diff --git a/conf/modules.config b/conf/modules.config index 5bed5c451..70a8ceca8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -819,6 +819,26 @@ process { ] } + withName: UNIFY_TARPMIR { + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { split(\$3, arr, \",\"); print \$1, \$2, arr[1], arr[2], \"tarpmir\" }'" + ext.suffix = "tarpmir.tsv" + publishDir = [ + path: { "${params.outdir}/mirna_prediction/binding_sites/tools/tarpmir/unified" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + + withName: UNIFY_PITA { + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$2, \$1, \$3, \$4, \"pita\" }'" + ext.suffix = "pita.tsv" + publishDir = [ + path: { "${params.outdir}/mirna_prediction/binding_sites/tools/pita/unified" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + withName: COMBINE_BINDINGSITES { ext.prefix = "bindingsites.tsv" } @@ -1042,6 +1062,26 @@ process { ] } + withName: TARPMIR { + ext.prefix = { "${meta.id}.tarpmir" } + publishDir = [ + path: { "${params.outdir}/mirna_prediction/binding_sites/tools/tarpmir/output" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + pattern: "*.bp" + ] + } + + withName: PITA { + ext.prefix = { "${meta.id}.pita" } + publishDir = [ + path: { "${params.outdir}/mirna_prediction/binding_sites/tools/pita/output" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + pattern: "*.tab" + ] + } + withName: MIRNA_TARGETS { publishDir = [ path: { "${params.outdir}/mirna_prediction/binding_sites/targets" }, @@ -1059,7 +1099,7 @@ process { ] } - withName: MAJORITY_VOTE { + withName: MIRNA_MAJORITYVOTE { publishDir = [ path: { "${params.outdir}/mirna_prediction/binding_sites/majority_vote" }, mode: params.publish_dir_mode, @@ -1067,7 +1107,7 @@ process { ] } - withName: '.*:MIRNA_PREDICTION:COMPUTE_CORRELATIONS' { + withName: '.*:MIRNA_PREDICTION:MIRNA_COMPUTECORRELATIONS' { publishDir = [ path: { "${params.outdir}/mirna_prediction/correlation" }, mode: params.publish_dir_mode, diff --git a/modules/local/ciriquant/de/main.nf b/modules/local/ciriquant/de/main.nf index 0e3eb14a8..3795151e9 100644 --- a/modules/local/ciriquant/de/main.nf +++ b/modules/local/ciriquant/de/main.nf @@ -8,8 +8,8 @@ process CIRIQUANT_DE { tuple val(meta), path(library), path(expression), path(gene) output: - tuple val(meta), path("${circ_path}"), emit: circ - tuple val(meta), path("${gene_path}"), emit: gene + tuple val(meta), path("${circ_path}"), emit: circ, optional: true + tuple val(meta), path("${gene_path}"), emit: gene, optional: true path "versions.yml", emit: versions when: diff --git a/modules/local/combinebeds/filter/templates/filter.py b/modules/local/combinebeds/filter/templates/filter.py index be3525909..a29991217 100644 --- a/modules/local/combinebeds/filter/templates/filter.py +++ b/modules/local/combinebeds/filter/templates/filter.py @@ -74,6 +74,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: continue memberships = series.to_list() dataset = upsetplot.from_memberships(memberships) + # TODO: Make this more robust for large datasets upsetplot.plot(dataset, orientation='horizontal', show_counts=True, diff --git a/modules/local/deseq2/gene_normalization/main.nf b/modules/local/deseq2/gene_normalization/main.nf new file mode 100644 index 000000000..390a042da --- /dev/null +++ b/modules/local/deseq2/gene_normalization/main.nf @@ -0,0 +1,32 @@ +process GENE_NORMALIZATION { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioconductor-deseq2:1.34.0--r41hc247a5b_3' : + 'biocontainers/bioconductor-deseq2:1.34.0--r41hc247a5b_3' }" + + input: + tuple val(meta), path(counts) + + output: + tuple val(meta), path("${meta.id}.normalized_counts.tsv"), emit: normalized + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'gene_deseq_normalization.R' + + stub: + """ + touch ${meta.id}.normalized_counts.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))") + END_VERSIONS + """ +} diff --git a/modules/local/deseq2/gene_normalization/templates/gene_deseq_normalization.R b/modules/local/deseq2/gene_normalization/templates/gene_deseq_normalization.R new file mode 100644 index 000000000..6d6f86c85 --- /dev/null +++ b/modules/local/deseq2/gene_normalization/templates/gene_deseq_normalization.R @@ -0,0 +1,54 @@ +#!/usr/bin/env Rscript + +library(DESeq2) + +raw_counts <- read.table("$counts", sep = "\\t", header = TRUE, stringsAsFactors = FALSE, check.names = FALSE) +raw_counts <- raw_counts[ , -2] # drop gene ids +rownames(raw_counts) <- raw_counts\$tx +data <- round(raw_counts[, -1]) + +samples <- colnames(raw_counts)[-c(1)] + + +transcript_names <- data.frame(tx = raw_counts\$tx, order = seq_len(nrow(raw_counts))) + +# normalize using DeSeq2, Library Size Estimation +meta_data <- data.frame(samples) +row.names(meta_data) <- meta_data\$samples +all(colnames(data) %in% rownames(meta_data)) +all(colnames(data) == rownames(meta_data)) + +dds <- DESeqDataSetFromMatrix(countData = data, colData = meta_data, design = ~ 1) +dds <- estimateSizeFactors(dds) +sizeFactors(dds) +normalized_counts <- DESeq2::counts(dds, normalized = TRUE) + +# add tx IDs back to counts table +merged_data <- merge(transcript_names, normalized_counts, + by.x = "tx", by.y = "row.names") + +merged_data <- merged_data[order(merged_data\$order), ] + +norm_data <- subset(merged_data, select = -c(order)) + +write.table(norm_data, paste0("${meta.id}.normalized_counts.tsv"), quote = FALSE, sep = "\\t", row.names = FALSE) + +# TODO: (Can be done later) Add support for Samplesheet so that we can eliminate batch effects + + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] +deseq2.version <- as.character(packageVersion('DESeq2')) + +writeLines( + c( + '"${task.process}":', + paste(' r-base:', r.version), + paste(' bioconductor-deseq2:', deseq2.version) + ), +'versions.yml') diff --git a/modules/local/deseq2/normalization/environment.yml b/modules/local/deseq2/mirna_normalization/environment.yml similarity index 100% rename from modules/local/deseq2/normalization/environment.yml rename to modules/local/deseq2/mirna_normalization/environment.yml diff --git a/modules/local/deseq2/normalization/main.nf b/modules/local/deseq2/mirna_normalization/main.nf similarity index 96% rename from modules/local/deseq2/normalization/main.nf rename to modules/local/deseq2/mirna_normalization/main.nf index 74cb8b5a3..0af4fa1a1 100644 --- a/modules/local/deseq2/normalization/main.nf +++ b/modules/local/deseq2/mirna_normalization/main.nf @@ -1,4 +1,4 @@ -process DESEQ2_NORMALIZATION { +process MIRNA_NORMALIZATION { tag "$meta.id" label 'process_single' diff --git a/modules/local/deseq2/normalization/templates/deseq_normalization.R b/modules/local/deseq2/mirna_normalization/templates/deseq_normalization.R similarity index 100% rename from modules/local/deseq2/normalization/templates/deseq_normalization.R rename to modules/local/deseq2/mirna_normalization/templates/deseq_normalization.R diff --git a/modules/local/compute_correlations/environment.yml b/modules/local/mirna/computecorrelations/environment.yml similarity index 100% rename from modules/local/compute_correlations/environment.yml rename to modules/local/mirna/computecorrelations/environment.yml diff --git a/modules/local/compute_correlations/main.nf b/modules/local/mirna/computecorrelations/main.nf similarity index 95% rename from modules/local/compute_correlations/main.nf rename to modules/local/mirna/computecorrelations/main.nf index 4a72b5eb8..b44b8fd4f 100644 --- a/modules/local/compute_correlations/main.nf +++ b/modules/local/mirna/computecorrelations/main.nf @@ -1,4 +1,4 @@ -process COMPUTE_CORRELATIONS { +process MIRNA_COMPUTECORRELATIONS { tag "$meta.id" label 'process_single' diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/mirna/computecorrelations/templates/compute_correlations.R similarity index 100% rename from modules/local/compute_correlations/templates/compute_correlations.R rename to modules/local/mirna/computecorrelations/templates/compute_correlations.R diff --git a/modules/local/mirna_filtering/main.nf b/modules/local/mirna/filtering/main.nf similarity index 100% rename from modules/local/mirna_filtering/main.nf rename to modules/local/mirna/filtering/main.nf diff --git a/modules/local/mirna_filtering/templates/mirna_filtering.R b/modules/local/mirna/filtering/templates/mirna_filtering.R similarity index 100% rename from modules/local/mirna_filtering/templates/mirna_filtering.R rename to modules/local/mirna/filtering/templates/mirna_filtering.R diff --git a/modules/local/majority_vote/environment.yml b/modules/local/mirna/majorityvote/environment.yml similarity index 100% rename from modules/local/majority_vote/environment.yml rename to modules/local/mirna/majorityvote/environment.yml diff --git a/modules/local/majority_vote/main.nf b/modules/local/mirna/majorityvote/main.nf similarity index 72% rename from modules/local/majority_vote/main.nf rename to modules/local/mirna/majorityvote/main.nf index 33f417ba2..241c59f53 100644 --- a/modules/local/majority_vote/main.nf +++ b/modules/local/mirna/majorityvote/main.nf @@ -1,6 +1,6 @@ -process MAJORITY_VOTE { +process MIRNA_MAJORITYVOTE { tag "$meta.id" - label 'process_medium' + label 'process_high' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -11,9 +11,9 @@ process MAJORITY_VOTE { tuple val(meta), path(bindingsites) output: - tuple val(meta), path("${meta.id}.majority.tsv"), emit: tsv - tuple val(meta), path("${meta.id}.targets.tsv") , emit: targets - path "versions.yml" , emit: versions + tuple val(meta), path("${meta.id}.majority.tsv") , emit: tsv + tuple val(meta), path("${meta.id}.targets.tsv") , emit: targets + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -25,6 +25,7 @@ process MAJORITY_VOTE { stub: """ touch ${meta.id}.majority.tsv + touch ${meta.id}.targets.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/mirna/majorityvote/templates/majority.py similarity index 57% rename from modules/local/majority_vote/templates/majority.py rename to modules/local/mirna/majorityvote/templates/majority.py index 4812301ad..f8940bcd6 100644 --- a/modules/local/majority_vote/templates/majority.py +++ b/modules/local/mirna/majorityvote/templates/majority.py @@ -1,32 +1,25 @@ #!/usr/bin/env python3 - import platform - import polars as pl import yaml -paths = "${bindingsites}".split(" ") - -df = pl.scan_csv(paths, - separator="\\t", - has_header=False, - new_columns=['mirna', 'target', 'start', 'end', 'tool']) - -df = df.select(["mirna", "target", "tool"]) +df = pl.scan_csv("*.tsv", + separator="\\t", + has_header=False, + new_columns=['mirna', 'target', 'start', 'end', 'tool']) -df = df.group_by(['mirna', 'target']).agg(pl.col("tool").n_unique()) +df = df.select("mirna", "target", "tool") +df = df.group_by('mirna', 'target').agg(pl.col("tool").n_unique()) -df = df.filter(pl.col("tool") > int("${min_tools}")) \ - .select(["mirna", "target"]) +df = df.filter(pl.col("tool") >= int("${min_tools}")) +df = df.select("mirna", "target") df = df.collect() - df.write_csv('${meta.id}.majority.tsv', separator='\\t', include_header=False) # Create targets file df = df.group_by('mirna').agg(pl.col("target").str.concat(",")) - df.write_csv('${meta.id}.targets.tsv', separator='\\t', include_header=False) # Create version file @@ -39,3 +32,4 @@ with open("versions.yml", "w") as f: f.write(yaml.dump(versions)) + diff --git a/modules/local/mirna_targets/main.nf b/modules/local/mirna/targets/main.nf similarity index 97% rename from modules/local/mirna_targets/main.nf rename to modules/local/mirna/targets/main.nf index e525a9f5e..ea931cdd2 100644 --- a/modules/local/mirna_targets/main.nf +++ b/modules/local/mirna/targets/main.nf @@ -31,7 +31,7 @@ process MIRNA_TARGETS { bedtools intersect -a targetscan.bed -b miranda.bed | awk '{print \$6}' > mirna_type ## remove duplicate miRNA entries at MRE sites. - ## strategy: sory by circs, sort by start position, sort by site type - the goal is to take the best site type (i.e rank site type found at MRE site). + ## strategy: sort by circs, sort by start position, sort by site type - the goal is to take the best site type (i.e rank site type found at MRE site). paste ${prefix}.mirnas.tmp mirna_type | sort -k3n -k2n -k7r | awk -v OFS="\\t" '{print \$4,\$1,\$2,\$3,\$5,\$6,\$7}' | awk -F "\\t" '{if (!seen[\$1,\$2,\$3,\$4,\$5,\$6]++)print}' | sort -k1,1 -k3n > ${prefix}.mirna_targets.tmp echo -e "circRNA\\tmiRNA\\tStart\\tEnd\\tScore\\tEnergy_KcalMol\\tSite_type" | cat - ${prefix}.mirna_targets.tmp > ${prefix}.mirna_targets.txt diff --git a/modules/local/pita/main.nf b/modules/local/pita/main.nf new file mode 100644 index 000000000..b64d19510 --- /dev/null +++ b/modules/local/pita/main.nf @@ -0,0 +1,34 @@ +process PITA { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" + + input: + tuple val(meta), path(fasta) + tuple val(meta2), path(mature) + + output: + tuple val(meta), path("*.tab"), emit: tsv + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template "pita_prediction.pl" + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.tab + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + END_VERSIONS + """ +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/AUTHORS b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/AUTHORS new file mode 100755 index 000000000..a1946e083 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/AUTHORS @@ -0,0 +1,4 @@ +Ivo Hofacker (all parts) +Peter Stadler (design, documentation, cluster algorithms) +Walter Fontana (suboptimal folding, pre-historic implementation of mfe folding) +Stefan Wuchty (suboptimal folding) diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/COPYING b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/COPYING new file mode 100755 index 000000000..c3eb63c1c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/COPYING @@ -0,0 +1,19 @@ + Disclaimer and Copyright + +The programs, library and source code of the Vienna RNA Package are free +software. They are distributed in the hope that they will be useful +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + +Permission is granted for research, educational, and commercial use +and modification so long as 1) the package and any derived works are not +redistributed for any fee, other than media costs, 2) proper credit is +given to the authors and the Institute for Theoretical Chemistry of the +University of Vienna. + +If you want to include this software in a commercial product, please contact +the authors. + +Note that the file ./lib/naview.c has its own copyright attached. +The ./Readseq/ directory contains a modified version of Don Gilbert's +public domain readseq program. diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/ChangeLog b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/ChangeLog new file mode 100755 index 000000000..e9b9cff85 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/ChangeLog @@ -0,0 +1,123 @@ +2006-01-18 Ivo Hofacker + + * cleanup berni partition cofold code, including several bug fixes + +2006-01-16 Ivo Hofacker + + * update RNAplfold to working version + * add PS_dot_plot_turn() in PS_dot.c + +2005-11-07 Ivo Hofacker + + * add new utilities colorna and coloraln + +2005-10-11 Christoph Flamm + + * adapt PS_rna_plot() for drawing co-folded structures + +2005-07-24 Ivo Hofacker + + * fix a few memory problems in structure comparison routines + +2005-04-30 Ivo Hofacker + + * add folding of circular RNAs + +2005-03-11 Ivo Hofacker + + * add -mis option to RNAalifold to give "most informative + sequence" as consensus + +2005-02-10 Ivo Hofacker + + * move alifold() into the library + +2004-12-22 Stephan Bernhart + + * add partition function version of RNAcofold + +2004-12-23 Ivo Hofacker + + * add RNApaln for fast structural alignments (RNApdist improvement) + +2004-08-12 Ivo Hofacker + + * fix constrained folding in stochastic backtracking + +2004-07-21 Ivo Hofacker + + * add RNAduplex, to compute hybrid structures without + intra-molecular pairs + +2004-02-09 Ivo Hofacker + + * fix bug in fold that caused segfaults when using Intel compiler + * add computation of ensemble diversity to RNAfold + +2003-09-10 Ivo Hofacker + + * add annotation options to RNAplot + +2003-08-04 Ivo Hofacker + + * stochastic backtracking finally works. Try e.g. + RNAsubopt -p 10 + +2003-07-18 Ivo Hofacker + + * add relplot.pl and rotate_ss.pl utilities for reliability + annotation and rotation of rna structure plots + +2003-01-29 Ivo Hofacker + + * add RNALfold program to compute locally optimal structures with + maximum pair span. + * add RNAcofold for computing hybrid structure + +2002-11-07 Ivo Hofacker + + * change Make_bp_profile() and profile_edit_distance() to use + simple (float *) arrays; makes Perl access much easier. + RNApdist -B now works again + +2002-10-28 Ivo Hofacker + + * Improved Perl module with pod documentation; allow to write + things like + ($structure, $energy) = RNA::fold($seq); + Compatibility warning: the ptrvalue() and related functions are + gone, see the pod documentation for alternatives. + +2002-10-29 Ivo Hofacker + + * added svg structure plots in PS_dot.c and RNAplot + +2002-08-15 Ivo Hofacker + + * Improve reading of clustal files (alifold) + * add a sample alifold.cgi script + +2001-09-18 Ivo Hofacker + + * moved suboptimal folding into the library, thus it's now + accessible from the Perl module + +2001-08-31 Ivo Hofacker + + * added co-folding support in energy_of_struct(), and thus RNAeval + +2001-04-30 Ivo Hofacker + + * switch from handcrafted makefiles to automake and autoconf + +2001-04-05 Ivo Hofacker + + * added PS_rna_plot_a to produce structure plots with annotation + +2001-03-03 Ivo Hofacker + + * add alifold; predict consensus structures from alignment + +2000-09-28 Ivo Hofacker + + * add -d3 option to RNAfold for co-axial stacking diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/AD_main.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/AD_main.Po new file mode 100755 index 000000000..9ce06a81e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/AD_main.Po @@ -0,0 +1 @@ +# dummy diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/AS_main.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/AS_main.Po new file mode 100755 index 000000000..9ce06a81e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/AS_main.Po @@ -0,0 +1 @@ +# dummy diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/PS3D.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/PS3D.Po new file mode 100755 index 000000000..9ce06a81e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/PS3D.Po @@ -0,0 +1 @@ +# dummy diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/cluster.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/cluster.Po new file mode 100755 index 000000000..9ce06a81e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/cluster.Po @@ -0,0 +1 @@ +# dummy diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/distance_matrix.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/distance_matrix.Po new file mode 100755 index 000000000..9ce06a81e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/distance_matrix.Po @@ -0,0 +1 @@ +# dummy diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/split.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/split.Po new file mode 100755 index 000000000..9ce06a81e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/split.Po @@ -0,0 +1 @@ +# dummy diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/statgeom.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/statgeom.Po new file mode 100755 index 000000000..9ce06a81e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/statgeom.Po @@ -0,0 +1 @@ +# dummy diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/treeplot.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/treeplot.Po new file mode 100755 index 000000000..9ce06a81e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/.deps/treeplot.Po @@ -0,0 +1 @@ +# dummy diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AD_main.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AD_main.c new file mode 100755 index 000000000..a5b22f85e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AD_main.c @@ -0,0 +1,85 @@ +#include +#include +#include +#include "split.h" +#include "cluster.h" +#include "distance_matrix.h" +#include "treeplot.h" +#include "utils.h" + + +#define PUBLIC +#define PRIVATE static + +PRIVATE void usage(void); + +main(int argc, char *argv[]) +{ + int i,j; + float **dm; + Split *S; + Union *U; + char type[5]; + + short Do_Split=1, Do_Wards=0, Do_Nj=0; + + for (i=1; i %s\n",type); + + if(Do_Split) { + S = split_decomposition(dm); + sort_Split(S); + print_Split(S); + free_Split(S); + } + if(Do_Wards) { + U = wards_cluster(dm); + + printf_phylogeny(U,"W"); + PSplot_phylogeny(U,"wards.ps","Ward's Method"); + free(U); + } + if(Do_Nj) { + U = neighbour_joining(dm); + printf_phylogeny(U,"Nj"); + PSplot_phylogeny(U,"nj.ps","Neighbor Joining"); + free(U); + } + free_distance_matrix(dm); + } + return 0; +} + + +PRIVATE void usage(void) +{ + nrerror("usage: AnalyseDist [-X[swn]]"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AS_main.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AS_main.c new file mode 100755 index 000000000..c516f32c7 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AS_main.c @@ -0,0 +1,292 @@ +#include +#include +#include "distance_matrix.h" +#include "statgeom.h" +#include "split.h" +#include "cluster.h" +#include "treeplot.h" +#include "utils.h" + + +#define PUBLIC +#define PRIVATE static + +PRIVATE char scale1[] = "....,....1....,....2....,....3....,....4"; +PRIVATE char scale2[] = "....,....5....,....6....,....7....,....8"; + +PRIVATE void usage(void); + +main(int argc, char *argv[]) +{ + int n,i,j,l; + int intty; + int outtty; + char *mask, junk[20]; + char **s; + char **ss[4]; + float *B; + float **dm; + Split *S; + Union *U; + char DistAlgorithm='H'; + int nn[4]; + short Do_Split=0, Do_Wards=0, Do_Stg=1, Do_4_Stg=0, Do_Nj=0, Do_Mat=0; + float per_digit, per_gap; + + mask = space(sizeof(char)*54); + strcpy (mask,"%ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz"); + for (i=1; i %s\n","H (Hamming Distance)"); + break; + case 'A' : + dm = StrEdit_SimpleDistMatrix(s,n); + printf("> %s\n","A (Needleman-Wunsch Distance)"); + break; + case 'G' : + dm = StrEdit_GotohDistMatrix(s,n); + printf("> %s\n","G (Gotoh Distance)"); + break; + default: + nrerror("This can't happen."); + } + } + if(Do_Split) { + S = split_decomposition(dm); + sort_Split(S); + print_Split(S); + free_Split(S); + } + if(Do_Wards) { + U = wards_cluster(dm); + printf_phylogeny(U,"W"); + PSplot_phylogeny(U,"wards.ps","Ward's Method"); + free(U); + } + if(Do_Nj) { + U = neighbour_joining(dm); + printf_phylogeny(U,"Nj"); + PSplot_phylogeny(U,"nj.ps","Neighbor Joining"); + free(U); + } + if(Do_Mat) printf_distance_matrix(dm); + } + + if (dm!=NULL) free_distance_matrix(dm); + for(i=0;i Y x [comments] +.br +where 'x' gives the number of taxa, 'Y' is a single character that +indicates the type of distance and 'comment' is an arbitrary comment. +This matches the output format of, e.g., RNAdistance. +The input data file may contain arbitrary lines before and after the +distance matrix. All lines beginning with '> ' that are not of the +above form are written to stdout. The programm continues reading +until it encounters an EOF condition or the terminator character '@'. +.br +A list of taxa names can be specified in the input stream. The list +must begin with a line of the form +.br +* [fname] +.br +if fname is present, it will be used to name the postscript output files. +The entries have the form 'x : Taxon', +where x is the number of taxon, i.e., the corresponding row and column +of the distance matrix. The taxa list need not be complete. It must +end however with a line beginning with '*' or any of the separator +characters. The taxa list is printed on top of the output. + +.SH OPTIONS + +.IP \fB\-X[swn]\fI\fP +specifies the analysis methods to be used. +.IP \fB[s]\fI\fP +Split decomposition. +.IP \fB[w]\fI\fP +Cluster analysis using Ward's method. A PostScript file named '[fname_]wards.ps' +is created containing a drawing of the tree. +.IP \fB[n]\fI\fP +Cluster analysis using Saitou's neighbour joining method. +A PostScript file named '[fname_]nj.ps' is created containing a drawing of the tree. + +.SH REFERENCES + +The method of split decomposition was proposed by H.J. Bandelt and +A.W.M. Dress (Adv Math, 92:1992,47). +.br +The variance method for cluster analysis is due to H.J. Ward. +(J Amer Stat Ass, 58:1963,236). +.br +The neighbour joining method was published by Saitou and Nei +(Mol Biol Evol, 4:1987,406). +.br +This program is part of the Vienna RNA Package. + +.SH WARNING +This a beta test version. + +.SH VERSION +This man page is part of the Vienna RNA Package version 1.2 +.SH AUTHOR +Peter F Stadler and Ivo L Hofacker. +.SH BUGS +Comments should be sent to ivo@tbi.univie.ac.at. +.br diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AnalyseSeqs.1 b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AnalyseSeqs.1 new file mode 100755 index 000000000..c5ace8f92 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/AnalyseSeqs.1 @@ -0,0 +1,168 @@ +.TH ANALYSESEQS l +.ER +.SH NAME +AnalyseSeqs \- Analyse a set of sequences of common length +.SH SYNOPSIS +\fBAnalyseSeqs [\-X[\fIbswn\fP]] [\-Q] [\-M{mask}[+|!]] [\-D{H|A|G}] [\-d{S|H|D|B}] +.SH DESCRIPTION +.I AnalyseSeqs +reads a set of sequences from stdin and tries a variety of methods +for sequence analysis on them. Currently available are: +.br +Statistical geometry for quadruples of sequences; THIS IS +PRELIMINARY AND NOT WELL TESTED BY NOW. +.br +split decomposition; +neighbour joining and Ward's variance method for reconstructing +phylogenies using various distance measures. +For statistical geometry and the cluster methods PostScript output +is available. +.br +The program continues reading until it encounters one of the +separator characters '@' or '%'. Only sequences of alphabetical +characters or of a specified alphabet are processed, all other +lines are ignored. The program stops reading +if it either encounters an EOF condition, or if there are no +valid sequence data between two lines beginning with separator +characters. +.br +A list of taxa names can be specified in the input stream. The list +begins with a line beginning with '*'. Optionally, a file name prefix +[fn] for the PostScript output can be specified in this line. +The entries have the form 'x : Taxon', +where x is the number of taxon, i.e., of the corresponding entry in +the list of input sequences. The taxa list need not be complete. It must +end, however, with a line beginning with '*' or any of the separator +characters. The taxa list is printed on top of the output. The specified +taxa names are used as labels in the PostScript output. + +.SH OPTIONS +.IP \fB\-X[bswn]\fI\fP +specifies the analysis methods to be used. +.IP \fB[b]\fI\fP +Statistical Geometry. A PostScript file named '[fn_]box.ps' giving a +graphical representation of the statistical geometry is created. The +resulting box is a good measure of 'tree likeness' of the data set. +This is the default. +.IP \fB[s]\fI\fP +Split decomposition. +.IP \fB[w]\fI\fP +Cluster analysis using Ward's method. A PostScript file named '[fn_]wards.ps' +is created containing a drawing of the tree. +.IP \fB[n]\fI\fP +Cluster analysis using Saitou's neighbour joining method. A PostScript +file named '[fn_]nj.ps' is created containing a drawing of the tree. + +.IP \fB\-Q\fB +indicates that a statistical geometry analysis is to be performed +comparing four data sets, for instance to confirm the significance of +a proposed phylogeny. This option is only useful for statistical +geometry analysis and hence the -X option is ignored. Each of the +four data sets must be of the form +.br +* [filename_prefix] +.br +# number +.br +[list of taxa names] +.br +* +.br +list of sequences +.br +% +.br +where number is 1,2,3,4 for the four groups to be compared. + +.IP \fB\-M{mask}[+|!]\fB +allows to specify a mask for the input file. '{mask}' can be one +of the following letters indicating a predefined alphabet or +the %-sign followed by all characters to be accepted. A + sign +at the very end of the mask indicates that the input is to be +handled case sensitive. Default is conversion of the input to +upper case. A ! sign can be used to convert the input data to +RY code: GgAaXx -> R, UuCcKkTt -> Y, all other letters are +converted to *. +.IP \fB-Ma\fI\fP +all letters A-Z and a-z. +.IP \fB-Mu\fI\fP +uppercase letters. +.IP \fB-Ml\fI\fP +lowercase letters. +.IP \fB-Mc\fI\fP +digits [0-9]. +.IP \fB-Mn\fI\fP +all alphanumeric characters. +.IP \fB-MR\fI\fP +RNA alphabet (GCAUgcau). +.IP \fB-MD\fI\fP +DNA alphabet (GCATgcat). +.IP \fB-MA\fI\fP +Amino acids in one-letter code. +.IP \fB-MS\fI\fP +Secondary strcutures coded as '^.()' +.IP \fB-M%alphabet\fI\fP +use the specified alphabet. + +.IP \fB\-D\fB +specifies the algorithm to be used for calculating the +distance matrix of the input data set. Available are +.IP \fB-DH\fI\fP +Hamming Distance +.IP \fB-DA[,cost]\fI\fB +Simple alignment distance according to Needleman and Wunsch. +A gap cost different from 1. can be specified after the comma. +.IP \fB-DG[,cost1,cost2]\fI\fB +Gotoh's distance with gap cost function +g(k) = cost2+cost1*(k-1). cost2<=cost1 has to be fulfilled. +Default values are cost1=1., cost2=1., yielding the same +distance as option A. +.br +ONLY THE HAMMING DISTANCE IS WELL TESTED BY NOW !!! + +.IP \fB\-d\fB +specifies the edit cost matrix to be used. Available are +.IP \fB-dS\fI\fP +simple distance. Indel and substitution of different characters +all have cost 1. The indel cost can be set by specifying the +gap costs with the algorithm options -DA and -DG. This is the +default. +.IP \fB-dH\fI\fP +A distance matrix for RNA secondary structures. Inspired by +Hogeweg's similarity measure (J.Mol.Biol 1988). +Gap-function is set automatically. +.IP \fB-dD\fI\fP +Dayhoff's matrix for amino acid distances. +.IP \fB-dB\fI\fP +Distinguish purines and pyrimidines only. +CAUTION this option of course influences only the calculation of distances. +It does NOT affect computation of the statistical geometry. This is +done directly on the sequences. If you want to do statistical geometry on +RY sequences use the ! sign with the -M option, for instance -MR!. + +.SH REFERENCES +The method of statistical geometry has been introduced by +M. Eigen, R. Winkler-Oswatitsch and A.W.M. Dress +(Proc Natl Acad Sci, 85:1988,5912). +The method of split decomposition was proposed by +H.J. Bandelt and A.W.M. Dress +(Adv Math, 92:1992,47). +The variance method for cluster analysis is due to H.J. Ward +(J Amer Stat Ass, 58:1963,236). +The neighbour joining method was published by Saitou and Nei +(Mol Biol Evol, 4:1987,406). + +This program is part of the Vienna RNA Package + +.SH WARNING +This is the beta test version. Some options or combinations +of options may still produce nonsense. Please send bug reports to +ivo@tbi.univie.ac.at. + +.SH VERSION +This man page is part of the Vienna RNA Package version 1.2. +.SH AUTHOR +Peter F Stadler, Ivo L. Hofacker. +.SH BUGS +Comments should be sent to ivo@itc.univie.ac.at. +.br diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/Makefile new file mode 100755 index 000000000..c8c35badc --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/Makefile @@ -0,0 +1,507 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# Cluster/Makefile. Generated from Makefile.in by configure. + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005 Free Software Foundation, Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + + + + +SOURCES = $(AnalyseDists_SOURCES) $(AnalyseSeqs_SOURCES) + +srcdir = . +top_srcdir = .. + +pkgdatadir = $(datadir)/ViennaRNA +pkglibdir = $(libdir)/ViennaRNA +pkgincludedir = $(includedir)/ViennaRNA +top_builddir = .. +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +INSTALL = /usr/bin/install -c +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +build_triplet = x86_64-unknown-linux-gnu +host_triplet = x86_64-unknown-linux-gnu +bin_PROGRAMS = AnalyseDists$(EXEEXT) AnalyseSeqs$(EXEEXT) +subdir = Cluster +DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \ + $(srcdir)/Makefile.in +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.in +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_CLEAN_FILES = +am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(man1dir)" +binPROGRAMS_INSTALL = $(INSTALL_PROGRAM) +PROGRAMS = $(bin_PROGRAMS) +am_AnalyseDists_OBJECTS = split.$(OBJEXT) distance_matrix.$(OBJEXT) \ + cluster.$(OBJEXT) treeplot.$(OBJEXT) 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$(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) +ACLOCAL = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run aclocal-1.9 +AMDEP_FALSE = # +AMDEP_TRUE = +AMTAR = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run tar +AUTOCONF = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run autoconf +AUTOHEADER = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run autoheader +AUTOMAKE = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run automake-1.9 +AWK = gawk +CC = gcc +CCDEPMODE = depmode=gcc3 +CFLAGS = -g -O2 +CPP = gcc -E +CPPFLAGS = +CYGPATH_W = echo +DEFS = -DHAVE_CONFIG_H +DEPDIR = .deps +ECHO_C = +ECHO_N = -n +ECHO_T = +EGREP = grep -E +EXEEXT = +INSTALL_DATA = ${INSTALL} -m 644 +INSTALL_PROGRAM = ${INSTALL} +INSTALL_SCRIPT = ${INSTALL} +INSTALL_STRIP_PROGRAM = ${SHELL} $(install_sh) -c -s +ISODATE = 2006-06-13 +LDFLAGS = +LIBOBJS = +LIBS = +LTLIBOBJS = +MAKEINFO = ${SHELL} 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b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/PS3D.c new file mode 100755 index 000000000..7af4de63c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/PS3D.c @@ -0,0 +1,143 @@ +#include +#include +#include "utils.h" + +#define PUBLIC +#define PRIVATE static + +PUBLIC void ps3d_Preambel(FILE *fp, float view[3], float axis[3], char *projtype); +PUBLIC void PS_DrawSimplifiedBox(float X,float Y, float Z, float T, float P, FILE *fp); + + +PUBLIC void ps3d_Preambel(FILE *fp, float view[3], float axis[3], char *projtype) +{ + fprintf(fp,"%%!PS\n"); + fprintf(fp,"%%%%Title: RNA DotPlot\n"); + fprintf(fp,"%%%%Creator: RNAfold V.01.002c - by Oymolon\n"); + fprintf(fp,"%%%%CreationDate: %s", time_stamp()); +/* fprintf(fp,"%%%%BoundingBox: 66 211 518 662\n"); */ + fprintf(fp,"%%%%Pages: 1\n"); + fprintf(fp,"%%%%EndComments: Geil eyh !?\n"); + fprintf(fp,"%%Viewing vector\n"); + fprintf(fp,"/v1 { %f } def\n", view[0]); + fprintf(fp,"/v2 { %f } def\n", view[1]); + fprintf(fp,"/v3 { %f } def\n", view[2]); + fprintf(fp,"/a1 { %f } def\n", axis[0]); + fprintf(fp,"/a2 { %f } def\n", axis[1]); + fprintf(fp,"/a3 { %f } def\n", axis[2]); + fprintf(fp,"%%Define some coefficients for the projections.\n"); + fprintf(fp,"/y1a { v2 a3 mul v3 a2 mul sub } def\n"); + fprintf(fp,"/y2a { v3 a1 mul v1 a3 mul sub } def\n"); + fprintf(fp,"/y3a { v1 a2 mul v2 a1 mul sub } def\n"); + fprintf(fp,"/ya_len { y1a y1a mul y2a y2a mul y3a y3a mul add add sqrt } def\n"); + fprintf(fp,"/x1a { v2 y3a mul v3 y2a mul sub } def\n"); + fprintf(fp,"/x2a { v3 y1a mul v1 y3a mul sub } def\n"); + fprintf(fp,"/x3a { v1 y2a mul v2 y1a mul sub } def\n"); + fprintf(fp,"/xa_len { x1a x1a mul x2a x2a mul x3a x3a mul add add sqrt } def\n"); + fprintf(fp,"/x1 { x1a xa_len div } def\n"); + fprintf(fp,"/x2 { x2a xa_len div } def\n"); + fprintf(fp,"/x3 { x3a xa_len div } def\n"); + fprintf(fp,"/y1 { y1a ya_len div } def\n"); + fprintf(fp,"/y2 { y2a ya_len div } def\n"); + fprintf(fp,"/y3 { y3a ya_len div } def\n"); + fprintf(fp,"/sx { v1 v3 div } def\n"); + fprintf(fp,"/sy { v2 v3 div } def\n"); + fprintf(fp,"/v_len { v1 v1 mul v2 v2 mul v3 v3 mul add add sqrt } def\n"); + fprintf(fp,"/u_len { v1 v1 mul v2 v2 mul add sqrt } def\n"); + fprintf(fp,"/u1 { v2 u_len div } def\n"); + fprintf(fp,"/u2 { v1 neg u_len div } def\n"); + fprintf(fp,"/w1 { v1 v3 mul neg u_len div v_len div } def\n"); + fprintf(fp,"/w2 { v2 v3 mul neg u_len div v_len div } def\n"); + fprintf(fp,"/w3 { v1 v1 mul v2 v2 mul add u_len div v_len div } def\n"); + fprintf(fp,"%%Projection Operators\n"); + fprintf(fp,"%% Projection onto x-y plane in direction v\n"); + fprintf(fp,"/ProjXY { dup sx mul 4 -1 roll exch sub \n"); + fprintf(fp," 3 1 roll sy mul sub \n"); + fprintf(fp," } def \n"); + fprintf(fp,"%% Normal Projection onto a plane normal to (v1,v2,v3!=0)\n"); + fprintf(fp,"/Projnn { w3 mul 3 1 roll dup w2 mul 3 1 roll u2 mul exch \n"); + fprintf(fp," dup w1 mul 3 1 roll u1 mul add 4 1 roll add add \n"); + fprintf(fp," } def \n"); + fprintf(fp,"%% General Normal Projection\n"); + fprintf(fp,"/ProjN { dup y3 mul 4 1 roll x3 mul 3 1 roll dup \n"); + fprintf(fp," y2 mul 5 1 roll x2 mul 3 1 roll dup y1 mul \n"); + fprintf(fp," 6 1 roll x1 mul add add 4 1 roll add add \n"); + fprintf(fp," } def\n"); + fprintf(fp,"/Proj { Proj%s } def\n", projtype); + fprintf(fp,"/L3 { Proj lineto } def\n"); + fprintf(fp,"/RL3 { Proj rlineto } def\n"); + fprintf(fp,"/M3 { Proj moveto } def\n"); + fprintf(fp,"/RM3 { Proj rmoveto } def\n"); + fprintf(fp,"%% end 3D macros\n\n"); +} + +PUBLIC void PS_DrawSimplifiedBox(float X,float Y, float Z, float T, float P, FILE *fp) +{ + float t1, p1, t, lw; + t1 = T/sqrt(2.); + p1 = P/sqrt(3.); + t = X+t1+2*p1; /* approximate size */ + lw = 0.001*t; + fprintf(fp,"/scaling_factor { %f } def \n", 400./t); + fprintf(fp,"%f %f %f Proj \n", X+t1, Y+t1, Z+t1); + fprintf(fp,"scaling_factor mul 2 div 300 sub neg exch \n" ); + fprintf(fp,"scaling_factor mul 2 div 400 sub neg translate \n"); + fprintf(fp,"scaling_factor dup scale\n"); + fprintf(fp,"newpath\n"); + fprintf(fp,"%f setlinewidth\n",lw); + fprintf(fp,"0 0 0 M3\n"); + fprintf(fp,"%f %f %f L3\n", X , 0. , 0. ); + fprintf(fp,"%f %f %f L3\n", X+t1 , t1 , 0. ); + fprintf(fp,"%f %f %f L3\n", X+t1 , Y+t1 , 0. ); + fprintf(fp,"%f %f %f L3\n", t1 , Y+t1 , 0. ); + fprintf(fp,"%f %f %f L3\n", 0. , Y , 0. ); + fprintf(fp,"%f %f %f L3\n", 0. , 0. , 0. ); + fprintf(fp,"%f %f %f L3\n", 0. , 0. , Z ); + fprintf(fp,"%f %f %f L3\n", 0. , t1 , Z+t1 ); + fprintf(fp,"%f %f %f L3\n", 0. , Y+t1 , Z+t1 ); + fprintf(fp,"%f %f %f L3\n", 0. , Y+t1 , t1 ); + fprintf(fp,"%f %f %f L3\n", 0. , Y , 0. ); + fprintf(fp,"%f %f %f L3\n", 0. , 0. , 0. ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", t1 , Y+t1 , 0. ); + fprintf(fp,"%f %f %f L3\n", 0. , Y+t1 , t1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", X+t1 , t1 , 0. ); + fprintf(fp,"%f %f %f L3\n", X+t1 , 0. , t1 ); + fprintf(fp,"%f %f %f L3\n", X+t1 , 0. , Z+t1 ); + fprintf(fp,"%f %f %f L3\n", X+t1 , Y , Z+t1 ); + fprintf(fp,"%f %f %f L3\n", X+t1 , Y+t1 , Z ); + fprintf(fp,"%f %f %f L3\n", X+t1 , Y+t1 , 0. ); + fprintf(fp,"%f %f %f L3\n", X+t1 , t1 , 0. ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", X+t1 , 0. , Z+t1 ); + fprintf(fp,"%f %f %f L3\n", t1 , 0. , Z+t1 ); + fprintf(fp,"%f %f %f L3\n", 0. , t1 , Z+t1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", X+t1 , Y , Z+t1 ); + fprintf(fp,"%f %f %f L3\n", X , Y+t1 , Z+t1 ); + fprintf(fp,"%f %f %f L3\n", 0. , Y+t1 , Z+t1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", X , 0. , 0. ); + fprintf(fp,"%f %f %f L3\n", X+t1 , 0. , t1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", 0. , 0. , Z ); + fprintf(fp,"%f %f %f L3\n", t1 , 0. , Z+t1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", X+t1 , Y+t1 , Z ); + fprintf(fp,"%f %f %f L3\n", X , Y+t1 , Z+t1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", 0. , 0. , 0. ); + fprintf(fp,"%f %f %f RL3\n", -p1 , -p1 , -p1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", X+t1 , Y+t1 , 0. ); + fprintf(fp,"%f %f %f RL3\n", p1 , p1 , -p1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", X+t1 , 0. , Z+t1 ); + fprintf(fp,"%f %f %f RL3\n", p1 , -p1 , p1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"%f %f %f M3\n", 0. , Y+t1 , Z+t1 ); + fprintf(fp,"%f %f %f RL3\n", -p1 , p1 , p1 ); + fprintf(fp,"stroke\n"); + fprintf(fp,"showpage\n"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/PS3D.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/PS3D.h new file mode 100755 index 000000000..842e59011 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/PS3D.h @@ -0,0 +1,2 @@ +extern void ps3d_Preambel(FILE *fp, float view[3], float axis[3], char *projtype); +extern void PS_DrawSimplifiedBox(float X,float Y, float Z, float T, float P, FILE *fp); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/StrEdit_CostMatrix.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/StrEdit_CostMatrix.h new file mode 100755 index 000000000..25e45ad66 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/StrEdit_CostMatrix.h @@ -0,0 +1,107 @@ +#define DINF 100000.0 +#define GAP 1.0 + +/* -------------------------------------------------------------------------- */ + +/* BinCode: 'B' ... RNA sequences, but RY-distance only */ + +char StrEdit_BinCodeA[6] = "_GCAU"; +/* _ G C A U */ +float StrEdit_BinCodeM[5][5] = + { { 5., 1., 1., 1., 1. }, /* _ */ + { 1., 0., 1., 0., 1. }, /* G */ + { 1., 1., 0., 1., 0. }, /* C */ + { 1., 0., 1., 0., 1. }, /* A */ + { 1., 1., 0., 1., 0. } }; /* U */ + +/* -------------------------------------------------------------------------- */ + +/* Dayhoff: 'D' ... Dayhoff's matrix for Amino Acids */ +/* CAUTION THIS IS A SIMILARITY MATRIX !!! */ + +char StrEdit_DayhoffA[22] = +"_CSTPAGNDEQHRKMILVFYW"; +float StrEdit_DayhoffM[21][21] = +/* _ C S T P A G N D E Q H R K M I L V F Y W */ + {{21.,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP}, /* _ ... < ~gap~ > */ + {GAP,12., 0.,-2.,-3.,-2.,-3.,-4.,-5.,-5.,-5.,-3.,-4.,-5.,-5.,-2.,-6.,-2.,-4., 0.,-8.}, /* C ... Cysteine */ + {GAP, 0., 2., 1., 1., 1., 1., 1., 0., 0.,-1.,-1., 0., 0.,-2.,-1.,-3.,-1.,-3.,-3.,-2.}, /* S ... Serine */ + {GAP,-2., 1., 3., 0., 1., 0., 0., 0., 0.,-1.,-1.,-1., 0.,-1., 0.,-2., 0.,-3.,-3.,-5.}, /* T ... Threonine */ + {GAP,-3., 1., 0., 6., 1.,-1.,-1.,-1.,-1., 0., 0., 0.,-1.,-2.,-2.,-3.,-1.,-5.,-5.,-6.}, /* P ... Proline */ + {GAP,-2., 1., 1., 1., 2., 1., 0., 0., 0., 0.,-1.,-2.,-1.,-1.,-1.,-2., 0.,-4.,-3.,-6.}, /* A ... Alanine */ + {GAP,-3., 1., 0.,-1., 1., 5., 0., 1., 0.,-1.,-2.,-3.,-2.,-3.,-3.,-4.,-1.,-5.,-5.,-7.}, /* G ... Glycine */ + {GAP,-4., 1., 0.,-1., 0., 0., 2., 2., 2., 1., 2., 0., 1.,-2.,-2.,-3.,-2.,-4.,-2.,-4.}, /* N ... Asparagine */ + {GAP,-5., 0., 0.,-1., 0., 1., 2., 4., 3., 2., 1.,-1., 0.,-3.,-2.,-4.,-2.,-6.,-4.,-7.}, /* D ... Aspartic A */ + {GAP,-5., 0., 0.,-1., 0., 0., 1., 3., 4., 2., 1.,-1., 0.,-2.,-2.,-3.,-2.,-5.,-4.,-7.}, /* E ... Glutamic A */ + {GAP,-5.,-1.,-1., 0., 0.,-1., 1., 2., 2., 4., 3., 3., 1.,-1.,-2.,-2.,-2.,-5.,-4.,-5.}, /* Q ... Glutamine */ + {GAP,-3.,-1.,-1., 0.,-1.,-2., 2., 1., 1., 3., 6., 2., 0.,-2.,-2.,-2.,-2.,-2., 0.,-3.}, /* H ... Histidine */ + {GAP,-4., 0.,-1., 0.,-2.,-3., 0.,-1.,-1., 1., 2., 6., 3., 0.,-2.,-3.,-2.,-4.,-4.,-2.}, /* R ... Arginine */ + {GAP,-5., 0., 0.,-1.,-1.,-2., 1., 0., 0., 1., 0., 2., 5., 0.,-2.,-3.,-2.,-5.,-4.,-3.}, /* K ... Lysine */ + {GAP,-5.,-2.,-1.,-2.,-1.,-3.,-2.,-3.,-2.,-1.,-2., 0., 0., 6., 2., 4., 2., 0.,-2.,-4.}, /* M ... Methionine */ + {GAP,-2.,-1., 0.,-2.,-1.,-3.,-2.,-2.,-2.,-2.,-2.,-2.,-2., 2., 5., 2., 4., 1.,-1.,-5.}, /* I ... Isoleucine */ + {GAP,-6.,-3.,-2.,-3.,-2.,-4.,-3.,-4.,-3.,-2.,-2.,-3.,-3., 4., 2., 6., 2., 2.,-1.,-2.}, /* L ... Leucine */ + {GAP,-2.,-1., 0.,-1., 0.,-1.,-2.,-2.,-2.,-2.,-2.,-2.,-2., 2., 4., 2., 4.,-1.,-2.,-6.}, /* V ... Valine */ + {GAP,-4.,-3.,-3.,-5.,-4.,-5.,-4.,-6.,-5.,-5.,-2.,-4.,-5., 0., 1., 2.,-1., 9., 7., 0.}, /* F ... Phenylalanine */ + {GAP, 0.,-3.,-3.,-5.,-3.,-5.,-2.,-4.,-4.,-4., 0.,-4.,-4.,-2.,-1.,-1.,-2., 7.,10., 0.}, /* Y ... Tyrosine */ + {GAP,-8.,-2.,-5.,-6.,-6.,-7.,-4.,-7.,-7.,-5.,-3.,-2.,-2.,-4.,-5.,-2.,-6., 0., 0.,17.}}; /* W ... Tryptophane */ + +/* -------------------------------------------------------------------------- */ + +/* Hogeweg: 'H' ... Hogeweg's matrix for String Edit of Secondary Structures */ + +char StrEdit_HogewegA[6]="_.^()"; +float StrEdit_HogewegM[5][5] = +/* _ . ^ ( ) */ + { { 5., GAP, GAP, GAP, GAP }, /* _ ... */ + { GAP, 0., 1., 1., 1. }, /* . ... unpaired */ + { GAP, 1., 0., 1., 1. }, /* ^ ... hairpin-unpaired */ + { GAP, 1., 1., 0., DINF }, /* ( ... paired upstream */ + { GAP, 1., 1., DINF, 0. } }; /* ) ... paired downstream */ + +/* -------------------------------------------------------------------------- */ + +char StrEdit_GLHA[22] = "_ACDEFGHIKLMNPQRSTVWY"; +float StrEdit_GLHM[21][21] = { + {21.,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP}, + {GAP, 0.000, .156, .150, .148, .730, .045, .455, .346, .193, .335, + 1.018, .140, .058, .237, .308, .046, .010, .246, .124, .977}, /* ALA */ + {GAP, .156, 0.000, .219, .206, .779, .188, .412, .389, .150, .318, + .870, .183, .198, .225, .256, .149, .149, .289, .073, .940}, /* CYS */ + {GAP, .150, .219,0.000, .017, .840, .120, .337, .494, .129, .479, + 1.071, .047, .114, .122, .206, .108, .157, .395, .194, .963}, /* ASP */ + {GAP, .148, .206, .017,0.000, .836, .122, .328, .493, .114, .473, + 1.057, .030, .117, .110, .194, .103, .154, .393, .181, .950}, /* GLU */ + {GAP, .730, .779, .840, .836,0.000, .753,1.036, .595, .864, .586, + 1.301, .822, .763, .900, .957, .761, .729, .617, .726, .920}, /* PHE */ + {GAP, .045, .188, .120, .122, .753,0.000, .444, .376, .193, .377, + 1.055, .124, .014, .224, .302, .046, .054, .279, .157, .989}, /* GLY */ + {GAP, .455, .412, .337, .328,1.036, .444,0.000, .785, .279, .718, + 1.044, .321, .442, .225, .171, .411, .459, .682, .404, .824}, /* HIS */ + {GAP, .346, .389, .494, .493, .595, .376, .785,0.000, .513, .159, + 1.006, .485, .385, .575, .631, .391, .340, .103, .385,1.143}, /* ILE */ + {GAP, .193, .150, .129, .114, .864, .193, .279, .513,0.000, .461, + .954, .093, .194, .077, .119, .152, .193, .410, .152, .919}, /* LYS */ + {GAP, .335, .318, .479, .473, .586, .377, .718, .159, .461,0.000, + .872, .456, .389, .530, .571, .372, .327, .142, .319,1.035}, /* LEU */ + {GAP, 1.018, .870,1.071,1.057,1.301,1.055,1.044,1.006, .954, .872, + 0.000,1.033,1.065,1.013, .966,1.018,1.010, .977, .921,1.282}, /* MET */ + {GAP, .140, .183, .047, .030, .822, .124, .321, .485, .093, .456, + 1.033,0.000, .122, .102, .184, .095, .146, .383, .156, .930}, /* ASN */ + {GAP, .058, .198, .114, .117, .763, .014, .442, .385, .194, .389, + 1.065, .122,0.000, .222, .301, .054, .067, .289, .168, .996}, /* PRO */ + {GAP, .237, .225, .122, .110, .900, .224, .225, .575, .077, .530, + 1.013, .102, .222,0.000, .086, .192, .241, .472, .216, .910}, /* GLN */ + {GAP, .308, .256, .206, .194, .957, .302, .171, .631, .119, .571, + .966, .184, .301, .086,0.000, .265, .310, .528, .261, .901}, /* ARG */ + {GAP, .046, .149, .108, .103, .761, .046, .411, .391, .152, .372, + 1.018, .095, .054, .192, .265,0.000, .051, .289, .117, .963}, /* SER */ + {GAP, .010, .149, .157, .154, .729, .054, .459, .340, .193, .327, + 1.010, .146, .067, .241, .310, .051,0.000, .239, .119, .979}, /* THR */ + {GAP, .246, .289, .395, .393, .617, .279, .682, .103, .410, .142, + .977, .383, .289, .472, .528, .289, .239,0.000, .282,1.076}, /* VAL */ + {GAP, .124, .073, .194, .181, .726, .157, .404, .385, .152, .319, + .921, .156, .168, .216, .261, .117, .119, .282,0.000, .893}, /* TRP */ + {GAP, .977, .940, .963, .950, .920, .989, .824,1.143, .919,1.035, + 1.282, .930, .996, .910, .901, .963, .979,1.076, .893,0.000}, /* TYR */ +}; + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/cluster.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/cluster.c new file mode 100755 index 000000000..3cf754036 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/cluster.c @@ -0,0 +1,281 @@ +/* Last changed Time-stamp: <95/07/12 19:52:41 ivo> */ +/* + Cluster Analysis using Ward's Method + Ward J Amer Stat Ass, 58 (1963), p236 + c Peter Stadler and Ivo Hofacker +*/ +#include +#include +#include +#include "utils.h" + +#define PUBLIC +#define PRIVATE static + +#define INFINITY 1000000 + +typedef struct{ + int set1; + int set2; + float distance; + float distance2; + } Union; + +typedef struct { + int type; + int weight; + int father; + int sons; + int leftmostleaf; + } Postorder_list; + +PUBLIC Union *wards_cluster(float **clmat); +PUBLIC Union *neighbour_joining(float **clmat); +PUBLIC void printf_phylogeny(Union *tree, char *type); + + +/*--------------------------------------------------------------------*/ + +PUBLIC Union *wards_cluster(float **clmat) +{ + float **d; + int *indic; + int *size; + float *help; + Union *tree; + + float min,deno,xa,xb,x; + int i,j,step,s=0,t=0,n; + + n= (int)(clmat[0][0]); + + size = (int *) space((n+1)*sizeof(int)); + d = (float **) space((n+1)*sizeof(float *)); + for(i=0;i<=n;i++) + d[i] = (float *) space((n+1)*sizeof(float)); + indic = (int *) space((n+1)*sizeof(int)); + help = (float *) space((n+1)*sizeof(float)); + tree = (Union *) space((n+1)*sizeof(Union)); + + tree[0].set1 = n; + tree[0].set2 = 0; + tree[0].distance = 0.0; + tree[0].distance2 = 0.0; + + for (i=1;i<=n;i++) size[i]=1; + for (i=1; i<=n; i++){ + for(j=1; j<=n; j++){ + d[i][j] = clmat[i][j]; + } + } + + /* look for the indices [s,t] with minimum d[s][t]*/ + for(step=1;step %d %s ( Phylogeny using ",n, type); + switch(type[0]){ + case 'W' : + printf("Ward's Method )\n"); + printf("> Nodes Variance\n"); + for(i=1; i Nodes Branch Length in Tree\n"); + for(i=1; i +#include +#include +#include +#include "utils.h" +#include "StrEdit_CostMatrix.h" + +#define PUBLIC +#define PRIVATE static +#define MAXSEQS 1000 +#define MIN(A, B) ((A) < (B) ? (A) : (B)) +#define MIN3(A,B,C) (MIN((MIN((A),(B))),(C))) +#define MAX(A, B) ((A) > (B) ? (A) : (B)) + +PUBLIC float **read_distance_matrix(char type[]); +PUBLIC char **read_sequence_list(int *n_of_seqs, char *mask); +PUBLIC float **Hamming_Distance_Matrix(char **seqs, int n_of_seqs); +PUBLIC float **StrEdit_SimpleDistMatrix(char **seqs, int n_of_seqs); +PUBLIC float **StrEdit_GotohDistMatrix(char **seqs, int n_of_seqs); +PUBLIC void free_distance_matrix(float **x); +PUBLIC void printf_distance_matrix(float **x); +PUBLIC void printf_taxa_list(void); +PUBLIC char *get_taxon_label(int whoami); +PUBLIC float StrEdit_SimpleDist(char *str1, char *str2); +PUBLIC float StrEdit_GotohDist(char *str1, char *str2); +PUBLIC void Set_StrEdit_CostMatrix(char type); +PUBLIC void Set_StrEdit_GapCosts(float per_digit, float per_gap); + +/* NOTE: x[0][0] = (float)size_of_matrix; */ + +PRIVATE void read_taxa_list(void); +PRIVATE int string_consists_of(char line[],char *mask); +PRIVATE float StrEditCost( int i, int j, char *T1, char *T2); +PRIVATE int decode(char id); + +PRIVATE char Taxa_List[MAXSEQS][50]; +PRIVATE int Taxa_Numbers[MAXSEQS]; +PRIVATE int N_of_named_taxa=0; +PRIVATE char *file_name; +PRIVATE char N_of_infiles=0; +PRIVATE float **StrEdit_CostMatrix; +PRIVATE char *StrEdit_ValidAlphabet; +PRIVATE float StrEdit_GapCost = 1.; +PRIVATE float StrEdit_GotohAlpha = 1.; +PRIVATE float StrEdit_GotohBeta = 1.; + + + +PUBLIC float **read_distance_matrix(char type[]) +{ + char *line; + float **D; + float tmp; + int i,j,size; + + while(1) { + type[0]= '\0'; + size = 0; + D = NULL; + if ((line = get_line(stdin))==NULL) return NULL; + if (*line =='@') return NULL; + if (*line =='*') { + N_of_infiles++; + if(file_name) free(file_name); + + if(strlen(line)>1) { + file_name = (char *) space(sizeof(char)*strlen(line)); + sscanf(line,"*%s",file_name); + } else { + file_name = (char *) space(10); + sprintf(file_name,"%d",N_of_infiles); + } + read_taxa_list(); + } + else if (*line=='>') { + int r; + size = 0; + r = sscanf(line,"> %1s%*[ ] %d", type, &size); + fprintf(stderr, "%d ", r); + if (r==EOF) return NULL; + if((r==2)&&(size>1)) { + D=(float **)space((size+1)*sizeof(float *)); + for(i=0; i<=size; i++) + D[i] = (float *)space((size+1)*sizeof(float)); + D[0][0] = (float)size; + D[1][1] = 0.0; + for(i=2; i<= size; i++) { + D[i][i] = 0.0; + for(j=1; j1) { + file_name = (char *) space(sizeof(char)*strlen(line)); + sscanf(line,"*%s",file_name); + } else { + file_name = (char *) space(10); + sprintf(file_name,"%d",N_of_infiles); + } + read_taxa_list(); + free(line); + continue; + } + + len = strlen(line); + if(string_consists_of(line,mask)){ + if(mask[0]=='%') { + for(i=0;i false */ + return 1; /* loop left after last char -> true */ +} +/* -------------------------------------------------------------------------- */ + +PUBLIC void free_distance_matrix(float **x) +{ + int i,n; + n=(int) x[0][0]; + for(i=0;i<=n;i++) free(x[i]); + free(x); + x=NULL; +} + +/* -------------------------------------------------------------------------- */ + +PUBLIC void printf_distance_matrix(float **x) +{ + int i,j,n; + n=(int) x[0][0]; + printf("> X %d\n",n); + if(n>1){ + for(i=2;i<=n;i++) { + for(j=1;j0){ + printf("* List of Taxa: %s\n", file_name); + for(i=0;i0) i1 = decode(T1[i-1]); else i1 = 0; + if(j>0) j1 = decode(T2[j-1]); else j1 = 0; + if(StrEdit_CostMatrix==NULL) { + if(i&&j) return (float)(i1!=j1); + else return (float) StrEdit_GapCost; + } + else return (float) StrEdit_CostMatrix[i1][j1]; +} + +/* -------------------------------------------------------------------------- */ + +PRIVATE int decode(char id) +{ + int n,alen; + + if (!StrEdit_ValidAlphabet) return (int)id; + alen = strlen(StrEdit_ValidAlphabet); + if(!alen) return (int)id; + + for(n=0;n set to ~gap~\n"); + return 0; +} + +/* -------------------------------------------------------------------------- */ + +PUBLIC void Set_StrEdit_CostMatrix(char type) +{ + int i,j; + if(StrEdit_ValidAlphabet) { + free(StrEdit_ValidAlphabet); + StrEdit_ValidAlphabet = NULL; + } + if(StrEdit_CostMatrix) { + free(StrEdit_CostMatrix); + StrEdit_CostMatrix = NULL; + } + switch(type){ + case 'D' : + StrEdit_ValidAlphabet = (char*) space((20+2)*sizeof(char)); + strcpy(StrEdit_ValidAlphabet,StrEdit_DayhoffA); + StrEdit_CostMatrix = (float**) space((20+1)*sizeof(float*)); + for(i=0;i<=20;i++) + StrEdit_CostMatrix[i] = (float*)space((20+1)*sizeof(float)); + for(i=1;i<=20;i++) { + for(j=1;j<=20;j++) { + StrEdit_CostMatrix[i][j] = + MAX(StrEdit_DayhoffM[i][i],StrEdit_DayhoffM[j][j])- + StrEdit_DayhoffM[i][j]; + } + StrEdit_CostMatrix[i][0] = StrEdit_DayhoffM[i][i]; + StrEdit_CostMatrix[0][i] = StrEdit_DayhoffM[i][i]; + } + StrEdit_CostMatrix[0][0] = StrEdit_DayhoffM[0][0]; + break; + case 'A' : + StrEdit_ValidAlphabet = (char*) space((20+2)*sizeof(char)); + strcpy(StrEdit_ValidAlphabet,StrEdit_GLHA); + StrEdit_CostMatrix = (float**) space((20+1)*sizeof(float*)); + for(i=0;i<=20;i++) + StrEdit_CostMatrix[i] = (float*)space((20+1)*sizeof(float)); + for(i=1;i<=20;i++) { + for(j=1;j<=20;j++) + StrEdit_CostMatrix[i][j] = StrEdit_GLHM[i][j]; + StrEdit_CostMatrix[i][0] = StrEdit_CostMatrix[0][i] = + StrEdit_GapCost; + } + StrEdit_CostMatrix[0][0] = StrEdit_GLHM[0][0]; + break; + case 'B' : + StrEdit_ValidAlphabet = space((4+2)*sizeof(char)); + strcpy(StrEdit_ValidAlphabet,StrEdit_BinCodeA); + StrEdit_CostMatrix = (float**) space((4+1)*sizeof(float*)); + for(i=0;i<=4;i++) + StrEdit_CostMatrix[i] = (float*)space((4+1)*sizeof(float)); + for(i=0;i<=4;i++) + for(j=0;j<=4;j++) + StrEdit_CostMatrix[i][j] = StrEdit_BinCodeM[i][j]; + break; + case 'H' : + StrEdit_ValidAlphabet = space((4+2)*sizeof(char)); + strcpy(StrEdit_ValidAlphabet,StrEdit_HogewegA); + StrEdit_CostMatrix = (float**) space((4+1)*sizeof(float*)); + for(i=0;i<=4;i++) + StrEdit_CostMatrix[i] = (float*)space((4+1)*sizeof(float)); + for(i=0;i<=4;i++) + for(j=0;j<=4;j++) + StrEdit_CostMatrix[i][j] = StrEdit_HogewegM[i][j]; + StrEdit_GotohAlpha = 3.; + StrEdit_GotohBeta = 0.; + break; + default: + if(!StrEdit_GapCost) StrEdit_GapCost = 1.; /* This is the simple distance */ + } +} + +/* -------------------------------------------------------------------------- */ + +PUBLIC void Set_StrEdit_GapCosts(float per_digit, float per_gap) +{ + if(per_gap==0.) per_gap = per_digit; + if(per_digit<0) nrerror("Gap Costs invalid."); + if(per_digit>per_gap) nrerror("Gap Costs invalid."); + + StrEdit_GapCost = per_digit; + StrEdit_GotohAlpha = per_digit; /* Gotoh gap function g(k) = a + b(k-1) */ + StrEdit_GotohBeta = per_gap; + +} + +/* -------------------------------------------------------------------------- */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/distance_matrix.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/distance_matrix.h new file mode 100755 index 000000000..896598c75 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/distance_matrix.h @@ -0,0 +1,14 @@ +extern float **read_distance_matrix(char type[]); +extern char **read_sequence_list(int *n_of_seqs,char *mask); +extern float **Hamming_Distance_Matrix(char **seqs, int n_of_seqs); +extern float **StrEdit_SimpleDistMatrix(char **seqs, int n_of_seqs); +extern float **StrEdit_GotohDistMatrix(char **seqs, int n_of_seqs); +extern char *get_taxon_label(int whoami); +extern void free_distance_matrix(float **x); +extern void printf_distance_matrix(float **x); +extern void printf_taxa_list(void); +extern float StrEdit_SimpleDist(char *str1, char *str2); +extern float StrEdit_GotohDist(char *str1, char *str2); +extern void Set_StrEdit_CostMatrix(char type); +extern void Set_StrEdit_GapCosts(float per_digit, float per_gap); + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/split.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/split.c new file mode 100755 index 000000000..7d2d77de3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/split.c @@ -0,0 +1,332 @@ +/* Last changed Time-stamp: <95/07/12 19:49:53 ivo>*/ +/* + Split Decomposition of Distance Matrices + as described by H.J.Bandelt and A.W.M.Dress + Adv Math, 92 (1992) p47 + c Peter Stadler and Ivo L. Hofacker +*/ +#include +#include +#include +#include "utils.h" + +#define PUBLIC +#define PRIVATE static +#define DEBUG 0 +#define SHORT_OUTPUT 1 + +#define DINFTY 1.e32 +#define ZERO 1.e-10 + + +typedef struct { + short *splitlist[2]; + int splitsize; + double isolation_index; } Split; + +PUBLIC Split *split_decomposition(float **dist); +PUBLIC void free_Split(Split *x); +PUBLIC void print_Split(Split *x); +PUBLIC void sort_Split(Split *x); + +PUBLIC Split *split_decomposition(float **dist) +{ + + int elm, n_of_splits; + short *full_slots; + int i,j,sp,new_sp,spp; + int i2,j1,j2,maxlen; + int x,y,z; + double alpha,beta,tmp; + double test1,test2; + Split *SD, *S; + int number_of_points; + + number_of_points = (int) dist[0][0]; + + /* Initialize */ + elm = 2; + n_of_splits = 1; + maxlen = (number_of_points+1)*(number_of_points+1); + full_slots = (short *) space(2*(maxlen+1)*sizeof(short)); + full_slots[1]=1; + + SD = space((maxlen+1)*sizeof(Split)); + + SD[0].splitlist[0] = NULL; + SD[0].splitlist[1] = NULL; + SD[0].splitsize = 1; + SD[0].isolation_index = 0.0; + /**/ + SD[1].splitlist[0] = (short *) space((number_of_points+1)*sizeof(short)); + SD[1].splitlist[0][0] = number_of_points; + SD[1].splitlist[0][1] = 1; + SD[1].splitlist[1] = (short *) space((number_of_points+1)*sizeof(short)); + SD[1].splitlist[1][1] = 2; + SD[1].splitsize = 1; + SD[1].isolation_index = dist[1][2]; + + + /* Iteration */ + + for( elm=3; elm <= number_of_points; elm++){ + + for (sp=1, spp=n_of_splits;sp<=n_of_splits; sp++){ + + SD[sp].splitlist[0][0] = elm; + + /* 1. Split = {old_A | old_B+{elm}} */ + + alpha = 2.0*SD[sp].isolation_index; + for(i2=1; i2<=(elm - SD[sp].splitsize); i2++){ + if(i2==(elm-SD[sp].splitsize)) { + x = elm; + } + else{ + x= SD[sp].splitlist[1][i2]; + } + for(j1=1; j1 <= SD[sp].splitsize; j1++){ + y= SD[sp].splitlist[0][j1]; + for(j2=1; j2 <= (SD[sp].splitsize); j2++){ + z= SD[sp].splitlist[0][j2]; + + /* calculate the value beta = beta(elm,x; y,z) */ + + beta = dist[elm][y] + dist[x][z]; + tmp = dist[elm][z] + dist[x][y]; + if(tmp>beta) beta=tmp; + tmp = dist[elm][x] + dist[y][z]; + if(tmp>beta) beta=tmp; + beta -= ( dist[elm][x] + dist[y][z] ); + + if(beta ZERO){ + /* add {old_A | old_B + {elm}} to the split-list */ + spp++; + full_slots[spp] =1; + SD[spp].splitsize = SD[sp].splitsize; + SD[spp].isolation_index = alpha; + SD[spp].splitlist[0] = (short *) space((number_of_points+1)*sizeof(short)); + SD[spp].splitlist[0][0] = elm; + SD[spp].splitlist[1] = (short *) space((number_of_points+1)*sizeof(short)); + for(i=1; i<=SD[spp].splitsize; i++) + SD[spp].splitlist[0][i] = SD[sp].splitlist[0][i]; + for(i=1; i<=(elm-1-SD[spp].splitsize); i++) + SD[spp].splitlist[1][i] = SD[sp].splitlist[1][i]; + SD[spp].splitlist[1][elm-SD[spp].splitsize] = elm; + } + + /* 2. Split = {old_A+{elm} | old_B} */ + + alpha = 2.0*SD[sp].isolation_index; + for(i2=1; i2<= (SD[sp].splitsize+1); i2++){ + if(i2==(SD[sp].splitsize+1)){ + x= elm; + } + else + { + x= SD[sp].splitlist[0][i2]; + } + for(j1=1; j1 <= (elm-1-SD[sp].splitsize); j1++){ + y= SD[sp].splitlist[1][j1]; + for(j2=1; j2 <= (elm-1-SD[sp].splitsize); j2++){ + z= SD[sp].splitlist[1][j2]; + + /* calculate the value beta = beta(elm,x; y,z) */ + + beta = dist[elm][y] + dist[x][z]; + tmp = dist[elm][z] + dist[x][y]; + if(tmp>beta) beta=tmp; + tmp = dist[elm][x] + dist[y][z]; + if(tmp>beta) beta=tmp; + beta -= ( dist[elm][x] + dist[y][z] ); + + if(beta ZERO){ + /* replace {old_A | old_B} by {old_A+{elm} | old_B} in the splitlist */ + SD[sp].splitsize++; + SD[sp].splitlist[0][SD[sp].splitsize] = elm; + SD[sp].isolation_index = alpha; + } + else{ + /* remove {old_A | old_B} from the split list */ + full_slots[sp] = 0; + free(SD[sp].splitlist[0]); + SD[sp].splitlist[0] = NULL; + free(SD[sp].splitlist[1]); + SD[sp].splitlist[1] = NULL; + SD[sp].splitsize = 0; + SD[sp].isolation_index = 0.0; + } + } + + /* 3. Split = { {elm} | {1,...,elm-1} } */ + + alpha=DINFTY; + for(i=1;i<=elm-1;i++){ + for(j=1; j<=elm-1;j++){ + tmp = dist[elm][i]+dist[elm][j] - dist[i][j]; + if( tmp < alpha) alpha = tmp; + } + } + alpha/=2.; + if (alpha > ZERO){ + spp++; + full_slots[spp] = 1; + SD[spp].splitsize = 1; + SD[spp].isolation_index = alpha; + SD[spp].splitlist[0] = (short *) space((number_of_points+1)*sizeof(short)); + SD[spp].splitlist[0][0] = elm; + SD[spp].splitlist[1] = (short *) space((number_of_points+1)*sizeof(short)); + SD[spp].splitlist[0][1] = elm; + for (i=1; i<= elm-1; i++) + SD[spp].splitlist[1][i] = i; + } + /* note that spp now points to the last entry in the splitlist !!! */ + + /* garbage collection .... unfortunately a bit boring */ + + for ( sp=1, new_sp=0; sp<= spp; sp++ ){ + if (full_slots[sp]){ + new_sp++; + if(sp != new_sp){ + /* copy all the junk from sp to new_sp */ + full_slots[new_sp]=1; full_slots[sp]=0; + SD[new_sp].splitsize = SD[sp].splitsize; + SD[new_sp].isolation_index = SD[sp].isolation_index; + if(SD[new_sp].splitlist[0]==NULL) + SD[new_sp].splitlist[0] = (short *) space((number_of_points+1)*sizeof(short)); + if(SD[new_sp].splitlist[1]==NULL) + SD[new_sp].splitlist[1] = (short *) space((number_of_points+1)*sizeof(short)); + for(i=0;i<=elm;i++){ + SD[new_sp].splitlist[0][i] = SD[sp].splitlist[0][i]; + SD[new_sp].splitlist[1][i] = SD[sp].splitlist[1][i]; + } + free(SD[sp].splitlist[0]); + SD[sp].splitlist[0] = NULL; + free(SD[sp].splitlist[1]); + SD[sp].splitlist[1] = NULL; + SD[sp].splitsize = 0; + SD[sp].isolation_index = 0.0; + } + } + } + n_of_splits = new_sp; + SD[0].splitsize = n_of_splits; +#if DEBUG + for(test1=0, i=2; i<=elm; i++) for( j=1; j %d Split Decomposition",x[0].splitsize); + for (k=1; k<=x[0].splitsize; k++) { + if( (x[k].splitlist[0])&&(x[k].splitlist[1]) ) { + printf("\n%3d %8.4f : {",k,x[k].isolation_index); + for(j=1;j<=x[k].splitsize;j++) + printf(" %3d",x[k].splitlist[0][j]); + printf(" |"); +#if SHORT_OUTPUT + printf(" ..."); +#else + for(j=1;j<=(x[k].splitlist[0][0]-x[k].splitsize);j++) + printf(" %3d",x[k].splitlist[1][j]); + printf(" } "); +#endif + } + } + printf("\n %8.4f : { [Split prime fraction] }\n", x[0].isolation_index); +} + + +/* -------------------------------------------------------------------------- */ + +int CompareSplit(const void *v1 , const void *v2) +{ + Split *S1, *S2; + + S1 = (Split *) v1; S2 = (Split *) v2; + if(S1->isolation_index < S2->isolation_index) return +1; + if(S2->isolation_index < S1->isolation_index) return -1; + return 0; +} + +/* -------------------------------------------------------------------------- */ + +PUBLIC void sort_Split(Split *x) +{ + int i,j; + int t1; + + qsort((void *) &(x[1]), x[0].splitsize ,sizeof(Split),CompareSplit ); + + for(i=1; i<=x[0].splitsize; i++) { + if(x[i].splitsize > x[i].splitlist[0][0]-x[i].splitsize) { + for(j=1; j<=x[i].splitsize; j++) { + t1 = x[i].splitlist[0][j]; + x[i].splitlist[0][j] = x[i].splitlist[1][j]; + x[i].splitlist[1][j] = t1; + } + x[i].splitsize = x[i].splitlist[0][0]-x[i].splitsize; + } + } +} + + +/* -------------------------------------------------------------------------- */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/split.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/split.h new file mode 100755 index 000000000..caa7079e5 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/split.h @@ -0,0 +1,14 @@ +typedef struct { + int *split_list[2]; + int split_size; + double isolation_index; } Split; + +extern Split *split_decomposition(float **dist); +extern void free_Split(Split *x); +extern void sort_Split(Split *x); +extern void print_Split(Split *x); + + +/* Auxiliary information contained in datatype 'Split': + Split[0].splitsize .... contains the total number of splits. +*/ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/statgeom.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/statgeom.c new file mode 100755 index 000000000..4bd03a5ce --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/statgeom.c @@ -0,0 +1,513 @@ +/* Quadruple Statistics on an arbitrary alphabet + + Vienna RNA Package --- Peter F Stadler 1993 + +*/ + +#include +#include +#include +#include "utils.h" +#include "PS3D.h" +#include "distance_matrix.h" + +#define PUBLIC +#define PRIVATE static + +#define MIN2(A, B) ((A) < (B) ? (A) : (B)) +#define MIN4(A, B, C, D) MIN2( (MIN2((A),(B))), (MIN2((C),(D))) ) +#define MAX2(A, B) ((A) > (B) ? (A) : (B)) +#define MAX4(A, B, C, D) MAX2( (MAX2((A),(B))), (MAX2((C),(D))) ) + +PRIVATE int IBox[16]; + + +PUBLIC float *statgeom(char **seqs, int n_of_seqs); +PUBLIC float *statgeom4(char **ss[4], int nn[4]); +PUBLIC void printf_stg(float *B); + +PRIVATE void SingleBox(char *x1, char *x2, char *x3, char *x4); +PRIVATE void SortSingleBox(void); + +/* ----------------------------------------------------------------------- */ + +PUBLIC float *statgeom(char **seqs, int n_of_seqs) +{ + int i,j,k,l; + int i1; + + float *B; + float temp; + + if(n_of_seqs < 4) { + fprintf(stderr,"Less than 4 sequences for statistical geometry.\n"); + return NULL; + } + + B = (float *) space(16*sizeof(float)); + + for(i=3; i Statistical Geometry.\n"); + printf("> %d (sequence length)\n", (int) B[0]); + printf("> AAAA\n"); + printf(" %7.5f\n", B[1]); + printf("> BAAA ABAA AABA AAAB\n"); + printf(" %7.5f %7.5f %7.5f %7.5f\n", B[2],B[3],B[4],B[5]); + printf("> AABB ABAB ABBA\n"); + printf(" %7.5f %7.5f %7.5f\n", B[6],B[7],B[8]); + printf("> AABC ABAC ABCA BAAC BACA BCAA\n"); + printf(" %7.5f %7.5f %7.5f %7.5f %7.5f %7.5f\n" + ,B[9],B[10],B[11],B[12],B[13],B[14]); + printf("> ABCD\n"); + printf(" %7.5f\n",B[15]); +} + +/* ------------------------------------------------------------------------- */ + + +PUBLIC void SimplifiedBox(float *B, char *filename) +{ + char *tmp, temp[50]; + float X,Y,Z; + float T,P; + float t1, t2, t3, t4; + float p1, p2, p3, p4; + float x1, x2, y1, y2,z1,z2; + FILE *fp; + float view[3] = {0.3, 1.5, 0.1}; + float axis[3] = {1.0, 0.0, 0.0}; + + t1 = B[9]+B[10]+B[11]+B[15]; + t2 = B[9]+B[12]+B[13]+B[15]; + t3 = B[10]+B[12]+B[14]+B[15]; + t4 = B[11]+B[13]+B[14]+B[15]; + + p1 = B[2]; p2 = B[3]; p3 = B[4]; p4 = B[5]; + + x1 = B[6] + B[14]; + x2 = B[6] + B[9]; + y1 = B[7] + B[13]; + y2 = B[7] + B[10]; + z1 = B[8] + B[12]; + z2 = B[8] + B[11]; + + X = (x1+x2)/2.; Y = (y1+y2)/2.; Z = (z1+z2)/2; + T = (t1+t2+t3+t4)/4.; + P = (p1+p2+p3+p4)/4.; + + printf("> X = %7.5f \n",X); + printf("> Y = %7.5f \n",Y); + printf("> Z = %7.5f \n",Z); + printf("> T = %7.5f \n",T); + printf("> P = %7.5f \n",P); + + tmp = get_taxon_label(-1); /* retrieve the dataset identifier */ + + temp[0]='\0'; + if(tmp) { strcat(temp,tmp);strcat(temp,"_"); free(tmp); } + strcat(temp,filename); + + fp = fopen(temp,"w"); + if (fp!=NULL) { + ps3d_Preambel(fp, view, axis, "N"); + PS_DrawSimplifiedBox(X,Y,Z,T,P, fp); + fclose(fp); + } else fprintf(stderr,"couldn't open %s -- not drawing box\n", temp); +} + + + +/* ------------------------------------------------------------------------- */ + +PRIVATE void SingleBox(char *x1, char *x2, char *x3, char *x4) +{ + int len,i1,j1,k1,i,M,m; + int d[4]; + char t[4]; + + len=strlen(x1); + if(strlen(x2)!=len) nrerror("Sequences of unequal length in 'SingleBox'"); + if(strlen(x3)!=len) nrerror("Sequences of unequal length in 'SingleBox'"); + if(strlen(x4)!=len) nrerror("Sequences of unequal length in 'SingleBox'"); + + IBox[0] = len; + for(i=1; i<=15; i++) IBox[i] = 0; + + for(i1=0;i1= IBox[14] ) { /* 1,2 > 3,4 */ + IBB[9] = IBox[9]; + IBB[14] = IBox[14]; + if( IBox[7] >= IBox[8] ) { /* 13|24 */ + IBB[7] = IBox[7]; + IBB[8] = IBox[8]; + if( IBox[10] >= IBox[13] ) { /* 1>2>3>4 */ + IBB[10] = IBox[10]; + IBB[13] = IBox[13]; + IBB[11] = IBox[11]; + IBB[12] = IBox[12]; + s[0]=0; s[1]=1; s[2]=2; s[3]=3; /* 1 2 3 4 */ + } + else { /* 2>1>4>3 */ + IBB[10] = IBox[13]; + IBB[13] = IBox[10]; + IBB[11] = IBox[12]; + IBB[12] = IBox[11]; + s[0]=1; s[1]=0; s[2]=3; s[3]=2; /* 2 1 4 3 */ + } + } + else { /* 14|23 */ + IBB[7] = IBox[8]; + IBB[8] = IBox[7]; + if( IBox[11] >= IBox[12]) { /* 1>2>4>3 */ + IBB[10] = IBox[11]; + IBB[13] = IBox[12]; + IBB[11] = IBox[10]; + IBB[12] = IBox[13]; + s[0]=0; s[1]=1; s[2]=3; s[3]=2; /* 1 2 4 3 */ + } + else { /* 2>1>3>4 */ + IBB[10] = IBox[12]; + IBB[13] = IBox[11]; + IBB[11] = IBox[13]; + IBB[12] = IBox[10]; + s[0]=1; s[1]=0; s[2]=2; s[3]=3; /* 2 1 3 4 */ + } + } + } + else { /* 3,4 > 1,2 */ + IBB[9] = IBox[14]; + IBB[14]= IBox[9]; + if( IBox[7] >= IBox[8] ) { /* 31|42 */ + IBB[7] = IBox[7]; + IBB[8] = IBox[8]; + if(IBox[10] >= IBox[13]) { /* 3>4>1>2 */ + IBB[10] = IBox[10]; + IBB[13] = IBox[13]; + IBB[11] = IBox[12]; + IBB[12] = IBox[11]; + s[0]=2; s[1]=3; s[2]=0; s[3]=1; /* 3 4 1 2 */ + } + else { /* */ + IBB[10] = IBox[13]; + IBB[13] = IBox[10]; + IBB[11] = IBox[11]; + IBB[12] = IBox[12]; + s[0]=3; s[1]=2; s[2]=1; s[3]=0; /* 4 3 2 1 */ + } + } + else { /* 32|14 */ + IBB[7] = IBox[8]; + IBB[8] = IBox[7]; + if( IBox[11] >= IBox[12]) { /* 3>4>2>1 */ + IBB[10] = IBox[12]; + IBB[13] = IBox[11]; + IBB[11] = IBox[10]; + IBB[12] = IBox[13]; + s[0]=2; s[1]=3; s[2]=1; s[3]=0; /* 3 4 2 1 */ + } + else { /* 2>1>3>4 */ + IBB[10] = IBox[10]; + IBB[13] = IBox[13]; + IBB[11] = IBox[12]; + IBB[12] = IBox[11]; + s[0]=2; s[1]=3; s[2]=0; s[3]=1; /* 3 4 1 2 */ + } + } + } + } + else if (M == IBox[7] ) { /* 13|24 */ + IBB[6] = IBox[7]; + if( IBox[10] >= IBox[13] ) { /* 1,3 > 2,4 */ + IBB[9] = IBox[10]; + IBB[14] = IBox[13]; + if( IBox[6] >= IBox[8]) { /* 12|34 */ + IBB[7] = IBox[6]; + IBB[8] = IBox[8]; + if( IBox[9] >= IBox[14] ) { /* 1,2>3,4 */ + IBB[10] = IBox[9]; + IBB[13] = IBox[14]; + IBB[11] = IBox[11]; + IBB[12] = IBox[12]; + s[0]=0; s[1]=2; s[2]=1; s[3]=3; /* 1 3 2 4 */ + } + else { + IBB[10] = IBox[14]; + IBB[13] = IBox[9]; + IBB[11] = IBox[12]; + IBB[12] = IBox[11]; + s[0]=2; s[1]=0; s[2]=3; s[3]=1; /* 3 1 4 2 */ + } + } + else { /* 14|23 */ + IBB[7] = IBox[8]; + IBB[8] = IBox[6]; + if( IBox[11] >= IBox[12] ){ /* 1,4 > 2,3 */ + IBB[10] = IBox[11]; + IBB[13] = IBox[12]; + IBB[11] = IBox[9]; + IBB[12] = IBox[14]; + s[0]=0; s[1]=2; s[2]=3; s[3]=1; /* 1 3 4 2 */ + } + else { + IBB[10] = IBox[12]; + IBB[13] = IBox[11]; + IBB[11] = IBox[14]; + IBB[12] = IBox[9]; + s[0]=2; s[1]=0; s[2]=1; s[3]=3; /* 3 1 2 4 */ + } + } + } + else { /* 2,4 > 1,3 */ + IBB[9] = IBox[13]; + IBB[14] = IBox[10]; + if( IBox[6] >= IBox[8]) { /* 21|43 */ + IBB[7] = IBox[6]; + IBB[8] = IBox[8]; + if( IBox[9] >= IBox[14] ) { /* 2,1>4,3 */ + IBB[10] = IBox[9]; + IBB[13] = IBox[14]; + IBB[11] = IBox[12]; + IBB[12] = IBox[11]; + s[0]=1; s[1]=3; s[2]=0; s[3]=2; /* 2 4 1 3 */ + } + else { + IBB[10] = IBox[14]; + IBB[13] = IBox[9]; + IBB[11] = IBox[11]; + IBB[12] = IBox[12]; + s[0]=3; s[1]=1; s[2]=2; s[3]=0; /* 4 2 3 1 */ + } + } + else { /* 14|23 */ + IBB[7] = IBox[8]; + IBB[8] = IBox[6]; + if( IBox[11] >= IBox[12] ){ /* 1,4 > 2,3 */ + IBB[10] = IBox[11]; + IBB[13] = IBox[12]; + IBB[11] = IBox[14]; + IBB[12] = IBox[9]; + s[0]=3; s[1]=1; s[2]=0; s[3]=2; /* 4 2 1 3 */ + } + else { + IBB[10] = IBox[12]; + IBB[13] = IBox[11]; + IBB[11] = IBox[9]; + IBB[12] = IBox[14]; + s[0]=1; s[1]=3; s[2]=2; s[3]=0; /* 2 4 3 1 */ + } + } + } + } + else { /* 14 | 23 */ + IBB[6] = IBox[8]; + if( IBox[11] >= IBox[12] ) { /* 1,4 > 2,3 */ + IBB[9] = IBox[11]; + IBB[14] = IBox[12]; + if(IBox[6] >= IBox[7]) { /* 12|34 */ + IBB[7] = IBox[6]; + IBB[8] = IBox[7]; + if(IBox[9] >= IBox[14]) { /* 1,2>3,4 */ + IBB[10] = IBox[9]; + IBB[13] = IBox[14]; + IBB[11] = IBox[10]; + IBB[12] = IBox[13]; + s[0]=0; s[1]=3; s[2]=1; s[3]=2; /* 1 4 2 3 */ + } + else { /* 4,3>2,1 */ + IBB[10] = IBox[14]; + IBB[13] = IBox[9]; + IBB[11] = IBox[13]; + IBB[12] = IBox[10]; + s[0]=3; s[1]=0; s[2]=2; s[3]=1; /* 4 1 3 2 */ + } + } + else { /* 13|24 */ + IBB[7] = IBox[7]; + IBB[8] = IBox[6]; + if( IBox[10] >= IBox[13]) { /* 1,3 > 2,4 */ + IBB[10] = IBox[10]; + IBB[13] = IBox[13]; + IBB[11] = IBox[9]; + IBB[12] = IBox[14]; + s[0]=0; s[1]=3; s[2]=2; s[3]=1; /* 1 4 3 2 */ + } + else { + IBB[10] = IBox[13]; + IBB[13] = IBox[10]; + IBB[11] = IBox[14]; + IBB[12] = IBox[9]; + s[0]=3; s[1]=0; s[2]=1; s[3]=2; /* 4 1 2 3 */ + } + } + } + else { /* 2,3 > 1,4 */ + IBB[9] = IBox[12]; + IBB[14] = IBox[11]; + if(IBox[6] >= IBox[7]) { /* 34|12 */ + IBB[7] = IBox[6]; + IBB[8] = IBox[7]; + if(IBox[9] >= IBox[14]) { /* 2,1>4,3 */ + IBB[10] = IBox[9]; + IBB[13] = IBox[14]; + IBB[11] = IBox[13]; + IBB[12] = IBox[10]; + s[0]=1; s[1]=2; s[2]=0; s[3]=3; /* 2 3 1 4 */ + } + else { /* 4,3>2,1 */ + IBB[10] = IBox[14]; + IBB[13] = IBox[9]; + IBB[11] = IBox[10]; + IBB[12] = IBox[13]; + s[0]=2; s[1]=1; s[2]=3; s[3]=0; /* 3 2 4 1 */ + } + } + else { /* 31|42 */ + IBB[7] = IBox[7]; + IBB[8] = IBox[6]; + if( IBox[10] >= IBox[13]) { /* 1,3 > 2,4 */ + IBB[10] = IBox[10]; + IBB[13] = IBox[13]; + IBB[11] = IBox[14]; + IBB[12] = IBox[9]; + s[0]=2; s[1]=1; s[2]=0; s[3]=4; /* 3 2 1 4 */ + } + else { + IBB[10] = IBox[13]; + IBB[13] = IBox[10]; + IBB[11] = IBox[9]; + IBB[12] = IBox[14]; + s[0]=1; s[1]=2; s[2]=3; s[3]=0; /* 2 3 4 1 */ + } + } + } + } + /* HEUREKA */ + IBB[0] = IBox[0]; + IBB[1] = IBox[1]; + IBB[2] = IBox[2+s[0]]; + IBB[3] = IBox[2+s[1]]; + IBB[4] = IBox[2+s[2]]; + IBB[5] = IBox[2+s[3]]; + /* + IBB[6...14] see above :-) + */ + IBB[15] = IBox[15]; + + for(i=0;i<=15;i++) IBox[i] = IBB[i]; +} + +/* ----------------------------------------------------------------------- */ + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/statgeom.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/statgeom.h new file mode 100755 index 000000000..751191736 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/statgeom.h @@ -0,0 +1,5 @@ +extern float *statgeom(char **seqs, int n_of_seqs); +extern float *statgeom4(char **ss[4], int nn[4]); +extern void printf_stg(float *B); +extern void SimplifiedBox(float *B, char *filename); + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/treeplot.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/treeplot.c new file mode 100755 index 000000000..7a53260d5 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/treeplot.c @@ -0,0 +1,359 @@ +#include +#include +#include +#include "distance_matrix.h" +#include "utils.h" + +#define PUBLIC +#define PRIVATE static +#define MAX(A, B) ((A) > (B) ? (A) : (B)) +#define MIN(A, B) ((A) < (B) ? (A) : (B)) + +#define MAXTAXA_FOR_LABELS 200 + +typedef struct{ + int set1; + int set2; + float distance; + float distance2; + } Union; + +typedef struct _Node_ { + float height; + float brr; + float brl; + int whoami; + int size; + struct _Node_ *father; + struct _Node_ *left; + struct _Node_ *right; + } Node; + +PUBLIC void PSplot_phylogeny(Union *cluster, char *filename, char *type); + +PRIVATE Node *W2Phylo(Union *cluster); +PRIVATE Node *Nj2Phylo(Union *cluster); +PRIVATE void free_phylo_tree(Node *root); +PRIVATE void fill_height_into_tree(Node *root); +PRIVATE void fill_br_from_height(Node *root); +PRIVATE void plot_branch(Node *root, FILE *fp); +PRIVATE void format_number(float x); + +PRIVATE char str[10]; +PRIVATE float threshold; +PRIVATE int print_labels=1; + +/* --------------------------------------------------------------------------*/ + +PUBLIC void PSplot_phylogeny(Union *cluster, char *filename, char *type) +{ + int n; + char outfile[50]; + char *tmp, *tfont; + Node *root; + Node *tempnode; + FILE *fp; + float xsize, ysize, tfontsize, lfontsize, lwidth; + + n = cluster[0].set1; + switch(type[0]) { + case 'W' : + root = W2Phylo(cluster); + break; + case 'N' : + root = Nj2Phylo(cluster); + break; + default : + return; + } + + outfile[0] = '\0'; + tmp = get_taxon_label(-1); /* retrieve data set identifier */ + if(tmp) {strcat(outfile,tmp); strcat(outfile,"_"); free(tmp);} + strcat(outfile,filename); + + fp = fopen(outfile,"w"); + if (fp==NULL) { + fprintf(stderr,"couldn't open %s -- not doing treeplot\n", outfile); + return; + } + xsize = root->size; + tempnode = root; + while(tempnode->right) + tempnode = tempnode->right; + ysize = tempnode->height; + threshold = ysize*0.06; + + lwidth = MIN(1.5, 8/sqrt((double)n)); + tfontsize = MIN(15,550./(10+n)); + lfontsize = 2./3.*tfontsize; + if (n>30) tfont = "Helvetica"; + else tfont = "Times-Roman"; + if(n > MAXTAXA_FOR_LABELS) print_labels=0; + else print_labels=1; + fprintf(fp,"%%!PS-Adobe-2.0 EPSF-1.2\n"); + fprintf(fp,"%%%%Title: TreePlot (%s)\n",type); + fprintf(fp,"%%%%Creator: AnalyseDists\n"); + fprintf(fp,"%%%%CreationDate: %s", time_stamp()); + /* BoundingBox is only approximate */ + fprintf(fp,"%%%%BoundingBox: 35 45 535 640\n"); + fprintf(fp,"%%%%Pages: 1\n"); + fprintf(fp,"%%%%EndComments: No comment!\n"); + fprintf(fp,"288.5 50 translate\n"); + fprintf(fp,"%3.1f setlinewidth\n" + "/cmtx matrix currentmatrix def\n", lwidth); + fprintf(fp,"500 %g div 360 %g div scale\n", xsize, ysize); + fprintf(fp,"/rotshow {gsave cmtx setmatrix\n"); + fprintf(fp," 90 rotate 5 %4.1f rmoveto show grestore} def\n", + -tfontsize/4); + fprintf(fp,"/cshow {gsave cmtx setmatrix\n" + " /Helvetica findfont %4.1f scalefont setfont\n" + " 90 rotate 0 %3.1f rmoveto\n" + " dup stringwidth pop 2 div neg 0 rmoveto show\n" + " grestore} def\n", lfontsize, lfontsize/5); + fprintf(fp,"/%s findfont %4.1f scalefont setfont\n", tfont, tfontsize); + + fprintf(fp,"0 0 moveto\n"); + plot_branch(root,fp); + + fprintf(fp,"cmtx setmatrix stroke\nshowpage\n"); + free_phylo_tree(root); + fclose(fp); + +} + +/* --------------------------------------------------------------------------*/ + +PRIVATE Node *W2Phylo(Union *cluster) +{ + int i,n; + float b; + Node **taxa; + Node *father; + + n=cluster[0].set1; + taxa = (Node **) space(sizeof(Node*)*(n+1)); + + b = sqrt(MAX(cluster[n-1].distance,0.)); + for(i=1;i<=n;i++){ + taxa[i] = (Node *) space(sizeof(Node)); + taxa[i]->whoami = i; + taxa[i]->size = 1; + taxa[i]->height = b; + } + + for(i=1;iwhoami = 0; + father->left = taxa[cluster[i].set1]; + father->right = taxa[cluster[i].set2]; + father->size = father->left->size+father->right->size; + b = sqrt(MAX(cluster[n-1].distance-cluster[i].distance,0.)); + father->height = b; + father->left->father = father; + father->right->father = father; + taxa[cluster[i].set1] = father; + } + free(taxa); + father->whoami = -1; + fill_br_from_height(father); + return father; +} + + +/* --------------------------------------------------------------------------*/ + +PRIVATE void fill_br_from_height(Node *root) +{ + root->brr = root->right->height - root->height; + root->brl = root->left->height - root->height; + if(!root->left->whoami) fill_br_from_height(root->left); + if(!root->right->whoami) fill_br_from_height(root->right); + return; +} + +/* -------------------------------------------------------------------------- */ +#define ORDER(X) \ +if ((X)->brl>(X)->brr) { \ + xnode=(X)->right; \ + (X)->right=(X)->left; \ + (X)->left=xnode; \ + br = (X)->brr; \ + (X)->brr=(X)->brl; \ + (X)->brl=br; \ +} + + + +PRIVATE Node *Nj2Phylo(Union *cluster) +{ + int i,n, br; + float h1,h2,maxdist,dist; + Node **taxa; + Node *father; + Node *topnode; /* of the longest path in the tree */ + Node *tempnode, *xnode; + Node *root; + + maxdist = 0.; + n=cluster[0].set1; + taxa = (Node **) space(sizeof(Node*)*(n+1)); + + for(i=1;i<=n;i++){ + taxa[i] = (Node *) space(sizeof(Node)); + taxa[i]->whoami = i; + taxa[i]->size = 1; + } + + for(i=1;iwhoami = 0; + h1 = cluster[i].distance +taxa[cluster[i].set1]->height; + h2 = cluster[i].distance2+taxa[cluster[i].set2]->height; + dist = h1 + h2; + if(dist > maxdist) { + maxdist = dist; + topnode = father; + } + if(h1<=h2) { + father->brr = cluster[i].distance2; + father->brl = cluster[i].distance; + father->left = taxa[cluster[i].set1]; + father->right = taxa[cluster[i].set2]; + } + else { + father->brr = cluster[i].distance; + father->brl = cluster[i].distance2; + father->left = taxa[cluster[i].set2]; + father->right = taxa[cluster[i].set1]; + } + father->height = MAX(h1,h2); + father->size = father->left->size + father->right->size; + father->left->father = father; + father->right->father = father; + taxa[cluster[i].set1] = father; + } + + /* new root is inserted in the middle of the longest path */ + dist = maxdist/2.; + tempnode = topnode; + while (tempnode->height > dist) + tempnode = tempnode->right; + + topnode = tempnode->father; + /* new root must go between topnode and tempnode */ + h1 = dist - tempnode->height; + h2 = topnode->height - dist ; + + root = (Node *) space(sizeof(Node)); + root->father = NULL; + root->whoami = -1; + root->right = tempnode; + root->left = topnode; + root->height = 0.0; + root->brr = h1; + root->brl = h2; + root->size = n; + + topnode->size = n - tempnode->size; + + tempnode = root; + while(topnode->father) { + topnode->right = topnode->father; + topnode->brr = topnode->father->brr; + topnode->father = tempnode; + tempnode = topnode; + topnode = topnode->right; + topnode->size = tempnode->size - tempnode->left->size; + ORDER(tempnode); + } + /* topnode is now old root, remove it */ + if (tempnode->right==topnode) { + tempnode->right = topnode->left; + tempnode->brr = topnode->brr + topnode->brl; + tempnode->right->father = tempnode; + } else { + tempnode->left = topnode->left; + tempnode->brl = topnode->brr + topnode->brl; + tempnode->left->father = tempnode; + } + free(topnode); + ORDER(root); + + fill_height_into_tree(root); + + return root; +} + +/* -------------------------------------------------------------------------- */ + +PRIVATE void fill_height_into_tree(Node *root) +{ + if(root->whoami>0) return; + root->left->height = root->height + root->brl; + root->right->height = root->height + root->brr; + fill_height_into_tree(root->left); + fill_height_into_tree(root->right); + return; +} + +/* -------------------------------------------------------------------------- */ + +PRIVATE void free_phylo_tree(Node *root) { + if(root->left) free_phylo_tree(root->left); + if(root->right) free_phylo_tree(root->right); + free(root); +} + + +/* -------------------------------------------------------------------------- */ + +PRIVATE void plot_branch(Node *root, FILE *fp) +{ + char *label; + + fprintf(fp,"currentpoint %g 0 rlineto 0 %g rlineto \n", + -(float)(root->left->size)/2., root->brr); + if((print_labels)&&(root->brr > threshold)) { + format_number(root->brr); + fprintf(fp,"currentpoint 0 %g rlineto \n", -root->brr/2.); + fprintf(fp,"(%s) cshow moveto\n", str); + } + if(root->right->whoami==0) plot_branch(root->right,fp); + else if(print_labels) { + label = get_taxon_label(root->right->whoami); + fprintf(fp, "(%s) rotshow\n", label); + free(label); + } + fprintf(fp,"moveto\n"); + fprintf(fp,"currentpoint %g 0 rlineto 0 %g rlineto \n", + +(float)(root->right->size)/2., root->brl); + if((print_labels)&&(root->brl > threshold)) { + format_number(root->brl); + fprintf(fp,"currentpoint 0 %g rlineto \n", -root->brl/2.); + fprintf(fp,"(%s) cshow moveto\n",str); + } + if(root->left->whoami==0) plot_branch(root->left,fp); + else if(print_labels) { + label = get_taxon_label(root->left->whoami); + fprintf(fp, "(%s) rotshow\n", label); + free(label); + } + fprintf(fp,"moveto\n"); +} + +/* -------------------------------------------------------------------------- */ + +PRIVATE void format_number(float x) +{ + if(x >= 1.e5) { sprintf(str, "%4.1g",x ); return;} + if(x >= 100) { sprintf(str, "%.0f" ,x ); return;} + if(x >= 10) { sprintf(str, "%.1f", x ); return;} + if(x >= 1) { sprintf(str, "%.2f", x ); return;} + if(x >= 0.1) { sprintf(str, "%.2f", x ); return;} + if(x >= 0.01) { sprintf(str, "%.3f", x ); return;} + sprintf(str, "%4.1g",x ); + return; +} + +/* -------------------------------------------------------------------------- */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/treeplot.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/treeplot.h new file mode 100755 index 000000000..7897809a6 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/treeplot.h @@ -0,0 +1 @@ +extern void PSplot_phylogeny(Union *cluster, char *filename, char *type); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/utils.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/utils.h new file mode 100755 index 000000000..b0cbae0c8 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Cluster/utils.h @@ -0,0 +1,13 @@ +/* Header file for utils.c */ + +extern void *space(unsigned size); +extern void nrerror(char *message); +extern double urn(); +extern int int_urn(int from, int to); +extern void filecopy(FILE *from, FILE *to); +extern char *time_stamp(); +extern char *random_string(int l, char *symbols); +extern int hamming(char *s1, char *s2); +extern char *get_line(FILE *fp); +extern unsigned short xsubi[3]; + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/Makefile new file mode 100755 index 000000000..f7ad3d306 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/Makefile @@ -0,0 +1,378 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# H/Makefile. Generated from Makefile.in by configure. + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005 Free Software Foundation, Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + + + +srcdir = . +top_srcdir = .. + +pkgdatadir = $(datadir)/ViennaRNA +pkglibdir = $(libdir)/ViennaRNA +pkgincludedir = $(includedir)/ViennaRNA +top_builddir = .. +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +INSTALL = /usr/bin/install -c +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +build_triplet = x86_64-unknown-linux-gnu +host_triplet = x86_64-unknown-linux-gnu +subdir = H +DIST_COMMON = $(pkginclude_HEADERS) $(srcdir)/Makefile.am \ + $(srcdir)/Makefile.in +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.in +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_CLEAN_FILES = +SOURCES = +DIST_SOURCES = +am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; 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+/* write PostScript drawing of structure to file */ +extern int PS_rna_plot_a(char *string, char *structure, char *file, char *pre, char *post); +/* write PostScript drawing of structure to file with annotation */ +extern int gmlRNA(char *string, char *structure, char *ssfile, char option); +/* structure drawing in gml */ +extern int ssv_rna_plot(char *string, char *structure, char *ssfile); +/*write coord file for SStructView */ +extern int svg_rna_plot(char *string, char *structure, char *ssfile); +/*write RNAplot in SVG */ +extern int xrna_plot(char *string, char *structure, char *ssfile); +/*write .ss file for further editing in XRNA */ +extern int PS_dot_plot(char *string, char *file); +/* produce a PostScript dot plot of the pair probability matix */ +extern int rna_plot_type; /* 0= simple coordinates, 1= naview */ + +typedef struct cpair { + int i,j,mfe; + float p, hue, sat; +} cpair; +extern int PS_color_dot_plot(char *string, cpair *pi, char *filename); + +typedef struct plist { + int i; + int j; + float p; +}plist; +extern int PS_dot_plot_list(char *seq, char *filename, struct plist *pl, + struct plist *mf, char *comment); +extern int PS_dot_plot_turn(char *seq, struct plist *pl, char *filename, + int winSize); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/ProfileAln.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/ProfileAln.h new file mode 100755 index 000000000..4462e119c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/ProfileAln.h @@ -0,0 +1,10 @@ +#ifndef PROFILEALN_H +#define PROFILEALN_H + +extern float profile_aln(const float *T1, const char *seq1, + const float *T2, const char *seq2); + +extern int set_paln_params(double gap_open, double gap_ext, + double seqweight, int free_ends); + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/RNAstruct.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/RNAstruct.h new file mode 100755 index 000000000..eb6cf2468 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/RNAstruct.h @@ -0,0 +1,37 @@ +#define STRUC 1000 + +extern char *b2HIT(const char *structure); /* Full -> HIT [incl. root] */ +extern char *b2C(const char *structure); /* Full -> Coarse [incl. root] */ +extern char *b2Shapiro(const char *structure); /* Full -> weighted Shapiro [i.r.] */ +extern char *add_root(const char *); /* {Tree} -> ({Tree}R) */ + +extern char *expand_Shapiro(const char *coarse); +/* add S for stacks to coarse struct */ +extern char *expand_Full(const char *structure); /* Full -> FFull */ +extern char *unexpand_Full(const char *ffull); /* FFull -> Full */ +extern char *unweight(const char *wcoarse); /* remove weights from coarse struct */ + +extern void unexpand_aligned_F(char *align[2]); + +extern void parse_structure(const char *structure); /* make structure statistics */ + +extern int loop_size[STRUC]; /* loop sizes of a structure */ +extern int helix_size[STRUC]; /* helix sizes of a structure */ +extern int loop_degree[STRUC]; /* loop degrees of a structure */ +extern int loops; /* n of loops and stacks */ +extern int unpaired, pairs; /* n of unpaired digits and pairs */ + +/* + Example: + .((..(((...)))..((..)))). is the bracket or full tree + becomes expanded: - expand_Full() - + ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R) + HIT: - b2HIT() - + ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R) + Coarse: - b2C() - + ((H)((H)M)R) + becomes expanded: - expand_Shapiro() - + (((((H)S)((H)S)M)S)R) + weighted Shapiro: - b2Shapiro() - + ((((((H3)S3)((H2)S2)M4)S2)E2)R) +*/ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/alifold.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/alifold.h new file mode 100755 index 000000000..bec45ed5f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/alifold.h @@ -0,0 +1,14 @@ +extern float alifold(char **strings, char *structure); +extern void free_alifold_arrays(void); +extern void update_alifold_params(void); +extern double cv_fact /* =1 */; +extern double nc_fact /* =1 */; +typedef struct { + short i; /* i,j in [0, n-1] */ + short j; + float p; /* probability */ + float ent; /* pseudo entropy for p(i,j) = S_i + S_j - p_ij*ln(p_ij) */ + short bp[8]; /* frequencies of pair_types */ + char comp; /* 1 iff pair is in mfe structure */ +} pair_info; +extern float alipf_fold(char **sequences, char *structure, pair_info **pi); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/aln_util.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/aln_util.h new file mode 100755 index 000000000..1109b6f31 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/aln_util.h @@ -0,0 +1,8 @@ +#ifndef ALN_UTIL_H +#define ALN_UTIL_H + +extern int read_clustal(FILE *clust, char *AlignedSeqs[], char *names[]); +extern /*@only@*/ /*@notnull@*/ char *consensus(const char *AS[]); +extern /*@only@*/ /*@notnull@*/ char *consens_mis(const char *AS[]); + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/cofold.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/cofold.h new file mode 100755 index 000000000..90e559d46 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/cofold.h @@ -0,0 +1,6 @@ +/* function from fold.c */ +extern float cofold(char *sequence, char *structure); +/* calculate energy of string on structure */ +extern void free_co_arrays(void); /* free arrays for mfe folding */ +extern void initialize_cofold(int length); /* allocate arrays for folding */ +extern void update_cofold_params(void); /* recalculate parameters */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/dist_vars.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/dist_vars.h new file mode 100755 index 000000000..926972054 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/dist_vars.h @@ -0,0 +1,31 @@ +#ifndef DIST_VARS_H +#define DIST_VARS_H +/* Global variables for Distance-Package */ + +extern int edit_backtrack; /* set to 1 if you want backtracking */ + +extern char *aligned_line[4]; /* containes alignment after backtracking */ + +extern int cost_matrix; /* 0 usual costs (default), 1 Shapiro's costs */ + +/* Global type defs for Distance-Package */ + +typedef struct { + int type; + int weight; + int father; + int sons; + int leftmostleaf; + } Postorder_list; + +typedef struct { + Postorder_list *postorder_list; + int *keyroots; + } Tree; + +typedef struct { + int type; + int sign; + float weight; + } swString; +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/duplex.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/duplex.h new file mode 100755 index 000000000..4d54c6170 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/duplex.h @@ -0,0 +1,14 @@ +#ifndef DUPLEX_H +#define DUPLEX_H + +typedef struct { + int i; + int j; + char *structure; + float energy; +} duplexT; + +extern duplexT duplexfold(const char *s1, const char *s2); +extern duplexT *duplex_subopt(const char *s1, const char *s2, int delta, int w); + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/edit_cost.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/edit_cost.h new file mode 100755 index 000000000..d1cc12d68 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/edit_cost.h @@ -0,0 +1,54 @@ +/* + +cost.h :: global variables for Edit Costs + included by treedist.c and stringdist.c + +*/ +#define PRIVATE static + +PRIVATE char sep = ':'; +PRIVATE char *coding = "Null:U:P:H:B:I:M:S:E:R"; + +#define INF 10000 /* infinity */ + +typedef int CostMatrix[10][10]; + +PRIVATE CostMatrix *EditCost; /* will point to UsualCost or ShapiroCost */ + +PRIVATE CostMatrix UsualCost = +{ + +/* Null, U, P, H, B, I, M, S, E, R */ + + { 0, 1, 2, 2, 2, 2, 2, 1, 1, INF}, /* Null replaced */ + { 1, 0, 1, INF, INF, INF, INF, INF, INF, INF}, /* U replaced */ + { 2, 1, 0, INF, INF, INF, INF, INF, INF, INF}, /* P replaced */ + { 2, INF, INF, 0, 2, 2, 2, INF, INF, INF}, /* H replaced */ + { 2, INF, INF, 2, 0, 1, 2, INF, INF, INF}, /* B replaced */ + { 2, INF, INF, 2, 1, 0, 2, INF, INF, INF}, /* I replaced */ + { 2, INF, INF, 2, 2, 2, 0, INF, INF, INF}, /* M replaced */ + { 1, INF, INF, INF, INF, INF, INF, 0, INF, INF}, /* S replaced */ + { 1, INF, INF, INF, INF, INF, INF, INF, 0, INF}, /* E replaced */ + { INF, INF, INF, INF, INF, INF, INF, INF, INF, 0}, /* R replaced */ + +}; + + +PRIVATE CostMatrix ShapiroCost = +{ + +/* Null, U, P, H, B, I, M, S, E, R */ + + { 0, 1, 2, 100, 5, 5, 75, 5, 5, INF}, /* Null replaced */ + { 1, 0, 1, INF, INF, INF, INF, INF, INF, INF}, /* U replaced */ + { 2, 1, 0, INF, INF, INF, INF, INF, INF, INF}, /* P replaced */ + { 100, INF, INF, 0, 8, 8, 8, INF, INF, INF}, /* H replaced */ + { 5, INF, INF, 8, 0, 3, 8, INF, INF, INF}, /* B replaced */ + { 5, INF, INF, 8, 3, 0, 8, INF, INF, INF}, /* I replaced */ + { 75, INF, INF, 8, 8, 8, 0, INF, INF, INF}, /* M replaced */ + { 5, INF, INF, INF, INF, INF, INF, 0, INF, INF}, /* S replaced */ + { 5, INF, INF, INF, INF, INF, INF, INF, 0, INF}, /* E replaced */ + { INF, INF, INF, INF, INF, INF, INF, INF, INF, 0}, /* R replaced */ + +}; + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/energy_const.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/energy_const.h new file mode 100755 index 000000000..04892da4d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/energy_const.h @@ -0,0 +1,23 @@ +/* + + energy constants, formerly defined in + energy_par.h + + customized for use with RNAedit by + S.Kopp, IMB-Jena, Germany, Mar 1996 + +*/ + +#ifndef _ENERGY_CONST_H +#define _ENERGY_CONST_H 1 + +#define GASCONST 1.98717 /* in [cal/K] */ +#define K0 273.15 +#define INF 1000000 +#define FORBIDDEN 9999 +#define BONUS 10000 +#define NBPAIRS 7 +#define TURN 3 +#define MAXLOOP 30 + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/energy_par.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/energy_par.h new file mode 100755 index 000000000..fee8e3c6d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/energy_par.h @@ -0,0 +1,60 @@ +/* + prototypes for energy_par.c +*/ + +#include "energy_const.h" + +extern double lxc37; /* parameter for logarithmic loop + energy extrapolation */ + +extern int stack37[NBPAIRS+1][NBPAIRS+1]; +extern int enthalpies[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */ +extern int entropies[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */ + +extern int hairpin37[31]; +extern int bulge37[31]; +extern int internal_loop37[31]; +extern int internal2_energy; +extern int old_mismatch_37[NBPAIRS+1][5][5]; +extern int mismatchI37[NBPAIRS+1][5][5]; /* interior loop mismatches */ +extern int mismatchH37[NBPAIRS+1][5][5]; /* same for hairpins */ +extern int mismatchM37[NBPAIRS+1][5][5]; /* same for multiloops */ +extern int mism_H[NBPAIRS+1][5][5]; /* mismatch enthalpies */ + +extern int dangle5_37[NBPAIRS+1][5]; /* 5' dangle exterior of pair */ +extern int dangle3_37[NBPAIRS+1][5]; /* 3' dangle */ +extern int dangle3_H[NBPAIRS+1][5]; /* corresponding enthalpies */ +extern int dangle5_H[NBPAIRS+1][5]; + +extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */ +extern int int11_H[NBPAIRS+1][NBPAIRS+1][5][5]; + +extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */ +extern int int21_H[NBPAIRS+1][NBPAIRS+1][5][5][5]; + +extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */ +extern int int22_H[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; + +/* constants for linearly destabilizing contributions for multi-loops + F = ML_closing + ML_intern*(k-1) + ML_BASE*u */ +extern int ML_BASE37; +extern int ML_closing37; +extern int ML_intern37; + +/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */ +/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */ +extern int MAX_NINIO; /* maximum correction */ +extern int F_ninio37[5]; + +/* penalty for helices terminated by AU (actually not GC) */ +extern int TerminalAU; +/* penalty for forming bi-molecular duplex */ +extern int DuplexInit; +/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */ +extern char Tetraloops[]; /* string containing the special tetraloops */ +extern int TETRA_ENERGY37[]; /* Bonus energy for special tetraloops */ +extern int TETRA_ENTH37; +extern char Triloops[]; /* string containing the special triloops */ +extern int Triloop_E37[]; /* Bonus energy for special Triloops */ + +extern double Tmeasure; /* temperature of param measurements */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/fold.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/fold.h new file mode 100755 index 000000000..703aa2d0f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/fold.h @@ -0,0 +1,8 @@ +/* function from fold.c */ +extern float fold(const char *sequence, char *structure); +/* calculate mfe-structure of sequence */ +extern float energy_of_struct(const char *string, const char *structure); +/* calculate energy of string on structure */ +extern void free_arrays(void); /* free arrays for mfe folding */ +extern void initialize_fold(int length); /* allocate arrays for folding */ +extern void update_fold_params(void); /* recalculate parameters */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/fold_vars.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/fold_vars.h new file mode 100755 index 000000000..815e790c6 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/fold_vars.h @@ -0,0 +1,36 @@ +/* to use floats instead of doubles in pf_fold() comment next line */ +#define LARGE_PF +#ifdef LARGE_PF +#define FLT_OR_DBL double +#else +#define FLT_OR_DBL float +#endif + +extern int noGU; /* GU not allowed at all */ +extern int no_closingGU; /* GU allowed only inside stacks */ +extern int tetra_loop; /* Fold with specially stable 4-loops */ +extern int energy_set; /* 0 = BP; 1=any mit GC; 2=any mit AU-parameter */ +extern int dangles; /* use dangling end energies (not in part_func!) */ +/*@null@*/ +extern char *nonstandards; /* contains allowed non standard bases */ +extern double temperature; /* rescale parameters to this temperature */ +extern int james_rule; /* interior loops of size 2 get energy 0.8Kcal and + no mismatches, default 1 */ +extern int logML; /* use logarithmic multiloop energy function */ +extern int cut_point; /* first position of 2nd strand for co-folding */ + +typedef struct bond { /* base pair */ + int i; + int j; +} bondT; +extern bondT *base_pair; /* list of base pairs */ + +extern FLT_OR_DBL *pr; /* base pairing prob. matrix */ +extern int *iindx; /* pr[i,j] -> pr[iindx[i]-j] */ +extern double pf_scale; /* scaling factor to avoid float overflows*/ +extern int fold_constrained; /* fold with constraints */ +extern int do_backtrack; /* calculate pair prob matrix in part_func() */ +extern int noLonelyPairs; /* avoid helices of length 1 */ +extern char backtrack_type; /* usually 'F'; 'C' require (1,N) to be bonded; + 'M' seq is part of a multi loop */ +char * option_string(void); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/inverse.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/inverse.h new file mode 100755 index 000000000..e443dc7ba --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/inverse.h @@ -0,0 +1,18 @@ +/* prototypes from inverse.c */ +extern char *symbolset; /* alphabet default is "AUGC" */ +extern float inverse_fold(char *start, const char *target); +/* find sequences with predefined structure. + the found sequence is written to start, + return value is + energy_of_struct(start, target) - fold(start, structure), + i.e. 0. if search was successful; */ + +extern float inverse_pf_fold(char *start, const char *target); +/* inverse folding maximising the frequency of target in the + ensemble of structures, final sequence is written to start, returns + energy_of_struct(start, target) - part_func(start, structure) +*/ +extern float final_cost; /* when to stop inverse_pf_fold() */ +extern int give_up; /* default 0: try to minimize structure distance even if + no exact solution can be found */ + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/pair_mat.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/pair_mat.h new file mode 100755 index 000000000..0e4b2a09d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/pair_mat.h @@ -0,0 +1,117 @@ +#include +#define NBASES 8 +/*@notnull@*/ +static const char Law_and_Order[] = "_ACGUTXKI"; +static int BP_pair[NBASES][NBASES]= +/* _ A C G U X K I */ +{{ 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 5, 0, 0, 5}, + { 0, 0, 0, 1, 0, 0, 0, 0}, + { 0, 0, 2, 0, 3, 0, 0, 0}, + { 0, 6, 0, 4, 0, 0, 0, 6}, + { 0, 0, 0, 0, 0, 0, 2, 0}, + { 0, 0, 0, 0, 0, 1, 0, 0}, + { 0, 6, 0, 0, 5, 0, 0, 0}}; + +#define MAXALPHA 20 /* maximal length of alphabet */ + +static short alias[MAXALPHA+1]; +static int pair[MAXALPHA+1][MAXALPHA+1]; +/* rtype[pair[i][j]]:=pair[j][i] */ +static int rtype[8] = {0, 2, 1, 4, 3, 6, 5, 7}; + +/* for backward compatibility */ +#define ENCODE(C) encode_char(c) + +static int encode_char(char c) { + /* return numerical representation of base used e.g. in pair[][] */ + int code; + if (energy_set>0) code = (int) (c-'A')+1; + else { + char *pos; + pos = strchr(Law_and_Order, c); + if (pos==NULL) code=0; + else code = (int) (pos-Law_and_Order); + if (code>4) code--; /* make T and U equivalent */ + } + return code; +} + +/*@+boolint +charint@*/ +/*@null@*/ +extern char *nonstandards; +extern void nrerror(const char message[]); +static void make_pair_matrix(void) +{ + int i,j; + + if (energy_set==0) { + for (i=0; i<5; i++) alias[i] = (short) i; + alias[5] = 3; /* X <-> G */ + alias[6] = 2; /* K <-> C */ + alias[7] = 0; /* I <-> default base '@' */ + for (i=0; i G */ + alias[i++] = 2; /* B <-> C */ + } + for (i=1; i GC */ + i++; + pair[i][i-1] = 1; /* BA <-> CG */ + } + } + else if (energy_set==2) { + for (i=1; i A*/ + alias[i++] = 4; /* B <-> U */ + } + for (i=1; i AU */ + i++; + pair[i][i-1] = 6; /* BA <-> UA */ + } + } + else if (energy_set==3) { + for (i=1; i G */ + alias[i++] = 2; /* B <-> C */ + alias[i++] = 1; /* C <-> A */ + alias[i++] = 4; /* D <-> U */ + } + for (i=1; i GC */ + i++; + pair[i][i-1] = 1; /* BA <-> CG */ + i++; + pair[i][i+1] = 5; /* CD <-> AU */ + i++; + pair[i][i-1] = 6; /* DC <-> UA */ + } + } + else nrerror("What energy_set are YOU using??"); + for (i=0; i<=MAXALPHA; i++) { + for (j=0; j<=MAXALPHA; j++) + rtype[pair[i][j]] = pair[j][i]; + } + } +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/params.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/params.h new file mode 100755 index 000000000..46d6122f4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/params.h @@ -0,0 +1,32 @@ +#include "energy_const.h" +typedef struct { + int id; + int stack[NBPAIRS+1][NBPAIRS+1]; + int hairpin[31]; + int bulge[MAXLOOP+1]; + int internal_loop[MAXLOOP+1]; + int mismatchI[NBPAIRS+1][5][5]; + int mismatchH[NBPAIRS+1][5][5]; + int mismatchM[NBPAIRS+1][5][5]; + int dangle5[NBPAIRS+1][5]; + int dangle3[NBPAIRS+1][5]; + int int11[NBPAIRS+1][NBPAIRS+1][5][5]; + int int21[NBPAIRS+1][NBPAIRS+1][5][5][5]; + int int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; + int F_ninio[5]; + double lxc; + int MLbase; + int MLintern[NBPAIRS+1]; + int MLclosing; + int TerminalAU; + int DuplexInit; + int TETRA_ENERGY[200]; + char Tetraloops[1401]; + int Triloop_E[40]; + char Triloops[241]; + double temperature; +} paramT; + +extern paramT *scale_parameters(void); +extern paramT *copy_parameters(void); +extern paramT *set_parameters(paramT *dest); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/part_func.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/part_func.h new file mode 100755 index 000000000..633f18984 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/part_func.h @@ -0,0 +1,8 @@ +/* functions from part_func.c */ +extern float pf_fold(char *sequence, char *structure); +/* calculate partition function and base pair probabilities */ +extern void init_pf_fold(int length); /* allocate space for pf_fold() */ +extern void free_pf_arrays(void); /* free arrays from pf_fold() */ +extern void update_pf_params(int length); /*recalculate energy parameters */ +extern char bppm_symbol(const float *x); /* string representation of structure */ +extern double mean_bp_dist(int length); /* mean pair distance of ensemble */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/part_func_co.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/part_func_co.h new file mode 100755 index 000000000..484d34d92 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/part_func_co.h @@ -0,0 +1,56 @@ +/* functions from part_func.c */ +/* calculate partition function and base pair probabilities */ +#define LARGE_PF +#ifdef LARGE_PF +#define FLT_OR_DBL double +#else +#define FLT_OR_DBL float +#endif +extern int mirnatog; /*toggles no intrabp in 2nd mol*/ + +typedef struct cofoldF { + /* free energies for: */ + double F0AB; /* null model without DuplexInit */ + double FAB; /* all states with DuplexInit corretion */ + double FcAB; /* true hybrid states only */ + double FA; /* monomer A */ + double FB; /* monomer B */ +} cofoldF; + +extern cofoldF co_pf_fold(char *sequence, char *structure); /* calculate partition function and base pair probabilities */ +extern void init_co_pf_fold(int length); +extern void free_co_pf_arrays(void); +extern void update_co_pf_params(int length); /*recalculate energy parameters */ +extern char co_bppm_symbol(float *x); /* string representation of structure */ +extern void compute_probabilities(double FAB, double FEA, double FEB, + struct plist *prAB, + struct plist *prA, struct plist *prB, + int Alength); + + +typedef struct ConcEnt { + double A0; /*start concentration A*/ + double B0; /*start concentration B*/ + double ABc; /*End concentration AB*/ + double AAc; + double BBc; + double Ac; + double Bc; +} ConcEnt; + + + +typedef struct pairpro{ + struct plist *AB; + struct plist *AA; + struct plist *A; + struct plist *B; + struct plist *BB; +}pairpro; + + +extern struct ConcEnt *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double * startconc); + +extern struct plist *get_plist(struct plist *pl, int length, double cut_off); + +extern int make_probsum(int length, char *name); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/profiledist.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/profiledist.h new file mode 100755 index 000000000..c1507de73 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/profiledist.h @@ -0,0 +1,14 @@ + +extern float *Make_bp_profile(int length); +/* condense pair probability matrix pr into a vector containing probabilities + for upstream paired, downstream paired and unpaired. This resulting + probability profile is used as input for profile_edit_distance */ + +extern float profile_edit_distance(const float *T1, const float *T2); +/* align two probability profiles */ + +extern void print_bppm(const float *T); +/* print string representation of probability profile */ + +extern void free_profile(float *T); +/* free space allocated in Make_bp_profile */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/stringdist.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/stringdist.h new file mode 100755 index 000000000..ba3383d40 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/stringdist.h @@ -0,0 +1,7 @@ +#ifndef DIST_VARS_H +#include "dist_vars.h" /* defines the type Tree */ +#endif +extern swString *Make_swString(char *string); +/* make input for string_edit_distance */ +extern float string_edit_distance(swString *T1, swString *T2); +/* compare to structures using string alignment */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/subopt.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/subopt.h new file mode 100755 index 000000000..b20643abf --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/subopt.h @@ -0,0 +1,12 @@ +/* subopt.h */ +typedef struct { + float energy; /* energy of structure */ + char *structure; +} SOLUTION; + +extern SOLUTION *subopt (char *seq, char *sequence, int delta, FILE *fp); + /* returns list of subopt structures or writes to fp */ + +extern int subopt_sorted; /* sort output by energy */ + +/* End of file */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/treedist.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/treedist.h new file mode 100755 index 000000000..fd928c393 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/treedist.h @@ -0,0 +1,8 @@ +#ifndef DIST_VARS_H +#include "dist_vars.h" /* defines the type Tree */ +#endif +extern Tree *make_tree(char *struc); /* make input for tree_edit_distance */ +extern float tree_edit_distance(Tree *T1, Tree *T2); +/* compare to structures using tree editing */ +extern void print_tree(Tree *t); /* mainly for debugging */ +extern void free_tree(Tree *t); /* free space allocated by make_tree */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/utils.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/utils.h new file mode 100755 index 000000000..2fda4f110 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/H/utils.h @@ -0,0 +1,41 @@ +/* Header file for utils.c */ +#ifdef HAVE_CONFIG_H +#include +#endif +#ifdef WITH_DMALLOC +/* use dmalloc library to check for memory management bugs */ +#include "dmalloc.h" +#define space(S) calloc(1,(S)) +#else +extern /*@only@*/ /*@notnull@*/ +void *space(unsigned size) /*@ensures MaxSet(result) == (size-1);@*/; + /* allocate space safely */ +extern /*@only@*/ /*@notnull@*/ +void *xrealloc(/*@null@*/ /*@only@*/ /*@out@*/ /*@returned@*/ void *p, unsigned size) /*@modifies *p @*/ /*@ensures MaxSet(result) == (size-1) @*/; +#endif + +extern /*@exits@*/ void nrerror(const char message[]); /* die with error message */ +extern void init_rand(void); /* make random number seeds */ +extern unsigned short xsubi[3]; /* current 48bit random number */ +extern double urn(void); /* random number from [0..1] */ +extern int int_urn(int from, int to); /* random integer */ +extern void filecopy(FILE *from, FILE *to); /* inefficient `cp' */ +extern /*@observer@*/ char *time_stamp(void); /* current date in a string */ +extern /*@only@*/ /*@notnull@*/ char *random_string(int l, const char symbols[]); +/* random string of length l using characters from symbols[] */ +extern int hamming(const char *s1, const char *s2); +/* calculate hamming distance */ +extern /*@only@*/ /*@null@*/ char *get_line(const FILE *fp); /* read one (arbitrary length) line from fp */ + + +extern char *pack_structure(const char *struc); +/* pack secondary secondary structure, 5:1 compression using base 3 encoding */ +extern char *unpack_structure(const char *packed); +/* unpack sec structure packed with pack_structure() */ +extern short *make_pair_table(const char *structure); +/* returns a newly allocated table, such that: table[i]=j if (i.j) pair or + 0 if i is unpaired, table[0] contains the length of the structure. */ + +extern int bp_distance(const char *str1, const char *str2); +/* dist = {number of base pairs in one structure but not in the other} + same as edit distance with open-pair close-pair as move-set */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/INSTALL b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/INSTALL new file mode 100755 index 000000000..40e573981 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/INSTALL @@ -0,0 +1,91 @@ +Installation: + +This package uses GNU autoconf generated configure scripts, see the +file INSTALL.configure for generic configure documentation. + +Quickstart: Usually you'll just have to type: +---------- + ./configure + make +and (as root) + make install + +Install Paths: +------------- +The main programs, library, man, and info pages are +installed in the usual places by default +(i.e. /usr/local/{bin,lib,man,info}). In addition the following +install paths are used: +header files /usr/local/include/ViennaRNA [includedir/ViennaRNA] +parameter files /usr/local/share/ViennaRNA [datadir/ViennaRNA] +extra scripts /usr/local/share/ViennaRNA/bin [datadir/ViennaRNA/bin] +documentation /usr/local/share/ViennaRNA/doc [datadir/ViennaRNA/doc] + +All these locations can be changed by calling ./configure with +appropriate options. + +If you like having all software packages separated in their own directories +you could run e.g.: +./configure --prefix=/opt/packages/ViennaRNA --datadir=/opt/packages/ViennaRNA +resulting in /opt/packages/ViennaRNA/{bin,lib,man,info,include,doc} directories + +The installed location of the Perl module is determined by Perl's own +configuration, independent of any configure options. +To leave out the Perl modules run + ./configure --without-perl + +The programs AnalyseSeqs and AnalyseDists offer some cluster analysis +tools (split decomposition, statistical geometry, neighbor joining, +Ward's method) for sequences and distance data. To also build these +programs add --with-cluster to your configure options. + +This release includes the RNAforester and Kinfold programs, which can also +be obtained as independent packages. Running ./configure in the ViennaRNA +directory will configure those two packages as well. However, for detailed +information and compile time options, see the README and INSTALL files in +the respective subdirectories. + +The Kinfold program can be used to simulate the folding dynamics of an +RNA molecule, and is compiled by default. Use the --without-kinfold +option to skip compiling Kinfold. + +The RNAforester program is used for comparing secondary structures using +tree alignment. To compile RNAforester you'll need to first install the +g2 graphic library, then run configure with the --with-forester option. + +Calculation of partition functions (via RNAfold -p) uses double +precision floats by default, to avoid overflow errors on longer sequences. +If your machine has little memory and you dont't plan to fold sequences +over 1000 bases in length you can compile the package to do the computions +in single precision by giving ./configure the --enable-floatpf option. + +Memory requirements for a sequence of length n will be approximately +12*n^2 bytes for RNAfold -p in the double precision version, and + 4*n^2 bytes for the minimum free energy alone. + + +The readseq program is not integrated in the build process. If desired, +install readseq manually, following the instructions in the readseq +directory. + +There are man pages for all executables, the library is documented in +./man/RNAlib.texinfo. You can either print this file as a manual using +TeX (if you don't have texinfo.tex installed use the .dvi file) or use +it as online documentation if you have the GNU texinfo package installed. +Documentation in HTML can be found at http://www.tbi.univie.ac.at/~ivo/RNA/ + + +System specific notes: +calculating the partition function for long sequences ( >400 bases) +generates a lot of floating point underflows. On some system this can slow +down the calculation dramatically because an exception is invoked for each +underflow. How to avoid this problem is highly system specific: + +On SunOS 4.1 the remedy is calling nonstandard_arithmetic() add a -DSUN4 to +the CFLAGS in lib/makefile to do this. Use CC=gcc since SUN's standard cc +doesn't understand ANSI C. + +On HP machines running hpux-9 or hpux-10 add -DHP9 to the CFLAGS so that +fpsetfastmode() will be called. + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/INSTALL.configure b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/INSTALL.configure new file mode 100755 index 000000000..b42a17ac4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/INSTALL.configure @@ -0,0 +1,182 @@ +Basic Installation +================== + + These are generic installation instructions. + + The `configure' shell script attempts to guess correct values for +various system-dependent variables used during compilation. It uses +those values to create a `Makefile' in each directory of the package. +It may also create one or more `.h' files containing system-dependent +definitions. Finally, it creates a shell script `config.status' that +you can run in the future to recreate the current configuration, a file +`config.cache' that saves the results of its tests to speed up +reconfiguring, and a file `config.log' containing compiler output +(useful mainly for debugging `configure'). + + If you need to do unusual things to compile the package, please try +to figure out how `configure' could check whether to do them, and mail +diffs or instructions to the address given in the `README' so they can +be considered for the next release. If at some point `config.cache' +contains results you don't want to keep, you may remove or edit it. + + The file `configure.in' is used to create `configure' by a program +called `autoconf'. You only need `configure.in' if you want to change +it or regenerate `configure' using a newer version of `autoconf'. + +The simplest way to compile this package is: + + 1. `cd' to the directory containing the package's source code and type + `./configure' to configure the package for your system. If you're + using `csh' on an old version of System V, you might need to type + `sh ./configure' instead to prevent `csh' from trying to execute + `configure' itself. + + Running `configure' takes awhile. While running, it prints some + messages telling which features it is checking for. + + 2. Type `make' to compile the package. + + 3. Optionally, type `make check' to run any self-tests that come with + the package. + + 4. Type `make install' to install the programs and any data files and + documentation. + + 5. You can remove the program binaries and object files from the + source code directory by typing `make clean'. To also remove the + files that `configure' created (so you can compile the package for + a different kind of computer), type `make distclean'. There is + also a `make maintainer-clean' target, but that is intended mainly + for the package's developers. If you use it, you may have to get + all sorts of other programs in order to regenerate files that came + with the distribution. + +Compilers and Options +===================== + + Some systems require unusual options for compilation or linking that +the `configure' script does not know about. You can give `configure' +initial values for variables by setting them in the environment. Using +a Bourne-compatible shell, you can do that on the command line like +this: + CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure + +Or on systems that have the `env' program, you can do it like this: + env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure + +Compiling For Multiple Architectures +==================================== + + You can compile the package for more than one kind of computer at the +same time, by placing the object files for each architecture in their +own directory. To do this, you must use a version of `make' that +supports the `VPATH' variable, such as GNU `make'. `cd' to the +directory where you want the object files and executables to go and run +the `configure' script. `configure' automatically checks for the +source code in the directory that `configure' is in and in `..'. + + If you have to use a `make' that does not supports the `VPATH' +variable, you have to compile the package for one architecture at a time +in the source code directory. After you have installed the package for +one architecture, use `make distclean' before reconfiguring for another +architecture. + +Installation Names +================== + + By default, `make install' will install the package's files in +`/usr/local/bin', `/usr/local/man', etc. You can specify an +installation prefix other than `/usr/local' by giving `configure' the +option `--prefix=PATH'. + + You can specify separate installation prefixes for +architecture-specific files and architecture-independent files. If you +give `configure' the option `--exec-prefix=PATH', the package will use +PATH as the prefix for installing programs and libraries. +Documentation and other data files will still use the regular prefix. + + In addition, if you use an unusual directory layout you can give +options like `--bindir=PATH' to specify different values for particular +kinds of files. Run `configure --help' for a list of the directories +you can set and what kinds of files go in them. + + If the package supports it, you can cause programs to be installed +with an extra prefix or suffix on their names by giving `configure' the +option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. + +Optional Features +================= + + Some packages pay attention to `--enable-FEATURE' options to +`configure', where FEATURE indicates an optional part of the package. +They may also pay attention to `--with-PACKAGE' options, where PACKAGE +is something like `gnu-as' or `x' (for the X Window System). The +`README' should mention any `--enable-' and `--with-' options that the +package recognizes. + + For packages that use the X Window System, `configure' can usually +find the X include and library files automatically, but if it doesn't, +you can use the `configure' options `--x-includes=DIR' and +`--x-libraries=DIR' to specify their locations. + +Specifying the System Type +========================== + + There may be some features `configure' can not figure out +automatically, but needs to determine by the type of host the package +will run on. Usually `configure' can figure that out, but if it prints +a message saying it can not guess the host type, give it the +`--host=TYPE' option. TYPE can either be a short name for the system +type, such as `sun4', or a canonical name with three fields: + CPU-COMPANY-SYSTEM + +See the file `config.sub' for the possible values of each field. If +`config.sub' isn't included in this package, then this package doesn't +need to know the host type. + + If you are building compiler tools for cross-compiling, you can also +use the `--target=TYPE' option to select the type of system they will +produce code for and the `--build=TYPE' option to select the type of +system on which you are compiling the package. + +Sharing Defaults +================ + + If you want to set default values for `configure' scripts to share, +you can create a site shell script called `config.site' that gives +default values for variables like `CC', `cache_file', and `prefix'. +`configure' looks for `PREFIX/share/config.site' if it exists, then +`PREFIX/etc/config.site' if it exists. Or, you can set the +`CONFIG_SITE' environment variable to the location of the site script. +A warning: not all `configure' scripts look for a site script. + +Operation Controls +================== + + `configure' recognizes the following options to control how it +operates. + +`--cache-file=FILE' + Use and save the results of the tests in FILE instead of + `./config.cache'. Set FILE to `/dev/null' to disable caching, for + debugging `configure'. + +`--help' + Print a summary of the options to `configure', and exit. + +`--quiet' +`--silent' +`-q' + Do not print messages saying which checks are being made. To + suppress all normal output, redirect it to `/dev/null' (any error + messages will still be shown). + +`--srcdir=DIR' + Look for the package's source code in directory DIR. Usually + `configure' can determine that directory automatically. + +`--version' + Print the version of Autoconf used to generate the `configure' + script, and exit. + +`configure' also accepts some other, not widely useful, options. diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/baum.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/baum.Po new file mode 100755 index 000000000..a96f3cb76 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/baum.Po @@ -0,0 +1,103 @@ +baum.o baum.o: baum.c /usr/include/stdio.h /usr/include/features.h \ + /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h /usr/include/assert.h ../H/fold_vars.h \ + ../H/fold.h ../H/utils.h ./config.h ../H/pair_mat.h \ + /usr/include/ctype.h nachbar.h globals.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +/usr/include/assert.h: + +../H/fold_vars.h: + +../H/fold.h: + +../H/utils.h: + +./config.h: + +../H/pair_mat.h: + +/usr/include/ctype.h: + +nachbar.h: + +globals.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/cache.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/cache.Po new file mode 100755 index 000000000..fb3bc9243 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/cache.Po @@ -0,0 +1,102 @@ +cache.o cache.o: cache.c /usr/include/stdio.h /usr/include/features.h \ + /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/string.h \ + /usr/include/bits/string.h /usr/include/bits/string2.h ../H/utils.h \ + ./config.h cache_util.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/utils.h: + +./config.h: + +cache_util.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/getopt.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/getopt.Po new file mode 100755 index 000000000..f4e11a5e1 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/getopt.Po @@ -0,0 +1,49 @@ +getopt.o getopt.o: getopt.c ./config.h /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/gnu-versions.h + +./config.h: + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/gnu-versions.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/getopt1.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/getopt1.Po new file mode 100755 index 000000000..114d616f4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/getopt1.Po @@ -0,0 +1,51 @@ +getopt1.o getopt1.o: getopt1.c ./config.h getopt.h /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/gnu-versions.h + +./config.h: + +getopt.h: + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/gnu-versions.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/globals.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/globals.Po new file mode 100755 index 000000000..9eab258c2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/globals.Po @@ -0,0 +1,104 @@ +globals.o globals.o: globals.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h /usr/include/assert.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h ./getopt.h ../H/utils.h ./config.h globals.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +/usr/include/assert.h: + +/usr/include/errno.h: + +/usr/include/bits/errno.h: + +/usr/include/linux/errno.h: + +/usr/include/asm/errno.h: + +./getopt.h: + +../H/utils.h: + +./config.h: + +globals.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/main.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/main.Po new file mode 100755 index 000000000..d70751c2b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/main.Po @@ -0,0 +1,114 @@ +main.o main.o: main.c /usr/include/stdio.h /usr/include/features.h \ + /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h /usr/include/assert.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h ./getopt.h ../H/fold_vars.h ../H/fold.h \ + baum.h nachbar.h cache_util.h ../H/utils.h ./config.h globals.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +/usr/include/assert.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +./getopt.h: + +../H/fold_vars.h: + +../H/fold.h: + +baum.h: + +nachbar.h: + +cache_util.h: + +../H/utils.h: + +./config.h: + +globals.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/nachbar.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/nachbar.Po new file mode 100755 index 000000000..0efa1acd9 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/.deps/nachbar.Po @@ -0,0 +1,133 @@ +nachbar.o nachbar.o: nachbar.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h globals.h \ + /usr/include/assert.h ../H/fold_vars.h ../H/energy_const.h ../H/utils.h \ + ./config.h cache_util.h baum.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h: + +/usr/include/limits.h: + +/usr/include/bits/posix1_lim.h: + +/usr/include/bits/local_lim.h: + +/usr/include/linux/limits.h: + +/usr/include/bits/posix2_lim.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +globals.h: + +/usr/include/assert.h: + +../H/fold_vars.h: + +../H/energy_const.h: + +../H/utils.h: + +./config.h: + +cache_util.h: + +baum.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/AUTHORS b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/AUTHORS new file mode 100755 index 000000000..bfcbc6adc --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/AUTHORS @@ -0,0 +1,2 @@ +Christoph Flamm and +Ivo L. Hofacker diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/COPYING b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/COPYING new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/ChangeLog b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/ChangeLog new file mode 100755 index 000000000..68c4b46a9 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/ChangeLog @@ -0,0 +1,3 @@ +2001-08-01 Christoph Flamm, Ivo L. 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install-exec \ + install-exec-am install-info install-info-am install-man \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-generic pdf pdf-am ps ps-am uninstall uninstall-am \ + uninstall-info-am + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/README b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/README new file mode 100755 index 000000000..518bbc096 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/README @@ -0,0 +1,55 @@ +---------- +Folding Modes: + +(1) default mode: + start structure is open chain + stop structure is minimum free enegy structure + example: hairpin.log, traj + ../Kinfold --log hpin --num 10 <./hpin.in>& traj + +(2) multi-stop mode: + start structure is open chain + stop structure(s) are 2nd and following lines in hpin.in + example: hairpin.e.log, traj.e + ../Kinfold --stop --log hpin.e --num 10 <./hpin.in>& traj.e + +(3) refolding mode: + start structure is 2nd line in hpin.in + stop structure(s) are 3rd and following lines in hpin.in + example: hairpin.ae.log, traj.ae + ../Kinfold --start --stop --log hpin.ae --num 10 <./hpin.in>& traj.ae + +if you don't want to log the trajectories use option --silent +(trajectory files can get petty huge) + +---------- +Output: + +(A) log files (on each line you find): + randon seed + stop-structure-label or O ( for didn't reach stop-structure(s) ) + first passage time + stop-structure if stop-structure-label equals O + +(B) trajectory files (on each line you find): + structure + energy + time + number of neighbours of structure (only with --verbose) + code for the move (only with --verbose) + (i=base pair insert move, + d=base pair delete move, + s,S=base pair shift move, + I=base pair double insert move (only with --noLP) + D=base pair double delete move (only with --noLP) + ) + code for type of structure (only with --verbose) + (1=strict local minimum, + 2=degenerate local minimum, + 0=anything else + ) + stop-structure-label or O ( for didn't reach stop-structure(s) ) + +---------- +canonical example: hpin.nolp, traj.nolp + ../Kinfold --verbose --noLP --num 10 --log hpin.nolp < ./hpin.in > traj.nolp diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.ae.log b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.ae.log new file mode 100755 index 000000000..89bb1cd31 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.ae.log @@ -0,0 +1,20 @@ +#< +#Date: Thu Aug 2 15:09:44 2001 +#EnergyModel: dangle=2 Temp=37.0 logML=logarithmic Par=VRNA-1.4 +#MoveSet: noShift=off noLP=off +#Simulation: num=10 time=500.00 seed=clock fpt=on mc=Kawasaki +#Output: log=hairpin.ae silent=on lmin=off cut=20.00 +#ACUGAUCGUAGUCAC +#((((....))))... ( 0.40) +#..((((....)))). ( -0.60) X01 +(20760 15209 5246) X01 67.304 +(45270 55184 46987) X01 89.090 +(53914 48671 9491) X01 8.332 +(44432 62476 30554) X01 21.474 +(21206 16128 4429) X01 31.761 +( 5998 36361 17232) X01 33.787 +(35376 54746 29922) X01 4.436 +(51998 14938 13352) X01 38.070 +(17648 21853 64886) X01 51.808 +(16304 9322 17404) X01 30.137 +(46698 42323 39623) diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.e.log b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.e.log new file mode 100755 index 000000000..14aca2060 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.e.log @@ -0,0 +1,21 @@ +#< +#Date: Thu Aug 2 15:12:23 2001 +#EnergyModel: dangle=2 Temp=37.0 logML=logarithmic Par=VRNA-1.4 +#MoveSet: noShift=off noLP=off +#Simulation: num=10 time=500.00 seed=clock fpt=on mc=Kawasaki +#Output: log=hairpin.e silent=on lmin=off cut=20.00 +#ACUGAUCGUAGUCAC +#............... ( 0.00) +#..((((....)))). ( -0.60) X01 +#((((....))))... ( 0.40) X02 +(20919 15209 5246) X01 9.495 +(37503 34287 60895) X01 5.325 +(32207 13446 53388) X01 6.008 +(45167 5229 23791) X02 4.194 +(45433 53919 17806) X02 5.419 +(10205 8134 35980) X01 32.380 +(36817 5241 15865) X01 4.066 +(22891 28285 5106) X02 9.916 +(11239 25108 29130) X01 6.766 +(29917 23269 27183) X01 11.207 +(11597 13711 6518) diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.in new file mode 100755 index 000000000..18ef58629 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.in @@ -0,0 +1,3 @@ +ACUGAUCGUAGUCAC +((((....))))... +..((((....)))). diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.log b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.log new file mode 100755 index 000000000..5b22424ff --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.log @@ -0,0 +1,20 @@ +#< +#Date: Thu Aug 2 15:07:51 2001 +#EnergyModel: dangle=2 Temp=37.0 logML=logarithmic Par=VRNA-1.4 +#MoveSet: noShift=off noLP=off +#Simulation: num=10 time=500.00 seed=clock fpt=on mc=Kawasaki +#Output: log=hairpin silent=on lmin=off cut=20.00 +#ACUGAUCGUAGUCAC +#............... ( 0.00) +#..((((....)))). ( -0.60) X01 +(20647 15209 5246) X01 3.761 +(45273 46965 58195) X01 59.663 +(38349 38236 54635) X01 2.485 +( 2807 18778 20846) X01 8.455 +( 9813 63338 21421) X01 7.325 +(36623 13209 39161) X01 7.609 +(15011 38369 16622) X01 6.431 +(38685 28037 30315) X01 8.799 +(59813 28723 56993) X01 3.397 +(12419 11904 47612) X01 29.864 +(41943 21469 46941) diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.nolp.log b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.nolp.log new file mode 100755 index 000000000..4e15c052a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/hpin.nolp.log @@ -0,0 +1,20 @@ +#< +#Date: Thu Aug 2 16:24:42 2001 +#EnergyModel: dangle=2 Temp=37.0 logML=logarithmic Par=VRNA-1.4 +#MoveSet: noShift=off noLP=on +#Simulation: num=10 time=500.00 seed=clock fpt=on mc=Kawasaki +#Output: log=hpin.nolp silent=off lmin=off cut=20.00 +#ACUGAUCGUAGUCAC +#............... ( 0.00) +#..((((....)))). ( -0.60) X01 +(25258 15209 5246) X01 2.860 +(44730 44944 54555) X01 4.393 +(45786 38897 9635) X01 5.149 +( 1138 2575 3872) X01 1.976 +(18170 22215 30745) X01 11.294 +(15062 36074 3444) X01 25.262 +(45366 51780 48872) X01 5.836 +(47174 49996 2611) X01 4.510 +(36794 62744 9691) X01 14.810 +(48262 52565 918) X01 17.438 +(54706 34016 15011) diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/traj b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/traj new file mode 100755 index 000000000..74be8538a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Example/traj @@ -0,0 +1,312 @@ +............... 0.00 0.314 24 i 1 +.......(....).. 2.10 0.516 10 d 0 +............... 0.00 0.903 24 i 1 +.(.....)....... 3.10 0.934 10 d 0 +............... 0.00 1.603 24 i 1 +....(......)... 4.80 1.606 11 d 0 +............... 0.00 1.983 24 i 1 +.......(....).. 2.10 1.999 10 d 0 +............... 0.00 2.325 24 i 1 +.......(......) 3.20 2.391 9 d 0 +............... 0.00 2.631 24 i 1 +...(........).. 1.80 2.701 12 i 0 +...((......)).. 0.70 3.004 9 i 0 +..(((......))). 0.20 3.254 8 d 0 +...((......)).. 0.70 3.608 9 i 0 +...(((....))).. -0.10 3.670 7 i 0 +..((((....)))). -0.60 3.761 6 _ 1 X1 +............... 0.00 0.400 24 i 1 +.....(...)..... 5.60 0.412 14 d 0 +............... 0.00 1.284 24 i 1 +.......(....).. 2.10 1.430 10 s 0 +.......(......) 3.20 1.436 9 d 0 +............... 0.00 3.099 24 i 1 +.......(....).. 2.10 3.144 10 s 0 +.(.....)....... 3.10 3.257 10 i 0 +((.....))...... 1.80 9.410 6 d 1 +(.......)...... 4.20 9.419 9 i 0 +((.....))...... 1.80 14.566 6 d 1 +.(.....)....... 3.10 14.611 10 s 0 +.(........).... 2.80 14.660 12 d 0 +............... 0.00 14.671 24 i 1 +(.......)...... 4.20 14.695 9 d 0 +............... 0.00 15.196 24 i 1 +.(........).... 2.80 15.444 12 d 0 +............... 0.00 15.498 24 i 1 +(..........)... 5.40 15.499 16 d 0 +............... 0.00 15.856 24 i 1 +..(....)....... 4.20 15.857 13 s 0 +..(..........). 5.20 15.873 16 d 0 +............... 0.00 16.005 24 i 1 +(.......)...... 4.20 16.027 9 d 0 +............... 0.00 16.203 24 i 1 +.(........).... 2.80 16.271 12 d 0 +............... 0.00 17.060 24 i 1 +.......(....).. 2.10 17.098 10 s 0 +.......(......) 3.20 17.102 9 i 0 +.......((....)) 2.80 17.212 6 d 1 +.......(......) 3.20 17.263 9 d 0 +............... 0.00 18.446 24 i 1 +.......(....).. 2.10 18.687 10 d 0 +............... 0.00 20.230 24 i 1 +..(......)..... 4.80 20.249 10 i 0 +.((......)).... 2.00 20.775 8 i 0 +.(((....))).... 1.10 21.103 6 i 0 +((((....))))... 0.40 21.150 5 d 1 +.(((....))).... 1.10 21.538 6 i 0 +((((....))))... 0.40 21.606 5 d 1 +(((......)))... 1.30 21.741 7 i 0 +((((....))))... 0.40 21.903 5 d 1 +.(((....))).... 1.10 22.125 6 i 0 +((((....))))... 0.40 23.012 5 d 1 +.(((....))).... 1.10 23.126 6 i 0 +((((....))))... 0.40 23.598 5 d 1 +(((......)))... 1.30 26.216 7 d 0 +.((......)).... 2.00 26.323 8 i 0 +.(((....))).... 1.10 26.344 6 d 0 +..((....))..... 3.90 26.485 8 i 0 +.(((....))).... 1.10 26.607 6 i 0 +((((....))))... 0.40 27.374 5 S 1 +(((.(...))))... 4.80 27.394 5 S 0 +((((....))))... 0.40 28.384 5 d 1 +(((......)))... 1.30 28.561 7 d 0 +.((......)).... 2.00 28.923 8 i 0 +.(((....))).... 1.10 29.158 6 i 0 +((((....))))... 0.40 29.370 5 d 1 +.(((....))).... 1.10 29.647 6 i 0 +((((....))))... 0.40 29.732 5 d 1 +.(((....))).... 1.10 30.038 6 i 0 +((((....))))... 0.40 30.183 5 d 1 +(((......)))... 1.30 30.218 7 i 0 +((((....))))... 0.40 33.237 5 d 1 +.(((....))).... 1.10 34.478 6 i 0 +((((....))))... 0.40 34.894 5 d 1 +.(((....))).... 1.10 34.941 6 i 0 +((((....))))... 0.40 35.253 5 d 1 +(((......)))... 1.30 35.383 7 i 0 +(((.(...))))... 4.80 35.404 5 S 0 +((((....))))... 0.40 35.652 5 d 1 +.(((....))).... 1.10 35.804 6 i 0 +((((....))))... 0.40 36.163 5 d 1 +.(((....))).... 1.10 36.782 6 i 0 +((((....))))... 0.40 37.013 5 d 1 +.(((....))).... 1.10 37.094 6 d 0 +.((......)).... 2.00 37.123 8 d 0 +.(........).... 2.80 37.152 12 d 0 +............... 0.00 39.960 24 i 1 +........(....). 5.10 39.975 11 d 0 +............... 0.00 41.639 24 i 1 +.(........).... 2.80 41.656 12 S 0 +.....(....).... 5.00 41.704 14 d 2 +............... 0.00 42.031 24 i 1 +(.......)...... 4.20 42.085 9 d 0 +............... 0.00 44.421 24 i 1 +.......(....).. 2.10 44.636 10 d 0 +............... 0.00 45.440 24 i 1 +.....(...)..... 5.60 45.445 14 d 0 +............... 0.00 46.263 24 i 1 +.(.....)....... 3.10 46.322 10 d 0 +............... 0.00 47.704 24 i 1 +.......(....).. 2.10 47.841 10 d 0 +............... 0.00 47.995 24 i 1 +...(.......)... 5.80 48.005 12 d 0 +............... 0.00 48.081 24 i 1 +.......(....).. 2.10 48.103 10 d 0 +............... 0.00 50.047 24 i 1 +......(...).... 5.00 50.050 13 d 2 +............... 0.00 50.580 24 i 1 +.......(....).. 2.10 50.623 10 d 0 +............... 0.00 53.181 24 i 1 +...(........).. 1.80 53.313 12 d 0 +............... 0.00 57.201 24 i 1 +.....(...)..... 5.60 57.204 14 d 0 +............... 0.00 57.493 24 i 1 +.......(....).. 2.10 57.544 10 d 0 +............... 0.00 57.667 24 i 1 +...(....)...... 4.90 57.690 13 d 0 +............... 0.00 58.504 24 i 1 +...(........).. 1.80 58.513 12 i 0 +..((........)). 1.30 59.207 11 i 0 +..(((......))). 0.20 59.523 8 i 0 +..((((....)))). -0.60 59.663 6 _ 1 X1 +............... 0.00 1.169 24 i 1 +...(........).. 1.80 1.236 12 i 0 +...((......)).. 0.70 1.461 9 i 0 +...(((....))).. -0.10 1.605 7 i 0 +..((((....)))). -0.60 2.485 6 _ 1 X1 +............... 0.00 1.158 24 i 1 +.....(.......). 5.50 1.172 10 d 2 +............... 0.00 2.459 24 i 1 +...(........).. 1.80 2.461 12 d 0 +............... 0.00 3.842 24 i 1 +...(........).. 1.80 3.903 12 d 0 +............... 0.00 4.947 24 i 1 +.(........).... 2.80 5.126 12 d 0 +............... 0.00 6.931 24 i 1 +...(........).. 1.80 6.991 12 i 0 +..((........)). 1.30 7.231 11 i 0 +..(((......))). 0.20 7.336 8 d 0 +...((......)).. 0.70 7.551 9 i 0 +..(((......))). 0.20 7.597 8 i 0 +..((((....)))). -0.60 8.455 6 _ 1 X1 +............... 0.00 0.898 24 i 1 +.......(....).. 2.10 0.904 10 d 0 +............... 0.00 1.771 24 i 1 +...(........).. 1.80 1.819 12 d 0 +............... 0.00 4.058 24 i 1 +.(........).... 2.80 4.166 12 d 0 +............... 0.00 4.949 24 i 1 +...(........).. 1.80 4.971 12 i 0 +...((......)).. 0.70 5.245 9 i 0 +..(((......))). 0.20 5.512 8 d 0 +...((......)).. 0.70 5.594 9 i 0 +...(((....))).. -0.10 6.930 7 i 0 +..((((....)))). -0.60 7.325 6 _ 1 X1 +............... 0.00 0.459 24 i 1 +...(........).. 1.80 0.584 12 d 0 +............... 0.00 1.684 24 i 1 +...(........).. 1.80 1.694 12 d 0 +............... 0.00 2.900 24 i 1 +.(........).... 2.80 3.049 12 d 0 +............... 0.00 3.478 24 i 1 +...(........).. 1.80 3.532 12 S 0 +.......(....).. 2.10 3.579 10 d 0 +............... 0.00 5.797 24 i 1 +..(.......).... 4.90 5.810 12 d 0 +............... 0.00 5.961 24 i 1 +...(........).. 1.80 6.140 12 d 0 +............... 0.00 6.310 24 i 1 +...(........).. 1.80 6.403 12 i 0 +...((......)).. 0.70 6.428 9 i 0 +..(((......))). 0.20 6.555 8 i 0 +..((((....)))). -0.60 7.609 6 _ 1 X1 +............... 0.00 0.088 24 i 1 +....(......)... 4.80 0.111 11 d 0 +............... 0.00 1.787 24 i 1 +..(.......).... 4.90 1.795 12 d 0 +............... 0.00 1.880 24 i 1 +...(....)...... 4.90 1.883 13 d 0 +............... 0.00 2.082 24 i 1 +.......(....).. 2.10 2.143 10 d 0 +............... 0.00 2.598 24 i 1 +...(........).. 1.80 2.606 12 d 0 +............... 0.00 3.354 24 i 1 +(.......)...... 4.20 3.363 9 d 0 +............... 0.00 4.364 24 i 1 +...(........).. 1.80 4.600 12 d 0 +............... 0.00 4.649 24 i 1 +.......(....).. 2.10 4.740 10 d 0 +............... 0.00 4.839 24 i 1 +...(........).. 1.80 4.912 12 i 0 +..((........)). 1.30 5.364 11 i 0 +..(((......))). 0.20 5.839 8 i 0 +..((((....)))). -0.60 6.431 6 _ 1 X1 +............... 0.00 0.176 24 i 1 +.......(...)... 6.30 0.183 13 d 0 +............... 0.00 4.665 24 i 1 +....(......)... 4.80 4.708 11 d 0 +............... 0.00 4.856 24 i 1 +(.......)...... 4.20 4.859 9 d 0 +............... 0.00 4.927 24 i 1 +.(.....)....... 3.10 4.957 10 i 0 +((.....))...... 1.80 6.571 6 d 1 +.(.....)....... 3.10 6.601 10 d 0 +............... 0.00 6.680 24 i 1 +.......(....).. 2.10 7.314 10 S 0 +...(........).. 1.80 7.318 12 i 0 +...((......)).. 0.70 7.403 9 i 0 +...(((....))).. -0.10 7.583 7 d 0 +...((......)).. 0.70 8.001 9 i 0 +..(((......))). 0.20 8.143 8 d 0 +...((......)).. 0.70 8.335 9 i 0 +...(((....))).. -0.10 8.692 7 i 0 +..((((....)))). -0.60 8.799 6 _ 1 X1 +............... 0.00 0.074 24 i 1 +.......(....).. 2.10 0.075 10 d 0 +............... 0.00 0.312 24 i 1 +....(......)... 4.80 0.353 11 i 0 +...((......)).. 0.70 0.538 9 i 0 +...(((....))).. -0.10 3.151 7 i 0 +..((((....)))). -0.60 3.397 6 _ 1 X1 +............... 0.00 0.793 24 i 1 +.......(....).. 2.10 0.820 10 d 0 +............... 0.00 1.892 24 i 1 +...(........).. 1.80 1.898 12 d 0 +............... 0.00 2.653 24 i 1 +.....(.......). 5.50 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17.438 2 _ 1 X1 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/INSTALL b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/INSTALL new file mode 100755 index 000000000..b42a17ac4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/INSTALL @@ -0,0 +1,182 @@ +Basic Installation +================== + + These are generic installation instructions. + + The `configure' shell script attempts to guess correct values for +various system-dependent variables used during compilation. It uses +those values to create a `Makefile' in each directory of the package. +It may also create one or more `.h' files containing system-dependent +definitions. Finally, it creates a shell script `config.status' that +you can run in the future to recreate the current configuration, a file +`config.cache' that saves the results of its tests to speed up +reconfiguring, and a file `config.log' containing compiler output +(useful mainly for debugging `configure'). + + If you need to do unusual things to compile the package, please try +to figure out how `configure' could check whether to do them, and mail +diffs or instructions to the address given in the `README' so they can +be considered for the next release. If at some point `config.cache' +contains results you don't want to keep, you may remove or edit it. + + The file `configure.in' is used to create `configure' by a program +called `autoconf'. You only need `configure.in' if you want to change +it or regenerate `configure' using a newer version of `autoconf'. + +The simplest way to compile this package is: + + 1. `cd' to the directory containing the package's source code and type + `./configure' to configure the package for your system. If you're + using `csh' on an old version of System V, you might need to type + `sh ./configure' instead to prevent `csh' from trying to execute + `configure' itself. + + Running `configure' takes awhile. While running, it prints some + messages telling which features it is checking for. + + 2. Type `make' to compile the package. + + 3. Optionally, type `make check' to run any self-tests that come with + the package. + + 4. Type `make install' to install the programs and any data files and + documentation. + + 5. You can remove the program binaries and object files from the + source code directory by typing `make clean'. To also remove the + files that `configure' created (so you can compile the package for + a different kind of computer), type `make distclean'. There is + also a `make maintainer-clean' target, but that is intended mainly + for the package's developers. If you use it, you may have to get + all sorts of other programs in order to regenerate files that came + with the distribution. + +Compilers and Options +===================== + + Some systems require unusual options for compilation or linking that +the `configure' script does not know about. You can give `configure' +initial values for variables by setting them in the environment. Using +a Bourne-compatible shell, you can do that on the command line like +this: + CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure + +Or on systems that have the `env' program, you can do it like this: + env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure + +Compiling For Multiple Architectures +==================================== + + You can compile the package for more than one kind of computer at the +same time, by placing the object files for each architecture in their +own directory. To do this, you must use a version of `make' that +supports the `VPATH' variable, such as GNU `make'. `cd' to the +directory where you want the object files and executables to go and run +the `configure' script. `configure' automatically checks for the +source code in the directory that `configure' is in and in `..'. + + If you have to use a `make' that does not supports the `VPATH' +variable, you have to compile the package for one architecture at a time +in the source code directory. After you have installed the package for +one architecture, use `make distclean' before reconfiguring for another +architecture. + +Installation Names +================== + + By default, `make install' will install the package's files in +`/usr/local/bin', `/usr/local/man', etc. You can specify an +installation prefix other than `/usr/local' by giving `configure' the +option `--prefix=PATH'. + + You can specify separate installation prefixes for +architecture-specific files and architecture-independent files. If you +give `configure' the option `--exec-prefix=PATH', the package will use +PATH as the prefix for installing programs and libraries. +Documentation and other data files will still use the regular prefix. + + In addition, if you use an unusual directory layout you can give +options like `--bindir=PATH' to specify different values for particular +kinds of files. Run `configure --help' for a list of the directories +you can set and what kinds of files go in them. + + If the package supports it, you can cause programs to be installed +with an extra prefix or suffix on their names by giving `configure' the +option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. + +Optional Features +================= + + Some packages pay attention to `--enable-FEATURE' options to +`configure', where FEATURE indicates an optional part of the package. +They may also pay attention to `--with-PACKAGE' options, where PACKAGE +is something like `gnu-as' or `x' (for the X Window System). The +`README' should mention any `--enable-' and `--with-' options that the +package recognizes. + + For packages that use the X Window System, `configure' can usually +find the X include and library files automatically, but if it doesn't, +you can use the `configure' options `--x-includes=DIR' and +`--x-libraries=DIR' to specify their locations. + +Specifying the System Type +========================== + + There may be some features `configure' can not figure out +automatically, but needs to determine by the type of host the package +will run on. Usually `configure' can figure that out, but if it prints +a message saying it can not guess the host type, give it the +`--host=TYPE' option. TYPE can either be a short name for the system +type, such as `sun4', or a canonical name with three fields: + CPU-COMPANY-SYSTEM + +See the file `config.sub' for the possible values of each field. If +`config.sub' isn't included in this package, then this package doesn't +need to know the host type. + + If you are building compiler tools for cross-compiling, you can also +use the `--target=TYPE' option to select the type of system they will +produce code for and the `--build=TYPE' option to select the type of +system on which you are compiling the package. + +Sharing Defaults +================ + + If you want to set default values for `configure' scripts to share, +you can create a site shell script called `config.site' that gives +default values for variables like `CC', `cache_file', and `prefix'. +`configure' looks for `PREFIX/share/config.site' if it exists, then +`PREFIX/etc/config.site' if it exists. Or, you can set the +`CONFIG_SITE' environment variable to the location of the site script. +A warning: not all `configure' scripts look for a site script. + +Operation Controls +================== + + `configure' recognizes the following options to control how it +operates. + +`--cache-file=FILE' + Use and save the results of the tests in FILE instead of + `./config.cache'. Set FILE to `/dev/null' to disable caching, for + debugging `configure'. + +`--help' + Print a summary of the options to `configure', and exit. + +`--quiet' +`--silent' +`-q' + Do not print messages saying which checks are being made. To + suppress all normal output, redirect it to `/dev/null' (any error + messages will still be shown). + +`--srcdir=DIR' + Look for the package's source code in directory DIR. Usually + `configure' can determine that directory automatically. + +`--version' + Print the version of Autoconf used to generate the `configure' + script, and exit. + +`configure' also accepts some other, not widely useful, options. diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Kinfold b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Kinfold new file mode 100755 index 000000000..92e9c5829 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Kinfold differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Makefile new file mode 100755 index 000000000..9ef004e58 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/Makefile @@ -0,0 +1,670 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# Makefile. 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Hofacker + + for the energy evaluation Kinfold uses routines from + the Vienna-RNA-Package Version 1.4. + you can download the source code for Vienna-RNA-Package from + http://www.tbi.univie.ac.at/~ivo/RNA/ + +Comments are welcome. + + - Christoph Flamm, diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/acinclude.m4 b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/acinclude.m4 new file mode 100755 index 000000000..01c514d0d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/acinclude.m4 @@ -0,0 +1,53 @@ +dnl -*-autoconf-*- + +AC_DEFUN([AC_PATH_VRNA], +[AC_MSG_CHECKING([for ViennaRNA package]) +if test -z "$ac_VRNA_includes"; then + for ac_dir in \ + ../H \ + /usr/local/include/ViennaRNA \ + /usr/local/include \ + /usr/include/ViennaRNA \ + /usr/local/ViennaRNA/H \ + /usr/local/share/ViennaRNA/include \ + /opt/ViennaRNA/include \ + ;\ + do + if test -r "$ac_dir/part_func.h"; then + ac_VRNA_includes=$ac_dir + break + fi + done +fi +if test $ac_VRNA_includes; then + CPPFLAGS="$CPPFLAGS -I$ac_VRNA_includes" +fi + +if [[ -d ../lib ] && [ "$ac_VRNA_includes" = "../H" ]]; then + ac_VRNA_lib=../lib +fi + +if test -z "$ac_VRNA_lib"; then +for ac_dir in `echo "$ac_VRNA_includes" | sed -e s/include/lib/ -e s/H$/lib/` \ + /usr/local/lib \ + ; \ +do + for ac_extension in a so sl; do + if test -r $ac_dir/libRNA.$ac_extension; then + ac_VRNA_lib=$ac_dir + break 2 + fi + done +done +fi # $ac_VRNA_lib = NO +if test $ac_VRNA_lib; then + LDFLAGS="-L$ac_VRNA_lib $LDFLAGS" +fi +AC_MSG_RESULT([ headers in "$ac_VRNA_includes" and library... 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We just wanted to have am__tar + # and am__untar set. + test -n "${am_cv_prog_tar_$1}" && break + + # tar/untar a dummy directory, and stop if the command works + rm -rf conftest.dir + mkdir conftest.dir + echo GrepMe > conftest.dir/file + AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar]) + rm -rf conftest.dir + if test -s conftest.tar; then + AM_RUN_LOG([$am__untar /dev/null 2>&1 && break + fi +done +rm -rf conftest.dir + +AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool]) +AC_MSG_RESULT([$am_cv_prog_tar_$1])]) +AC_SUBST([am__tar]) +AC_SUBST([am__untar]) +]) # _AM_PROG_TAR + +m4_include([acinclude.m4]) diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/baum.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/baum.c new file mode 100755 index 000000000..8e9a451d7 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/baum.c @@ -0,0 +1,726 @@ +/* + Last changed Time-stamp: <2006-01-16 11:27:31 ivo> + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: baum.c,v 1.5 2006/01/16 10:37:47 ivo Exp $ +*/ + +#include +#include +#include +#include +#include "fold_vars.h" +#include "fold.h" +#include "utils.h" +#include "pair_mat.h" +#include "nachbar.h" +#include "globals.h" + + +#define MYTURN 4 +#define ORDER(x,y) if ((x)->nummer>(y)->nummer) {tempb=x; x=y; y=tempb;} + +/* item of structure ringlist */ +typedef struct _baum { + int nummer; /* number of base in sequence */ + char typ; /* 'r' virtualroot, 'p' or 'q' paired, 'u' unpaired */ + unsigned short base; /* 0<->unknown, 1<->A, 2<->C, 3<->G, 4<->U */ + struct _baum *up; + struct _baum *next; + struct _baum *prev; + struct _baum *down; +} baum; + +static char UNUSED rcsid[]="$Id: baum.c,v 1.5 2006/01/16 10:37:47 ivo Exp $"; +static int poListop = 0; /* polist counter = no_of_bp */ +static short *pairList; +static short *typeList; +static short *aliasList; +static baum *rl; /* ringlist */ +static baum *wurzl; /* virtualroot of ringlist-tree */ +static baum **poList; /* post order list of bp's */ +static char **ptype; + +static int comp_struc(const void *A, const void *B); +extern int energy_of_struct_pt (char *string, + short * ptable, short *s, short *s1); +/* PUBLIC FUNCTIONES */ +void ini_or_reset_rl (void); +void move_it (void); +void update_tree (int i, int j); +void clean_up_rl (void); + +/* PRIVATE FUNCTIONES */ +static void ini_ringlist(void); +static void reset_ringlist(void); +static void struc2tree (char *struc); +static void close_bp (baum *i, baum *j); +static void open_bp (baum *i); +static void make_poList (baum *root); +static void inb (baum *root); +static void inb_nolp (baum *root); +static void dnb (baum *rli); +static void dnb_nolp (baum *rli); +static void fnb (baum *rli); +static void make_ptypes(const short *S); +/* debugging tool(s) */ +#if 0 +static void rl_status(void); +#endif + +/* convert structure in bracked-dot-notation to a ringlist-tree */ +static void struc2tree(char *struc) { + char* struc_copy; + int ipos, jpos, balance = 0; + baum *rli, *rlj; + + struc_copy = (char *)calloc(GSV.len+1, sizeof(char)); + assert(struc_copy); + strcpy(struc_copy,struc); + + for (ipos = 0; ipos < GSV.len; ipos++) { + if (struc_copy[ipos] == ')') { + jpos = ipos; + struc_copy[ipos] = '.'; + balance++; + while (struc_copy[--ipos] != '('); + struc_copy[ipos] = '.'; + balance--; + rli = &rl[ipos]; + rlj = &rl[jpos]; + close_bp(rli, rlj); + } + } + + if (balance) { + fprintf(stderr, + "struc2tree(): start structure is not balanced !\n%s\n%s\n", + GAV.farbe, struc); + exit(1); + } + + poListop = 1; + make_poList(NULL); + GSV.currE = GSV.startE = + (float )energy_of_struct_pt(GAV.farbe, + pairList, typeList, aliasList) / 100.0; + free(struc_copy); +} + +/**/ +static void ini_ringlist(void) { + int i; + + /* needed by function energy_of_struct_pt() from Vienna-RNA-1.4 */ + pairList = (short *)calloc(GSV.len + 2, sizeof(short)); + assert(pairList != NULL); + typeList = (short *)calloc(GSV.len + 2, sizeof(short)); + assert(typeList != NULL); + aliasList = (short *)calloc(GSV.len + 2, sizeof(short)); + assert(aliasList != NULL); + pairList[0] = typeList[0] = aliasList[0] = GSV.len; + ptype = (char **)calloc(GSV.len + 2, sizeof(char *)); + assert(ptype != NULL); + for (i=0; i<=GSV.len; i++) { + ptype[i] = (char*)calloc(GSV.len + 2, sizeof(char)); + assert(ptype[i] != NULL); + } + + /* allocate virtual root */ + wurzl = (baum *)calloc(1, sizeof(baum)); + assert(wurzl != NULL); + /* allocate ringList */ + rl = (baum *)calloc(GSV.len+1, sizeof(baum)); + assert(rl != NULL); + /* allocate PostOrderList */ + poList = (baum **)calloc(GSV.len+2, sizeof(baum *)); + assert(poList != NULL); + + /* initialize virtualroot */ + wurzl->typ = 'r'; + wurzl->nummer = -1; + /* connect virtualroot to ringlist-tree in down direction */ + wurzl->down = &rl[GSV.len]; + /* initialize post-order list */ + poList[poListop++] = wurzl; + + make_pair_matrix(); + + /* initialize rest of ringlist-tree */ + for(i = 0; i < GSV.len; i++) { + int c; + GAV.currform[i] = '.'; + GAV.prevform[i] = 'x'; + pairList[i+1] = 0; + rl[i].typ = 'u'; + /* decode base to numeric value */ + c = encode_char(GAV.farbe[i]); + rl[i].base = typeList[i+1] = c; + aliasList[i+1] = alias[typeList[i+1]]; + /* astablish links for node of the ringlist-tree */ + rl[i].nummer = i; + rl[i].next = &rl[i+1]; + rl[i].prev = ((i == 0) ? &rl[GSV.len] : &rl[i-1]); + rl[i].up = rl[i].down = NULL; + } + GAV.currform[GSV.len] = GAV.prevform[GSV.len] = '\0'; + make_ptypes(aliasList); + + rl[i].nummer = i; + rl[i].base = 0; + /* make ringlist circular in next, prev direction */ + rl[i].next = &rl[0]; + rl[i].prev = &rl[i-1]; + /* make virtual basepair for virtualroot */ + rl[i].up = wurzl; + rl[i].typ = 'x'; +} + +/**/ +void ini_or_reset_rl(void) { + + /* if there is no ringList-tree make a new one */ + if (wurzl == NULL) { + ini_ringlist(); + + /* start structure */ + struc2tree(GAV.startform); + GSV.currE = GSV.startE = energy_of_struct(GAV.farbe, GAV.startform); + + + /* stop structure(s) */ + if ( GTV.stop ) { + int i; + + qsort(GAV.stopform, GSV.maxS, sizeof(char *), comp_struc); + for (i = 0; i< GSV.maxS; i++) + GAV.sE[i] = energy_of_struct(GAV.farbe_full, GAV.stopform[i]); + } + else { + if(GTV.noLP) + noLonelyPairs=1; + initialize_fold(GSV.len); + /* fold sequence to get Minimum free energy structure (Mfe) */ + GAV.sE[0] = fold(GAV.farbe_full, GAV.stopform[0]); + free_arrays(); + /* revaluate energy of Mfe (maye differ if --logML=logarthmic */ + GAV.sE[0] = energy_of_struct(GAV.farbe_full, GAV.stopform[0]); + } + GSV.stopE = GAV.sE[0]; + ini_nbList(strlen(GAV.farbe_full)*strlen(GAV.farbe_full)); + } + else { + /* reset ringlist-tree to start conditions */ + reset_ringlist(); + if(GTV.start) struc2tree(GAV.startform); + else { + GSV.currE = GSV.startE; + poListop = 1; + } + } +} + +/**/ +static void reset_ringlist(void) { + int i; + + for(i = 0; i < GSV.len; i++) { + GAV.currform[i] = '.'; + GAV.prevform[i] = 'x'; + pairList[i+1] = 0; + rl[i].typ = 'u'; + rl[i].next = &rl[i + 1]; + rl[i].prev = ((i == 0) ? &rl[GSV.len] : &rl[i - 1]); + rl[i].up = rl[i].down = NULL; + } + rl[i].next = &rl[0]; + rl[i].prev = &rl[i-1]; + rl[i].up = wurzl; +} + +/* update ringlist-tree */ +void update_tree(int i, int j) { + + baum *rli, *rlj, *tempb; + + if ( abs(i) < GSV.len) { /* >> single basepair move */ + if ((i > 0) && (j > 0)) { /* insert */ + rli = &rl[i-1]; + rlj = &rl[j-1]; + close_bp(rli, rlj); + } + else if ((i < 0)&&(j < 0)) { /* delete */ + i = -i; + rli = &rl[i-1]; + open_bp(rli); + } + else { /* shift */ + if (i > 0) { /* i remains the same, j shifts */ + j=-j; + rli=&rl[i-1]; + rlj=&rl[j-1]; + open_bp(rli); + ORDER(rli, rlj); + close_bp(rli, rlj); + } + else { /* j remains the same, i shifts */ + baum *old_rli; + i = -i; + rli = &rl[i-1]; + rlj = &rl[j-1]; + old_rli = rlj->up; + open_bp(old_rli); + ORDER(rli, rlj); + close_bp(rli, rlj); + } + } + } /* << single basepair move */ + else { /* >> double basepair move */ + if ((i > 0) && (j > 0)) { /* insert */ + rli = &rl[i-GSV.len-2]; + rlj = &rl[j-GSV.len-2]; + close_bp(rli->next, rlj->prev); + close_bp(rli, rlj); + } + else if ((i < 0)&&(j < 0)) { /* delete */ + i = -i; + rli = &rl[i-GSV.len-2]; + open_bp(rli); + open_bp(rli->next); + } + } /* << double basepair move */ + + poListop = 1; + make_poList(NULL); +} + +/* open a particular base pair */ +void open_bp(baum *i) { + + baum *in; /* points to i->next */ + + /* change string representation */ + GAV.currform[i->nummer] = '.'; + GAV.currform[i->down->nummer] = '.'; + + /* change pairtable representation */ + pairList[1 + i->nummer] = 0; + pairList[1 + i->down->nummer] = 0; + + /* change tree representation */ + in = i->next; + i->typ = 'u'; + i->down->typ = 'u'; + i->next = i->down->next; + i->next->prev = i; + in->prev = i->down; + i->down->next = in; + i->down = in->prev->up = NULL; +} + +/* close a particular base pair */ +void close_bp (baum *i, baum *j) { + + baum *jn; /* points to j->next */ + + /* change string representation */ + GAV.currform[i->nummer] = '('; + GAV.currform[j->nummer] = ')'; + + /* change pairtable representation */ + pairList[1 + i->nummer] = 1+ j->nummer; + pairList[1 + j->nummer] = 1 + i->nummer; + + /* change tree representation */ + jn = j->next; + i->typ = 'p'; + j->typ = 'q'; + i->down = j; + j->up = i; + i->next->prev = j; + j->next->prev = i; + j->next = i->next; + i->next = jn; +} + +/* for a given tree, generate postorder-list */ +static void make_poList (baum *root) { + + baum *stop, *rli; + + if (!root) root = wurzl; + stop = root->down; + + /* foreach base in ringlist ... */ + for (rli = stop->next; rli != stop; rli = rli->next) { + /* ... explore subtee if bp found */ + if (rli->typ == 'p') { + /* fprintf(stderr, "%d >%d<\n", poListop, rli->nummer); */ + poList[poListop++] = rli; + if ( poListop > GSV.len+1 ) { + fprintf(stderr, "Something went wrong in make_poList()\n"); + exit(1); + } + make_poList(rli); + } + } + return; +} + +/* for a given ringlist, generate all structures + with one additional basepair */ +static void inb(baum *root) { + + int EoT = 0; + baum *stop,*rli,*rlj; + + stop=root->down; + /* loop ringlist over all possible i positions */ + for(rli=stop->next;rli!=stop;rli=rli->next){ + /* potential i-position is already paired */ + if(rli->typ=='p') continue; + /* loop ringlist over all possible j positions */ + for(rlj=rli->next;rlj!=stop;rlj=rlj->next){ + /* base pair must enclose at least 3 bases */ + if(rlj->nummer - rli->nummer < MYTURN) continue; + /* potential j-position is already paired */ + if(rlj->typ=='p') continue; + /* if i-j can form a base pair ... */ + if(ptype[rli->nummer][rlj->nummer]){ + /* close the base bair and ... */ + close_bp(rli,rlj); + /* ... evaluate energy of the structure */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* open the base pair again... */ + open_bp(rli); + /* ... and put the move and the enegy + of the structure into the neighbour list */ + update_nbList(1 + rli->nummer, 1 + rlj->nummer, EoT); + } + } + } +} + +/* for a given ringlist, generate all structures (canonical) + with one additional base pair (BUT WITHOUT ISOLATED BASE PAIRS) */ +static void inb_nolp(baum *root) { + + int EoT = 0; + baum *stop, *rli, *rlj; + + stop = root->down; + /* loop ringlist over all possible i positions */ + for (rli=stop->next;rli!=stop;rli=rli->next) { + /* potential i-position is already paired */ + if (rli->typ=='p') continue; + /* loop ringlist over all possible j positions */ + for (rlj=rli->next;rlj!=stop;rlj=rlj->next) { + /* base pair must enclose at least 3 bases */ + if (rlj->nummer - rli->nummer < MYTURN) continue; + /* potential j-position is already paired */ + if (rlj->typ=='p') continue; + /* if i-j can form a base pair ... */ + if (ptype[rli->nummer][rlj->nummer]) { + /* ... and extends a helix ... */ + if (((rli->prev==stop && rlj->next==stop) && stop->typ != 'x') || + (rli->next == rlj->prev)) { + /* ... close the base bair and ... */ + close_bp(rli,rlj); + /* ... evaluate energy of the structure */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* open the base pair again... */ + open_bp(rli); + /* ... and put the move and the enegy + of the structure into the neighbour list */ + update_nbList(1 + rli->nummer, 1 + rlj->nummer, EoT); + } + /* if double insertion is possible ... */ + else if ((rlj->nummer - rli->nummer >= MYTURN+2)&& + (rli->next->typ != 'p' && rlj->prev->typ != 'p') && + (rli->next->next != rlj->prev->prev) && + (ptype[rli->next->nummer][rlj->prev->nummer])) { + /* close the two base bair and ... */ + close_bp(rli->next, rlj->prev); + close_bp(rli, rlj); + /* ... evaluate energy of the structure */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* open the two base pair again ... */ + open_bp(rli); + open_bp(rli->next); + /* ... and put the move and the enegy + of the structure into the neighbour list */ + update_nbList(1+rli->nummer+GSV.len+1, 1+rlj->nummer+GSV.len+1, EoT); + } + } + } + } +} + +/* for a given ringlist, generate all structures + with one less base pair */ +static void dnb(baum *rli){ + + int EoT = 0; + baum *rlj; + + rlj=rli->down; + open_bp(rli); + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + close_bp(rli,rlj); + update_nbList(-(1 + rli->nummer), -(1 + rlj->nummer), EoT); +} + +/* for a given ringlist, generate all structures (canonical) + with one less base pair (BUT WITHOUT ISOLATED BASE PAIRS) */ +static void dnb_nolp(baum *rli) { + + int EoT = 0; + baum *rlj; + baum *rlin = NULL; /* pointers to following pair in helix, if any */ + baum *rljn = NULL; + baum *rlip = NULL; /* pointers to preceding pair in helix, if any */ + baum *rljp = NULL; + + rlj = rli->down; + + /* immediate interior base pair ? */ + if (rlj->next == rlj->prev) { + rlin = rlj->next; + rljn = rlin->down; + } + + /* immediate exterior base pair and not virtualroot ? */ + if (rli->prev == rli->next && rli->next->typ != 'x') { + rlip = rli->next->up; + rljp = rli->next; + } + + /* double delete ? */ + if (rlip==NULL && rlin && rljn->next != rljn->prev ) { + /* open the two base pairs ... */ + open_bp(rli); + open_bp(rlin); + /* ... evaluate energy of the structure ... */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* ... and put the move and the enegy + of the structure into the neighbour list ... */ + update_nbList(-(1+rli->nummer+GSV.len+1),-(1+rlj->nummer+GSV.len+1), EoT); + /* ... and close the two base pairs again */ + close_bp(rlin, rljn); + close_bp(rli, rlj); + } else { /* single delete */ + /* the following will work only if boolean expr are shortcicuited */ + if (rlip==NULL || (rlip->prev == rlip->next && rlip->prev->typ != 'x')) + if (rlin ==NULL || (rljn->next == rljn->prev)) { + /* open the base pair ... */ + open_bp(rli); + /* ... evaluate energy of the structure ... */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* ... and put the move and the enegy + of the structure into the neighbour list ... */ + update_nbList(-(1 + rli->nummer),-(1 + rlj->nummer), EoT); + /* and close the base pair again */ + close_bp(rli, rlj); + } + } +} + +/* for a given ringlist, generate all structures + with one shifted base pair */ +static void fnb(baum *rli) { + + int EoT = 0, x; + baum *rlj, *stop, *help_rli, *help_rlj; + + stop = rli->down; + + /* examin interior loop of bp(ij); (.......) + i of j move -> <- */ + for (rlj = stop->next; rlj != stop; rlj = rlj->next) { + /* prevent shifting to paired position */ + if ((rlj->typ=='p')||(rlj->typ=='q')) continue; + /* j-position of base pair shifts to k position (ij)->(ik) inummer-rli->nummer >= MYTURN) + && (ptype[rli->nummer][rlj->nummer]) ) { + /* open original basepair */ + open_bp(rli); + /* close shifted version of original basepair */ + close_bp(rli, rlj); + /* evaluate energy of the structure */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* put the move and the enegy of the structure into the neighbour list */ + update_nbList(1+rli->nummer, -(1+rlj->nummer), EoT); + /* open shifted basepair */ + open_bp(rli); + /* restore original basepair */ + close_bp(rli, stop); + } + /* i-position of base pair shifts to position k (ij)->(kj) inummer-rlj->nummer >= MYTURN) + && (ptype[stop->nummer][rlj->nummer]) ) { + /* open original basepair */ + open_bp(rli); + /* close shifted version of original basepair */ + close_bp(rlj, stop); + /* evaluate energy of the structure */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* put the move and the enegy of the structure into the neighbour list */ + update_nbList(-(1 + rlj->nummer), 1 + stop->nummer, EoT); + /* open shifted basepair */ + open_bp(rlj); + /* restore original basepair */ + close_bp(rli, stop); + } + } + /* examin exterior loop of bp(ij); (.......) + i or j moves <- -> */ + for (rlj=rli->next;rlj!=rli;rlj=rlj->next) { + if ((rlj->typ=='p') || (rlj->typ=='q' ) || (rlj->typ=='x')) continue; + x=rlj->nummer-rli->nummer; + if (x<0) x=-x; + /* j-position of base pair shifts to position k */ + if ((x >= MYTURN) && (ptype[rli->nummer][rlj->nummer])) { + if (rli->nummernummer) { + help_rli=rli; + help_rlj=rlj; + } + else { + help_rli=rlj; + help_rlj=rli; + } + /* open original basepair */ + open_bp(rli); + /* close shifted version of original basepair */ + close_bp(help_rli,help_rlj); + /* evaluate energy of the structure */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* put the move and the enegy of the structure into the neighbour list */ + update_nbList(1 + rli->nummer, -(1 + rlj->nummer), EoT); + /* open shifted base pair */ + open_bp(help_rli); + /* restore original basepair */ + close_bp(rli,stop); + } + x = rlj->nummer-stop->nummer; + if (x < 0) x = -x; + /* i-position of base pair shifts to position k */ + if ((x >= MYTURN) && (ptype[stop->nummer][rlj->nummer])) { + if (stop->nummer < rlj->nummer) { + help_rli = stop; + help_rlj = rlj; + } + else { + help_rli = rlj; + help_rlj = stop; + } + /* open original basepair */ + open_bp(rli); + /* close shifted version of original basepair */ + close_bp(help_rli, help_rlj); + /* evaluate energy of the structure */ + EoT = energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList); + /* put the move and the enegy of the structure into the neighbour list */ + update_nbList(-(1 + rlj->nummer), 1 + stop->nummer, EoT); + /* open shifted basepair */ + open_bp(help_rli); + /* restore original basepair */ + close_bp(rli,stop); + } + } +} + +/* for a given tree (structure), + generate all neighbours according to moveset */ +void move_it (void) { + int i; + + GSV.currE = + energy_of_struct_pt(GAV.farbe, pairList, typeList, aliasList)/100.; + + if ( GTV.noLP ) { /* canonical neighbours only */ + for (i = 0; i < poListop; i++) { + /* canonical base pair insert neighbours */ + inb_nolp(poList[i]); + + if (i > 0) { /* virtual root bp should never be removed !!! */ + /* canonical base pair delete neighbours */ + dnb_nolp(poList[i]); + } + } + } + else { /* all neighbours */ + for (i = 0; i < poListop; i++) { + /* base pair insert neighbours */ + inb(poList[i]); + + if (i > 0) { /* virtual root bp should never be removed !!! */ + /* base pair delete neighbours */ + dnb(poList[i]); + /* base pair shift neighbours */ + if ( GTV.noShift == 0 ) fnb(poList[i]); + } + } + } +} + +/**/ +void clean_up_rl(void) { + + free(pairList); pairList=NULL; + free(typeList); typeList = NULL; + free(aliasList); aliasList = NULL; + free(rl); rl=NULL; + free(wurzl); wurzl=NULL; + free(poList); poList=NULL; poListop=0; +} + +/**/ +static int comp_struc(const void *A, const void *B) { + int aE, bE; + aE = (int)(100 * energy_of_struct(GAV.farbe_full, ((char **)A)[0])); + bE = (int)(100 * energy_of_struct(GAV.farbe_full, ((char **)B)[0])); + return (aE-bE); +} + +#if 0 +/**/ +static void rl_status(void) { + + int i; + + printf("\n%s\n%s\n", GAV.farbe, GAV.currform); + for (i=0; i <= GSV.len; i++) { + printf("%2d %c %c %2d %2d %2d %2d\n", + rl[i].nummer, + i == GSV.len ? 'X': GAV.farbe[i], + rl[i].typ, + rl[i].up==NULL?0:(rl[i].up)->nummer, + rl[i].down==NULL?0:(rl[i].down)->nummer, + (rl[i].prev)->nummer, + (rl[i].next)->nummer); + } + printf("---\n"); +} +#endif + +#define TURN MYTURN-1 +static void make_ptypes(const short *S) { + int n,i,j,k,l; + n=S[0]; + for (k=1; kn) continue; + type = pair[S[i]][S[j]]; + while ((i>=1)&&(j<=n)) { + if ((i>1)&&(j + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: baum.h,v 1.1.1.1 2001/08/02 16:48:58 xtof Exp $ +*/ + +#ifndef BAUM_H +#define BAUM_H + +/* used in main.c */ +extern void ini_or_reset_rl(void); +extern void move_it(void); +extern void clean_up_rl(void); + +/* used in nachbar.c */ +extern void update_tree(int i,int j); + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/baum.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/baum.o new file mode 100755 index 000000000..d67934622 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/baum.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache.c new file mode 100755 index 000000000..14e4cc908 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache.c @@ -0,0 +1,131 @@ +/* + Last changed Time-stamp: <2001-08-02 14:59:19 xtof> + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: cache.c,v 1.2 2005/02/16 17:00:48 ivo Exp $ +*/ + +#include +#include +#include +#include +#include "utils.h" +#include "cache_util.h" + +/* + modify cache_f(), cache_comp() and the typedef of cache_entry + in cache_utils.h to suit your application +*/ + +/* PUBLIC FUNCTIONES */ +cache_entry *lookup_cache (char *x); +int write_cache (cache_entry *x); +/* void delete_cache (cache_entry *x); */ +void kill_cache(); +void initialize_cache(); + +/* PRIVATE FUNCTIONES */ +/* static int cache_comp(cache_entry *x, cache_entry *y); */ +static unsigned cache_f (char *x); + +/* #define CACHESIZE 67108864 -1 */ /* 2^26 -1 must be power of 2 -1 */ +/* #define CACHESIZE 33554432 -1 */ /* 2^25 -1 must be power of 2 -1 */ +/* #define CACHESIZE 16777216 -1 */ /* 2^24 -1 must be power of 2 -1 */ +/* #define CACHESIZE 4194304 -1 */ /* 2^22 -1 must be power of 2 -1 */ +#define CACHESIZE 1048576 -1 /* 2^20 -1 must be power of 2 -1 */ +/* #define CACHESIZE 262144 -1 */ /* 2^18 -1 must be power of 2 -1 */ +/* next is default */ +/* #define CACHESIZE 65536 -1 */ /* 2^16 -1 must be power of 2 -1 */ +/* #define CACHESIZE 16384 -1 */ /* 2^14 -1 must be power of 2 -1 */ +/* #define CACHESIZE 4096 -1 */ /* 2^12 -1 must be power of 2 -1 */ + +static cache_entry *cachetab[CACHESIZE+1]; +static char UNUSED rcsid[] ="$Id: cache.c,v 1.2 2005/02/16 17:00:48 ivo Exp $"; +unsigned long collisions=0; + +/* stolen from perl source */ +char coeff[] = { + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1, + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1, + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1, + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1, + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1, + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1, + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1, + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1}; + +/* key must not be longer than 128 */ +#pragma inline (cache_f) +unsigned cache_f(char *x) { + register char *s; + register int i; + register unsigned cache; + + s = x; + + for (i=0, cache = 0; + /* while */ *s; + s++, i++ , cache *= 5 ) { + cache += *s * coeff[i]; + } + + /* divide through CACHESIZE for normalization */ + return ((cache) & (CACHESIZE)); +} + + +/* returns NULL unless x is in the cache */ +cache_entry *lookup_cache (char *x) { + int cacheval; + cache_entry *c; + + cacheval=cache_f(x); + if ((c=cachetab[cacheval])) + if (strcmp(c->structure,x)==0) return c; + + return NULL; +} + +/* returns 1 if x already was in the cache */ +int write_cache (cache_entry *x) { + int cacheval; + cache_entry *c; + + cacheval=cache_f(x->structure); + if ((c=cachetab[cacheval])) { + free(c->structure); + free(c->neighbors); + free(c->rates); + free(c); + } + cachetab[cacheval]=x; + return 0; +} + +/**/ +void initialize_cache () { } + +/**/ +void kill_cache () { + int i; + + for (i=0;istructure); + free (cachetab[i]->neighbors); + free (cachetab[i]->rates); + free (cachetab[i]); + } + cachetab[i]=NULL; + } +} + +#if 0 +/**/ +static int cache_comp(cache_entry *x, cache_entry *y) { + return strcmp(((cache_entry *)x)->structure, ((cache_entry *)y)->structure); +} +#endif + +/* End of file */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache.o new file mode 100755 index 000000000..a3caf7a17 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache_util.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache_util.h new file mode 100755 index 000000000..47ed1fa9f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/cache_util.h @@ -0,0 +1,32 @@ +/* + Last changed Time-stamp: <2001-08-02 14:58:06 xtof> + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: cache_util.h,v 1.1.1.1 2001/08/02 16:48:58 xtof Exp $ +*/ + +#ifndef CACHE_UTIL_H +#define CACHE_UTIL_H + +#ifdef __GNUC__ +#define UNUSED __attribute__ ((unused)) +#else +#define UNUSED +#endif + +typedef struct { + char *structure; + int top; /* number of neighbors */ + int lmin; /* is a local minimum ? */ + double flux; /* sum of rates */ + double energy; /* energy of this structure */ + short *neighbors; + float *rates; +} cache_entry; + +extern cache_entry *lookup_cache (char *x); +extern int write_cache (cache_entry *x); +void kill_cache(void); + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.h new file mode 100755 index 000000000..fb0f7d73b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.h @@ -0,0 +1,74 @@ +/* config.h. Generated by configure. */ +/* config.h.in. Generated from configure.in by autoheader. */ + +/* Define to 1 if you have the header file. */ +#define HAVE_FOLD_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_INTTYPES_H 1 + +/* Define to 1 if you have the `m' library (-lm). */ +#define HAVE_LIBM 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_LIMITS_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_MEMORY_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STDINT_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STDLIB_H 1 + +/* Define to 1 if you have the `strdup' function. */ +/* #undef HAVE_STRDUP */ + +/* Define to 1 if you have the header file. */ +#define HAVE_STRINGS_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STRING_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_SYS_STAT_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_SYS_TIME_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_SYS_TYPES_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_UNISTD_H 1 + +/* Name of package */ +#define PACKAGE "kinfold" + +/* Define to the address where bug reports for this package should be sent. */ +#define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" + +/* Define to the full name of this package. */ +#define PACKAGE_NAME "Kinfold" + +/* Define to the full name and version of this package. */ +#define PACKAGE_STRING "Kinfold 1.0" + +/* Define to the one symbol short name of this package. */ +#define PACKAGE_TARNAME "kinfold" + +/* Define to the version of this package. */ +#define PACKAGE_VERSION "1.0" + +/* Define to 1 if you have the ANSI C header files. */ +/* #undef STDC_HEADERS */ + +/* Version number of package */ +#define VERSION "1.0" + +/* Define if using the dmalloc debugging malloc package */ +/* #undef WITH_DMALLOC */ + +/* Define to empty if `const' does not conform to ANSI C. */ +/* #undef const */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.h.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.h.in new file mode 100755 index 000000000..7224bfa2b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.h.in @@ -0,0 +1,73 @@ +/* config.h.in. Generated from configure.in by autoheader. */ + +/* Define to 1 if you have the header file. */ +#undef HAVE_FOLD_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_INTTYPES_H + +/* Define to 1 if you have the `m' library (-lm). */ +#undef HAVE_LIBM + +/* Define to 1 if you have the header file. */ +#undef HAVE_LIMITS_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_MEMORY_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDINT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDLIB_H + +/* Define to 1 if you have the `strdup' function. */ +#undef HAVE_STRDUP + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRINGS_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRING_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_STAT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_TIME_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_TYPES_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_UNISTD_H + +/* Name of package */ +#undef PACKAGE + +/* Define to the address where bug reports for this package should be sent. */ +#undef PACKAGE_BUGREPORT + +/* Define to the full name of this package. */ +#undef PACKAGE_NAME + +/* Define to the full name and version of this package. */ +#undef PACKAGE_STRING + +/* Define to the one symbol short name of this package. */ +#undef PACKAGE_TARNAME + +/* Define to the version of this package. */ +#undef PACKAGE_VERSION + +/* Define to 1 if you have the ANSI C header files. */ +#undef STDC_HEADERS + +/* Version number of package */ +#undef VERSION + +/* Define if using the dmalloc debugging malloc package */ +#undef WITH_DMALLOC + +/* Define to empty if `const' does not conform to ANSI C. */ +#undef const diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.log b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.log new file mode 100755 index 000000000..5e2ff49ca --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.log @@ -0,0 +1,653 @@ +This file contains any messages produced by compilers while +running configure, to aid debugging if configure makes a mistake. + +It was created by Kinfold configure 1.0, which was +generated by GNU Autoconf 2.59. Invocation command line was + + $ ./configure --prefix=/usr/local --cache-file=/dev/null --srcdir=. + +## --------- ## +## Platform. ## +## --------- ## + +hostname = mcluster02 +uname -m = x86_64 +uname -r = 2.6.9-34.ELsmp +uname -s = Linux +uname -v = #1 SMP Fri Feb 24 16:56:28 EST 2006 + +/usr/bin/uname -p = unknown +/bin/uname -X = unknown + +/bin/arch = x86_64 +/usr/bin/arch -k = unknown +/usr/convex/getsysinfo = unknown +hostinfo = unknown +/bin/machine = unknown +/usr/bin/oslevel = unknown +/bin/universe = unknown + +PATH: /storage/appl/n1ge6u7/bin/lx24-amd64 +PATH: /opt/sun/n1gc/bin +PATH: /usr/local/bin +PATH: /bin +PATH: /usr/bin +PATH: /opt/c3-4/ +PATH: /usr/X11R6/bin +PATH: /usr/local/bin +PATH: /usr/local/bin/X11R5 +PATH: /usr/local/X11R5/bin +PATH: /usr/X11R6/bin +PATH: /home/rabani/Develop/perl/GeneXPress +PATH: /home/rabani/Develop/perl/Genome +PATH: /home/rabani/Develop/perl/Lib +PATH: /home/rabani/Develop/perl/Parsers +PATH: /home/rabani/Develop/perl/RNA +PATH: /home/rabani/Develop/perl/Sequence +PATH: /home/rabani/Develop/perl/System +PATH: /home/rabani/Develop/perl/Web +PATH: /home/rabani/Develop/perl/Web/DataDir +PATH: /home/rabani/Develop/genie_release64/Programs +PATH: /storage/appl/matlab14.3/bin +PATH: /home/rabani + + +## ----------- ## +## Core tests. ## +## ----------- ## + +configure:1364: checking for a BSD-compatible install +configure:1419: result: /usr/bin/install -c +configure:1430: checking whether build environment is sane +configure:1473: result: yes +configure:1538: checking for gawk +configure:1554: found /bin/gawk +configure:1564: result: gawk +configure:1574: checking whether make sets $(MAKE) +configure:1594: result: yes +configure:1763: checking if malloc debugging is wanted +configure:1784: result: no +configure:1835: checking for gcc +configure:1851: found /usr/bin/gcc +configure:1861: result: gcc +configure:2105: checking for C compiler version +configure:2108: gcc --version &5 +gcc (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2) +Copyright (C) 2004 Free Software Foundation, Inc. +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + +configure:2111: $? = 0 +configure:2113: gcc -v &5 +Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.5/specs +Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux +Thread model: posix +gcc version 3.4.5 20051201 (Red Hat 3.4.5-2) +configure:2116: $? = 0 +configure:2118: gcc -V &5 +gcc: `-V' option must have argument +configure:2121: $? = 1 +configure:2144: checking for C compiler default output file name +configure:2147: gcc conftest.c >&5 +configure:2150: $? = 0 +configure:2196: result: a.out +configure:2201: checking whether the C compiler works +configure:2207: ./a.out +configure:2210: $? = 0 +configure:2227: result: yes +configure:2234: checking whether we are cross compiling +configure:2236: result: no +configure:2239: checking for suffix of executables +configure:2241: gcc -o conftest conftest.c >&5 +configure:2244: $? = 0 +configure:2269: result: +configure:2275: checking for suffix of object files +configure:2296: gcc -c conftest.c >&5 +configure:2299: $? = 0 +configure:2321: result: o +configure:2325: checking whether we are using the GNU C compiler +configure:2349: gcc -c conftest.c >&5 +configure:2355: $? = 0 +configure:2359: test -z + || test ! -s conftest.err +configure:2362: $? = 0 +configure:2365: test -s conftest.o +configure:2368: $? = 0 +configure:2381: result: yes +configure:2387: checking whether gcc accepts -g +configure:2408: gcc -c -g conftest.c >&5 +configure:2414: $? = 0 +configure:2418: test -z + || test ! -s conftest.err +configure:2421: $? = 0 +configure:2424: test -s conftest.o +configure:2427: $? = 0 +configure:2438: result: yes +configure:2455: checking for gcc option to accept ANSI C +configure:2525: gcc -c -g -O2 conftest.c >&5 +configure:2531: $? = 0 +configure:2535: test -z + || test ! -s conftest.err +configure:2538: $? = 0 +configure:2541: test -s conftest.o +configure:2544: $? = 0 +configure:2562: result: none needed +configure:2580: gcc -c -g -O2 conftest.c >&5 +conftest.c:2: error: syntax error before "me" +configure:2586: $? = 1 +configure: failed program was: +| #ifndef __cplusplus +| choke me +| #endif +configure:2730: checking for style of include used by make +configure:2758: result: GNU +configure:2786: checking dependency style of gcc +configure:2876: result: gcc3 +configure:2893: checking whether make sets $(MAKE) +configure:2913: result: yes +configure:2937: checking build system type +configure:2955: result: x86_64-unknown-linux-gnu +configure:2963: checking host system type +configure:2977: result: x86_64-unknown-linux-gnu +configure:3000: checking for ViennaRNA package +configure:3043: result: headers in "../H" and library... "../lib" +configure:3050: checking for exp in -lm +configure:3080: gcc -o conftest -g -O2 -I../H -L../lib conftest.c -lm >&5 +conftest.c:18: warning: conflicting types for built-in function 'exp' +configure:3086: $? = 0 +configure:3090: test -z + || test ! -s conftest.err +configure:3093: $? = 0 +configure:3096: test -s conftest +configure:3099: $? = 0 +configure:3112: result: yes +configure:3132: checking how to run the C preprocessor +configure:3167: gcc -E -I../H conftest.c +configure:3173: $? = 0 +configure:3205: gcc -E -I../H conftest.c +conftest.c:12:28: ac_nonexistent.h: No such file or directory +configure:3211: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "Kinfold" +| #define PACKAGE_TARNAME "kinfold" +| #define PACKAGE_VERSION "1.0" +| #define PACKAGE_STRING "Kinfold 1.0" +| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" +| #define PACKAGE "kinfold" +| #define VERSION "1.0" +| #define HAVE_LIBM 1 +| /* end confdefs.h. */ +| #include +configure:3250: result: gcc -E +configure:3274: gcc -E -I../H conftest.c +configure:3280: $? = 0 +configure:3312: gcc -E -I../H conftest.c +conftest.c:12:28: ac_nonexistent.h: No such file or directory +configure:3318: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "Kinfold" +| #define PACKAGE_TARNAME "kinfold" +| #define PACKAGE_VERSION "1.0" +| #define PACKAGE_STRING "Kinfold 1.0" +| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" +| #define PACKAGE "kinfold" +| #define VERSION "1.0" +| #define HAVE_LIBM 1 +| /* end confdefs.h. */ +| #include +configure:3362: checking for egrep +configure:3372: result: grep -E +configure:3377: checking for ANSI C header files +configure:3402: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3408: $? = 0 +configure:3412: test -z + || test ! -s conftest.err +configure:3415: $? = 0 +configure:3418: test -s conftest.o +configure:3421: $? = 0 +configure:3510: gcc -o conftest -g -O2 -I../H -L../lib conftest.c -lRNA -lm >&5 +/usr/bin/ld: skipping incompatible ../lib/libRNA.a when searching for -lRNA +/usr/bin/ld: cannot find -lRNA +collect2: ld returned 1 exit status +configure:3513: $? = 1 +configure: program exited with status 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "Kinfold" +| #define PACKAGE_TARNAME "kinfold" +| #define PACKAGE_VERSION "1.0" +| #define PACKAGE_STRING "Kinfold 1.0" +| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" +| #define PACKAGE "kinfold" +| #define VERSION "1.0" +| #define HAVE_LIBM 1 +| /* end confdefs.h. */ +| #include +| #if ((' ' & 0x0FF) == 0x020) +| # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +| # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +| #else +| # define ISLOWER(c) (('a' <= (c) && (c) <= 'i') || ('j' <= (c) && (c) <= 'r') || ('s' <= (c) && (c) <= 'z')) +| # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +| #endif +| +| #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +| int +| main () +| { +| int i; +| for (i = 0; i < 256; i++) +| if (XOR (islower (i), ISLOWER (i)) +| || toupper (i) != TOUPPER (i)) +| exit(2); +| exit (0); +| } +configure:3533: result: no +configure:3557: checking for sys/types.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3557: checking for sys/stat.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3557: checking for stdlib.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3557: checking for string.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3557: checking for memory.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3557: checking for strings.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3557: checking for inttypes.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3557: checking for stdint.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3557: checking for unistd.h +configure:3573: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3579: $? = 0 +configure:3583: test -z + || test ! -s conftest.err +configure:3586: $? = 0 +configure:3589: test -s conftest.o +configure:3592: $? = 0 +configure:3603: result: yes +configure:3632: checking limits.h usability +configure:3644: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3650: $? = 0 +configure:3654: test -z + || test ! -s conftest.err +configure:3657: $? = 0 +configure:3660: test -s conftest.o +configure:3663: $? = 0 +configure:3673: result: yes +configure:3677: checking limits.h presence +configure:3687: gcc -E -I../H conftest.c +configure:3693: $? = 0 +configure:3713: result: yes +configure:3748: checking for limits.h +configure:3755: result: yes +configure:3632: checking sys/time.h usability +configure:3644: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3650: $? = 0 +configure:3654: test -z + || test ! -s conftest.err +configure:3657: $? = 0 +configure:3660: test -s conftest.o +configure:3663: $? = 0 +configure:3673: result: yes +configure:3677: checking sys/time.h presence +configure:3687: gcc -E -I../H conftest.c +configure:3693: $? = 0 +configure:3713: result: yes +configure:3748: checking for sys/time.h +configure:3755: result: yes +configure:3623: checking for unistd.h +configure:3628: result: yes +configure:3632: checking fold.h usability +configure:3644: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3650: $? = 0 +configure:3654: test -z + || test ! -s conftest.err +configure:3657: $? = 0 +configure:3660: test -s conftest.o +configure:3663: $? = 0 +configure:3673: result: yes +configure:3677: checking fold.h presence +configure:3687: gcc -E -I../H conftest.c +configure:3693: $? = 0 +configure:3713: result: yes +configure:3748: checking for fold.h +configure:3755: result: yes +configure:3769: checking for an ANSI C-conforming const +configure:3836: gcc -c -g -O2 -I../H conftest.c >&5 +configure:3842: $? = 0 +configure:3846: test -z + || test ! -s conftest.err +configure:3849: $? = 0 +configure:3852: test -s conftest.o +configure:3855: $? = 0 +configure:3866: result: yes +configure:3881: checking for strdup +configure:3938: gcc -o conftest -g -O2 -I../H -L../lib conftest.c -lRNA -lm >&5 +conftest.c:49: warning: conflicting types for built-in function 'strdup' +/usr/bin/ld: skipping incompatible ../lib/libRNA.a when searching for -lRNA +/usr/bin/ld: cannot find -lRNA +collect2: ld returned 1 exit status +configure:3944: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "Kinfold" +| #define PACKAGE_TARNAME "kinfold" +| #define PACKAGE_VERSION "1.0" +| #define PACKAGE_STRING "Kinfold 1.0" +| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" +| #define PACKAGE "kinfold" +| #define VERSION "1.0" +| #define HAVE_LIBM 1 +| #define HAVE_SYS_TYPES_H 1 +| #define HAVE_SYS_STAT_H 1 +| #define HAVE_STDLIB_H 1 +| #define HAVE_STRING_H 1 +| #define HAVE_MEMORY_H 1 +| #define HAVE_STRINGS_H 1 +| #define HAVE_INTTYPES_H 1 +| #define HAVE_STDINT_H 1 +| #define HAVE_UNISTD_H 1 +| #define HAVE_LIMITS_H 1 +| #define HAVE_SYS_TIME_H 1 +| #define HAVE_UNISTD_H 1 +| #define HAVE_FOLD_H 1 +| /* end confdefs.h. */ +| /* Define strdup to an innocuous variant, in case declares strdup. +| For example, HP-UX 11i declares gettimeofday. */ +| #define strdup innocuous_strdup +| +| /* System header to define __stub macros and hopefully few prototypes, +| which can conflict with char strdup (); below. +| Prefer to if __STDC__ is defined, since +| exists even on freestanding compilers. */ +| +| #ifdef __STDC__ +| # include +| #else +| # include +| #endif +| +| #undef strdup +| +| /* Override any gcc2 internal prototype to avoid an error. */ +| #ifdef __cplusplus +| extern "C" +| { +| #endif +| /* We use char because int might match the return type of a gcc2 +| builtin and then its argument prototype would still apply. */ +| char strdup (); +| /* The GNU C library defines this for functions which it implements +| to always fail with ENOSYS. Some functions are actually named +| something starting with __ and the normal name is an alias. */ +| #if defined (__stub_strdup) || defined (__stub___strdup) +| choke me +| #else +| char (*f) () = strdup; +| #endif +| #ifdef __cplusplus +| } +| #endif +| +| int +| main () +| { +| return f != strdup; +| ; +| return 0; +| } +configure:3969: result: no +configure:4090: creating ./config.status + +## ---------------------- ## +## Running config.status. ## +## ---------------------- ## + +This file was extended by Kinfold config.status 1.0, which was +generated by GNU Autoconf 2.59. Invocation command line was + + CONFIG_FILES = + CONFIG_HEADERS = + CONFIG_LINKS = + CONFIG_COMMANDS = + $ ./config.status + +on mcluster02 + +config.status:699: creating Makefile +config.status:699: creating Example/Makefile +config.status:803: creating config.h +config.status:917: config.h is unchanged +config.status:1097: executing depfiles commands + +## ---------------- ## +## Cache variables. ## +## ---------------- ## + +ac_cv_build=x86_64-unknown-linux-gnu +ac_cv_build_alias=x86_64-unknown-linux-gnu +ac_cv_c_compiler_gnu=yes +ac_cv_c_const=yes +ac_cv_env_CC_set= +ac_cv_env_CC_value= +ac_cv_env_CFLAGS_set= +ac_cv_env_CFLAGS_value= +ac_cv_env_CPPFLAGS_set= +ac_cv_env_CPPFLAGS_value= +ac_cv_env_CPP_set= +ac_cv_env_CPP_value= +ac_cv_env_LDFLAGS_set= +ac_cv_env_LDFLAGS_value= +ac_cv_env_build_alias_set= +ac_cv_env_build_alias_value= +ac_cv_env_host_alias_set= +ac_cv_env_host_alias_value= +ac_cv_env_target_alias_set= +ac_cv_env_target_alias_value= +ac_cv_exeext= +ac_cv_func_strdup=no +ac_cv_header_fold_h=yes +ac_cv_header_inttypes_h=yes +ac_cv_header_limits_h=yes +ac_cv_header_memory_h=yes +ac_cv_header_stdc=no +ac_cv_header_stdint_h=yes +ac_cv_header_stdlib_h=yes +ac_cv_header_string_h=yes +ac_cv_header_strings_h=yes +ac_cv_header_sys_stat_h=yes +ac_cv_header_sys_time_h=yes +ac_cv_header_sys_types_h=yes +ac_cv_header_unistd_h=yes +ac_cv_host=x86_64-unknown-linux-gnu +ac_cv_host_alias=x86_64-unknown-linux-gnu +ac_cv_lib_m_exp=yes +ac_cv_objext=o +ac_cv_path_install='/usr/bin/install -c' +ac_cv_prog_AWK=gawk +ac_cv_prog_CPP='gcc -E' +ac_cv_prog_ac_ct_CC=gcc +ac_cv_prog_cc_g=yes +ac_cv_prog_cc_stdc= +ac_cv_prog_egrep='grep -E' +ac_cv_prog_make_make_set=yes +am_cv_CC_dependencies_compiler_type=gcc3 + +## ----------------- ## +## Output variables. ## +## ----------------- ## + +ACLOCAL='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run aclocal-1.9' +AMDEPBACKSLASH='\' +AMDEP_FALSE='#' +AMDEP_TRUE='' +AMTAR='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run tar' +AUTOCONF='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run autoconf' +AUTOHEADER='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run autoheader' +AUTOMAKE='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run automake-1.9' +AWK='gawk' +CC='gcc' +CCDEPMODE='depmode=gcc3' +CFLAGS='-g -O2' +CPP='gcc -E' +CPPFLAGS=' -I../H' +CYGPATH_W='echo' +DEFS='-DHAVE_CONFIG_H' +DEPDIR='.deps' +ECHO_C='' +ECHO_N='-n' +ECHO_T='' +EGREP='grep -E' +EXEEXT='' +INSTALL_DATA='${INSTALL} -m 644' +INSTALL_PROGRAM='${INSTALL}' +INSTALL_SCRIPT='${INSTALL}' +INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s' +ISODATE='2006-06-13' +LDFLAGS='-L../lib ' +LIBOBJS='' +LIBS='-lRNA -lm ' +LTLIBOBJS='' +MAKEINFO='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run makeinfo' +OBJEXT='o' +PACKAGE='kinfold' +PACKAGE_BUGREPORT='rna@tbi.univie.ac.at' +PACKAGE_NAME='Kinfold' +PACKAGE_STRING='Kinfold 1.0' +PACKAGE_TARNAME='kinfold' +PACKAGE_VERSION='1.0' +PATH_SEPARATOR=':' +SET_MAKE='' +SHELL='/bin/sh' +STRIP='' +VERSION='1.0' +ac_ct_CC='gcc' +ac_ct_STRIP='' +am__fastdepCC_FALSE='#' +am__fastdepCC_TRUE='' +am__include='include' +am__leading_dot='.' +am__quote='' +am__tar='${AMTAR} chof - "$$tardir"' +am__untar='${AMTAR} xf -' +bindir='${exec_prefix}/bin' +build='x86_64-unknown-linux-gnu' +build_alias='' +build_cpu='x86_64' +build_os='linux-gnu' +build_vendor='unknown' +datadir='${prefix}/share' +exec_prefix='${prefix}' +host='x86_64-unknown-linux-gnu' +host_alias='' +host_cpu='x86_64' +host_os='linux-gnu' +host_vendor='unknown' +includedir='${prefix}/include' +infodir='${prefix}/info' +install_sh='/home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/install-sh' +libdir='${exec_prefix}/lib' +libexecdir='${exec_prefix}/libexec' +localstatedir='${prefix}/var' +mandir='${prefix}/man' +mkdir_p='mkdir -p --' +oldincludedir='/usr/include' +prefix='/usr/local' +program_transform_name='s,x,x,' +sbindir='${exec_prefix}/sbin' +sharedstatedir='${prefix}/com' +sysconfdir='${prefix}/etc' +target_alias='' + +## ----------- ## +## confdefs.h. ## +## ----------- ## + +#define HAVE_FOLD_H 1 +#define HAVE_INTTYPES_H 1 +#define HAVE_LIBM 1 +#define HAVE_LIMITS_H 1 +#define HAVE_MEMORY_H 1 +#define HAVE_STDINT_H 1 +#define HAVE_STDLIB_H 1 +#define HAVE_STRINGS_H 1 +#define HAVE_STRING_H 1 +#define HAVE_SYS_STAT_H 1 +#define HAVE_SYS_TIME_H 1 +#define HAVE_SYS_TYPES_H 1 +#define HAVE_UNISTD_H 1 +#define HAVE_UNISTD_H 1 +#define PACKAGE "kinfold" +#define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" +#define PACKAGE_NAME "Kinfold" +#define PACKAGE_STRING "Kinfold 1.0" +#define PACKAGE_TARNAME "kinfold" +#define PACKAGE_VERSION "1.0" +#define VERSION "1.0" + +configure: exit 0 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.status b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.status new file mode 100755 index 000000000..4be07f4d2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/config.status @@ -0,0 +1,1188 @@ +#! /bin/sh +# Generated by configure. +# Run this file to recreate the current configuration. +# Compiler output produced by configure, useful for debugging +# configure, is in config.log if it exists. + +debug=false +ac_cs_recheck=false +ac_cs_silent=false +SHELL=${CONFIG_SHELL-/bin/sh} +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## + +# Be Bourne compatible +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' +elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then + set -o posix +fi +DUALCASE=1; export DUALCASE # for MKS sh + +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + + +# Work around bugs in pre-3.0 UWIN ksh. +$as_unset ENV MAIL MAILPATH +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +for as_var in \ + LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ + LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ + LC_TELEPHONE LC_TIME +do + if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then + eval $as_var=C; export $as_var + else + $as_unset $as_var + fi +done + +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)$' \| \ + . : '\(.\)' 2>/dev/null || +echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } + /^X\/\(\/\/\)$/{ s//\1/; q; } + /^X\/\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + + +# PATH needs CR, and LINENO needs CR and PATH. +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + echo "#! /bin/sh" >conf$$.sh + echo "exit 0" >>conf$$.sh + chmod +x conf$$.sh + if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then + PATH_SEPARATOR=';' + else + PATH_SEPARATOR=: + fi + rm -f conf$$.sh +fi + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" || { + # Find who we are. Look in the path if we contain no path at all + # relative or not. + case $0 in + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done + + ;; + esac + # We did not find ourselves, most probably we were run as `sh COMMAND' + # in which case we are not to be found in the path. + if test "x$as_myself" = x; then + as_myself=$0 + fi + if test ! -f "$as_myself"; then + { { echo "$as_me:$LINENO: error: cannot find myself; rerun with an absolute path" >&5 +echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2;} + { (exit 1); exit 1; }; } + fi + case $CONFIG_SHELL in + '') + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for as_base in sh bash ksh sh5; do + case $as_dir in + /*) + if ("$as_dir/$as_base" -c ' + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then + $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } + $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } + CONFIG_SHELL=$as_dir/$as_base + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$0" ${1+"$@"} + fi;; + esac + done +done +;; + esac + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line before each line; the second 'sed' does the real + # work. The second script uses 'N' to pair each line-number line + # with the numbered line, and appends trailing '-' during + # substitution so that $LINENO is not a special case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) + sed '=' <$as_myself | + sed ' + N + s,$,-, + : loop + s,^\(['$as_cr_digits']*\)\(.*\)[$]LINENO\([^'$as_cr_alnum'_]\),\1\2\1\3, + t loop + s,-$,, + s,^['$as_cr_digits']*\n,, + ' >$as_me.lineno && + chmod +x $as_me.lineno || + { { echo "$as_me:$LINENO: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&5 +echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2;} + { (exit 1); exit 1; }; } + + # Don't try to exec as it changes $[0], causing all sort of problems + # (the dirname of $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensible to this). + . ./$as_me.lineno + # Exit status is that of the last command. + exit +} + + +case `echo "testing\c"; echo 1,2,3`,`echo -n testing; echo 1,2,3` in + *c*,-n*) ECHO_N= ECHO_C=' +' ECHO_T=' ' ;; + *c*,* ) ECHO_N=-n ECHO_C= ECHO_T= ;; + *) ECHO_N= ECHO_C='\c' ECHO_T= ;; +esac + +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +rm -f conf$$ conf$$.exe conf$$.file +echo >conf$$.file +if ln -s conf$$.file conf$$ 2>/dev/null; then + # We could just check for DJGPP; but this test a) works b) is more generic + # and c) will remain valid once DJGPP supports symlinks (DJGPP 2.04). + if test -f conf$$.exe; then + # Don't use ln at all; we don't have any links + as_ln_s='cp -p' + else + as_ln_s='ln -s' + fi +elif ln conf$$.file conf$$ 2>/dev/null; then + as_ln_s=ln +else + as_ln_s='cp -p' +fi +rm -f conf$$ conf$$.exe conf$$.file + +if mkdir -p . 2>/dev/null; then + as_mkdir_p=: +else + test -d ./-p && rmdir ./-p + as_mkdir_p=false +fi + +as_executable_p="test -f" + +# Sed expression to map a string onto a valid CPP name. +as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" + +# Sed expression to map a string onto a valid variable name. +as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" + + +# IFS +# We need space, tab and new line, in precisely that order. +as_nl=' +' +IFS=" $as_nl" + +# CDPATH. +$as_unset CDPATH + +exec 6>&1 + +# Open the log real soon, to keep \$[0] and so on meaningful, and to +# report actual input values of CONFIG_FILES etc. instead of their +# values after options handling. Logging --version etc. is OK. +exec 5>>config.log +{ + echo + sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX +## Running $as_me. ## +_ASBOX +} >&5 +cat >&5 <<_CSEOF + +This file was extended by Kinfold $as_me 1.0, which was +generated by GNU Autoconf 2.59. Invocation command line was + + CONFIG_FILES = $CONFIG_FILES + CONFIG_HEADERS = $CONFIG_HEADERS + CONFIG_LINKS = $CONFIG_LINKS + CONFIG_COMMANDS = $CONFIG_COMMANDS + $ $0 $@ + +_CSEOF +echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 +echo >&5 +config_files=" Makefile Example/Makefile" +config_headers=" config.h" +config_commands=" depfiles" + +ac_cs_usage="\ +\`$as_me' instantiates files from templates according to the +current configuration. + +Usage: $0 [OPTIONS] [FILE]... + + -h, --help print this help, then exit + -V, --version print version number, then exit + -q, --quiet do not print progress messages + -d, --debug don't remove temporary files + --recheck update $as_me by reconfiguring in the same conditions + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE + +Configuration files: +$config_files + +Configuration headers: +$config_headers + +Configuration commands: +$config_commands + +Report bugs to ." +ac_cs_version="\ +Kinfold config.status 1.0 +configured by ./configure, generated by GNU Autoconf 2.59, + with options \"'--prefix=/usr/local' '--cache-file=/dev/null' '--srcdir=.'\" + +Copyright (C) 2003 Free Software Foundation, Inc. +This config.status script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it." +srcdir=. +INSTALL="/usr/bin/install -c" +# If no file are specified by the user, then we need to provide default +# value. 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Disable this feature. + alias -g '${1+"$@"}'='"$@"' +elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then + set -o posix +fi +DUALCASE=1; export DUALCASE # for MKS sh + +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + + +# Work around bugs in pre-3.0 UWIN ksh. +$as_unset ENV MAIL MAILPATH +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +for as_var in \ + LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ + LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ + LC_TELEPHONE LC_TIME +do + if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then + eval $as_var=C; export $as_var + else + $as_unset $as_var + fi +done + +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)$' \| \ + . : '\(.\)' 2>/dev/null || +echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } + /^X\/\(\/\/\)$/{ s//\1/; q; } + /^X\/\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + + +# PATH needs CR, and LINENO needs CR and PATH. +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + echo "#! /bin/sh" >conf$$.sh + echo "exit 0" >>conf$$.sh + chmod +x conf$$.sh + if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then + PATH_SEPARATOR=';' + else + PATH_SEPARATOR=: + fi + rm -f conf$$.sh +fi + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" || { + # Find who we are. 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See below for descriptions of some of the useful variables. + +Defaults for the options are specified in brackets. + +Configuration: + -h, --help display this help and exit + --help=short display options specific to this package + --help=recursive display the short help of all the included packages + -V, --version display version information and exit + -q, --quiet, --silent do not print \`checking...' messages + --cache-file=FILE cache test results in FILE [disabled] + -C, --config-cache alias for \`--cache-file=config.cache' + -n, --no-create do not create output files + --srcdir=DIR find the sources in DIR [configure dir or \`..'] + +_ACEOF + + cat <<_ACEOF +Installation directories: + --prefix=PREFIX install architecture-independent files in PREFIX + [$ac_default_prefix] + --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX + [PREFIX] + +By default, \`make install' will install all the files in +\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify +an installation prefix other than \`$ac_default_prefix' using \`--prefix', +for instance \`--prefix=\$HOME'. + +For better control, use the options below. + +Fine tuning of the installation directories: + --bindir=DIR user executables [EPREFIX/bin] + --sbindir=DIR system admin executables [EPREFIX/sbin] + --libexecdir=DIR program executables [EPREFIX/libexec] + --datadir=DIR read-only architecture-independent data [PREFIX/share] + --sysconfdir=DIR read-only single-machine data [PREFIX/etc] + --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] + --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --libdir=DIR object code libraries [EPREFIX/lib] + --includedir=DIR C header files [PREFIX/include] + --oldincludedir=DIR C header files for non-gcc [/usr/include] + --infodir=DIR info documentation [PREFIX/info] + --mandir=DIR man documentation [PREFIX/man] +_ACEOF + + cat <<\_ACEOF + +Program names: + --program-prefix=PREFIX prepend PREFIX to installed program names + --program-suffix=SUFFIX append SUFFIX to installed program names + --program-transform-name=PROGRAM run sed PROGRAM on installed program names + +System types: + --build=BUILD configure for building on BUILD [guessed] + --host=HOST cross-compile to build programs to run on HOST [BUILD] +_ACEOF +fi + +if test -n "$ac_init_help"; then + case $ac_init_help in + short | recursive ) echo "Configuration of Kinfold 1.0:";; + esac + cat <<\_ACEOF + +Optional Features: + --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no) + --enable-FEATURE[=ARG] include FEATURE [ARG=yes] + --disable-dependency-tracking speeds up one-time build + --enable-dependency-tracking do not reject slow dependency extractors + +Optional Packages: + --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] + --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) + --with-dmalloc use dmalloc, as in + http://www.dmalloc.com/dmalloc.tar.gz + --with-ViennaRNA-include where to search for ViennaRNA header files + --with-ViennaRNA-lib where to search for libRNA.a + +Some influential environment variables: + CC C compiler command + CFLAGS C compiler flags + LDFLAGS linker flags, e.g. -L if you have libraries in a + nonstandard directory + CPPFLAGS C/C++ preprocessor flags, e.g. -I if you have + headers in a nonstandard directory + CPP C preprocessor + +Use these variables to override the choices made by `configure' or to help +it to find libraries and programs with nonstandard names/locations. + +Report bugs to . +_ACEOF +fi + +if test "$ac_init_help" = "recursive"; then + # If there are subdirs, report their specific --help. + ac_popdir=`pwd` + for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue + test -d $ac_dir || continue + ac_builddir=. + +if test "$ac_dir" != .; then + ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'` + # A "../" for each directory in $ac_dir_suffix. + ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'` +else + ac_dir_suffix= ac_top_builddir= +fi + +case $srcdir in + .) # No --srcdir option. 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Use of quotes ensures accuracy. + *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; + esac + fi +done +if $ac_cache_corrupted; then + { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 +echo "$as_me: error: changes in the environment can compromise the build" >&2;} + { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 +echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} + { (exit 1); exit 1; }; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + + + + + + + + + + + + + + + + + + + + + + + + + + + +am__api_version="1.9" +ac_aux_dir= +for ac_dir in $srcdir $srcdir/.. $srcdir/../..; do + if test -f $ac_dir/install-sh; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install-sh -c" + break + elif test -f $ac_dir/install.sh; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install.sh -c" + break + elif test -f $ac_dir/shtool; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/shtool install -c" + break + fi +done +if test -z "$ac_aux_dir"; then + { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&5 +echo "$as_me: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&2;} + { (exit 1); exit 1; }; } +fi +ac_config_guess="$SHELL $ac_aux_dir/config.guess" +ac_config_sub="$SHELL $ac_aux_dir/config.sub" +ac_configure="$SHELL $ac_aux_dir/configure" # This should be Cygnus configure. + +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 +echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6 +if test -z "$INSTALL"; then +if test "${ac_cv_path_install+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + done + done + ;; +esac +done + + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. We don't cache a + # path for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the path is relative. + INSTALL=$ac_install_sh + fi +fi +echo "$as_me:$LINENO: result: $INSTALL" >&5 +echo "${ECHO_T}$INSTALL" >&6 + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' + +echo "$as_me:$LINENO: checking whether build environment is sane" >&5 +echo $ECHO_N "checking whether build environment is sane... $ECHO_C" >&6 +# Just in case +sleep 1 +echo timestamp > conftest.file +# Do `set' in a subshell so we don't clobber the current shell's +# arguments. Must try -L first in case configure is actually a +# symlink; some systems play weird games with the mod time of symlinks +# (eg FreeBSD returns the mod time of the symlink's containing +# directory). +if ( + set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null` + if test "$*" = "X"; then + # -L didn't work. + set X `ls -t $srcdir/configure conftest.file` + fi + rm -f conftest.file + if test "$*" != "X $srcdir/configure conftest.file" \ + && test "$*" != "X conftest.file $srcdir/configure"; then + + # If neither matched, then we have a broken ls. This can happen + # if, for instance, CONFIG_SHELL is bash and it inherits a + # broken ls alias from the environment. This has actually + # happened. Such a system could not be considered "sane". + { { echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&5 +echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&2;} + { (exit 1); exit 1; }; } + fi + + test "$2" = conftest.file + ) +then + # Ok. + : +else + { { echo "$as_me:$LINENO: error: newly created file is older than distributed files! +Check your system clock" >&5 +echo "$as_me: error: newly created file is older than distributed files! +Check your system clock" >&2;} + { (exit 1); exit 1; }; } +fi +echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 +test "$program_prefix" != NONE && + program_transform_name="s,^,$program_prefix,;$program_transform_name" +# Use a double $ so make ignores it. +test "$program_suffix" != NONE && + program_transform_name="s,\$,$program_suffix,;$program_transform_name" +# Double any \ or $. echo might interpret backslashes. +# By default was `s,x,x', remove it if useless. +cat <<\_ACEOF >conftest.sed +s/[\\$]/&&/g;s/;s,x,x,$// +_ACEOF +program_transform_name=`echo $program_transform_name | sed -f conftest.sed` +rm conftest.sed + +# expand $ac_aux_dir to an absolute path +am_aux_dir=`cd $ac_aux_dir && pwd` + +test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing" +# Use eval to expand $SHELL +if eval "$MISSING --run true"; then + am_missing_run="$MISSING --run " +else + am_missing_run= + { echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5 +echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;} +fi + +if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then + # We used to keeping the `.' as first argument, in order to + # allow $(mkdir_p) to be used without argument. As in + # $(mkdir_p) $(somedir) + # where $(somedir) is conditionally defined. However this is wrong + # for two reasons: + # 1. if the package is installed by a user who cannot write `.' + # make install will fail, + # 2. the above comment should most certainly read + # $(mkdir_p) $(DESTDIR)$(somedir) + # so it does not work when $(somedir) is undefined and + # $(DESTDIR) is not. + # To support the latter case, we have to write + # test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir), + # so the `.' trick is pointless. + mkdir_p='mkdir -p --' +else + # On NextStep and OpenStep, the `mkdir' command does not + # recognize any option. It will interpret all options as + # directories to create, and then abort because `.' already + # exists. + for d in ./-p ./--version; + do + test -d $d && rmdir $d + done + # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists. + if test -f "$ac_aux_dir/mkinstalldirs"; then + mkdir_p='$(mkinstalldirs)' + else + mkdir_p='$(install_sh) -d' + fi +fi + +for ac_prog in gawk mawk nawk awk +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_AWK+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$AWK"; then + ac_cv_prog_AWK="$AWK" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_AWK="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +AWK=$ac_cv_prog_AWK +if test -n "$AWK"; then + echo "$as_me:$LINENO: result: $AWK" >&5 +echo "${ECHO_T}$AWK" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$AWK" && break +done + +echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6 +set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y,:./+-,___p_,'` +if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.make <<\_ACEOF +all: + @echo 'ac_maketemp="$(MAKE)"' +_ACEOF +# GNU make sometimes prints "make[1]: Entering...", which would confuse us. +eval `${MAKE-make} -f conftest.make 2>/dev/null | grep temp=` +if test -n "$ac_maketemp"; then + eval ac_cv_prog_make_${ac_make}_set=yes +else + eval ac_cv_prog_make_${ac_make}_set=no +fi +rm -f conftest.make +fi +if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then + echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + SET_MAKE= +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 + SET_MAKE="MAKE=${MAKE-make}" +fi + +rm -rf .tst 2>/dev/null +mkdir .tst 2>/dev/null +if test -d .tst; then + am__leading_dot=. +else + am__leading_dot=_ +fi +rmdir .tst 2>/dev/null + +# test to see if srcdir already configured +if test "`cd $srcdir && pwd`" != "`pwd`" && + test -f $srcdir/config.status; then + { { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5 +echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;} + { (exit 1); exit 1; }; } +fi + +# test whether we have cygpath +if test -z "$CYGPATH_W"; then + if (cygpath --version) >/dev/null 2>/dev/null; then + CYGPATH_W='cygpath -w' + else + CYGPATH_W=echo + fi +fi + + +# Define the identity of the package. + PACKAGE='kinfold' + VERSION='1.0' + + +cat >>confdefs.h <<_ACEOF +#define PACKAGE "$PACKAGE" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define VERSION "$VERSION" +_ACEOF + +# Some tools Automake needs. + +ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"} + + +AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"} + + +AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"} + + +AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"} + + +MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"} + +install_sh=${install_sh-"$am_aux_dir/install-sh"} + +# Installed binaries are usually stripped using `strip' when the user +# run `make install-strip'. However `strip' might not be the right +# tool to use in cross-compilation environments, therefore Automake +# will honor the `STRIP' environment variable to overrule this program. +if test "$cross_compiling" != no; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. +set dummy ${ac_tool_prefix}strip; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_STRIP+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$STRIP"; then + ac_cv_prog_STRIP="$STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_STRIP="${ac_tool_prefix}strip" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +STRIP=$ac_cv_prog_STRIP +if test -n "$STRIP"; then + echo "$as_me:$LINENO: result: $STRIP" >&5 +echo "${ECHO_T}$STRIP" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_STRIP"; then + ac_ct_STRIP=$STRIP + # Extract the first word of "strip", so it can be a program name with args. +set dummy strip; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_STRIP"; then + ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_STRIP="strip" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + test -z "$ac_cv_prog_ac_ct_STRIP" && ac_cv_prog_ac_ct_STRIP=":" +fi +fi +ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP +if test -n "$ac_ct_STRIP"; then + echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 +echo "${ECHO_T}$ac_ct_STRIP" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + STRIP=$ac_ct_STRIP +else + STRIP="$ac_cv_prog_STRIP" +fi + +fi +INSTALL_STRIP_PROGRAM="\${SHELL} \$(install_sh) -c -s" + +# We need awk for the "check" target. The system "awk" is bad on +# some platforms. +# Always define AMTAR for backward compatibility. + +AMTAR=${AMTAR-"${am_missing_run}tar"} + +am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' + + + + + + +echo "$as_me:$LINENO: checking if malloc debugging is wanted" >&5 +echo $ECHO_N "checking if malloc debugging is wanted... $ECHO_C" >&6 + +# Check whether --with-dmalloc or --without-dmalloc was given. +if test "${with_dmalloc+set}" = set; then + withval="$with_dmalloc" + if test "$withval" = yes; then + echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + +cat >>confdefs.h <<\_ACEOF +#define WITH_DMALLOC 1 +_ACEOF + + LIBS="$LIBS -ldmalloc" + LDFLAGS="$LDFLAGS -g" +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi; + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $# != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CC" && break +done + + CC=$ac_ct_CC +fi + +fi + + +test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files a.out a.exe b.out" +# Try to create an executable without -o first, disregard a.out. +# It will help us diagnose broken compilers, and finding out an intuition +# of exeext. +echo "$as_me:$LINENO: checking for C compiler default output file name" >&5 +echo $ECHO_N "checking for C compiler default output file name... $ECHO_C" >&6 +ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` +if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 + (eval $ac_link_default) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # Find the output, starting from the most likely. This scheme is +# not robust to junk in `.', hence go to wildcards (a.*) only as a last +# resort. + +# Be careful to initialize this variable, since it used to be cached. +# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. +ac_cv_exeext= +# b.out is created by i960 compilers. +for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out +do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) + ;; + conftest.$ac_ext ) + # This is the source file. + ;; + [ab].out ) + # We found the default executable, but exeext='' is most + # certainly right. + break;; + *.* ) + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + # FIXME: I believe we export ac_cv_exeext for Libtool, + # but it would be cool to find out if it's true. Does anybody + # maintain Libtool? --akim. + export ac_cv_exeext + break;; + * ) + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: C compiler cannot create executables +See \`config.log' for more details." >&5 +echo "$as_me: error: C compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; } +fi + +ac_exeext=$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_file" >&5 +echo "${ECHO_T}$ac_file" >&6 + +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether the C compiler works" >&5 +echo $ECHO_N "checking whether the C compiler works... $ECHO_C" >&6 +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. +if test "$cross_compiling" != yes; then + if { ac_try='./$ac_file' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { echo "$as_me:$LINENO: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + fi + fi +fi +echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + +rm -f a.out a.exe conftest$ac_cv_exeext b.out +ac_clean_files=$ac_clean_files_save +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 +echo "$as_me:$LINENO: result: $cross_compiling" >&5 +echo "${ECHO_T}$cross_compiling" >&6 + +echo "$as_me:$LINENO: checking for suffix of executables" >&5 +echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + export ac_cv_exeext + break;; + * ) break;; + esac +done +else + { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +echo "${ECHO_T}$ac_cv_exeext" >&6 + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +echo "$as_me:$LINENO: checking for suffix of object files" >&5 +echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 +if test "${ac_cv_objext+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.o conftest.obj +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; + *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest.$ac_cv_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 +echo "${ECHO_T}$ac_cv_objext" >&6 +OBJEXT=$ac_cv_objext +ac_objext=$OBJEXT +echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 +if test "${ac_cv_c_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 +GCC=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +CFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 +echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cc_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 +echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_prog_cc_stdc=no +ac_save_CC=$CC +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std1 is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std1. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +# Don't try gcc -ansi; that turns off useful extensions and +# breaks some systems' header files. +# AIX -qlanglvl=ansi +# Ultrix and OSF/1 -std1 +# HP-UX 10.20 and later -Ae +# HP-UX older versions -Aa -D_HPUX_SOURCE +# SVR4 -Xc -D__EXTENSIONS__ +for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_stdc=$ac_arg +break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext +done +rm -f conftest.$ac_ext conftest.$ac_objext +CC=$ac_save_CC + +fi + +case "x$ac_cv_prog_cc_stdc" in + x|xno) + echo "$as_me:$LINENO: result: none needed" >&5 +echo "${ECHO_T}none needed" >&6 ;; + *) + echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 + CC="$CC $ac_cv_prog_cc_stdc" ;; +esac + +# Some people use a C++ compiler to compile C. Since we use `exit', +# in C++ we need to declare it. In case someone uses the same compiler +# for both compiling C and C++ we need to have the C++ compiler decide +# the declaration of exit, since it's the most demanding environment. +cat >conftest.$ac_ext <<_ACEOF +#ifndef __cplusplus + choke me +#endif +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +#include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +DEPDIR="${am__leading_dot}deps" + + ac_config_commands="$ac_config_commands depfiles" + + +am_make=${MAKE-make} +cat > confinc << 'END' +am__doit: + @echo done +.PHONY: am__doit +END +# If we don't find an include directive, just comment out the code. +echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5 +echo $ECHO_N "checking for style of include used by $am_make... $ECHO_C" >&6 +am__include="#" +am__quote= +_am_result=none +# First try GNU make style include. +echo "include confinc" > confmf +# We grep out `Entering directory' and `Leaving directory' +# messages which can occur if `w' ends up in MAKEFLAGS. +# In particular we don't look at `^make:' because GNU make might +# be invoked under some other name (usually "gmake"), in which +# case it prints its new name instead of `make'. +if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then + am__include=include + am__quote= + _am_result=GNU +fi +# Now try BSD make style include. +if test "$am__include" = "#"; then + echo '.include "confinc"' > confmf + if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then + am__include=.include + am__quote="\"" + _am_result=BSD + fi +fi + + +echo "$as_me:$LINENO: result: $_am_result" >&5 +echo "${ECHO_T}$_am_result" >&6 +rm -f confinc confmf + +# Check whether --enable-dependency-tracking or --disable-dependency-tracking was given. +if test "${enable_dependency_tracking+set}" = set; then + enableval="$enable_dependency_tracking" + +fi; +if test "x$enable_dependency_tracking" != xno; then + am_depcomp="$ac_aux_dir/depcomp" + AMDEPBACKSLASH='\' +fi + + +if test "x$enable_dependency_tracking" != xno; then + AMDEP_TRUE= + AMDEP_FALSE='#' +else + AMDEP_TRUE='#' + AMDEP_FALSE= +fi + + + + +depcc="$CC" am_compiler_list= + +echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 +echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6 +if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then + # We make a subdir and do the tests there. Otherwise we can end up + # making bogus files that we don't know about and never remove. For + # instance it was reported that on HP-UX the gcc test will end up + # making a dummy file named `D' -- because `-MD' means `put the output + # in D'. + mkdir conftest.dir + # Copy depcomp to subdir because otherwise we won't find it if we're + # using a relative directory. + cp "$am_depcomp" conftest.dir + cd conftest.dir + # We will build objects and dependencies in a subdirectory because + # it helps to detect inapplicable dependency modes. For instance + # both Tru64's cc and ICC support -MD to output dependencies as a + # side effect of compilation, but ICC will put the dependencies in + # the current directory while Tru64 will put them in the object + # directory. + mkdir sub + + am_cv_CC_dependencies_compiler_type=none + if test "$am_compiler_list" = ""; then + am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp` + fi + for depmode in $am_compiler_list; do + # Setup a source with many dependencies, because some compilers + # like to wrap large dependency lists on column 80 (with \), and + # we should not choose a depcomp mode which is confused by this. + # + # We need to recreate these files for each test, as the compiler may + # overwrite some of them when testing with obscure command lines. + # This happens at least with the AIX C compiler. + : > sub/conftest.c + for i in 1 2 3 4 5 6; do + echo '#include "conftst'$i'.h"' >> sub/conftest.c + # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with + # Solaris 8's {/usr,}/bin/sh. + touch sub/conftst$i.h + done + echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf + + case $depmode in + nosideeffect) + # after this tag, mechanisms are not by side-effect, so they'll + # only be used when explicitly requested + if test "x$enable_dependency_tracking" = xyes; then + continue + else + break + fi + ;; + none) break ;; + esac + # We check with `-c' and `-o' for the sake of the "dashmstdout" + # mode. It turns out that the SunPro C++ compiler does not properly + # handle `-M -o', and we need to detect this. + if depmode=$depmode \ + source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \ + depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \ + $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \ + >/dev/null 2>conftest.err && + grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 && + grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 && + ${MAKE-make} -s -f confmf > /dev/null 2>&1; then + # icc doesn't choke on unknown options, it will just issue warnings + # or remarks (even with -Werror). So we grep stderr for any message + # that says an option was ignored or not supported. + # When given -MP, icc 7.0 and 7.1 complain thusly: + # icc: Command line warning: ignoring option '-M'; no argument required + # The diagnosis changed in icc 8.0: + # icc: Command line remark: option '-MP' not supported + if (grep 'ignoring option' conftest.err || + grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else + am_cv_CC_dependencies_compiler_type=$depmode + break + fi + fi + done + + cd .. + rm -rf conftest.dir +else + am_cv_CC_dependencies_compiler_type=none +fi + +fi +echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5 +echo "${ECHO_T}$am_cv_CC_dependencies_compiler_type" >&6 +CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type + + + +if + test "x$enable_dependency_tracking" != xno \ + && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then + am__fastdepCC_TRUE= + am__fastdepCC_FALSE='#' +else + am__fastdepCC_TRUE='#' + am__fastdepCC_FALSE= +fi + + +echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6 +set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y,:./+-,___p_,'` +if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.make <<\_ACEOF +all: + @echo 'ac_maketemp="$(MAKE)"' +_ACEOF +# GNU make sometimes prints "make[1]: Entering...", which would confuse us. +eval `${MAKE-make} -f conftest.make 2>/dev/null | grep temp=` +if test -n "$ac_maketemp"; then + eval ac_cv_prog_make_${ac_make}_set=yes +else + eval ac_cv_prog_make_${ac_make}_set=no +fi +rm -f conftest.make +fi +if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then + echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + SET_MAKE= +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 + SET_MAKE="MAKE=${MAKE-make}" +fi + + + ac_config_headers="$ac_config_headers config.h" + + + + +ISODATE=`date +%Y-%m-%d` + + +# Make sure we can run config.sub. +$ac_config_sub sun4 >/dev/null 2>&1 || + { { echo "$as_me:$LINENO: error: cannot run $ac_config_sub" >&5 +echo "$as_me: error: cannot run $ac_config_sub" >&2;} + { (exit 1); exit 1; }; } + +echo "$as_me:$LINENO: checking build system type" >&5 +echo $ECHO_N "checking build system type... $ECHO_C" >&6 +if test "${ac_cv_build+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_build_alias=$build_alias +test -z "$ac_cv_build_alias" && + ac_cv_build_alias=`$ac_config_guess` +test -z "$ac_cv_build_alias" && + { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5 +echo "$as_me: error: cannot guess build type; you must specify one" >&2;} + { (exit 1); exit 1; }; } +ac_cv_build=`$ac_config_sub $ac_cv_build_alias` || + { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_build_alias failed" >&5 +echo "$as_me: error: $ac_config_sub $ac_cv_build_alias failed" >&2;} + { (exit 1); exit 1; }; } + +fi +echo "$as_me:$LINENO: result: $ac_cv_build" >&5 +echo "${ECHO_T}$ac_cv_build" >&6 +build=$ac_cv_build +build_cpu=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` +build_vendor=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` +build_os=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` + + +echo "$as_me:$LINENO: checking host system type" >&5 +echo $ECHO_N "checking host system type... $ECHO_C" >&6 +if test "${ac_cv_host+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_host_alias=$host_alias +test -z "$ac_cv_host_alias" && + ac_cv_host_alias=$ac_cv_build_alias +ac_cv_host=`$ac_config_sub $ac_cv_host_alias` || + { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_host_alias failed" >&5 +echo "$as_me: error: $ac_config_sub $ac_cv_host_alias failed" >&2;} + { (exit 1); exit 1; }; } + +fi +echo "$as_me:$LINENO: result: $ac_cv_host" >&5 +echo "${ECHO_T}$ac_cv_host" >&6 +host=$ac_cv_host +host_cpu=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` +host_vendor=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` +host_os=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` + + + + +# Check whether --with-ViennaRNA-include or --without-ViennaRNA-include was given. +if test "${with_ViennaRNA_include+set}" = set; then + withval="$with_ViennaRNA_include" + ac_VRNA_includes="$withval" +fi; + + +# Check whether --with-ViennaRNA-lib or --without-ViennaRNA-lib was given. +if test "${with_ViennaRNA_lib+set}" = set; then + withval="$with_ViennaRNA_lib" + ac_VRNA_lib="$withval" +fi; + +echo "$as_me:$LINENO: checking for ViennaRNA package" >&5 +echo $ECHO_N "checking for ViennaRNA package... $ECHO_C" >&6 +if test -z "$ac_VRNA_includes"; then + for ac_dir in \ + ../H \ + /usr/local/include/ViennaRNA \ + /usr/local/include \ + /usr/include/ViennaRNA \ + /usr/local/ViennaRNA/H \ + /usr/local/share/ViennaRNA/include \ + /opt/ViennaRNA/include \ + ;\ + do + if test -r "$ac_dir/part_func.h"; then + ac_VRNA_includes=$ac_dir + break + fi + done +fi +if test $ac_VRNA_includes; then + CPPFLAGS="$CPPFLAGS -I$ac_VRNA_includes" +fi + +if [ -d ../lib ] && [ "$ac_VRNA_includes" = "../H" ]; then + ac_VRNA_lib=../lib +fi + +if test -z "$ac_VRNA_lib"; then +for ac_dir in `echo "$ac_VRNA_includes" | sed -e s/include/lib/ -e s/H$/lib/` \ + /usr/local/lib \ + ; \ +do + for ac_extension in a so sl; do + if test -r $ac_dir/libRNA.$ac_extension; then + ac_VRNA_lib=$ac_dir + break 2 + fi + done +done +fi # $ac_VRNA_lib = NO +if test $ac_VRNA_lib; then + LDFLAGS="-L$ac_VRNA_lib $LDFLAGS" +fi +echo "$as_me:$LINENO: result: headers in \"$ac_VRNA_includes\" and library... \"$ac_VRNA_lib\"" >&5 +echo "${ECHO_T} headers in \"$ac_VRNA_includes\" and library... \"$ac_VRNA_lib\"" >&6 + + + + + +echo "$as_me:$LINENO: checking for exp in -lm" >&5 +echo $ECHO_N "checking for exp in -lm... $ECHO_C" >&6 +if test "${ac_cv_lib_m_exp+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lm $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char exp (); +int +main () +{ +exp (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_m_exp=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_m_exp=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_m_exp" >&5 +echo "${ECHO_T}$ac_cv_lib_m_exp" >&6 +if test $ac_cv_lib_m_exp = yes; then + cat >>confdefs.h <<_ACEOF +#define HAVE_LIBM 1 +_ACEOF + + LIBS="-lm $LIBS" + +fi + + +LIBS="-lRNA ${LIBS}" + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 +echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6 +# On Suns, sometimes $CPP names a directory. +if test -n "$CPP" && test -d "$CPP"; then + CPP= +fi +if test -z "$CPP"; then + if test "${ac_cv_prog_CPP+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + # Double quotes because CPP needs to be expanded + for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" + do + ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether non-existent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # Broken: success on invalid input. +continue +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + break +fi + + done + ac_cv_prog_CPP=$CPP + +fi + CPP=$ac_cv_prog_CPP +else + ac_cv_prog_CPP=$CPP +fi +echo "$as_me:$LINENO: result: $CPP" >&5 +echo "${ECHO_T}$CPP" >&6 +ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether non-existent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # Broken: success on invalid input. +continue +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : +else + { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&5 +echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +echo "$as_me:$LINENO: checking for egrep" >&5 +echo $ECHO_N "checking for egrep... $ECHO_C" >&6 +if test "${ac_cv_prog_egrep+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if echo a | (grep -E '(a|b)') >/dev/null 2>&1 + then ac_cv_prog_egrep='grep -E' + else ac_cv_prog_egrep='egrep' + fi +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_egrep" >&5 +echo "${ECHO_T}$ac_cv_prog_egrep" >&6 + EGREP=$ac_cv_prog_egrep + + +echo "$as_me:$LINENO: checking for ANSI C header files" >&5 +echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 +if test "${ac_cv_header_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_header_stdc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_header_stdc=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + +if test $ac_cv_header_stdc = yes; then + # SunOS 4.x string.h does not declare mem*, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "memchr" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "free" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. + if test "$cross_compiling" = yes; then + : +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#if ((' ' & 0x0FF) == 0x020) +# define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +#else +# define ISLOWER(c) \ + (('a' <= (c) && (c) <= 'i') \ + || ('j' <= (c) && (c) <= 'r') \ + || ('s' <= (c) && (c) <= 'z')) +# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +#endif + +#define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +int +main () +{ + int i; + for (i = 0; i < 256; i++) + if (XOR (islower (i), ISLOWER (i)) + || toupper (i) != TOUPPER (i)) + exit(2); + exit (0); +} +_ACEOF +rm -f conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: program exited with status $ac_status" >&5 +echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no +fi +rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +fi +fi +echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 +echo "${ECHO_T}$ac_cv_header_stdc" >&6 +if test $ac_cv_header_stdc = yes; then + +cat >>confdefs.h <<\_ACEOF +#define STDC_HEADERS 1 +_ACEOF + +fi + +# On IRIX 5.3, sys/types and inttypes.h are conflicting. + + + + + + + + + +for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ + inttypes.h stdint.h unistd.h +do +as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` +echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + eval "$as_ac_Header=yes" +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +eval "$as_ac_Header=no" +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 +if test `eval echo '${'$as_ac_Header'}'` = yes; then + cat >>confdefs.h <<_ACEOF +#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + + + + + +for ac_header in limits.h sys/time.h unistd.h fold.h +do +as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 +else + # Is the header compilable? +echo "$as_me:$LINENO: checking $ac_header usability" >&5 +echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_header_compiler=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_header_compiler=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +echo "${ECHO_T}$ac_header_compiler" >&6 + +# Is the header present? +echo "$as_me:$LINENO: checking $ac_header presence" >&5 +echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include <$ac_header> +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + ac_header_preproc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi +rm -f conftest.err conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +echo "${ECHO_T}$ac_header_preproc" >&6 + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + ( + cat <<\_ASBOX +## ----------------------------------- ## +## Report this to rna@tbi.univie.ac.at ## +## ----------------------------------- ## +_ASBOX + ) | + sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac +echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 + +fi +if test `eval echo '${'$as_ac_Header'}'` = yes; then + cat >>confdefs.h <<_ACEOF +#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + +echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 +echo $ECHO_N "checking for an ANSI C-conforming const... $ECHO_C" >&6 +if test "${ac_cv_c_const+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +/* FIXME: Include the comments suggested by Paul. */ +#ifndef __cplusplus + /* Ultrix mips cc rejects this. */ + typedef int charset[2]; + const charset x; + /* SunOS 4.1.1 cc rejects this. */ + char const *const *ccp; + char **p; + /* NEC SVR4.0.2 mips cc rejects this. */ + struct point {int x, y;}; + static struct point const zero = {0,0}; + /* AIX XL C 1.02.0.0 rejects this. + It does not let you subtract one const X* pointer from another in + an arm of an if-expression whose if-part is not a constant + expression */ + const char *g = "string"; + ccp = &g + (g ? g-g : 0); + /* HPUX 7.0 cc rejects these. */ + ++ccp; + p = (char**) ccp; + ccp = (char const *const *) p; + { /* SCO 3.2v4 cc rejects this. */ + char *t; + char const *s = 0 ? (char *) 0 : (char const *) 0; + + *t++ = 0; + } + { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ + int x[] = {25, 17}; + const int *foo = &x[0]; + ++foo; + } + { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ + typedef const int *iptr; + iptr p = 0; + ++p; + } + { /* AIX XL C 1.02.0.0 rejects this saying + "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ + struct s { int j; const int *ap[3]; }; + struct s *b; b->j = 5; + } + { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ + const int foo = 10; + } +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_c_const=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_c_const=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5 +echo "${ECHO_T}$ac_cv_c_const" >&6 +if test $ac_cv_c_const = no; then + +cat >>confdefs.h <<\_ACEOF +#define const +_ACEOF + +fi + + + +for ac_func in strdup +do +as_ac_var=`echo "ac_cv_func_$ac_func" | $as_tr_sh` +echo "$as_me:$LINENO: checking for $ac_func" >&5 +echo $ECHO_N "checking for $ac_func... $ECHO_C" >&6 +if eval "test \"\${$as_ac_var+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_$ac_func) || defined (__stub___$ac_func) +choke me +#else +char (*f) () = $ac_func; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != $ac_func; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + eval "$as_ac_var=yes" +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +eval "$as_ac_var=no" +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_var'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_var'}'`" >&6 +if test `eval echo '${'$as_ac_var'}'` = yes; then + cat >>confdefs.h <<_ACEOF +#define `echo "HAVE_$ac_func" | $as_tr_cpp` 1 +_ACEOF + +fi +done + + + ac_config_files="$ac_config_files Makefile Example/Makefile" +cat >confcache <<\_ACEOF +# This file is a shell script that caches the results of configure +# tests run on this system so they can be shared between configure +# scripts and configure runs, see configure's option --config-cache. +# It is not useful on other systems. If it contains results you don't +# want to keep, you may remove or edit it. +# +# config.status only pays attention to the cache file if you give it +# the --recheck option to rerun configure. +# +# `ac_cv_env_foo' variables (set or unset) will be overridden when +# loading this file, other *unset* `ac_cv_foo' will be assigned the +# following values. + +_ACEOF + +# The following way of writing the cache mishandles newlines in values, +# but we know of no workaround that is simple, portable, and efficient. +# So, don't put newlines in cache variables' values. +# Ultrix sh set writes to stderr and can't be redirected directly, +# and sets the high bit in the cache file unless we assign to the vars. +{ + (set) 2>&1 | + case `(ac_space=' '; set | grep ac_space) 2>&1` in + *ac_space=\ *) + # `set' does not quote correctly, so add quotes (double-quote + # substitution turns \\\\ into \\, and sed turns \\ into \). + sed -n \ + "s/'/'\\\\''/g; + s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" + ;; + *) + # `set' quotes correctly as required by POSIX, so do not add quotes. + sed -n \ + "s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1=\\2/p" + ;; + esac; +} | + sed ' + t clear + : clear + s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/ + t end + /^ac_cv_env/!s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/ + : end' >>confcache +if diff $cache_file confcache >/dev/null 2>&1; then :; else + if test -w $cache_file; then + test "x$cache_file" != "x/dev/null" && echo "updating cache $cache_file" + cat confcache >$cache_file + else + echo "not updating unwritable cache $cache_file" + fi +fi +rm -f confcache + +test "x$prefix" = xNONE && prefix=$ac_default_prefix +# Let make expand exec_prefix. +test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' + +# VPATH may cause trouble with some makes, so we remove $(srcdir), +# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and +# trailing colons and then remove the whole line if VPATH becomes empty +# (actually we leave an empty line to preserve line numbers). +if test "x$srcdir" = x.; then + ac_vpsub='/^[ ]*VPATH[ ]*=/{ +s/:*\$(srcdir):*/:/; +s/:*\${srcdir}:*/:/; +s/:*@srcdir@:*/:/; +s/^\([^=]*=[ ]*\):*/\1/; +s/:*$//; +s/^[^=]*=[ ]*$//; +}' +fi + +DEFS=-DHAVE_CONFIG_H + +ac_libobjs= +ac_ltlibobjs= +for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue + # 1. 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Invocation command line was + + CONFIG_FILES = $CONFIG_FILES + CONFIG_HEADERS = $CONFIG_HEADERS + CONFIG_LINKS = $CONFIG_LINKS + CONFIG_COMMANDS = $CONFIG_COMMANDS + $ $0 $@ + +_CSEOF +echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 +echo >&5 +_ACEOF + +# Files that config.status was made for. +if test -n "$ac_config_files"; then + echo "config_files=\"$ac_config_files\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_headers"; then + echo "config_headers=\"$ac_config_headers\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_links"; then + echo "config_links=\"$ac_config_links\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_commands"; then + echo "config_commands=\"$ac_config_commands\"" >>$CONFIG_STATUS +fi + +cat >>$CONFIG_STATUS <<\_ACEOF + +ac_cs_usage="\ +\`$as_me' instantiates files from templates according to the +current configuration. + +Usage: $0 [OPTIONS] [FILE]... + + -h, --help print this help, then exit + -V, --version print version number, then exit + -q, --quiet do not print progress messages + -d, --debug don't remove temporary files + --recheck update $as_me by reconfiguring in the same conditions + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE + +Configuration files: +$config_files + +Configuration headers: +$config_headers + +Configuration commands: +$config_commands + +Report bugs to ." +_ACEOF + +cat >>$CONFIG_STATUS <<_ACEOF +ac_cs_version="\\ +Kinfold config.status 1.0 +configured by $0, generated by GNU Autoconf 2.59, + with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\" + +Copyright (C) 2003 Free Software Foundation, Inc. +This config.status script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it." +srcdir=$srcdir +INSTALL="$INSTALL" +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF +# If no file are specified by the user, then we need to provide default +# value. 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Make it in the build tree +# simply because there is no reason to put it here, and in addition, +# creating and moving files from /tmp can sometimes cause problems. +# Create a temporary directory, and hook for its removal unless debugging. +$debug || +{ + trap 'exit_status=$?; rm -rf $tmp && exit $exit_status' 0 + trap '{ (exit 1); exit 1; }' 1 2 13 15 +} + +# Create a (secure) tmp directory for tmp files. + +{ + tmp=`(umask 077 && mktemp -d -q "./confstatXXXXXX") 2>/dev/null` && + test -n "$tmp" && test -d "$tmp" +} || +{ + tmp=./confstat$$-$RANDOM + (umask 077 && mkdir $tmp) +} || +{ + echo "$me: cannot create a temporary directory in ." >&2 + { (exit 1); exit 1; } +} + +_ACEOF + +cat >>$CONFIG_STATUS <<_ACEOF + +# +# CONFIG_FILES section. +# + +# No need to generate the scripts if there are no CONFIG_FILES. +# This happens for instance when ./config.status config.h +if test -n "\$CONFIG_FILES"; then + # Protect against being on the right side of a sed subst in config.status. + sed 's/,@/@@/; s/@,/@@/; s/,;t t\$/@;t t/; /@;t t\$/s/[\\\\&,]/\\\\&/g; + s/@@/,@/; s/@@/@,/; s/@;t t\$/,;t t/' >\$tmp/subs.sed <<\\CEOF +s,@SHELL@,$SHELL,;t t +s,@PATH_SEPARATOR@,$PATH_SEPARATOR,;t t +s,@PACKAGE_NAME@,$PACKAGE_NAME,;t t +s,@PACKAGE_TARNAME@,$PACKAGE_TARNAME,;t t +s,@PACKAGE_VERSION@,$PACKAGE_VERSION,;t t +s,@PACKAGE_STRING@,$PACKAGE_STRING,;t t +s,@PACKAGE_BUGREPORT@,$PACKAGE_BUGREPORT,;t t +s,@exec_prefix@,$exec_prefix,;t t +s,@prefix@,$prefix,;t t +s,@program_transform_name@,$program_transform_name,;t t +s,@bindir@,$bindir,;t t +s,@sbindir@,$sbindir,;t t +s,@libexecdir@,$libexecdir,;t t +s,@datadir@,$datadir,;t t +s,@sysconfdir@,$sysconfdir,;t t +s,@sharedstatedir@,$sharedstatedir,;t t +s,@localstatedir@,$localstatedir,;t t +s,@libdir@,$libdir,;t t +s,@includedir@,$includedir,;t t +s,@oldincludedir@,$oldincludedir,;t t +s,@infodir@,$infodir,;t t +s,@mandir@,$mandir,;t t +s,@build_alias@,$build_alias,;t t +s,@host_alias@,$host_alias,;t t +s,@target_alias@,$target_alias,;t t +s,@DEFS@,$DEFS,;t t +s,@ECHO_C@,$ECHO_C,;t t +s,@ECHO_N@,$ECHO_N,;t t +s,@ECHO_T@,$ECHO_T,;t t +s,@LIBS@,$LIBS,;t t +s,@INSTALL_PROGRAM@,$INSTALL_PROGRAM,;t t +s,@INSTALL_SCRIPT@,$INSTALL_SCRIPT,;t t +s,@INSTALL_DATA@,$INSTALL_DATA,;t t +s,@CYGPATH_W@,$CYGPATH_W,;t t +s,@PACKAGE@,$PACKAGE,;t t +s,@VERSION@,$VERSION,;t t +s,@ACLOCAL@,$ACLOCAL,;t t +s,@AUTOCONF@,$AUTOCONF,;t t +s,@AUTOMAKE@,$AUTOMAKE,;t t +s,@AUTOHEADER@,$AUTOHEADER,;t t +s,@MAKEINFO@,$MAKEINFO,;t t +s,@install_sh@,$install_sh,;t t +s,@STRIP@,$STRIP,;t t +s,@ac_ct_STRIP@,$ac_ct_STRIP,;t t +s,@INSTALL_STRIP_PROGRAM@,$INSTALL_STRIP_PROGRAM,;t t +s,@mkdir_p@,$mkdir_p,;t t +s,@AWK@,$AWK,;t t +s,@SET_MAKE@,$SET_MAKE,;t t +s,@am__leading_dot@,$am__leading_dot,;t t +s,@AMTAR@,$AMTAR,;t t +s,@am__tar@,$am__tar,;t t +s,@am__untar@,$am__untar,;t t +s,@CC@,$CC,;t t +s,@CFLAGS@,$CFLAGS,;t t +s,@LDFLAGS@,$LDFLAGS,;t t +s,@CPPFLAGS@,$CPPFLAGS,;t t +s,@ac_ct_CC@,$ac_ct_CC,;t t +s,@EXEEXT@,$EXEEXT,;t t +s,@OBJEXT@,$OBJEXT,;t t +s,@DEPDIR@,$DEPDIR,;t t +s,@am__include@,$am__include,;t t +s,@am__quote@,$am__quote,;t t +s,@AMDEP_TRUE@,$AMDEP_TRUE,;t t +s,@AMDEP_FALSE@,$AMDEP_FALSE,;t t +s,@AMDEPBACKSLASH@,$AMDEPBACKSLASH,;t t +s,@CCDEPMODE@,$CCDEPMODE,;t t +s,@am__fastdepCC_TRUE@,$am__fastdepCC_TRUE,;t t +s,@am__fastdepCC_FALSE@,$am__fastdepCC_FALSE,;t t +s,@ISODATE@,$ISODATE,;t t +s,@build@,$build,;t t +s,@build_cpu@,$build_cpu,;t t +s,@build_vendor@,$build_vendor,;t t +s,@build_os@,$build_os,;t t +s,@host@,$host,;t t +s,@host_cpu@,$host_cpu,;t t +s,@host_vendor@,$host_vendor,;t t +s,@host_os@,$host_os,;t t +s,@CPP@,$CPP,;t t +s,@EGREP@,$EGREP,;t t +s,@LIBOBJS@,$LIBOBJS,;t t +s,@LTLIBOBJS@,$LTLIBOBJS,;t t +CEOF + +_ACEOF + + cat >>$CONFIG_STATUS <<\_ACEOF + # Split the substitutions into bite-sized pieces for seds with + # small command number limits, like on Digital OSF/1 and HP-UX. + ac_max_sed_lines=48 + ac_sed_frag=1 # Number of current file. + ac_beg=1 # First line for current file. + ac_end=$ac_max_sed_lines # Line after last line for current file. + ac_more_lines=: + ac_sed_cmds= + while $ac_more_lines; do + if test $ac_beg -gt 1; then + sed "1,${ac_beg}d; ${ac_end}q" $tmp/subs.sed >$tmp/subs.frag + else + sed "${ac_end}q" $tmp/subs.sed >$tmp/subs.frag + fi + if test ! 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Generated by config.status. */ + if test x"$ac_file" = x-; then + configure_input= + else + configure_input="$ac_file. " + fi + configure_input=$configure_input"Generated from `echo $ac_file_in | + sed 's,.*/,,'` by configure." + + # First look for the input files in the build tree, otherwise in the + # src tree. + ac_file_inputs=`IFS=: + for f in $ac_file_in; do + case $f in + -) echo $tmp/stdin ;; + [\\/$]*) + # Absolute (can't be DOS-style, as IFS=:) + test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + echo "$f";; + *) # Relative + if test -f "$f"; then + # Build tree + echo "$f" + elif test -f "$srcdir/$f"; then + # Source tree + echo "$srcdir/$f" + else + # /dev/null tree + { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + fi;; + esac + done` || { (exit 1); exit 1; } +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF + sed "$ac_vpsub +$extrasub +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF +:t +/@[a-zA-Z_][a-zA-Z_0-9]*@/!b +s,@configure_input@,$configure_input,;t t +s,@srcdir@,$ac_srcdir,;t t +s,@abs_srcdir@,$ac_abs_srcdir,;t t +s,@top_srcdir@,$ac_top_srcdir,;t t +s,@abs_top_srcdir@,$ac_abs_top_srcdir,;t t +s,@builddir@,$ac_builddir,;t t +s,@abs_builddir@,$ac_abs_builddir,;t t +s,@top_builddir@,$ac_top_builddir,;t t +s,@abs_top_builddir@,$ac_abs_top_builddir,;t t +s,@INSTALL@,$ac_INSTALL,;t t +" $ac_file_inputs | (eval "$ac_sed_cmds") >$tmp/out + rm -f $tmp/stdin + if test x"$ac_file" != x-; then + mv $tmp/out $ac_file + else + cat $tmp/out + rm -f $tmp/out + fi + +done +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF + +# +# CONFIG_HEADER section. +# + +# These sed commands are passed to sed as "A NAME B NAME C VALUE D", where +# NAME is the cpp macro being defined and VALUE is the value it is being given. +# +# ac_d sets the value in "#define NAME VALUE" lines. +ac_dA='s,^\([ ]*\)#\([ ]*define[ ][ ]*\)' +ac_dB='[ ].*$,\1#\2' +ac_dC=' ' +ac_dD=',;t' +# ac_u turns "#undef NAME" without trailing blanks into "#define NAME VALUE". +ac_uA='s,^\([ ]*\)#\([ ]*\)undef\([ ][ ]*\)' +ac_uB='$,\1#\2define\3' +ac_uC=' ' +ac_uD=',;t' + +for ac_file in : $CONFIG_HEADERS; do test "x$ac_file" = x: && continue + # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in". + case $ac_file in + - | *:- | *:-:* ) # input from stdin + cat >$tmp/stdin + ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;; + *:* ) ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;; + * ) ac_file_in=$ac_file.in ;; + esac + + test x"$ac_file" != x- && { echo "$as_me:$LINENO: creating $ac_file" >&5 +echo "$as_me: creating $ac_file" >&6;} + + # First look for the input files in the build tree, otherwise in the + # src tree. + ac_file_inputs=`IFS=: + for f in $ac_file_in; do + case $f in + -) echo $tmp/stdin ;; + [\\/$]*) + # Absolute (can't be DOS-style, as IFS=:) + test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + # Do quote $f, to prevent DOS paths from being IFS'd. + echo "$f";; + *) # Relative + if test -f "$f"; then + # Build tree + echo "$f" + elif test -f "$srcdir/$f"; then + # Source tree + echo "$srcdir/$f" + else + # /dev/null tree + { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + fi;; + esac + done` || { (exit 1); exit 1; } + # Remove the trailing spaces. + sed 's/[ ]*$//' $ac_file_inputs >$tmp/in + +_ACEOF + +# Transform confdefs.h into two sed scripts, `conftest.defines' and +# `conftest.undefs', that substitutes the proper values into +# config.h.in to produce config.h. The first handles `#define' +# templates, and the second `#undef' templates. +# And first: Protect against being on the right side of a sed subst in +# config.status. Protect against being in an unquoted here document +# in config.status. +rm -f conftest.defines conftest.undefs +# Using a here document instead of a string reduces the quoting nightmare. +# Putting comments in sed scripts is not portable. +# +# `end' is used to avoid that the second main sed command (meant for +# 0-ary CPP macros) applies to n-ary macro definitions. +# See the Autoconf documentation for `clear'. +cat >confdef2sed.sed <<\_ACEOF +s/[\\&,]/\\&/g +s,[\\$`],\\&,g +t clear +: clear +s,^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*\)\(([^)]*)\)[ ]*\(.*\)$,${ac_dA}\1${ac_dB}\1\2${ac_dC}\3${ac_dD},gp +t end +s,^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)$,${ac_dA}\1${ac_dB}\1${ac_dC}\2${ac_dD},gp +: end +_ACEOF +# If some macros were called several times there might be several times +# the same #defines, which is useless. Nevertheless, we may not want to +# sort them, since we want the *last* AC-DEFINE to be honored. +uniq confdefs.h | sed -n -f confdef2sed.sed >conftest.defines +sed 's/ac_d/ac_u/g' conftest.defines >conftest.undefs +rm -f confdef2sed.sed + +# This sed command replaces #undef with comments. This is necessary, for +# example, in the case of _POSIX_SOURCE, which is predefined and required +# on some systems where configure will not decide to define it. +cat >>conftest.undefs <<\_ACEOF +s,^[ ]*#[ ]*undef[ ][ ]*[a-zA-Z_][a-zA-Z_0-9]*,/* & */, +_ACEOF + +# Break up conftest.defines because some shells have a limit on the size +# of here documents, and old seds have small limits too (100 cmds). +echo ' # Handle all the #define templates only if necessary.' >>$CONFIG_STATUS +echo ' if grep "^[ ]*#[ ]*define" $tmp/in >/dev/null; then' >>$CONFIG_STATUS +echo ' # If there are no defines, we may have an empty if/fi' >>$CONFIG_STATUS +echo ' :' >>$CONFIG_STATUS +rm -f conftest.tail +while grep . conftest.defines >/dev/null +do + # Write a limited-size here document to $tmp/defines.sed. + echo ' cat >$tmp/defines.sed <>$CONFIG_STATUS + # Speed up: don't consider the non `#define' lines. + echo '/^[ ]*#[ ]*define/!b' >>$CONFIG_STATUS + # Work around the forget-to-reset-the-flag bug. + echo 't clr' >>$CONFIG_STATUS + echo ': clr' >>$CONFIG_STATUS + sed ${ac_max_here_lines}q conftest.defines >>$CONFIG_STATUS + echo 'CEOF + sed -f $tmp/defines.sed $tmp/in >$tmp/out + rm -f $tmp/in + mv $tmp/out $tmp/in +' >>$CONFIG_STATUS + sed 1,${ac_max_here_lines}d conftest.defines >conftest.tail + rm -f conftest.defines + mv conftest.tail conftest.defines +done +rm -f conftest.defines +echo ' fi # grep' >>$CONFIG_STATUS +echo >>$CONFIG_STATUS + +# Break up conftest.undefs because some shells have a limit on the size +# of here documents, and old seds have small limits too (100 cmds). +echo ' # Handle all the #undef templates' >>$CONFIG_STATUS +rm -f conftest.tail +while grep . conftest.undefs >/dev/null +do + # Write a limited-size here document to $tmp/undefs.sed. + echo ' cat >$tmp/undefs.sed <>$CONFIG_STATUS + # Speed up: don't consider the non `#undef' + echo '/^[ ]*#[ ]*undef/!b' >>$CONFIG_STATUS + # Work around the forget-to-reset-the-flag bug. + echo 't clr' >>$CONFIG_STATUS + echo ': clr' >>$CONFIG_STATUS + sed ${ac_max_here_lines}q conftest.undefs >>$CONFIG_STATUS + echo 'CEOF + sed -f $tmp/undefs.sed $tmp/in >$tmp/out + rm -f $tmp/in + mv $tmp/out $tmp/in +' >>$CONFIG_STATUS + sed 1,${ac_max_here_lines}d conftest.undefs >conftest.tail + rm -f conftest.undefs + mv conftest.tail conftest.undefs +done +rm -f conftest.undefs + +cat >>$CONFIG_STATUS <<\_ACEOF + # Let's still pretend it is `configure' which instantiates (i.e., don't + # use $as_me), people would be surprised to read: + # /* config.h. Generated by config.status. */ + if test x"$ac_file" = x-; then + echo "/* Generated by configure. */" >$tmp/config.h + else + echo "/* $ac_file. Generated by configure. */" >$tmp/config.h + fi + cat $tmp/in >>$tmp/config.h + rm -f $tmp/in + if test x"$ac_file" != x-; then + if diff $ac_file $tmp/config.h >/dev/null 2>&1; then + { echo "$as_me:$LINENO: $ac_file is unchanged" >&5 +echo "$as_me: $ac_file is unchanged" >&6;} + else + ac_dir=`(dirname "$ac_file") 2>/dev/null || +$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$ac_file" : 'X\(//\)[^/]' \| \ + X"$ac_file" : 'X\(//\)$' \| \ + X"$ac_file" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$ac_file" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + { if $as_mkdir_p; then + mkdir -p "$ac_dir" + else + as_dir="$ac_dir" + as_dirs= + while test ! -d "$as_dir"; do + as_dirs="$as_dir $as_dirs" + as_dir=`(dirname "$as_dir") 2>/dev/null || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + done + test ! -n "$as_dirs" || mkdir $as_dirs + fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5 +echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;} + { (exit 1); exit 1; }; }; } + + rm -f $ac_file + mv $tmp/config.h $ac_file + fi + else + cat $tmp/config.h + rm -f $tmp/config.h + fi +# Compute $ac_file's index in $config_headers. +_am_stamp_count=1 +for _am_header in $config_headers :; do + case $_am_header in + $ac_file | $ac_file:* ) + break ;; + * ) + _am_stamp_count=`expr $_am_stamp_count + 1` ;; + esac +done +echo "timestamp for $ac_file" >`(dirname $ac_file) 2>/dev/null || +$as_expr X$ac_file : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X$ac_file : 'X\(//\)[^/]' \| \ + X$ac_file : 'X\(//\)$' \| \ + X$ac_file : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X$ac_file | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'`/stamp-h$_am_stamp_count +done +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF + +# +# CONFIG_COMMANDS section. +# +for ac_file in : $CONFIG_COMMANDS; do test "x$ac_file" = x: && continue + ac_dest=`echo "$ac_file" | sed 's,:.*,,'` + ac_source=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_dir=`(dirname "$ac_dest") 2>/dev/null || +$as_expr X"$ac_dest" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$ac_dest" : 'X\(//\)[^/]' \| \ + X"$ac_dest" : 'X\(//\)$' \| \ + X"$ac_dest" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$ac_dest" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + { if $as_mkdir_p; then + mkdir -p "$ac_dir" + else + as_dir="$ac_dir" + as_dirs= + while test ! -d "$as_dir"; do + as_dirs="$as_dir $as_dirs" + as_dir=`(dirname "$as_dir") 2>/dev/null || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + done + test ! -n "$as_dirs" || mkdir $as_dirs + fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5 +echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;} + { (exit 1); exit 1; }; }; } + + ac_builddir=. + +if test "$ac_dir" != .; then + ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'` + # A "../" for each directory in $ac_dir_suffix. + ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'` +else + ac_dir_suffix= ac_top_builddir= +fi + +case $srcdir in + .) # No --srcdir option. We are building in place. + ac_srcdir=. + if test -z "$ac_top_builddir"; then + ac_top_srcdir=. + else + ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` + fi ;; + [\\/]* | ?:[\\/]* ) # Absolute path. + ac_srcdir=$srcdir$ac_dir_suffix; + ac_top_srcdir=$srcdir ;; + *) # Relative path. + ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix + ac_top_srcdir=$ac_top_builddir$srcdir ;; +esac + +# Do not use `cd foo && pwd` to compute absolute paths, because +# the directories may not exist. +case `pwd` in +.) ac_abs_builddir="$ac_dir";; +*) + case "$ac_dir" in + .) ac_abs_builddir=`pwd`;; + [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";; + *) ac_abs_builddir=`pwd`/"$ac_dir";; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_top_builddir=${ac_top_builddir}.;; +*) + case ${ac_top_builddir}. in + .) ac_abs_top_builddir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;; + *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_srcdir=$ac_srcdir;; +*) + case $ac_srcdir in + .) ac_abs_srcdir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;; + *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_top_srcdir=$ac_top_srcdir;; +*) + case $ac_top_srcdir in + .) ac_abs_top_srcdir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;; + *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;; + esac;; +esac + + + { echo "$as_me:$LINENO: executing $ac_dest commands" >&5 +echo "$as_me: executing $ac_dest commands" >&6;} + case $ac_dest in + depfiles ) test x"$AMDEP_TRUE" != x"" || for mf in $CONFIG_FILES; do + # Strip MF so we end up with the name of the file. + mf=`echo "$mf" | sed -e 's/:.*$//'` + # Check whether this is an Automake generated Makefile or not. + # We used to match only the files named `Makefile.in', but + # some people rename them; so instead we look at the file content. + # Grep'ing the first line is not enough: some people post-process + # each Makefile.in and add a new line on top of each file to say so. + # So let's grep whole file. + if grep '^#.*generated by automake' $mf > /dev/null 2>&1; then + dirpart=`(dirname "$mf") 2>/dev/null || +$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$mf" : 'X\(//\)[^/]' \| \ + X"$mf" : 'X\(//\)$' \| \ + X"$mf" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$mf" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + else + continue + fi + # Extract the definition of DEPDIR, am__include, and am__quote + # from the Makefile without running `make'. + DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"` + test -z "$DEPDIR" && continue + am__include=`sed -n 's/^am__include = //p' < "$mf"` + test -z "am__include" && continue + am__quote=`sed -n 's/^am__quote = //p' < "$mf"` + # When using ansi2knr, U may be empty or an underscore; expand it + U=`sed -n 's/^U = //p' < "$mf"` + # Find all dependency output files, they are included files with + # $(DEPDIR) in their names. We invoke sed twice because it is the + # simplest approach to changing $(DEPDIR) to its actual value in the + # expansion. + for file in `sed -n " + s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \ + sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do + # Make sure the directory exists. + test -f "$dirpart/$file" && continue + fdir=`(dirname "$file") 2>/dev/null || +$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$file" : 'X\(//\)[^/]' \| \ + X"$file" : 'X\(//\)$' \| \ + X"$file" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$file" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + { if $as_mkdir_p; then + mkdir -p $dirpart/$fdir + else + as_dir=$dirpart/$fdir + as_dirs= + while test ! -d "$as_dir"; do + as_dirs="$as_dir $as_dirs" + as_dir=`(dirname "$as_dir") 2>/dev/null || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + done + test ! -n "$as_dirs" || mkdir $as_dirs + fi || { { echo "$as_me:$LINENO: error: cannot create directory $dirpart/$fdir" >&5 +echo "$as_me: error: cannot create directory $dirpart/$fdir" >&2;} + { (exit 1); exit 1; }; }; } + + # echo "creating $dirpart/$file" + echo '# dummy' > "$dirpart/$file" + done +done + ;; + esac +done +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF + +{ (exit 0); exit 0; } +_ACEOF +chmod +x $CONFIG_STATUS +ac_clean_files=$ac_clean_files_save + + +# configure is writing to config.log, and then calls config.status. +# config.status does its own redirection, appending to config.log. +# Unfortunately, on DOS this fails, as config.log is still kept open +# by configure, so config.status won't be able to write to it; its +# output is simply discarded. So we exec the FD to /dev/null, +# effectively closing config.log, so it can be properly (re)opened and +# appended to by config.status. When coming back to configure, we +# need to make the FD available again. +if test "$no_create" != yes; then + ac_cs_success=: + ac_config_status_args= + test "$silent" = yes && + ac_config_status_args="$ac_config_status_args --quiet" + exec 5>/dev/null + $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false + exec 5>>config.log + # Use ||, not &&, to avoid exiting from the if with $? = 1, which + # would make configure fail if this is the last instruction. + $ac_cs_success || { (exit 1); exit 1; } +fi + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/configure.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/configure.in new file mode 100755 index 000000000..d1dad181c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/configure.in @@ -0,0 +1,55 @@ +dnl Process this file with autoconf to produce a configure script. +AC_INIT([Kinfold], [1.0], [rna@tbi.univie.ac.at]) + +dnl Every other copy of the package version number gets its value from here +AM_INIT_AUTOMAKE + +dnl configure options +AM_WITH_DMALLOC + +dnl Checks for programs. +AC_PROG_CC +AC_PROG_MAKE_SET + +dnl create a config.h file (Automake will add -DHAVE_CONFIG_H) +AM_CONFIG_HEADER(config.h) + +AC_SUBST(VERSION) + +ISODATE=`date +%Y-%m-%d` +AC_SUBST(ISODATE) + +AC_CANONICAL_HOST + +AC_ARG_WITH(ViennaRNA-include, + [ --with-ViennaRNA-include where to search for ViennaRNA header files], + ac_VRNA_includes="$withval", + ) + +AC_ARG_WITH(ViennaRNA-lib, + [ --with-ViennaRNA-lib where to search for libRNA.a], + ac_VRNA_lib="$withval", + ) + +AC_PATH_VRNA + +dnl Checks for libraries. +dnl Replace `main' with a function in -lm: +AC_CHECK_LIB(m, exp) + +dnl checking for -lRNA will fail if both are built simultaneously +dnl AC_CHECK_LIB(RNA, fold) +LIBS=["-lRNA ${LIBS}"] + + +dnl Checks for header files. +AC_HEADER_STDC +AC_CHECK_HEADERS(limits.h sys/time.h unistd.h fold.h) + +dnl Checks for typedefs, structures, and compiler characteristics. +AC_C_CONST + +dnl Checks for library functions. +AC_CHECK_FUNCS(strdup) + +AC_OUTPUT(Makefile Example/Makefile) diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.c new file mode 100755 index 000000000..4744e4339 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.c @@ -0,0 +1,1055 @@ +/* Getopt for GNU. + NOTE: getopt is now part of the C library, so if you don't know what + "Keep this file name-space clean" means, talk to drepper@gnu.org + before changing it! + + Copyright (C) 1987, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 2000 + Free Software Foundation, Inc. + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Library General Public License as + published by the Free Software Foundation; either version 2 of the + License, or (at your option) any later version. + + The GNU C Library is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Library General Public License for more details. + + You should have received a copy of the GNU Library General Public + License along with the GNU C Library; see the file COPYING.LIB. If not, + write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, + Boston, MA 02111-1307, USA. */ + +/* This tells Alpha OSF/1 not to define a getopt prototype in . + Ditto for AIX 3.2 and . */ +#ifndef _NO_PROTO +# define _NO_PROTO +#endif + +#ifdef HAVE_CONFIG_H +# include +#endif + +#if !defined __STDC__ || !__STDC__ +/* This is a separate conditional since some stdc systems + reject `defined (const)'. */ +# ifndef const +# define const +# endif +#endif + +#include + +/* Comment out all this code if we are using the GNU C Library, and are not + actually compiling the library itself. This code is part of the GNU C + Library, but also included in many other GNU distributions. Compiling + and linking in this code is a waste when using the GNU C library + (especially if it is a shared library). Rather than having every GNU + program understand `configure --with-gnu-libc' and omit the object files, + it is simpler to just do this in the source for each such file. */ + +#define GETOPT_INTERFACE_VERSION 2 +#if !defined _LIBC && defined __GLIBC__ && __GLIBC__ >= 2 +# include +# if _GNU_GETOPT_INTERFACE_VERSION == GETOPT_INTERFACE_VERSION +# define ELIDE_CODE +# endif +#endif + +#ifndef ELIDE_CODE + + +/* This needs to come after some library #include + to get __GNU_LIBRARY__ defined. */ +#ifdef __GNU_LIBRARY__ +/* Don't include stdlib.h for non-GNU C libraries because some of them + contain conflicting prototypes for getopt. */ +# include +# include +#endif /* GNU C library. */ + +#ifdef VMS +# include +# if HAVE_STRING_H - 0 +# include +# endif +#endif + +#ifndef _ +/* This is for other GNU distributions with internationalized messages. + When compiling libc, the _ macro is predefined. */ +# ifdef HAVE_LIBINTL_H +# include +# define _(msgid) gettext (msgid) +# else +# define _(msgid) (msgid) +# endif +#endif + +/* This version of `getopt' appears to the caller like standard Unix `getopt' + but it behaves differently for the user, since it allows the user + to intersperse the options with the other arguments. + + As `getopt' works, it permutes the elements of ARGV so that, + when it is done, all the options precede everything else. Thus + all application programs are extended to handle flexible argument order. + + Setting the environment variable POSIXLY_CORRECT disables permutation. + Then the behavior is completely standard. + + GNU application programs can use a third alternative mode in which + they can distinguish the relative order of options and other arguments. */ + +#include "getopt.h" + +/* For communication from `getopt' to the caller. + When `getopt' finds an option that takes an argument, + the argument value is returned here. + Also, when `ordering' is RETURN_IN_ORDER, + each non-option ARGV-element is returned here. */ + +char *optarg; + +/* Index in ARGV of the next element to be scanned. + This is used for communication to and from the caller + and for communication between successive calls to `getopt'. + + On entry to `getopt', zero means this is the first call; initialize. + + When `getopt' returns -1, this is the index of the first of the + non-option elements that the caller should itself scan. + + Otherwise, `optind' communicates from one call to the next + how much of ARGV has been scanned so far. */ + +/* 1003.2 says this must be 1 before any call. */ +int optind = 1; + +/* Formerly, initialization of getopt depended on optind==0, which + causes problems with re-calling getopt as programs generally don't + know that. */ + +int __getopt_initialized; + +/* The next char to be scanned in the option-element + in which the last option character we returned was found. + This allows us to pick up the scan where we left off. + + If this is zero, or a null string, it means resume the scan + by advancing to the next ARGV-element. */ + +static char *nextchar; + +/* Callers store zero here to inhibit the error message + for unrecognized options. */ + +int opterr = 1; + +/* Set to an option character which was unrecognized. + This must be initialized on some systems to avoid linking in the + system's own getopt implementation. */ + +int optopt = '?'; + +/* Describe how to deal with options that follow non-option ARGV-elements. + + If the caller did not specify anything, + the default is REQUIRE_ORDER if the environment variable + POSIXLY_CORRECT is defined, PERMUTE otherwise. + + REQUIRE_ORDER means don't recognize them as options; + stop option processing when the first non-option is seen. + This is what Unix does. + This mode of operation is selected by either setting the environment + variable POSIXLY_CORRECT, or using `+' as the first character + of the list of option characters. + + PERMUTE is the default. We permute the contents of ARGV as we scan, + so that eventually all the non-options are at the end. This allows options + to be given in any order, even with programs that were not written to + expect this. + + RETURN_IN_ORDER is an option available to programs that were written + to expect options and other ARGV-elements in any order and that care about + the ordering of the two. We describe each non-option ARGV-element + as if it were the argument of an option with character code 1. + Using `-' as the first character of the list of option characters + selects this mode of operation. + + The special argument `--' forces an end of option-scanning regardless + of the value of `ordering'. In the case of RETURN_IN_ORDER, only + `--' can cause `getopt' to return -1 with `optind' != ARGC. */ + +static enum +{ + REQUIRE_ORDER, PERMUTE, RETURN_IN_ORDER +} ordering; + +/* Value of POSIXLY_CORRECT environment variable. */ +static char *posixly_correct; + +#ifdef __GNU_LIBRARY__ +/* We want to avoid inclusion of string.h with non-GNU libraries + because there are many ways it can cause trouble. + On some systems, it contains special magic macros that don't work + in GCC. */ +# include +# define my_index strchr +#else + +# if HAVE_STRING_H +# include +# else +# include +# endif + +/* Avoid depending on library functions or files + whose names are inconsistent. */ + +#ifndef getenv +extern char *getenv (); +#endif + +static char * +my_index (str, chr) + const char *str; + int chr; +{ + while (*str) + { + if (*str == chr) + return (char *) str; + str++; + } + return 0; +} + +/* If using GCC, we can safely declare strlen this way. + If not using GCC, it is ok not to declare it. */ +#ifdef __GNUC__ +/* Note that Motorola Delta 68k R3V7 comes with GCC but not stddef.h. + That was relevant to code that was here before. */ +# if (!defined __STDC__ || !__STDC__) && !defined strlen +/* gcc with -traditional declares the built-in strlen to return int, + and has done so at least since version 2.4.5. -- rms. */ +extern int strlen (const char *); +# endif /* not __STDC__ */ +#endif /* __GNUC__ */ + +#endif /* not __GNU_LIBRARY__ */ + +/* Handle permutation of arguments. */ + +/* Describe the part of ARGV that contains non-options that have + been skipped. `first_nonopt' is the index in ARGV of the first of them; + `last_nonopt' is the index after the last of them. */ + +static int first_nonopt; +static int last_nonopt; + +#ifdef _LIBC +/* Bash 2.0 gives us an environment variable containing flags + indicating ARGV elements that should not be considered arguments. */ + +/* Defined in getopt_init.c */ +extern char *__getopt_nonoption_flags; + +static int nonoption_flags_max_len; +static int nonoption_flags_len; + +static int original_argc; +static char *const *original_argv; + +/* Make sure the environment variable bash 2.0 puts in the environment + is valid for the getopt call we must make sure that the ARGV passed + to getopt is that one passed to the process. */ +static void +__attribute__ ((unused)) +store_args_and_env (int argc, char *const *argv) +{ + /* XXX This is no good solution. We should rather copy the args so + that we can compare them later. But we must not use malloc(3). */ + original_argc = argc; + original_argv = argv; +} +# ifdef text_set_element +text_set_element (__libc_subinit, store_args_and_env); +# endif /* text_set_element */ + +# define SWAP_FLAGS(ch1, ch2) \ + if (nonoption_flags_len > 0) \ + { \ + char __tmp = __getopt_nonoption_flags[ch1]; \ + __getopt_nonoption_flags[ch1] = __getopt_nonoption_flags[ch2]; \ + __getopt_nonoption_flags[ch2] = __tmp; \ + } +#else /* !_LIBC */ +# define SWAP_FLAGS(ch1, ch2) +#endif /* _LIBC */ + +/* Exchange two adjacent subsequences of ARGV. + One subsequence is elements [first_nonopt,last_nonopt) + which contains all the non-options that have been skipped so far. + The other is elements [last_nonopt,optind), which contains all + the options processed since those non-options were skipped. + + `first_nonopt' and `last_nonopt' are relocated so that they describe + the new indices of the non-options in ARGV after they are moved. */ + +#if defined __STDC__ && __STDC__ +static void exchange (char **); +#endif + +static void +exchange (argv) + char **argv; +{ + int bottom = first_nonopt; + int middle = last_nonopt; + int top = optind; + char *tem; + + /* Exchange the shorter segment with the far end of the longer segment. + That puts the shorter segment into the right place. + It leaves the longer segment in the right place overall, + but it consists of two parts that need to be swapped next. */ + +#ifdef _LIBC + /* First make sure the handling of the `__getopt_nonoption_flags' + string can work normally. Our top argument must be in the range + of the string. */ + if (nonoption_flags_len > 0 && top >= nonoption_flags_max_len) + { + /* We must extend the array. The user plays games with us and + presents new arguments. */ + char *new_str = malloc (top + 1); + if (new_str == NULL) + nonoption_flags_len = nonoption_flags_max_len = 0; + else + { + memset (__mempcpy (new_str, __getopt_nonoption_flags, + nonoption_flags_max_len), + '\0', top + 1 - nonoption_flags_max_len); + nonoption_flags_max_len = top + 1; + __getopt_nonoption_flags = new_str; + } + } +#endif + + while (top > middle && middle > bottom) + { + if (top - middle > middle - bottom) + { + /* Bottom segment is the short one. */ + int len = middle - bottom; + register int i; + + /* Swap it with the top part of the top segment. */ + for (i = 0; i < len; i++) + { + tem = argv[bottom + i]; + argv[bottom + i] = argv[top - (middle - bottom) + i]; + argv[top - (middle - bottom) + i] = tem; + SWAP_FLAGS (bottom + i, top - (middle - bottom) + i); + } + /* Exclude the moved bottom segment from further swapping. */ + top -= len; + } + else + { + /* Top segment is the short one. */ + int len = top - middle; + register int i; + + /* Swap it with the bottom part of the bottom segment. */ + for (i = 0; i < len; i++) + { + tem = argv[bottom + i]; + argv[bottom + i] = argv[middle + i]; + argv[middle + i] = tem; + SWAP_FLAGS (bottom + i, middle + i); + } + /* Exclude the moved top segment from further swapping. */ + bottom += len; + } + } + + /* Update records for the slots the non-options now occupy. */ + + first_nonopt += (optind - last_nonopt); + last_nonopt = optind; +} + +/* Initialize the internal data when the first call is made. */ + +#if defined __STDC__ && __STDC__ +static const char *_getopt_initialize (int, char *const *, const char *); +#endif +static const char * +_getopt_initialize (argc, argv, optstring) + int argc; + char *const *argv; + const char *optstring; +{ + /* Start processing options with ARGV-element 1 (since ARGV-element 0 + is the program name); the sequence of previously skipped + non-option ARGV-elements is empty. */ + + first_nonopt = last_nonopt = optind; + + nextchar = NULL; + + posixly_correct = getenv ("POSIXLY_CORRECT"); + + /* Determine how to handle the ordering of options and nonoptions. */ + + if (optstring[0] == '-') + { + ordering = RETURN_IN_ORDER; + ++optstring; + } + else if (optstring[0] == '+') + { + ordering = REQUIRE_ORDER; + ++optstring; + } + else if (posixly_correct != NULL) + ordering = REQUIRE_ORDER; + else + ordering = PERMUTE; + +#ifdef _LIBC + if (posixly_correct == NULL + && argc == original_argc && argv == original_argv) + { + if (nonoption_flags_max_len == 0) + { + if (__getopt_nonoption_flags == NULL + || __getopt_nonoption_flags[0] == '\0') + nonoption_flags_max_len = -1; + else + { + const char *orig_str = __getopt_nonoption_flags; + int len = nonoption_flags_max_len = strlen (orig_str); + if (nonoption_flags_max_len < argc) + nonoption_flags_max_len = argc; + __getopt_nonoption_flags = + (char *) malloc (nonoption_flags_max_len); + if (__getopt_nonoption_flags == NULL) + nonoption_flags_max_len = -1; + else + memset (__mempcpy (__getopt_nonoption_flags, orig_str, len), + '\0', nonoption_flags_max_len - len); + } + } + nonoption_flags_len = nonoption_flags_max_len; + } + else + nonoption_flags_len = 0; +#endif + + return optstring; +} + +/* Scan elements of ARGV (whose length is ARGC) for option characters + given in OPTSTRING. + + If an element of ARGV starts with '-', and is not exactly "-" or "--", + then it is an option element. The characters of this element + (aside from the initial '-') are option characters. If `getopt' + is called repeatedly, it returns successively each of the option characters + from each of the option elements. + + If `getopt' finds another option character, it returns that character, + updating `optind' and `nextchar' so that the next call to `getopt' can + resume the scan with the following option character or ARGV-element. + + If there are no more option characters, `getopt' returns -1. + Then `optind' is the index in ARGV of the first ARGV-element + that is not an option. (The ARGV-elements have been permuted + so that those that are not options now come last.) + + OPTSTRING is a string containing the legitimate option characters. + If an option character is seen that is not listed in OPTSTRING, + return '?' after printing an error message. If you set `opterr' to + zero, the error message is suppressed but we still return '?'. + + If a char in OPTSTRING is followed by a colon, that means it wants an arg, + so the following text in the same ARGV-element, or the text of the following + ARGV-element, is returned in `optarg'. Two colons mean an option that + wants an optional arg; if there is text in the current ARGV-element, + it is returned in `optarg', otherwise `optarg' is set to zero. + + If OPTSTRING starts with `-' or `+', it requests different methods of + handling the non-option ARGV-elements. + See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above. + + Long-named options begin with `--' instead of `-'. + Their names may be abbreviated as long as the abbreviation is unique + or is an exact match for some defined option. If they have an + argument, it follows the option name in the same ARGV-element, separated + from the option name by a `=', or else the in next ARGV-element. + When `getopt' finds a long-named option, it returns 0 if that option's + `flag' field is nonzero, the value of the option's `val' field + if the `flag' field is zero. + + The elements of ARGV aren't really const, because we permute them. + But we pretend they're const in the prototype to be compatible + with other systems. + + LONGOPTS is a vector of `struct option' terminated by an + element containing a name which is zero. + + LONGIND returns the index in LONGOPT of the long-named option found. + It is only valid when a long-named option has been found by the most + recent call. + + If LONG_ONLY is nonzero, '-' as well as '--' can introduce + long-named options. */ + +int +_getopt_internal (argc, argv, optstring, longopts, longind, long_only) + int argc; + char *const *argv; + const char *optstring; + const struct option *longopts; + int *longind; + int long_only; +{ + int print_errors = opterr; + if (optstring[0] == ':') + print_errors = 0; + + optarg = NULL; + + if (optind == 0 || !__getopt_initialized) + { + if (optind == 0) + optind = 1; /* Don't scan ARGV[0], the program name. */ + optstring = _getopt_initialize (argc, argv, optstring); + __getopt_initialized = 1; + } + + /* Test whether ARGV[optind] points to a non-option argument. + Either it does not have option syntax, or there is an environment flag + from the shell indicating it is not an option. The later information + is only used when the used in the GNU libc. */ +#ifdef _LIBC +# define NONOPTION_P (argv[optind][0] != '-' || argv[optind][1] == '\0' \ + || (optind < nonoption_flags_len \ + && __getopt_nonoption_flags[optind] == '1')) +#else +# define NONOPTION_P (argv[optind][0] != '-' || argv[optind][1] == '\0') +#endif + + if (nextchar == NULL || *nextchar == '\0') + { + /* Advance to the next ARGV-element. */ + + /* Give FIRST_NONOPT & LAST_NONOPT rational values if OPTIND has been + moved back by the user (who may also have changed the arguments). */ + if (last_nonopt > optind) + last_nonopt = optind; + if (first_nonopt > optind) + first_nonopt = optind; + + if (ordering == PERMUTE) + { + /* If we have just processed some options following some non-options, + exchange them so that the options come first. */ + + if (first_nonopt != last_nonopt && last_nonopt != optind) + exchange ((char **) argv); + else if (last_nonopt != optind) + first_nonopt = optind; + + /* Skip any additional non-options + and extend the range of non-options previously skipped. */ + + while (optind < argc && NONOPTION_P) + optind++; + last_nonopt = optind; + } + + /* The special ARGV-element `--' means premature end of options. + Skip it like a null option, + then exchange with previous non-options as if it were an option, + then skip everything else like a non-option. */ + + if (optind != argc && !strcmp (argv[optind], "--")) + { + optind++; + + if (first_nonopt != last_nonopt && last_nonopt != optind) + exchange ((char **) argv); + else if (first_nonopt == last_nonopt) + first_nonopt = optind; + last_nonopt = argc; + + optind = argc; + } + + /* If we have done all the ARGV-elements, stop the scan + and back over any non-options that we skipped and permuted. */ + + if (optind == argc) + { + /* Set the next-arg-index to point at the non-options + that we previously skipped, so the caller will digest them. */ + if (first_nonopt != last_nonopt) + optind = first_nonopt; + return -1; + } + + /* If we have come to a non-option and did not permute it, + either stop the scan or describe it to the caller and pass it by. */ + + if (NONOPTION_P) + { + if (ordering == REQUIRE_ORDER) + return -1; + optarg = argv[optind++]; + return 1; + } + + /* We have found another option-ARGV-element. + Skip the initial punctuation. */ + + nextchar = (argv[optind] + 1 + + (longopts != NULL && argv[optind][1] == '-')); + } + + /* Decode the current option-ARGV-element. */ + + /* Check whether the ARGV-element is a long option. + + If long_only and the ARGV-element has the form "-f", where f is + a valid short option, don't consider it an abbreviated form of + a long option that starts with f. Otherwise there would be no + way to give the -f short option. + + On the other hand, if there's a long option "fubar" and + the ARGV-element is "-fu", do consider that an abbreviation of + the long option, just like "--fu", and not "-f" with arg "u". + + This distinction seems to be the most useful approach. */ + + if (longopts != NULL + && (argv[optind][1] == '-' + || (long_only && (argv[optind][2] || !my_index (optstring, argv[optind][1]))))) + { + char *nameend; + const struct option *p; + const struct option *pfound = NULL; + int exact = 0; + int ambig = 0; + int indfound = -1; + int option_index; + + for (nameend = nextchar; *nameend && *nameend != '='; nameend++) + /* Do nothing. */ ; + + /* Test all long options for either exact match + or abbreviated matches. */ + for (p = longopts, option_index = 0; p->name; p++, option_index++) + if (!strncmp (p->name, nextchar, nameend - nextchar)) + { + if ((unsigned int) (nameend - nextchar) + == (unsigned int) strlen (p->name)) + { + /* Exact match found. */ + pfound = p; + indfound = option_index; + exact = 1; + break; + } + else if (pfound == NULL) + { + /* First nonexact match found. */ + pfound = p; + indfound = option_index; + } + else + /* Second or later nonexact match found. */ + ambig = 1; + } + + if (ambig && !exact) + { + if (print_errors) + fprintf (stderr, _("%s: option `%s' is ambiguous\n"), + argv[0], argv[optind]); + nextchar += strlen (nextchar); + optind++; + optopt = 0; + return '?'; + } + + if (pfound != NULL) + { + option_index = indfound; + optind++; + if (*nameend) + { + /* Don't test has_arg with >, because some C compilers don't + allow it to be used on enums. */ + if (pfound->has_arg) + optarg = nameend + 1; + else + { + if (print_errors) + { + if (argv[optind - 1][1] == '-') + /* --option */ + fprintf (stderr, + _("%s: option `--%s' doesn't allow an argument\n"), + argv[0], pfound->name); + else + /* +option or -option */ + fprintf (stderr, + _("%s: option `%c%s' doesn't allow an argument\n"), + argv[0], argv[optind - 1][0], pfound->name); + } + + nextchar += strlen (nextchar); + + optopt = pfound->val; + return '?'; + } + } + else if (pfound->has_arg == 1) + { + if (optind < argc) + optarg = argv[optind++]; + else + { + if (print_errors) + fprintf (stderr, + _("%s: option `%s' requires an argument\n"), + argv[0], argv[optind - 1]); + nextchar += strlen (nextchar); + optopt = pfound->val; + return optstring[0] == ':' ? ':' : '?'; + } + } + nextchar += strlen (nextchar); + if (longind != NULL) + *longind = option_index; + if (pfound->flag) + { + *(pfound->flag) = pfound->val; + return 0; + } + return pfound->val; + } + + /* Can't find it as a long option. If this is not getopt_long_only, + or the option starts with '--' or is not a valid short + option, then it's an error. + Otherwise interpret it as a short option. */ + if (!long_only || argv[optind][1] == '-' + || my_index (optstring, *nextchar) == NULL) + { + if (print_errors) + { + if (argv[optind][1] == '-') + /* --option */ + fprintf (stderr, _("%s: unrecognized option `--%s'\n"), + argv[0], nextchar); + else + /* +option or -option */ + fprintf (stderr, _("%s: unrecognized option `%c%s'\n"), + argv[0], argv[optind][0], nextchar); + } + nextchar = (char *) ""; + optind++; + optopt = 0; + return '?'; + } + } + + /* Look at and handle the next short option-character. */ + + { + char c = *nextchar++; + char *temp = my_index (optstring, c); + + /* Increment `optind' when we start to process its last character. */ + if (*nextchar == '\0') + ++optind; + + if (temp == NULL || c == ':') + { + if (print_errors) + { + if (posixly_correct) + /* 1003.2 specifies the format of this message. */ + fprintf (stderr, _("%s: illegal option -- %c\n"), + argv[0], c); + else + fprintf (stderr, _("%s: invalid option -- %c\n"), + argv[0], c); + } + optopt = c; + return '?'; + } + /* Convenience. Treat POSIX -W foo same as long option --foo */ + if (temp[0] == 'W' && temp[1] == ';') + { + char *nameend; + const struct option *p; + const struct option *pfound = NULL; + int exact = 0; + int ambig = 0; + int indfound = 0; + int option_index; + + /* This is an option that requires an argument. */ + if (*nextchar != '\0') + { + optarg = nextchar; + /* If we end this ARGV-element by taking the rest as an arg, + we must advance to the next element now. */ + optind++; + } + else if (optind == argc) + { + if (print_errors) + { + /* 1003.2 specifies the format of this message. */ + fprintf (stderr, _("%s: option requires an argument -- %c\n"), + argv[0], c); + } + optopt = c; + if (optstring[0] == ':') + c = ':'; + else + c = '?'; + return c; + } + else + /* We already incremented `optind' once; + increment it again when taking next ARGV-elt as argument. */ + optarg = argv[optind++]; + + /* optarg is now the argument, see if it's in the + table of longopts. */ + + for (nextchar = nameend = optarg; *nameend && *nameend != '='; nameend++) + /* Do nothing. */ ; + + /* Test all long options for either exact match + or abbreviated matches. */ + for (p = longopts, option_index = 0; p->name; p++, option_index++) + if (!strncmp (p->name, nextchar, nameend - nextchar)) + { + if ((unsigned int) (nameend - nextchar) == strlen (p->name)) + { + /* Exact match found. */ + pfound = p; + indfound = option_index; + exact = 1; + break; + } + else if (pfound == NULL) + { + /* First nonexact match found. */ + pfound = p; + indfound = option_index; + } + else + /* Second or later nonexact match found. */ + ambig = 1; + } + if (ambig && !exact) + { + if (print_errors) + fprintf (stderr, _("%s: option `-W %s' is ambiguous\n"), + argv[0], argv[optind]); + nextchar += strlen (nextchar); + optind++; + return '?'; + } + if (pfound != NULL) + { + option_index = indfound; + if (*nameend) + { + /* Don't test has_arg with >, because some C compilers don't + allow it to be used on enums. */ + if (pfound->has_arg) + optarg = nameend + 1; + else + { + if (print_errors) + fprintf (stderr, _("\ +%s: option `-W %s' doesn't allow an argument\n"), + argv[0], pfound->name); + + nextchar += strlen (nextchar); + return '?'; + } + } + else if (pfound->has_arg == 1) + { + if (optind < argc) + optarg = argv[optind++]; + else + { + if (print_errors) + fprintf (stderr, + _("%s: option `%s' requires an argument\n"), + argv[0], argv[optind - 1]); + nextchar += strlen (nextchar); + return optstring[0] == ':' ? ':' : '?'; + } + } + nextchar += strlen (nextchar); + if (longind != NULL) + *longind = option_index; + if (pfound->flag) + { + *(pfound->flag) = pfound->val; + return 0; + } + return pfound->val; + } + nextchar = NULL; + return 'W'; /* Let the application handle it. */ + } + if (temp[1] == ':') + { + if (temp[2] == ':') + { + /* This is an option that accepts an argument optionally. */ + if (*nextchar != '\0') + { + optarg = nextchar; + optind++; + } + else + optarg = NULL; + nextchar = NULL; + } + else + { + /* This is an option that requires an argument. */ + if (*nextchar != '\0') + { + optarg = nextchar; + /* If we end this ARGV-element by taking the rest as an arg, + we must advance to the next element now. */ + optind++; + } + else if (optind == argc) + { + if (print_errors) + { + /* 1003.2 specifies the format of this message. */ + fprintf (stderr, + _("%s: option requires an argument -- %c\n"), + argv[0], c); + } + optopt = c; + if (optstring[0] == ':') + c = ':'; + else + c = '?'; + } + else + /* We already incremented `optind' once; + increment it again when taking next ARGV-elt as argument. */ + optarg = argv[optind++]; + nextchar = NULL; + } + } + return c; + } +} + +int +getopt (argc, argv, optstring) + int argc; + char *const *argv; + const char *optstring; +{ + return _getopt_internal (argc, argv, optstring, + (const struct option *) 0, + (int *) 0, + 0); +} + +#endif /* Not ELIDE_CODE. */ + +#ifdef TEST + +/* Compile with -DTEST to make an executable for use in testing + the above definition of `getopt'. */ + +int +main (argc, argv) + int argc; + char **argv; +{ + int c; + int digit_optind = 0; + + while (1) + { + int this_option_optind = optind ? optind : 1; + + c = getopt (argc, argv, "abc:d:0123456789"); + if (c == -1) + break; + + switch (c) + { + case '0': + case '1': + case '2': + case '3': + case '4': + case '5': + case '6': + case '7': + case '8': + case '9': + if (digit_optind != 0 && digit_optind != this_option_optind) + printf ("digits occur in two different argv-elements.\n"); + digit_optind = this_option_optind; + printf ("option %c\n", c); + break; + + case 'a': + printf ("option a\n"); + break; + + case 'b': + printf ("option b\n"); + break; + + case 'c': + printf ("option c with value `%s'\n", optarg); + break; + + case '?': + break; + + default: + printf ("?? getopt returned character code 0%o ??\n", c); + } + } + + if (optind < argc) + { + printf ("non-option ARGV-elements: "); + while (optind < argc) + printf ("%s ", argv[optind++]); + printf ("\n"); + } + + exit (0); +} + +#endif /* TEST */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.h new file mode 100755 index 000000000..b0147e9d2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.h @@ -0,0 +1,169 @@ +/* Declarations for getopt. + Copyright (C) 1989,90,91,92,93,94,96,97,98 Free Software Foundation, Inc. + This file is part of the GNU C Library. + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Library General Public License as + published by the Free Software Foundation; either version 2 of the + License, or (at your option) any later version. + + The GNU C Library is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Library General Public License for more details. + + You should have received a copy of the GNU Library General Public + License along with the GNU C Library; see the file COPYING.LIB. If not, + write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, + Boston, MA 02111-1307, USA. */ + +#ifndef _GETOPT_H + +#ifndef __need_getopt +# define _GETOPT_H 1 +#endif + +#ifdef __cplusplus +extern "C" { +#endif + +/* For communication from `getopt' to the caller. + When `getopt' finds an option that takes an argument, + the argument value is returned here. + Also, when `ordering' is RETURN_IN_ORDER, + each non-option ARGV-element is returned here. */ + +extern char *optarg; + +/* Index in ARGV of the next element to be scanned. + This is used for communication to and from the caller + and for communication between successive calls to `getopt'. + + On entry to `getopt', zero means this is the first call; initialize. + + When `getopt' returns -1, this is the index of the first of the + non-option elements that the caller should itself scan. + + Otherwise, `optind' communicates from one call to the next + how much of ARGV has been scanned so far. */ + +extern int optind; + +/* Callers store zero here to inhibit the error message `getopt' prints + for unrecognized options. */ + +extern int opterr; + +/* Set to an option character which was unrecognized. */ + +extern int optopt; + +#ifndef __need_getopt +/* Describe the long-named options requested by the application. + The LONG_OPTIONS argument to getopt_long or getopt_long_only is a vector + of `struct option' terminated by an element containing a name which is + zero. + + The field `has_arg' is: + no_argument (or 0) if the option does not take an argument, + required_argument (or 1) if the option requires an argument, + optional_argument (or 2) if the option takes an optional argument. + + If the field `flag' is not NULL, it points to a variable that is set + to the value given in the field `val' when the option is found, but + left unchanged if the option is not found. + + To have a long-named option do something other than set an `int' to + a compiled-in constant, such as set a value from `optarg', set the + option's `flag' field to zero and its `val' field to a nonzero + value (the equivalent single-letter option character, if there is + one). For long options that have a zero `flag' field, `getopt' + returns the contents of the `val' field. */ + +struct option +{ +# if defined __STDC__ && __STDC__ + const char *name; +# else + char *name; +# endif + /* has_arg can't be an enum because some compilers complain about + type mismatches in all the code that assumes it is an int. */ + int has_arg; + int *flag; + int val; +}; + +/* Names for the values of the `has_arg' field of `struct option'. */ + +# define no_argument 0 +# define required_argument 1 +# define optional_argument 2 +#endif /* need getopt */ + + +/* Get definitions and prototypes for functions to process the + arguments in ARGV (ARGC of them, minus the program name) for + options given in OPTS. + + Return the option character from OPTS just read. Return -1 when + there are no more options. For unrecognized options, or options + missing arguments, `optopt' is set to the option letter, and '?' is + returned. + + The OPTS string is a list of characters which are recognized option + letters, optionally followed by colons, specifying that that letter + takes an argument, to be placed in `optarg'. + + If a letter in OPTS is followed by two colons, its argument is + optional. This behavior is specific to the GNU `getopt'. + + The argument `--' causes premature termination of argument + scanning, explicitly telling `getopt' that there are no more + options. + + If OPTS begins with `--', then non-option arguments are treated as + arguments to the option '\0'. This behavior is specific to the GNU + `getopt'. */ + +#if defined __STDC__ && __STDC__ +# ifdef __GNU_LIBRARY__ +/* Many other libraries have conflicting prototypes for getopt, with + differences in the consts, in stdlib.h. To avoid compilation + errors, only prototype getopt for the GNU C library. */ +extern int getopt (int __argc, char *const *__argv, const char *__shortopts); +# else /* not __GNU_LIBRARY__ */ +extern int getopt (); +# endif /* __GNU_LIBRARY__ */ + +# ifndef __need_getopt +extern int getopt_long (int __argc, char *const *__argv, const char *__shortopts, + const struct option *__longopts, int *__longind); +extern int getopt_long_only (int __argc, char *const *__argv, + const char *__shortopts, + const struct option *__longopts, int *__longind); + +/* Internal only. Users should not call this directly. */ +extern int _getopt_internal (int __argc, char *const *__argv, + const char *__shortopts, + const struct option *__longopts, int *__longind, + int __long_only); +# endif +#else /* not __STDC__ */ +extern int getopt (); +# ifndef __need_getopt +extern int getopt_long (); +extern int getopt_long_only (); + +extern int _getopt_internal (); +# endif +#endif /* __STDC__ */ + +#ifdef __cplusplus +} +#endif + +/* Make sure we later can get all the definitions and declarations. */ +#undef __need_getopt + +#endif /* getopt.h */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.o new file mode 100755 index 000000000..db55539aa Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt1.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt1.c new file mode 100755 index 000000000..3d264f2db --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt1.c @@ -0,0 +1,188 @@ +/* getopt_long and getopt_long_only entry points for GNU getopt. + Copyright (C) 1987,88,89,90,91,92,93,94,96,97,98 + Free Software Foundation, Inc. + This file is part of the GNU C Library. + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Library General Public License as + published by the Free Software Foundation; either version 2 of the + License, or (at your option) any later version. + + The GNU C Library is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Library General Public License for more details. + + You should have received a copy of the GNU Library General Public + License along with the GNU C Library; see the file COPYING.LIB. If not, + write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, + Boston, MA 02111-1307, USA. */ + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "getopt.h" + +#if !defined __STDC__ || !__STDC__ +/* This is a separate conditional since some stdc systems + reject `defined (const)'. */ +#ifndef const +#define const +#endif +#endif + +#include + +/* Comment out all this code if we are using the GNU C Library, and are not + actually compiling the library itself. This code is part of the GNU C + Library, but also included in many other GNU distributions. Compiling + and linking in this code is a waste when using the GNU C library + (especially if it is a shared library). Rather than having every GNU + program understand `configure --with-gnu-libc' and omit the object files, + it is simpler to just do this in the source for each such file. */ + +#define GETOPT_INTERFACE_VERSION 2 +#if !defined _LIBC && defined __GLIBC__ && __GLIBC__ >= 2 +#include +#if _GNU_GETOPT_INTERFACE_VERSION == GETOPT_INTERFACE_VERSION +#define ELIDE_CODE +#endif +#endif + +#ifndef ELIDE_CODE + + +/* This needs to come after some library #include + to get __GNU_LIBRARY__ defined. */ +#ifdef __GNU_LIBRARY__ +#include +#endif + +#ifndef NULL +#define NULL 0 +#endif + +int +getopt_long (argc, argv, options, long_options, opt_index) + int argc; + char *const *argv; + const char *options; + const struct option *long_options; + int *opt_index; +{ + return _getopt_internal (argc, argv, options, long_options, opt_index, 0); +} + +/* Like getopt_long, but '-' as well as '--' can indicate a long option. + If an option that starts with '-' (not '--') doesn't match a long option, + but does match a short option, it is parsed as a short option + instead. */ + +int +getopt_long_only (argc, argv, options, long_options, opt_index) + int argc; + char *const *argv; + const char *options; + const struct option *long_options; + int *opt_index; +{ + return _getopt_internal (argc, argv, options, long_options, opt_index, 1); +} + + +#endif /* Not ELIDE_CODE. */ + +#ifdef TEST + +#include + +int +main (argc, argv) + int argc; + char **argv; +{ + int c; + int digit_optind = 0; + + while (1) + { + int this_option_optind = optind ? optind : 1; + int option_index = 0; + static struct option long_options[] = + { + {"add", 1, 0, 0}, + {"append", 0, 0, 0}, + {"delete", 1, 0, 0}, + {"verbose", 0, 0, 0}, + {"create", 0, 0, 0}, + {"file", 1, 0, 0}, + {0, 0, 0, 0} + }; + + c = getopt_long (argc, argv, "abc:d:0123456789", + long_options, &option_index); + if (c == -1) + break; + + switch (c) + { + case 0: + printf ("option %s", long_options[option_index].name); + if (optarg) + printf (" with arg %s", optarg); + printf ("\n"); + break; + + case '0': + case '1': + case '2': + case '3': + case '4': + case '5': + case '6': + case '7': + case '8': + case '9': + if (digit_optind != 0 && digit_optind != this_option_optind) + printf ("digits occur in two different argv-elements.\n"); + digit_optind = this_option_optind; + printf ("option %c\n", c); + break; + + case 'a': + printf ("option a\n"); + break; + + case 'b': + printf ("option b\n"); + break; + + case 'c': + printf ("option c with value `%s'\n", optarg); + break; + + case 'd': + printf ("option d with value `%s'\n", optarg); + break; + + case '?': + break; + + default: + printf ("?? getopt returned character code 0%o ??\n", c); + } + } + + if (optind < argc) + { + printf ("non-option ARGV-elements: "); + while (optind < argc) + printf ("%s ", argv[optind++]); + printf ("\n"); + } + + exit (0); +} + +#endif /* TEST */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt1.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt1.o new file mode 100755 index 000000000..7a36c6f5f Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/getopt1.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.c new file mode 100755 index 000000000..2a544812d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.c @@ -0,0 +1,428 @@ +/* + Last changed Time-stamp: <2005-02-18 14:25:33 ivo> + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: globals.c,v 1.5 2005/02/18 13:29:04 ivo Exp $ +*/ + +#include +#include +#include +#include +#include +#include +#include "utils.h" +#include "globals.h" + +/* forward declarations privat functions */ +static void ini_globs(void); +static void ini_gtoggles (void); +static void ini_gvars(void); +static void ini_garrays (void); +static void usage(int status); +static void display_settings(void); +static void display_fileformat(void); +static char *verbose(int optval, const char *which); +static int process_options (int argc, char *argv[]); + +static char UNUSED rcsid[] ="$Id: globals.c,v 1.5 2005/02/18 13:29:04 ivo Exp $"; +#define MAXMSG 8 +static char msg[MAXMSG][60] = +{{"off"}, + {"on"}, + {"current time"}, + {"take from input file"}, + {"open chain"}, + {"mfe structure of sequence"}, + {"ViennaRNA-Package-1.4 defaults"}, + {""} +}; + +static struct option const long_options[] = +{ {"dangle", required_argument, 0, 0}, + {"Temp", required_argument, 0, 0}, + {"Par", required_argument, 0, 0}, + {"logML", no_argument, >V.logML, 0}, + {"noShift", no_argument, >V.noShift, 1}, + {"noLP", no_argument, >V.noLP, 1}, + {"seed", required_argument, 0, 0}, + {"time", required_argument, 0, 0}, + {"num", required_argument, 0, 0}, + {"start", no_argument, >V.start, 1}, + {"stop", no_argument, >V.stop, 1}, + {"fpt", no_argument, >V.fpt, 0}, + {"met", no_argument, >V.mc, 1}, + {"grow", required_argument, 0, 0}, + {"glen", required_argument, 0, 0}, + {"log", required_argument, 0, 0}, + {"silent", no_argument, 0, 0}, + {"lmin", no_argument, >V.lmin, 1}, + {"cut", required_argument, 0, 0}, + {"help", no_argument, 0, 'h'}, + {"verbose", no_argument, 0, 0}, + {NULL, 0, NULL, 0} +}; + +/**/ +void decode_switches(int argc, char *argv[]) { + ini_globs(); + strcpy(GAV.ProgramName, argv[0]); + process_options(argc, argv); +} + +/**/ +void clean_up_globals(void) { + int i; + free(GAV.ProgramName); + free(GAV.ParamFile); + free(GAV.BaseName); + free(GAV.farbe); + free(GAV.farbe_full); + free(GAV.startform); + free(GAV.currform); + free(GAV.prevform); + for (i = 0; i < GSV.maxS; i++) free(GAV.stopform[i]); + free(GAV.stopform); + free(GAV.sE); +} + +/**/ +static void usage(int status) { + fprintf(stderr, "\n%s - Kinetic Folding Program for Nucleic Acids -\n", + GAV.ProgramName); + fprintf(stderr, "Usage: %s [OPTION] < FILE\n", GAV.ProgramName); + fprintf(stderr, + "Options:\n" + " EnergyModel\n" + " --dangle <0|1|2> set dangling end model to (non|normal|double)\n" + " --Temp set simulation temperature to \n" + " --Par use energy-parameter-file \n" + " --logML use linear multiloop-function not logarithmic\n" + " MoveSet\n" + " --noShift turn off shift-moves\n" + " --noLP forbit structures with isolated base-pairs\n" + " Simulation\n" + " --seed set random seed to \n" + " --time set maxtime of simulation to \n" + " --num set number of simulations to \n" + " --start set start structure\n" + " --stop set stop structure(s)\n" + " --met use Metropolis rule not Kawasaki rule\n" + " --fpt stop stop structure(s) is reached\n" + " --grow grow chain every time steps\n" + " Output\n" + " --log set basename of log-file to \n" + " --err set basename of error-log-file to \n" + " --silent no output to stdout\n" + " --verbose more information to stdout\n" + " --lmin output only local minima to stdout\n" + " --cut output structures with E <= to stdout\n"); + display_settings(); + display_fileformat(); + exit (status); +} + +/**/ +static void display_fileformat(void) { + fprintf(stderr, + "Input File Format:\n" + "1st line sequence\n" + "2nd line start structure (if option --start is used)\n" + "following lines stop structures\n\n"); +} + +/**/ +void log_prog_params(FILE *FP) { + fprintf( FP, + "#<\n#Date: %s" + "#EnergyModel: dangle=%d Temp=%.1f logML=%s Par=%s\n" + "#MoveSet: noShift=%s noLP=%s\n" + "#Simulation: num=%d time=%.2f seed=%s fpt=%s mc=%s\n" + "#Output: log=%s silent=%s lmin=%s cut=%.2f\n", + time_stamp(), + GTV.dangle, + GSV.Temp, + verbose(GTV.logML, "logML"), + GAV.ParamFile, + verbose(GTV.noShift, NULL), + verbose(GTV.noLP, NULL), + GSV.num, + GSV.time, + verbose(GTV.seed, "seed"), + verbose(GTV.fpt, NULL), + verbose(GTV.mc, "met"), + GAV.BaseName, + verbose(GTV.silent, NULL), + verbose(GTV.lmin, NULL), + GSV.cut); + fflush(FP); +} + +/**/ +void log_start_stop(FILE *FP) { + int i; + fprintf(FP, "#%s\n#%s (%6.2f)\n", GAV.farbe, GAV.startform, GSV.startE); + for (i = 0; i < GSV.maxS; i++) { + fprintf(FP, "#%s (%6.2f) X%02d\n", GAV.stopform[i], GAV.sE[i], i+1); + } + fprintf(FP, "(%-5hu %5hu %5hu)", GAV.subi[0], GAV.subi[1], GAV.subi[2]); + fflush(FP); +} + +/**/ +static void display_settings(void) { + fprintf(stderr, + "Default Settings:\n" + " EnergyModel\n" + " --dangle = %d\n" + " --Temp = %.2f\n" + " --Par = %s\n" + " --logML = %s\n" + " MoveSet\n" + " --noShift = %s\n" + " --noLP = %s\n" + " Simulation\n" + " --seed = %s\n" + " --time = %.1f\n" + " --num = %d\n" + " --start = %s\n" + " --stop = %s\n" + " --met = %s\n" + " --fpt = %s\n" + " Output\n" + " --log = %s\n" + " --silent = %s\n" + " --verbose = %s\n" + " --lmin = %s\n" + " --cut = %.2f\n", + GTV.dangle, + GSV.Temp, + GAV.ParamFile, + verbose(GTV.logML, "logML"), + verbose(GTV.noShift, NULL), + verbose(GTV.noLP, NULL), + verbose(GTV.seed, "seed"), + GSV.time, + GSV.num, + verbose(GTV.start, "start"), + verbose(GTV.stop, "stop"), + verbose(GTV.mc, "met"), + verbose(GTV.fpt, NULL), + GAV.BaseName, + verbose(GTV.silent, NULL), + verbose(GTV.verbose, NULL), + verbose(GTV.lmin, NULL), + GSV.cut); +} + +/**/ +static char *verbose (int optval, const char *which) { + if (which == NULL) return msg[optval]; + else { + if ( strcmp(which, "seed") == 0 ) { + if (optval == 0 ) return "clock"; + else { + sprintf(msg[MAXMSG - 1], + "%hu %hu %hu", GAV.subi[0], GAV.subi[1],GAV.subi[2]); + return msg[MAXMSG - 1]; + } + } + + if ( strcmp(which, "met") == 0 ) { + if ( optval == 0 ) return "Kawasaki"; + else return "Metropolis"; + } + + if ( strcmp(which, "logML") == 0 ) { + if ( optval == 0 ) return "linear"; + else return "logarithmic"; + } + + if ( strcmp(which, "start") == 0 ) { + if ( optval == 0 ) return "OpenChain"; + else return "input file"; + } + + if ( strcmp(which, "stop") == 0 ) { + if ( optval == 0 ) return "Mfe"; + else return "input file"; + } + } + return "hae?"; +} + +/**/ +static void ini_globs (void) { + ini_gtoggles(); + ini_gvars(); + ini_garrays(); +} + +/**/ +static int process_options (int argc, char *argv[]) { + int c, itmp; + float ftmp; + double dtmp; + int option_index = 0; + while ((c = getopt_long (argc, argv, "h", + long_options, &option_index)) != EOF) { + switch (c) { + case 0: + if (strcmp(long_options[option_index].name,"dangle")==0) { + itmp = -1; + if (sscanf(optarg, "%d", &itmp) == 0) + usage(EXIT_FAILURE); + else if (itmp == 0 || itmp == 1 || itmp == 2 || itmp == 3) + GTV.dangle = itmp; + else { + fprintf(stderr, "Value of --dangle must be 0|1|2 >%d<\n", itmp); + usage (EXIT_FAILURE); + } + } + + if (strcmp(long_options[option_index].name,"Temp")==0) { + ftmp = -1.0; + if (sscanf(optarg, "%f", &ftmp) == 0) + usage(EXIT_FAILURE); + else if ( ftmp >= 0 ) + GSV.Temp = ftmp; + else { + fprintf(stderr, "Value of --Temp must be >= 0 >%.2f<\n", ftmp); + usage (EXIT_FAILURE); + } + } + + if (strcmp(long_options[option_index].name,"Par")==0) { + if (sscanf(optarg, "%s", GAV.ParamFile) == 0) + usage(EXIT_FAILURE); + else { + GTV.Par = 1; + } + } + + if (strcmp(long_options[option_index].name,"silent")==0) { + GTV.silent = 1; + GTV.verbose = 0; + } + + if (strcmp(long_options[option_index].name,"verbose")==0) { + if (GTV.silent == 0) + GTV.verbose = 1; + } + + if (strcmp(long_options[option_index].name,"seed")==0) { + if (sscanf(optarg, "%hu=%hu=%hu", + &GAV.subi[0], &GAV.subi[1], &GAV.subi[2]) == 0) + usage(EXIT_FAILURE); + else GTV.seed = 1; + } + + if (strcmp(long_options[option_index].name,"time")==0) { + dtmp = -1.0; + if (sscanf(optarg, "%lf", &dtmp) == 0) + usage(EXIT_FAILURE); + else if ( dtmp > 0 ) + GSV.time = dtmp; + else { + fprintf(stderr, "Value of --time must be > 0 >%lf<\n", dtmp); + usage(EXIT_FAILURE); + } + } + + if (strcmp(long_options[option_index].name,"num")==0) { + itmp = -1; + if (sscanf(optarg, "%d", &itmp) == 0) + usage(EXIT_FAILURE); + else if ( itmp > 0 ) + GSV.num = itmp; + else { + fprintf(stderr, "Value of --num must be > 0 >%d<\n", itmp); + usage(EXIT_FAILURE); + } + } + + if (strcmp(long_options[option_index].name,"log")==0) + if (sscanf(optarg, "%s", GAV.BaseName) == 0) + usage(EXIT_FAILURE); + + if (strcmp(long_options[option_index].name,"cut")==0) + if (sscanf(optarg, "%f", &GSV.cut) == 0) + usage(EXIT_FAILURE); + + if (strcmp(long_options[option_index].name,"grow")==0) + if (sscanf(optarg, "%lf", &GSV.grow) == 0) + usage(EXIT_FAILURE); + + if (strcmp(long_options[option_index].name,"glen")==0) + if (sscanf(optarg, "%d", &GSV.glen) == 0) + usage(EXIT_FAILURE); + + break; + + case 'h': + usage (0); + default: + usage (EXIT_FAILURE); + } + } + return optind; +} + +/**/ +static void ini_gtoggles(void) { + GTV.Par = 0; + GTV.seed = 0; + GTV.dangle = 2; + GTV.logML = 1; + GTV.noLP = 0; + GTV.noShift = 0; + GTV.start = 0; + GTV.stop = 0; + GTV.silent = 0; + GTV.verbose = 0; + GTV.lmin = 0; + GTV.fpt = 1; + GTV.mc = 0; +} + +/**/ +static void ini_gvars(void) { + GSV.len = 0; + GSV.num = 1; + GSV.maxS = 99; + GSV.cut = 20; + GSV.Temp = 37.0; + GSV.startE = 0.0; + GSV.stopE = 0.0; + GSV.currE = 0.0; + GSV.time = 500.0; + GSV.simTime = 0.0; + GSV.glen = 15; +} + +/**/ +static void ini_garrays(void) { + GAV.ProgramName = (char *)calloc((size_t)256, sizeof(char)); + assert(GAV.ProgramName != NULL); + GAV.ParamFile = (char *)calloc((size_t)256, sizeof(char)); + assert(GAV.ParamFile != NULL); + strcpy(GAV.ParamFile,"VRNA-1.4"); + GAV.BaseName = (char *)calloc((size_t)256, sizeof(char)); + assert(GAV.BaseName != NULL); + strcpy(GAV.BaseName, "kinout"); + GAV.stopform = (char **)calloc(GSV.maxS + 1, sizeof(char *)); + assert(GAV.stopform != NULL); + GAV.farbe = NULL; + GAV.startform = NULL; + GAV.currform = NULL; + GAV.prevform = NULL; +} + +/* End of file */ + + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.h new file mode 100755 index 000000000..a58c0f3c5 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.h @@ -0,0 +1,76 @@ +/* + Last changed Time-stamp: <2005-02-16 13:16:43 ivo> + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: globals.h,v 1.2 2005/02/16 17:00:48 ivo Exp $ +*/ + +#ifndef GLOBDEFS_H +#define GLOBDEFS_H + +#ifdef __GNUC__ +#define UNUSED __attribute__ ((unused)) +#else +#define UNUSED +#endif + +typedef struct _GlobVars { + int len; + int num; + int maxS; + int steps; + float cut; + float Temp; + float startE; + float stopE; + float currE; + double grow; + int glen; + double time; + double simTime; +} GlobVars; + +typedef struct _GlobArrays { + char *ParamFile; + char *ProgramName; + char *BaseName; /* output file basename */ + char *farbe; /* sequence */ + char *farbe_full; /* full sequence (for chain growth simulation) */ + char *startform; /* start structure */ + char **stopform; /* stop structure(s) */ + char *currform; /* current structure */ + char *prevform; /* current structure of previous time step */ + float *sE; /* energy(s) of stop structure(s) */ + unsigned short subi[3]; /* seeds for random-number-generator */ +} GlobArrays; + +typedef struct _GlobToogles { + int Par; + int seed; + int dangle; + int logML; + int noLP; + int noShift; + int start; + int stop; + int silent; + int lmin; + int fpt; + int mc; + int verbose; +} GlobToggles; + +void decode_switches(int argc, char *argv[]); +void clean_up_globals(void); +void log_prog_params(FILE *FP); +void log_start_stop(FILE *FP); + +GlobVars GSV; +GlobArrays GAV; +GlobToggles GTV; + +#endif + + +/* End of file */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.o new file mode 100755 index 000000000..f2a6185de Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/globals.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/main.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/main.c new file mode 100755 index 000000000..8ca00522c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/main.c @@ -0,0 +1,234 @@ +/* + Last changed Time-stamp: <2005-02-18 14:24:41 ivo> + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: main.c,v 1.3 2005/02/18 13:29:04 ivo Exp $ +*/ + +#include +#include +#include +#include +#include +#include +#include "fold_vars.h" +#include "fold.h" +#include "baum.h" +#include "nachbar.h" +#include "cache_util.h" +#include "utils.h" +#include "globals.h" + +static char UNUSED rcsid[] ="$Id: main.c,v 1.3 2005/02/18 13:29:04 ivo Exp $"; +extern void read_parameter_file(const char fname[]); +extern void get_from_cache(cache_entry *c); + +/* PRIVAT FUNCTIONS */ +static void ini_energy_model(void); +static void read_data(void); +static char *getline(FILE *fp); +static void clean_up(void); + +/**/ +int main(int argc, char *argv[]) { + int i; + char * start; + + /* + process command-line optiones + */ + decode_switches(argc, argv); + + /* + initialize energy parameters + */ + ini_energy_model(); + + /* + read input file + */ + read_data(); + + /* + perform GSV.num simulations + */ + + start = strdup(GAV.startform); /* remember startform for next run */ + for (i = 0; i < GSV.num; i++) { + + /* + initialize or reset ringlist to start conditions + */ + if (GSV.grow>0) { + if (strlen(GAV.farbe)>GSV.glen) { + start[GSV.glen] = '\0'; + GAV.farbe[GSV.glen] = '\0'; + strcpy(GAV.startform,start); + strcpy(GAV.currform,start); + GSV.len=GSV.glen; + } + clean_up_rl(); + } + ini_or_reset_rl(); + + /* + perform simulation + */ + for (GSV.steps = 1;; GSV.steps++) { + cache_entry *c; + + /* + take neighbourhood of current structure from cache if there + else generate it from scratch + */ + if ( (c = lookup_cache(GAV.currform)) ) get_from_cache(c); + else move_it(); + + /* + select a structure from neighbourhood of current structure + and make it to the new current structure. + stop simulation if stop condition is met. + */ + if ( sel_nb() > 0 ) break; + + /* if (GSV.grow>0) grow_chain(); */ + } + } + + /* + clean up memory + */ + free(start); + clean_up(); + return(0); +} + +/**/ +static void ini_energy_model(void) { + if ( !GTV.seed ) { + init_rand(); + GAV.subi[0] = xsubi[0]; + GAV.subi[1] = xsubi[1]; + GAV.subi[2] = xsubi[2]; + } + else { + xsubi[0] = GAV.subi[0]; + xsubi[1] = GAV.subi[1]; + xsubi[2] = GAV.subi[2]; + } + logML = GTV.logML; + dangles = GTV.dangle; + temperature = GSV.Temp; + if( GTV.Par ) read_parameter_file(GAV.ParamFile); + update_fold_params(); +} + +/**/ +static void read_data(void) { + char *ctmp, **s; + int i, len; + + /* + read sequence + */ + ctmp = getline(stdin); + len = strlen(ctmp); + GAV.farbe = (char *)calloc(len+1, sizeof(char)); + assert(GAV.farbe != NULL); + sscanf(ctmp, "%s", GAV.farbe); + GSV.len = strlen(GAV.farbe); + for (i = 0; i < len; i++) GAV.farbe[i] = toupper(GAV.farbe[i]); + free (ctmp); + /* allocate some global arrays */ + GAV.currform = (char *)calloc(GSV.len +1, sizeof(char)); + assert(GAV.currform != NULL); + GAV.prevform = (char *)calloc(GSV.len +1, sizeof(char)); + assert(GAV.prevform != NULL); + GAV.startform = (char *)calloc(GSV.len +1, sizeof(char)); + assert(GAV.startform != NULL); + + /* + read start structure + */ + if (GTV.start) { + ctmp = getline(stdin); + len = strlen(ctmp); + sscanf(ctmp, "%s", GAV.startform); + + if (strlen(GAV.startform) != GSV.len) { + fprintf(stderr, + "read_data():\n%s\n%s\n unequal length!\n", + GAV.farbe, GAV.startform); + exit(1); + } + free (ctmp); + } + else { /* start structure is open chain */ + for (i = 0; i< GSV.len; i++) GAV.startform[i] = '.'; + } + + /* + read stop structure(s) + */ + if (GTV.stop) { + s = GAV.stopform; + while (( ctmp = getline(stdin))) { + *s = (char *)calloc(GSV.len+1, sizeof(char)); + sscanf(ctmp, "%s", *s); + + if ( (s-GAV.stopform) >= GSV.maxS ) { + fprintf(stderr, + "WARNING: Can handle a maximum of %d stop structures\n", + GSV.maxS ); + break; + } + + if (strlen(*s) != GSV.len) { + fprintf(stderr, "read_data():\n%s\n%s\n unequal length!\n", + GAV.farbe, *s); + exit(1); + } + + s++; + free (ctmp); + } + GSV.maxS = (s-GAV.stopform); + } + else { + GSV.maxS = 1; + GAV.stopform[0] = (char *)calloc(GSV.len+1, sizeof(char)); + } + + GAV.farbe_full = strdup(GAV.farbe); + + GAV.sE = (float *)calloc(GSV.maxS, sizeof(float)); +} + +/**/ +static char *getline(FILE *fp) { + char s[512], *line, *cp; + + line = NULL; + do { + if (fgets(s, 512, fp) == NULL) break; + cp = strchr(s, '\n'); + if (cp != NULL) *cp = '\0'; + if (line == NULL) { + line = (char *)calloc((strlen(s) + 1), sizeof(char)); + assert(line != NULL); + } + else + line = (char *)realloc(line, strlen(s) + strlen(line) + 1); + strcat(line, s); + } while(cp == NULL); + return(line); +} + +/**/ +void clean_up(void) { + clean_up_globals(); + clean_up_rl(); + clean_up_nbList(); + kill_cache(); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/main.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/main.o new file mode 100755 index 000000000..48988d33b Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/main.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/nachbar.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/nachbar.c new file mode 100755 index 000000000..cecde545a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/nachbar.c @@ -0,0 +1,330 @@ +/* + Last changed Time-stamp: <2006-01-16 11:28:43 ivo> + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: nachbar.c,v 1.6 2006/01/16 10:38:11 ivo Exp $ +*/ + +#include +#include +#include +#include +#include +#include +#include +#include "globals.h" +#include "assert.h" +#include "fold_vars.h" +#include "energy_const.h" +#include "utils.h" +#include "cache_util.h" +#include "baum.h" + +static char UNUSED rcsid[]="$Id: nachbar.c,v 1.6 2006/01/16 10:38:11 ivo Exp $"; + +/* arrays */ +static short *neighbor_list=NULL; +static float *bmf; /* boltzmann weight of structure */ + +/* variables */ +/* static double highestE = -1000.0; */ +/* static double OhighestE = -1000.0; */ +/* static char *highestS, *OhighestS; */ +static int lmin = 1; +static int top = 0; +static int is_from_cache = 0; +/* static double meanE = 0.0; */ +static double totalflux = 0.0; +static double Zeit = 0.0; +static double zeitInc = 0.0; +static double _RT = 0.6; + +/* public functiones */ +void ini_nbList(int chords); +void update_nbList(int i, int j, int iE); +int sel_nb(void); +void clean_up_nbList(void); +extern void update_tree(int i, int j); + +/* privat functiones */ +static void reset_nbList(void); +static void grow_chain(void); +static FILE *logFP=NULL; + +/**/ +void ini_nbList(int chords) { + char logFN[256]; + + _RT = (((temperature + K0) * GASCONST) / 1000.0); + if (neighbor_list!=NULL) return; + /* + list for move coding + make room for 2*chords neighbors (safe bet) + */ + if (chords == 0) chords = 1; + neighbor_list = (short *)calloc(4*chords, sizeof(short)); + assert(neighbor_list != NULL); + /* + list for Boltzmann-factors + */ + bmf = (float *)calloc(2*chords, sizeof(double)); + assert(bmf != NULL); + + /* open log-file */ + logFP = fopen(strcat(strcpy(logFN, GAV.BaseName), ".log"), "a+"); + assert(logFP != NULL); + + /* log initial condition */ + log_prog_params(logFP); + log_start_stop(logFP); +} + +/**/ +void update_nbList(int i, int j, int iE) { + double E, dE, p; + + E = (double)iE/100.; + neighbor_list[2*top] = (short )i; + neighbor_list[2*top+1] = (short )j; + + /* compute rates and some statistics */ + /* meanE += E; */ + dE = E-GSV.currE; + if( GTV.mc ) { + /* metropolis rule */ + if (dE < 0) p = 1; + else p = exp(-(dE / _RT)); + } + else /* kawasaki rule */ + p = exp(-0.5 * (dE / _RT)); + + totalflux += p; + bmf[top++] = (float )p; + if (dE < 0) lmin = 0; + if ((dE == 0) && (lmin==1)) lmin = 2; +} + +/**/ +void get_from_cache(cache_entry *c) { + top = c->top; + totalflux = c->flux; + GSV.currE = c->energy; + lmin = c->lmin; + memcpy(neighbor_list, c->neighbors, 2*top*sizeof(short)); + memcpy(bmf, c->rates, top*sizeof(float)); + is_from_cache = 1; +} + +/**/ +void put_in_cache(void) { + cache_entry *c; + + if ((c = (cache_entry *) malloc(sizeof(cache_entry)))==NULL) { + fprintf(stderr, "out of memory\n"); exit(255); + } +/* c->structure = strdup(GAV.currform); */ + c->structure = (char *) calloc(GSV.len+1, sizeof(char)); + strcpy(c->structure, GAV.currform); + c->neighbors = (short *) malloc(top*2*sizeof(short)); + memcpy(c->neighbors,neighbor_list,top*2*sizeof(short)); + c->rates = (float *) malloc(top*sizeof(float)); + memcpy(c->rates, bmf, top*sizeof(float)); + c->top = top; + c->lmin = lmin; + c->flux = totalflux; + c->energy = GSV.currE; + write_cache(c); +} + +/*============*/ + +int sel_nb(void) { + + char trans, **s; + int next; + double pegel = 0.0, schwelle = 0.0, zufall = 0.0; + int found_stop=0; + + /* before we select a move, store current conformation in cache */ + /* ... unless it just came from there */ + if ( !is_from_cache ) put_in_cache(); + is_from_cache = 0; + + /* draw 2 different a random number */ + schwelle = urn(); + while ( zufall==0 ) zufall = urn(); + + /* advance internal clock */ + if (totalflux>0) + zeitInc = (log(1. / zufall) / totalflux); + else { + if (GSV.grow>0) zeitInc=GSV.grow; + else zeitInc = GSV.time; + } + + Zeit += zeitInc; + if (GSV.grow>0 && GSV.len < strlen(GAV.farbe_full)) grow_chain(); + + /* meanE /= (double)top; */ + + /* normalize boltzmann weights */ + schwelle *=totalflux; + + /* and choose a neighbour structure next */ + for (next = 0; next < top; next++) { + pegel += bmf[next]; + if (pegel > schwelle) break; + } + + /* in case of rounding errors */ + if (next==top) next=top-1; + + /* + process termination contitiones + */ + /* is current structure identical to a stop structure ?*/ + for (found_stop = 0, s = GAV.stopform; *s; s++) { + if (strcmp(*s, GAV.currform) == 0) { + found_stop = (s - GAV.stopform) + 1; + break; + } + } + + if ( ((found_stop > 0) && (GTV.fpt == 1)) || (Zeit > GSV.time) ) { + /* met condition to stop simulation */ + + /* this gose to stdout */ + if ( !GTV.silent ) { + printf("%s %6.2f %10.3f", GAV.currform, GSV.currE, Zeit); + if ( GTV.verbose ) printf("%4d _ %d", top, lmin); + if (found_stop) printf(" X%d\n", found_stop);/* found a stop structure */ + else printf(" O\n"); /* time for simulation is exceeded */ + fflush(stdout); + } + + /* this goes to log */ + /* comment log steps of simulation as well !!! %6.2f round */ + if ( found_stop ) fprintf(logFP," X%02d %12.3f\n", found_stop, Zeit); + else fprintf(logFP," O %12.3f %d %s\n", Zeit, lmin, GAV.currform); + GAV.subi[0] = xsubi[0]; + GAV.subi[1] = xsubi[1]; + GAV.subi[2] = xsubi[2]; + fprintf(logFP, "(%5hu %5hu %5hu)", GAV.subi[0], GAV.subi[1], GAV.subi[2]); + fflush(logFP); + + Zeit = 0.0; + /* highestE = OhighestE = -1000.0; */ + reset_nbList(); + return(1); + } + else { + /* continue simulation */ + int flag = 0; + if( (!GTV.silent) && (GSV.currE <= GSV.stopE+GSV.cut) ) { + if (!GTV.lmin || (lmin==1 && strcmp(GAV.prevform, GAV.currform) != 0)) { + char format[64]; + flag = 1; + sprintf(format, "%%-%ds %%6.2f %%10.3f", strlen(GAV.farbe_full)); + printf(format, GAV.currform, GSV.currE, Zeit); + } + if ( flag && GTV.verbose ) { + int ii, jj; + if (next<0) trans='g'; /* growth */ + else { + ii = neighbor_list[2*next]; + jj = neighbor_list[2*next+1]; + if (abs(ii) < GSV.len) { + if ((ii > 0) && (jj > 0)) trans = 'i'; + else if ((ii < 0) && (jj < 0)) trans = 'd'; + else if ((ii > 0) && (jj < 0)) trans = 's'; + else trans = 'S'; + } else { + if ((ii > 0) && (jj > 0)) trans = 'I'; + else trans = 'D'; + } + } + printf("%4d %c %d", top, trans, lmin); + } + if (flag) printf("\n"); + } + } + + + /* store last lmin seen, so we can avoid printing the same lmin twice */ + if (lmin==1) + strcpy(GAV.prevform, GAV.currform); + +#if 0 + if (lmin==1) { + /* went back to previous lmin */ + if (strcmp(GAV.prevform, GAV.currform) == 0) { + if (OhighestE < highestE) { + highestE = OhighestE; /* delete loop */ + strcpy(highestS, OhighestS); + } + } else { + strcpy(GAV.prevform, GAV.currform); + OhighestE = 10000.; + } + } + + if ( strcmp(GAV.currform, GAV.startform)==0 ) { + OhighestE = highestE = -1000.; + highestS[0] = 0; + } + + /* log highes energy */ + if (GSV.currE > highestE) { + OhighestE = highestE; + highestE = GSV.currE; + strcpy(OhighestS, highestS); + strcpy(highestS, GAV.currform); + } +#endif + + if (next>=0) update_tree(neighbor_list[2*next], neighbor_list[2*next+1]); + else { + clean_up_rl(); ini_or_reset_rl(); + } + + reset_nbList(); + return(0); +} + +/*==========================*/ +static void reset_nbList(void) { + + top = 0; + totalflux = 0.0; + /* meanE = 0.0; */ + lmin = 1; +} + +/*======================*/ +void clean_up_nbList(void){ + + free(neighbor_list); + free(bmf); + fprintf(logFP,"\n"); + fclose(logFP); +} + +/*======================*/ +static void grow_chain(void){ + int newl; + /* note Zeit=0 corresponds to chain length GSV.glen */ + if (Zeit<(GSV.len+1-GSV.glen) * GSV.grow) return; + newl = GSV.len+1; + Zeit = (newl-GSV.glen) * GSV.grow; + top=0; /* prevent structure move in sel_nb */ + + if (GSV.len + c Christoph Flamm and Ivo L Hofacker + {xtof,ivo}@tbi.univie.ac.at + Kinfold: $Name: $ + $Id: nachbar.h,v 1.2 2005/02/16 17:00:48 ivo Exp $ +*/ + +#ifndef NACHBAR_H +#define NACHBAR_H + +/* used in baum.c */ +extern void ini_nbList(int chords); +extern void update_nbList(int i,int j, int iE); + +/* used in main.c */ +extern int sel_nb(void); +extern void clean_up_nbList(void); + +extern void grow_chain(void); +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/nachbar.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/nachbar.o new file mode 100755 index 000000000..1ebb04335 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/nachbar.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/stamp-h1 b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/stamp-h1 new file mode 100755 index 000000000..4547fe1b5 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Kinfold/stamp-h1 @@ -0,0 +1 @@ +timestamp for config.h diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Makefile new file mode 100755 index 000000000..f5afa2b30 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Makefile @@ -0,0 +1,635 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# Makefile. 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RNAforester was written by Matthias + Hoechsmann +- The Kinfold program for stochastic simulation of folding trajectories is + no included in the package, see the Kinfold subdirectory. +- cofolding of two structures now supports suboptimal folding and + partition function folding (still experimental). + ATTENTION: Energies of hybrid structures now inlcude the Duplex-initiation + energy, which was neglected in previous version. +- RNAplfold is a partition function variant of RNALfold. It computes the + mean probability of a (local) base pair averaged over all sequence + windows that contain the pair. +- new utilities to color alignments and consensus structures + +Version 1.5pre +----------- +- ViennaRNA now uses autoconfig generated configure scripts for even better + portability (should compile on any UNIX, Linux, MacOS X, Windows with + Cygwin). +- The new RNAalifold program predicts consensus structures for a set of + aligned sequences. +- Complete suboptimal folding is now integrated in the library. +- Beginning support for co-folding of two strands: energy_of_struct() and + RNAeval can now compute energies of duplex structures. +- RNAcofold predicts hybrid structures of two RNA strands +- RNAduplex predicts hybrid structures, while allowing only inter-molecular + base pairs (useful for finding potential binding sites) +- RNALfold predicts locally stable structures in long sequences. +- Major changes to Perl module. See the pod documentation (perldoc RNA). +- RNAsubopt can do stochastic backtracking to produce samples of suboptimal + structures with Boltzmann statistics. +- New utilities to rotate secondary structure plots and annotate them with + reliability data. +- Various small bug fixes + +Version 1.4 +----------- +- New Turner parameters as described in Mathews et.al. JMB v288, 1999. + Small changes to format of parameter files (old param files won't work!) +- mfe and suboptimal folding will produce only structures without isolated + pairs if noLonelyPairs=1 (-noLP option), for partition function folding + pairs that can only occur as isolated pairs are not formed. +- setting dangles=3 (-d3 option) will allow co-axial stacking of adjacent + helices in mfe folding and energy_of_struct(). + +Version 1.3.1 +------------- +- RNAheat would produce spikes in the specific heat because dangling end + energies did not go smoothly to 0. +- PS dot plots now have an option to use a log scale (edit _dp.ps file + and set logscale to true). + +Version 1.3 +----------- +- Secondary structure plots now use E. Bruccoleri's naview routines for + layout by default. New utility RNAplot produces secondary structure plots + from structures in bracket notation with several options. +- New -d2 option in RNAfold and RNAeval sets dangles=2, which makes + energy_of_struct() and fold() treat dangling ends as in pf_fold(). + -noLP option in RNAfold etc sets noLonelyPairs=1, which avoids most + structures containing lonely base pairs (helices of length 1). +- new utility functions pack_structure() unpack_structure() make_pair_table() + and bp_distance(). RNAdistance adds bp_distance() via -DP switch. +- First release of RNAsubopt for complete suboptimal folding. +- fixed bug in asymmetry penalty for interior loops. +- Default compilation now uses doubles for partition function folding. + +Version 1.2.1 +------------- +- Fixed bug in version 1.2 of the RNAheat program causing overflow errors + for most input sequences. +- The PS_dot_plot() and PS_rna_plot() routines now return an int. The return + value is 0 if the file could not be written, 1 otherwise. +- This version contains the alpha version of a perl5 module, which let's you + access all the capabilities of the Vienna RNA library from perl scripts. + +Version 1.2 +----------- +- New energy parameters from (Walter et.al 1994). +- Energy parameters can be read from file. +- RNAeval and energy_of_struct() support logarithmic energy function for + multi-loops. +- gmlRNA() produces secondary structure drawing in gml (Graph Meta Language). +- Many bug fixes. diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile new file mode 100755 index 000000000..e40112b09 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile @@ -0,0 +1,319 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# Perl/Makefile. Generated from Makefile.in by configure. + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005 Free Software Foundation, Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + + +SOURCES = RNA.i ptr2array.i Makefile.PL + +srcdir = . +top_srcdir = .. + +pkgdatadir = $(datadir)/ViennaRNA +pkglibdir = $(libdir)/ViennaRNA +pkgincludedir = $(includedir)/ViennaRNA +top_builddir = .. +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +INSTALL = /usr/bin/install -c +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +build_triplet = x86_64-unknown-linux-gnu +host_triplet = x86_64-unknown-linux-gnu +subdir = Perl +DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.in +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_CLEAN_FILES = +DIST_SOURCES = +DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) +ACLOCAL = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run aclocal-1.9 +AMDEP_FALSE = # +AMDEP_TRUE = +AMTAR = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run tar +AUTOCONF = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run autoconf +AUTOHEADER = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run autoheader +AUTOMAKE = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run automake-1.9 +AWK = gawk +CC = gcc +CCDEPMODE = depmode=gcc3 +CFLAGS = -g -O2 +CPP = gcc -E +CPPFLAGS = +CYGPATH_W = echo +DEFS = -DHAVE_CONFIG_H +DEPDIR = .deps +ECHO_C = +ECHO_N = -n +ECHO_T = +EGREP = grep -E +EXEEXT = +INSTALL_DATA = ${INSTALL} -m 644 +INSTALL_PROGRAM = ${INSTALL} +INSTALL_SCRIPT = ${INSTALL} +INSTALL_STRIP_PROGRAM = ${SHELL} $(install_sh) -c -s +ISODATE = 2006-06-13 +LDFLAGS = +LIBOBJS = +LIBS = +LTLIBOBJS = +MAKEINFO = ${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/missing --run makeinfo +MAKE_CLUSTER_FALSE = +MAKE_CLUSTER_TRUE = # +MAKE_FORESTER_FALSE = # +MAKE_FORESTER_TRUE = +MAKE_KINFOLD_FALSE = # +MAKE_KINFOLD_TRUE = +MAKE_PERL_EXT_FALSE = # +MAKE_PERL_EXT_TRUE = +OBJEXT = o +PACKAGE = ViennaRNA +PACKAGE_BUGREPORT = rna@tbi.univie.ac.at +PACKAGE_NAME = ViennaRNA +PACKAGE_STRING = ViennaRNA 1.6 +PACKAGE_TARNAME = ViennaRNA +PACKAGE_VERSION = 1.6 +PATH_SEPARATOR = : +PerlCmd = /usr/bin/perl +RANLIB = ranlib +SET_MAKE = +SHELL = /bin/sh +STRIP = +VERSION = 1.6 +ac_ct_CC = gcc +ac_ct_RANLIB = ranlib +ac_ct_STRIP = +am__fastdepCC_FALSE = # +am__fastdepCC_TRUE = +am__include = include +am__leading_dot = . +am__quote = +am__tar = ${AMTAR} chof - "$$tardir" +am__untar = ${AMTAR} xf - +bindir = ${exec_prefix}/bin +build = x86_64-unknown-linux-gnu +build_alias = +build_cpu = x86_64 +build_os = linux-gnu +build_vendor = unknown +datadir = ${prefix}/share +exec_prefix = ${prefix} +host = x86_64-unknown-linux-gnu +host_alias = +host_cpu = x86_64 +host_os = linux-gnu +host_vendor = unknown +includedir = ${prefix}/include +infodir = ${prefix}/info +install_sh = /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/install-sh +libdir = ${exec_prefix}/lib +libexecdir = ${exec_prefix}/libexec +localstatedir = ${prefix}/var +mandir = ${prefix}/man +mkdir_p = mkdir -p -- +oldincludedir = /usr/include +prefix = /usr/local +program_transform_name = s,x,x, +sbindir = ${exec_prefix}/sbin +sharedstatedir = ${prefix}/com +subdirs = RNAforester Kinfold +sysconfdir = ${prefix}/etc +target_alias = +SOURCES = RNA.i ptr2array.i Makefile.PL +EXTRA_DIST = RNA.pm RNA_wrap.c RNAfold.pl test.pl RNAfold.cgi RNA.i Makefile.PL +all: all-am + +.SUFFIXES: +$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) + @for dep in $?; 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s/SWIGTYPE_p_unsigned_short/SWIGTYPE_p_short/' RNA_wrap.c + +all-local: RNA_wrap.c Makefile.perl + $(MAKE) -f Makefile.perl + +install-exec-local: all-local + $(MAKE) -f Makefile.perl install + +check-local: all-local + $(MAKE) -f Makefile.perl test + +mostlyclean-local: Makefile.perl + $(MAKE) -f Makefile.perl clean +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.PL b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.PL new file mode 100755 index 000000000..bb18cfc69 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.PL @@ -0,0 +1,12 @@ +# File : Makefile.PL +use ExtUtils::MakeMaker; +WriteMakefile( + MAKEFILE => "Makefile.perl", + NAME => "RNA", + LIBS => ["-lm"], + MYEXTLIB => "../lib/libRNA.a", + PM => {"RNA.pm", '$(INST_LIBDIR)/RNA.pm'}, + OBJECT => "RNA_wrap.o", + AUTHOR => 'Ivo Hofacker ', + VERSION => 0.2 +); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.am b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.am new file mode 100755 index 000000000..a6a1474a3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.am @@ -0,0 +1,23 @@ +SOURCES = RNA.i ptr2array.i Makefile.PL + +EXTRA_DIST = RNA.pm RNA_wrap.c RNAfold.pl test.pl RNAfold.cgi RNA.i Makefile.PL + +Makefile.perl: Makefile.PL Makefile + @PerlCmd@ Makefile.PL + +# the perl command repairs some errors in the SWIG CVS version +RNA_wrap.c: RNA.i + swig -perl5 -shadow RNA.i +# @PerlCmd@ -i -npe 's/\A\s+\;\s+\Z//; s/SWIGTYPE_p_unsigned_short/SWIGTYPE_p_short/' RNA_wrap.c + +all-local: RNA_wrap.c Makefile.perl + $(MAKE) -f Makefile.perl + +install-exec-local: all-local + $(MAKE) -f Makefile.perl install + +check-local: all-local + $(MAKE) -f Makefile.perl test + +mostlyclean-local: Makefile.perl + $(MAKE) -f Makefile.perl clean diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.in new file mode 100755 index 000000000..0acb53e40 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.in @@ -0,0 +1,319 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005 Free Software Foundation, Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +@SET_MAKE@ +SOURCES = RNA.i ptr2array.i Makefile.PL + +srcdir = @srcdir@ +top_srcdir = @top_srcdir@ +VPATH = @srcdir@ +pkgdatadir = $(datadir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkgincludedir = $(includedir)/@PACKAGE@ +top_builddir = .. +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +INSTALL = @INSTALL@ +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +build_triplet = @build@ +host_triplet = @host@ +subdir = Perl +DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.in +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_CLEAN_FILES = +DIST_SOURCES = +DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) +ACLOCAL = @ACLOCAL@ +AMDEP_FALSE = @AMDEP_FALSE@ +AMDEP_TRUE = @AMDEP_TRUE@ +AMTAR = @AMTAR@ +AUTOCONF = @AUTOCONF@ +AUTOHEADER = @AUTOHEADER@ +AUTOMAKE = @AUTOMAKE@ +AWK = @AWK@ +CC = @CC@ +CCDEPMODE = @CCDEPMODE@ +CFLAGS = @CFLAGS@ +CPP = @CPP@ +CPPFLAGS = @CPPFLAGS@ +CYGPATH_W = @CYGPATH_W@ +DEFS = @DEFS@ +DEPDIR = @DEPDIR@ +ECHO_C = @ECHO_C@ +ECHO_N = @ECHO_N@ +ECHO_T = @ECHO_T@ +EGREP = @EGREP@ +EXEEXT = @EXEEXT@ +INSTALL_DATA = @INSTALL_DATA@ +INSTALL_PROGRAM = @INSTALL_PROGRAM@ +INSTALL_SCRIPT = @INSTALL_SCRIPT@ +INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@ +ISODATE = @ISODATE@ +LDFLAGS = @LDFLAGS@ +LIBOBJS = @LIBOBJS@ +LIBS = @LIBS@ +LTLIBOBJS = @LTLIBOBJS@ +MAKEINFO = @MAKEINFO@ +MAKE_CLUSTER_FALSE = @MAKE_CLUSTER_FALSE@ +MAKE_CLUSTER_TRUE = @MAKE_CLUSTER_TRUE@ +MAKE_FORESTER_FALSE = @MAKE_FORESTER_FALSE@ +MAKE_FORESTER_TRUE = @MAKE_FORESTER_TRUE@ +MAKE_KINFOLD_FALSE = @MAKE_KINFOLD_FALSE@ +MAKE_KINFOLD_TRUE = @MAKE_KINFOLD_TRUE@ +MAKE_PERL_EXT_FALSE = @MAKE_PERL_EXT_FALSE@ +MAKE_PERL_EXT_TRUE = @MAKE_PERL_EXT_TRUE@ +OBJEXT = @OBJEXT@ +PACKAGE = @PACKAGE@ +PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ +PACKAGE_NAME = @PACKAGE_NAME@ +PACKAGE_STRING = @PACKAGE_STRING@ +PACKAGE_TARNAME = @PACKAGE_TARNAME@ +PACKAGE_VERSION = @PACKAGE_VERSION@ +PATH_SEPARATOR = @PATH_SEPARATOR@ +PerlCmd = @PerlCmd@ +RANLIB = @RANLIB@ +SET_MAKE = @SET_MAKE@ +SHELL = @SHELL@ +STRIP = @STRIP@ +VERSION = @VERSION@ +ac_ct_CC = @ac_ct_CC@ +ac_ct_RANLIB = @ac_ct_RANLIB@ +ac_ct_STRIP = @ac_ct_STRIP@ +am__fastdepCC_FALSE = @am__fastdepCC_FALSE@ +am__fastdepCC_TRUE = @am__fastdepCC_TRUE@ +am__include = @am__include@ +am__leading_dot = @am__leading_dot@ +am__quote = @am__quote@ +am__tar = @am__tar@ +am__untar = @am__untar@ +bindir = @bindir@ +build = @build@ +build_alias = @build_alias@ +build_cpu = @build_cpu@ +build_os = @build_os@ +build_vendor = @build_vendor@ +datadir = @datadir@ +exec_prefix = @exec_prefix@ +host = @host@ +host_alias = @host_alias@ +host_cpu = @host_cpu@ +host_os = @host_os@ +host_vendor = @host_vendor@ +includedir = @includedir@ +infodir = @infodir@ +install_sh = @install_sh@ +libdir = @libdir@ +libexecdir = @libexecdir@ +localstatedir = @localstatedir@ +mandir = @mandir@ +mkdir_p = @mkdir_p@ +oldincludedir = @oldincludedir@ +prefix = @prefix@ +program_transform_name = @program_transform_name@ +sbindir = @sbindir@ +sharedstatedir = @sharedstatedir@ +subdirs = @subdirs@ +sysconfdir = @sysconfdir@ +target_alias = @target_alias@ +SOURCES = RNA.i ptr2array.i Makefile.PL +EXTRA_DIST = RNA.pm RNA_wrap.c RNAfold.pl test.pl RNAfold.cgi RNA.i Makefile.PL +all: all-am + +.SUFFIXES: +$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) + @for dep in $?; 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s/SWIGTYPE_p_unsigned_short/SWIGTYPE_p_short/' RNA_wrap.c + +all-local: RNA_wrap.c Makefile.perl + $(MAKE) -f Makefile.perl + +install-exec-local: all-local + $(MAKE) -f Makefile.perl install + +check-local: all-local + $(MAKE) -f Makefile.perl test + +mostlyclean-local: Makefile.perl + $(MAKE) -f Makefile.perl clean +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.perl b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.perl new file mode 100755 index 000000000..a8492194d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/Makefile.perl @@ -0,0 +1,830 @@ +# This Makefile is for the RNA extension to perl. +# +# It was generated automatically by MakeMaker version +# 6.03 (Revision: 1.63) from the contents of +# Makefile.PL. Don't edit this file, edit Makefile.PL instead. +# +# ANY CHANGES MADE HERE WILL BE LOST! +# +# MakeMaker ARGV: () +# +# MakeMaker Parameters: + +# AUTHOR => q[Ivo Hofacker ] +# LIBS => [q[-lm]] +# MAKEFILE => q[Makefile.perl] +# MYEXTLIB => q[../lib/libRNA.a] +# NAME => q[RNA] +# OBJECT => q[RNA_wrap.o] +# PM => { RNA.pm=>q[$(INST_LIBDIR)/RNA.pm] } +# VERSION => q[0.2] + +# --- MakeMaker post_initialize section: + + +# --- MakeMaker const_config section: + +# These definitions are from config.sh (via /usr/lib/perl5/5.8.0/i386-linux-thread-multi/Config.pm) + +# They may have been overridden via Makefile.PL or on the command line +AR = ar +CC = gcc +CCCDLFLAGS = -fPIC +CCDLFLAGS = -rdynamic -Wl,-rpath,/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE +DLEXT = so +DLSRC = dl_dlopen.xs +LD = gcc +LDDLFLAGS = -shared -L/usr/local/lib +LDFLAGS = -L/usr/local/lib +LIBC = /lib/libc-2.3.2.so +LIB_EXT = .a +OBJ_EXT = .o +OSNAME = linux +OSVERS = 2.4.21-23.elsmp +RANLIB = : +SO = so +EXE_EXT = +FULL_AR = /usr/bin/ar + + +# --- MakeMaker constants section: +AR_STATIC_ARGS = cr +NAME = RNA +DISTNAME = RNA +NAME_SYM = RNA +VERSION = 0.2 +VERSION_SYM = 0_2 +XS_VERSION = 0.2 +INST_ARCHLIB = blib/arch +INST_SCRIPT = blib/script +INST_BIN = blib/bin +INST_LIB = blib/lib +INSTALLDIRS = site +PREFIX = /usr +SITEPREFIX = /usr +VENDORPREFIX = /usr +INSTALLPRIVLIB = /usr/lib/perl5/5.8.0 +INSTALLSITELIB = /usr/lib/perl5/site_perl/5.8.0 +INSTALLVENDORLIB = /usr/lib/perl5/vendor_perl/5.8.0 +INSTALLARCHLIB = /usr/lib/perl5/5.8.0/i386-linux-thread-multi +INSTALLSITEARCH = /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi +INSTALLVENDORARCH = /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi +INSTALLBIN = /usr/bin +INSTALLSITEBIN = /usr/bin +INSTALLVENDORBIN = /usr/bin +INSTALLSCRIPT = /usr/bin +PERL_LIB = /usr/lib/perl5/5.8.0 +PERL_ARCHLIB = /usr/lib/perl5/5.8.0/i386-linux-thread-multi +SITELIBEXP = /usr/lib/perl5/site_perl/5.8.0 +SITEARCHEXP = /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi +LIBPERL_A = libperl.a +MYEXTLIB = ../lib/libRNA.a +FIRST_MAKEFILE = Makefile +MAKE_APERL_FILE = Makefile.aperl +PERLMAINCC = $(CC) +PERL_INC = /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE +PERL = /usr/bin/perl +FULLPERL = /usr/bin/perl +PERLRUN = $(PERL) +FULLPERLRUN = $(FULLPERL) +PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +ABSPERL = $(PERL) +ABSPERLRUN = $(ABSPERL) +ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +FULL_AR = /usr/bin/ar +PERL_CORE = 0 +NOOP = $(SHELL) -c true +NOECHO = @ + +VERSION_MACRO = VERSION +DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\" +XS_VERSION_MACRO = XS_VERSION +XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\" +PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc + +MAKEMAKER = /usr/lib/perl5/5.8.0/ExtUtils/MakeMaker.pm +MM_VERSION = 6.03 + +# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle). +# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle) +# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar) +# DLBASE = Basename part of dynamic library. May be just equal BASEEXT. +FULLEXT = RNA +BASEEXT = RNA +PARENT_NAME = +DLBASE = $(BASEEXT) +OBJECT = RNA_wrap$(OBJ_EXT) +LDFROM = $(OBJECT) +LINKTYPE = dynamic + +# Handy lists of source code files: +XS_FILES= +C_FILES = RNA_wrap.c +O_FILES = RNA_wrap.o +H_FILES = +MAN1PODS = +MAN3PODS = RNA.pm +INST_MAN1DIR = blib/man1 +MAN1EXT = 1 +INSTALLMAN1DIR = /usr/share/man/man1 +INSTALLSITEMAN1DIR = /usr/share/man/man1 +INSTALLVENDORMAN1DIR = /usr/share/man/man1 +INST_MAN3DIR = blib/man3 +MAN3EXT = 3pm +INSTALLMAN3DIR = /usr/share/man/man3 +INSTALLSITEMAN3DIR = /usr/share/man/man3 +INSTALLVENDORMAN3DIR = /usr/share/man/man3 +PERM_RW = 644 +PERM_RWX = 755 + +# work around a famous dec-osf make(1) feature(?): +makemakerdflt: all + +.SUFFIXES: .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT) + +# Nick wanted to get rid of .PRECIOUS. I don't remember why. I seem to recall, that +# some make implementations will delete the Makefile when we rebuild it. Because +# we call false(1) when we rebuild it. So make(1) is not completely wrong when it +# does so. Our milage may vary. +# .PRECIOUS: Makefile # seems to be not necessary anymore + +.PHONY: all config static dynamic test linkext manifest + +# Where is the Config information that we are using/depend on +CONFIGDEP = $(PERL_ARCHLIB)/Config.pm $(PERL_INC)/config.h + +# Where to put things: +INST_LIBDIR = $(INST_LIB) +INST_ARCHLIBDIR = $(INST_ARCHLIB) + +INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT) +INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT) + +INST_STATIC = $(INST_ARCHAUTODIR)/$(BASEEXT)$(LIB_EXT) +INST_DYNAMIC = $(INST_ARCHAUTODIR)/$(DLBASE).$(DLEXT) +INST_BOOT = $(INST_ARCHAUTODIR)/$(BASEEXT).bs + +EXPORT_LIST = + +PERL_ARCHIVE = + +PERL_ARCHIVE_AFTER = + +TO_INST_PM = RNA.pm + +PM_TO_BLIB = RNA.pm \ + $(INST_LIBDIR)/RNA.pm + + +# --- MakeMaker tool_autosplit section: +# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto +AUTOSPLITFILE = $(PERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1) ;' + + + +# --- MakeMaker tool_xsubpp section: + +XSUBPPDIR = /usr/lib/perl5/5.8.0/ExtUtils +XSUBPP = $(XSUBPPDIR)/xsubpp +XSPROTOARG = +XSUBPPDEPS = $(XSUBPPDIR)/typemap $(XSUBPP) +XSUBPPARGS = -typemap $(XSUBPPDIR)/typemap +XSUBPP_EXTRA_ARGS = + + +# --- MakeMaker tools_other section: + +SHELL = /bin/sh +CHMOD = chmod +CP = cp +LD = gcc +MV = mv +NOOP = $(SHELL) -c true +RM_F = rm -f +RM_RF = rm -rf +TEST_F = test -f +TOUCH = touch +UMASK_NULL = umask 0 +DEV_NULL = > /dev/null 2>&1 + +# The following is a portable way to say mkdir -p +# To see which directories are created, change the if 0 to if 1 +MKPATH = $(PERLRUN) "-MExtUtils::Command" -e mkpath + +# This helps us to minimize the effect of the .exists files A yet +# better solution would be to have a stable file in the perl +# distribution with a timestamp of zero. But this solution doesn't +# need any changes to the core distribution and works with older perls +EQUALIZE_TIMESTAMP = $(PERLRUN) "-MExtUtils::Command" -e eqtime + +# Here we warn users that an old packlist file was found somewhere, +# and that they should call some uninstall routine +WARN_IF_OLD_PACKLIST = $(PERL) -we 'exit unless -f $$ARGV[0];' \ +-e 'print "WARNING: I have found an old package in\n";' \ +-e 'print "\t$$ARGV[0].\n";' \ +-e 'print "Please make sure the two installations are not conflicting\n";' + +UNINST=0 +VERBINST=0 + +MOD_INSTALL = $(PERL) "-I$(INST_LIB)" "-I$(PERL_LIB)" "-MExtUtils::Install" \ +-e "install({@ARGV},'$(VERBINST)',0,'$(UNINST)');" + +DOC_INSTALL = $(PERL) -e '$$\="\n\n";' \ +-e 'print "=head2 ", scalar(localtime), ": C<", shift, ">", " L<", $$arg=shift, "|", $$arg, ">";' \ +-e 'print "=over 4";' \ +-e 'while (defined($$key = shift) and defined($$val = shift)){print "=item *";print "C<$$key: $$val>";}' \ +-e 'print "=back";' + +UNINSTALL = $(PERLRUN) "-MExtUtils::Install" \ +-e 'uninstall($$ARGV[0],1,1); print "\nUninstall is deprecated. Please check the";' \ +-e 'print " packlist above carefully.\n There may be errors. Remove the";' \ +-e 'print " appropriate files manually.\n Sorry for the inconveniences.\n"' + + +# --- MakeMaker dist section: +ZIPFLAGS = -r +TO_UNIX = @$(NOOP) +TAR = tar +POSTOP = @$(NOOP) +ZIP = zip +DIST_DEFAULT = tardist +CI = ci -u +SHAR = shar +COMPRESS = gzip --best +DIST_CP = best +PREOP = @$(NOOP) +TARFLAGS = cvf +DISTVNAME = $(DISTNAME)-$(VERSION) +SUFFIX = .gz +RCS_LABEL = rcs -Nv$(VERSION_SYM): -q + + +# --- MakeMaker macro section: + + +# --- MakeMaker depend section: + + +# --- MakeMaker cflags section: + +CCFLAGS = -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm +OPTIMIZE = -O2 -g -pipe -march=i386 -mcpu=i686 +PERLTYPE = +MPOLLUTE = + + +# --- MakeMaker const_loadlibs section: + +# RNA might depend on some other libraries: +# See ExtUtils::Liblist for details +# +EXTRALIBS = -lm +LDLOADLIBS = -lm +BSLOADLIBS = +LD_RUN_PATH = /lib + + +# --- MakeMaker const_cccmd section: +CCCMD = $(CC) -c $(PASTHRU_INC) $(INC) \ + $(CCFLAGS) $(OPTIMIZE) \ + $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \ + $(XS_DEFINE_VERSION) + +# --- MakeMaker post_constants section: + + +# --- MakeMaker pasthru section: + +PASTHRU = LIB="$(LIB)"\ + LIBPERL_A="$(LIBPERL_A)"\ + LINKTYPE="$(LINKTYPE)"\ + PREFIX="$(PREFIX)"\ + OPTIMIZE="$(OPTIMIZE)"\ + PASTHRU_DEFINE="$(PASTHRU_DEFINE)"\ + PASTHRU_INC="$(PASTHRU_INC)" + + +# --- MakeMaker c_o section: + +.c.i: + gcc -E -c $(PASTHRU_INC) $(INC) \ + $(CCFLAGS) $(OPTIMIZE) \ + $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \ + $(XS_DEFINE_VERSION) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c > $*.i + +.c.s: + $(CCCMD) -S $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c + +.c$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c + +.C$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.C + +.cpp$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cpp + +.cxx$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cxx + +.cc$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cc + + +# --- MakeMaker xs_c section: + +.xs.c: + $(PERLRUN) $(XSUBPP) $(XSPROTOARG) $(XSUBPPARGS) $(XSUBPP_EXTRA_ARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c + + +# --- MakeMaker xs_o section: + +.xs$(OBJ_EXT): + $(PERLRUN) $(XSUBPP) $(XSPROTOARG) $(XSUBPPARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c + + +# --- MakeMaker top_targets section: + +all :: pure_all manifypods + @$(NOOP) + +pure_all :: config pm_to_blib subdirs linkext + @$(NOOP) + +subdirs :: $(MYEXTLIB) + @$(NOOP) + +config :: Makefile.perl $(INST_LIBDIR)/.exists + @$(NOOP) + +config :: $(INST_ARCHAUTODIR)/.exists + @$(NOOP) + +config :: $(INST_AUTODIR)/.exists + @$(NOOP) + +$(INST_AUTODIR)/.exists :: /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h + @$(MKPATH) $(INST_AUTODIR) + @$(EQUALIZE_TIMESTAMP) /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h $(INST_AUTODIR)/.exists + + -@$(CHMOD) $(PERM_RWX) $(INST_AUTODIR) + +$(INST_LIBDIR)/.exists :: /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h + @$(MKPATH) $(INST_LIBDIR) + @$(EQUALIZE_TIMESTAMP) /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h $(INST_LIBDIR)/.exists + + -@$(CHMOD) $(PERM_RWX) $(INST_LIBDIR) + +$(INST_ARCHAUTODIR)/.exists :: /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h + @$(MKPATH) $(INST_ARCHAUTODIR) + @$(EQUALIZE_TIMESTAMP) /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h $(INST_ARCHAUTODIR)/.exists + + -@$(CHMOD) $(PERM_RWX) $(INST_ARCHAUTODIR) + +config :: $(INST_MAN3DIR)/.exists + @$(NOOP) + + +$(INST_MAN3DIR)/.exists :: /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h + @$(MKPATH) $(INST_MAN3DIR) + @$(EQUALIZE_TIMESTAMP) /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h $(INST_MAN3DIR)/.exists + + -@$(CHMOD) $(PERM_RWX) $(INST_MAN3DIR) + +help: + perldoc ExtUtils::MakeMaker + + +# --- MakeMaker linkext section: + +linkext :: $(LINKTYPE) + @$(NOOP) + + +# --- MakeMaker dlsyms section: + + +# --- MakeMaker dynamic section: + +## $(INST_PM) has been moved to the all: target. +## It remains here for awhile to allow for old usage: "make dynamic" +#dynamic :: Makefile.perl $(INST_DYNAMIC) $(INST_BOOT) $(INST_PM) +dynamic :: Makefile.perl $(INST_DYNAMIC) $(INST_BOOT) + @$(NOOP) + + +# --- MakeMaker dynamic_bs section: + +BOOTSTRAP = RNA.bs + +# As Mkbootstrap might not write a file (if none is required) +# we use touch to prevent make continually trying to remake it. +# The DynaLoader only reads a non-empty file. +$(BOOTSTRAP): Makefile.perl $(INST_ARCHAUTODIR)/.exists + @echo "Running Mkbootstrap for $(NAME) ($(BSLOADLIBS))" + @$(PERLRUN) \ + "-MExtUtils::Mkbootstrap" \ + -e "Mkbootstrap('$(BASEEXT)','$(BSLOADLIBS)');" + @$(TOUCH) $(BOOTSTRAP) + $(CHMOD) $(PERM_RW) $@ + +$(INST_BOOT): $(BOOTSTRAP) $(INST_ARCHAUTODIR)/.exists + @rm -rf $(INST_BOOT) + -cp $(BOOTSTRAP) $(INST_BOOT) + $(CHMOD) $(PERM_RW) $@ + + +# --- MakeMaker dynamic_lib section: + +# This section creates the dynamically loadable $(INST_DYNAMIC) +# from $(OBJECT) and possibly $(MYEXTLIB). +ARMAYBE = : +OTHERLDFLAGS = +INST_DYNAMIC_DEP = + +$(INST_DYNAMIC): $(OBJECT) $(MYEXTLIB) $(BOOTSTRAP) $(INST_ARCHAUTODIR)/.exists $(EXPORT_LIST) $(PERL_ARCHIVE) $(PERL_ARCHIVE_AFTER) $(INST_DYNAMIC_DEP) + $(RM_F) $@ + LD_RUN_PATH="$(LD_RUN_PATH)" $(LD) $(LDDLFLAGS) $(LDFROM) $(OTHERLDFLAGS) -o $@ $(MYEXTLIB) $(PERL_ARCHIVE) $(LDLOADLIBS) $(PERL_ARCHIVE_AFTER) $(EXPORT_LIST) + $(CHMOD) $(PERM_RWX) $@ + + +# --- MakeMaker static section: + +## $(INST_PM) has been moved to the all: target. +## It remains here for awhile to allow for old usage: "make static" +#static :: Makefile.perl $(INST_STATIC) $(INST_PM) +static :: Makefile.perl $(INST_STATIC) + @$(NOOP) + + +# --- MakeMaker static_lib section: + +$(INST_STATIC): $(OBJECT) $(MYEXTLIB) $(INST_ARCHAUTODIR)/.exists + $(RM_RF) $@ + cp $(MYEXTLIB) $@ + $(FULL_AR) $(AR_STATIC_ARGS) $@ $(OBJECT) && $(RANLIB) $@ + $(CHMOD) $(PERM_RWX) $@ + @echo "$(EXTRALIBS)" > $(INST_ARCHAUTODIR)/extralibs.ld + + + +# --- MakeMaker manifypods section: +POD2MAN_EXE = /usr/bin/pod2man +POD2MAN = $(PERL) -we '%m=@ARGV;for (keys %m){' \ +-e 'next if -e $$m{$$_} && -M $$m{$$_} < -M $$_ && -M $$m{$$_} < -M "Makefile.perl";' \ +-e 'print "Manifying $$m{$$_}\n";' \ +-e 'system(q[$(PERLRUN) $(POD2MAN_EXE) ].qq[$$_>$$m{$$_}])==0 or warn "Couldn\047t install $$m{$$_}\n";' \ +-e 'chmod(oct($(PERM_RW)), $$m{$$_}) or warn "chmod $(PERM_RW) $$m{$$_}: $$!\n";}' + +manifypods : pure_all RNA.pm + @$(POD2MAN) \ + RNA.pm \ + $(INST_MAN3DIR)/RNA.$(MAN3EXT) + +# --- MakeMaker processPL section: + + +# --- MakeMaker installbin section: + + +# --- MakeMaker subdirs section: + +# none + +# --- MakeMaker clean section: + +# Delete temporary files but do not touch installed files. We don't delete +# the Makefile here so a later make realclean still has a makefile to use. + +clean :: + -rm -rf ./blib $(MAKE_APERL_FILE) $(INST_ARCHAUTODIR)/extralibs.all perlmain.c tmon.out mon.out so_locations pm_to_blib *$(OBJ_EXT) *$(LIB_EXT) perl.exe perl perl$(EXE_EXT) $(BOOTSTRAP) $(BASEEXT).bso $(BASEEXT).def lib$(BASEEXT).def $(BASEEXT).exp $(BASEEXT).x core core.*perl.*.? *perl.core + -mv Makefile.perl Makefile.perl.old $(DEV_NULL) + + +# --- MakeMaker realclean section: + +# Delete temporary files (via clean) and also delete installed files +realclean purge :: clean + rm -rf $(INST_AUTODIR) $(INST_ARCHAUTODIR) + rm -rf $(DISTVNAME) + rm -f $(INST_DYNAMIC) $(INST_BOOT) + rm -f $(INST_STATIC) + rm -f $(INST_LIBDIR)/RNA.pm + rm -rf Makefile.perl Makefile.perl.old + + +# --- MakeMaker dist_basics section: +distclean :: realclean distcheck + $(NOECHO) $(NOOP) + +distcheck : + $(PERLRUN) "-MExtUtils::Manifest=fullcheck" -e fullcheck + +skipcheck : + $(PERLRUN) "-MExtUtils::Manifest=skipcheck" -e skipcheck + +manifest : + $(PERLRUN) "-MExtUtils::Manifest=mkmanifest" -e mkmanifest + +veryclean : realclean + $(RM_F) *~ *.orig */*~ */*.orig + + + +# --- MakeMaker dist_core section: + +dist : $(DIST_DEFAULT) + @$(PERL) -le 'print "Warning: Makefile possibly out of date with $$vf" if ' \ + -e '-e ($$vf="$(VERSION_FROM)") and -M $$vf < -M "Makefile.perl";' + +tardist : $(DISTVNAME).tar$(SUFFIX) + +zipdist : $(DISTVNAME).zip + +$(DISTVNAME).tar$(SUFFIX) : distdir + $(PREOP) + $(TO_UNIX) + $(TAR) $(TARFLAGS) $(DISTVNAME).tar $(DISTVNAME) + $(RM_RF) $(DISTVNAME) + $(COMPRESS) $(DISTVNAME).tar + $(POSTOP) + +$(DISTVNAME).zip : distdir + $(PREOP) + $(ZIP) $(ZIPFLAGS) $(DISTVNAME).zip $(DISTVNAME) + $(RM_RF) $(DISTVNAME) + $(POSTOP) + +uutardist : $(DISTVNAME).tar$(SUFFIX) + uuencode $(DISTVNAME).tar$(SUFFIX) \ + $(DISTVNAME).tar$(SUFFIX) > \ + $(DISTVNAME).tar$(SUFFIX)_uu + +shdist : distdir + $(PREOP) + $(SHAR) $(DISTVNAME) > $(DISTVNAME).shar + $(RM_RF) $(DISTVNAME) + $(POSTOP) + + +# --- MakeMaker dist_dir section: +distdir : + $(RM_RF) $(DISTVNAME) + $(PERLRUN) "-MExtUtils::Manifest=manicopy,maniread" \ + -e "manicopy(maniread(),'$(DISTVNAME)', '$(DIST_CP)');" + + + +# --- MakeMaker dist_test section: + +disttest : distdir + cd $(DISTVNAME) && $(ABSPERLRUN) Makefile.PL + cd $(DISTVNAME) && $(MAKE) $(PASTHRU) + cd $(DISTVNAME) && $(MAKE) test $(PASTHRU) + + +# --- MakeMaker dist_ci section: + +ci : + $(PERLRUN) "-MExtUtils::Manifest=maniread" \ + -e "@all = keys %{ maniread() };" \ + -e 'print("Executing $(CI) @all\n"); system("$(CI) @all");' \ + -e 'print("Executing $(RCS_LABEL) ...\n"); system("$(RCS_LABEL) @all");' + + +# --- MakeMaker install section: + +install :: all pure_install doc_install + +install_perl :: all pure_perl_install doc_perl_install + +install_site :: all pure_site_install doc_site_install + +install_vendor :: all pure_vendor_install doc_vendor_install + +pure_install :: pure_$(INSTALLDIRS)_install + +doc_install :: doc_$(INSTALLDIRS)_install + @echo Appending installation info to $(INSTALLARCHLIB)/perllocal.pod + +pure__install : pure_site_install + @echo INSTALLDIRS not defined, defaulting to INSTALLDIRS=site + +doc__install : doc_site_install + @echo INSTALLDIRS not defined, defaulting to INSTALLDIRS=site + +pure_perl_install :: + @$(MOD_INSTALL) \ + read $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist \ + write $(INSTALLARCHLIB)/auto/$(FULLEXT)/.packlist \ + $(INST_LIB) $(INSTALLPRIVLIB) \ + $(INST_ARCHLIB) $(INSTALLARCHLIB) \ + $(INST_BIN) $(INSTALLBIN) \ + $(INST_SCRIPT) $(INSTALLSCRIPT) \ + $(INST_MAN1DIR) $(INSTALLMAN1DIR) \ + $(INST_MAN3DIR) $(INSTALLMAN3DIR) + @$(WARN_IF_OLD_PACKLIST) \ + $(SITEARCHEXP)/auto/$(FULLEXT) + + +pure_site_install :: + @$(MOD_INSTALL) \ + read $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist \ + write $(INSTALLSITEARCH)/auto/$(FULLEXT)/.packlist \ + $(INST_LIB) $(INSTALLSITELIB) \ + $(INST_ARCHLIB) $(INSTALLSITEARCH) \ + $(INST_BIN) $(INSTALLSITEBIN) \ + $(INST_SCRIPT) $(INSTALLSCRIPT) \ + $(INST_MAN1DIR) $(INSTALLSITEMAN1DIR) \ + $(INST_MAN3DIR) $(INSTALLSITEMAN3DIR) + @$(WARN_IF_OLD_PACKLIST) \ + $(PERL_ARCHLIB)/auto/$(FULLEXT) + +pure_vendor_install :: + @$(MOD_INSTALL) \ + $(INST_LIB) $(INSTALLVENDORLIB) \ + $(INST_ARCHLIB) $(INSTALLVENDORARCH) \ + $(INST_BIN) $(INSTALLVENDORBIN) \ + $(INST_SCRIPT) $(INSTALLSCRIPT) \ + $(INST_MAN1DIR) $(INSTALLVENDORMAN1DIR) \ + $(INST_MAN3DIR) $(INSTALLVENDORMAN3DIR) + +doc_perl_install :: + -@$(MKPATH) $(INSTALLARCHLIB) + -@$(DOC_INSTALL) \ + "Module" "$(NAME)" \ + "installed into" "$(INSTALLPRIVLIB)" \ + LINKTYPE "$(LINKTYPE)" \ + VERSION "$(VERSION)" \ + EXE_FILES "$(EXE_FILES)" \ + >> $(INSTALLARCHLIB)/perllocal.pod + +doc_site_install :: + -@$(MKPATH) $(INSTALLARCHLIB) + -@$(DOC_INSTALL) \ + "Module" "$(NAME)" \ + "installed into" "$(INSTALLSITELIB)" \ + LINKTYPE "$(LINKTYPE)" \ + VERSION "$(VERSION)" \ + EXE_FILES "$(EXE_FILES)" \ + >> $(INSTALLSITEARCH)/perllocal.pod + +doc_vendor_install :: + + +uninstall :: uninstall_from_$(INSTALLDIRS)dirs + +uninstall_from_perldirs :: + @$(UNINSTALL) $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist + +uninstall_from_sitedirs :: + @$(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist + + +# --- MakeMaker force section: +# Phony target to force checking subdirectories. +FORCE: + @$(NOOP) + + +# --- MakeMaker perldepend section: + +PERL_HDRS = \ + $(PERL_INC)/EXTERN.h \ + $(PERL_INC)/INTERN.h \ + $(PERL_INC)/XSUB.h \ + $(PERL_INC)/av.h \ + $(PERL_INC)/cc_runtime.h \ + $(PERL_INC)/config.h \ + $(PERL_INC)/cop.h \ + $(PERL_INC)/cv.h \ + $(PERL_INC)/dosish.h \ + $(PERL_INC)/embed.h \ + $(PERL_INC)/embedvar.h \ + $(PERL_INC)/fakethr.h \ + $(PERL_INC)/form.h \ + $(PERL_INC)/gv.h \ + $(PERL_INC)/handy.h \ + $(PERL_INC)/hv.h \ + $(PERL_INC)/intrpvar.h \ + $(PERL_INC)/iperlsys.h \ + $(PERL_INC)/keywords.h \ + $(PERL_INC)/mg.h \ + $(PERL_INC)/nostdio.h \ + $(PERL_INC)/op.h \ + $(PERL_INC)/opcode.h \ + $(PERL_INC)/opnames.h \ + $(PERL_INC)/patchlevel.h \ + $(PERL_INC)/perl.h \ + $(PERL_INC)/perlapi.h \ + $(PERL_INC)/perlio.h \ + $(PERL_INC)/perlsdio.h \ + $(PERL_INC)/perlsfio.h \ + $(PERL_INC)/perlvars.h \ + $(PERL_INC)/perly.h \ + $(PERL_INC)/pp.h \ + $(PERL_INC)/pp_proto.h \ + $(PERL_INC)/proto.h \ + $(PERL_INC)/regcomp.h \ + $(PERL_INC)/regexp.h \ + $(PERL_INC)/regnodes.h \ + $(PERL_INC)/scope.h \ + $(PERL_INC)/sv.h \ + $(PERL_INC)/thrdvar.h \ + $(PERL_INC)/thread.h \ + $(PERL_INC)/unixish.h \ + $(PERL_INC)/utf8.h \ + $(PERL_INC)/util.h \ + $(PERL_INC)/warnings.h + +$(OBJECT) : $(PERL_HDRS) + + +# --- MakeMaker makefile section: + +$(OBJECT) : $(FIRST_MAKEFILE) + +# We take a very conservative approach here, but it\'s worth it. +# We move Makefile to Makefile.old here to avoid gnu make looping. +Makefile.perl : Makefile.PL $(CONFIGDEP) + @echo "Makefile out-of-date with respect to $?" + @echo "Cleaning current config before rebuilding Makefile..." + -@$(RM_F) Makefile.perl.old + -@$(MV) Makefile.perl Makefile.perl.old + -$(MAKE) -f Makefile.perl.old clean $(DEV_NULL) || $(NOOP) + $(PERLRUN) Makefile.PL + @echo "==> Your Makefile has been rebuilt. <==" + @echo "==> Please rerun the make command. <==" + false + + + +# --- MakeMaker staticmake section: + +# --- MakeMaker makeaperl section --- +MAP_TARGET = perl +FULLPERL = /usr/bin/perl + +$(MAP_TARGET) :: static $(MAKE_APERL_FILE) + $(MAKE) -f $(MAKE_APERL_FILE) $@ + +$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE) + @echo Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET) + @$(PERLRUNINST) \ + Makefile.PL DIR= \ + MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \ + MAKEAPERL=1 NORECURS=1 CCCDLFLAGS= + + +# --- MakeMaker test section: + +TEST_VERBOSE=0 +TEST_TYPE=test_$(LINKTYPE) +TEST_FILE = test.pl +TEST_FILES = +TESTDB_SW = -d + +testdb :: testdb_$(LINKTYPE) + +test :: $(TEST_TYPE) + +test_dynamic :: pure_all + PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + +testdb_dynamic :: pure_all + PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + +test_ : test_dynamic + +test_static :: pure_all $(MAP_TARGET) + PERL_DL_NONLAZY=1 ./$(MAP_TARGET) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + +testdb_static :: pure_all $(MAP_TARGET) + PERL_DL_NONLAZY=1 ./$(MAP_TARGET) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + + + +# --- MakeMaker ppd section: +# Creates a PPD (Perl Package Description) for a binary distribution. +ppd: + @$(PERL) -e "print qq{\n\t$(DISTNAME)\n\t\n\tIvo Hofacker <ivo\@tbi.univie.ac.at>\n}" > $(DISTNAME).ppd + @$(PERL) -e "print qq{\t\n}" >> $(DISTNAME).ppd + @$(PERL) -e "print qq{\t\t\n\t\t\n\t\t\n\t\n\n}" >> $(DISTNAME).ppd + +# --- MakeMaker pm_to_blib section: + +pm_to_blib: $(TO_INST_PM) + @$(PERLRUNINST) "-MExtUtils::Install" \ + -e "pm_to_blib({qw{RNA.pm $(INST_LIBDIR)/RNA.pm}},'$(INST_LIB)/auto','$(PM_FILTER)')" + @$(TOUCH) $@ + +# --- MakeMaker selfdocument section: + + +# --- MakeMaker postamble section: + + +# End. diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA.bs b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA.bs new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA.i b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA.i new file mode 100755 index 000000000..c408b19c2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA.i @@ -0,0 +1,455 @@ +%module RNA +//%pragma(perl5) modulecode="@EXPORT=qw(fold);" +%pragma(perl5) include="RNA.pod" +%{ +#include "../H/utils.h" +#include "../H/fold_vars.h" +#undef fold +#include "../H/fold.h" +#include "../H/cofold.h" +#include "../H/part_func.h" +#include "../H/PS_dot.h" +#include "../H/inverse.h" +#include "../H/RNAstruct.h" +#include "../H/treedist.h" +#include "../H/stringdist.h" +#include "../H/profiledist.h" +#include "../H/dist_vars.h" +#include "../H/pair_mat.h" +#include "../H/subopt.h" +#include "../H/energy_const.h" +#include "../H/params.h" +%} +// +%include carrays.i +%array_functions(int, intP); +%array_class(int, intArray); +%array_functions(float, floatP); +%array_class(float, floatArray); +%array_functions(double, doubleP); +%array_class(double, doubleArray); +%array_functions(short, shortP); +%include cdata.i + +%constant double VERSION = 0.3; +%include typemaps.i +%typemap(perl5,in) FILE * { + if (SvOK($input)) /* check for undef */ + $1 = PerlIO_findFILE(IoIFP(sv_2io($input))); + else $1 = NULL; +} + +%typemap(python,in) FILE * { + if (PyFile_Check($input)) /* check for undef */ + $1 = PyFile_AsFile($input); + else $1 = NULL; +} + +//%title "Interface to the Vienna RNA library" +//%section "Folding Routines" +//%subsection "Minimum free Energy Folding" + +%rename (fold) my_fold; + +%{ + char *my_fold(char *string, char *constraints, float *energy) { + char *struc; + float en; + struc = calloc(strlen(string)+1,sizeof(char)); + if (constraints && fold_constrained) + strncpy(struc, constraints, strlen(string)); + *energy = fold(string, struc); + if (constraints) + strncpy(constraints, struc, strlen(constraints)); + return(struc); + } +%} + +%newobject my_fold; +char *my_fold(char *string, char *constraints = NULL, float *OUTPUT); +%ignore fold; +%include "../H/fold.h" + +%rename (cofold) my_cofold; + +%{ + char *my_cofold(char *string, char *constraints, float *energy) { + char *struc; + float en; + struc = calloc(strlen(string)+1,sizeof(char)); + if (constraints && fold_constrained) + strncpy(struc, constraints, strlen(string)); + *energy = cofold(string, struc); + if (constraints) + strncpy(constraints, struc, strlen(constraints)); + return(struc); + } +%} + +%newobject my_cofold; +char *my_cofold(char *string, char *constraints = NULL, float *OUTPUT); +%ignore cofold; +%include "../H/cofold.h" + +//%subsection "Partition function Folding" + +%rename (pf_fold) my_pf_fold; +%{ + char *my_pf_fold(char *string, char *constraints, float *energy) { + char *struc; + float en; + struc = calloc(strlen(string)+1,sizeof(char)); + if (constraints && fold_constrained) + strncpy(struc, constraints, strlen(string)); + *energy = pf_fold(string, struc); + if (constraints) + strncpy(constraints, struc, strlen(constraints)); + return(struc); + } +%} + +%newobject my_pf_fold; +char *my_pf_fold(char *string, char *constraints = NULL, float *OUTPUT); + +%ignore pf_fold; +%include "../H/part_func.h" + +%newobject pbacktrack; +extern char *pbacktrack(char *sequence); + +//%subsection "Inverse Folding" + +%rename (inverse_fold) my_inverse_fold; +%{ + char *my_inverse_fold(char *start, const char *target, float *cost) { + char *seq; + int n; + n = strlen(target); + seq = random_string(n, symbolset); + if (start) + strncpy(seq, start, strlen(start)); + *cost = inverse_fold(seq, target); + if (start) + /* for backward compatibility modify start */ + strncpy(start, seq, strlen(start)); + return(seq); + } +%} + +%newobject my_inverse_fold; +char * my_inverse_fold(char *start, const char *target, float *OUTPUT); + +%rename (inverse_pf_fold) my_inverse_pf_fold; +%{ + char *my_inverse_pf_fold(char *start, const char *target, float *cost) { + char *seq; + int n; + n = strlen(target); + seq = random_string(n, symbolset); + if (start) strncpy(seq, start, n); + *cost = inverse_pf_fold(seq, target); + if (start) + /* for backward compatibility modify start */ + strncpy(start, seq, strlen(start)); + return(seq); + } +%} + +%newobject my_inverse_pf_fold; +char * my_inverse_pf_fold(char *start, const char *target, float *OUTPUT); + +%ignore inverse_fold; +%ignore inverse_pf_fold; +%include "../H/inverse.h" + +//%subsection "Global Variables to Modify Folding" +//extern double *pr; /* base pairing prob. matrix */ +%include "../H/fold_vars.h" +%extend bondT { + bondT *get(int i) { + return self+i; + } +} + +//%include "../H/subopt.h" +// from subopt.h + +typedef struct { + float energy; /* energy of structure */ + char *structure; +} SOLUTION; + +%newobject subopt; +extern SOLUTION *subopt (char *seq, char *constraint, int delta, FILE *fp=NULL); + +extern int subopt_sorted; /* sort output by energy */ +%extend SOLUTION { + SOLUTION *get(int i) { +// static int size=-1; +// if (size<0) { +// SOLUTION *s; +// for (s=self; s->structure; s++); +// size= (int) (s-self); +// } +// if (i>=size) { +// warn("value out of range"); +// return NULL; +// } + return self+i; + } + + int size() { + SOLUTION *s; + for (s=self; s->structure; s++); + return (int)(s-self); + } + + ~SOLUTION() { + SOLUTION *s; + for (s=self; s->structure; s++) free(s->structure); + free(self); + } +} +%{ +double get_pr(int i, int j) { + int ii; + if (i>j) {ii=i; i=j; j=ii;} + return pr[iindx[i]-j]; +} +%} +double get_pr(int i, int j); +/* Get probability of pair i.j from the pr array */ + +//%section "Parsing and Comparing Structures" +// from RNAstruct.h + +%newobject b2HIT; +%newobject b2C; +%newobject b2Shapiro; +%newobject add_root; +%newobject expand_Shapiro; +%newobject expand_Full; +%newobject unexpand_Full; +%newobject unweight; +char *b2HIT(char *structure); // Full -> HIT [incl. root] +char *b2C(char *structure); // Full -> Coarse [incl. root] +char *b2Shapiro(char *structure); // Full -> weighted Shapiro [i.r] +char *add_root(char *); // {Tree} -> ({Tree}R) +char *expand_Shapiro(char *coarse); // add S for stacks to coarse struct +char *expand_Full(char *structure); // Full -> FFull +char *unexpand_Full(char *ffull); // FFull -> Full +char *unweight(char *wcoarse); // remove weights from coarse struct +void unexpand_aligned_F(char *align[2]); +void parse_structure(char *structure); // make structure statistics +int loop_size[1000]; // loop sizes of a structure +int helix_size[1000]; // helix sizes of a structure +int loop_degree[1000]; // loop degrees of a structure +int loops; // n of loops and stacks +int unpaired, pairs; // n of unpaired digits and pairs + +%include "../H/treedist.h" +%include "../H/stringdist.h" +%newobject Make_bp_profile; +%include "../H/profiledist.h" +// from dist_vars.h +int edit_backtrack; /* set to 1 if you want backtracking */ +char *aligned_line[2]; /* containes alignment after backtracking */ +int cost_matrix; /* 0 usual costs (default), 1 Shapiro's costs */ + +//%section "Utilities" +%newobject space; +%newobject time_stamp; +%newobject random_string; +%newobject get_line; +%newobject pack_structure; +%newobject unpack_structure; +%newobject make_pair_table; + +%include "../H/utils.h" + +// from read_epars.c +extern void read_parameter_file(char *fname); +/* read energy parameters from file */ +extern void write_parameter_file(char *fname); +/* write energy parameters to file */ + +// this doesn't work currently +%inline %{ +void *deref_any(void **ptr, int index) { + /* dereference arbitray pointer */ + return (void *) ptr[index]; +} +%} + +// from params.h + +extern paramT *scale_parameters(void); +extern paramT *copy_parameters(void); +extern paramT *set_parameters(paramT *dest); +%{ +char *get_aligned_line(int i) { + i = i % 2; + return aligned_line[i]; +} +%} + +char *get_aligned_line(int); + + + +//%include ptr2array.i + + + +%inline %{ + short *make_loop_index(const char *structure) { + /* number each position by which loop it belongs to (positions start at 0) */ + int i,j,hx,l,nl; + int length; + short *stack; + short *loop; + length = strlen(structure); + stack = (short *) space(sizeof(short)*(length+1)); + loop = (short *) space(sizeof(short)*(length+2)); + hx=l=nl=0; + for (i=0; i0) + l = loop[stack[hx-1]]; /* index of enclosing loop */ + else l=0; /* external loop has index 0 */ + if (hx<0) { + fprintf(stderr, "%s\n", structure); + nrerror("unbalanced brackets in make_pair_table"); + } + } + } + free(stack); + return loop; + } +%} + +%inline %{ +float energy_of_move(const char *string, char *structure, int mi, int mj) { + extern int energy_of_struct_pt(const char *string, short * ptable, + short *s, short *s1); +#define ILLEGAL 999.; + int i,j,hx,l,nl; + int length; + short *stack, *table, *loop; + short *S, *S1; + int energy; + + if (mj<0) { + if ((structure[-mi]!='(') || (structure[-mj]!=')')) + return 1001; /* illegal delete pair */ + } else + if ((structure[mi]!='.') || (structure[mj]!='.')) + return 1002; /* illegal add pair */ + + /* make the pair table and loop index l*/ + length = strlen(structure); + stack = (short *) space(sizeof(short)*(length+1)); + loop = (short *) space(sizeof(short)*(length+2)); + table = (short *) space(sizeof(short)*(length+2)); + table[0] = length; + hx=l=nl=0; + for (i=1; i<=length; i++) { + if (structure[i-1] == '(') { + nl++; l=nl; + stack[hx++]=i; + } + loop[i]=l; + if (structure[i-1] ==')') { + j=stack[--hx]; + if (hx>0) + l = loop[stack[hx-1]]; /* index of enclosing loop */ + else l=0; /* external loop has index 0 */ + if (hx<0) { + fprintf(stderr, "%s\n", structure); + nrerror("unbalanced brackets in energy_of_move"); + } + table[i]=j; + table[j]=i; + } + } + if (hx!=0) { + fprintf(stderr, "%s\n", structure); + nrerror("unbalanced brackets in energy_of_move"); + } + + if (loop[abs(mi)+1] != loop[abs(mj)+1]) { /* not in same loop => illegal */ + free(stack); + free(loop); + free(table); + return 1003.; + } + + /* if we get here the move is legal */ + if (mj<0) { /* delete pair */ + structure[-mi] = '.'; + structure[-mj] = '.'; + table[-mi+1] = table[-mj+1] = 0; + } else { /* insert pair */ + structure[mi] = '('; + structure[mj] = ')'; + table[mi+1] = mj+1; + table[mj+1] = mi+1; + } + + S = (short *) space(sizeof(short)*(length+1)); + S[0] = length; + for (i=1; i<=length; i++) { + char *pos; + pos = strchr(Law_and_Order, string[i-1]); + if (pos==NULL) S[i]=0; + else S[i] = pos-Law_and_Order; + } + + energy = energy_of_struct_pt(string, table, S, S); + + free(S); + free(stack); + free(loop); + free(table); + return (float) energy/100.; +} +%} + +%init %{ +/* work around segfault when script tries to free symbolset */ + +symbolset = (char *) space(21); +strcpy(symbolset, "AUGC"); + +%} + + +// Convert Perl array reference int a char ** +// not needed curently +//%typemap(perl5,in) char ** { +// AV *tempav; +// I32 len; +// int i; +// SV **tv; +// if (!SvROK($input)) croak("$input is not a reference."); +// if (SvTYPE(SvRV($input)) != SVt_PVAV) croak("$input is not an array."); +// tempav = (AV*)SvRV($input); +// len = av_len(tempav); +// $1 = (char **) malloc((len+2)*sizeof(char *)); +// for (i = 0; i <= len; i++) { +// tv = av_fetch(tempav, i, 0); +// $1[i] = (char *) SvPV(*tv,PL_na); +// } +// $1[i] = 0; +//} +// This cleans up our char ** array after the function call +//%typemap(perl5,freearg) char ** { +// free($1); +//} +%include "../H/PS_dot.h" diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA.pm b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA.pm new file mode 100755 index 000000000..a4cb55d54 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA.pm @@ -0,0 +1,1075 @@ +# This file was automatically generated by SWIG +package RNA; +require Exporter; +require DynaLoader; +@ISA = qw(Exporter DynaLoader); +package RNAc; +bootstrap RNA; +package RNA; +@EXPORT = qw( ); +=head1 NAME + +RNA - interface to the Vienna RNA library (libRNA.a) +Version 0.3 + +=head1 SYNOPSIS + + use RNA; + $seq = "CGCAGGGAUACCCGCG"; + ($struct, $mfe) = RNA::fold($seq); #predict mfe structure of $seq + RNA::PS_rna_plot($seq, $struct, "rna.ps"); # write PS plot to rna.ps + $F = RNA::pf_fold($seq); # compute partition function and pair pobabilities + RNA::PS_dot_plot($seq, "dot.ps"); # write dot plot to dot.ps + ... + +=head1 DESCRIPTION + +The RNA.pm package gives access to almost all functions in the libRNA.a +library of the Vienna RNA PACKAGE. The Perl wrapper is generated using +SWIG http://www.swig.org/ with relatively little manual intervention. +For each C function in the library the perl package provides a function +of the same name and calling convention (with few exceptions). For +detailed information you should therefore also consult the documentation +of the library (info RNAlib). + +Note that in general C arrays are wrapped into opaque objects that can +only be accessed via helper functions. SWIG provides a couple of general +purpose helper functions, see the section at the end of this file. C +structures are wrapped into Perl objects using SWIG's shadow class +mechanism, resulting in a tied hash with keys named after the structure +members. + +For the interrested reader we list for each scalar type of the +corepsonding C variable in brackets, and point out the header files +containing the C declaration. + +=head2 Folding Routines + +Minimum free Energy Folding (from fold.h) + +=over 4 + +=item fold SEQUENCE + +=item fold SEQUENCE, CONSTRAINTS + +computes the minimum free energy structure of the string SEQUENCE and returns +the predicted structure and energy, e.g. + + ($structure, $mfe) = RNA::fold("UGUGUCGAUGUGCUAU"); + +If a second argument is supplied and +L<$fold_constrained|/$fold_constrained>==1 the CONSTRAINTS string is +used to specify constraints on the predicted structure. The +characters '|', 'x', '<', '>' mark bases that are paired, unpaired, +paired upstream, or downstream, respectively; matching brackets "( )" +denote base pairs, dots '.' are used for unconstrained bases. + +In the two argument version the CONSTRAINTS string is modified and holds the +predicted structure upon return. This is done for backwards compatibility only, +and might change in future versions. + +=item energy_of_struct SEQUENCE, STRUCTURE + +returns the energy of SEQUENCE on STRUCTURE (in kcal/mol). The string structure +must hold a valid secondary structure in bracket notation. + +=item update_fold_params + +recalculate the pair matrix and energy parameters after a change in folding +parameters. In many cases (such as changes to +L<$temperature|/$temperature>) the fold() routine will call +update_fold_params automatically when necessary. + +=item free_arrays + +frees memory allocated internally when calling L. + +=back + +Partition function Folding (from part_func.h) + +=over 4 + +=item pf_fold SEQUENCE + +=item pf_fold SEQUENCE, CONSTRAINTS + +calculates the partition function over all possible secondary +structures and the matrix of pair probabilities for SEQUENCE and +returns a two element list consisting of a string summarizing possible +structures. See below on how to access the pair probability matrix. As +with L the second argument can be used to specify folding +constraints. Constraints are implemented by excluding base pairings +that contradict the constraint, but without bonus +energies. Constraints of type '|' (paired base) are ignored. In the +two argument version CONSTRAINTS is modified to contain the structure +string on return (obsolete feature, for backwards compatibility only) + +=item get_pr I, J + +After calling C the global C variable C points to the +computed pair probabilities. Perl access to the C is facilitated by +the C helper function that looks up and returns the +probability of the pair (I,J). + +=item free_pf_arrays + +frees memory allocated for pf_fold + +=item update_pf_params LENGTH + +recalculate energy parameters for pf_fold. In most cases (such as +simple changes to L<$temperature|/$temperature>) C +will take appropriate action automatically. + +=back + +Suboptimal Folding (from subopt.h) + +=over 4 + +=item subopt SEQUENCE, CONSTRAINTS, DELTA + +=item subopt SEQUENCE, CONSTRAINTS, DELTA, FILEHANDLE + +compute all structures of SEQUENCE within DELTA*0.01 kcal/mol of the +optimum. If specified, results are written to FILEHANDLE and nothing +is returned. Else, the C function returnes a list of C structs of type +SOLUTION. The list is wrapped by SWIG as a perl object that can be +accesses as follows: + + $solution = subopt($seq, undef, 500); + for (0..$solution->size()-1) { + printf "%s %6.2f\n", $solution->get($_)->{structure}, + $solution->get($_)->{energy}; + } + +=back + +Inverse Folding (from inverse.h) + +=over 4 + +=item inverse_fold START, TARGET + +find a sequence that folds into structure TARGET, by optimizing the +sequence until its mfe structure (as returned by L) is +TARGET. Startpoint of the optimization is the sequence START. Returns +a list containing the sequence found and the final value of the cost +function, i.e. 0 if the search was successful. A random start sequence +can be generated using L. + +=item inverse_pf_fold START, TARGET + +optimizes a sequence (beginning with START) by maximising the +frequency of the structure TARGET in the thermodynamic ensemble +of structures. Returns a list containing the optimized sequence and +the final value of the cost function. The cost function is given by +C, i.e.C<-RT*log(p(TARGET))> + +=item $final_cost [float] + +holds the value of the cost function where the optimization in +C should stop. For values <=0 the optimization will +only terminate at a local optimimum (which might take very long to reach). + +=item $symbolset [char *] + +the string symbolset holds the allowed characters to be used by +C and C, the default alphabet is "AUGC" + + +=item $give_up [int] + +If non-zero stop optimization when its clear that no exact solution +can be found. Else continue and eventually return an approximate +solution. Default 0. + +=back + +Global Variables to Modify Folding (from fold_vars.h) + +=over 4 + +=item $noGU [int] + +Do not allow GU pairs to form, default 0. + +=item $no_closingGU [int] + +allow GU only inside stacks, default 0. + +=item $tetra_loop [int] + +Fold with specially stable 4-loops, default 1. + +=item $energy_set [int] + +0 = BP; 1=any mit GC; 2=any mit AU-parameter, default 0. + +=item $dangles [int] + +How to compute dangling ends. 0: no dangling end energies, 1: "normal" +dangling ends (default), 2: simplified dangling ends, 3: "normal" + +co-axial stacking. Note that L treats cases 1 and 3 +as 2. The same holds for the main computation in L, +however subopt will re-evalute energies using +L for cases 1 and 3. See the more +detailed discussion in RNAlib.texinfo. + +=item $nonstandards [char *] + +contains allowed non standard bases, default empty string "" + +=item $temperature [double] + +temperature in degrees Celsius for rescaling parameters, default 37C. + +=item $logML [int] + +use logarithmic multiloop energy function in +L, default 0. + +=item $noLonelyPairs [int] + +consider only structures without isolated base pairs (helices of length 1). +For L only eliminates pairs +that can B occur as isolated pairs. Default 0. + +=item $base_pair [struct bond *] + +list of base pairs from last call to L. Better use +the structure string returned by L. + +=item $pf_scale [double] + +scaling factor used by L to avoid overflows. Should +be set to exp(-F/(RT*length)) where F is a guess for the ensmble free +energy (e.g. use the mfe). + + +=item $fold_constrained [int] + +apply constraints in the folding algorithms, default 0. + +=item $do_backtrack [int] + +If 0 do not compute the pair probabilities in L +(only the partition function). Default 1. + +=item $backtrack_type [char] + +usually 'F'; 'C' require (1,N) to be bonded; 'M' backtrack as if the +sequence was part of a multi loop. Used by L + +=item $pr [double *] + +the base pairing prob. matrix computed by L. + +=item $iindx [int *] + +Array of indices for moving withing the C array. Better use +L. + + +=back + +=head2 Parsing and Comparing Structures + +from RNAstruct.h: these functions convert between strings +representating secondary structures with various levels of coarse +graining. See the documentation of the C library for details + +=over 4 + +=item b2HIT STRUCTURE + +Full -> HIT [incl. root] + +=item b2C STRUCTURE + +Full -> Coarse [incl. root] + +=item b2Shapiro STRUCTURE + +Full -> weighted Shapiro [i.r.] + +=item add_root STRUCTURE + +{Tree} -> ({Tree}R) + +=item expand_Shapiro COARSE + +add S for stacks to coarse struct + +=item expand_Full STRUCTURE + +Full -> FFull + +=item unexpand_Full FSTRUCTURE + +FFull -> Full + +=item unweight WCOARSE + +remove weights from coarse struct + +=item unexpand_aligned_F ALIGN + + + +=item parse_structure STRUCTURE + +computes structure statistics, and fills the following global variables: + +$loops [int] number of loops (and stacks) +$unpaired [int] number of unpaired positions +$pairs [int] number of paired positions +$loop_size[int *] holds all loop sizes +$loop_degree[int *] holds all loop degrees +$helix_size[int *] holds all helix lengths + +=back + +from treedist.h: routines for computing tree-edit distances between structures + +=over 4 + +=item make_tree STRUCTURE + +make input for tree_edit_distance (a Tree * pointer). + +=item tree_edit_distance T1, T2 + +compare to structures using tree editing. C, C must have been +created using C + +=item print_tree T + +mainly for debugging + +=item free_tree T + +free space allocated by make_tree + +=back + +from stringdist.h routines to compute structure distances via string-editing + +=over 4 + +=item Make_swString STRUCTURE + +[ returns swString * ] +make input for string_edit_distance + +=item string_edit_distance S1, S2 + +[ returns float ] +compare to structures using string alignment. C, C should be +created using C + +=back + +from profiledist + +=over + +=item Make_bp_profile LENGTH + +[ returns (float *) ] +condense pair probability matrix C into a vector containing +probabilities for upstream paired, downstream paired and +unpaired. This resulting probability profile is used as input for +profile_edit_distance + +=item profile_edit_distance T1, T2 + +[ returns float ] +align two probability profiles produced by C + +=item print_bppm T + +[ returns void ] +print string representation of probability profile + +=item free_profile T + +[ returns void ] +free space allocated in Make_bp_profile + +=back + +Global variables for computing structure distances + +=over 4 + +=item $edit_backtrack [int] + +set to 1 if you want backtracking + +=item $aligned_line [(char *)[2]] + +containes alignmed structures after computing structure distance with +C + +=item $cost_matrix [int] + +0 usual costs (default), 1 Shapiro's costs + +=back + +=head2 Utilities (from utils.h) + +=over 4 + +=item space SIZE + +allocate memory from C. Usually not needed in Perl + +=item nrerror MESSGAE + +die with error message. Better use Perl's C + +=item $xsubi [unsigned short[3]] + +libRNA uses the rand48 48bit random number generator if available, the +current random number is always stored in $xsubi. + +=item init_rand + +initialize the $xsubi random number from current time + +=item urn + +returns a random number between 0 and 1 using the random number +generator from the RNA library. + +=item int_urn FROM, TO + +returns random integer in the range [FROM..TO] + +=item time_stamp + +current date in a string. In perl you might as well use C + +=item random_string LENGTH, SYMBOLS + +returns a string of length LENGTH using characters from the string +SYMBOLS + +=item hamming S1, S2 + +calculate hamming distance of the strings C and C. + + +=item pack_structure STRUCTURE + +pack secondary structure, using a 5:1 compression via 3 +encoding. Returns the packed string. + +=item unpack_structure PACKED + +unpacks a secondary structure packed with pack_structure + +=item make_pair_table STRUCTURE + +returns a pair table as a newly allocated (short *) C array, such +that: table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] +contains the length of the structure. + +=item bp_distance STRUCTURE1, STRUCTURE2 + +returns the base pair distance of the two STRUCTURES. dist = {number +of base pairs in one structure but not in the other} same as edit +distance with open-pair close-pair as move-set + +=back + +from PS_plot.h + +=over 4 + +=item PS_rna_plot SEQUENCE, STRUCTURE, FILENAME + +write PostScript drawing of structure to FILENAME. Returns 1 on +sucess, 0 else. + +=item PS_rna_plot_a SEQUENCE, STRUCTURE, FILENAME, PRE, POST + +write PostScript drawing of structure to FILENAME. The strings PRE and +POST contain PostScript code that is included verbatim in the plot just +before (after) the data. Returns 1 on sucess, 0 else. + +=item gmlRNA SEQUENCE, STRUCTURE, FILENAME, OPTION + +write structure drawing in gml (Graph Meta Language) to +FILENAME. OPTION should be a single character. If uppercase the gml +output will include the SEQUENCE as node labels. IF OPTION equal 'x' +or 'X' write graph with coordinates (else only connectivity +information). Returns 1 on sucess, 0 else. + +=item ssv_rna_plot SEQUENCE, STRUCTURE, SSFILE + +write structure drfawing as coord file for SStructView Returns 1 on +sucess, 0 else. + +=item xrna_plot SEQUENCE, STRUCTURE, SSFILE + +write structure drawing as ".ss" file for further editing in XRNA. +Returns 1 on sucess, 0 else. + +=item PS_dot_plot SEQUENCE, FILENAME + +write a PostScript dot plot of the pair probability matix to +FILENAME. Returns 1 on sucess, 0 else. + +=item $rna_plot_type [int] + +Select layout algorithm for structure drawings. Currently available +0= simple coordinates, 1= naview, default 1. + +=back + +from read_epars.c + +=over 4 + +=item read_parameter_file FILENAME + +read energy parameters from FILENAME + +=item write_parameter_file FILENAME + +write energy parameters to FILENAME + +=back + +=head2 SWIG helper functions + +The package includes generic helper functions to access C arrays +of type C, C and C, such as: + +=over 4 + +=item intP_getitem POINTER, INDEX + +return the element INDEX from the array + +=item intP_setitem POINTER, INDEX, VALUE + +set element INDEX to VALUE + +=item new_intP NELEM + +allocate a new C array of integers with NELEM elements and return the pointer + +=item delete_intP POINTER + +deletes the C array by calling free() + +=back + +substituting C with C or C gives the corresponding +functions for arrays of float or double. You need to know the correct C +type however, and the function work only for arrays of simple types. + +On the lowest level the C function gives direct access to any data +in the form of a Perl string. + +=over + +=item cdata POINTER, SIZE + +copies SIZE bytes at POINTER to a Perl string (with binary data) + +=item memmove POINTER, STRING + +copies the (binary) string STRING to the memory location pointed to by +POINTER. + + +=back + +In combination with Perl's C this provides a generic way to convert +C data structures to Perl. E.g. + + RNA::parse_structure($structure); # fills the $RNA::loop_degree array + @ldegrees = unpack "I*", RNA::cdata($RNA::loop_degree, ($RNA::loops+1)*4); + +Warning: using these functions with wrong arguments will corrupt your +memory and lead to a segmentation fault. + +=head1 AUTHOR + +Ivo L. Hofacker + +=cut + +# ---------- BASE METHODS ------------- + +package RNA; + +sub TIEHASH { + my ($classname,$obj) = @_; + return bless $obj, $classname; +} + +sub CLEAR { } + +sub FIRSTKEY { } + +sub NEXTKEY { } + +sub FETCH { + my ($self,$field) = @_; + my $member_func = "swig_${field}_get"; + $self->$member_func(); +} + +sub STORE { + my ($self,$field,$newval) = @_; + my $member_func = "swig_${field}_set"; + $self->$member_func($newval); +} + +sub this { + my $ptr = shift; + return tied(%$ptr); +} + + +# ------- FUNCTION WRAPPERS -------- + +package RNA; + +*new_intP = *RNAc::new_intP; +*delete_intP = *RNAc::delete_intP; +*intP_getitem = *RNAc::intP_getitem; +*intP_setitem = *RNAc::intP_setitem; +*new_floatP = *RNAc::new_floatP; +*delete_floatP = *RNAc::delete_floatP; +*floatP_getitem = *RNAc::floatP_getitem; +*floatP_setitem = *RNAc::floatP_setitem; +*new_doubleP = *RNAc::new_doubleP; +*delete_doubleP = *RNAc::delete_doubleP; +*doubleP_getitem = *RNAc::doubleP_getitem; +*doubleP_setitem = *RNAc::doubleP_setitem; +*new_shortP = *RNAc::new_shortP; +*delete_shortP = *RNAc::delete_shortP; +*shortP_getitem = *RNAc::shortP_getitem; +*shortP_setitem = *RNAc::shortP_setitem; +*cdata = *RNAc::cdata; +*memmove = *RNAc::memmove; +*fold = *RNAc::fold; +*energy_of_struct = *RNAc::energy_of_struct; +*free_arrays = *RNAc::free_arrays; +*initialize_fold = *RNAc::initialize_fold; +*update_fold_params = *RNAc::update_fold_params; +*cofold = *RNAc::cofold; +*free_co_arrays = *RNAc::free_co_arrays; +*initialize_cofold = *RNAc::initialize_cofold; +*update_cofold_params = *RNAc::update_cofold_params; +*pf_fold = *RNAc::pf_fold; +*init_pf_fold = *RNAc::init_pf_fold; +*free_pf_arrays = *RNAc::free_pf_arrays; +*update_pf_params = *RNAc::update_pf_params; +*bppm_symbol = *RNAc::bppm_symbol; +*mean_bp_dist = *RNAc::mean_bp_dist; +*pbacktrack = *RNAc::pbacktrack; +*inverse_fold = *RNAc::inverse_fold; +*inverse_pf_fold = *RNAc::inverse_pf_fold; +*option_string = *RNAc::option_string; +*subopt = *RNAc::subopt; +*get_pr = *RNAc::get_pr; +*b2HIT = *RNAc::b2HIT; +*b2C = *RNAc::b2C; +*b2Shapiro = *RNAc::b2Shapiro; +*add_root = *RNAc::add_root; +*expand_Shapiro = *RNAc::expand_Shapiro; +*expand_Full = *RNAc::expand_Full; +*unexpand_Full = *RNAc::unexpand_Full; +*unweight = *RNAc::unweight; +*unexpand_aligned_F = *RNAc::unexpand_aligned_F; +*parse_structure = *RNAc::parse_structure; +*make_tree = *RNAc::make_tree; +*tree_edit_distance = *RNAc::tree_edit_distance; +*print_tree = *RNAc::print_tree; +*free_tree = *RNAc::free_tree; +*Make_swString = *RNAc::Make_swString; +*string_edit_distance = *RNAc::string_edit_distance; +*Make_bp_profile = *RNAc::Make_bp_profile; +*profile_edit_distance = *RNAc::profile_edit_distance; +*print_bppm = *RNAc::print_bppm; +*free_profile = *RNAc::free_profile; +*space = *RNAc::space; +*xrealloc = *RNAc::xrealloc; +*nrerror = *RNAc::nrerror; +*init_rand = *RNAc::init_rand; +*urn = *RNAc::urn; +*int_urn = *RNAc::int_urn; +*filecopy = *RNAc::filecopy; +*time_stamp = *RNAc::time_stamp; +*random_string = *RNAc::random_string; +*hamming = *RNAc::hamming; +*get_line = *RNAc::get_line; +*pack_structure = *RNAc::pack_structure; +*unpack_structure = *RNAc::unpack_structure; +*make_pair_table = *RNAc::make_pair_table; +*bp_distance = *RNAc::bp_distance; +*read_parameter_file = *RNAc::read_parameter_file; +*write_parameter_file = *RNAc::write_parameter_file; +*deref_any = *RNAc::deref_any; +*scale_parameters = *RNAc::scale_parameters; +*copy_parameters = *RNAc::copy_parameters; +*set_parameters = *RNAc::set_parameters; +*get_aligned_line = *RNAc::get_aligned_line; +*make_loop_index = *RNAc::make_loop_index; +*energy_of_move = *RNAc::energy_of_move; +*PS_rna_plot = *RNAc::PS_rna_plot; +*PS_rna_plot_a = *RNAc::PS_rna_plot_a; +*gmlRNA = *RNAc::gmlRNA; +*ssv_rna_plot = *RNAc::ssv_rna_plot; +*svg_rna_plot = *RNAc::svg_rna_plot; +*xrna_plot = *RNAc::xrna_plot; +*PS_dot_plot = *RNAc::PS_dot_plot; +*PS_color_dot_plot = *RNAc::PS_color_dot_plot; +*PS_dot_plot_list = *RNAc::PS_dot_plot_list; + +############# Class : RNA::intArray ############## + +package RNA::intArray; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = RNAc::new_intArray(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_intArray($self); + delete $OWNER{$self}; + } +} + +*getitem = *RNAc::intArray_getitem; +*setitem = *RNAc::intArray_setitem; +*cast = *RNAc::intArray_cast; +*frompointer = *RNAc::intArray_frompointer; +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::floatArray ############## + +package RNA::floatArray; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = RNAc::new_floatArray(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_floatArray($self); + delete $OWNER{$self}; + } +} + +*getitem = *RNAc::floatArray_getitem; +*setitem = *RNAc::floatArray_setitem; +*cast = *RNAc::floatArray_cast; +*frompointer = *RNAc::floatArray_frompointer; +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::doubleArray ############## + +package RNA::doubleArray; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = RNAc::new_doubleArray(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_doubleArray($self); + delete $OWNER{$self}; + } +} + +*getitem = *RNAc::doubleArray_getitem; +*setitem = *RNAc::doubleArray_setitem; +*cast = *RNAc::doubleArray_cast; +*frompointer = *RNAc::doubleArray_frompointer; +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::bondT ############## + +package RNA::bondT; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +*swig_i_get = *RNAc::bondT_i_get; +*swig_i_set = *RNAc::bondT_i_set; +*swig_j_get = *RNAc::bondT_j_get; +*swig_j_set = *RNAc::bondT_j_set; +*get = *RNAc::bondT_get; +sub new { + my $pkg = shift; + my $self = RNAc::new_bondT(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_bondT($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::SOLUTION ############## + +package RNA::SOLUTION; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +*swig_energy_get = *RNAc::SOLUTION_energy_get; +*swig_energy_set = *RNAc::SOLUTION_energy_set; +*swig_structure_get = *RNAc::SOLUTION_structure_get; +*swig_structure_set = *RNAc::SOLUTION_structure_set; +*get = *RNAc::SOLUTION_get; +*size = *RNAc::SOLUTION_size; +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_SOLUTION($self); + delete $OWNER{$self}; + } +} + +sub new { + my $pkg = shift; + my $self = RNAc::new_SOLUTION(@_); + bless $self, $pkg if defined($self); +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::cpair ############## + +package RNA::cpair; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +*swig_i_get = *RNAc::cpair_i_get; +*swig_i_set = *RNAc::cpair_i_set; +*swig_j_get = *RNAc::cpair_j_get; +*swig_j_set = *RNAc::cpair_j_set; +*swig_mfe_get = *RNAc::cpair_mfe_get; +*swig_mfe_set = *RNAc::cpair_mfe_set; +*swig_p_get = *RNAc::cpair_p_get; +*swig_p_set = *RNAc::cpair_p_set; +*swig_hue_get = *RNAc::cpair_hue_get; +*swig_hue_set = *RNAc::cpair_hue_set; +*swig_sat_get = *RNAc::cpair_sat_get; +*swig_sat_set = *RNAc::cpair_sat_set; +sub new { + my $pkg = shift; + my $self = RNAc::new_cpair(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_cpair($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::plist ############## + +package RNA::plist; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +*swig_i_get = *RNAc::plist_i_get; +*swig_i_set = *RNAc::plist_i_set; +*swig_j_get = *RNAc::plist_j_get; +*swig_j_set = *RNAc::plist_j_set; +*swig_p_get = *RNAc::plist_p_get; +*swig_p_set = *RNAc::plist_p_set; +sub new { + my $pkg = shift; + my $self = RNAc::new_plist(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_plist($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +# ------- VARIABLE STUBS -------- + +package RNA; + +*VERSION = *RNAc::VERSION; +*symbolset = *RNAc::symbolset; +*final_cost = *RNAc::final_cost; +*give_up = *RNAc::give_up; +*noGU = *RNAc::noGU; +*no_closingGU = *RNAc::no_closingGU; +*tetra_loop = *RNAc::tetra_loop; +*energy_set = *RNAc::energy_set; +*dangles = *RNAc::dangles; +*nonstandards = *RNAc::nonstandards; +*temperature = *RNAc::temperature; +*james_rule = *RNAc::james_rule; +*logML = *RNAc::logML; +*cut_point = *RNAc::cut_point; + +my %__base_pair_hash; +tie %__base_pair_hash,"RNA::bondT", $RNAc::base_pair; +$base_pair= \%__base_pair_hash; +bless $base_pair, RNA::bondT; +*pr = *RNAc::pr; +*iindx = *RNAc::iindx; +*pf_scale = *RNAc::pf_scale; +*fold_constrained = *RNAc::fold_constrained; +*do_backtrack = *RNAc::do_backtrack; +*noLonelyPairs = *RNAc::noLonelyPairs; +*backtrack_type = *RNAc::backtrack_type; +*subopt_sorted = *RNAc::subopt_sorted; +*loop_size = *RNAc::loop_size; +*helix_size = *RNAc::helix_size; +*loop_degree = *RNAc::loop_degree; +*loops = *RNAc::loops; +*unpaired = *RNAc::unpaired; +*pairs = *RNAc::pairs; +*edit_backtrack = *RNAc::edit_backtrack; +*aligned_line = *RNAc::aligned_line; +*cost_matrix = *RNAc::cost_matrix; +*xsubi = *RNAc::xsubi; +*rna_plot_type = *RNAc::rna_plot_type; +1; diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA_wrap.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA_wrap.c new file mode 100755 index 000000000..6aba3c290 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA_wrap.c @@ -0,0 +1,6502 @@ +/* ---------------------------------------------------------------------------- + * This file was automatically generated by SWIG (http://www.swig.org). + * Version 1.3.24 + * + * This file is not intended to be easily readable and contains a number of + * coding conventions designed to improve portability and efficiency. Do not make + * changes to this file unless you know what you are doing--modify the SWIG + * interface file instead. + * ----------------------------------------------------------------------------- */ + + +#ifndef SWIG_TEMPLATE_DISAMBIGUATOR +# if defined(__SUNPRO_CC) +# define SWIG_TEMPLATE_DISAMBIGUATOR template +# else +# define SWIG_TEMPLATE_DISAMBIGUATOR +# endif +#endif + +/*********************************************************************** + * swigrun.swg + * + * This file contains generic CAPI SWIG runtime support for pointer + * type checking. + * + ************************************************************************/ + +/* This should only be incremented when either the layout of swig_type_info changes, + or for whatever reason, the runtime changes incompatibly */ +#define SWIG_RUNTIME_VERSION "1" + +/* define SWIG_TYPE_TABLE_NAME as "SWIG_TYPE_TABLE" */ +#ifdef SWIG_TYPE_TABLE +#define SWIG_QUOTE_STRING(x) #x +#define SWIG_EXPAND_AND_QUOTE_STRING(x) SWIG_QUOTE_STRING(x) +#define SWIG_TYPE_TABLE_NAME SWIG_EXPAND_AND_QUOTE_STRING(SWIG_TYPE_TABLE) +#else +#define SWIG_TYPE_TABLE_NAME +#endif + +#include + +#ifndef SWIGINLINE +#if defined(__cplusplus) || (defined(__GNUC__) && !defined(__STRICT_ANSI__)) +# define SWIGINLINE inline +#else +# define SWIGINLINE +#endif +#endif + +/* + You can use the SWIGRUNTIME and SWIGRUNTIMEINLINE macros for + creating a static or dynamic library from the swig runtime code. + In 99.9% of the cases, swig just needs to declare them as 'static'. + + But only do this if is strictly necessary, ie, if you have problems + with your compiler or so. +*/ +#ifndef SWIGRUNTIME +#define SWIGRUNTIME static +#endif +#ifndef SWIGRUNTIMEINLINE +#define SWIGRUNTIMEINLINE SWIGRUNTIME SWIGINLINE +#endif + +#ifdef __cplusplus +extern "C" { +#endif + +typedef void *(*swig_converter_func)(void *); +typedef struct swig_type_info *(*swig_dycast_func)(void **); + +typedef struct swig_type_info { + const char *name; + swig_converter_func converter; + const char *str; + void *clientdata; + swig_dycast_func dcast; + struct swig_type_info *next; + struct swig_type_info *prev; +} swig_type_info; + +/* + Compare two type names skipping the space characters, therefore + "char*" == "char *" and "Class" == "Class", etc. + + Return 0 when the two name types are equivalent, as in + strncmp, but skipping ' '. +*/ +SWIGRUNTIME int +SWIG_TypeNameComp(const char *f1, const char *l1, + const char *f2, const char *l2) { + for (;(f1 != l1) && (f2 != l2); ++f1, ++f2) { + while ((*f1 == ' ') && (f1 != l1)) ++f1; + while ((*f2 == ' ') && (f2 != l2)) ++f2; + if (*f1 != *f2) return *f1 - *f2; + } + return (l1 - f1) - (l2 - f2); +} + +/* + Check type equivalence in a name list like ||... +*/ +SWIGRUNTIME int +SWIG_TypeEquiv(const char *nb, const char *tb) { + int equiv = 0; + const char* te = tb + strlen(tb); + const char* ne = nb; + while (!equiv && *ne) { + for (nb = ne; *ne; ++ne) { + if (*ne == '|') break; + } + equiv = SWIG_TypeNameComp(nb, ne, tb, te) == 0; + if (*ne) ++ne; + } + return equiv; +} + +/* + Register a type mapping with the type-checking +*/ +SWIGRUNTIME swig_type_info * +SWIG_TypeRegisterTL(swig_type_info **tl, swig_type_info *ti) { + swig_type_info *tc, *head, *ret, *next; + /* Check to see if this type has already been registered */ + tc = *tl; + while (tc) { + /* check simple type equivalence */ + int typeequiv = (strcmp(tc->name, ti->name) == 0); + /* check full type equivalence, resolving typedefs */ + if (!typeequiv) { + /* only if tc is not a typedef (no '|' on it) */ + if (tc->str && ti->str && !strstr(tc->str,"|")) { + typeequiv = SWIG_TypeEquiv(ti->str,tc->str); + } + } + if (typeequiv) { + /* Already exists in the table. Just add additional types to the list */ + if (ti->clientdata) tc->clientdata = ti->clientdata; + head = tc; + next = tc->next; + goto l1; + } + tc = tc->prev; + } + head = ti; + next = 0; + + /* Place in list */ + ti->prev = *tl; + *tl = ti; + + /* Build linked lists */ + l1: + ret = head; + tc = ti + 1; + /* Patch up the rest of the links */ + while (tc->name) { + head->next = tc; + tc->prev = head; + head = tc; + tc++; + } + if (next) next->prev = head; + head->next = next; + + return ret; +} + +/* + Check the typename +*/ +SWIGRUNTIME swig_type_info * +SWIG_TypeCheck(const char *c, swig_type_info *ty) { + swig_type_info *s; + if (!ty) return 0; /* Void pointer */ + s = ty->next; /* First element always just a name */ + do { + if (strcmp(s->name,c) == 0) { + if (s == ty->next) return s; + /* Move s to the top of the linked list */ + s->prev->next = s->next; + if (s->next) { + s->next->prev = s->prev; + } + /* Insert s as second element in the list */ + s->next = ty->next; + if (ty->next) ty->next->prev = s; + ty->next = s; + s->prev = ty; + return s; + } + s = s->next; + } while (s && (s != ty->next)); + return 0; +} + +/* + Cast a pointer up an inheritance hierarchy +*/ +SWIGRUNTIMEINLINE void * +SWIG_TypeCast(swig_type_info *ty, void *ptr) { + return ((!ty) || (!ty->converter)) ? ptr : (*ty->converter)(ptr); +} + +/* + Dynamic pointer casting. Down an inheritance hierarchy +*/ +SWIGRUNTIME swig_type_info * +SWIG_TypeDynamicCast(swig_type_info *ty, void **ptr) { + swig_type_info *lastty = ty; + if (!ty || !ty->dcast) return ty; + while (ty && (ty->dcast)) { + ty = (*ty->dcast)(ptr); + if (ty) lastty = ty; + } + return lastty; +} + +/* + Return the name associated with this type +*/ +SWIGRUNTIMEINLINE const char * +SWIG_TypeName(const swig_type_info *ty) { + return ty->name; +} + +/* + Return the pretty name associated with this type, + that is an unmangled type name in a form presentable to the user. +*/ +SWIGRUNTIME const char * +SWIG_TypePrettyName(const swig_type_info *type) { + /* The "str" field contains the equivalent pretty names of the + type, separated by vertical-bar characters. We choose + to print the last name, as it is often (?) the most + specific. */ + if (type->str != NULL) { + const char *last_name = type->str; + const char *s; + for (s = type->str; *s; s++) + if (*s == '|') last_name = s+1; + return last_name; + } + else + return type->name; +} + +/* + Search for a swig_type_info structure +*/ +SWIGRUNTIME swig_type_info * +SWIG_TypeQueryTL(swig_type_info *tl, const char *name) { + swig_type_info *ty = tl; + while (ty) { + if (ty->str && (SWIG_TypeEquiv(ty->str,name))) return ty; + if (ty->name && (strcmp(name,ty->name) == 0)) return ty; + ty = ty->prev; + } + return 0; +} + +/* + Set the clientdata field for a type +*/ +SWIGRUNTIME void +SWIG_TypeClientDataTL(swig_type_info *tl, swig_type_info *ti, void *clientdata) { + swig_type_info *tc, *equiv; + if (ti->clientdata) return; + /* if (ti->clientdata == clientdata) return; */ + ti->clientdata = clientdata; + equiv = ti->next; + while (equiv) { + if (!equiv->converter) { + tc = tl; + while (tc) { + if ((strcmp(tc->name, equiv->name) == 0)) + SWIG_TypeClientDataTL(tl,tc,clientdata); + tc = tc->prev; + } + } + equiv = equiv->next; + } +} + +/* + Pack binary data into a string +*/ +SWIGRUNTIME char * +SWIG_PackData(char *c, void *ptr, size_t sz) { + static char hex[17] = "0123456789abcdef"; + unsigned char *u = (unsigned char *) ptr; + const unsigned char *eu = u + sz; + register unsigned char uu; + for (; u != eu; ++u) { + uu = *u; + *(c++) = hex[(uu & 0xf0) >> 4]; + *(c++) = hex[uu & 0xf]; + } + return c; +} + +/* + Unpack binary data from a string +*/ +SWIGRUNTIME const char * +SWIG_UnpackData(const char *c, void *ptr, size_t sz) { + register unsigned char *u = (unsigned char *) ptr; + register const unsigned char *eu = u + sz; + for (; u != eu; ++u) { + register int d = *(c++); + register unsigned char uu = 0; + if ((d >= '0') && (d <= '9')) + uu = ((d - '0') << 4); + else if ((d >= 'a') && (d <= 'f')) + uu = ((d - ('a'-10)) << 4); + else + return (char *) 0; + d = *(c++); + if ((d >= '0') && (d <= '9')) + uu |= (d - '0'); + else if ((d >= 'a') && (d <= 'f')) + uu |= (d - ('a'-10)); + else + return (char *) 0; + *u = uu; + } + return c; +} + +/* + This function will propagate the clientdata field of type to any new + swig_type_info structures that have been added into the list of + equivalent types. It is like calling SWIG_TypeClientData(type, + clientdata) a second time. +*/ +SWIGRUNTIME void +SWIG_PropagateClientDataTL(swig_type_info *tl, swig_type_info *type) { + swig_type_info *equiv = type->next; + swig_type_info *tc; + if (!type->clientdata) return; + while (equiv) { + if (!equiv->converter) { + tc = tl; + while (tc) { + if ((strcmp(tc->name, equiv->name) == 0) && !tc->clientdata) + SWIG_TypeClientDataTL(tl,tc, type->clientdata); + tc = tc->prev; + } + } + equiv = equiv->next; + } +} + +/* + Pack 'void *' into a string buffer. +*/ +SWIGRUNTIME char * +SWIG_PackVoidPtr(char *buff, void *ptr, const char *name, size_t bsz) { + char *r = buff; + if ((2*sizeof(void *) + 2) > bsz) return 0; + *(r++) = '_'; + r = SWIG_PackData(r,&ptr,sizeof(void *)); + if (strlen(name) + 1 > (bsz - (r - buff))) return 0; + strcpy(r,name); + return buff; +} + +SWIGRUNTIME const char * +SWIG_UnpackVoidPtr(const char *c, void **ptr, const char *name) { + if (*c != '_') { + if (strcmp(c,"NULL") == 0) { + *ptr = (void *) 0; + return name; + } else { + return 0; + } + } + return SWIG_UnpackData(++c,ptr,sizeof(void *)); +} + +SWIGRUNTIME char * +SWIG_PackDataName(char *buff, void *ptr, size_t sz, const char *name, size_t bsz) { + char *r = buff; + size_t lname = (name ? strlen(name) : 0); + if ((2*sz + 2 + lname) > bsz) return 0; + *(r++) = '_'; + r = SWIG_PackData(r,ptr,sz); + if (lname) { + strncpy(r,name,lname+1); + } else { + *r = 0; + } + return buff; +} + +SWIGRUNTIME const char * +SWIG_UnpackDataName(const char *c, void *ptr, size_t sz, const char *name) { + if (*c != '_') { + if (strcmp(c,"NULL") == 0) { + memset(ptr,0,sz); + return name; + } else { + return 0; + } + } + return SWIG_UnpackData(++c,ptr,sz); +} + +#ifdef __cplusplus +} +#endif + +/*********************************************************************** + * common.swg + * + * This file contains generic SWIG runtime support for pointer + * type checking as well as a few commonly used macros to control + * external linkage. + * + * Author : David Beazley (beazley@cs.uchicago.edu) + * + * Copyright (c) 1999-2000, The University of Chicago + * + * This file may be freely redistributed without license or fee provided + * this copyright message remains intact. + ************************************************************************/ + + +#if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__) +# if !defined(STATIC_LINKED) +# define SWIGEXPORT(a) __declspec(dllexport) a +# else +# define SWIGEXPORT(a) a +# endif +#else +# define SWIGEXPORT(a) a +#endif + +#ifdef __cplusplus +extern "C" { +#endif + + +/*************************************************************************/ + + +/* The static type info list */ + +static swig_type_info *swig_type_list = 0; +static swig_type_info **swig_type_list_handle = &swig_type_list; + + +/* Register a type mapping with the type-checking */ +static swig_type_info * +SWIG_TypeRegister(swig_type_info *ti) { + return SWIG_TypeRegisterTL(swig_type_list_handle, ti); +} + +/* Search for a swig_type_info structure */ +static swig_type_info * +SWIG_TypeQuery(const char *name) { + return SWIG_TypeQueryTL(*swig_type_list_handle, name); +} + +/* Set the clientdata field for a type */ +static void +SWIG_TypeClientData(swig_type_info *ti, void *clientdata) { + SWIG_TypeClientDataTL(*swig_type_list_handle, ti, clientdata); +} + +/* This function will propagate the clientdata field of type to +* any new swig_type_info structures that have been added into the list +* of equivalent types. It is like calling +* SWIG_TypeClientData(type, clientdata) a second time. +*/ +static void +SWIG_PropagateClientData(swig_type_info *type) { + SWIG_PropagateClientDataTL(*swig_type_list_handle, type); +} + +#ifdef __cplusplus +} +#endif + +/* ---------------------------------------------------------------------- -*- c -*- + * perl5.swg + * + * Perl5 runtime library + * $Header: /cvsroot/swig/SWIG/Lib/perl5/perlrun.swg,v 1.20 2004/11/29 23:13:57 wuzzeb Exp $ + * ----------------------------------------------------------------------------- */ + +#define SWIGPERL +#define SWIGPERL5 +#ifdef __cplusplus +/* Needed on some windows machines---since MS plays funny games with the header files under C++ */ +#include +#include +extern "C" { +#endif +#include "EXTERN.h" +#include "perl.h" +#include "XSUB.h" + +/* Get rid of free and malloc defined by perl */ +#undef free +#undef malloc + +#ifndef pTHX_ +#define pTHX_ +#endif + +#include +#ifdef __cplusplus +} +#endif + +/* Macro to call an XS function */ + +#ifdef PERL_OBJECT +# define SWIG_CALLXS(_name) _name(cv,pPerl) +#else +# ifndef MULTIPLICITY +# define SWIG_CALLXS(_name) _name(cv) +# else +# define SWIG_CALLXS(_name) _name(PERL_GET_THX, cv) +# endif +#endif + +/* Contract support */ + +#define SWIG_contract_assert(expr,msg) if (!(expr)) { SWIG_croak(msg); } else + +/* Note: SwigMagicFuncHack is a typedef used to get the C++ compiler to just shut up already */ + +#ifdef PERL_OBJECT +#define MAGIC_PPERL CPerlObj *pPerl = (CPerlObj *) this; +typedef int (CPerlObj::*SwigMagicFunc)(SV *, MAGIC *); + +#ifdef __cplusplus +extern "C" { +#endif +typedef int (CPerlObj::*SwigMagicFuncHack)(SV *, MAGIC *); +#ifdef __cplusplus +} +#endif + +#define SWIG_MAGIC(a,b) (SV *a, MAGIC *b) +#define SWIGCLASS_STATIC +#else +#define MAGIC_PPERL +#define SWIGCLASS_STATIC static +#ifndef MULTIPLICITY +#define SWIG_MAGIC(a,b) (SV *a, MAGIC *b) +typedef int (*SwigMagicFunc)(SV *, MAGIC *); + +#ifdef __cplusplus +extern "C" { +#endif +typedef int (*SwigMagicFuncHack)(SV *, MAGIC *); +#ifdef __cplusplus +} +#endif + + +#else +#define SWIG_MAGIC(a,b) (struct interpreter *interp, SV *a, MAGIC *b) +typedef int (*SwigMagicFunc)(struct interpreter *, SV *, MAGIC *); +#ifdef __cplusplus +extern "C" { +#endif +typedef int (*SwigMagicFuncHack)(struct interpreter *, SV *, MAGIC *); +#ifdef __cplusplus +} +#endif + +#endif +#endif + +#if defined(WIN32) && defined(PERL_OBJECT) && !defined(PerlIO_exportFILE) +#define PerlIO_exportFILE(fh,fl) (FILE*)(fh) +#endif + +/* Modifications for newer Perl 5.005 releases */ + +#if !defined(PERL_REVISION) || ((PERL_REVISION >= 5) && ((PERL_VERSION < 5) || ((PERL_VERSION == 5) && (PERL_SUBVERSION < 50)))) +# ifndef PL_sv_yes +# define PL_sv_yes sv_yes +# endif +# ifndef PL_sv_undef +# define PL_sv_undef sv_undef +# endif +# ifndef PL_na +# define PL_na na +# endif +#endif + +#include + +#ifdef __cplusplus +extern "C" { +#endif + +#define SWIG_OWNER 1 +#define SWIG_SHADOW 2 + +/* Common SWIG API */ + +#ifdef PERL_OBJECT +# define SWIG_ConvertPtr(obj, pp, type, flags) \ + SWIG_Perl_ConvertPtr(pPerl, obj, pp, type, flags) +# define SWIG_NewPointerObj(p, type, flags) \ + SWIG_Perl_NewPointerObj(pPerl, p, type, flags) +# define SWIG_MakePackedObj(sv, p, s, type) \ + SWIG_Perl_MakePackedObj(pPerl, sv, p, s, type) +# define SWIG_ConvertPacked(obj, p, s, type, flags) \ + SWIG_Perl_ConvertPacked(pPerl, obj, p, s, type, flags) + +#else +# define SWIG_ConvertPtr(obj, pp, type, flags) \ + SWIG_Perl_ConvertPtr(obj, pp, type, flags) +# define SWIG_NewPointerObj(p, type, flags) \ + SWIG_Perl_NewPointerObj(p, type, flags) +# define SWIG_MakePackedObj(sv, p, s, type) \ + SWIG_Perl_MakePackedObj(sv, p, s, type ) +# define SWIG_ConvertPacked(obj, p, s, type, flags) \ + SWIG_Perl_ConvertPacked(obj, p, s, type, flags) +#endif + +/* Perl-specific API */ +#ifdef PERL_OBJECT +# define SWIG_MakePtr(sv, ptr, type, flags) \ + SWIG_Perl_MakePtr(pPerl, sv, ptr, type, flags) +# define SWIG_SetError(str) \ + SWIG_Perl_SetError(pPerl, str) +#else +# define SWIG_MakePtr(sv, ptr, type, flags) \ + SWIG_Perl_MakePtr(sv, ptr, type, flags) +# define SWIG_SetError(str) \ + SWIG_Perl_SetError(str) +# define SWIG_SetErrorSV(str) \ + SWIG_Perl_SetErrorSV(str) +#endif + +#define SWIG_SetErrorf SWIG_Perl_SetErrorf + + +#ifdef PERL_OBJECT +# define SWIG_MAYBE_PERL_OBJECT CPerlObj *pPerl, +#else +# define SWIG_MAYBE_PERL_OBJECT +#endif + +static swig_type_info ** +SWIG_Perl_GetTypeListHandle() { + static void *type_pointer = (void *)0; + SV *pointer; + + /* first check if pointer already created */ + if (!type_pointer) { + pointer = get_sv("swig_runtime_data::type_pointer" SWIG_RUNTIME_VERSION SWIG_TYPE_TABLE_NAME, FALSE); + if (pointer && SvOK(pointer)) { + type_pointer = INT2PTR(swig_type_info **, SvIV(pointer)); + } + } + + return (swig_type_info **) type_pointer; +} + +/* + Search for a swig_type_info structure + */ +SWIGRUNTIMEINLINE swig_type_info * +SWIG_Perl_GetTypeList() { + swig_type_info **tlh = SWIG_Perl_GetTypeListHandle(); + return tlh ? *tlh : (swig_type_info*)0; +} + +#define SWIG_Runtime_GetTypeList SWIG_Perl_GetTypeList + +static swig_type_info * +SWIG_Perl_TypeCheckRV(SWIG_MAYBE_PERL_OBJECT SV *rv, swig_type_info *ty) { + swig_type_info *s; + if (!ty) return 0; /* Void pointer */ + s = ty->next; /* First element always just a name */ + do { + if (sv_derived_from(rv, (char *) s->name)) { + if (s == ty->next) return s; + /* Move s to the top of the linked list */ + s->prev->next = s->next; + if (s->next) { + s->next->prev = s->prev; + } + /* Insert s as second element in the list */ + s->next = ty->next; + if (ty->next) ty->next->prev = s; + ty->next = s; + s->prev = ty; + return s; + } + s = s->next; + } while (s && (s != ty->next)); + return 0; +} + +/* Function for getting a pointer value */ + +static int +SWIG_Perl_ConvertPtr(SWIG_MAYBE_PERL_OBJECT SV *sv, void **ptr, swig_type_info *_t, int flags) { + swig_type_info *tc; + void *voidptr = (void *)0; + + /* If magical, apply more magic */ + if (SvGMAGICAL(sv)) + mg_get(sv); + + /* Check to see if this is an object */ + if (sv_isobject(sv)) { + SV *tsv = (SV*) SvRV(sv); + IV tmp = 0; + if ((SvTYPE(tsv) == SVt_PVHV)) { + MAGIC *mg; + if (SvMAGICAL(tsv)) { + mg = mg_find(tsv,'P'); + if (mg) { + sv = mg->mg_obj; + if (sv_isobject(sv)) { + tmp = SvIV((SV*)SvRV(sv)); + } + } + } else { + return -1; + } + } else { + tmp = SvIV((SV*)SvRV(sv)); + } + voidptr = (void *)tmp; + if (!_t) { + *(ptr) = voidptr; + return 0; + } + } else if (! SvOK(sv)) { /* Check for undef */ + *(ptr) = (void *) 0; + return 0; + } else if (SvTYPE(sv) == SVt_RV) { /* Check for NULL pointer */ + *(ptr) = (void *) 0; + if (!SvROK(sv)) + return 0; + else + return -1; + } else { /* Don't know what it is */ + *(ptr) = (void *) 0; + return -1; + } + if (_t) { + /* Now see if the types match */ + char *_c = HvNAME(SvSTASH(SvRV(sv))); + tc = SWIG_TypeCheck(_c,_t); + if (!tc) { + *ptr = voidptr; + return -1; + } + *ptr = SWIG_TypeCast(tc,voidptr); + return 0; + } + *ptr = voidptr; + return 0; +} + +static void +SWIG_Perl_MakePtr(SWIG_MAYBE_PERL_OBJECT SV *sv, void *ptr, swig_type_info *t, int flags) { + if (ptr && (flags & SWIG_SHADOW)) { + SV *self; + SV *obj=newSV(0); + HV *hash=newHV(); + HV *stash; + sv_setref_pv(obj, (char *) t->name, ptr); + stash=SvSTASH(SvRV(obj)); + if (flags & SWIG_OWNER) { + HV *hv; + GV *gv=*(GV**)hv_fetch(stash, "OWNER", 5, TRUE); + if (!isGV(gv)) + gv_init(gv, stash, "OWNER", 5, FALSE); + hv=GvHVn(gv); + hv_store_ent(hv, obj, newSViv(1), 0); + } + sv_magic((SV *)hash, (SV *)obj, 'P', Nullch, 0); + SvREFCNT_dec(obj); + self=newRV_noinc((SV *)hash); + sv_setsv(sv, self); + SvREFCNT_dec((SV *)self); + sv_bless(sv, stash); + } + else { + sv_setref_pv(sv, (char *) t->name, ptr); + } +} + +static SWIGINLINE SV * +SWIG_Perl_NewPointerObj(SWIG_MAYBE_PERL_OBJECT void *ptr, swig_type_info *t, int flags) { + SV *result = sv_newmortal(); + SWIG_MakePtr(result, ptr, t, flags); + return result; +} + +static void + SWIG_Perl_MakePackedObj(SWIG_MAYBE_PERL_OBJECT SV *sv, void *ptr, int sz, swig_type_info *type) { + char result[1024]; + char *r = result; + if ((2*sz + 1 + strlen(type->name)) > 1000) return; + *(r++) = '_'; + r = SWIG_PackData(r,ptr,sz); + strcpy(r,type->name); + sv_setpv(sv, result); +} + +/* Convert a packed value value */ +static int +SWIG_Perl_ConvertPacked(SWIG_MAYBE_PERL_OBJECT SV *obj, void *ptr, int sz, swig_type_info *ty, int flags) { + swig_type_info *tc; + const char *c = 0; + + if ((!obj) || (!SvOK(obj))) return -1; + c = SvPV(obj, PL_na); + /* Pointer values must start with leading underscore */ + if (*c != '_') return -1; + c++; + c = SWIG_UnpackData(c,ptr,sz); + if (ty) { + tc = SWIG_TypeCheck(c,ty); + if (!tc) return -1; + } + return 0; +} + +static SWIGINLINE void +SWIG_Perl_SetError(SWIG_MAYBE_PERL_OBJECT const char *error) { + if (error) sv_setpv(perl_get_sv("@", TRUE), error); +} + +static SWIGINLINE void +SWIG_Perl_SetErrorSV(SWIG_MAYBE_PERL_OBJECT SV *error) { + if (error) sv_setsv(perl_get_sv("@", TRUE), error); +} + +static void +SWIG_Perl_SetErrorf(const char *fmt, ...) { + va_list args; + va_start(args, fmt); + sv_vsetpvfn(perl_get_sv("@", TRUE), fmt, strlen(fmt), &args, Null(SV**), 0, Null(bool*)); + va_end(args); +} + +/* Macros for low-level exception handling */ +#define SWIG_fail goto fail +#define SWIG_croak(x) { SWIG_SetError(x); goto fail; } +#define SWIG_croakSV(x) { SWIG_SetErrorSV(x); goto fail; } +/* most preprocessors do not support vararg macros :-( */ +/* #define SWIG_croakf(x...) { SWIG_SetErrorf(x); goto fail; } */ + + +typedef XS(SwigPerlWrapper); +typedef SwigPerlWrapper *SwigPerlWrapperPtr; + +/* Structure for command table */ +typedef struct { + const char *name; + SwigPerlWrapperPtr wrapper; +} swig_command_info; + +/* Information for constant table */ + +#define SWIG_INT 1 +#define SWIG_FLOAT 2 +#define SWIG_STRING 3 +#define SWIG_POINTER 4 +#define SWIG_BINARY 5 + +/* Constant information structure */ +typedef struct swig_constant_info { + int type; + const char *name; + long lvalue; + double dvalue; + void *pvalue; + swig_type_info **ptype; +} swig_constant_info; + +#ifdef __cplusplus +} +#endif + +/* Structure for variable table */ +typedef struct { + const char *name; + SwigMagicFunc set; + SwigMagicFunc get; + swig_type_info **type; +} swig_variable_info; + +/* Magic variable code */ +#ifndef PERL_OBJECT +#define swig_create_magic(s,a,b,c) _swig_create_magic(s,a,b,c) + #ifndef MULTIPLICITY + static void _swig_create_magic(SV *sv, char *name, int (*set)(SV *, MAGIC *), int (*get)(SV *,MAGIC *)) { + #else + static void _swig_create_magic(SV *sv, char *name, int (*set)(struct interpreter*, SV *, MAGIC *), int (*get)(struct interpreter*, SV *,MAGIC *)) { + #endif +#else +# define swig_create_magic(s,a,b,c) _swig_create_magic(pPerl,s,a,b,c) +static void _swig_create_magic(CPerlObj *pPerl, SV *sv, const char *name, int (CPerlObj::*set)(SV *, MAGIC *), int (CPerlObj::*get)(SV *, MAGIC *)) { +#endif + MAGIC *mg; + sv_magic(sv,sv,'U',(char *) name,strlen(name)); + mg = mg_find(sv,'U'); + mg->mg_virtual = (MGVTBL *) malloc(sizeof(MGVTBL)); + mg->mg_virtual->svt_get = (SwigMagicFuncHack) get; + mg->mg_virtual->svt_set = (SwigMagicFuncHack) set; + mg->mg_virtual->svt_len = 0; + mg->mg_virtual->svt_clear = 0; + mg->mg_virtual->svt_free = 0; +} + + + + + + +#ifdef do_open + #undef do_open +#endif +#ifdef do_close + #undef do_close +#endif +#ifdef scalar + #undef scalar +#endif +#ifdef list + #undef list +#endif +#ifdef apply + #undef apply +#endif +#ifdef convert + #undef convert +#endif +#ifdef Error + #undef Error +#endif +#ifdef form + #undef form +#endif +#ifdef vform + #undef vform +#endif +#ifdef LABEL + #undef LABEL +#endif +#ifdef METHOD + #undef METHOD +#endif +#ifdef Move + #undef Move +#endif +#ifdef yylex + #undef yylex +#endif +#ifdef yyparse + #undef yyparse +#endif +#ifdef yyerror + #undef yyerror +#endif +#ifdef invert + #undef invert +#endif +#ifdef ref + #undef ref +#endif +#ifdef ENTER + #undef ENTER +#endif + + +/* -------- TYPES TABLE (BEGIN) -------- */ + +#define SWIGTYPE_p_SOLUTION swig_types[0] +#define SWIGTYPE_p_intArray swig_types[1] +#define SWIGTYPE_p_double swig_types[2] +#define SWIGTYPE_p_bond swig_types[3] +#define SWIGTYPE_p_plist swig_types[4] +#define SWIGTYPE_p_cpair swig_types[5] +#define SWIGTYPE_p_swString swig_types[6] +#define SWIGTYPE_p_float swig_types[7] +#define SWIGTYPE_p_void swig_types[8] +#define SWIGTYPE_p_floatArray swig_types[9] +#define SWIGTYPE_p_doubleArray swig_types[10] +#define SWIGTYPE_p_p_void swig_types[11] +#define SWIGTYPE_p_short swig_types[12] +#define SWIGTYPE_p_p_char swig_types[13] +#define SWIGTYPE_p_char swig_types[14] +#define SWIGTYPE_p_unsigned_short swig_types[15] +#define SWIGTYPE_p_paramT swig_types[16] +#define SWIGTYPE_p_Tree swig_types[17] +#define SWIGTYPE_p_FILE swig_types[18] +#define SWIGTYPE_p_int swig_types[19] +static swig_type_info *swig_types[21]; + +/* -------- TYPES TABLE (END) -------- */ + +#define SWIG_init boot_RNA + +#define SWIG_name "RNAc::boot_RNA" +#define SWIG_prefix "RNAc::" + +#ifdef __cplusplus +extern "C" +#endif +#ifndef PERL_OBJECT +#ifndef MULTIPLICITY +SWIGEXPORT(void) SWIG_init (CV* cv); +#else +SWIGEXPORT(void) SWIG_init (pTHXo_ CV* cv); +#endif +#else +SWIGEXPORT(void) SWIG_init (CV *cv, CPerlObj *); +#endif + + +#include "../H/utils.h" +#include "../H/fold_vars.h" +#undef fold +#include "../H/fold.h" +#include "../H/cofold.h" +#include "../H/part_func.h" +#include "../H/PS_dot.h" +#include "../H/inverse.h" +#include "../H/RNAstruct.h" +#include "../H/treedist.h" +#include "../H/stringdist.h" +#include "../H/profiledist.h" +#include "../H/dist_vars.h" +#include "../H/pair_mat.h" +#include "../H/subopt.h" +#include "../H/energy_const.h" +#include "../H/params.h" + + +static int *new_intP(int nelements) { + return (int *) calloc(nelements,sizeof(int)); +} + +static void delete_intP(int *ary) { + free(ary); +} + +static int intP_getitem(int *ary, int index) { + return ary[index]; +} +static void intP_setitem(int *ary, int index, int value) { + ary[index] = value; +} + + +typedef int intArray; + +static intArray *new_intArray(int nelements){ + return (int *) calloc(nelements,sizeof(int)); +} +static void delete_intArray(intArray *self){ + free(self); +} +static int intArray_getitem(intArray *self,int index){ + return self[index]; +} +static void intArray_setitem(intArray *self,int index,int value){ + self[index] = value; +} +static int *intArray_cast(intArray *self){ + return self; +} +static intArray *intArray_frompointer(int *t){ + return (intArray *) t; +} + +static float *new_floatP(int nelements) { + return (float *) calloc(nelements,sizeof(float)); +} + +static void delete_floatP(float *ary) { + free(ary); +} + +static float floatP_getitem(float *ary, int index) { + return ary[index]; +} +static void floatP_setitem(float *ary, int index, float value) { + ary[index] = value; +} + + +typedef float floatArray; + +static floatArray *new_floatArray(int nelements){ + return (float *) calloc(nelements,sizeof(float)); +} +static void delete_floatArray(floatArray *self){ + free(self); +} +static float floatArray_getitem(floatArray *self,int index){ + return self[index]; +} +static void floatArray_setitem(floatArray *self,int index,float value){ + self[index] = value; +} +static float *floatArray_cast(floatArray *self){ + return self; +} +static floatArray *floatArray_frompointer(float *t){ + return (floatArray *) t; +} + +static double *new_doubleP(int nelements) { + return (double *) calloc(nelements,sizeof(double)); +} + +static void delete_doubleP(double *ary) { + free(ary); +} + +static double doubleP_getitem(double *ary, int index) { + return ary[index]; +} +static void doubleP_setitem(double *ary, int index, double value) { + ary[index] = value; +} + + +typedef double doubleArray; + +static doubleArray *new_doubleArray(int nelements){ + return (double *) calloc(nelements,sizeof(double)); +} +static void delete_doubleArray(doubleArray *self){ + free(self); +} +static double doubleArray_getitem(doubleArray *self,int index){ + return self[index]; +} +static void doubleArray_setitem(doubleArray *self,int index,double value){ + self[index] = value; +} +static double *doubleArray_cast(doubleArray *self){ + return self; +} +static doubleArray *doubleArray_frompointer(double *t){ + return (doubleArray *) t; +} + +static short *new_shortP(int nelements) { + return (short *) calloc(nelements,sizeof(short)); +} + +static void delete_shortP(short *ary) { + free(ary); +} + +static short shortP_getitem(short *ary, int index) { + return ary[index]; +} +static void shortP_setitem(short *ary, int index, short value) { + ary[index] = value; +} + + +typedef struct SWIGCDATA { + char *data; + int len; +} SWIGCDATA; + + + +static SWIGCDATA cdata_void(void *ptr, int nelements) { + + + + SWIGCDATA d; + d.data = (char *) ptr; + + + + d.len = nelements; + + return d; +} + + + char *my_fold(char *string, char *constraints, float *energy) { + char *struc; + float en; + struc = calloc(strlen(string)+1,sizeof(char)); + if (constraints && fold_constrained) + strncpy(struc, constraints, strlen(string)); + *energy = fold(string, struc); + if (constraints) + strncpy(constraints, struc, strlen(constraints)); + return(struc); + } + +float energy_of_struct(char const *,char const *); +void free_arrays(void); +void initialize_fold(int); +void update_fold_params(void); + + char *my_cofold(char *string, char *constraints, float *energy) { + char *struc; + float en; + struc = calloc(strlen(string)+1,sizeof(char)); + if (constraints && fold_constrained) + strncpy(struc, constraints, strlen(string)); + *energy = cofold(string, struc); + if (constraints) + strncpy(constraints, struc, strlen(constraints)); + return(struc); + } + +void free_co_arrays(void); +void initialize_cofold(int); +void update_cofold_params(void); + + char *my_pf_fold(char *string, char *constraints, float *energy) { + char *struc; + float en; + struc = calloc(strlen(string)+1,sizeof(char)); + if (constraints && fold_constrained) + strncpy(struc, constraints, strlen(string)); + *energy = pf_fold(string, struc); + if (constraints) + strncpy(constraints, struc, strlen(constraints)); + return(struc); + } + +void init_pf_fold(int); +void free_pf_arrays(void); +void update_pf_params(int); +char bppm_symbol(float const *); +double mean_bp_dist(int); +char *pbacktrack(char *); + + char *my_inverse_fold(char *start, const char *target, float *cost) { + char *seq; + int n; + n = strlen(target); + seq = random_string(n, symbolset); + if (start) + strncpy(seq, start, strlen(start)); + *cost = inverse_fold(seq, target); + if (start) + /* for backward compatibility modify start */ + strncpy(start, seq, strlen(start)); + return(seq); + } + + + char *my_inverse_pf_fold(char *start, const char *target, float *cost) { + char *seq; + int n; + n = strlen(target); + seq = random_string(n, symbolset); + if (start) strncpy(seq, start, n); + *cost = inverse_pf_fold(seq, target); + if (start) + /* for backward compatibility modify start */ + strncpy(start, seq, strlen(start)); + return(seq); + } + +extern char *symbolset; +extern float final_cost; +extern int give_up; +extern int noGU; +extern int no_closingGU; +extern int tetra_loop; +extern int energy_set; +extern int dangles; +extern char *nonstandards; +extern double temperature; +extern int james_rule; +extern int logML; +extern int cut_point; +static bondT *bondT_get(bondT *self,int i){ + return self+i; + } +extern bondT *base_pair; +extern double *pr; +extern int *iindx; +extern double pf_scale; +extern int fold_constrained; +extern int do_backtrack; +extern int noLonelyPairs; +extern char backtrack_type; +static SOLUTION *SOLUTION_get(SOLUTION *self,int i){ +// static int size=-1; +// if (size<0) { +// SOLUTION *s; +// for (s=self; s->structure; s++); +// size= (int) (s-self); +// } +// if (i>=size) { +// warn("value out of range"); +// return NULL; +// } + return self+i; + } +static int SOLUTION_size(SOLUTION *self){ + SOLUTION *s; + for (s=self; s->structure; s++); + return (int)(s-self); + } +static void delete_SOLUTION(SOLUTION *self){ + SOLUTION *s; + for (s=self; s->structure; s++) free(s->structure); + free(self); + } +SOLUTION *subopt(char *,char *,int,FILE *); +extern int subopt_sorted; + +double get_pr(int i, int j) { + int ii; + if (i>j) {ii=i; i=j; j=ii;} + return pr[iindx[i]-j]; +} + +Tree *make_tree(char *); +float tree_edit_distance(Tree *,Tree *); +void print_tree(Tree *); +void free_tree(Tree *); +swString *Make_swString(char *); +float string_edit_distance(swString *,swString *); +float *Make_bp_profile(int); +float profile_edit_distance(float const *,float const *); +void print_bppm(float const *); +void free_profile(float *); +void *space(unsigned int); +void *xrealloc(void *,unsigned int); +void nrerror(char const []); +void init_rand(void); +extern unsigned short xsubi[3]; +double urn(void); +int int_urn(int,int); +void filecopy(FILE *,FILE *); +char *time_stamp(void); +char *random_string(int,char const []); +int hamming(char const *,char const *); +char *get_line(FILE const *); +char *pack_structure(char const *); +char *unpack_structure(char const *); +short *make_pair_table(char const *); +int bp_distance(char const *,char const *); +void read_parameter_file(char *); +void write_parameter_file(char *); + +void *deref_any(void **ptr, int index) { + /* dereference arbitray pointer */ + return (void *) ptr[index]; +} + +paramT *scale_parameters(void); +paramT *copy_parameters(void); +paramT *set_parameters(paramT *); + +char *get_aligned_line(int i) { + i = i % 2; + return aligned_line[i]; +} + + + short *make_loop_index(const char *structure) { + /* number each position by which loop it belongs to (positions start at 0) */ + int i,j,hx,l,nl; + int length; + short *stack; + short *loop; + length = strlen(structure); + stack = (short *) space(sizeof(short)*(length+1)); + loop = (short *) space(sizeof(short)*(length+2)); + hx=l=nl=0; + for (i=0; i0) + l = loop[stack[hx-1]]; /* index of enclosing loop */ + else l=0; /* external loop has index 0 */ + if (hx<0) { + fprintf(stderr, "%s\n", structure); + nrerror("unbalanced brackets in make_pair_table"); + } + } + } + free(stack); + return loop; + } + + +float energy_of_move(const char *string, char *structure, int mi, int mj) { + extern int energy_of_struct_pt(const char *string, short * ptable, + short *s, short *s1); +#define ILLEGAL 999.; + int i,j,hx,l,nl; + int length; + short *stack, *table, *loop; + short *S, *S1; + int energy; + + if (mj<0) { + if ((structure[-mi]!='(') || (structure[-mj]!=')')) + return 1001; /* illegal delete pair */ + } else + if ((structure[mi]!='.') || (structure[mj]!='.')) + return 1002; /* illegal add pair */ + + /* make the pair table and loop index l*/ + length = strlen(structure); + stack = (short *) space(sizeof(short)*(length+1)); + loop = (short *) space(sizeof(short)*(length+2)); + table = (short *) space(sizeof(short)*(length+2)); + table[0] = length; + hx=l=nl=0; + for (i=1; i<=length; i++) { + if (structure[i-1] == '(') { + nl++; l=nl; + stack[hx++]=i; + } + loop[i]=l; + if (structure[i-1] ==')') { + j=stack[--hx]; + if (hx>0) + l = loop[stack[hx-1]]; /* index of enclosing loop */ + else l=0; /* external loop has index 0 */ + if (hx<0) { + fprintf(stderr, "%s\n", structure); + nrerror("unbalanced brackets in energy_of_move"); + } + table[i]=j; + table[j]=i; + } + } + if (hx!=0) { + fprintf(stderr, "%s\n", structure); + nrerror("unbalanced brackets in energy_of_move"); + } + + if (loop[abs(mi)+1] != loop[abs(mj)+1]) { /* not in same loop => illegal */ + free(stack); + free(loop); + free(table); + return 1003.; + } + + /* if we get here the move is legal */ + if (mj<0) { /* delete pair */ + structure[-mi] = '.'; + structure[-mj] = '.'; + table[-mi+1] = table[-mj+1] = 0; + } else { /* insert pair */ + structure[mi] = '('; + structure[mj] = ')'; + table[mi+1] = mj+1; + table[mj+1] = mi+1; + } + + S = (short *) space(sizeof(short)*(length+1)); + S[0] = length; + for (i=1; i<=length; i++) { + char *pos; + pos = strchr(Law_and_Order, string[i-1]); + if (pos==NULL) S[i]=0; + else S[i] = pos-Law_and_Order; + } + + energy = energy_of_struct_pt(string, table, S, S); + + free(S); + free(stack); + free(loop); + free(table); + return (float) energy/100.; +} + +int PS_rna_plot(char *,char *,char *); +int PS_rna_plot_a(char *,char *,char *,char *,char *); +int gmlRNA(char *,char *,char *,char); +int ssv_rna_plot(char *,char *,char *); +int svg_rna_plot(char *,char *,char *); +int xrna_plot(char *,char *,char *); +int PS_dot_plot(char *,char *); +extern int rna_plot_type; +int PS_color_dot_plot(char *,cpair *,char *); +int PS_dot_plot_list(char *,char *,struct plist *,struct plist *,char *); +#ifdef PERL_OBJECT +#define MAGIC_CLASS _wrap_RNA_var:: +class _wrap_RNA_var : public CPerlObj { +public: +#else +#define MAGIC_CLASS +#endif +SWIGCLASS_STATIC int swig_magic_readonly(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + sv = sv; mg = mg; + croak("Value is read-only."); + return 0; +} +SWIGCLASS_STATIC int _wrap_set_symbolset(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + char *_a = (char *) SvPV(sv,PL_na); + if (symbolset) free((char *) symbolset); + symbolset = (char *) malloc(strlen(_a)+1); + strcpy((char *)symbolset,_a); + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_symbolset(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + if (symbolset) { + sv_setpv((SV*)sv, (char *) symbolset); + } else { + sv_setsv((SV*)sv, &PL_sv_undef); + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_final_cost(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + final_cost = (float) SvNV(sv); + + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_final_cost(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setnv(sv, (double) final_cost); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_give_up(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + give_up = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_give_up(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) give_up); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_noGU(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + noGU = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_noGU(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) noGU); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_no_closingGU(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + no_closingGU = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_no_closingGU(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) no_closingGU); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_tetra_loop(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + tetra_loop = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_tetra_loop(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) tetra_loop); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_energy_set(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + energy_set = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_energy_set(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) energy_set); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_dangles(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + dangles = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_dangles(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) dangles); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_nonstandards(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + char *_a = (char *) SvPV(sv,PL_na); + if (nonstandards) free((char *) nonstandards); + nonstandards = (char *) malloc(strlen(_a)+1); + strcpy((char *)nonstandards,_a); + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_nonstandards(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + if (nonstandards) { + sv_setpv((SV*)sv, (char *) nonstandards); + } else { + sv_setsv((SV*)sv, &PL_sv_undef); + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_temperature(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + temperature = (double) SvNV(sv); + + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_temperature(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setnv(sv, (double) temperature); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_james_rule(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + james_rule = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_james_rule(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) james_rule); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_logML(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + logML = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_logML(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) logML); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_cut_point(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + cut_point = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_cut_point(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) cut_point); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_base_pair(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + void *temp; + if (SWIG_ConvertPtr(sv, (void **) &base_pair, SWIGTYPE_p_bond,0) < 0) { + croak("Type error in argument $argnum of base_pair. Expected _p_bond"); + } + base_pair = (bondT *) temp; + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_base_pair(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(SvRV(sv),(IV) base_pair); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_pr(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + void *temp; + if (SWIG_ConvertPtr(sv, (void **) &pr, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument $argnum of pr. Expected _p_double"); + } + pr = (double *) temp; + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_pr(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(SvRV(sv),(IV) pr); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_iindx(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + void *temp; + if (SWIG_ConvertPtr(sv, (void **) &iindx, SWIGTYPE_p_int,0) < 0) { + croak("Type error in argument $argnum of iindx. Expected _p_int"); + } + iindx = (int *) temp; + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_iindx(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(SvRV(sv),(IV) iindx); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_pf_scale(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + pf_scale = (double) SvNV(sv); + + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_pf_scale(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setnv(sv, (double) pf_scale); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_fold_constrained(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + fold_constrained = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_fold_constrained(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) fold_constrained); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_do_backtrack(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + do_backtrack = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_do_backtrack(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) do_backtrack); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_noLonelyPairs(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + noLonelyPairs = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_noLonelyPairs(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) noLonelyPairs); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_backtrack_type(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + backtrack_type = (char) *SvPV(sv,PL_na); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_backtrack_type(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setpvn((SV *) sv, &backtrack_type, 1); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_subopt_sorted(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + subopt_sorted = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_subopt_sorted(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) subopt_sorted); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_loop_size(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + int i; + int *temp; + int *b = (int *) loop_size; + if (SWIG_ConvertPtr(sv, (void **) &temp, SWIGTYPE_p_int,0) < 0) { + croak("Type error in argument $argnum of loop_size. Expected _p_int"); + } + for (i = 0; i < 1000; i++) b[i] = temp[i]; + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_loop_size(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(SvRV(sv),(IV) loop_size); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_helix_size(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + int i; + int *temp; + int *b = (int *) helix_size; + if (SWIG_ConvertPtr(sv, (void **) &temp, SWIGTYPE_p_int,0) < 0) { + croak("Type error in argument $argnum of helix_size. Expected _p_int"); + } + for (i = 0; i < 1000; i++) b[i] = temp[i]; + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_helix_size(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(SvRV(sv),(IV) helix_size); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_loop_degree(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + int i; + int *temp; + int *b = (int *) loop_degree; + if (SWIG_ConvertPtr(sv, (void **) &temp, SWIGTYPE_p_int,0) < 0) { + croak("Type error in argument $argnum of loop_degree. Expected _p_int"); + } + for (i = 0; i < 1000; i++) b[i] = temp[i]; + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_loop_degree(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(SvRV(sv),(IV) loop_degree); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_loops(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + loops = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_loops(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) loops); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_unpaired(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + unpaired = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_unpaired(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) unpaired); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_pairs(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + pairs = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_pairs(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) pairs); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_edit_backtrack(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + edit_backtrack = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_edit_backtrack(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) edit_backtrack); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_aligned_line(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + int i; + char * *temp; + char * *b = (char * *) aligned_line; + if (SWIG_ConvertPtr(sv, (void **) &temp, SWIGTYPE_p_p_char,0) < 0) { + croak("Type error in argument $argnum of aligned_line. Expected _p_p_char"); + } + for (i = 0; i < 2; i++) b[i] = temp[i]; + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_aligned_line(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(SvRV(sv),(IV) aligned_line); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_cost_matrix(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + cost_matrix = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_cost_matrix(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) cost_matrix); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_xsubi(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + { + int i; + unsigned short *temp; + unsigned short *b = (unsigned short *) xsubi; + if (SWIG_ConvertPtr(sv, (void **) &temp, SWIGTYPE_p_unsigned_short,0) < 0) { + croak("Type error in argument $argnum of xsubi. Expected _p_unsigned_short"); + } + for (i = 0; i < 3; i++) b[i] = temp[i]; + } + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_xsubi(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(SvRV(sv),(IV) xsubi); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_set_rna_plot_type(pTHX_ SV* sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + rna_plot_type = (int) SvIV(sv); + return 1; +} + + +SWIGCLASS_STATIC int _wrap_val_rna_plot_type(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + mg = mg; + sv_setiv(sv, (IV) rna_plot_type); + return 1; +} + + + + +#ifdef PERL_OBJECT +}; +#endif + +#ifdef __cplusplus +extern "C" { +#endif +XS(_wrap_new_intP) { + { + int arg1 ; + int *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_intP(nelements);"); + } + arg1 = (int) SvIV(ST(0)); + result = (int *)new_intP(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_int, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_intP) { + { + int *arg1 = (int *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_intP(ary);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_int,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_intP. Expected _p_int"); + } + } + delete_intP(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_intP_getitem) { + { + int *arg1 = (int *) 0 ; + int arg2 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: intP_getitem(ary,index);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_int,0) < 0) { + SWIG_croak("Type error in argument 1 of intP_getitem. Expected _p_int"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (int)intP_getitem(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_intP_setitem) { + { + int *arg1 = (int *) 0 ; + int arg2 ; + int arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: intP_setitem(ary,index,value);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_int,0) < 0) { + SWIG_croak("Type error in argument 1 of intP_setitem. Expected _p_int"); + } + } + arg2 = (int) SvIV(ST(1)); + arg3 = (int) SvIV(ST(2)); + intP_setitem(arg1,arg2,arg3); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_intArray) { + { + int arg1 ; + intArray *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_intArray(nelements);"); + } + arg1 = (int) SvIV(ST(0)); + result = (intArray *)new_intArray(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_intArray, SWIG_SHADOW|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_intArray) { + { + intArray *arg1 = (intArray *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_intArray(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_intArray,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_intArray. Expected _p_intArray"); + } + } + delete_intArray(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_intArray_getitem) { + { + intArray *arg1 = (intArray *) 0 ; + int arg2 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: intArray_getitem(self,index);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_intArray,0) < 0) { + SWIG_croak("Type error in argument 1 of intArray_getitem. Expected _p_intArray"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (int)intArray_getitem(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_intArray_setitem) { + { + intArray *arg1 = (intArray *) 0 ; + int arg2 ; + int arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: intArray_setitem(self,index,value);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_intArray,0) < 0) { + SWIG_croak("Type error in argument 1 of intArray_setitem. Expected _p_intArray"); + } + } + arg2 = (int) SvIV(ST(1)); + arg3 = (int) SvIV(ST(2)); + intArray_setitem(arg1,arg2,arg3); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_intArray_cast) { + { + intArray *arg1 = (intArray *) 0 ; + int *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: intArray_cast(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_intArray,0) < 0) { + SWIG_croak("Type error in argument 1 of intArray_cast. Expected _p_intArray"); + } + } + result = (int *)intArray_cast(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_int, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_intArray_frompointer) { + { + int *arg1 = (int *) 0 ; + intArray *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: intArray_frompointer(t);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_int,0) < 0) { + SWIG_croak("Type error in argument 1 of intArray_frompointer. Expected _p_int"); + } + } + result = (intArray *)intArray_frompointer(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_intArray, SWIG_SHADOW|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_floatP) { + { + int arg1 ; + float *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_floatP(nelements);"); + } + arg1 = (int) SvIV(ST(0)); + result = (float *)new_floatP(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_float, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_floatP) { + { + float *arg1 = (float *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_floatP(ary);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_floatP. Expected _p_float"); + } + } + delete_floatP(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_floatP_getitem) { + { + float *arg1 = (float *) 0 ; + int arg2 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: floatP_getitem(ary,index);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 1 of floatP_getitem. Expected _p_float"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (float)floatP_getitem(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_floatP_setitem) { + { + float *arg1 = (float *) 0 ; + int arg2 ; + float arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: floatP_setitem(ary,index,value);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 1 of floatP_setitem. Expected _p_float"); + } + } + arg2 = (int) SvIV(ST(1)); + arg3 = (float) SvNV(ST(2)); + + floatP_setitem(arg1,arg2,arg3); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_floatArray) { + { + int arg1 ; + floatArray *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_floatArray(nelements);"); + } + arg1 = (int) SvIV(ST(0)); + result = (floatArray *)new_floatArray(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_floatArray, SWIG_SHADOW|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_floatArray) { + { + floatArray *arg1 = (floatArray *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_floatArray(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_floatArray,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_floatArray. Expected _p_floatArray"); + } + } + delete_floatArray(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_floatArray_getitem) { + { + floatArray *arg1 = (floatArray *) 0 ; + int arg2 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: floatArray_getitem(self,index);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_floatArray,0) < 0) { + SWIG_croak("Type error in argument 1 of floatArray_getitem. Expected _p_floatArray"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (float)floatArray_getitem(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_floatArray_setitem) { + { + floatArray *arg1 = (floatArray *) 0 ; + int arg2 ; + float arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: floatArray_setitem(self,index,value);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_floatArray,0) < 0) { + SWIG_croak("Type error in argument 1 of floatArray_setitem. Expected _p_floatArray"); + } + } + arg2 = (int) SvIV(ST(1)); + arg3 = (float) SvNV(ST(2)); + + floatArray_setitem(arg1,arg2,arg3); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_floatArray_cast) { + { + floatArray *arg1 = (floatArray *) 0 ; + float *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: floatArray_cast(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_floatArray,0) < 0) { + SWIG_croak("Type error in argument 1 of floatArray_cast. Expected _p_floatArray"); + } + } + result = (float *)floatArray_cast(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_float, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_floatArray_frompointer) { + { + float *arg1 = (float *) 0 ; + floatArray *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: floatArray_frompointer(t);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 1 of floatArray_frompointer. Expected _p_float"); + } + } + result = (floatArray *)floatArray_frompointer(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_floatArray, SWIG_SHADOW|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_doubleP) { + { + int arg1 ; + double *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_doubleP(nelements);"); + } + arg1 = (int) SvIV(ST(0)); + result = (double *)new_doubleP(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_double, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_doubleP) { + { + double *arg1 = (double *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_doubleP(ary);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_double,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_doubleP. Expected _p_double"); + } + } + delete_doubleP(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_doubleP_getitem) { + { + double *arg1 = (double *) 0 ; + int arg2 ; + double result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: doubleP_getitem(ary,index);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_double,0) < 0) { + SWIG_croak("Type error in argument 1 of doubleP_getitem. Expected _p_double"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (double)doubleP_getitem(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_doubleP_setitem) { + { + double *arg1 = (double *) 0 ; + int arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: doubleP_setitem(ary,index,value);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_double,0) < 0) { + SWIG_croak("Type error in argument 1 of doubleP_setitem. Expected _p_double"); + } + } + arg2 = (int) SvIV(ST(1)); + arg3 = (double) SvNV(ST(2)); + + doubleP_setitem(arg1,arg2,arg3); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_doubleArray) { + { + int arg1 ; + doubleArray *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_doubleArray(nelements);"); + } + arg1 = (int) SvIV(ST(0)); + result = (doubleArray *)new_doubleArray(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_doubleArray, SWIG_SHADOW|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_doubleArray) { + { + doubleArray *arg1 = (doubleArray *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_doubleArray(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_doubleArray,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_doubleArray. Expected _p_doubleArray"); + } + } + delete_doubleArray(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_doubleArray_getitem) { + { + doubleArray *arg1 = (doubleArray *) 0 ; + int arg2 ; + double result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: doubleArray_getitem(self,index);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_doubleArray,0) < 0) { + SWIG_croak("Type error in argument 1 of doubleArray_getitem. Expected _p_doubleArray"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (double)doubleArray_getitem(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_doubleArray_setitem) { + { + doubleArray *arg1 = (doubleArray *) 0 ; + int arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: doubleArray_setitem(self,index,value);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_doubleArray,0) < 0) { + SWIG_croak("Type error in argument 1 of doubleArray_setitem. Expected _p_doubleArray"); + } + } + arg2 = (int) SvIV(ST(1)); + arg3 = (double) SvNV(ST(2)); + + doubleArray_setitem(arg1,arg2,arg3); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_doubleArray_cast) { + { + doubleArray *arg1 = (doubleArray *) 0 ; + double *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: doubleArray_cast(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_doubleArray,0) < 0) { + SWIG_croak("Type error in argument 1 of doubleArray_cast. Expected _p_doubleArray"); + } + } + result = (double *)doubleArray_cast(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_double, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_doubleArray_frompointer) { + { + double *arg1 = (double *) 0 ; + doubleArray *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: doubleArray_frompointer(t);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_double,0) < 0) { + SWIG_croak("Type error in argument 1 of doubleArray_frompointer. Expected _p_double"); + } + } + result = (doubleArray *)doubleArray_frompointer(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_doubleArray, SWIG_SHADOW|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_shortP) { + { + int arg1 ; + short *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_shortP(nelements);"); + } + arg1 = (int) SvIV(ST(0)); + result = (short *)new_shortP(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_short, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_shortP) { + { + short *arg1 = (short *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_shortP(ary);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_short,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_shortP. Expected _p_short"); + } + } + delete_shortP(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_shortP_getitem) { + { + short *arg1 = (short *) 0 ; + int arg2 ; + short result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: shortP_getitem(ary,index);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_short,0) < 0) { + SWIG_croak("Type error in argument 1 of shortP_getitem. Expected _p_short"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (short)shortP_getitem(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_shortP_setitem) { + { + short *arg1 = (short *) 0 ; + int arg2 ; + short arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: shortP_setitem(ary,index,value);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_short,0) < 0) { + SWIG_croak("Type error in argument 1 of shortP_setitem. Expected _p_short"); + } + } + arg2 = (int) SvIV(ST(1)); + arg3 = (short) SvIV(ST(2)); + shortP_setitem(arg1,arg2,arg3); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cdata) { + { + void *arg1 = (void *) 0 ; + int arg2 ; + SWIGCDATA result; + int argvi = 0; + dXSARGS; + + arg2 = 1; + if ((items < 1) || (items > 2)) { + SWIG_croak("Usage: cdata(ptr,nelements);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, 0,0) < 0) { + SWIG_croak("Type error in argument 1 of cdata. Expected _p_void"); + } + } + if (items > 1) { + arg2 = (int) SvIV(ST(1)); + } + result = cdata_void(arg1,arg2); + + { + ST(argvi) = sv_newmortal(); + sv_setpvn((SV*)ST(argvi++),(&result)->data,(&result)->len); + } + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_memmove) { + { + void *arg1 = (void *) 0 ; + void *arg2 = (void *) 0 ; + int arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: memmove(data,indata,inlen);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, 0,0) < 0) { + SWIG_croak("Type error in argument 1 of memmove. Expected _p_void"); + } + } + { + STRLEN temp; + arg2 = (void *) SvPV(ST(1),temp); + arg3 = (int) temp; + } + memmove(arg1,(void const *)arg2,arg3); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_fold) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) NULL ; + float *arg3 = (float *) 0 ; + char *result; + float temp3 ; + int argvi = 0; + dXSARGS; + + arg3 = &temp3; + if ((items < 1) || (items > 2)) { + SWIG_croak("Usage: fold(string,constraints);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (items > 1) { + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + } + result = (char *)my_fold(arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + { + if (argvi >= items) { + EXTEND(sp,1); + } + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi),(double) *(arg3)); + argvi++; + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_energy_of_struct) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: energy_of_struct(string,structure);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + result = (float)energy_of_struct((char const *)arg1,(char const *)arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_free_arrays) { + { + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: free_arrays();"); + } + free_arrays(); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_initialize_fold) { + { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: initialize_fold(length);"); + } + arg1 = (int) SvIV(ST(0)); + initialize_fold(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_update_fold_params) { + { + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: update_fold_params();"); + } + update_fold_params(); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cofold) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) NULL ; + float *arg3 = (float *) 0 ; + char *result; + float temp3 ; + int argvi = 0; + dXSARGS; + + arg3 = &temp3; + if ((items < 1) || (items > 2)) { + SWIG_croak("Usage: cofold(string,constraints);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (items > 1) { + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + } + result = (char *)my_cofold(arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + { + if (argvi >= items) { + EXTEND(sp,1); + } + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi),(double) *(arg3)); + argvi++; + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_free_co_arrays) { + { + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: free_co_arrays();"); + } + free_co_arrays(); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_initialize_cofold) { + { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: initialize_cofold(length);"); + } + arg1 = (int) SvIV(ST(0)); + initialize_cofold(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_update_cofold_params) { + { + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: update_cofold_params();"); + } + update_cofold_params(); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_pf_fold) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) NULL ; + float *arg3 = (float *) 0 ; + char *result; + float temp3 ; + int argvi = 0; + dXSARGS; + + arg3 = &temp3; + if ((items < 1) || (items > 2)) { + SWIG_croak("Usage: pf_fold(string,constraints);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (items > 1) { + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + } + result = (char *)my_pf_fold(arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + { + if (argvi >= items) { + EXTEND(sp,1); + } + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi),(double) *(arg3)); + argvi++; + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_init_pf_fold) { + { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: init_pf_fold(length);"); + } + arg1 = (int) SvIV(ST(0)); + init_pf_fold(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_free_pf_arrays) { + { + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: free_pf_arrays();"); + } + free_pf_arrays(); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_update_pf_params) { + { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: update_pf_params(length);"); + } + arg1 = (int) SvIV(ST(0)); + update_pf_params(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_bppm_symbol) { + { + float *arg1 = (float *) 0 ; + char result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: bppm_symbol(x);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 1 of bppm_symbol. Expected _p_float"); + } + } + result = (char)bppm_symbol((float const *)arg1); + + ST(argvi) = sv_newmortal(); + sv_setpvn((SV*)ST(argvi++), &result, 1); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_mean_bp_dist) { + { + int arg1 ; + double result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: mean_bp_dist(length);"); + } + arg1 = (int) SvIV(ST(0)); + result = (double)mean_bp_dist(arg1); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_pbacktrack) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: pbacktrack(sequence);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)pbacktrack(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_inverse_fold) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + float *arg3 = (float *) 0 ; + char *result; + float temp3 ; + int argvi = 0; + dXSARGS; + + arg3 = &temp3; + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: inverse_fold(start,target);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + result = (char *)my_inverse_fold(arg1,(char const *)arg2,arg3); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + { + if (argvi >= items) { + EXTEND(sp,1); + } + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi),(double) *(arg3)); + argvi++; + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_inverse_pf_fold) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + float *arg3 = (float *) 0 ; + char *result; + float temp3 ; + int argvi = 0; + dXSARGS; + + arg3 = &temp3; + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: inverse_pf_fold(start,target);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + result = (char *)my_inverse_pf_fold(arg1,(char const *)arg2,arg3); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + { + if (argvi >= items) { + EXTEND(sp,1); + } + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi),(double) *(arg3)); + argvi++; + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_bondT_i_set) { + { + bondT *arg1 = (bondT *) 0 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: bondT_i_set(self,i);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_bond,0) < 0) { + SWIG_croak("Type error in argument 1 of bondT_i_set. Expected _p_bond"); + } + } + arg2 = (int) SvIV(ST(1)); + if (arg1) (arg1)->i = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_bondT_i_get) { + { + bondT *arg1 = (bondT *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: bondT_i_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_bond,0) < 0) { + SWIG_croak("Type error in argument 1 of bondT_i_get. Expected _p_bond"); + } + } + result = (int) ((arg1)->i); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_bondT_j_set) { + { + bondT *arg1 = (bondT *) 0 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: bondT_j_set(self,j);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_bond,0) < 0) { + SWIG_croak("Type error in argument 1 of bondT_j_set. Expected _p_bond"); + } + } + arg2 = (int) SvIV(ST(1)); + if (arg1) (arg1)->j = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_bondT_j_get) { + { + bondT *arg1 = (bondT *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: bondT_j_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_bond,0) < 0) { + SWIG_croak("Type error in argument 1 of bondT_j_get. Expected _p_bond"); + } + } + result = (int) ((arg1)->j); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_bondT_get) { + { + bondT *arg1 = (bondT *) 0 ; + int arg2 ; + bondT *result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: bondT_get(self,i);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_bond,0) < 0) { + SWIG_croak("Type error in argument 1 of bondT_get. Expected _p_bond"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (bondT *)bondT_get(arg1,arg2); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_bond, SWIG_SHADOW|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_bondT) { + { + bondT *result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: new_bondT();"); + } + result = (bondT *)(bondT *) calloc(1, sizeof(bondT)); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_bond, SWIG_SHADOW|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_bondT) { + { + bondT *arg1 = (bondT *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_bondT(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_bond,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_bondT. Expected _p_bond"); + } + } + free((char *) arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_option_string) { + { + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: option_string();"); + } + result = (char *)option_string(); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_SOLUTION_energy_set) { + { + SOLUTION *arg1 = (SOLUTION *) 0 ; + float arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: SOLUTION_energy_set(self,energy);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_SOLUTION,0) < 0) { + SWIG_croak("Type error in argument 1 of SOLUTION_energy_set. Expected _p_SOLUTION"); + } + } + arg2 = (float) SvNV(ST(1)); + + if (arg1) (arg1)->energy = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_SOLUTION_energy_get) { + { + SOLUTION *arg1 = (SOLUTION *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: SOLUTION_energy_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_SOLUTION,0) < 0) { + SWIG_croak("Type error in argument 1 of SOLUTION_energy_get. Expected _p_SOLUTION"); + } + } + result = (float) ((arg1)->energy); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_SOLUTION_structure_set) { + { + SOLUTION *arg1 = (SOLUTION *) 0 ; + char *arg2 = (char *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: SOLUTION_structure_set(self,structure);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_SOLUTION,0) < 0) { + SWIG_croak("Type error in argument 1 of SOLUTION_structure_set. Expected _p_SOLUTION"); + } + } + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + { + if (arg1->structure) free((char*)arg1->structure); + if (arg2) { + arg1->structure = (char *) malloc(strlen(arg2)+1); + strcpy((char*)arg1->structure,arg2); + } else { + arg1->structure = 0; + } + } + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_SOLUTION_structure_get) { + { + SOLUTION *arg1 = (SOLUTION *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: SOLUTION_structure_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_SOLUTION,0) < 0) { + SWIG_croak("Type error in argument 1 of SOLUTION_structure_get. Expected _p_SOLUTION"); + } + } + result = (char *) ((arg1)->structure); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_SOLUTION_get) { + { + SOLUTION *arg1 = (SOLUTION *) 0 ; + int arg2 ; + SOLUTION *result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: SOLUTION_get(self,i);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_SOLUTION,0) < 0) { + SWIG_croak("Type error in argument 1 of SOLUTION_get. Expected _p_SOLUTION"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (SOLUTION *)SOLUTION_get(arg1,arg2); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_SOLUTION, SWIG_SHADOW|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_SOLUTION_size) { + { + SOLUTION *arg1 = (SOLUTION *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: SOLUTION_size(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_SOLUTION,0) < 0) { + SWIG_croak("Type error in argument 1 of SOLUTION_size. Expected _p_SOLUTION"); + } + } + result = (int)SOLUTION_size(arg1); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_SOLUTION) { + { + SOLUTION *arg1 = (SOLUTION *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_SOLUTION(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_SOLUTION,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_SOLUTION. Expected _p_SOLUTION"); + } + } + delete_SOLUTION(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_SOLUTION) { + { + SOLUTION *result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: new_SOLUTION();"); + } + result = (SOLUTION *)(SOLUTION *) calloc(1, sizeof(SOLUTION)); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_SOLUTION, SWIG_SHADOW|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_subopt) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + int arg3 ; + FILE *arg4 = (FILE *) NULL ; + SOLUTION *result; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 4)) { + SWIG_croak("Usage: subopt(seq,constraint,delta,fp);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + arg3 = (int) SvIV(ST(2)); + if (items > 3) { + { + if (SvOK(ST(3))) /* check for undef */ + arg4 = PerlIO_findFILE(IoIFP(sv_2io(ST(3)))); + else arg4 = NULL; + } + } + result = (SOLUTION *)subopt(arg1,arg2,arg3,arg4); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_SOLUTION, SWIG_SHADOW|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_get_pr) { + { + int arg1 ; + int arg2 ; + double result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: get_pr(i,j);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + result = (double)get_pr(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_b2HIT) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: b2HIT(structure);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)b2HIT(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_b2C) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: b2C(structure);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)b2C(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_b2Shapiro) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: b2Shapiro(structure);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)b2Shapiro(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_add_root) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: add_root(char *);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)add_root(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_expand_Shapiro) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: expand_Shapiro(coarse);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)expand_Shapiro(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_expand_Full) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: expand_Full(structure);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)expand_Full(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_unexpand_Full) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: unexpand_Full(ffull);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)unexpand_Full(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_unweight) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: unweight(wcoarse);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)unweight(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_unexpand_aligned_F) { + { + char **arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: unexpand_aligned_F(align);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_p_char,0) < 0) { + SWIG_croak("Type error in argument 1 of unexpand_aligned_F. Expected _p_p_char"); + } + } + unexpand_aligned_F(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_parse_structure) { + { + char *arg1 = (char *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: parse_structure(structure);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + parse_structure(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_make_tree) { + { + char *arg1 = (char *) 0 ; + Tree *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: make_tree(struc);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (Tree *)make_tree(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_Tree, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_tree_edit_distance) { + { + Tree *arg1 = (Tree *) 0 ; + Tree *arg2 = (Tree *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: tree_edit_distance(T1,T2);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_Tree,0) < 0) { + SWIG_croak("Type error in argument 1 of tree_edit_distance. Expected _p_Tree"); + } + } + { + if (SWIG_ConvertPtr(ST(1), (void **) &arg2, SWIGTYPE_p_Tree,0) < 0) { + SWIG_croak("Type error in argument 2 of tree_edit_distance. Expected _p_Tree"); + } + } + result = (float)tree_edit_distance(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_print_tree) { + { + Tree *arg1 = (Tree *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: print_tree(t);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_Tree,0) < 0) { + SWIG_croak("Type error in argument 1 of print_tree. Expected _p_Tree"); + } + } + print_tree(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_free_tree) { + { + Tree *arg1 = (Tree *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: free_tree(t);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_Tree,0) < 0) { + SWIG_croak("Type error in argument 1 of free_tree. Expected _p_Tree"); + } + } + free_tree(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_Make_swString) { + { + char *arg1 = (char *) 0 ; + swString *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: Make_swString(string);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (swString *)Make_swString(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_swString, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_string_edit_distance) { + { + swString *arg1 = (swString *) 0 ; + swString *arg2 = (swString *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: string_edit_distance(T1,T2);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_swString,0) < 0) { + SWIG_croak("Type error in argument 1 of string_edit_distance. Expected _p_swString"); + } + } + { + if (SWIG_ConvertPtr(ST(1), (void **) &arg2, SWIGTYPE_p_swString,0) < 0) { + SWIG_croak("Type error in argument 2 of string_edit_distance. Expected _p_swString"); + } + } + result = (float)string_edit_distance(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_Make_bp_profile) { + { + int arg1 ; + float *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: Make_bp_profile(length);"); + } + arg1 = (int) SvIV(ST(0)); + result = (float *)Make_bp_profile(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_float, 0|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_profile_edit_distance) { + { + float *arg1 = (float *) 0 ; + float *arg2 = (float *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: profile_edit_distance(T1,T2);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 1 of profile_edit_distance. Expected _p_float"); + } + } + { + if (SWIG_ConvertPtr(ST(1), (void **) &arg2, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 2 of profile_edit_distance. Expected _p_float"); + } + } + result = (float)profile_edit_distance((float const *)arg1,(float const *)arg2); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_print_bppm) { + { + float *arg1 = (float *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: print_bppm(T);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 1 of print_bppm. Expected _p_float"); + } + } + print_bppm((float const *)arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_free_profile) { + { + float *arg1 = (float *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: free_profile(T);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_float,0) < 0) { + SWIG_croak("Type error in argument 1 of free_profile. Expected _p_float"); + } + } + free_profile(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_space) { + { + unsigned int arg1 ; + void *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: space(size);"); + } + arg1 = (unsigned int) SvUV(ST(0)); + result = (void *)space(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_void, 0|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_xrealloc) { + { + void *arg1 = (void *) 0 ; + unsigned int arg2 ; + void *result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: xrealloc(p,size);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, 0,0) < 0) { + SWIG_croak("Type error in argument 1 of xrealloc. Expected _p_void"); + } + } + arg2 = (unsigned int) SvUV(ST(1)); + result = (void *)xrealloc(arg1,arg2); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_void, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_nrerror) { + { + char *arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: nrerror(message);"); + } + arg1 = SvPV(ST(0),PL_na); + + nrerror((char const (*))arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_init_rand) { + { + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: init_rand();"); + } + init_rand(); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_urn) { + { + double result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: urn();"); + } + result = (double)urn(); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_int_urn) { + { + int arg1 ; + int arg2 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: int_urn(from,to);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + result = (int)int_urn(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_filecopy) { + { + FILE *arg1 = (FILE *) 0 ; + FILE *arg2 = (FILE *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: filecopy(from,to);"); + } + { + if (SvOK(ST(0))) /* check for undef */ + arg1 = PerlIO_findFILE(IoIFP(sv_2io(ST(0)))); + else arg1 = NULL; + } + { + if (SvOK(ST(1))) /* check for undef */ + arg2 = PerlIO_findFILE(IoIFP(sv_2io(ST(1)))); + else arg2 = NULL; + } + filecopy(arg1,arg2); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_time_stamp) { + { + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: time_stamp();"); + } + result = (char *)time_stamp(); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_random_string) { + { + int arg1 ; + char *arg2 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: random_string(l,symbols);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = SvPV(ST(1),PL_na); + + result = (char *)random_string(arg1,(char const (*))arg2); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_hamming) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: hamming(s1,s2);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + result = (int)hamming((char const *)arg1,(char const *)arg2); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_get_line) { + { + FILE *arg1 = (FILE *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: get_line(fp);"); + } + { + if (SvOK(ST(0))) /* check for undef */ + arg1 = PerlIO_findFILE(IoIFP(sv_2io(ST(0)))); + else arg1 = NULL; + } + result = (char *)get_line((FILE const *)arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_pack_structure) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: pack_structure(struc);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)pack_structure((char const *)arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_unpack_structure) { + { + char *arg1 = (char *) 0 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: unpack_structure(packed);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (char *)unpack_structure((char const *)arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + free(result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_make_pair_table) { + { + char *arg1 = (char *) 0 ; + short *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: make_pair_table(structure);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (short *)make_pair_table((char const *)arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_short, 0|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_bp_distance) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: bp_distance(str1,str2);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + result = (int)bp_distance((char const *)arg1,(char const *)arg2); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_read_parameter_file) { + { + char *arg1 = (char *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: read_parameter_file(fname);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + read_parameter_file(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_write_parameter_file) { + { + char *arg1 = (char *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: write_parameter_file(fname);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + write_parameter_file(arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_deref_any) { + { + void **arg1 = (void **) 0 ; + int arg2 ; + void *result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: deref_any(ptr,index);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_p_void,0) < 0) { + SWIG_croak("Type error in argument 1 of deref_any. Expected _p_p_void"); + } + } + arg2 = (int) SvIV(ST(1)); + result = (void *)deref_any(arg1,arg2); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_void, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_scale_parameters) { + { + paramT *result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: scale_parameters();"); + } + result = (paramT *)scale_parameters(); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_paramT, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_copy_parameters) { + { + paramT *result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: copy_parameters();"); + } + result = (paramT *)copy_parameters(); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_paramT, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_set_parameters) { + { + paramT *arg1 = (paramT *) 0 ; + paramT *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: set_parameters(dest);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_paramT,0) < 0) { + SWIG_croak("Type error in argument 1 of set_parameters. Expected _p_paramT"); + } + } + result = (paramT *)set_parameters(arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_paramT, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_get_aligned_line) { + { + int arg1 ; + char *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: get_aligned_line(int);"); + } + arg1 = (int) SvIV(ST(0)); + result = (char *)get_aligned_line(arg1); + + ST(argvi) = sv_newmortal(); + if (result) { + sv_setpv((SV*)ST(argvi++), (char *) result); + } else { + sv_setsv((SV*)ST(argvi++), &PL_sv_undef); + } + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_make_loop_index) { + { + char *arg1 = (char *) 0 ; + short *result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: make_loop_index(structure);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (short *)make_loop_index((char const *)arg1); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_short, 0|0); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_energy_of_move) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + int arg3 ; + int arg4 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + SWIG_croak("Usage: energy_of_move(string,structure,mi,mj);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + arg3 = (int) SvIV(ST(2)); + arg4 = (int) SvIV(ST(3)); + result = (float)energy_of_move((char const *)arg1,arg2,arg3,arg4); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_PS_rna_plot) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + char *arg3 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: PS_rna_plot(string,structure,file);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + if (!SvOK((SV*) ST(2))) arg3 = 0; + else arg3 = (char *) SvPV(ST(2), PL_na); + result = (int)PS_rna_plot(arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_PS_rna_plot_a) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + char *arg3 = (char *) 0 ; + char *arg4 = (char *) 0 ; + char *arg5 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 5) || (items > 5)) { + SWIG_croak("Usage: PS_rna_plot_a(string,structure,file,pre,post);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + if (!SvOK((SV*) ST(2))) arg3 = 0; + else arg3 = (char *) SvPV(ST(2), PL_na); + if (!SvOK((SV*) ST(3))) arg4 = 0; + else arg4 = (char *) SvPV(ST(3), PL_na); + if (!SvOK((SV*) ST(4))) arg5 = 0; + else arg5 = (char *) SvPV(ST(4), PL_na); + result = (int)PS_rna_plot_a(arg1,arg2,arg3,arg4,arg5); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_gmlRNA) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + char *arg3 = (char *) 0 ; + char arg4 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + SWIG_croak("Usage: gmlRNA(string,structure,ssfile,option);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + if (!SvOK((SV*) ST(2))) arg3 = 0; + else arg3 = (char *) SvPV(ST(2), PL_na); + arg4 = (char) *SvPV(ST(3),PL_na); + result = (int)gmlRNA(arg1,arg2,arg3,arg4); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_ssv_rna_plot) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + char *arg3 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: ssv_rna_plot(string,structure,ssfile);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + if (!SvOK((SV*) ST(2))) arg3 = 0; + else arg3 = (char *) SvPV(ST(2), PL_na); + result = (int)ssv_rna_plot(arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_svg_rna_plot) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + char *arg3 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: svg_rna_plot(string,structure,ssfile);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + if (!SvOK((SV*) ST(2))) arg3 = 0; + else arg3 = (char *) SvPV(ST(2), PL_na); + result = (int)svg_rna_plot(arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_xrna_plot) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + char *arg3 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: xrna_plot(string,structure,ssfile);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + if (!SvOK((SV*) ST(2))) arg3 = 0; + else arg3 = (char *) SvPV(ST(2), PL_na); + result = (int)xrna_plot(arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_PS_dot_plot) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: PS_dot_plot(string,file);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + result = (int)PS_dot_plot(arg1,arg2); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_i_set) { + { + cpair *arg1 = (cpair *) 0 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: cpair_i_set(self,i);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_i_set. Expected _p_cpair"); + } + } + arg2 = (int) SvIV(ST(1)); + if (arg1) (arg1)->i = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_i_get) { + { + cpair *arg1 = (cpair *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: cpair_i_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_i_get. Expected _p_cpair"); + } + } + result = (int) ((arg1)->i); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_j_set) { + { + cpair *arg1 = (cpair *) 0 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: cpair_j_set(self,j);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_j_set. Expected _p_cpair"); + } + } + arg2 = (int) SvIV(ST(1)); + if (arg1) (arg1)->j = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_j_get) { + { + cpair *arg1 = (cpair *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: cpair_j_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_j_get. Expected _p_cpair"); + } + } + result = (int) ((arg1)->j); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_mfe_set) { + { + cpair *arg1 = (cpair *) 0 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: cpair_mfe_set(self,mfe);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_mfe_set. Expected _p_cpair"); + } + } + arg2 = (int) SvIV(ST(1)); + if (arg1) (arg1)->mfe = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_mfe_get) { + { + cpair *arg1 = (cpair *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: cpair_mfe_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_mfe_get. Expected _p_cpair"); + } + } + result = (int) ((arg1)->mfe); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_p_set) { + { + cpair *arg1 = (cpair *) 0 ; + float arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: cpair_p_set(self,p);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_p_set. Expected _p_cpair"); + } + } + arg2 = (float) SvNV(ST(1)); + + if (arg1) (arg1)->p = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_p_get) { + { + cpair *arg1 = (cpair *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: cpair_p_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_p_get. Expected _p_cpair"); + } + } + result = (float) ((arg1)->p); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_hue_set) { + { + cpair *arg1 = (cpair *) 0 ; + float arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: cpair_hue_set(self,hue);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_hue_set. Expected _p_cpair"); + } + } + arg2 = (float) SvNV(ST(1)); + + if (arg1) (arg1)->hue = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_hue_get) { + { + cpair *arg1 = (cpair *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: cpair_hue_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_hue_get. Expected _p_cpair"); + } + } + result = (float) ((arg1)->hue); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_sat_set) { + { + cpair *arg1 = (cpair *) 0 ; + float arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: cpair_sat_set(self,sat);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_sat_set. Expected _p_cpair"); + } + } + arg2 = (float) SvNV(ST(1)); + + if (arg1) (arg1)->sat = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_cpair_sat_get) { + { + cpair *arg1 = (cpair *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: cpair_sat_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of cpair_sat_get. Expected _p_cpair"); + } + } + result = (float) ((arg1)->sat); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_cpair) { + { + cpair *result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: new_cpair();"); + } + result = (cpair *)(cpair *) calloc(1, sizeof(cpair)); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_cpair, SWIG_SHADOW|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_cpair) { + { + cpair *arg1 = (cpair *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_cpair(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_cpair. Expected _p_cpair"); + } + } + free((char *) arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_PS_color_dot_plot) { + { + char *arg1 = (char *) 0 ; + cpair *arg2 = (cpair *) 0 ; + char *arg3 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + SWIG_croak("Usage: PS_color_dot_plot(string,pi,filename);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + { + if (SWIG_ConvertPtr(ST(1), (void **) &arg2, SWIGTYPE_p_cpair,0) < 0) { + SWIG_croak("Type error in argument 2 of PS_color_dot_plot. Expected _p_cpair"); + } + } + if (!SvOK((SV*) ST(2))) arg3 = 0; + else arg3 = (char *) SvPV(ST(2), PL_na); + result = (int)PS_color_dot_plot(arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_plist_i_set) { + { + plist *arg1 = (plist *) 0 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: plist_i_set(self,i);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 1 of plist_i_set. Expected _p_plist"); + } + } + arg2 = (int) SvIV(ST(1)); + if (arg1) (arg1)->i = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_plist_i_get) { + { + plist *arg1 = (plist *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: plist_i_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 1 of plist_i_get. Expected _p_plist"); + } + } + result = (int) ((arg1)->i); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_plist_j_set) { + { + plist *arg1 = (plist *) 0 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: plist_j_set(self,j);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 1 of plist_j_set. Expected _p_plist"); + } + } + arg2 = (int) SvIV(ST(1)); + if (arg1) (arg1)->j = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_plist_j_get) { + { + plist *arg1 = (plist *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: plist_j_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 1 of plist_j_get. Expected _p_plist"); + } + } + result = (int) ((arg1)->j); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_plist_p_set) { + { + plist *arg1 = (plist *) 0 ; + float arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: plist_p_set(self,p);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 1 of plist_p_set. Expected _p_plist"); + } + } + arg2 = (float) SvNV(ST(1)); + + if (arg1) (arg1)->p = arg2; + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_plist_p_get) { + { + plist *arg1 = (plist *) 0 ; + float result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: plist_p_get(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 1 of plist_p_get. Expected _p_plist"); + } + } + result = (float) ((arg1)->p); + + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi++), (double) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_new_plist) { + { + plist *result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: new_plist();"); + } + result = (plist *)(plist *) calloc(1, sizeof(plist)); + + ST(argvi) = sv_newmortal(); + SWIG_MakePtr(ST(argvi++), (void *) result, SWIGTYPE_p_plist, SWIG_SHADOW|SWIG_OWNER); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_delete_plist) { + { + plist *arg1 = (plist *) 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_plist(self);"); + } + { + if (SWIG_ConvertPtr(ST(0), (void **) &arg1, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 1 of delete_plist. Expected _p_plist"); + } + } + free((char *) arg1); + + + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + +XS(_wrap_PS_dot_plot_list) { + { + char *arg1 = (char *) 0 ; + char *arg2 = (char *) 0 ; + struct plist *arg3 = (struct plist *) 0 ; + struct plist *arg4 = (struct plist *) 0 ; + char *arg5 = (char *) 0 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 5) || (items > 5)) { + SWIG_croak("Usage: PS_dot_plot_list(string,filename,pl,mf,comment);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + if (!SvOK((SV*) ST(1))) arg2 = 0; + else arg2 = (char *) SvPV(ST(1), PL_na); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 3 of PS_dot_plot_list. Expected _p_plist"); + } + } + { + if (SWIG_ConvertPtr(ST(3), (void **) &arg4, SWIGTYPE_p_plist,0) < 0) { + SWIG_croak("Type error in argument 4 of PS_dot_plot_list. Expected _p_plist"); + } + } + if (!SvOK((SV*) ST(4))) arg5 = 0; + else arg5 = (char *) SvPV(ST(4), PL_na); + result = (int)PS_dot_plot_list(arg1,arg2,arg3,arg4,arg5); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); + fail: + ; + } + croak(Nullch); +} + + + +/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */ + +static void *_p_floatArrayTo_p_float(void *x) { + return (void *)((float *) ((floatArray *) x)); +} +static void *_p_intArrayTo_p_int(void *x) { + return (void *)((int *) ((intArray *) x)); +} +static void *_p_doubleArrayTo_p_double(void *x) { + return (void *)((double *) ((doubleArray *) x)); +} +static swig_type_info _swigt__p_SOLUTION[] = {{"RNA::SOLUTION", 0, "SOLUTION *", 0, 0, 0, 0},{"RNA::SOLUTION", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_intArray[] = {{"RNA::intArray", 0, "struct intArray *|intArray *", 0, 0, 0, 0},{"RNA::intArray", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_double[] = {{"_p_double", 0, "double *", 0, 0, 0, 0},{"RNA::doubleArray", _p_doubleArrayTo_p_double, 0, 0, 0, 0, 0},{"_p_double", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_bond[] = {{"RNA::bondT", 0, "struct bond *|bondT *", 0, 0, 0, 0},{"RNA::bondT", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_plist[] = {{"RNA::plist", 0, "struct plist *", 0, 0, 0, 0},{"RNA::plist", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_cpair[] = {{"RNA::cpair", 0, "struct cpair *|cpair *", 0, 0, 0, 0},{"RNA::cpair", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_swString[] = {{"_p_swString", 0, "swString *", 0, 0, 0, 0},{"_p_swString", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_float[] = {{"_p_float", 0, "float *", 0, 0, 0, 0},{"_p_float", 0, 0, 0, 0, 0, 0},{"RNA::floatArray", _p_floatArrayTo_p_float, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_void[] = {{"_p_void", 0, "void *", 0, 0, 0, 0},{"_p_void", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_floatArray[] = {{"RNA::floatArray", 0, "struct floatArray *|floatArray *", 0, 0, 0, 0},{"RNA::floatArray", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_doubleArray[] = {{"RNA::doubleArray", 0, "struct doubleArray *|doubleArray *", 0, 0, 0, 0},{"RNA::doubleArray", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_p_void[] = {{"_p_p_void", 0, "void **", 0, 0, 0, 0},{"_p_p_void", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_short[] = {{"_p_short", 0, "short *", 0, 0, 0, 0},{"_p_short", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_p_char[] = {{"_p_p_char", 0, "char **", 0, 0, 0, 0},{"_p_p_char", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_char[] = {{"_p_char", 0, "char *", 0, 0, 0, 0},{"_p_char", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_unsigned_short[] = {{"_p_unsigned_short", 0, "unsigned short *", 0, 0, 0, 0},{"_p_unsigned_short", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_paramT[] = {{"_p_paramT", 0, "paramT *", 0, 0, 0, 0},{"_p_paramT", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_Tree[] = {{"_p_Tree", 0, "Tree *", 0, 0, 0, 0},{"_p_Tree", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_FILE[] = {{"_p_FILE", 0, "FILE *", 0, 0, 0, 0},{"_p_FILE", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; +static swig_type_info _swigt__p_int[] = {{"_p_int", 0, "int *", 0, 0, 0, 0},{"RNA::intArray", _p_intArrayTo_p_int, 0, 0, 0, 0, 0},{"_p_int", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}}; + +static swig_type_info *swig_types_initial[] = { +_swigt__p_SOLUTION, +_swigt__p_intArray, +_swigt__p_double, +_swigt__p_bond, +_swigt__p_plist, +_swigt__p_cpair, +_swigt__p_swString, +_swigt__p_float, +_swigt__p_void, +_swigt__p_floatArray, +_swigt__p_doubleArray, +_swigt__p_p_void, +_swigt__p_short, +_swigt__p_p_char, +_swigt__p_char, +_swigt__p_unsigned_short, +_swigt__p_paramT, +_swigt__p_Tree, +_swigt__p_FILE, +_swigt__p_int, +0 +}; + + +/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (END) -------- */ + +static swig_constant_info swig_constants[] = { +{ SWIG_FLOAT, (char *) SWIG_prefix "VERSION", 0, (double) 0.3, 0, 0}, +{0,0,0,0,0,0} +}; +#ifdef __cplusplus +} +#endif +static swig_variable_info swig_variables[] = { + { "RNAc::symbolset", MAGIC_CLASS _wrap_set_symbolset, MAGIC_CLASS _wrap_val_symbolset,0 }, + { "RNAc::final_cost", MAGIC_CLASS _wrap_set_final_cost, MAGIC_CLASS _wrap_val_final_cost,0 }, + { "RNAc::give_up", MAGIC_CLASS _wrap_set_give_up, MAGIC_CLASS _wrap_val_give_up,0 }, + { "RNAc::noGU", MAGIC_CLASS _wrap_set_noGU, MAGIC_CLASS _wrap_val_noGU,0 }, + { "RNAc::no_closingGU", MAGIC_CLASS _wrap_set_no_closingGU, MAGIC_CLASS _wrap_val_no_closingGU,0 }, + { "RNAc::tetra_loop", MAGIC_CLASS _wrap_set_tetra_loop, MAGIC_CLASS _wrap_val_tetra_loop,0 }, + { "RNAc::energy_set", MAGIC_CLASS _wrap_set_energy_set, MAGIC_CLASS _wrap_val_energy_set,0 }, + { "RNAc::dangles", MAGIC_CLASS _wrap_set_dangles, MAGIC_CLASS _wrap_val_dangles,0 }, + { "RNAc::nonstandards", MAGIC_CLASS _wrap_set_nonstandards, MAGIC_CLASS _wrap_val_nonstandards,0 }, + { "RNAc::temperature", MAGIC_CLASS _wrap_set_temperature, MAGIC_CLASS _wrap_val_temperature,0 }, + { "RNAc::james_rule", MAGIC_CLASS _wrap_set_james_rule, MAGIC_CLASS _wrap_val_james_rule,0 }, + { "RNAc::logML", MAGIC_CLASS _wrap_set_logML, MAGIC_CLASS _wrap_val_logML,0 }, + { "RNAc::cut_point", MAGIC_CLASS _wrap_set_cut_point, MAGIC_CLASS _wrap_val_cut_point,0 }, + { "RNAc::base_pair", MAGIC_CLASS _wrap_set_base_pair, MAGIC_CLASS _wrap_val_base_pair,&SWIGTYPE_p_bond }, + { "RNAc::pr", MAGIC_CLASS _wrap_set_pr, MAGIC_CLASS _wrap_val_pr,&SWIGTYPE_p_double }, + { "RNAc::iindx", MAGIC_CLASS _wrap_set_iindx, MAGIC_CLASS _wrap_val_iindx,&SWIGTYPE_p_int }, + { "RNAc::pf_scale", MAGIC_CLASS _wrap_set_pf_scale, MAGIC_CLASS _wrap_val_pf_scale,0 }, + { "RNAc::fold_constrained", MAGIC_CLASS _wrap_set_fold_constrained, MAGIC_CLASS _wrap_val_fold_constrained,0 }, + { "RNAc::do_backtrack", MAGIC_CLASS _wrap_set_do_backtrack, MAGIC_CLASS _wrap_val_do_backtrack,0 }, + { "RNAc::noLonelyPairs", MAGIC_CLASS _wrap_set_noLonelyPairs, MAGIC_CLASS _wrap_val_noLonelyPairs,0 }, + { "RNAc::backtrack_type", MAGIC_CLASS _wrap_set_backtrack_type, MAGIC_CLASS _wrap_val_backtrack_type,0 }, + { "RNAc::subopt_sorted", MAGIC_CLASS _wrap_set_subopt_sorted, MAGIC_CLASS _wrap_val_subopt_sorted,0 }, + { "RNAc::loop_size", MAGIC_CLASS _wrap_set_loop_size, MAGIC_CLASS _wrap_val_loop_size,&SWIGTYPE_p_int }, + { "RNAc::helix_size", MAGIC_CLASS _wrap_set_helix_size, MAGIC_CLASS _wrap_val_helix_size,&SWIGTYPE_p_int }, + { "RNAc::loop_degree", MAGIC_CLASS _wrap_set_loop_degree, MAGIC_CLASS _wrap_val_loop_degree,&SWIGTYPE_p_int }, + { "RNAc::loops", MAGIC_CLASS _wrap_set_loops, MAGIC_CLASS _wrap_val_loops,0 }, + { "RNAc::unpaired", MAGIC_CLASS _wrap_set_unpaired, MAGIC_CLASS _wrap_val_unpaired,0 }, + { "RNAc::pairs", MAGIC_CLASS _wrap_set_pairs, MAGIC_CLASS _wrap_val_pairs,0 }, + { "RNAc::edit_backtrack", MAGIC_CLASS _wrap_set_edit_backtrack, MAGIC_CLASS _wrap_val_edit_backtrack,0 }, + { "RNAc::aligned_line", MAGIC_CLASS _wrap_set_aligned_line, MAGIC_CLASS _wrap_val_aligned_line,&SWIGTYPE_p_p_char }, + { "RNAc::cost_matrix", MAGIC_CLASS _wrap_set_cost_matrix, MAGIC_CLASS _wrap_val_cost_matrix,0 }, + { "RNAc::xsubi", MAGIC_CLASS _wrap_set_xsubi, MAGIC_CLASS _wrap_val_xsubi,&SWIGTYPE_p_unsigned_short }, + { "RNAc::rna_plot_type", MAGIC_CLASS _wrap_set_rna_plot_type, MAGIC_CLASS _wrap_val_rna_plot_type,0 }, +{0,0,0,0} +}; +static swig_command_info swig_commands[] = { +{"RNAc::new_intP", _wrap_new_intP}, +{"RNAc::delete_intP", _wrap_delete_intP}, +{"RNAc::intP_getitem", _wrap_intP_getitem}, +{"RNAc::intP_setitem", _wrap_intP_setitem}, +{"RNAc::new_intArray", _wrap_new_intArray}, +{"RNAc::delete_intArray", _wrap_delete_intArray}, +{"RNAc::intArray_getitem", _wrap_intArray_getitem}, +{"RNAc::intArray_setitem", _wrap_intArray_setitem}, +{"RNAc::intArray_cast", _wrap_intArray_cast}, +{"RNAc::intArray_frompointer", _wrap_intArray_frompointer}, +{"RNAc::new_floatP", _wrap_new_floatP}, +{"RNAc::delete_floatP", _wrap_delete_floatP}, +{"RNAc::floatP_getitem", _wrap_floatP_getitem}, +{"RNAc::floatP_setitem", _wrap_floatP_setitem}, +{"RNAc::new_floatArray", _wrap_new_floatArray}, +{"RNAc::delete_floatArray", _wrap_delete_floatArray}, +{"RNAc::floatArray_getitem", _wrap_floatArray_getitem}, +{"RNAc::floatArray_setitem", _wrap_floatArray_setitem}, +{"RNAc::floatArray_cast", _wrap_floatArray_cast}, +{"RNAc::floatArray_frompointer", _wrap_floatArray_frompointer}, +{"RNAc::new_doubleP", _wrap_new_doubleP}, +{"RNAc::delete_doubleP", _wrap_delete_doubleP}, +{"RNAc::doubleP_getitem", _wrap_doubleP_getitem}, +{"RNAc::doubleP_setitem", _wrap_doubleP_setitem}, +{"RNAc::new_doubleArray", _wrap_new_doubleArray}, +{"RNAc::delete_doubleArray", _wrap_delete_doubleArray}, +{"RNAc::doubleArray_getitem", _wrap_doubleArray_getitem}, +{"RNAc::doubleArray_setitem", _wrap_doubleArray_setitem}, +{"RNAc::doubleArray_cast", _wrap_doubleArray_cast}, +{"RNAc::doubleArray_frompointer", _wrap_doubleArray_frompointer}, +{"RNAc::new_shortP", _wrap_new_shortP}, +{"RNAc::delete_shortP", _wrap_delete_shortP}, +{"RNAc::shortP_getitem", _wrap_shortP_getitem}, +{"RNAc::shortP_setitem", _wrap_shortP_setitem}, +{"RNAc::cdata", _wrap_cdata}, +{"RNAc::memmove", _wrap_memmove}, +{"RNAc::fold", _wrap_fold}, +{"RNAc::energy_of_struct", _wrap_energy_of_struct}, +{"RNAc::free_arrays", _wrap_free_arrays}, +{"RNAc::initialize_fold", _wrap_initialize_fold}, +{"RNAc::update_fold_params", _wrap_update_fold_params}, +{"RNAc::cofold", _wrap_cofold}, +{"RNAc::free_co_arrays", _wrap_free_co_arrays}, +{"RNAc::initialize_cofold", _wrap_initialize_cofold}, +{"RNAc::update_cofold_params", _wrap_update_cofold_params}, +{"RNAc::pf_fold", _wrap_pf_fold}, +{"RNAc::init_pf_fold", _wrap_init_pf_fold}, +{"RNAc::free_pf_arrays", _wrap_free_pf_arrays}, +{"RNAc::update_pf_params", _wrap_update_pf_params}, +{"RNAc::bppm_symbol", _wrap_bppm_symbol}, +{"RNAc::mean_bp_dist", _wrap_mean_bp_dist}, +{"RNAc::pbacktrack", _wrap_pbacktrack}, +{"RNAc::inverse_fold", _wrap_inverse_fold}, +{"RNAc::inverse_pf_fold", _wrap_inverse_pf_fold}, +{"RNAc::bondT_i_set", _wrap_bondT_i_set}, +{"RNAc::bondT_i_get", _wrap_bondT_i_get}, +{"RNAc::bondT_j_set", _wrap_bondT_j_set}, +{"RNAc::bondT_j_get", _wrap_bondT_j_get}, +{"RNAc::bondT_get", _wrap_bondT_get}, +{"RNAc::new_bondT", _wrap_new_bondT}, +{"RNAc::delete_bondT", _wrap_delete_bondT}, +{"RNAc::option_string", _wrap_option_string}, +{"RNAc::SOLUTION_energy_set", _wrap_SOLUTION_energy_set}, +{"RNAc::SOLUTION_energy_get", _wrap_SOLUTION_energy_get}, +{"RNAc::SOLUTION_structure_set", _wrap_SOLUTION_structure_set}, +{"RNAc::SOLUTION_structure_get", _wrap_SOLUTION_structure_get}, +{"RNAc::SOLUTION_get", _wrap_SOLUTION_get}, +{"RNAc::SOLUTION_size", _wrap_SOLUTION_size}, +{"RNAc::delete_SOLUTION", _wrap_delete_SOLUTION}, +{"RNAc::new_SOLUTION", _wrap_new_SOLUTION}, +{"RNAc::subopt", _wrap_subopt}, +{"RNAc::get_pr", _wrap_get_pr}, +{"RNAc::b2HIT", _wrap_b2HIT}, +{"RNAc::b2C", _wrap_b2C}, +{"RNAc::b2Shapiro", _wrap_b2Shapiro}, +{"RNAc::add_root", _wrap_add_root}, +{"RNAc::expand_Shapiro", _wrap_expand_Shapiro}, +{"RNAc::expand_Full", _wrap_expand_Full}, +{"RNAc::unexpand_Full", _wrap_unexpand_Full}, +{"RNAc::unweight", _wrap_unweight}, +{"RNAc::unexpand_aligned_F", _wrap_unexpand_aligned_F}, +{"RNAc::parse_structure", _wrap_parse_structure}, +{"RNAc::make_tree", _wrap_make_tree}, +{"RNAc::tree_edit_distance", _wrap_tree_edit_distance}, +{"RNAc::print_tree", _wrap_print_tree}, +{"RNAc::free_tree", _wrap_free_tree}, +{"RNAc::Make_swString", _wrap_Make_swString}, +{"RNAc::string_edit_distance", _wrap_string_edit_distance}, +{"RNAc::Make_bp_profile", _wrap_Make_bp_profile}, +{"RNAc::profile_edit_distance", _wrap_profile_edit_distance}, +{"RNAc::print_bppm", _wrap_print_bppm}, +{"RNAc::free_profile", _wrap_free_profile}, +{"RNAc::space", _wrap_space}, +{"RNAc::xrealloc", _wrap_xrealloc}, +{"RNAc::nrerror", _wrap_nrerror}, +{"RNAc::init_rand", _wrap_init_rand}, +{"RNAc::urn", _wrap_urn}, +{"RNAc::int_urn", _wrap_int_urn}, +{"RNAc::filecopy", _wrap_filecopy}, +{"RNAc::time_stamp", _wrap_time_stamp}, +{"RNAc::random_string", _wrap_random_string}, +{"RNAc::hamming", _wrap_hamming}, +{"RNAc::get_line", _wrap_get_line}, +{"RNAc::pack_structure", _wrap_pack_structure}, +{"RNAc::unpack_structure", _wrap_unpack_structure}, +{"RNAc::make_pair_table", _wrap_make_pair_table}, +{"RNAc::bp_distance", _wrap_bp_distance}, +{"RNAc::read_parameter_file", _wrap_read_parameter_file}, +{"RNAc::write_parameter_file", _wrap_write_parameter_file}, +{"RNAc::deref_any", _wrap_deref_any}, +{"RNAc::scale_parameters", _wrap_scale_parameters}, +{"RNAc::copy_parameters", _wrap_copy_parameters}, +{"RNAc::set_parameters", _wrap_set_parameters}, +{"RNAc::get_aligned_line", _wrap_get_aligned_line}, +{"RNAc::make_loop_index", _wrap_make_loop_index}, +{"RNAc::energy_of_move", _wrap_energy_of_move}, +{"RNAc::PS_rna_plot", _wrap_PS_rna_plot}, +{"RNAc::PS_rna_plot_a", _wrap_PS_rna_plot_a}, +{"RNAc::gmlRNA", _wrap_gmlRNA}, +{"RNAc::ssv_rna_plot", _wrap_ssv_rna_plot}, +{"RNAc::svg_rna_plot", _wrap_svg_rna_plot}, +{"RNAc::xrna_plot", _wrap_xrna_plot}, +{"RNAc::PS_dot_plot", _wrap_PS_dot_plot}, +{"RNAc::cpair_i_set", _wrap_cpair_i_set}, +{"RNAc::cpair_i_get", _wrap_cpair_i_get}, +{"RNAc::cpair_j_set", _wrap_cpair_j_set}, +{"RNAc::cpair_j_get", _wrap_cpair_j_get}, +{"RNAc::cpair_mfe_set", _wrap_cpair_mfe_set}, +{"RNAc::cpair_mfe_get", _wrap_cpair_mfe_get}, +{"RNAc::cpair_p_set", _wrap_cpair_p_set}, +{"RNAc::cpair_p_get", _wrap_cpair_p_get}, +{"RNAc::cpair_hue_set", _wrap_cpair_hue_set}, +{"RNAc::cpair_hue_get", _wrap_cpair_hue_get}, +{"RNAc::cpair_sat_set", _wrap_cpair_sat_set}, +{"RNAc::cpair_sat_get", _wrap_cpair_sat_get}, +{"RNAc::new_cpair", _wrap_new_cpair}, +{"RNAc::delete_cpair", _wrap_delete_cpair}, +{"RNAc::PS_color_dot_plot", _wrap_PS_color_dot_plot}, +{"RNAc::plist_i_set", _wrap_plist_i_set}, +{"RNAc::plist_i_get", _wrap_plist_i_get}, +{"RNAc::plist_j_set", _wrap_plist_j_set}, +{"RNAc::plist_j_get", _wrap_plist_j_get}, +{"RNAc::plist_p_set", _wrap_plist_p_set}, +{"RNAc::plist_p_get", _wrap_plist_p_get}, +{"RNAc::new_plist", _wrap_new_plist}, +{"RNAc::delete_plist", _wrap_delete_plist}, +{"RNAc::PS_dot_plot_list", _wrap_PS_dot_plot_list}, +{0,0} +}; + + +static void SWIG_Perl_SetTypeListHandle(swig_type_info **handle) { + SV *pointer; + + /* create a new pointer */ + pointer = get_sv("swig_runtime_data::type_pointer" SWIG_RUNTIME_VERSION SWIG_TYPE_TABLE_NAME, TRUE); + sv_setiv(pointer, PTR2IV(swig_type_list_handle)); +} + +static swig_type_info ** +SWIG_Perl_LookupTypePointer(swig_type_info **type_list_handle) { + swig_type_info **type_pointer; + + /* first check if module already created */ + type_pointer = SWIG_Perl_GetTypeListHandle(); + if (type_pointer) { + return type_pointer; + } else { + /* create a new module and variable */ + SWIG_Perl_SetTypeListHandle(type_list_handle); + return type_list_handle; + } +} + + +#ifdef __cplusplus +extern "C" +#endif + +XS(SWIG_init) { + dXSARGS; + int i; + static int _init = 0; + if (!_init) { + swig_type_list_handle = SWIG_Perl_LookupTypePointer(swig_type_list_handle); + for (i = 0; swig_types_initial[i]; i++) { + swig_types[i] = SWIG_TypeRegister(swig_types_initial[i]); + } + _init = 1; + } + + /* Install commands */ + for (i = 0; swig_commands[i].name; i++) { + newXS((char*) swig_commands[i].name,swig_commands[i].wrapper, (char*)__FILE__); + } + + /* Install variables */ + for (i = 0; swig_variables[i].name; i++) { + SV *sv; + sv = perl_get_sv((char*) swig_variables[i].name, TRUE | 0x2); + if (swig_variables[i].type) { + SWIG_MakePtr(sv,(void *)1, *swig_variables[i].type,0); + } else { + sv_setiv(sv,(IV) 0); + } + swig_create_magic(sv, (char *) swig_variables[i].name, swig_variables[i].set, swig_variables[i].get); + } + + /* Install constant */ + for (i = 0; swig_constants[i].type; i++) { + SV *sv; + sv = perl_get_sv((char*)swig_constants[i].name, TRUE | 0x2); + switch(swig_constants[i].type) { + case SWIG_INT: + sv_setiv(sv, (IV) swig_constants[i].lvalue); + break; + case SWIG_FLOAT: + sv_setnv(sv, (double) swig_constants[i].dvalue); + break; + case SWIG_STRING: + sv_setpv(sv, (char *) swig_constants[i].pvalue); + break; + case SWIG_POINTER: + SWIG_MakePtr(sv, swig_constants[i].pvalue, *(swig_constants[i].ptype),0); + break; + case SWIG_BINARY: + SWIG_MakePackedObj(sv, swig_constants[i].pvalue, swig_constants[i].lvalue, *(swig_constants[i].ptype)); + break; + default: + break; + } + SvREADONLY_on(sv); + } + + SWIG_TypeClientData(SWIGTYPE_p_intArray, (void*) "RNA::intArray"); + SWIG_TypeClientData(SWIGTYPE_p_floatArray, (void*) "RNA::floatArray"); + SWIG_TypeClientData(SWIGTYPE_p_doubleArray, (void*) "RNA::doubleArray"); + SWIG_TypeClientData(SWIGTYPE_p_bond, (void*) "RNA::bondT"); + SWIG_TypeClientData(SWIGTYPE_p_SOLUTION, (void*) "RNA::SOLUTION"); + + /* work around segfault when script tries to free symbolset */ + + symbolset = (char *) space(21); + strcpy(symbolset, "AUGC"); + + + SWIG_TypeClientData(SWIGTYPE_p_cpair, (void*) "RNA::cpair"); + SWIG_TypeClientData(SWIGTYPE_p_plist, (void*) "RNA::plist"); + ST(0) = &PL_sv_yes; + XSRETURN(1); +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA_wrap.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA_wrap.o new file mode 100755 index 000000000..ba5cde282 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNA_wrap.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNAfold.cgi b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNAfold.cgi new file mode 100755 index 000000000..6e6ab568f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNAfold.cgi @@ -0,0 +1,386 @@ +#!/usr/bin/perl +# -*-Perl-*- +# Last changed Time-stamp: <2002-11-19 15:40:22 ivo> +# CGI script for a Web-based RNA fold server +# you need to have the perl5 RNA module installed +# that comes as part of the Vienna RNA package + +use strict; +use CGI qw/ :standard /; +use CGI::Carp qw(fatalsToBrowser); +use HTML::Entities; +use URI::Escape; +use RNA; +use Chart::Lines; +use vars qw/$hdir $maxlength $ssv_home $ssv_url $paramdir $serverroot/; + +# please configure these variables for your site + +$paramdir = '/var/www/RNA'; # directory where parameters files etc are stored +$serverroot = '/u/html'; # where your web pages lie +$hdir = "/RNAfold_dir"; # output directory (relative to $serverroot) +$maxlength = 500; # only process sequences up to this length +$ssv_home = "http://smi-web.stanford.edu/projects/helix/sstructview/home.html"; +$ssv_url = "/~ivo/RNA/SStructView.zip"; + +my $query = new CGI; + +if ($query->param) { + &do_work($query); +} else { + &print_header($query); +} + +&print_tail; +print $query->end_html,"\n"; + +sub print_header { + my($query, $cookie) = @_; + if ($cookie) { + print $query->header(-expires=>'+1m', + -cookie=>$cookie); + } else { + print $query->header(-expires=>'+1m'); + } + print $query->start_html(-title=>"RNAfold input form", + -author=>'ivo@tbi.univie.ac.at', + -BGCOLOR=>'#f8f8ff'); + print "\n

Vienna RNA Secondary Structure Prediction

\n"; + print "

", + "A web interface to the RNAfold programm

\n"; + + print "This server will predict secondary structures of single stranded\n", + "RNA or DNA sequences. If the options look confusing read the\n", + "", + "help page

\n"; + + print "News: based on ViennaRNA-1.5
\n", + "Try the new SVG plot if your browser supports it!\n

\n"; + &print_prompt($query); +} + +sub print_prompt { + my($query) = @_; + + print $query->startform(-action=>'/cgi-bin/RNAfold.cgi#Results'); + print "Name of sequence ", + "(choose a unique identifier)
\n> "; + print $query->textfield('name'); + + + print "

\nType in your sequence\nTs will be ", + "automatically replaced by Us.\nAny symbols except ", + "AUCGTXKI will be interpreted as nonbonding bases. ", + "Maximum sequence length is currently $maxlength
\n"; + + print $query->textarea(-name=>'Sequence', + -rows=>5, + -columns=>70, + -default=>""); + + print "

\nChoose Fold Algorithm
\n"; + + print $query->popup_menu(-name => 'pffold', + -values => ['mfe','pf'], + -default => 'pf', + -labels => {'mfe', 'minimum free energy only', + 'pf', + 'partition function and pair probabilities'} + ); + print $query->popup_menu(-name => 'Params', + -values => ['RNA','oldRNA','DNA'], + -default => 'RNA', + -labels => {'RNA', 'use RNA parameters', + 'oldRNA', 'old RNA parameters', + 'DNA', 'use DNA parameters'} + ); + + print "

Options to modify the fold algorithm

\n"; + print "Rescale energy parameters to temperature\n", + $query->textfield(-name=>'Temp', + -default=>37, + -size=>3); + print "C

\n"; + print $query->checkbox_group( + -name=>'toggles', + -values=>['-4', '-d', '-noGU', '-noCloseGU', + '-noLP'], + -labels=>{'-4', 'no special tetraloops', + '-d', 'no dangling end energies', + '-noGU', 'no GU pairs', + '-noCloseGU', + 'no GU pairs at the end of helices', + '-noLP', 'avoid isolated base pairs' + }, + -linebreak=>'yes', + -defaults=>[]); + + print "\n
", + "Should we produce a mountain plot of the structure? \n", + $query->checkbox(-name=>'plot', -checked=>'ON'); + print "\n
View a plot of the mfe structure inline using\n", + "an SVG image (may requires plugin)\n", + $query->checkbox(-name=>'SVG', checked=>'ON'); + print "
\nor using the SStructView java applet?\n", + $query->checkbox(-name=>'SSview'); + + print "

\n",$query->reset, "\n"; + print $query->submit('Action','Fold it'), "\n"; + print $query->endform, "\n"; + + if (!$query->param) { + my @old_files = $query->cookie('old_files'); + if (@old_files) { + print "

The results from your last run should still be in\n"; + foreach my $f (@old_files) { + print " $f"; + } + print ".\n"; + } + } + print "

\n"; +} + +sub do_work { +# setpriority(PRIO_PROCESS, 0, 19); + my($query) = @_; + my($OK_CHARS) = '-a-zA-Z0-9_.@ '; + my($RNAfold_id, $junk); + my($WORK_DIR) = $serverroot . $hdir; + my($sfact) = 1.02; + chdir $WORK_DIR || die("can't change directory"); + + # clean old files + foreach my $f (< *.ps *.png *.coords *.svg>) { + unlink($f) if (-M $f)>1.5; + } + + my $Sequence = $query->param('Sequence'); + if (length($Sequence) < 1) { # do nothing + &print_header($query); + return; + } + $Sequence =~ s/[\n\s]//gm; # remove whitespace and linebreaks + $Sequence = uc $Sequence; # upper case + if ($query->param('Params') eq 'DNA') { + $Sequence =~ s/U/T/g; # U -> T + } else { + $Sequence =~ s/T/U/g; # T -> U + } + + my $name = $query->param('name'); + + my $options = ""; + $options .= " -p" if ($query->param('pffold') eq 'pf'); + $options .= " -P dna.par" if $query->param('Params') eq 'DNA'; + $options .= " -P vienna13.par" if $query->param('Params') eq 'oldRNA'; + $options .= " " . join(' ', $query->param('toggles')); + $RNA::tetra_loop = 0 if $options =~ /-4/; + $RNA::dangles = 0 if $options =~ /-d/; + $RNA::noGU = 1 if $options =~ /-noGU/; + $RNA::no_closingGU = 1 if $options =~ /-noCloseGU/; + $RNA::noLonelyPairs = 1 if $options =~ /-noLP/; + + if ($query->param('Temp') =~ /([-+]?\d+\.?\d*)/) { + $RNA::temperature = $1; + $options .= " -T $1" if $1 != 37; + } + + # remove strange characters, so we can pass strings to shell + $options =~ s/[^$OK_CHARS]//go; + if ($name =~ /(\S+)/) { + $name = $1; + } else { + $name = "s$$"; + } + + $name =~ s/\///g; # no / allowed in file names + my $fname_ss = $name . "_ss.ps"; + my $fname_dp = ($options =~ /-p /)?($name . "_dp.ps"):""; + my $fname_co = $name . ".coords"; + my $fname_svg = $name . ".svg"; + my $ss_escaped = uri_escape($fname_ss); + my $dp_escaped = uri_escape($fname_dp); + my $png_escaped = uri_escape($name . ".png"); + + my $the_cookie = $query->cookie(-name=>'old_files', + -value=>[$ss_escaped,$dp_escaped,$png_escaped], + -expires=>'+1d', + -path=>'/cgi-bin'); + + &print_header($query, $the_cookie); # don't print anything before this line + + print "

Here are your results

\n"; + + if ($query->param('Params') eq 'DNA') { + print "DNA parameters provided by courtesy of " . + "", + "John SantaLucia Jr.
\n", + "In any publication using these relsults, please cite:
\n", + "SantaLucia, J Jr (1998) ", + "\"A unified view of polymer, dumbbell, and oligonucleotide DNA ", + "nearest-neighbor thermodynamics.\"\n", + "Proc. Natl. Acad. Sci. USA 95, 1460-1465.\n", + "

\n"; + } else { + print "RNA parameters are described in
\n" . + "D.H. Mathews, J. Sabina, M. Zucker and H. Turner\n", + "\"Expanded Sequence Dependence of Thermodynamic Parameters ", + "Provides Robust Prediction of RNA Secondary Structure\",\n", + "JMB, 288, pp 911-940, 1999
\n"; + } +# print $query->query_string, "
\n"; + my $length = length($Sequence); + if ($length > $maxlength) { + print "Sorry, this interface is still being tested.\n", + "Currently, sequences longer than $maxlength bases will currently ", + "not be processed. Your sequence has length $length.
\n"; + return; + } + + print "An equivalent RNAfold command line would have been
\n"; + print "RNAfold $options

\n"; + if ($query->param('Params') eq 'DNA') { + RNA::read_parameter_file("$paramdir/dna.par"); + } elsif ($query->param('Params') eq 'oldRNA') { + RNA::read_parameter_file("$paramdir/vienna13.par"); + } + + my ($structure, $mfe) = RNA::fold($Sequence); + print "The optimal secondary structure in bracket notation is given below\n"; + my $eseq = $Sequence; + encode_entities($eseq); + + print "

\n";
+   print "> $name\n$eseq\n$structure";
+   printf " (%6.2f)\n", $mfe;
+   print "

\n"; + print "The minimum free energy in kcal/mol is given in parenthesis.\n"; + + if (!($structure =~ /\(/)) {$RNA::rna_plot_type = 0}; + RNA::PS_rna_plot($Sequence, $structure, $fname_ss); + print "You may look at the PostScript drawing of the structure\n"; + my $efname = $fname_ss; encode_entities($efname); + print "in $efname.

\n"; + + if ($options =~ /-p/) { + $RNA::dangles = 2 if $RNA::dangles; + my $min_en = RNA::energy_of_struct($Sequence, $structure); + my $kT = ($RNA::temperature+273.15)*1.98717/1000.; # in Kcal + $RNA::pf_scale = exp(-($sfact*$min_en)/$kT/$length); + my ($pf_struct, $energy) = RNA::pf_fold($Sequence); + print "The free energy of the thermodynamic ensemble is "; + printf "%6.2f kcal/mol\n", $energy; + RNA::PS_dot_plot($Sequence, $fname_dp); + print "
The PostScript dot plot containing the base pair ", + "probabilities is in\n", + encode_entities($fname_dp), ".\n"; + } + print "

"; + + mountain($name, $structure, $options) if $query->param('plot') eq 'on'; + + if ($query->param('SSview') eq 'on') { + my $ret = RNA::ssv_rna_plot($Sequence, $structure, $fname_co); + if ($ret == 0) { + print "error: ssv_rna_plot plot failed, sorry

\n"; + return; + } + my $escaped = uri_escape($fname_co); + print "Please be patient while the applet is loading
\n"; + print "\n", + "\n", + "\n", +# "\n", + "\n", + "
\n"; + print "For information on the java applet see the ", + "SStructView home page

\n"; + } + + if ($query->param('SVG') eq 'on') { + my $ret = RNA::svg_rna_plot($Sequence, $structure, $fname_svg); + if ($ret == 0) { + print "error: svg_rna_plot plot failed, sorry

\n"; + return; + } + my $escaped = uri_escape($fname_svg); + print "
\n"; + print 'Note: you need the ', + "Adobe SVG plugin or an SVG enabled browser to view the graphics
\n"; + } + + print "Your output files will be deleted from this server after one day.\n"; + +# $myself = $query->self_url; +# print "
Back to the input form"; + print "
Scroll back to the top to submit another sequence.\n"; + + my ($user,$system,$cuser,$csystem) = times; + print "
Time used for this call ",$user+$system, " seconds\n"; + print "
\n"; +} + +sub print_tail { + print <Ivo Hofacker + <ivo\@tbi.univie.ac.at> +
+ Vienna RNA Home Page +END +} + +sub mountain { + my($name, $structure, $options) = @_; + my $length = length $structure; + my $width = 480; + my $height = 300; + + # FIXME: legend_lables when doing mfe only + my $skip = 10**(int (log($length)/log(10.) - 0.5)); + my $obj = Chart::Lines->new( $width, $height ); + $obj->set ('title' => $name, + 'x_label' => 'Position', + 'y_label' => 'Height', + 'min_val' => 0, + 'legend_labels' => ['mfe'], + 'skip_x_ticks' => $skip); + + $obj->add_dataset ((0..$length)); + + #my $bp = $RNA::base_pair; + #my $npair = RNA::bond_i_get($bp); + my @mp = (0); # valid indices 1..length + my $h = 0; + foreach (split(//, $structure)) { + $h-- if $_ eq ')'; + push @mp, $h; + $h++ if $_ eq '('; + } + warn "illegal structure $structure" if $mp[-1] != 0; + $obj->add_dataset (@mp[0..$length]); # @mp[1..$length] ?? + + if ($options =~ /-p/) { # we have base pairing probs + $obj->set('legend_labels' => ['mfe', 'pf']); + my $bpp = RNA::Make_bp_profile($length); + my @bpp = unpack("f*",RNA::cdata($bpp, ($length+1)*4*3)); + $mp[0] = $mp[1] = 0; # use indices [1..length] + for my $i (1..$length) { + $mp[$i] -= $bpp[$i*3+2]; # paired downstream + $mp[$i+1] = $mp[$i] + $bpp[$i*3+1]; # upstream + } + + $obj->add_dataset (@mp[0..$length]); + } + + $name .= ".png"; + $obj->png("$name"); + my $png_escaped = uri_escape($name); + print "\"Mountain

\n"; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNAfold.pl b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNAfold.pl new file mode 100755 index 000000000..b719d0226 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/RNAfold.pl @@ -0,0 +1,141 @@ +#!/usr/bin/perl +# -*-Perl-*- +# Last changed Time-stamp: <2003-02-03 18:27:19 ivo> + +use RNA; +use Getopt::Long; +use strict; +use warnings; + + Getopt::Long::config("no_ignore_case"); + +use vars qw/$opt_debug $opt_v $ParamFile $pf $ns_bases/; +my $sfact=1.07; +&usage() unless GetOptions("p|p1" => \$pf, + "p0" => sub {$pf=1; $RNA::do_backtrack=0}, + "C" => \$RNA::fold_constrained, + "T=f" => \$RNA::temperature, + "4" => sub {$RNA::tetra_loop = 0}, + "d|d0" => sub {$RNA::dangles=0}, + "d2" => sub {$RNA::dangles=2},, + "noGU" => \$RNA::noGU, + "noCloseGU" => \$RNA::no_closingGU, + "noLP" => \$RNA::noLonelyPairs, + "e=i" => \$RNA::energy_set, + "P=s" => \$ParamFile, + "nsp=s" => \$ns_bases, + "S=f" => \$sfact); + + RNA::read_parameter_file($ParamFile) if ($ParamFile); + +if ($ns_bases) { + $RNA::nonstandards = ""; + foreach my $p ( split(/,/, $ns_bases) ) { + if ($p =~ s/^-//) { + $RNA::nonstandards .= reverse($p) + } + $RNA::nonstandards .= $p; + } + print "$RNA::nonstandards\n"; +} + +my $istty = (-t STDIN) && (-t STDOUT); +if (($RNA::fold_constrained)&&($istty)) { +print < : base i is paired with a base j>i +matching brackets ( ): base i pairs base j +END +} + +if ($istty) { + print "\nInput string (upper or lower case); @ to quit\n"; + for (1..8) { print "....,....$_";} + print "\n"; +} +my $fname; +while (<>) { # main loop: continue until end of file + my ($string, $cstruc, $structure, $min_en); + # skip comment lines and get filenames + if (/^>\s*(\S*)/) { + $fname = $1; + next; + } + last if (/^@/); + + if (/(\S+)/) { + $string = $1; + } else { + next; + } + + $string = uc($string); + my $length = length($string); + printf("length = %d\n", $length) if ($istty); + + if ($RNA::fold_constrained) { + $_ = <>; + $cstruc = $1 if (/(\S+)/); + die("constraint string has wrong length") + if (length($cstruc)!=$length); + ($structure, $min_en) = RNA::fold($string, $structure); + } else { + ($structure, $min_en) = RNA::fold($string); + } + print "$string\n$structure"; + if ($istty) { + printf("\n minimum free energy = %6.2f kcal/mol\n", $min_en); + } else { + printf(" (%6.2f)\n", $min_en); + } + my $ffname = ($fname) ? ($fname . '_ss.ps') : 'rna.ps'; + RNA::PS_rna_plot($string, $structure, $ffname); + + if ($pf) { + + # recompute with dangles as in pf_fold() + $RNA::dangles=2 if ($RNA::dangles); + $min_en = RNA::energy_of_struct($string, $structure); + + my $kT = ($RNA::temperature+273.15)*1.98717/1000.; # in Kcal + $RNA::pf_scale = exp(-($sfact*$min_en)/$kT/$length); + print STDERR "scaling factor $RNA::pf_scale\n" if ($length>2000); + + $structure = $cstruc if ($RNA::fold_constrained); + my $energy = RNA::pf_fold($string, $structure); + + if ($RNA::do_backtrack) { + print $structure; + printf(" [%6.2f]\n", $energy) if (!$istty); + print "\n"; + } + if (($istty)||(!$RNA::do_backtrack)) { + printf(" free energy of ensemble = %6.2f kcal/mol\n", $energy); + printf(" frequency of mfe structure in ensemble %g\n", + exp(($energy-$min_en)/$kT)); + } + + if ($RNA::do_backtrack) { + $ffname = ($fname)?($fname . "_dp.ps"):"dot.ps"; + &RNA::PS_dot_plot($string, $ffname); + } + } + undef $fname; +} + + RNA::free_pf_arrays() if ($pf); + RNA::free_arrays(); + +sub usage() +{ + die("usage: " . + "RNAfold [-p[0]] [-C] [-T temp] [-4] [-d] [-noGU] [-noCloseGU]\n" . + " [-e e_set] [-P paramfile] [-nsp pairs] [-S scale]"); +} + + +# End of file diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/arch/auto/RNA/.exists b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/arch/auto/RNA/.exists new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/arch/auto/RNA/RNA.bs b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/arch/auto/RNA/RNA.bs new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/arch/auto/RNA/RNA.so b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/arch/auto/RNA/RNA.so new file mode 100755 index 000000000..530ce938f Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/arch/auto/RNA/RNA.so differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/lib/.exists b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/lib/.exists new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/lib/RNA.pm b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/lib/RNA.pm new file mode 100755 index 000000000..a4cb55d54 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/lib/RNA.pm @@ -0,0 +1,1075 @@ +# This file was automatically generated by SWIG +package RNA; +require Exporter; +require DynaLoader; +@ISA = qw(Exporter DynaLoader); +package RNAc; +bootstrap RNA; +package RNA; +@EXPORT = qw( ); +=head1 NAME + +RNA - interface to the Vienna RNA library (libRNA.a) +Version 0.3 + +=head1 SYNOPSIS + + use RNA; + $seq = "CGCAGGGAUACCCGCG"; + ($struct, $mfe) = RNA::fold($seq); #predict mfe structure of $seq + RNA::PS_rna_plot($seq, $struct, "rna.ps"); # write PS plot to rna.ps + $F = RNA::pf_fold($seq); # compute partition function and pair pobabilities + RNA::PS_dot_plot($seq, "dot.ps"); # write dot plot to dot.ps + ... + +=head1 DESCRIPTION + +The RNA.pm package gives access to almost all functions in the libRNA.a +library of the Vienna RNA PACKAGE. The Perl wrapper is generated using +SWIG http://www.swig.org/ with relatively little manual intervention. +For each C function in the library the perl package provides a function +of the same name and calling convention (with few exceptions). For +detailed information you should therefore also consult the documentation +of the library (info RNAlib). + +Note that in general C arrays are wrapped into opaque objects that can +only be accessed via helper functions. SWIG provides a couple of general +purpose helper functions, see the section at the end of this file. C +structures are wrapped into Perl objects using SWIG's shadow class +mechanism, resulting in a tied hash with keys named after the structure +members. + +For the interrested reader we list for each scalar type of the +corepsonding C variable in brackets, and point out the header files +containing the C declaration. + +=head2 Folding Routines + +Minimum free Energy Folding (from fold.h) + +=over 4 + +=item fold SEQUENCE + +=item fold SEQUENCE, CONSTRAINTS + +computes the minimum free energy structure of the string SEQUENCE and returns +the predicted structure and energy, e.g. + + ($structure, $mfe) = RNA::fold("UGUGUCGAUGUGCUAU"); + +If a second argument is supplied and +L<$fold_constrained|/$fold_constrained>==1 the CONSTRAINTS string is +used to specify constraints on the predicted structure. The +characters '|', 'x', '<', '>' mark bases that are paired, unpaired, +paired upstream, or downstream, respectively; matching brackets "( )" +denote base pairs, dots '.' are used for unconstrained bases. + +In the two argument version the CONSTRAINTS string is modified and holds the +predicted structure upon return. This is done for backwards compatibility only, +and might change in future versions. + +=item energy_of_struct SEQUENCE, STRUCTURE + +returns the energy of SEQUENCE on STRUCTURE (in kcal/mol). The string structure +must hold a valid secondary structure in bracket notation. + +=item update_fold_params + +recalculate the pair matrix and energy parameters after a change in folding +parameters. In many cases (such as changes to +L<$temperature|/$temperature>) the fold() routine will call +update_fold_params automatically when necessary. + +=item free_arrays + +frees memory allocated internally when calling L. + +=back + +Partition function Folding (from part_func.h) + +=over 4 + +=item pf_fold SEQUENCE + +=item pf_fold SEQUENCE, CONSTRAINTS + +calculates the partition function over all possible secondary +structures and the matrix of pair probabilities for SEQUENCE and +returns a two element list consisting of a string summarizing possible +structures. See below on how to access the pair probability matrix. As +with L the second argument can be used to specify folding +constraints. Constraints are implemented by excluding base pairings +that contradict the constraint, but without bonus +energies. Constraints of type '|' (paired base) are ignored. In the +two argument version CONSTRAINTS is modified to contain the structure +string on return (obsolete feature, for backwards compatibility only) + +=item get_pr I, J + +After calling C the global C variable C points to the +computed pair probabilities. Perl access to the C is facilitated by +the C helper function that looks up and returns the +probability of the pair (I,J). + +=item free_pf_arrays + +frees memory allocated for pf_fold + +=item update_pf_params LENGTH + +recalculate energy parameters for pf_fold. In most cases (such as +simple changes to L<$temperature|/$temperature>) C +will take appropriate action automatically. + +=back + +Suboptimal Folding (from subopt.h) + +=over 4 + +=item subopt SEQUENCE, CONSTRAINTS, DELTA + +=item subopt SEQUENCE, CONSTRAINTS, DELTA, FILEHANDLE + +compute all structures of SEQUENCE within DELTA*0.01 kcal/mol of the +optimum. If specified, results are written to FILEHANDLE and nothing +is returned. Else, the C function returnes a list of C structs of type +SOLUTION. The list is wrapped by SWIG as a perl object that can be +accesses as follows: + + $solution = subopt($seq, undef, 500); + for (0..$solution->size()-1) { + printf "%s %6.2f\n", $solution->get($_)->{structure}, + $solution->get($_)->{energy}; + } + +=back + +Inverse Folding (from inverse.h) + +=over 4 + +=item inverse_fold START, TARGET + +find a sequence that folds into structure TARGET, by optimizing the +sequence until its mfe structure (as returned by L) is +TARGET. Startpoint of the optimization is the sequence START. Returns +a list containing the sequence found and the final value of the cost +function, i.e. 0 if the search was successful. A random start sequence +can be generated using L. + +=item inverse_pf_fold START, TARGET + +optimizes a sequence (beginning with START) by maximising the +frequency of the structure TARGET in the thermodynamic ensemble +of structures. Returns a list containing the optimized sequence and +the final value of the cost function. The cost function is given by +C, i.e.C<-RT*log(p(TARGET))> + +=item $final_cost [float] + +holds the value of the cost function where the optimization in +C should stop. For values <=0 the optimization will +only terminate at a local optimimum (which might take very long to reach). + +=item $symbolset [char *] + +the string symbolset holds the allowed characters to be used by +C and C, the default alphabet is "AUGC" + + +=item $give_up [int] + +If non-zero stop optimization when its clear that no exact solution +can be found. Else continue and eventually return an approximate +solution. Default 0. + +=back + +Global Variables to Modify Folding (from fold_vars.h) + +=over 4 + +=item $noGU [int] + +Do not allow GU pairs to form, default 0. + +=item $no_closingGU [int] + +allow GU only inside stacks, default 0. + +=item $tetra_loop [int] + +Fold with specially stable 4-loops, default 1. + +=item $energy_set [int] + +0 = BP; 1=any mit GC; 2=any mit AU-parameter, default 0. + +=item $dangles [int] + +How to compute dangling ends. 0: no dangling end energies, 1: "normal" +dangling ends (default), 2: simplified dangling ends, 3: "normal" + +co-axial stacking. Note that L treats cases 1 and 3 +as 2. The same holds for the main computation in L, +however subopt will re-evalute energies using +L for cases 1 and 3. See the more +detailed discussion in RNAlib.texinfo. + +=item $nonstandards [char *] + +contains allowed non standard bases, default empty string "" + +=item $temperature [double] + +temperature in degrees Celsius for rescaling parameters, default 37C. + +=item $logML [int] + +use logarithmic multiloop energy function in +L, default 0. + +=item $noLonelyPairs [int] + +consider only structures without isolated base pairs (helices of length 1). +For L only eliminates pairs +that can B occur as isolated pairs. Default 0. + +=item $base_pair [struct bond *] + +list of base pairs from last call to L. Better use +the structure string returned by L. + +=item $pf_scale [double] + +scaling factor used by L to avoid overflows. Should +be set to exp(-F/(RT*length)) where F is a guess for the ensmble free +energy (e.g. use the mfe). + + +=item $fold_constrained [int] + +apply constraints in the folding algorithms, default 0. + +=item $do_backtrack [int] + +If 0 do not compute the pair probabilities in L +(only the partition function). Default 1. + +=item $backtrack_type [char] + +usually 'F'; 'C' require (1,N) to be bonded; 'M' backtrack as if the +sequence was part of a multi loop. Used by L + +=item $pr [double *] + +the base pairing prob. matrix computed by L. + +=item $iindx [int *] + +Array of indices for moving withing the C array. Better use +L. + + +=back + +=head2 Parsing and Comparing Structures + +from RNAstruct.h: these functions convert between strings +representating secondary structures with various levels of coarse +graining. See the documentation of the C library for details + +=over 4 + +=item b2HIT STRUCTURE + +Full -> HIT [incl. root] + +=item b2C STRUCTURE + +Full -> Coarse [incl. root] + +=item b2Shapiro STRUCTURE + +Full -> weighted Shapiro [i.r.] + +=item add_root STRUCTURE + +{Tree} -> ({Tree}R) + +=item expand_Shapiro COARSE + +add S for stacks to coarse struct + +=item expand_Full STRUCTURE + +Full -> FFull + +=item unexpand_Full FSTRUCTURE + +FFull -> Full + +=item unweight WCOARSE + +remove weights from coarse struct + +=item unexpand_aligned_F ALIGN + + + +=item parse_structure STRUCTURE + +computes structure statistics, and fills the following global variables: + +$loops [int] number of loops (and stacks) +$unpaired [int] number of unpaired positions +$pairs [int] number of paired positions +$loop_size[int *] holds all loop sizes +$loop_degree[int *] holds all loop degrees +$helix_size[int *] holds all helix lengths + +=back + +from treedist.h: routines for computing tree-edit distances between structures + +=over 4 + +=item make_tree STRUCTURE + +make input for tree_edit_distance (a Tree * pointer). + +=item tree_edit_distance T1, T2 + +compare to structures using tree editing. C, C must have been +created using C + +=item print_tree T + +mainly for debugging + +=item free_tree T + +free space allocated by make_tree + +=back + +from stringdist.h routines to compute structure distances via string-editing + +=over 4 + +=item Make_swString STRUCTURE + +[ returns swString * ] +make input for string_edit_distance + +=item string_edit_distance S1, S2 + +[ returns float ] +compare to structures using string alignment. C, C should be +created using C + +=back + +from profiledist + +=over + +=item Make_bp_profile LENGTH + +[ returns (float *) ] +condense pair probability matrix C into a vector containing +probabilities for upstream paired, downstream paired and +unpaired. This resulting probability profile is used as input for +profile_edit_distance + +=item profile_edit_distance T1, T2 + +[ returns float ] +align two probability profiles produced by C + +=item print_bppm T + +[ returns void ] +print string representation of probability profile + +=item free_profile T + +[ returns void ] +free space allocated in Make_bp_profile + +=back + +Global variables for computing structure distances + +=over 4 + +=item $edit_backtrack [int] + +set to 1 if you want backtracking + +=item $aligned_line [(char *)[2]] + +containes alignmed structures after computing structure distance with +C + +=item $cost_matrix [int] + +0 usual costs (default), 1 Shapiro's costs + +=back + +=head2 Utilities (from utils.h) + +=over 4 + +=item space SIZE + +allocate memory from C. Usually not needed in Perl + +=item nrerror MESSGAE + +die with error message. Better use Perl's C + +=item $xsubi [unsigned short[3]] + +libRNA uses the rand48 48bit random number generator if available, the +current random number is always stored in $xsubi. + +=item init_rand + +initialize the $xsubi random number from current time + +=item urn + +returns a random number between 0 and 1 using the random number +generator from the RNA library. + +=item int_urn FROM, TO + +returns random integer in the range [FROM..TO] + +=item time_stamp + +current date in a string. In perl you might as well use C + +=item random_string LENGTH, SYMBOLS + +returns a string of length LENGTH using characters from the string +SYMBOLS + +=item hamming S1, S2 + +calculate hamming distance of the strings C and C. + + +=item pack_structure STRUCTURE + +pack secondary structure, using a 5:1 compression via 3 +encoding. Returns the packed string. + +=item unpack_structure PACKED + +unpacks a secondary structure packed with pack_structure + +=item make_pair_table STRUCTURE + +returns a pair table as a newly allocated (short *) C array, such +that: table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] +contains the length of the structure. + +=item bp_distance STRUCTURE1, STRUCTURE2 + +returns the base pair distance of the two STRUCTURES. dist = {number +of base pairs in one structure but not in the other} same as edit +distance with open-pair close-pair as move-set + +=back + +from PS_plot.h + +=over 4 + +=item PS_rna_plot SEQUENCE, STRUCTURE, FILENAME + +write PostScript drawing of structure to FILENAME. Returns 1 on +sucess, 0 else. + +=item PS_rna_plot_a SEQUENCE, STRUCTURE, FILENAME, PRE, POST + +write PostScript drawing of structure to FILENAME. The strings PRE and +POST contain PostScript code that is included verbatim in the plot just +before (after) the data. Returns 1 on sucess, 0 else. + +=item gmlRNA SEQUENCE, STRUCTURE, FILENAME, OPTION + +write structure drawing in gml (Graph Meta Language) to +FILENAME. OPTION should be a single character. If uppercase the gml +output will include the SEQUENCE as node labels. IF OPTION equal 'x' +or 'X' write graph with coordinates (else only connectivity +information). Returns 1 on sucess, 0 else. + +=item ssv_rna_plot SEQUENCE, STRUCTURE, SSFILE + +write structure drfawing as coord file for SStructView Returns 1 on +sucess, 0 else. + +=item xrna_plot SEQUENCE, STRUCTURE, SSFILE + +write structure drawing as ".ss" file for further editing in XRNA. +Returns 1 on sucess, 0 else. + +=item PS_dot_plot SEQUENCE, FILENAME + +write a PostScript dot plot of the pair probability matix to +FILENAME. Returns 1 on sucess, 0 else. + +=item $rna_plot_type [int] + +Select layout algorithm for structure drawings. Currently available +0= simple coordinates, 1= naview, default 1. + +=back + +from read_epars.c + +=over 4 + +=item read_parameter_file FILENAME + +read energy parameters from FILENAME + +=item write_parameter_file FILENAME + +write energy parameters to FILENAME + +=back + +=head2 SWIG helper functions + +The package includes generic helper functions to access C arrays +of type C, C and C, such as: + +=over 4 + +=item intP_getitem POINTER, INDEX + +return the element INDEX from the array + +=item intP_setitem POINTER, INDEX, VALUE + +set element INDEX to VALUE + +=item new_intP NELEM + +allocate a new C array of integers with NELEM elements and return the pointer + +=item delete_intP POINTER + +deletes the C array by calling free() + +=back + +substituting C with C or C gives the corresponding +functions for arrays of float or double. You need to know the correct C +type however, and the function work only for arrays of simple types. + +On the lowest level the C function gives direct access to any data +in the form of a Perl string. + +=over + +=item cdata POINTER, SIZE + +copies SIZE bytes at POINTER to a Perl string (with binary data) + +=item memmove POINTER, STRING + +copies the (binary) string STRING to the memory location pointed to by +POINTER. + + +=back + +In combination with Perl's C this provides a generic way to convert +C data structures to Perl. E.g. + + RNA::parse_structure($structure); # fills the $RNA::loop_degree array + @ldegrees = unpack "I*", RNA::cdata($RNA::loop_degree, ($RNA::loops+1)*4); + +Warning: using these functions with wrong arguments will corrupt your +memory and lead to a segmentation fault. + +=head1 AUTHOR + +Ivo L. Hofacker + +=cut + +# ---------- BASE METHODS ------------- + +package RNA; + +sub TIEHASH { + my ($classname,$obj) = @_; + return bless $obj, $classname; +} + +sub CLEAR { } + +sub FIRSTKEY { } + +sub NEXTKEY { } + +sub FETCH { + my ($self,$field) = @_; + my $member_func = "swig_${field}_get"; + $self->$member_func(); +} + +sub STORE { + my ($self,$field,$newval) = @_; + my $member_func = "swig_${field}_set"; + $self->$member_func($newval); +} + +sub this { + my $ptr = shift; + return tied(%$ptr); +} + + +# ------- FUNCTION WRAPPERS -------- + +package RNA; + +*new_intP = *RNAc::new_intP; +*delete_intP = *RNAc::delete_intP; +*intP_getitem = *RNAc::intP_getitem; +*intP_setitem = *RNAc::intP_setitem; +*new_floatP = *RNAc::new_floatP; +*delete_floatP = *RNAc::delete_floatP; +*floatP_getitem = *RNAc::floatP_getitem; +*floatP_setitem = *RNAc::floatP_setitem; +*new_doubleP = *RNAc::new_doubleP; +*delete_doubleP = *RNAc::delete_doubleP; +*doubleP_getitem = *RNAc::doubleP_getitem; +*doubleP_setitem = *RNAc::doubleP_setitem; +*new_shortP = *RNAc::new_shortP; +*delete_shortP = *RNAc::delete_shortP; +*shortP_getitem = *RNAc::shortP_getitem; +*shortP_setitem = *RNAc::shortP_setitem; +*cdata = *RNAc::cdata; +*memmove = *RNAc::memmove; +*fold = *RNAc::fold; +*energy_of_struct = *RNAc::energy_of_struct; +*free_arrays = *RNAc::free_arrays; +*initialize_fold = *RNAc::initialize_fold; +*update_fold_params = *RNAc::update_fold_params; +*cofold = *RNAc::cofold; +*free_co_arrays = *RNAc::free_co_arrays; +*initialize_cofold = *RNAc::initialize_cofold; +*update_cofold_params = *RNAc::update_cofold_params; +*pf_fold = *RNAc::pf_fold; +*init_pf_fold = *RNAc::init_pf_fold; +*free_pf_arrays = *RNAc::free_pf_arrays; +*update_pf_params = *RNAc::update_pf_params; +*bppm_symbol = *RNAc::bppm_symbol; +*mean_bp_dist = *RNAc::mean_bp_dist; +*pbacktrack = *RNAc::pbacktrack; +*inverse_fold = *RNAc::inverse_fold; +*inverse_pf_fold = *RNAc::inverse_pf_fold; +*option_string = *RNAc::option_string; +*subopt = *RNAc::subopt; +*get_pr = *RNAc::get_pr; +*b2HIT = *RNAc::b2HIT; +*b2C = *RNAc::b2C; +*b2Shapiro = *RNAc::b2Shapiro; +*add_root = *RNAc::add_root; +*expand_Shapiro = *RNAc::expand_Shapiro; +*expand_Full = *RNAc::expand_Full; +*unexpand_Full = *RNAc::unexpand_Full; +*unweight = *RNAc::unweight; +*unexpand_aligned_F = *RNAc::unexpand_aligned_F; +*parse_structure = *RNAc::parse_structure; +*make_tree = *RNAc::make_tree; +*tree_edit_distance = *RNAc::tree_edit_distance; +*print_tree = *RNAc::print_tree; +*free_tree = *RNAc::free_tree; +*Make_swString = *RNAc::Make_swString; +*string_edit_distance = *RNAc::string_edit_distance; +*Make_bp_profile = *RNAc::Make_bp_profile; +*profile_edit_distance = *RNAc::profile_edit_distance; +*print_bppm = *RNAc::print_bppm; +*free_profile = *RNAc::free_profile; +*space = *RNAc::space; +*xrealloc = *RNAc::xrealloc; +*nrerror = *RNAc::nrerror; +*init_rand = *RNAc::init_rand; +*urn = *RNAc::urn; +*int_urn = *RNAc::int_urn; +*filecopy = *RNAc::filecopy; +*time_stamp = *RNAc::time_stamp; +*random_string = *RNAc::random_string; +*hamming = *RNAc::hamming; +*get_line = *RNAc::get_line; +*pack_structure = *RNAc::pack_structure; +*unpack_structure = *RNAc::unpack_structure; +*make_pair_table = *RNAc::make_pair_table; +*bp_distance = *RNAc::bp_distance; +*read_parameter_file = *RNAc::read_parameter_file; +*write_parameter_file = *RNAc::write_parameter_file; +*deref_any = *RNAc::deref_any; +*scale_parameters = *RNAc::scale_parameters; +*copy_parameters = *RNAc::copy_parameters; +*set_parameters = *RNAc::set_parameters; +*get_aligned_line = *RNAc::get_aligned_line; +*make_loop_index = *RNAc::make_loop_index; +*energy_of_move = *RNAc::energy_of_move; +*PS_rna_plot = *RNAc::PS_rna_plot; +*PS_rna_plot_a = *RNAc::PS_rna_plot_a; +*gmlRNA = *RNAc::gmlRNA; +*ssv_rna_plot = *RNAc::ssv_rna_plot; +*svg_rna_plot = *RNAc::svg_rna_plot; +*xrna_plot = *RNAc::xrna_plot; +*PS_dot_plot = *RNAc::PS_dot_plot; +*PS_color_dot_plot = *RNAc::PS_color_dot_plot; +*PS_dot_plot_list = *RNAc::PS_dot_plot_list; + +############# Class : RNA::intArray ############## + +package RNA::intArray; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = RNAc::new_intArray(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_intArray($self); + delete $OWNER{$self}; + } +} + +*getitem = *RNAc::intArray_getitem; +*setitem = *RNAc::intArray_setitem; +*cast = *RNAc::intArray_cast; +*frompointer = *RNAc::intArray_frompointer; +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::floatArray ############## + +package RNA::floatArray; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = RNAc::new_floatArray(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_floatArray($self); + delete $OWNER{$self}; + } +} + +*getitem = *RNAc::floatArray_getitem; +*setitem = *RNAc::floatArray_setitem; +*cast = *RNAc::floatArray_cast; +*frompointer = *RNAc::floatArray_frompointer; +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::doubleArray ############## + +package RNA::doubleArray; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = RNAc::new_doubleArray(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_doubleArray($self); + delete $OWNER{$self}; + } +} + +*getitem = *RNAc::doubleArray_getitem; +*setitem = *RNAc::doubleArray_setitem; +*cast = *RNAc::doubleArray_cast; +*frompointer = *RNAc::doubleArray_frompointer; +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::bondT ############## + +package RNA::bondT; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +*swig_i_get = *RNAc::bondT_i_get; +*swig_i_set = *RNAc::bondT_i_set; +*swig_j_get = *RNAc::bondT_j_get; +*swig_j_set = *RNAc::bondT_j_set; +*get = *RNAc::bondT_get; +sub new { + my $pkg = shift; + my $self = RNAc::new_bondT(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_bondT($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::SOLUTION ############## + +package RNA::SOLUTION; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +*swig_energy_get = *RNAc::SOLUTION_energy_get; +*swig_energy_set = *RNAc::SOLUTION_energy_set; +*swig_structure_get = *RNAc::SOLUTION_structure_get; +*swig_structure_set = *RNAc::SOLUTION_structure_set; +*get = *RNAc::SOLUTION_get; +*size = *RNAc::SOLUTION_size; +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_SOLUTION($self); + delete $OWNER{$self}; + } +} + +sub new { + my $pkg = shift; + my $self = RNAc::new_SOLUTION(@_); + bless $self, $pkg if defined($self); +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::cpair ############## + +package RNA::cpair; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +*swig_i_get = *RNAc::cpair_i_get; +*swig_i_set = *RNAc::cpair_i_set; +*swig_j_get = *RNAc::cpair_j_get; +*swig_j_set = *RNAc::cpair_j_set; +*swig_mfe_get = *RNAc::cpair_mfe_get; +*swig_mfe_set = *RNAc::cpair_mfe_set; +*swig_p_get = *RNAc::cpair_p_get; +*swig_p_set = *RNAc::cpair_p_set; +*swig_hue_get = *RNAc::cpair_hue_get; +*swig_hue_set = *RNAc::cpair_hue_set; +*swig_sat_get = *RNAc::cpair_sat_get; +*swig_sat_set = *RNAc::cpair_sat_set; +sub new { + my $pkg = shift; + my $self = RNAc::new_cpair(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_cpair($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : RNA::plist ############## + +package RNA::plist; +@ISA = qw( RNA ); +%OWNER = (); +%ITERATORS = (); +*swig_i_get = *RNAc::plist_i_get; +*swig_i_set = *RNAc::plist_i_set; +*swig_j_get = *RNAc::plist_j_get; +*swig_j_set = *RNAc::plist_j_set; +*swig_p_get = *RNAc::plist_p_get; +*swig_p_set = *RNAc::plist_p_set; +sub new { + my $pkg = shift; + my $self = RNAc::new_plist(@_); + bless $self, $pkg if defined($self); +} + +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + RNAc::delete_plist($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +# ------- VARIABLE STUBS -------- + +package RNA; + +*VERSION = *RNAc::VERSION; +*symbolset = *RNAc::symbolset; +*final_cost = *RNAc::final_cost; +*give_up = *RNAc::give_up; +*noGU = *RNAc::noGU; +*no_closingGU = *RNAc::no_closingGU; +*tetra_loop = *RNAc::tetra_loop; +*energy_set = *RNAc::energy_set; +*dangles = *RNAc::dangles; +*nonstandards = *RNAc::nonstandards; +*temperature = *RNAc::temperature; +*james_rule = *RNAc::james_rule; +*logML = *RNAc::logML; +*cut_point = *RNAc::cut_point; + +my %__base_pair_hash; +tie %__base_pair_hash,"RNA::bondT", $RNAc::base_pair; +$base_pair= \%__base_pair_hash; +bless $base_pair, RNA::bondT; +*pr = *RNAc::pr; +*iindx = *RNAc::iindx; +*pf_scale = *RNAc::pf_scale; +*fold_constrained = *RNAc::fold_constrained; +*do_backtrack = *RNAc::do_backtrack; +*noLonelyPairs = *RNAc::noLonelyPairs; +*backtrack_type = *RNAc::backtrack_type; +*subopt_sorted = *RNAc::subopt_sorted; +*loop_size = *RNAc::loop_size; +*helix_size = *RNAc::helix_size; +*loop_degree = *RNAc::loop_degree; +*loops = *RNAc::loops; +*unpaired = *RNAc::unpaired; +*pairs = *RNAc::pairs; +*edit_backtrack = *RNAc::edit_backtrack; +*aligned_line = *RNAc::aligned_line; +*cost_matrix = *RNAc::cost_matrix; +*xsubi = *RNAc::xsubi; +*rna_plot_type = *RNAc::rna_plot_type; +1; diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/lib/auto/RNA/.exists b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/lib/auto/RNA/.exists new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/man3/.exists b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/man3/.exists new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/man3/RNA.3pm b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/man3/RNA.3pm new file mode 100755 index 000000000..063e052a2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/blib/man3/RNA.3pm @@ -0,0 +1,588 @@ +.\" Automatically generated by Pod::Man v1.34, Pod::Parser v1.13 +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sh \" Subsection heading +.br +.if t .Sp +.ne 5 +.PP +\fB\\$1\fR +.PP +.. +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. | will give a +.\" real vertical bar. \*(C+ will give a nicer C++. Capital omega is used to +.\" do unbreakable dashes and therefore won't be available. \*(C` and \*(C' +.\" expand to `' in nroff, nothing in troff, for use with C<>. +.tr \(*W-|\(bv\*(Tr +.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' +.ie n \{\ +. ds -- \(*W- +. ds PI pi +. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch +. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch +. ds L" "" +. ds R" "" +. ds C` "" +. ds C' "" +'br\} +.el\{\ +. ds -- \|\(em\| +. ds PI \(*p +. ds L" `` +. ds R" '' +'br\} +.\" +.\" If the F register is turned on, we'll generate index entries on stderr for +.\" titles (.TH), headers (.SH), subsections (.Sh), items (.Ip), and index +.\" entries marked with X<> in POD. Of course, you'll have to process the +.\" output yourself in some meaningful fashion. +.if \nF \{\ +. de IX +. tm Index:\\$1\t\\n%\t"\\$2" +.. +. nr % 0 +. rr F +.\} +.\" +.\" For nroff, turn off justification. Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.hy 0 +.if n .na +.\" +.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). +.\" Fear. Run. Save yourself. No user-serviceable parts. +. \" fudge factors for nroff and troff +.if n \{\ +. ds #H 0 +. ds #V .8m +. ds #F .3m +. ds #[ \f1 +. ds #] \fP +.\} +.if t \{\ +. ds #H ((1u-(\\\\n(.fu%2u))*.13m) +. ds #V .6m +. ds #F 0 +. ds #[ \& +. ds #] \& +.\} +. \" simple accents for nroff and troff +.if n \{\ +. ds ' \& +. ds ` \& +. ds ^ \& +. ds , \& +. ds ~ ~ +. ds / +.\} +.if t \{\ +. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u" +. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u' +. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u' +. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u' +. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u' +. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u' +.\} +. \" troff and (daisy-wheel) nroff accents +.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V' +.ds 8 \h'\*(#H'\(*b\h'-\*(#H' +.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#] +.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H' +.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u' +.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#] +.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#] +.ds ae a\h'-(\w'a'u*4/10)'e +.ds Ae A\h'-(\w'A'u*4/10)'E +. \" corrections for vroff +.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u' +.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u' +. \" for low resolution devices (crt and lpr) +.if \n(.H>23 .if \n(.V>19 \ +\{\ +. ds : e +. ds 8 ss +. ds o a +. ds d- d\h'-1'\(ga +. ds D- D\h'-1'\(hy +. ds th \o'bp' +. ds Th \o'LP' +. ds ae ae +. ds Ae AE +.\} +.rm #[ #] #H #V #F C +.\" ======================================================================== +.\" +.IX Title "RNA 3" +.TH RNA 3 "2005-11-21" "perl v5.8.0" "User Contributed Perl Documentation" +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +.Vb 7 +\& use RNA; +\& $seq = "CGCAGGGAUACCCGCG"; +\& ($struct, $mfe) = RNA::fold($seq); #predict mfe structure of $seq +\& RNA::PS_rna_plot($seq, $struct, "rna.ps"); # write PS plot to rna.ps +\& $F = RNA::pf_fold($seq); # compute partition function and pair pobabilities +\& RNA::PS_dot_plot($seq, "dot.ps"); # write dot plot to dot.ps +\& ... +.Ve +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +The \s-1RNA\s0.pm package gives access to almost all functions in the libRNA.a +library of the Vienna \s-1RNA\s0 \s-1PACKAGE\s0. The Perl wrapper is generated using +\&\s-1SWIG\s0 http://www.swig.org/ with relatively little manual intervention. +For each C function in the library the perl package provides a function +of the same name and calling convention (with few exceptions). For +detailed information you should therefore also consult the documentation +of the library (info RNAlib). +.PP +Note that in general C arrays are wrapped into opaque objects that can +only be accessed via helper functions. \s-1SWIG\s0 provides a couple of general +purpose helper functions, see the section at the end of this file. C +structures are wrapped into Perl objects using \s-1SWIG\s0's shadow class +mechanism, resulting in a tied hash with keys named after the structure +members. +.PP +For the interrested reader we list for each scalar type of the +corepsonding C variable in brackets, and point out the header files +containing the C declaration. +.Sh "Folding Routines" +.IX Subsection "Folding Routines" +Minimum free Energy Folding (from fold.h) +.IP "fold \s-1SEQUENCE\s0" 4 +.IX Item "fold SEQUENCE" +.PD 0 +.IP "fold \s-1SEQUENCE\s0, \s-1CONSTRAINTS\s0" 4 +.IX Item "fold SEQUENCE, CONSTRAINTS" +.PD +computes the minimum free energy structure of the string \s-1SEQUENCE\s0 and returns +the predicted structure and energy, e.g. +.Sp +.Vb 1 +\& ($structure, $mfe) = RNA::fold("UGUGUCGAUGUGCUAU"); +.Ve +.Sp +If a second argument is supplied and +$fold_constrained==1 the \s-1CONSTRAINTS\s0 string is +used to specify constraints on the predicted structure. The +characters '|', 'x', '<', '>' mark bases that are paired, unpaired, +paired upstream, or downstream, respectively; matching brackets \*(L"( )\*(R" +denote base pairs, dots '.' are used for unconstrained bases. +.Sp +In the two argument version the \s-1CONSTRAINTS\s0 string is modified and holds the +predicted structure upon return. This is done for backwards compatibility only, +and might change in future versions. +.IP "energy_of_struct \s-1SEQUENCE\s0, \s-1STRUCTURE\s0" 4 +.IX Item "energy_of_struct SEQUENCE, STRUCTURE" +returns the energy of \s-1SEQUENCE\s0 on \s-1STRUCTURE\s0 (in kcal/mol). The string structure +must hold a valid secondary structure in bracket notation. +.IP "update_fold_params" 4 +.IX Item "update_fold_params" +recalculate the pair matrix and energy parameters after a change in folding +parameters. In many cases (such as changes to +$temperature) the \fIfold()\fR routine will call +update_fold_params automatically when necessary. +.IP "free_arrays" 4 +.IX Item "free_arrays" +frees memory allocated internally when calling fold. +.PP +Partition function Folding (from part_func.h) +.IP "pf_fold \s-1SEQUENCE\s0" 4 +.IX Item "pf_fold SEQUENCE" +.PD 0 +.IP "pf_fold \s-1SEQUENCE\s0, \s-1CONSTRAINTS\s0" 4 +.IX Item "pf_fold SEQUENCE, CONSTRAINTS" +.PD +calculates the partition function over all possible secondary +structures and the matrix of pair probabilities for \s-1SEQUENCE\s0 and +returns a two element list consisting of a string summarizing possible +structures. See below on how to access the pair probability matrix. As +with fold the second argument can be used to specify folding +constraints. Constraints are implemented by excluding base pairings +that contradict the constraint, but without bonus +energies. Constraints of type '|' (paired base) are ignored. In the +two argument version \s-1CONSTRAINTS\s0 is modified to contain the structure +string on return (obsolete feature, for backwards compatibility only) +.IP "get_pr I, J" 4 +.IX Item "get_pr I, J" +After calling \f(CW\*(C`pf_fold\*(C'\fR the global C variable \f(CW\*(C`pr\*(C'\fR points to the +computed pair probabilities. Perl access to the C is facilitated by +the \f(CW\*(C`get_pr\*(C'\fR helper function that looks up and returns the +probability of the pair (I,J). +.IP "free_pf_arrays" 4 +.IX Item "free_pf_arrays" +frees memory allocated for pf_fold +.IP "update_pf_params \s-1LENGTH\s0" 4 +.IX Item "update_pf_params LENGTH" +recalculate energy parameters for pf_fold. In most cases (such as +simple changes to $temperature) \f(CW\*(C`pf_fold\*(C'\fR +will take appropriate action automatically. +.PP +Suboptimal Folding (from subopt.h) +.IP "subopt \s-1SEQUENCE\s0, \s-1CONSTRAINTS\s0, \s-1DELTA\s0" 4 +.IX Item "subopt SEQUENCE, CONSTRAINTS, DELTA" +.PD 0 +.IP "subopt \s-1SEQUENCE\s0, \s-1CONSTRAINTS\s0, \s-1DELTA\s0, \s-1FILEHANDLE\s0" 4 +.IX Item "subopt SEQUENCE, CONSTRAINTS, DELTA, FILEHANDLE" +.PD +compute all structures of \s-1SEQUENCE\s0 within DELTA*0.01 kcal/mol of the +optimum. If specified, results are written to \s-1FILEHANDLE\s0 and nothing +is returned. Else, the C function returnes a list of C structs of type +\&\s-1SOLUTION\s0. The list is wrapped by \s-1SWIG\s0 as a perl object that can be +accesses as follows: +.Sp +.Vb 5 +\& $solution = subopt($seq, undef, 500); +\& for (0..$solution->size()-1) { +\& printf "%s %6.2f\en", $solution->get($_)->{structure}, +\& $solution->get($_)->{energy}; +\& } +.Ve +.PP +Inverse Folding (from inverse.h) +.IP "inverse_fold \s-1START\s0, \s-1TARGET\s0" 4 +.IX Item "inverse_fold START, TARGET" +find a sequence that folds into structure \s-1TARGET\s0, by optimizing the +sequence until its mfe structure (as returned by fold) is +\&\s-1TARGET\s0. Startpoint of the optimization is the sequence \s-1START\s0. Returns +a list containing the sequence found and the final value of the cost +function, i.e. 0 if the search was successful. A random start sequence +can be generated using random_string. +.IP "inverse_pf_fold \s-1START\s0, \s-1TARGET\s0" 4 +.IX Item "inverse_pf_fold START, TARGET" +optimizes a sequence (beginning with \s-1START\s0) by maximising the +frequency of the structure \s-1TARGET\s0 in the thermodynamic ensemble +of structures. Returns a list containing the optimized sequence and +the final value of the cost function. The cost function is given by +\&\f(CW\*(C`energy_of_struct(seq, TARGET) \- pf_fold(seq)\*(C'\fR, i.e.\f(CW\*(C`\-RT*log(p(TARGET))\*(C'\fR +.IP "$final_cost [float]" 4 +.IX Item "$final_cost [float]" +holds the value of the cost function where the optimization in +\&\f(CW\*(C`inverse_pf_fold\*(C'\fR should stop. For values <=0 the optimization will +only terminate at a local optimimum (which might take very long to reach). +.IP "$symbolset [char *]" 4 +.IX Item "$symbolset [char *]" +the string symbolset holds the allowed characters to be used by +\&\f(CW\*(C`inverse_fold\*(C'\fR and \f(CW\*(C`inverse_pf_fold\*(C'\fR, the default alphabet is \*(L"\s-1AUGC\s0\*(R" +.IP "$give_up [int]" 4 +.IX Item "$give_up [int]" +If non-zero stop optimization when its clear that no exact solution +can be found. Else continue and eventually return an approximate +solution. Default 0. +.PP +Global Variables to Modify Folding (from fold_vars.h) +.IP "$noGU [int]" 4 +.IX Item "$noGU [int]" +Do not allow \s-1GU\s0 pairs to form, default 0. +.IP "$no_closingGU [int]" 4 +.IX Item "$no_closingGU [int]" +allow \s-1GU\s0 only inside stacks, default 0. +.IP "$tetra_loop [int]" 4 +.IX Item "$tetra_loop [int]" +Fold with specially stable 4\-loops, default 1. +.IP "$energy_set [int]" 4 +.IX Item "$energy_set [int]" +0 = \s-1BP\s0; 1=any mit \s-1GC\s0; 2=any mit AU\-parameter, default 0. +.IP "$dangles [int]" 4 +.IX Item "$dangles [int]" +How to compute dangling ends. 0: no dangling end energies, 1: \*(L"normal\*(R" +dangling ends (default), 2: simplified dangling ends, 3: \*(L"normal\*(R" + +co-axial stacking. Note that pf_fold treats cases 1 and 3 +as 2. The same holds for the main computation in subopt, +however subopt will re-evalute energies using +energy_of_struct for cases 1 and 3. See the more +detailed discussion in RNAlib.texinfo. +.IP "$nonstandards [char *]" 4 +.IX Item "$nonstandards [char *]" +contains allowed non standard bases, default empty string "" +.IP "$temperature [double]" 4 +.IX Item "$temperature [double]" +temperature in degrees Celsius for rescaling parameters, default 37C. +.IP "$logML [int]" 4 +.IX Item "$logML [int]" +use logarithmic multiloop energy function in +energy_of_struct, default 0. +.IP "$noLonelyPairs [int]" 4 +.IX Item "$noLonelyPairs [int]" +consider only structures without isolated base pairs (helices of length 1). +For pf_fold only eliminates pairs +that can \fBonly\fR occur as isolated pairs. Default 0. +.IP "$base_pair [struct bond *]" 4 +.IX Item "$base_pair [struct bond *]" +list of base pairs from last call to fold. Better use +the structure string returned by fold. +.IP "$pf_scale [double]" 4 +.IX Item "$pf_scale [double]" +scaling factor used by pf_fold to avoid overflows. Should +be set to exp(\-F/(RT*length)) where F is a guess for the ensmble free +energy (e.g. use the mfe). +.IP "$fold_constrained [int]" 4 +.IX Item "$fold_constrained [int]" +apply constraints in the folding algorithms, default 0. +.IP "$do_backtrack [int]" 4 +.IX Item "$do_backtrack [int]" +If 0 do not compute the pair probabilities in pf_fold +(only the partition function). Default 1. +.IP "$backtrack_type [char]" 4 +.IX Item "$backtrack_type [char]" +usually 'F'; 'C' require (1,N) to be bonded; 'M' backtrack as if the +sequence was part of a multi loop. Used by inverse_fold +.IP "$pr [double *]" 4 +.IX Item "$pr [double *]" +the base pairing prob. matrix computed by pf_fold. +.IP "$iindx [int *]" 4 +.IX Item "$iindx [int *]" +Array of indices for moving withing the \f(CW\*(C`pr\*(C'\fR array. Better use +get_pr. +.Sh "Parsing and Comparing Structures" +.IX Subsection "Parsing and Comparing Structures" +from RNAstruct.h: these functions convert between strings +representating secondary structures with various levels of coarse +graining. See the documentation of the C library for details +.IP "b2HIT \s-1STRUCTURE\s0" 4 +.IX Item "b2HIT STRUCTURE" +Full \-> \s-1HIT\s0 [incl. root] +.IP "b2C \s-1STRUCTURE\s0" 4 +.IX Item "b2C STRUCTURE" +Full \-> Coarse [incl. root] +.IP "b2Shapiro \s-1STRUCTURE\s0" 4 +.IX Item "b2Shapiro STRUCTURE" +Full \-> weighted Shapiro [i.r.] +.IP "add_root \s-1STRUCTURE\s0" 4 +.IX Item "add_root STRUCTURE" +{Tree} \-> ({Tree}R) +.IP "expand_Shapiro \s-1COARSE\s0" 4 +.IX Item "expand_Shapiro COARSE" +add S for stacks to coarse struct +.IP "expand_Full \s-1STRUCTURE\s0" 4 +.IX Item "expand_Full STRUCTURE" +Full \-> FFull +.IP "unexpand_Full \s-1FSTRUCTURE\s0" 4 +.IX Item "unexpand_Full FSTRUCTURE" +FFull \-> Full +.IP "unweight \s-1WCOARSE\s0" 4 +.IX Item "unweight WCOARSE" +remove weights from coarse struct +.IP "unexpand_aligned_F \s-1ALIGN\s0" 4 +.IX Item "unexpand_aligned_F ALIGN" +.PD 0 +.IP "parse_structure \s-1STRUCTURE\s0" 4 +.IX Item "parse_structure STRUCTURE" +.PD +computes structure statistics, and fills the following global variables: +.Sp +$loops [int] number of loops (and stacks) +\&\f(CW$unpaired\fR [int] number of unpaired positions +\&\f(CW$pairs\fR [int] number of paired positions +\&\f(CW$loop_size\fR[int *] holds all loop sizes +\&\f(CW$loop_degree\fR[int *] holds all loop degrees +\&\f(CW$helix_size\fR[int *] holds all helix lengths +.PP +from treedist.h: routines for computing tree-edit distances between structures +.IP "make_tree \s-1STRUCTURE\s0" 4 +.IX Item "make_tree STRUCTURE" +make input for tree_edit_distance (a Tree * pointer). +.IP "tree_edit_distance T1, T2" 4 +.IX Item "tree_edit_distance T1, T2" +compare to structures using tree editing. \f(CW\*(C`T1\*(C'\fR, \f(CW\*(C`T2\*(C'\fR must have been +created using \f(CW\*(C`tree_edit_distance\*(C'\fR +.IP "print_tree T" 4 +.IX Item "print_tree T" +mainly for debugging +.IP "free_tree T" 4 +.IX Item "free_tree T" +free space allocated by make_tree +.PP +from stringdist.h routines to compute structure distances via string-editing +.IP "Make_swString \s-1STRUCTURE\s0" 4 +.IX Item "Make_swString STRUCTURE" +[ returns swString * ] +make input for string_edit_distance +.IP "string_edit_distance S1, S2" 4 +.IX Item "string_edit_distance S1, S2" +[ returns float ] +compare to structures using string alignment. \f(CW\*(C`S1\*(C'\fR, \f(CW\*(C`S2\*(C'\fR should be +created using \f(CW\*(C`Make_swString\*(C'\fR +.PP +from profiledist +.IP "Make_bp_profile \s-1LENGTH\s0" 4 +.IX Item "Make_bp_profile LENGTH" +[ returns (float *) ] +condense pair probability matrix \f(CW\*(C`pr\*(C'\fR into a vector containing +probabilities for upstream paired, downstream paired and +unpaired. This resulting probability profile is used as input for +profile_edit_distance +.IP "profile_edit_distance T1, T2" 4 +.IX Item "profile_edit_distance T1, T2" +[ returns float ] +align two probability profiles produced by \f(CW\*(C`Make_bp_profile\*(C'\fR +.IP "print_bppm T" 4 +.IX Item "print_bppm T" +[ returns void ] +print string representation of probability profile +.IP "free_profile T" 4 +.IX Item "free_profile T" +[ returns void ] +free space allocated in Make_bp_profile +.PP +Global variables for computing structure distances +.IP "$edit_backtrack [int]" 4 +.IX Item "$edit_backtrack [int]" +set to 1 if you want backtracking +.IP "$aligned_line [(char *)[2]]" 4 +.IX Item "$aligned_line [(char *)[2]]" +containes alignmed structures after computing structure distance with +\&\f(CW\*(C`edit_backtrack==1\*(C'\fR +.IP "$cost_matrix [int]" 4 +.IX Item "$cost_matrix [int]" +0 usual costs (default), 1 Shapiro's costs +.Sh "Utilities (from utils.h)" +.IX Subsection "Utilities (from utils.h)" +.IP "space \s-1SIZE\s0" 4 +.IX Item "space SIZE" +allocate memory from C. Usually not needed in Perl +.IP "nrerror \s-1MESSGAE\s0" 4 +.IX Item "nrerror MESSGAE" +die with error message. Better use Perl's \f(CW\*(C`die\*(C'\fR +.IP "$xsubi [unsigned short[3]]" 4 +.IX Item "$xsubi [unsigned short[3]]" +libRNA uses the rand48 48bit random number generator if available, the +current random number is always stored in \f(CW$xsubi\fR. +.IP "init_rand" 4 +.IX Item "init_rand" +initialize the \f(CW$xsubi\fR random number from current time +.IP "urn" 4 +.IX Item "urn" +returns a random number between 0 and 1 using the random number +generator from the \s-1RNA\s0 library. +.IP "int_urn \s-1FROM\s0, \s-1TO\s0" 4 +.IX Item "int_urn FROM, TO" +returns random integer in the range [\s-1FROM\s0..TO] +.IP "time_stamp" 4 +.IX Item "time_stamp" +current date in a string. In perl you might as well use \f(CW\*(C`locatime\*(C'\fR +.IP "random_string \s-1LENGTH\s0, \s-1SYMBOLS\s0" 4 +.IX Item "random_string LENGTH, SYMBOLS" +returns a string of length \s-1LENGTH\s0 using characters from the string +\&\s-1SYMBOLS\s0 +.IP "hamming S1, S2" 4 +.IX Item "hamming S1, S2" +calculate hamming distance of the strings \f(CW\*(C`S1\*(C'\fR and \f(CW\*(C`S2\*(C'\fR. +.IP "pack_structure \s-1STRUCTURE\s0" 4 +.IX Item "pack_structure STRUCTURE" +pack secondary structure, using a 5:1 compression via 3 +encoding. Returns the packed string. +.IP "unpack_structure \s-1PACKED\s0" 4 +.IX Item "unpack_structure PACKED" +unpacks a secondary structure packed with pack_structure +.IP "make_pair_table \s-1STRUCTURE\s0" 4 +.IX Item "make_pair_table STRUCTURE" +returns a pair table as a newly allocated (short *) C array, such +that: table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] +contains the length of the structure. +.IP "bp_distance \s-1STRUCTURE1\s0, \s-1STRUCTURE2\s0" 4 +.IX Item "bp_distance STRUCTURE1, STRUCTURE2" +returns the base pair distance of the two \s-1STRUCTURES\s0. dist = {number +of base pairs in one structure but not in the other} same as edit +distance with open-pair close-pair as move-set +.PP +from PS_plot.h +.IP "PS_rna_plot \s-1SEQUENCE\s0, \s-1STRUCTURE\s0, \s-1FILENAME\s0" 4 +.IX Item "PS_rna_plot SEQUENCE, STRUCTURE, FILENAME" +write PostScript drawing of structure to \s-1FILENAME\s0. Returns 1 on +sucess, 0 else. +.IP "PS_rna_plot_a \s-1SEQUENCE\s0, \s-1STRUCTURE\s0, \s-1FILENAME\s0, \s-1PRE\s0, \s-1POST\s0" 4 +.IX Item "PS_rna_plot_a SEQUENCE, STRUCTURE, FILENAME, PRE, POST" +write PostScript drawing of structure to \s-1FILENAME\s0. The strings \s-1PRE\s0 and +\&\s-1POST\s0 contain PostScript code that is included verbatim in the plot just +before (after) the data. Returns 1 on sucess, 0 else. +.IP "gmlRNA \s-1SEQUENCE\s0, \s-1STRUCTURE\s0, \s-1FILENAME\s0, \s-1OPTION\s0" 4 +.IX Item "gmlRNA SEQUENCE, STRUCTURE, FILENAME, OPTION" +write structure drawing in gml (Graph Meta Language) to +\&\s-1FILENAME\s0. \s-1OPTION\s0 should be a single character. If uppercase the gml +output will include the \s-1SEQUENCE\s0 as node labels. \s-1IF\s0 \s-1OPTION\s0 equal 'x' +or 'X' write graph with coordinates (else only connectivity +information). Returns 1 on sucess, 0 else. +.IP "ssv_rna_plot \s-1SEQUENCE\s0, \s-1STRUCTURE\s0, \s-1SSFILE\s0" 4 +.IX Item "ssv_rna_plot SEQUENCE, STRUCTURE, SSFILE" +write structure drfawing as coord file for SStructView Returns 1 on +sucess, 0 else. +.IP "xrna_plot \s-1SEQUENCE\s0, \s-1STRUCTURE\s0, \s-1SSFILE\s0" 4 +.IX Item "xrna_plot SEQUENCE, STRUCTURE, SSFILE" +write structure drawing as \*(L".ss\*(R" file for further editing in \s-1XRNA\s0. +Returns 1 on sucess, 0 else. +.IP "PS_dot_plot \s-1SEQUENCE\s0, \s-1FILENAME\s0" 4 +.IX Item "PS_dot_plot SEQUENCE, FILENAME" +write a PostScript dot plot of the pair probability matix to +\&\s-1FILENAME\s0. Returns 1 on sucess, 0 else. +.IP "$rna_plot_type [int]" 4 +.IX Item "$rna_plot_type [int]" +Select layout algorithm for structure drawings. Currently available +0= simple coordinates, 1= naview, default 1. +.PP +from read_epars.c +.IP "read_parameter_file \s-1FILENAME\s0" 4 +.IX Item "read_parameter_file FILENAME" +read energy parameters from \s-1FILENAME\s0 +.IP "write_parameter_file \s-1FILENAME\s0" 4 +.IX Item "write_parameter_file FILENAME" +write energy parameters to \s-1FILENAME\s0 +.Sh "\s-1SWIG\s0 helper functions" +.IX Subsection "SWIG helper functions" +The package includes generic helper functions to access C arrays +of type \f(CW\*(C`int\*(C'\fR, \f(CW\*(C`float\*(C'\fR and \f(CW\*(C`double\*(C'\fR, such as: +.IP "intP_getitem \s-1POINTER\s0, \s-1INDEX\s0" 4 +.IX Item "intP_getitem POINTER, INDEX" +return the element \s-1INDEX\s0 from the array +.IP "intP_setitem \s-1POINTER\s0, \s-1INDEX\s0, \s-1VALUE\s0" 4 +.IX Item "intP_setitem POINTER, INDEX, VALUE" +set element \s-1INDEX\s0 to \s-1VALUE\s0 +.IP "new_intP \s-1NELEM\s0" 4 +.IX Item "new_intP NELEM" +allocate a new C array of integers with \s-1NELEM\s0 elements and return the pointer +.IP "delete_intP \s-1POINTER\s0" 4 +.IX Item "delete_intP POINTER" +deletes the C array by calling \fIfree()\fR +.PP +substituting \f(CW\*(C`intP\*(C'\fR with \f(CW\*(C`floatP\*(C'\fR or \f(CW\*(C`doubleP\*(C'\fR gives the corresponding +functions for arrays of float or double. You need to know the correct C +type however, and the function work only for arrays of simple types. +.PP +On the lowest level the \f(CW\*(C`cdata\*(C'\fR function gives direct access to any data +in the form of a Perl string. +.IP "cdata \s-1POINTER\s0, \s-1SIZE\s0" 4 +.IX Item "cdata POINTER, SIZE" +copies \s-1SIZE\s0 bytes at \s-1POINTER\s0 to a Perl string (with binary data) +.IP "memmove \s-1POINTER\s0, \s-1STRING\s0" 4 +.IX Item "memmove POINTER, STRING" +copies the (binary) string \s-1STRING\s0 to the memory location pointed to by +\&\s-1POINTER\s0. +.PP +In combination with Perl's \f(CW\*(C`unpack\*(C'\fR this provides a generic way to convert +C data structures to Perl. E.g. +.PP +.Vb 2 +\& RNA::parse_structure($structure); # fills the $RNA::loop_degree array +\& @ldegrees = unpack "I*", RNA::cdata($RNA::loop_degree, ($RNA::loops+1)*4); +.Ve +.PP +Warning: using these functions with wrong arguments will corrupt your +memory and lead to a segmentation fault. +.SH "AUTHOR" +.IX Header "AUTHOR" +Ivo L. Hofacker diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/pm_to_blib b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/pm_to_blib new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/test.pl b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/test.pl new file mode 100755 index 000000000..0cd5b7d6f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Perl/test.pl @@ -0,0 +1,136 @@ +#!/usr/bin/perl -Iblib/arch -Iblib/lib + +# Last changed Time-stamp: <2005-07-23 16:04:56 ivo> + +######################### We start with some black magic to print on failure. +# (It may become useful if the test is moved to ./t subdirectory.) +use strict; +use Test; +use lib qw|blib/arch blib/lib|; + +BEGIN { plan tests => 19; } + +use RNA; +use warnings; + +######################### End of black magic. + +# Insert your test code below (better if it prints "ok 13" +# (correspondingly "not ok 13") depending on the success of chunk 13 +# of the test code): + +my $seq1 ="CGCAGGGAUACCCGCG"; +my $struc1="(((.((....)).)))"; +my $seq2 ="GCGCCCAUAGGGACGC"; +my $struc2="((((((...))).)))"; +# calculate a hamming distance (from util.c) +ok(RNA::hamming($seq1, $seq2), 16); + +# check a global variable +ok($RNA::temperature, 37); + +# fold a sequence + +# old obsolete way of calling fold() +my $struct = $seq1; # wierd way of allocating space +my $mfe=RNA::fold($seq1, $struct); +ok($struct, $struc1); + +# new better interface +($struct, $mfe) = RNA::fold($seq1); +ok($struct eq $struc1); +# check energy +ok(RNA::energy_of_struct($seq1,$struc1), $mfe); + +# check constrained folding +$RNA::fold_constrained = 1; +my($struct3, $cmfe) = RNA::fold($seq1, '....xx....xx...'); +ok($struct3, '(((..........)))'); +ok(RNA::energy_of_struct($seq1,$struct3), $cmfe); +$RNA::fold_constrained = 0; + +# test cofold +$RNA::cut_point = length($seq1)+1; +my($costruct, $comfe) = RNA::cofold($seq1 . $seq2); +ok($costruct, '(((.((....)).)))((((((...))).)))'); +$cmfe = RNA::energy_of_struct($seq1 . $seq2, $costruct); +ok(abs($comfe-$cmfe)<1e-5); +$RNA::cut_point=-1; + +# pf_fold +my $f = RNA::pf_fold($seq1, $struct); +ok(($f<$mfe)&&($mfe-$f<0.8)); + +# tree distance +my $xstruc = RNA::expand_Full($struc1); +my $T1 = RNA::make_tree($xstruc); +$xstruc = RNA::expand_Full($struc2); +my $T2 = RNA::make_tree($xstruc); +$RNA::edit_backtrack = 1; +my $tree_dist = RNA::tree_edit_distance($T1, $T2); +# print RNA::get_aligned_line(0), RNA::get_aligned_line(1),"\n"; +ok($tree_dist,4); + +# check access to a C array +#ok(RNA::ptrvalue($RNA::iindx,3),108); +ok(RNA::intP_getitem($RNA::iindx,3),108); + +#RNA::shortP_setitem($RNA::xsubi, 0, 171); +#RNA::shortP_setitem($RNA::xsubi, 1, 42); +#RNA::shortP_setitem($RNA::xsubi, 2, 93); +RNA::memmove($RNA::xsubi, pack('S3', 171,42,93)); +ok(pack('S3', 171,42,93), RNA::cdata($RNA::xsubi, 6)); + +# get a bp prob in two different ways +my $p1 = RNA::get_pr(2,15); +my $ii = RNA::intP_getitem($RNA::iindx, 2); +my $p2 = RNA::doubleP_getitem($RNA::pr, $ii-15); +ok(($p1<0.999) && ($p1>0.99) && (abs($p1-$p2)<1.2e-7)); + +my $bpf = RNA::Make_bp_profile(length($seq1)); +my @bpf = unpack("f*",RNA::cdata($bpf, length($seq1)*4*3)); +ok (($bpf[2*3]+$bpf[2*3+1]>.99999)&&$bpf[2*3+2]==0 && + ($bpf[2*3+1]>=$p1)); + +my $pack = RNA::pack_structure($struc1); +ok (RNA::unpack_structure($pack), $struc1); + + +RNA::parse_structure($struc1); +ok(($RNA::loops==2) && ($RNA::pairs==5)&&($RNA::unpaired==6) && + (RNA::intP_getitem($RNA::loop_degree,1)==2)); + + +RNA::PS_rna_plot($seq1, $struc1, "test_ss.ps"); +my $anote = "2 15 1 gmark\n" . "3 cmark\n"; +RNA::PS_rna_plot_a($seq1, $struc1, "test_ss_a.ps", undef, $anote); +RNA::PS_dot_plot($seq1, "test_dp.ps"); +RNA::ssv_rna_plot($seq1, $struct, "test.coord"); +# print "$seq1, $struct, $mfe, $f\n"; +print "please check the two postscript files test_ss.ps and test_dp.ps\n"; +RNA::write_parameter_file("test.par"); + +$RNA::symbolset = "GC"; +my $start = RNA::random_string(length $struc1, $RNA::symbolset); +my ($sinv, $cost) = RNA::inverse_fold($start, $struc1); +my ($ss, $en) = RNA::fold($sinv); +ok($ss, $struc1); + +RNA::free_pf_arrays(); +RNA::free_arrays(); + +$RNA::subopt_sorted = 1; +$RNA::noLonelyPairs = 1; +my $solution = RNA::subopt($seq1, undef, 500, undef); + +printf "%d suboptimals\n", $solution->size(); +for (0..$solution->size()) { + # the last access should produce a "value out of range" warning + printf "%s %6.2f\n", $solution->get($_)->{structure}, + $solution->get($_)->{energy} + if defined $solution->get($_); +} +$RNA::cut_point = 3; +my $e = RNA::energy_of_struct("GCGC", "(())"); +ok(int($e*100+0.5), 70); + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNALfold.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNALfold.Po new file mode 100755 index 000000000..4dcaeaf4b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNALfold.Po @@ -0,0 +1,120 @@ +RNALfold.o RNALfold.o: RNALfold.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/fold.h ../H/part_func.h \ + ../H/fold_vars.h ../H/utils.h ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/fold.h: + +../H/part_func.h: + +../H/fold_vars.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAalifold.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAalifold.Po new file mode 100755 index 000000000..1367f8ca7 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAalifold.Po @@ -0,0 +1,129 @@ +RNAalifold.o RNAalifold.o: RNAalifold.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/fold.h ../H/part_func.h \ + ../H/fold_vars.h ../H/PS_dot.h ../H/utils.h ../config.h ../H/pair_mat.h \ + ../H/alifold.h ../H/aln_util.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/fold.h: + +../H/part_func.h: + +../H/fold_vars.h: + +../H/PS_dot.h: + +../H/utils.h: + +../config.h: + +../H/pair_mat.h: + +../H/alifold.h: + +../H/aln_util.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAcofold.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAcofold.Po new file mode 100755 index 000000000..e1eaa6984 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAcofold.Po @@ -0,0 +1,127 @@ +RNAcofold.o RNAcofold.o: RNAcofold.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/PS_dot.h ../H/cofold.h ../H/fold.h \ + ../H/part_func_co.h ../H/part_func.h ../H/fold_vars.h ../H/utils.h \ + ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/PS_dot.h: + +../H/cofold.h: + +../H/fold.h: + +../H/part_func_co.h: + +../H/part_func.h: + +../H/fold_vars.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAddG.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAddG.Po new file mode 100755 index 000000000..16926a85e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAddG.Po @@ -0,0 +1,121 @@ +RNAddG.o RNAddG.o: RNAddG.c /usr/include/stdio.h /usr/include/features.h \ + /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/fold.h ../H/part_func.h \ + ../H/fold_vars.h ../H/PS_dot.h ../H/utils.h ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/fold.h: + +../H/part_func.h: + +../H/fold_vars.h: + +../H/PS_dot.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAddG4.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAddG4.Po new file mode 100755 index 000000000..2eaaa9223 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAddG4.Po @@ -0,0 +1,124 @@ +RNAddG4.o RNAddG4.o: RNAddG4.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/fold.h ../H/part_func.h \ + ../H/fold_vars.h ../H/PS_dot.h ../H/utils.h ../config.h ../H/duplex.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/fold.h: + +../H/part_func.h: + +../H/fold_vars.h: + +../H/PS_dot.h: + +../H/utils.h: + +../config.h: + +../H/duplex.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAdistance.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAdistance.Po new file mode 100755 index 000000000..7ec96ad1a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAdistance.Po @@ -0,0 +1,122 @@ +RNAdistance.o RNAdistance.o: RNAdistance.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/dist_vars.h ../H/RNAstruct.h \ + ../H/treedist.h ../H/stringdist.h ../H/utils.h ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/dist_vars.h: + +../H/RNAstruct.h: + +../H/treedist.h: + +../H/stringdist.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAduplex.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAduplex.Po new file mode 100755 index 000000000..121c5ba60 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAduplex.Po @@ -0,0 +1,107 @@ +RNAduplex.o RNAduplex.o: RNAduplex.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/ctype.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/duplex.h ../H/fold.h ../H/fold_vars.h \ + ../H/utils.h ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/duplex.h: + +../H/fold.h: + +../H/fold_vars.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAeval.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAeval.Po new file mode 100755 index 000000000..b5739b894 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAeval.Po @@ -0,0 +1,118 @@ +RNAeval.o RNAeval.o: RNAeval.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/fold_vars.h ../H/fold.h ../H/utils.h \ + ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/fold_vars.h: + +../H/fold.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAfold.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAfold.Po new file mode 100755 index 000000000..3eaa51480 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAfold.Po @@ -0,0 +1,122 @@ +RNAfold.o RNAfold.o: RNAfold.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/fold.h ../H/part_func.h \ + ../H/fold_vars.h ../H/PS_dot.h ../H/utils.h ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/fold.h: + +../H/part_func.h: + +../H/fold_vars.h: + +../H/PS_dot.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAheat.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAheat.Po new file mode 100755 index 000000000..f1ae75061 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAheat.Po @@ -0,0 +1,119 @@ +RNAheat.o RNAheat.o: RNAheat.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h /usr/include/ctype.h /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h ../H/utils.h \ + ../config.h ../H/fold_vars.h ../H/fold.h ../H/part_func.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +/usr/include/ctype.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +../H/utils.h: + +../config.h: + +../H/fold_vars.h: + +../H/fold.h: + +../H/part_func.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAinverse.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAinverse.Po new file mode 100755 index 000000000..ba74ed898 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAinverse.Po @@ -0,0 +1,122 @@ +RNAinverse.o RNAinverse.o: RNAinverse.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/inverse.h ../H/fold_vars.h ../H/fold.h \ + ../H/part_func.h ../H/utils.h ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/inverse.h: + +../H/fold_vars.h: + +../H/fold.h: + +../H/part_func.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAmotif_distance.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAmotif_distance.Po new file mode 100755 index 000000000..297871c49 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAmotif_distance.Po @@ -0,0 +1,122 @@ +RNAmotif_distance.o RNAmotif_distance.o: RNAmotif_distance.c \ + /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/dist_vars.h ../H/RNAstruct.h \ + ../H/treedist.h ../H/stringdist.h ../H/utils.h ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/dist_vars.h: + +../H/RNAstruct.h: + +../H/treedist.h: + +../H/stringdist.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAmotif_distance.Po~ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAmotif_distance.Po~ new file mode 100755 index 000000000..7ec96ad1a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAmotif_distance.Po~ @@ -0,0 +1,122 @@ +RNAdistance.o RNAdistance.o: RNAdistance.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/dist_vars.h ../H/RNAstruct.h \ + ../H/treedist.h ../H/stringdist.h ../H/utils.h ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/dist_vars.h: + +../H/RNAstruct.h: + +../H/treedist.h: + +../H/stringdist.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNApaln.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNApaln.Po new file mode 100755 index 000000000..46f257b23 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNApaln.Po @@ -0,0 +1,139 @@ +RNApaln.o RNApaln.o: RNApaln.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/errno.h /usr/include/bits/errno.h \ + /usr/include/linux/errno.h /usr/include/asm/errno.h \ + /usr/include/asm-x86_64/errno.h /usr/include/string.h \ + /usr/include/bits/string.h /usr/include/bits/string2.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h ../H/part_func.h \ + ../H/fold.h ../H/fold_vars.h ../H/profiledist.h ../H/dist_vars.h \ + ../H/utils.h ../config.h ../H/ProfileAln.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/errno.h: + +/usr/include/bits/errno.h: + +/usr/include/linux/errno.h: + +/usr/include/asm/errno.h: + +/usr/include/asm-x86_64/errno.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +../H/part_func.h: + +../H/fold.h: + +../H/fold_vars.h: + +../H/profiledist.h: + +../H/dist_vars.h: + +../H/utils.h: + +../config.h: + +../H/ProfileAln.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNApdist.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNApdist.Po new file mode 100755 index 000000000..e93a96bf4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNApdist.Po @@ -0,0 +1,135 @@ +RNApdist.o RNApdist.o: RNApdist.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/errno.h /usr/include/bits/errno.h \ + /usr/include/linux/errno.h /usr/include/asm/errno.h \ + /usr/include/asm-x86_64/errno.h /usr/include/string.h \ + /usr/include/bits/string.h /usr/include/bits/string2.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h ../H/part_func.h \ + ../H/fold_vars.h ../H/profiledist.h ../H/dist_vars.h ../H/utils.h \ + ../config.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/errno.h: + +/usr/include/bits/errno.h: + +/usr/include/linux/errno.h: + +/usr/include/asm/errno.h: + +/usr/include/asm-x86_64/errno.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +../H/part_func.h: + +../H/fold_vars.h: + +../H/profiledist.h: + +../H/dist_vars.h: + +../H/utils.h: + +../config.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAplfold.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAplfold.Po new file mode 100755 index 000000000..cac72381b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAplfold.Po @@ -0,0 +1,122 @@ +RNAplfold.o RNAplfold.o: RNAplfold.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/fold.h ../H/part_func.h \ + ../H/fold_vars.h ../H/utils.h ../config.h ../H/PS_dot.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/fold.h: + +../H/part_func.h: + +../H/fold_vars.h: + +../H/utils.h: + +../config.h: + +../H/PS_dot.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAplot.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAplot.Po new file mode 100755 index 000000000..8735197e4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAplot.Po @@ -0,0 +1,115 @@ +RNAplot.o RNAplot.o: RNAplot.c /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/confname.h \ + /usr/include/getopt.h ../H/utils.h ../config.h ../H/PS_dot.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +../H/utils.h: + +../config.h: + +../H/PS_dot.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAstats.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAstats.Po new file mode 100755 index 000000000..3950db63c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAstats.Po @@ -0,0 +1,122 @@ +RNAstats.o RNAstats.o: RNAstats.c ../config.h /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/part_func.h ../H/fold.h \ + ../H/fold_vars.h ../H/utils.h ../H/subopt.h + +../config.h: + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/part_func.h: + +../H/fold.h: + +../H/fold_vars.h: + +../H/utils.h: + +../H/subopt.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAsubopt.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAsubopt.Po new file mode 100755 index 000000000..dfdadd9e1 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/.deps/RNAsubopt.Po @@ -0,0 +1,122 @@ +RNAsubopt.o RNAsubopt.o: RNAsubopt.c ../config.h /usr/include/stdio.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ + /usr/include/gconv.h \ + /usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/stdlib.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ + /usr/include/alloca.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h /usr/include/ctype.h \ + /usr/include/string.h /usr/include/bits/string.h \ + /usr/include/bits/string2.h ../H/part_func.h ../H/fold.h \ + ../H/fold_vars.h ../H/utils.h ../H/subopt.h + +../config.h: + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/lib/gcc/x86_64-redhat-linux/3.4.5/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/ctype.h: + +/usr/include/string.h: + +/usr/include/bits/string.h: + +/usr/include/bits/string2.h: + +../H/part_func.h: + +../H/fold.h: + +../H/fold_vars.h: + +../H/utils.h: + +../H/subopt.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/Makefile new file mode 100755 index 000000000..08c498a46 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/Makefile @@ -0,0 +1,559 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# Progs/Makefile. Generated from Makefile.in by configure. + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005 Free Software Foundation, Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + + + +SOURCES = RNALfold.c RNAalifold.c RNAcofold.c RNAdistance.c RNAmotif_distance.c RNAduplex.c RNAeval.c RNAfold.c RNAheat.c RNAinverse.c RNApaln.c RNApdist.c RNAplfold.c RNAplot.c RNAsubopt.c RNAstats.c RNAddG.c RNAddG4.c + +srcdir = . +top_srcdir = .. + +pkgdatadir = $(datadir)/ViennaRNA +pkglibdir = $(libdir)/ViennaRNA +pkgincludedir = $(includedir)/ViennaRNA +top_builddir = .. +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +INSTALL = /usr/bin/install -c +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +build_triplet = x86_64-unknown-linux-gnu +host_triplet = x86_64-unknown-linux-gnu +bin_PROGRAMS = RNAfold$(EXEEXT) RNAeval$(EXEEXT) RNAheat$(EXEEXT) \ + RNApdist$(EXEEXT) RNAdistance$(EXEEXT) RNAmotif_distance$(EXEEXT) RNAinverse$(EXEEXT) \ + RNAplot$(EXEEXT) RNAsubopt$(EXEEXT) RNALfold$(EXEEXT) \ + RNAcofold$(EXEEXT) RNApaln$(EXEEXT) RNAduplex$(EXEEXT) \ + RNAalifold$(EXEEXT) RNAplfold$(EXEEXT) +subdir = Progs +DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.in +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_CLEAN_FILES = +am__installdirs = "$(DESTDIR)$(bindir)" +binPROGRAMS_INSTALL = $(INSTALL_PROGRAM) +PROGRAMS = $(bin_PROGRAMS) +RNALfold_SOURCES = RNALfold.c +RNALfold_OBJECTS = RNALfold.$(OBJEXT) +RNALfold_LDADD = $(LDADD) +RNALfold_DEPENDENCIES = ../lib/libRNA.a +RNAalifold_SOURCES = RNAalifold.c +RNAalifold_OBJECTS = RNAalifold.$(OBJEXT) +RNAalifold_LDADD = $(LDADD) +RNAalifold_DEPENDENCIES = ../lib/libRNA.a +RNAcofold_SOURCES = RNAcofold.c +RNAcofold_OBJECTS = RNAcofold.$(OBJEXT) +RNAcofold_LDADD = $(LDADD) +RNAcofold_DEPENDENCIES = ../lib/libRNA.a +RNAdistance_SOURCES = RNAdistance.c +RNAdistance_OBJECTS = RNAdistance.$(OBJEXT) +RNAdistance_LDADD = $(LDADD) +RNAdistance_DEPENDENCIES = ../lib/libRNA.a +RNAmotif_distance_SOURCES = RNAmotif_distance.c +RNAmotif_distance_OBJECTS = RNAmotif_distance.$(OBJEXT) +RNAmotif_distance_LDADD = $(LDADD) +RNAmotif_distance_DEPENDENCIES = ../lib/libRNA.a +RNAduplex_SOURCES = RNAduplex.c +RNAduplex_OBJECTS = RNAduplex.$(OBJEXT) +RNAduplex_LDADD = $(LDADD) +RNAduplex_DEPENDENCIES = ../lib/libRNA.a +RNAeval_SOURCES = RNAeval.c +RNAeval_OBJECTS = RNAeval.$(OBJEXT) +RNAeval_LDADD = $(LDADD) +RNAeval_DEPENDENCIES = ../lib/libRNA.a +RNAfold_SOURCES = RNAfold.c +RNAfold_OBJECTS = RNAfold.$(OBJEXT) +RNAfold_LDADD = $(LDADD) +RNAfold_DEPENDENCIES = ../lib/libRNA.a +RNAheat_SOURCES = RNAheat.c +RNAheat_OBJECTS = RNAheat.$(OBJEXT) +RNAheat_LDADD = $(LDADD) +RNAheat_DEPENDENCIES = ../lib/libRNA.a +RNAinverse_SOURCES = RNAinverse.c +RNAinverse_OBJECTS = RNAinverse.$(OBJEXT) +RNAinverse_LDADD = $(LDADD) +RNAinverse_DEPENDENCIES = ../lib/libRNA.a +RNApaln_SOURCES = RNApaln.c +RNApaln_OBJECTS = RNApaln.$(OBJEXT) +RNApaln_LDADD = $(LDADD) +RNApaln_DEPENDENCIES = ../lib/libRNA.a +RNApdist_SOURCES = RNApdist.c +RNApdist_OBJECTS = RNApdist.$(OBJEXT) +RNApdist_LDADD = $(LDADD) +RNApdist_DEPENDENCIES = 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uninstall-info-am + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold new file mode 100755 index 000000000..e158564ad Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold.c new file mode 100755 index 000000000..7e7a723a0 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold.c @@ -0,0 +1,247 @@ +/* Last changed Time-stamp: <2003-04-23 11:56:44 ivo> */ +/* + Ineractive Access to folding Routines + + c Ivo L Hofacker + Vienna RNA package +*/ + +#include +#include +#include +#include +#include +#include +#include "fold.h" +#include "part_func.h" +#include "fold_vars.h" +#include "utils.h" + +extern float Lfold(char *string, char *structure, int maxdist); +extern void read_parameter_file(const char fname[]); + +/*@unused@*/ +static char rcsid[] = "$Id: RNALfold.c,v 1.2 2003/07/14 13:38:47 ivo Exp $"; + +#define PRIVATE static + +static char scale1[] = "....,....1....,....2....,....3....,....4"; +static char scale2[] = "....,....5....,....6....,....7....,....8"; + +PRIVATE void usage(void); + +/*--------------------------------------------------------------------------*/ + +int main(int argc, char *argv[]) +{ + char *string, *line; + char *structure=NULL, *cstruc=NULL; + char fname[13], ffname[20], gfname[20]; + char *ParamFile=NULL; + char *ns_bases=NULL, *c; + int i, length, l, sym, r; + double energy, min_en; + double kT, sfact=1.07; + int pf=0, istty; + int noconv=0; + int maxdist=150; + + do_backtrack = 1; + string=NULL; + for (i=1; i : base i is paired with a base j>i\n"); + printf("matching brackets ( ): base i pairs base j\n"); + } + + do { /* main loop: continue until end of file */ + if (istty) { + printf("\nInput string (upper or lower case); @ to quit\n"); + printf("%s%s\n", scale1, scale2); + } + fname[0]='\0'; + if ((line = get_line(stdin))==NULL) break; + + /* skip comment lines and get filenames */ + while ((*line=='*')||(*line=='\0')||(*line=='>')) { + if (*line=='>') + (void) sscanf(line, ">%12s", fname); + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) break; + } + + if ((line ==NULL) || (strcmp(line, "@") == 0)) break; + + string = (char *) space(strlen(line)+1); + (void) sscanf(line,"%s",string); + free(line); + length = (int) strlen(string); + + structure = (char *) space((unsigned) length+1); + if (fold_constrained) { + cstruc = get_line(stdin); + if (cstruc!=NULL) + strncpy(structure, cstruc, length); + else + fprintf(stderr, "constraints missing\n"); + } + for (l = 0; l < length; l++) { + string[l] = toupper(string[l]); + if (!noconv && string[l] == 'T') string[l] = 'U'; + } + if (istty) + printf("length = %d\n", length); + + /* initialize_fold(length); */ + update_fold_params(); + min_en = Lfold(string, structure, maxdist); + printf("%s\n%s", string, structure); + if (istty) + printf("\n minimum free energy = %6.2f kcal/mol\n", min_en); + else + printf(" (%6.2f)\n", min_en); + + (void) fflush(stdout); + + if (pf) { + + if (dangles==1) { + dangles=2; /* recompute with dangles as in pf_fold() */ + min_en = energy_of_struct(string, structure); + dangles=1; + } + + kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */ + pf_scale = exp(-(sfact*min_en)/kT/length); + if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale); + + init_pf_fold(length); + + if (cstruc!=NULL) + strncpy(structure, cstruc, length+1); + energy = pf_fold(string, structure); + + if (do_backtrack) { + printf("%s", structure); + if (!istty) printf(" [%6.2f]\n", energy); + else printf("\n"); + } + if ((istty)||(!do_backtrack)) + printf(" free energy of ensemble = %6.2f kcal/mol\n", energy); + printf(" frequency of mfe structure in ensemble %g\n", + exp((energy-min_en)/kT)); + + if (do_backtrack) { + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_dp.ps"); + } else strcpy(ffname, "dot.ps"); + /* (void) PS_dot_plot(string, ffname); */ + } + free_pf_arrays(); + + } + if (cstruc!=NULL) free(cstruc); + (void) fflush(stdout); + free(string); + free(structure); + } while (1); + return 0; +} + +PRIVATE void usage(void) +{ + nrerror("usage:\n" + "RNALfold [-L span]\n" + " [-T temp] [-4] [-d[2|3]] [-noGU] [-noCloseGU]\n" + " [-noLP] [-P paramfile] [-nsp pairs] [-noconv]\n"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold.o new file mode 100755 index 000000000..187f0c0ff Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNALfold.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold new file mode 100755 index 000000000..9c17cc61c Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold.c new file mode 100755 index 000000000..8c5055d58 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold.c @@ -0,0 +1,406 @@ +/* Last changed Time-stamp: <2005-03-21 13:49:55 ivo> */ +/* + Access to alifold Routines + + c Ivo L Hofacker + Vienna RNA package +*/ + +#include +#include +#include +#include +#include +#include +#include "fold.h" +#include "part_func.h" +#include "fold_vars.h" +#include "PS_dot.h" +#include "utils.h" +#include "pair_mat.h" +#include "alifold.h" +#include "aln_util.h" +extern void read_parameter_file(const char fname[]); +/*@unused@*/ +static const char rcsid[] = "$Id: RNAalifold.c,v 1.13 2005/03/21 12:50:44 ivo Exp $"; + +#define PRIVATE static + +static const char scale[] = "....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +PRIVATE void /*@exits@*/ usage(void); +PRIVATE char *annote(const char *structure, const char *AS[]); +PRIVATE void print_pi(const pair_info pi, FILE *file); +PRIVATE cpair *make_color_pinfo(const pair_info *pi); +PRIVATE void mark_endgaps(char *seq, char egap); +/*--------------------------------------------------------------------------*/ +#define MAX_NUM_NAMES 500 +int main(int argc, char *argv[]) +{ + char *string; + char *structure=NULL, *cstruc=NULL; + char ffname[20], gfname[20], fname[13]=""; + char *ParamFile=NULL; + char *ns_bases=NULL, *c; + int n_seq, i, length, sym, r; + int endgaps=0, mis=0; + double min_en, real_en, sfact=1.07; + int pf=0, istty; + char *AS[MAX_NUM_NAMES]; /* aligned sequences */ + char *names[MAX_NUM_NAMES]; /* sequence names */ + FILE *clust_file = stdin; + + do_backtrack = 1; + string=NULL; + dangles=2; + for (i=1; i : base i is paired with a base j>i\n"); + printf("matching brackets ( ): base i pairs base j\n"); + } + if (fold_constrained) { + if (istty) printf("%s\n", scale); + cstruc = get_line(stdin); + } + + if (istty && (clust_file == stdin)) { + printf("\nInput aligned sequences in clustalw format\n"); + if (!fold_constrained) printf("%s\n", scale); + } + + n_seq = read_clustal(clust_file, AS, names); + if (endgaps) + for (i=0; i2000) fprintf(stderr, "scaling factor %f\n", pf_scale); + fflush(stdout); + + /* init_alipf_fold(length); */ + + if (cstruc!=NULL) + strncpy(structure, cstruc, length+1); + energy = alipf_fold(AS, structure, &pi); + + if (do_backtrack) { + printf("%s", structure); + if (!istty) printf(" [%6.2f]\n", energy); + else printf("\n"); + } + if ((istty)||(!do_backtrack)) + printf(" free energy of ensemble = %6.2f kcal/mol\n", energy); + printf(" frequency of mfe structure in ensemble %g\n", + exp((energy-min_en)/kT)); + + if (do_backtrack) { + FILE *aliout; + cpair *cp; + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_ali.out"); + } else strcpy(ffname, "alifold.out"); + aliout = fopen(ffname, "w"); + if (!aliout) { + fprintf(stderr, "can't open %s skipping output\n", ffname); + } else { + short *ptable; int k; + ptable = make_pair_table(mfe_struc); + fprintf(aliout, "%d sequence; length of alignment %d\n", + n_seq, length); + fprintf(aliout, "alifold output\n"); + for (k=0; pi[k].i>0; k++) { + pi[k].comp = (ptable[pi[k].i] == pi[k].j) ? 1:0; + print_pi(pi[k], aliout); + } + fprintf(aliout, "%s\n", structure); + free(ptable); + } + fclose(aliout); + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_dp.ps"); + } else strcpy(ffname, "alidot.ps"); + cp = make_color_pinfo(pi); + (void) PS_color_dot_plot(string, cp, ffname); + free(cp); + } + free(mfe_struc); + free(pi); + } + if (cstruc!=NULL) free(cstruc); + free(base_pair); + (void) fflush(stdout); + free(string); + free(structure); + for (i=0; AS[i]; i++) { + free(AS[i]); free(names[i]); + } + return 0; +} + +void mark_endgaps(char *seq, char egap) { + int i,n; + n = strlen(seq); + for (i=0; i0 && (seq[i]=='-'); i--) { + seq[i] = egap; + } +} + +void print_pi(const pair_info pi, FILE *file) { + const char *pname[8] = {"","CG","GC","GU","UG","AU","UA", "--"}; + int i; + + /* numbering starts with 1 in output */ + fprintf(file, "%5d %5d %2d %5.1f%% %7.3f", + pi.i, pi.j, pi.bp[0], 100.*pi.p, pi.ent); + for (i=1; i<=7; i++) + if (pi.bp[i]) fprintf(file, " %s:%-4d", pname[i], pi.bp[i]); + /* if ((!pi.sym)&&(pi.j>=0)) printf(" *"); */ + if (!pi.comp) fprintf(file, " +"); + fprintf(file, "\n"); +} + +#define MIN2(A, B) ((A) < (B) ? (A) : (B)) + +PRIVATE cpair *make_color_pinfo(const pair_info *pi) { + cpair *cp; + int i, n; + for (n=0; pi[n].i>0; n++); + cp = (cpair *) space(sizeof(cpair)*(n+1)); + for (i=0; i0) { + snprintf(pps, 64, "%d %d %d gmark\n", i, j, pfreq[0]); + strcat(ps, pps); + } + if (vi>1) { + snprintf(pps, 64, "%d cmark\n", i); + strcat(ps, pps); + } + if (vj>1) { + snprintf(pps, 64, "%d cmark\n", j); + strcat(ps, pps); + } + } + free(ptable); + return ps; +} + +/*-------------------------------------------------------------------------*/ + +PRIVATE void usage(void) +{ + nrerror("usage:\n" + "RNAalifold [-cv float] [-nc float] [-E] [-mis]\n" + " [-p[0]] [-C] [-T temp] [-4] [-d] [-noGU] [-noCloseGU]\n" + " [-noLP] [-e e_set] [-P paramfile] [-nsp pairs] [-S scale]\n" + ); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold.o new file mode 100755 index 000000000..557da475c Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAalifold.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold new file mode 100755 index 000000000..f7fcc1830 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold.c new file mode 100755 index 000000000..572768007 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold.c @@ -0,0 +1,624 @@ +/* Last changed Time-stamp: <2006-01-19 11:49:34 ivo> */ +/* + c Ivo L Hofacker, Vienna RNA package +*/ + +#include +#include +#include +#include +#include +#include +#include "PS_dot.h" +#include "cofold.h" +#include "fold.h" +#include "part_func_co.h" +#include "part_func.h" +#include "fold_vars.h" +#include "utils.h" + +extern void read_parameter_file(const char fname[]); + +/*@unused@*/ +static char rcsid[] = "$Id: RNAcofold.c,v 1.6 2006/01/19 11:30:04 ivo Exp $"; + +#define PRIVATE static + +static char scale[] = "....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +PRIVATE char *costring(char *string); +PRIVATE char *tokenize(char *line); +PRIVATE void usage(void); +PRIVATE cofoldF do_partfunc(char *string, int length, int Switch, struct plist **tpr, struct plist **mf); +PRIVATE double *read_concentrations(FILE *fp); +PRIVATE void do_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconces); +PRIVATE struct plist *get_mfe_plist(struct plist *pl); + +/*--------------------------------------------------------------------------*/ + +int main(int argc, char *argv[]) +{ + char *string, *line; + char *structure=NULL, *cstruc=NULL; + char fname[53], ffname[20]; + char *ParamFile=NULL; + char *ns_bases=NULL, *c; + char *Concfile; + int i, length, l, sym, r; + double min_en; + double kT, sfact=1.07; + int pf=0, istty; + int noconv=0; + int doT=0; /*compute dimere free energies etc.*/ + int doC=0; /*toggle to compute concentrations*/ + int doQ=0; /*toggle to compute prob of base being paired*/ + int cofi=0; /*toggle concentrations stdin / file*/ + struct plist *prAB; + struct plist *prAA; /*pair probabilities of AA dimer*/ + struct plist *prBB; + struct plist *prA; + struct plist *prB; + struct plist *mfAB; + struct plist *mfAA; /*pair mfobabilities of AA dimer*/ + struct plist *mfBB; + struct plist *mfA; + struct plist *mfB; + double *ConcAandB; + + do_backtrack = 1; + string=NULL; + Concfile=NULL; + for (i=1; i : base i is paired with a base j>i\n"); + printf("matching brackets ( ): base i pairs base j\n"); + } + + do { /* main loop: continue until end of file */ + cut_point = -1; + if (istty) { + printf("\nInput sequence(s); @ to quit\n"); + printf("Use '&' as spearator between 2 sequences that shall form a complex.\n"); + printf("%s\n", scale); + } + fname[0]='\0'; + if ((line = get_line(stdin))==NULL) break; + + /* skip comment lines and get filenames */ + while ((*line=='*')||(*line=='\0')||(*line=='>')) { + if (*line=='>') + (void) sscanf(line, ">%51s", fname); + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) break; + } + + if ((line ==NULL) || (strcmp(line, "@") == 0)) break; + + string = tokenize(line); /* frees line */ + + length = (int) strlen(string); + if (doC) { + FILE *fp; + if (cofi) { /* read from file */ + fp = fopen(Concfile, "r"); + if (fp==NULL) { + fprintf(stderr, "could not open concentration file %s", Concfile); + nrerror("\n"); + } + ConcAandB = read_concentrations(fp); + fclose(fp); + } else { + printf("Please enter concentrations [mol/l]\n format: ConcA ConcB\n return to end\n"); + ConcAandB = read_concentrations(stdin); + } + } + + structure = (char *) space((unsigned) length+1); + if (fold_constrained) { + cstruc = tokenize(get_line(stdin)); + if (cstruc!=NULL) + strncpy(structure, cstruc, length); + else + fprintf(stderr, "constraints missing\n"); + } + + for (l = 0; l < length; l++) { + string[l] = toupper(string[l]); + if (!noconv && string[l] == 'T') string[l] = 'U'; + } + if (istty) { + if (cut_point == -1) + printf("length = %d\n", length); + else + printf("length1 = %d\nlength2 = %d\n", + cut_point-1, length-cut_point+1); + } + + /*compute mfe of AB dimer*/ + min_en = cofold(string, structure); + mfAB=(struct plist *) space(sizeof(struct plist) * (length+1)); + mfAB=get_mfe_plist(mfAB); + + if (cut_point == -1) printf("%s\n%s", string, structure); /*no cofold*/ + + else { + char *pstring, *pstruct; + pstring = costring(string); + pstruct = costring(structure); + printf("%s\n%s", pstring, pstruct); + free(pstring); + free(pstruct); + } + if (istty) + printf("\n minimum free energy = %6.2f kcal/mol\n", min_en); + else + printf(" (%6.2f)\n", min_en); + + (void) fflush(stdout); + + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_ss.ps"); + } else { + strcpy(ffname, "rna.ps"); + } + if (length<2000) + (void) PS_rna_plot(string, structure, ffname); + else { + fprintf(stderr,"INFO: structure too long, not doing xy_plot\n"); + free_co_arrays(); + } + + /*compute partition function*/ + if (pf) { + cofoldF AB, AA, BB; + if (dangles==1) { + dangles=2; /* recompute with dangles as in pf_fold() */ + min_en = energy_of_struct(string, structure); + dangles=1; + } + + kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */ + pf_scale = exp(-(sfact*min_en)/kT/length); + if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale); + + init_co_pf_fold(length); + + if (cstruc!=NULL) + strncpy(structure, cstruc, length+1); + AB = co_pf_fold(string, structure); + + if (do_backtrack) { + char *costruc; + costruc = (char *) space(sizeof(char)*(strlen(structure)+2)); + if (cut_point<0) printf("%s", structure); + else { + strncpy(costruc, structure, cut_point-1); + strcat(costruc, "&"); + strcat(costruc, structure+cut_point-1); + printf("%s", costruc); + } + if (!istty) printf(" [%6.2f]\n", AB.FAB); + else printf("\n");/*8.6.04*/ + } + if ((istty)||(!do_backtrack)) + printf(" free energy of ensemble = %6.2f kcal/mol\n", AB.FAB); + printf(" frequency of mfe structure in ensemble %g", + exp((AB.FAB-min_en)/kT)); + + printf(" , delta G binding=%6.2f\n", AB.FcAB - AB.FA - AB.FB); + + prAB=(struct plist *) space(sizeof(struct plist) * (2*length)); + prAB=get_plist(prAB, length,0.00001); + + /* if (doQ) make_probsum(length,fname); */ /*compute prob of base paired*/ + free_co_arrays(); + if (doT) { /* cofold of all dimers, monomers */ + int Blength, Alength; + char *Astring, *Bstring; + char *Newstring; + char Newname[30]; + char comment[80]; + if (cut_point<0) { + printf("Sorry, i cannot do that with only one molecule, please give me two or leave it\n"); + free(mfAB); + free(prAB); + continue; + } + if (dangles==1) dangles=2; + Alength=cut_point-1; /*length of first molecule*/ + Blength=length-cut_point+1; /*length of 2nd molecule*/ + + Astring=(char *)space(sizeof(char)*(Alength+1));/*Sequence of first molecule*/ + Bstring=(char *)space(sizeof(char)*(Blength+1));/*Sequence of second molecule*/ + strncat(Astring,string,Alength); + strncat(Bstring,string+Alength,Blength); + + /* compute AA dimer */ + prAA=(struct plist *) space(sizeof(struct plist) * (4*Alength)); + mfAA=(struct plist *) space(sizeof(struct plist) * (Alength+1)); + AA=do_partfunc(Astring, Alength, 2, &prAA, &mfAA); + /* compute BB dimer */ + prBB=(struct plist *) space(sizeof(struct plist) * (4*Blength)); + mfBB=(struct plist *) space(sizeof(struct plist) * (Blength+1)); + BB=do_partfunc(Bstring, Blength, 2, &prBB, &mfBB); + /*free_co_pf_arrays();*/ + + /* compute A monomer */ + prA=(struct plist *) space(sizeof(struct plist) * (2*Alength)); + mfA=(struct plist *) space(sizeof(struct plist) * (Alength+1)); + do_partfunc(Astring, Alength, 1, &prA, &mfA); + + /* compute B monomer */ + prB=(struct plist *) space(sizeof(struct plist) * (2*Blength)); + mfB=(struct plist *) space(sizeof(struct plist) * (Blength+1)); + do_partfunc(Bstring, Blength, 1, &prB, &mfB); + + compute_probabilities(AB.F0AB, AB.FA, AB.FB, prAB, prA, prB, Alength); + compute_probabilities(AA.F0AB, AA.FA, AA.FA, prAA, prA, prA, Alength); + compute_probabilities(BB.F0AB, BB.FA, BB.FA, prBB, prA, prB, Blength); + printf("Free Energies:\nAB\t\tAA\t\tBB\t\tA\t\tB\n%.6f\t%6f\t%6f\t%6f\t%6f\n", + AB.FcAB, AA.FcAB, BB.FcAB, AB.FA, AB.FB); + + if (doC) { + do_concentrations(AB.FcAB, AA.FcAB, BB.FcAB, AB.FA, AB.FB, ConcAandB); + free(ConcAandB);/*freeen*/ + } + + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_dp5.ps"); + } else strcpy(ffname, "dot5.ps"); + /*output of the 5 dot plots*/ + + /*AB dot_plot*/ + /*write Free Energy into comment*/ + sprintf(comment,"\n%%Heterodimer AB FreeEnergy= %.9f\n", AB.FcAB); + /*reset cut_point*/ + cut_point=Alength+1; + /*write New name*/ + strcpy(Newname,"AB"); + strcat(Newname,ffname); + (void)PS_dot_plot_list(string, Newname, prAB, mfAB, comment); + + /*AA dot_plot*/ + sprintf(comment,"\n%%Homodimer AA FreeEnergy= %.9f\n",AA.FcAB); + /*write New name*/ + strcpy(Newname,"AA"); + strcat(Newname,ffname); + /*write AA sequence*/ + Newstring=(char*)space((2*Alength+1)*sizeof(char)); + strcpy(Newstring,Astring); + strcat(Newstring,Astring); + (void)PS_dot_plot_list(Newstring, Newname, prAA, mfAA, comment); + free(Newstring); + + /*BB dot_plot*/ + sprintf(comment,"\n%%Homodimer BB FreeEnergy= %.9f\n",BB.FcAB); + /*write New name*/ + strcpy(Newname,"BB"); + strcat(Newname,ffname); + /*write BB sequence*/ + Newstring=(char*)space((2*Blength+1)*sizeof(char)); + strcpy(Newstring,Bstring); + strcat(Newstring,Bstring); + /*reset cut_point*/ + cut_point=Blength+1; + (void)PS_dot_plot_list(Newstring, Newname, prBB, mfBB, comment); + free(Newstring); + + /*A dot plot*/ + /*reset cut_point*/ + cut_point=-1; + sprintf(comment,"\n%%Monomer A FreeEnergy= %.9f\n",AB.FA); + /*write New name*/ + strcpy(Newname,"A"); + strcat(Newname,ffname); + /*write BB sequence*/ + (void)PS_dot_plot_list(Astring, Newname, prA, mfA, comment); + + /*B monomer dot plot*/ + sprintf(comment,"\n%%Monomer B FreeEnergy= %.9f\n",AB.FB); + /*write New name*/ + strcpy(Newname,"B"); + strcat(Newname,ffname); + /*write BB sequence*/ + (void)PS_dot_plot_list(Bstring, Newname, prB, mfB, comment); + free(Astring); free(Bstring); free(prAB); free(prAA); free(prBB); free(prA); free(prB); + free(mfAB); free(mfAA); free(mfBB); free(mfA); free(mfB); + + } /*end if(doT)*/ + + }/*end if(pf)*/ + + + if (do_backtrack) { + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_dp.ps"); + } else strcpy(ffname, "dot.ps"); + + if (!doT) { + if (pf) { (void) PS_dot_plot_list(string, ffname, prAB, mfAB, "doof"); + free(prAB);} + free(mfAB); + } + } + if (!doT) free_co_pf_arrays(); + + + if (cstruc!=NULL) free(cstruc); + (void) fflush(stdout); + free(string); + free(structure); + } while (1); + return 0; +} + +PRIVATE char *tokenize(char *line) +{ + char *pos, *copy; + int cut = -1; + + copy = (char *) space(strlen(line)+1); + (void) sscanf(line, "%s", copy); + pos = strchr(copy, '&'); + if (pos) { + cut = (int) (pos-copy)+1; + if (cut >= strlen(copy)) cut = -1; + if (strchr(pos+1, '&')) nrerror("more than one cut-point in input"); + for (;*pos;pos++) *pos = *(pos+1); /* splice out the & */ + } + if (cut > -1) { + if (cut_point==-1) cut_point = cut; + else if (cut_point != cut) { + fprintf(stderr,"cut_point = %d cut = %d\n", cut_point, cut); + nrerror("Sequence and Structure have different cut points."); + } + } + free(line); + return copy; +} + +PRIVATE char *costring(char *string) +{ + char *ctmp; + int len; + + len = strlen(string); + ctmp = (char *)space((len+2) * sizeof(char)); + /* first sequence */ + (void) strncpy(ctmp, string, cut_point-1); + /* spacer */ + ctmp[cut_point-1] = '&'; + /* second sequence */ + (void) strcat(ctmp, string+cut_point-1); + + return ctmp; +} + +PRIVATE cofoldF do_partfunc(char *string, int length, int Switch, struct plist **tpr, struct plist **mfpl) { + /*compute mfe and partition function of dimere or monomer*/ + char *Newstring; + char *tempstruc; + double min_en; + double sfact=1.07; + double kT; + cofoldF X; + kT = (temperature+273.15)*1.98717/1000.; + switch (Switch) + { + case 1: /*monomer*/ + cut_point=-1; + tempstruc = (char *) space((unsigned)length+1); + min_en = fold(string, tempstruc); + pf_scale = exp(-(sfact*min_en)/kT/(length)); + *mfpl=get_mfe_plist(*mfpl); + free_arrays(); + /*En=pf_fold(string, tempstruc);*/ + init_co_pf_fold(length); + X=co_pf_fold(string, tempstruc); + + *tpr=get_plist(*tpr, length,0.00001); + free_co_pf_arrays(); + free(tempstruc); + break; + + case 2: /*dimer*/ + Newstring=(char *)space(sizeof(char)*(length*2+1)); + strcat(Newstring,string); + strcat(Newstring,string); + cut_point=length+1; + tempstruc = (char *) space((unsigned)length*2+1); + min_en = cofold(Newstring, tempstruc); + pf_scale =exp(-(sfact*min_en)/kT/(2*length)); + *mfpl=get_mfe_plist(*mfpl); + free_co_arrays(); + init_co_pf_fold(2*length); + X=co_pf_fold(Newstring, tempstruc); + *tpr=get_plist(*tpr, 2*length,0.00001); + free_co_pf_arrays(); + free(Newstring); + free(tempstruc); + break; + + default: + printf("Error in get_partfunc\n, computing neither mono- nor dimere!\n"); + exit (42); + + } + return X; +} + + +PRIVATE void do_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc) { + /* compute and print concentrations out of free energies, calls get_concentrations */ + struct ConcEnt *result; + int i, n; + + result=get_concentrations(FEAB, FEAA, FEBB, FEA, FEB, startconc); + + printf("Initial concentrations\t\trelative Equilibrium concentrations\n"); + printf("A\t\t B\t\t AB\t\t AA\t\t BB\t\t A\t\t B\n"); + for (n=0; (startconc[2*n]>0) || (startconc[2*n+1]>0); n++); /* count */ + for (i=0; i=2*n) { + n*=2; + startc=(double *)xrealloc(startc,(2*n+1)*sizeof(double)); + } + c = sscanf(line,"%lf %lf", &startc[i], &startc[i+1]); + free(line); + if (c<2) break; + i+=2; + } + startc[i]=startc[i+1]=0; + return startc; +} + +static struct plist *get_mfe_plist(struct plist *pl) { + /*get list of mfe structure out of base_pairs array*/ + int l; + for(l=1; l<=base_pair[0].i; l++) + { + pl[l-1].i=base_pair[l].i; + pl[l-1].j=base_pair[l].j; + pl[l-1].p=0.95; + } + pl[l-1].i=0; + pl[l-1].j=0; + pl[l-1].p=0.; + pl=(struct plist *)xrealloc(pl,l*sizeof(struct plist)); + return pl; +} + + +PRIVATE void usage(void) +{ + nrerror("usage:\n" + "RNAcofold [-a] [-c] [-f concfile]\n" + "[-p[0]] [-C] [-T temp] [-4] [-d[2|3]] [-noGU] [-noCloseGU]\n" + "[-noLP] [-e e_set] [-P paramfile] [-nsp pairs] [-S scale] " + "[-noconv]\n"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold.o new file mode 100755 index 000000000..7156ed19b Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAcofold.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG new file mode 100755 index 000000000..c8afdc51b Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG.c new file mode 100755 index 000000000..9ba5d6ead --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG.c @@ -0,0 +1,228 @@ +/* Last changed Time-stamp: <2005-09-22 10:10:55 ivo> */ +/* + * Ineractive Access to folding Routines + * + * c Ivo L Hofacker Vienna RNA package + */ + +#include +#include +#include +#include +#include +#include +#include "fold.h" +#include "part_func.h" +#include "fold_vars.h" +#include "PS_dot.h" +#include "utils.h" +/* @unused@ */ +static char rcsid[] = "$Id: RNAfold.c,v 1.18 2005/10/30 20:07:12 ivo Exp $"; + +#define PRIVATE static + +static char scale1[] = "....,....1....,....2....,....3....,....4"; +static char scale2[] = "....,....5....,....6....,....7....,....8"; + +PRIVATE void usage(void); + +/*--------------------------------------------------------------------------*/ + +int +main(int argc, char *argv[]) +{ + char *string, *line; + char *structure = NULL, *cstruc = NULL; + char *ParamFile = NULL; + char *ns_bases = NULL, *c; + int i, length, l, sym, r; + double energy, min_en; + double kT, sfact = 1.07; + int noconv = 0; + + float dG2; + double dG0, dG1, ddG, P; + + string = NULL; + for (i = 1; i < argc; i++) { + if (argv[i][0] == '-') + switch (argv[i][1]) { + case 'T': + if (argv[i][2] != '\0') + usage(); + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%lf", &temperature); + if (!r) + usage(); + break; + case 'n': + if (strcmp(argv[i], "-noGU") == 0) + noGU = 1; + if (strcmp(argv[i], "-noCloseGU") == 0) + no_closingGU = 1; + if (strcmp(argv[i], "-noLP") == 0) + noLonelyPairs = 1; + if (strcmp(argv[i], "-nsp") == 0) { + if (i == argc - 1) + usage(); + ns_bases = argv[++i]; + } + if (strcmp(argv[i], "-noconv") == 0) + noconv = 1; + break; + case '4': + tetra_loop = 0; + break; + case 'e': + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%d", &energy_set); + if (!r) + usage(); + break; + case 'S': + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%lf", &sfact); + if (!r) + usage(); + break; + case 'd': + dangles = 0; + if (argv[i][2] != '\0') { + r = sscanf(argv[i] + 2, "%d", &dangles); + if (r != 1) + usage(); + } + break; + case 'P': + if (i == argc - 1) + usage(); + ParamFile = argv[++i]; + break; + default: + usage(); + } + } + + if (ParamFile != NULL) + read_parameter_file(ParamFile); + + if (ns_bases != NULL) { + nonstandards = space(33); + c = ns_bases; + i = sym = 0; + if (*c == '-') { + sym = 1; + c++; + } + while (*c != '\0') { + if (*c != ',') { + nonstandards[i++] = *c++; + nonstandards[i++] = *c; + if ((sym) && (*c != *(c - 1))) { + nonstandards[i++] = *c; + nonstandards[i++] = *(c - 1); + } + } + c++; + } + } + + /* Some global parameters for the folding routines */ + do_backtrack = 0; + dangles = 2; + fold_constrained = 0; + + /* main loop: continue until end of file */ + + do { + + /* Read and prepare sequence and constraint ***************************/ + + if ((line = get_line(stdin)) == NULL) + break; + + string = (char *) space(strlen(line) + 1); + (void) sscanf(line, "%s", string); + free(line); + length = (int) strlen(string); + + structure = (char *) space((unsigned) length + 1); + + /* Always read folding constraint */ + if ((cstruc = get_line(stdin)) == NULL) + fprintf(stderr, "RNAdGG error: constraints missing\n"); + + if ((line = get_line(stdin)) == NULL) + fprintf (stderr, "RNAdGG error: dG2 missing\n"); + else + { + sscanf (line, "%f", &dG2); + free (line); + } + + for (l = 0; l < length; l++) { + string[l] = toupper(string[l]); + if (!noconv && string[l] == 'T') + string[l] = 'U'; + } + + /* Fold with no constraint ********************************************/ + + min_en = fold(string, structure); + printf ("%s\t", structure); + + kT = (temperature + 273.15) * 1.98717 / 1000.; /* in Kcal */ + pf_scale = exp(-(sfact * min_en) / kT / length); + init_pf_fold(length); + + dG0 = pf_fold(string, structure); + + free_pf_arrays(); + + /* Fold with constraint ***********************************************/ + + fold_constrained = 1; + strncpy(structure, cstruc, length + 1); + + min_en = fold(string, structure); + printf ("%s\t", structure); + + pf_scale = exp(-(sfact * min_en) / kT / length); + init_pf_fold(length); + + strncpy(structure, cstruc, length + 1); + dG1 = pf_fold(string, structure); + + free_pf_arrays(); + + /* Calculate and output ***********************************************/ + + ddG = dG1 + dG2 - dG0; + P = 1 / ( 1 + exp(ddG / kT) ); /* Probability of being bound */ + + printf ("%5.2f\t%5.2f\t%5.2f\t%5.2f\t%g\n", dG0, dG1, dG2, ddG, P); + + /* Free everything */ + + if (cstruc != NULL) + free(cstruc); + if (length >= 2000) + free(base_pair); + (void) fflush(stdout); + free(string); + free(structure); + } while (1); + return 0; +} + +PRIVATE void +usage(void) +{ + nrerror("usage:\n" + "RNAfold [-p[0]] [-C] [-T temp] [-4] [-d[2|3]] [-noGU] [-noCloseGU]\n" + " [-noLP] [-e e_set] [-P paramfile] [-nsp pairs] [-S scale]\n" + " [-noconv] \n"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG4 b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG4 new file mode 100755 index 000000000..a8fbee085 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG4 differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG4.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG4.c new file mode 100755 index 000000000..1a740b8d2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAddG4.c @@ -0,0 +1,402 @@ +/* Last changed Time-stamp: <2005-09-22 10:10:55 ivo> */ +/* + * Ineractive Access to folding Routines + * + * c Ivo L Hofacker Vienna RNA package + */ + +#include +#include +#include +#include +#include +#include +#include "fold.h" +#include "part_func.h" +#include "fold_vars.h" +#include "PS_dot.h" +#include "utils.h" +#include "duplex.h" + +static void print_struc(duplexT const *dup); +double LogOfSumOfExps (double* exps, int num_exps); + +/* @unused@ */ +static char rcsid[] = "$Id: RNAfold.c,v 1.18 2005/10/30 20:07:12 ivo Exp $"; + +#define PRIVATE static +#define MIN_NUMBER_TO_EXPONENTIATE -100 + +static char scale1[] = "....,....1....,....2....,....3....,....4"; +static char scale2[] = "....,....5....,....6....,....7....,....8"; + +PRIVATE void usage(void); + + +int array_size_i = 0; +int array_size_j = 0; +int *array_i; +int *array_j; +int five_prime_length = 0; +int E5p, E3p; +int debug_mode = 0; + +/*--------------------------------------------------------------------------*/ + +int +main(int argc, char *argv[]) +{ + char *string, *line; + char *structure = NULL, *constraint = NULL, *sub_target = NULL; + char *ParamFile = NULL; + char *ns_bases = NULL, *c; + int i, length, l, sym, r; + double energy, min_en; + double kT, sfact = 1.07; + int noconv = 0; + + duplexT hybrid; + + double dG0, dG1, dG2, P; + double ddG[50]; + double dG1array[50]; + double dG2array[50]; + + int n_exps = 0; + + + int restrict_from = 0; /* Where to start and end restriction of */ + int restrict_to = 0; /* mRNA folding so that miRNA can bind */ + int target_start = 0; /* Base where target starts */ + int upstream_rest = 0; /* Number of bases to be restricted upstream of target */ + + string = NULL; + for (i = 1; i < argc; i++) { + if (argv[i][0] == '-') + switch (argv[i][1]) { + case 'T': + if (argv[i][2] != '\0') + usage(); + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%lf", &temperature); + if (!r) + usage(); + break; + case 'n': + if (strcmp(argv[i], "-noGU") == 0) + noGU = 1; + if (strcmp(argv[i], "-noCloseGU") == 0) + no_closingGU = 1; + if (strcmp(argv[i], "-noLP") == 0) + noLonelyPairs = 1; + if (strcmp(argv[i], "-nsp") == 0) { + if (i == argc - 1) + usage(); + ns_bases = argv[++i]; + } + if (strcmp(argv[i], "-noconv") == 0) + noconv = 1; + break; + case '4': + tetra_loop = 0; + break; + case 'e': + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%d", &energy_set); + if (!r) + usage(); + break; + + case 'f': + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%i", &restrict_from); + if (!r) + usage(); + break; + + case 't': + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%i", &restrict_to); + if (!r) + usage(); + break; + + case 's': + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%i", &target_start); + if (!r) + usage(); + target_start--; /* zero-based */ + break; + + case 'u': + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%i", &upstream_rest); + if (!r) + usage(); + break; + + case 'S': + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%lf", &sfact); + if (!r) + usage(); + break; + case 'd': + dangles = 0; + if (argv[i][2] != '\0') { + r = sscanf(argv[i] + 2, "%d", &dangles); + if (r != 1) + usage(); + } + break; + case 'P': + if (i == argc - 1) + usage(); + ParamFile = argv[++i]; + break; + default: + usage(); + } + } + + if (ParamFile != NULL) + read_parameter_file(ParamFile); + + if (ns_bases != NULL) { + nonstandards = space(33); + c = ns_bases; + i = sym = 0; + if (*c == '-') { + sym = 1; + c++; + } + while (*c != '\0') { + if (*c != ',') { + nonstandards[i++] = *c++; + nonstandards[i++] = *c; + if ((sym) && (*c != *(c - 1))) { + nonstandards[i++] = *c; + nonstandards[i++] = *(c - 1); + } + } + c++; + } + } + + /* Some global parameters for the folding routines */ + do_backtrack = 0; + dangles = 2; + fold_constrained = 0; + + /* main loop: continue until end of file */ + + do { + + n_exps = 0; + + /* Read and prepare sequence ***************************/ + + if ((line = get_line(stdin)) == NULL) + break; + + string = (char *) space(strlen(line) + 1); + (void) sscanf(line, "%s", string); + free(line); + length = (int) strlen(string); + + structure = (char *) space((unsigned) length + 1); + constraint = (char *) space((unsigned) length + 1); + + sub_target = (char *) space(restrict_to + 1); + + + for (l = 0; l < length; l++) { + string[l] = toupper(string[l]); + if (!noconv && string[l] == 'T') + string[l] = 'U'; + } + + /* Fold with no constraint ********************************************/ + + min_en = fold(string, structure); + printf ("%s\t", structure); + + fold_constrained = 0; + + kT = (temperature + 273.15) * 1.98717 / 1000.; /* in Kcal */ + pf_scale = exp(-(sfact * min_en) / kT / length); + init_pf_fold(length); + + dG0 = pf_fold(string, structure); + + free_pf_arrays(); + + /* Create constraint sequence from length restrict_from to restrict_to */ + /* and calculate the fold for each constrain */ + + int i,j; + + for (i = restrict_from; i <= restrict_to; i++) + { + /* Build constraint string */ + + memset (constraint, ' ', length); + + for (j = (target_start + upstream_rest); j > (target_start - i); j--) + { + constraint[j] = 'x'; + } + + /* for (j = 0 - upstream_rest; j < i; j++) + { + constraint[j+target_start] = 'x'; + }*/ + + if (i < restrict_to) + constraint[target_start-i] = '|'; + + fold_constrained = 1; + strncpy(structure, constraint, length + 1); + + /* printf ("%d (from=%d; to=%d; upstream=%d): Constraint is: **%s**\n", i, restrict_from, restrict_to, upstream_rest, structure); */ + + /* Fold with constraint *******************************************/ + + min_en = fold(string, structure); + printf ("%s", structure); + if (i < restrict_to) + printf (";"); + + pf_scale = exp(-(sfact * min_en) / kT / length); + init_pf_fold(length); + + strncpy(structure, constraint, length + 1); + dG1 = pf_fold(string, structure); + + /* Call RNAduplex to calculate the hybridization energy */ + + /* strncpy (sub_target, string+target_start, i); + sub_target[i]='\x0'; */ + + + update_fold_params(); + + /* For future use: calcualte pf-like by summing many suboptimal structs + if (delta>=0) { + duplexT *sub; + subopt = duplex_subopt(s1, s2, delta, 0); + for (sub=subopt; sub->i >0; sub++) { + print_struc(sub); + free(sub->structure); + } + free(subopt); + } + */ + + /* hybrid = duplexfold(sub_target, miRNA); + /* print_struc(&hybrid); + free(hybrid.structure); */ + + printf ("\tno_hybrid_struct"); + + dG2 = 0; /*hybrid.energy; */ + + dG1array[n_exps] = dG1; + dG2array[n_exps] = dG2; + + ddG[n_exps++] = - (dG1 + dG2 - dG0); + /* printf ("dG0=%g, dG1=%g, dG2=%g, ddG=%g\t", dG0, dG1, dG2, -ddG[n_exps-1]); */ + } + + double ddGsum = -LogOfSumOfExps (ddG, n_exps); + + P = 1 / ( 1 + exp(ddGsum / kT) ); /* Probability of being bound */ + + printf ("\t%g\t", dG0); + + for (i=0; i= 2000) free(base_pair); + (void) fflush(stdout); + free(string); + free(structure); + free(constraint); + } while (1); + return 0; +} + +static void print_struc(duplexT const *dup) { + int l1; + l1 = strchr(dup->structure, '&')-dup->structure; + printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", dup->structure, dup->i+1-l1, + dup->i, dup->j, dup->j+strlen(dup->structure)-l1-2, dup->energy); +} + + +double LogOfSumOfExps (double* exps, int num_exps) +{ + + // compute log(exp(a_1)+exp(a_2)+...exp(a_n)) using: + // max(a_1,a_2,..a_n) + log(1+exp(a_2-max(a_1,a_2,..a_n))+...exp(a_n-max(a_1,a_2,..a_n))) + + double max_index = 0; + double max = exps[0]; + int i; + + for (i = 1; i < num_exps; ++i) + { + if (exps[i] > max) + { + max = exps[i]; + max_index = i; + } + } + + double remaining_summand = 1.0; + for (i = 0; i < num_exps; ++i) + { + if (i != max_index) + { + double difference = exps[i] - max; + if (difference > MIN_NUMBER_TO_EXPONENTIATE) + remaining_summand += exp(difference); + } + } + + double result = max + log(remaining_summand); + + return result; +} + + +PRIVATE void +usage(void) +{ + nrerror("usage:\n" + "RNAfold [-p[0]] [-C] [-T temp] [-4] [-d[2|3]] [-noGU] [-noCloseGU]\n" + " [-noLP] [-e e_set] [-P paramfile] [-nsp pairs] [-S scale]\n" + " [-noconv] \n\n" + " RNAddG special switches:\n" + " -f \n" + " -t \n" ); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance new file mode 100755 index 000000000..ee7546539 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance.c new file mode 100755 index 000000000..40022eb90 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance.c @@ -0,0 +1,548 @@ +/* + Distances of Secondary Structures + Walter Fontana, Ivo L Hofacker, Peter F Stadler + Vienna RNA Package +*/ +#include +#include +#include +#include +#include +#include +#include "dist_vars.h" +#include "RNAstruct.h" +#include "treedist.h" +#include "stringdist.h" +#include "utils.h" + +#define MAXNUM 1000 /* max number of structs for distance matrix */ + +#define PUBLIC +#define PRIVATE static +/*@unused@*/ +static char rcsid[] = "$Id: RNAdistance.c,v 1.8 2005/07/24 08:35:15 ivo Exp $"; +PRIVATE void command_line(int argc, char *argv[]); +PRIVATE void usage(void); +PRIVATE int parse_input(char *line); +PRIVATE int check_tree(char *line, char alpha[]); +PRIVATE int check_brackets(char *line); +PRIVATE void print_aligned_lines(FILE *somewhere); + +PRIVATE char ruler[] ="....,....1....,....2....,....3....,....4" +"....,....5....,....6....,....7....,....8"; +PRIVATE int types=1; +PRIVATE int task; +PRIVATE int taxa_list; +PRIVATE char outfile[50], *list_title; + +PRIVATE char ttype[10]="f"; +PRIVATE int n=0; + +int main(int argc, char *argv[]) +{ + char *line=NULL, *xstruc, *cc; + Tree *T[10][MAXNUM]; + int tree_types = 0, ttree; + swString *S[10][MAXNUM]; + char *P[MAXNUM]; /* structures for base pair distances */ + int string_types = 0, tstr; + int i,j, tt, istty, type; + int it, is; + FILE *somewhere=NULL; + + command_line(argc, argv); + + if((outfile[0]=='\0')&&(task==2)&&(edit_backtrack)) + strcpy(outfile,"backtrack.file"); + if(outfile[0]!='\0') somewhere = fopen(outfile,"w"); + if (somewhere==NULL) somewhere = stdout; + istty = isatty(fileno(stdin))&&isatty(fileno(stdout)); + + do { + if ((istty)&&(n==0)) { + printf("\nInput structure; @ to quit\n"); + printf("%s\n", ruler); + } + do { + if (line!=NULL) free(line); + line=get_line(stdin); + } while ((type=parse_input(line))==0); + + if (((type==999)||(type==888))&&(task==2)) { /* do matrices */ + if (taxa_list) + printf("* END of taxa list\n"); + + ttree = 0; tstr = 0; + for (tt=0; tt< types; tt++) { + printf("> %c %d\n", ttype[tt], n); + if(islower(ttype[tt])) { + for (i=1; i1) { + for (it=0, is=0, i=0; i1) { + for (it=0, is=0, i=0; i') { + if (taxa_list) + printf("%d :%s\n", n+1, line+1); + else printf("%s\n", line); + return 0; + } + + cp = strchr(line,' '); + if (cp) *cp='\0'; /* get rid of junk at the end of line */ + + switch (line[0]) { + case '.' : + type = 1; + break; + + case '(' : /* it's a tree */ + i=1; + xx = 0; + type = 4; /* coarse */ + rooted = 0; + while (line[i]) { + if (line[i]=='.'){ + type = 1; /* Full */ + break; + } + if ( (line[i]=='U')||(line[i]=='P') ) { + type = 2; /* FFull */ + xx = 1; + break; + } + if (line[i]=='S') { + type = 3; + xx = 1; + break; /* Shapiro tree */ + } + if ((line[i]!='(')&&(line[i]!=')')) xx = 1; + i++; + } + if(!xx) type =1; + + rooted = (line[strlen(line)-2]=='R'); + break; + case '@' : + return 999; + + default: + return 0; + } + + switch (type) { + case 1: + if(check_brackets(line)) + return 1; + break; + case 2: + if(check_tree(line,"UP") ) { + if(rooted) return 2; + else return -2; + } + break; + case 3: + if(check_tree(line,"HBIMSE") ){ + if(rooted) return -3; + else return -3; + } + break; + case 4: + if(check_tree(line,"HBIM") ){ + if(rooted) return 4; + else return -4; + } + break; + } + return 0; +} + +/*--------------------------------------------------------------------------*/ + + +PRIVATE int check_tree(char *line, char alpha[]) +{ + int n, i, o; + char *pos; + + n = (int) strlen(line); + + if( line[0] != '(' ) return 0; + i=o=1; + while( line[i] ){ + while( line[i] == '(' ){ + o++; + i++; + } + pos=strchr(alpha, (int)line[i]); + if (pos) { + while (isdigit((int) line[++i])); + if (line[i]!=')') return 0; + } + if (line[i]=='R') { + i++; + if ((i!=n-1)||(line[i]!=')')) return 0; + } + if (line[i]==')') { + o--; + if(o< 0) return 0; + if( (i0) return 0; + return 1; +} + +/*--------------------------------------------------------------------------*/ + + +PRIVATE int check_brackets(char *line) +{ + int i,o; + + i=o=0; + while( line[i] ){ + switch(line[i]) { + case '(' : + o++; + i++; + break; + case '.' : + i++; + break; + case ')' : + i++; + o--; + if(o<0) return 0; + break; + default: + return 0; + } + } + if (o>0) return 0; + return 1; +} + +/*--------------------------------------------------------------------------*/ + + +PRIVATE void command_line(int argc, char *argv[]) +{ + int i; + + edit_backtrack = 0; + types=1; ttype[0]='f'; task=1; + + for (i=1; i= argc) outfile[0] = '\0'; + else if (argv[i+1][0]=='-') outfile[0] = '\0'; + else { + i++; + strncpy(outfile,argv[i],49); + } + edit_backtrack = 1; + break; + default: + usage(); + } + } +} + +/*--------------------------------------------------------------------------*/ + +PRIVATE void print_aligned_lines(FILE *somewhere) +{ + if (edit_backtrack) { + fprintf(somewhere, "\n%s\n%s\n", aligned_line[0], aligned_line[1]); + fflush(somewhere); + } +} + +/*--------------------------------------------------------------------------*/ + +PRIVATE void usage(void) +{ + nrerror("usage: RNAdistance [-D[fhwcFHWCP]] [-X[p|m|f|c]] [-S] [-B [file]]"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance.o new file mode 100755 index 000000000..f6f5225c6 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAdistance.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex new file mode 100755 index 000000000..2b3085c79 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex.c new file mode 100755 index 000000000..d0d969a3e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex.c @@ -0,0 +1,301 @@ +/* Last changed Time-stamp: <2005-07-23 16:50:24 ivo> */ +/* + Compute duplex structure of two RNA strands + + c Ivo L Hofacker + Vienna RNA package +*/ + +#include +#include +#include +#include +#include +#include "duplex.h" +#include "fold.h" +#include "fold_vars.h" +#include "utils.h" + +extern void read_parameter_file(const char fname[]); +extern int subopt_sorted; +static void print_struc(duplexT const *dup); +void parse_mapping_array (int **map_array, int *array_size, char *arguments_string); + +/*@unused@*/ +static char rcsid[] = "$Id: RNAduplex.c,v 1.4 2005/07/24 08:35:15 ivo Exp $"; + +static char scale[] = "....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +static void usage(void); + +#define PRIVATE static + +int array_size_i = 0; +int array_size_j = 0; +int *array_i = NULL; +int *array_j = NULL; +int five_prime_length = 0; +int auto_five_prime_length = 0; +int E5p, E3p; +int debug_mode = 0; +int all_pairs = 0; + +/*--------------------------------------------------------------------------*/ + +int main(int argc, char *argv[]) +{ + char *s1, *s2, *line; + char fname[13]; + char tmp_string[255]; + char *ParamFile=NULL; + char *ns_bases=NULL, *c; + int i, l, sym, r; + double deltaf; + double kT, sfact=1.07; + int pf=0, istty, delta=-1; + int noconv=0; + int l1, l2; + + for (i=1; i=argc-1) usage(); + r=sscanf(argv[++i], "%lf", &deltaf); + if (r!=1) usage(); + delta = (int) (0.1+deltaf*100); + break; + case 's': subopt_sorted=1; + break; + case 'i': + if (i>=argc-1) usage(); + r=sscanf(argv[++i], "%s", tmp_string); + if (r!=1) usage(); + + parse_mapping_array (&array_i, &array_size_i, tmp_string); + break; + + case 'j': + if (i>=argc-1) usage(); + r=sscanf(argv[++i], "%s", tmp_string); + if (r!=1) usage(); + + parse_mapping_array (&array_j, &array_size_j, tmp_string); + break; + + case '5': + if (i>=argc-1) usage(); + r=sscanf(argv[++i], "%d", &five_prime_length); + if (r!=1) usage(); + if (five_prime_length == 0) auto_five_prime_length = 1; + break; + + case 'D': + if (i>=argc-1) usage(); + r=sscanf(argv[++i], "%d", &debug_mode); + if (r!=1) usage(); + break; + + case 'a': + if (i>=argc-1) usage(); + r=sscanf(argv[++i], "%d", &all_pairs); + if (r!=1) usage(); + break; + + case 'd': dangles=0; + if (argv[i][2]!='\0') { + r=sscanf(argv[i]+2, "%d", &dangles); + if (r!=1) usage(); + } + break; + case 'P': + if (i==argc-1) usage(); + ParamFile = argv[++i]; + break; + default: usage(); + } + } + + if (ParamFile != NULL) + read_parameter_file(ParamFile); + + if (ns_bases != NULL) { + nonstandards = space(33); + c=ns_bases; + i=sym=0; + if (*c=='-') { + sym=1; c++; + } + while (*c!='\0') { + if (*c!=',') { + nonstandards[i++]=*c++; + nonstandards[i++]=*c; + if ((sym)&&(*c!=*(c-1))) { + nonstandards[i++]=*c; + nonstandards[i++]=*(c-1); + } + } + c++; + } + } + istty = isatty(fileno(stdout))&&isatty(fileno(stdin)); + + do { /* main loop: continue until end of file */ + duplexT mfe, *subopt; + if (istty) { + printf("\nInput two sequences (one line each); @ to quit\n"); + printf("%s\n", scale); + } + fname[0]='\0'; + + if ((line = get_line(stdin))==NULL) break; + /* skip empty lines, comment lines, name lines */ + while (line && ((*line=='*')||(*line=='\0')||(*line=='>'))) { + printf("%s\n", line); free(line); + if ((line = get_line(stdin))==NULL) break; + } + if ((line ==NULL) || (strcmp(line, "@") == 0)) break; + + s1 = (char *) space(strlen(line)+1); + (void) sscanf(line,"%s",s1); free(line); + + if ((line = get_line(stdin))==NULL) break; + /* skip comment lines and get filenames */ + while ((*line=='*')||(*line=='\0')||(*line=='>')) { + printf("%s\n", line); free(line); + if ((line = get_line(stdin))==NULL) break; + } + if ((line ==NULL) || (strcmp(line, "@") == 0)) break; + + s2 = (char *) space(strlen(line)+1); + (void) sscanf(line,"%s",s2); free(line); + + + /* get force_binding strings */ + if (!all_pairs) + { + if ((line = get_line(stdin))==NULL) break; + (void) sscanf(line,"%s",tmp_string); free(line); + parse_mapping_array (&array_i, &array_size_i, tmp_string); + + if ((line = get_line(stdin))==NULL) break; + (void) sscanf(line,"%s",tmp_string); free(line); + parse_mapping_array (&array_j, &array_size_j, tmp_string); + } + + for (l = 0; l < strlen(s1); l++) { + s1[l] = toupper(s1[l]); + if (!noconv && s1[l] == 'T') s1[l] = 'U'; + } + for (l = 0; l < strlen(s2); l++) { + s2[l] = toupper(s2[l]); + if (!noconv && s2[l] == 'T') s2[l] = 'U'; + } + if (istty) + printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); + + /* initialize_fold(length); */ + update_fold_params(); + if (delta>=0) { + duplexT *sub; + subopt = duplex_subopt(s1, s2, delta, 0); + for (sub=subopt; sub->i >0; sub++) { + print_struc(sub); + free(sub->structure); + } + free(subopt); + } + else { + mfe = duplexfold(s1, s2); + + /* print_struc(&mfe); */ + + l1 = strchr(mfe.structure, '&') - mfe.structure; + l2 = strlen(mfe.structure) - l1 - 1; + + printf ("%s\t%d\t%d\t%d\t%d\t%d\t%d\t%5.2f\t%5.2f\t%5.2f\n", + mfe.structure, + mfe.i+1-l1, + mfe.i, + mfe.j, + mfe.j+l2-1, + l1, + l2, + mfe.energy, (float) (E5p) / 100., (float) (E3p) / 100.); + + + free(mfe.structure); + } + (void) fflush(stdout); + + (void) fflush(stdout); + free(s1); free(s2); + } while (1); + return 0; +} + +static void print_struc(duplexT const *dup) { + int l1; + l1 = strchr(dup->structure, '&')-dup->structure; + + + printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", dup->structure, dup->i+1-l1, + dup->i, dup->j, dup->j+strlen(dup->structure)-l1-2, dup->energy); +} + +static void usage(void) +{ + nrerror("usage:\n" + "RNAduplex [-e range] [-s]\n" + " [-T temp] [-4] [-d] [-noGU] [-noCloseGU]\n" + " [-noLP] [-P paramfile] [-nsp pairs] [-noconv]\n"); +} + +void parse_mapping_array (int **map_array, int *array_size, char *arguments_string) +{ + char *p; + int value; + int cur_array_size = 0; + + if (*map_array) free (*map_array); + + *map_array = (int *) space(sizeof(int) * (50)); + + p = strtok (arguments_string,","); + while (p != NULL) + { + value = atoi (p); + /* printf ("position %i: string=%s, value=%i\n", cur_array_size, p, value); */ + (*map_array)[cur_array_size++] = value; + p = strtok (NULL, ","); + } + + *array_size = cur_array_size; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex.o new file mode 100755 index 000000000..026b1f4c5 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAduplex.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval new file mode 100755 index 000000000..f70c774c0 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval.c new file mode 100755 index 000000000..78e520461 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval.c @@ -0,0 +1,229 @@ +/* Last changed Time-stamp: <2001-08-23 10:19:23 ivo> */ +/* + + Calculate Energy of given Sequences and Structures + c Ivo L Hofacker + Vienna RNA Pckage +*/ +#include +#include +#include +#include +#include +#include +#include +#include "fold_vars.h" +#include "fold.h" +#include "utils.h" +#ifdef __GNUC__ +#define UNUSED __attribute__ ((unused)) +#else +#define UNUSED +#endif + +/*@unused@*/ +static char UNUSED rcsid[]="$Id: RNAeval.c,v 1.8 2001/08/23 08:31:13 ivo Exp $"; + +#define PUBLIC +#define PRIVATE static + +static char scale[] = "....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +PRIVATE char *costring(char *string); +PRIVATE char *tokenize(char *line); +PRIVATE void usage(void); +extern int logML; +extern int cut_point; +extern int eos_debug; +extern void read_parameter_file(const char fname[]); + +int main(int argc, char *argv[]) +{ + char *line, *string, *structure; + char fname[12]; + char *ParamFile=NULL; + int i, l, length1, length2; + float energy; + int istty; + int noconv=0; + + string=NULL; + for (i=1; i')) { + if (*line=='>') + (void) sscanf(line, ">%s", fname); + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) break; + } + + if (line==NULL) break; + if (strcmp(line, "@") == 0) {free(line); break;} + + string = tokenize(line); + free(line); + length2 = (int) strlen(string); + + if ((line = get_line(stdin))==NULL) break; + /* skip comment lines */ + while ((*line=='*')||(*line=='\0')||(*line=='>')) { + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) break; + } + if (line==NULL) break; + if (strcmp(line, "@") == 0) {free(line); break;} + + structure = tokenize(line); + free(line); + length1 = (int) strlen(structure); + + if(length1!=length2) + nrerror("Sequence and Structure have unequal length."); + + for (l = 0; l < length1; l++) { + string[l] = toupper((int)string[l]); + if (!noconv && string[l] == 'T') string[l] = 'U'; + } + + if (istty) { + if (cut_point == -1) + printf("length = %d\n", length1); + else + printf("length1 = %d\nlength2 = %d\n", + cut_point-1, length1-cut_point+1); + } + + energy = energy_of_struct(string, structure); + if (cut_point == -1) + printf("%s\n%s", string, structure); + else { + char *pstring, *pstruct; + pstring = costring(string); + pstruct = costring(structure); + printf("%s\n%s", pstring, pstruct); + free(pstring); + free(pstruct); + } + if (istty) + printf("\n energy = %6.2f\n", energy); + else + printf(" (%6.2f)\n", energy); + + free(string); + free(structure); + (void) fflush(stdout); + } while (1); + return 0; +} + +PRIVATE char *tokenize(char *line) +{ + char *token, *copy, *ctmp; + int cut = -1; + + copy = (char *) space(strlen(line)+1); + ctmp = (char *) space(strlen(line)+1); + (void) sscanf(line, "%s", copy); + ctmp[0] = '\0'; + token = strtok(copy, "&"); + cut = strlen(token)+1; + while (token) { + strcat(ctmp, token); + token = strtok(NULL, "&"); + } + if (cut > strlen(ctmp)) cut = -1; + if (cut > -1) { + if (cut_point==-1) cut_point = cut; + else if (cut_point != cut) { + fprintf(stderr,"cut_point = %d cut = %d\n", cut_point, cut); + nrerror("Sequence and Structure have different cut points."); + } + } + free(copy); + + return ctmp; +} + +PRIVATE char *costring(char *string) +{ + char *ctmp; + int len; + + len = strlen(string); + ctmp = (char *)space((len+2) * sizeof(char)); + /* first sequence */ + (void) strncpy(ctmp, string, cut_point-1); + /* spacer */ + ctmp[cut_point-1] = '&'; + /* second sequence */ + (void) strcat(ctmp, string+cut_point-1); + + return ctmp; +} + +PRIVATE void usage(void) +{ + nrerror("usage: RNAeval [-T temp] [-4] [-d[0|1|2]] [-e e_set] [-logML] [-P paramfile]"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval.o new file mode 100755 index 000000000..625891745 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAeval.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold new file mode 100755 index 000000000..4245295d4 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold.c new file mode 100755 index 000000000..31ad377c0 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold.c @@ -0,0 +1,268 @@ +/* Last changed Time-stamp: <2005-09-22 10:10:55 ivo> */ +/* + Ineractive Access to folding Routines + + c Ivo L Hofacker + Vienna RNA package +*/ + +#include +#include +#include +#include +#include +#include +#include "fold.h" +#include "part_func.h" +#include "fold_vars.h" +#include "PS_dot.h" +#include "utils.h" +extern void read_parameter_file(const char fname[]); +extern float circfold(const char *string, char *structure); +/*@unused@*/ +static char rcsid[] = "$Id: RNAfold.c,v 1.18 2005/10/30 20:07:12 ivo Exp $"; + +#define PRIVATE static + +static char scale1[] = "....,....1....,....2....,....3....,....4"; +static char scale2[] = "....,....5....,....6....,....7....,....8"; + +PRIVATE void usage(void); + +/*--------------------------------------------------------------------------*/ + +int main(int argc, char *argv[]) +{ + char *string, *line; + char *structure=NULL, *cstruc=NULL; + char fname[13], ffname[20], gfname[20]; + char *ParamFile=NULL; + char *ns_bases=NULL, *c; + int i, length, l, sym, r; + double energy, min_en; + double kT, sfact=1.07; + int pf=0, istty; + int noconv=0; + int circ=0; + + do_backtrack = 1; + string=NULL; + for (i=1; i : base i is paired with a base j>i\n"); + printf("matching brackets ( ): base i pairs base j\n"); + } + + do { /* main loop: continue until end of file */ + if (istty) { + printf("\nInput string (upper or lower case); @ to quit\n"); + printf("%s%s\n", scale1, scale2); + } + fname[0]='\0'; + if ((line = get_line(stdin))==NULL) break; + + /* skip comment lines and get filenames */ + while ((*line=='*')||(*line=='\0')||(*line=='>')) { + if (*line=='>') + (void) sscanf(line, ">%12s", fname); + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) break; + } + + if ((line ==NULL) || (strcmp(line, "@") == 0)) break; + + string = (char *) space(strlen(line)+1); + (void) sscanf(line,"%s",string); + free(line); + length = (int) strlen(string); + + structure = (char *) space((unsigned) length+1); + if (fold_constrained) { + cstruc = get_line(stdin); + if (cstruc!=NULL) + strncpy(structure, cstruc, length); + else + fprintf(stderr, "constraints missing\n"); + } + for (l = 0; l < length; l++) { + string[l] = toupper(string[l]); + if (!noconv && string[l] == 'T') string[l] = 'U'; + } + if (istty) + printf("length = %d\n", length); + + /* initialize_fold(length); */ + if (circ) + min_en = circfold(string, structure); + else + min_en = fold(string, structure); + printf("%s\n%s", string, structure); + if (istty) + printf("\n minimum free energy = %6.2f kcal/mol\n", min_en); + else + printf(" (%6.2f)\n", min_en); + + (void) fflush(stdout); + + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_ss.ps"); + strcpy(gfname, fname); + strcat(gfname, "_ss.g"); + } else { + strcpy(ffname, "rna.ps"); + strcpy(gfname, "rna.g"); + } + if (length<2000) + (void) PS_rna_plot(string, structure, ffname); + else { + struct bond *bp; + fprintf(stderr,"INFO: structure too long, not doing xy_plot\n"); + + /* free mfe arrays but preserve base_pair for PS_dot_plot */ + bp = base_pair; base_pair = space(16); + free_arrays(); /* free's base_pair */ + base_pair = bp; + } + if (pf) { + if (circ) + nrerror("Currently no partition function for circular RNAs. Please implement it!"); + if (dangles==1) { + dangles=2; /* recompute with dangles as in pf_fold() */ + min_en = energy_of_struct(string, structure); + dangles=1; + } + + kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */ + pf_scale = exp(-(sfact*min_en)/kT/length); + if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale); + + init_pf_fold(length); + + if (cstruc!=NULL) + strncpy(structure, cstruc, length+1); + energy = pf_fold(string, structure); + + if (do_backtrack) { + printf("%s", structure); + if (!istty) printf(" [%6.2f]\n", energy); + else printf("\n"); + } + if ((istty)||(!do_backtrack)) + printf(" free energy of ensemble = %6.2f kcal/mol\n", energy); + printf(" frequency of mfe structure in ensemble %g; ", + exp((energy-min_en)/kT)); + if (do_backtrack) { + printf("ensemble diversity %-6.2f", mean_bp_dist(length)); + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_dp.ps"); + } else strcpy(ffname, "dot.ps"); + (void) PS_dot_plot(string, ffname); + } + printf("\n"); + free_pf_arrays(); + + } + if (cstruc!=NULL) free(cstruc); + if (length>=2000) free(base_pair); + (void) fflush(stdout); + free(string); + free(structure); + } while (1); + return 0; +} + +PRIVATE void usage(void) +{ + nrerror("usage:\n" + "RNAfold [-p[0]] [-C] [-T temp] [-4] [-d[2|3]] [-noGU] [-noCloseGU]\n" + " [-noLP] [-e e_set] [-P paramfile] [-nsp pairs] [-S scale]\n" + " [-noconv] [-circ] \n"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold.o new file mode 100755 index 000000000..22fadda5d Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAfold.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat new file mode 100755 index 000000000..8c671ca6e Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat.c new file mode 100755 index 000000000..f00a63519 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat.c @@ -0,0 +1,242 @@ +/* + Heat Capacity of RNA molecule + + c Ivo Hofacker and Peter Stadler + Vienna RNA package + + + calculates specific heat using C = - T d^2/dT^2 G(T) +*/ + +#include +#include +#include +#include +#include +#include +#include "utils.h" +#include "fold_vars.h" +#include "fold.h" +#include "part_func.h" +extern void read_parameter_file(const char fname[]); + +#define PRIVATE static +#define PUBLIC +#define MAXWIDTH 201 +/*@unused@*/ +static char rcsid[] = "$Id: RNAheat.c,v 1.12 2000/09/28 11:23:14 ivo Rel $"; + +PRIVATE float F[MAXWIDTH]; +PRIVATE float ddiff(float f[], float h, int m); +PRIVATE void usage(void); + +#define GASCONST 1.98717 /* in [cal/K] */ +#define K0 273.15 + +PRIVATE void heat_capacity(char *string, float T_min, float T_max, + float h, int m) +{ + int length, i; + char *structure; + float hc, kT, min_en; + + length = (int) strlen(string); + + do_backtrack = 0; + + temperature = T_min -m*h; + initialize_fold(length); + structure = (char *) space((unsigned) length+1); + min_en = fold(string, structure); + free(structure); free_arrays(); + kT = (temperature+K0)*GASCONST/1000; /* in kcal */ + pf_scale = exp(-(1.07*min_en)/kT/length ); + init_pf_fold(length); + + for (i=0; i<2*m+1; i++) { + F[i] = pf_fold(string, NULL); /* T_min -2h */ + temperature += h; + kT = (temperature+K0)*GASCONST/1000; + pf_scale=exp(-(F[i]/length +h*0.00727)/kT); /* try to extrapolate F */ + update_pf_params(length); + } + while (temperature <= (T_max+m*h+h)) { + + hc = - ddiff(F,h,m)* (temperature +K0 - m*h -h); + printf("%g %g\n", (temperature-m*h-h), hc); + + for (i=0; i<2*m; i++) + F[i] = F[i+1]; + F[2*m] = pf_fold(string, NULL); + temperature += h; + kT = (temperature+K0)*GASCONST/1000; + pf_scale=exp(-(F[i]/length +h*0.00727)/kT); + update_pf_params(length); + } + free_pf_arrays(); +} + +/* ------------------------------------------------------------------------- */ + +PRIVATE float ddiff(float f[], float h, int m) +{ + float fp; + int i; + float A, B; + A = (float)(m*(m+1)*(2*m+1)/3 ); /* 2*sum(x^2) */ + B = (float)(m*(m+1)*(2*m+1) ) * (float)(3*m*m+3*m-1) /15.; /* 2*sum(x^4) */ + + fp=0.; + for (i=0; i<2*m+1; i++) + fp += f[i]*( A - (float) ( (2*m+1)*(i-m)*(i-m)) ); + + fp /= ( ( A*A - B*( (float)(2*m+1) ) )*h*h/2. ); + return (float)fp; + +} + +/* ------------------------------------------------------------------------- */ + +static char scale1[] = "....,....1....,....2....,....3....,....4"; +static char scale2[] = "....,....5....,....6....,....7....,....8"; + +/*---------------------------------------------------------------------------*/ + +int main(int argc, char *argv[]) +{ + char *string, *line; + char *ns_bases=NULL, *c; + char *ParamFile=NULL; + int i, length, l, sym; + float T_min, T_max, h; + int mpoints; + int istty; + int noconv = 0; + + T_min=0.; T_max=100.; h=1; mpoints=2; + string=NULL; + dangles = 2; /* dangles can be 0 (no dangles) or 2, default is 2 */ + + for (i=1; i100) mpoints=100; + break; + case 'd': dangles=0; + break; + case 'P': + if (i==argc-1) usage(); + else + ParamFile= argv[++i]; + break; + default: usage(); + } + } + + if (ParamFile!=NULL) + read_parameter_file(ParamFile); + + if (ns_bases!=NULL) { + nonstandards = space(33); + c=ns_bases; + i=sym=0; + if (*c=='-') { + sym=1; c++; + } + while (*c!='\0') { + if (*c!=',') { + nonstandards[i++]=*c++; + nonstandards[i++]=*c; + if ((sym)&&(*c!=*(c-1))) { + nonstandards[i++]=*c; + nonstandards[i++]=*(c-1); + } + } + c++; + } + } + + istty = isatty(fileno(stdout))&&isatty(fileno(stdin)); + + do { + if (istty) { + printf("\nInput string (upper or lower case); @ to quit\n"); + printf("%s%s\n", scale1, scale2); + } + + if ((line = get_line(stdin))==NULL) break; + + /* skip comment lines and get filenames */ + while ((*line=='*')||(*line=='\0')||(*line=='>')) { + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) break; + } + if (line==NULL) break; + if (strcmp(line, "@") == 0) {free(line); break;} + + string = (char *) space(strlen(line)+1); + (void) sscanf(line,"%s",string); + free(line); + length = (int) strlen(string); + + for (l = 0; l < length; l++) { + string[l] = toupper(string[l]); + if (!noconv && string[l] == 'T') string[l] = 'U'; + } + + if (istty) + printf("length = %d\n", length); + + heat_capacity(string, T_min, T_max, h, mpoints); + free(string); + (void) fflush(stdout); + } while (1); + return 0; +} + +PRIVATE void usage(void) +{ + nrerror("usage: RNAheat [-Tmin t1] [-Tmax t2] [-h stepsize] [-m ipoints] [-4] [-d]\n" + " [-noGU] [-noCloseGU] [-noLP] [-e 1|2] [-P paramfile] [-nsp pairs]"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat.o new file mode 100755 index 000000000..399ead99a Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAheat.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse new file mode 100755 index 000000000..fab991e5e Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse.c new file mode 100755 index 000000000..ea92ab3d3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse.c @@ -0,0 +1,234 @@ +/* + Interactive access to inverse folding routines + c Ivo Hofacker, Peter Stadler + Vienna RNA Package +*/ +/* Last changed Time-stamp: <2000-09-28 14:58:05 ivo> */ +#include +#include +#include +#include +#include +#include +#include "inverse.h" +#include "fold_vars.h" +#include "fold.h" +#include "part_func.h" +#include "utils.h" +#ifdef dmalloc +#include "/usr/local/include/dmalloc.h" +#define space(X) calloc(1,(X)) +#endif + +#define PUBLIC +#define PRIVATE static +/*@unused@*/ +static char rcsid[] = "$Id: RNAinverse.c,v 1.11 2000/09/28 12:59:21 ivo Rel $"; +static char scale[] = "....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +#define REPEAT_DEFAULT 100 +#define INFINITY 100000 + +extern void read_parameter_file(const char fname[]); + +PRIVATE void usage(void); +extern int inv_verbose; + +int main(int argc, char *argv[]) +{ + char *start, *structure, *rstart, *str2, *line; + char *ParamFile=NULL; + int i,j, length, l, hd; + double energy=0., kT; + int pf, mfe, istty; + int repeat, found; + + do_backtrack = 0; pf = 0; mfe = 1; + repeat = 0; + init_rand(); + for (i=1; i')) { + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) break; + } + /* stop at eof or '@' */ + if (line==NULL) break; + if (strcmp(line, "@") == 0) {free(line); break;} + + structure = (char *) space(strlen(line)+1); + (void) sscanf(line,"%s",structure); /* scanf gets rid of trailing junk */ + free(line); + + length = (int) strlen(structure); + str2 = (char *) space((unsigned)length+1); + + if ((line = get_line(stdin))!=NULL) + if (strcmp(line, "@") == 0) {free(line); break;} + + start = (char *) space((unsigned) length+1); + if (line !=NULL) { + (void) strncpy(start, line, length); + free(line); + } + + if (istty) printf("length = %d\n", length); + + if (repeat!=0) found = (repeat>0)? repeat : (-repeat); + else found = 1; + + initialize_fold(length); + + rstart = (char *) space((unsigned)length+1); + while(found>0) { + char *string; + string = (char *) space((unsigned)length+1); + strcpy(string, start); + for (i=0; i=0) || (energy<=0.0) ) { + found--; + hd = hamming(rstart, string); + printf("%s %3d", string, hd); + if (energy>0) { /* no solution found */ + printf(" d= %g\n", energy); + if(istty) { + energy = fold(string,str2); + printf("%s\n", str2); + } + } else printf("\n"); + } + } + if (pf) { + if (!(mfe && give_up && (energy>0))) { + /* unless we gave up in the mfe part */ + double prob, min_en, sfact=1.07; + + /* get a reasonable pf_scale */ + min_en = fold(string,str2); + pf_scale = exp(-(sfact*min_en)/kT/length); + init_pf_fold(length); + + energy = inverse_pf_fold(string, structure); + prob = exp(-energy/kT); + hd = hamming(rstart, string); + printf("%s %3d (%g)\n", string, hd, prob); + free_pf_arrays(); + } + if (!mfe) found--; + } + (void) fflush(stdout); + free(string); + } + free(rstart); + free_arrays(); + + free(structure); + free(str2); + free(start); + (void) fflush(stdout); + } while (1); + return 0; +} + + +PRIVATE void usage(void) +{ + nrerror("usage: RNAinverse [-F[mp]] [-a ALPHABET] [-R [repeats]] [-f final]\n" + " [-T temp] [-4] [-d[2]] [-noGU] [-P paramfile] [-e e_set] [-v]"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse.o new file mode 100755 index 000000000..82a01b113 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAinverse.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance new file mode 100755 index 000000000..2659dcfb0 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.c new file mode 100755 index 000000000..46223bc7b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.c @@ -0,0 +1,251 @@ +/************************************************************************/ +/* Distances of Secondary Structures */ +/************************************************************************/ + + +#include +#include +#include +#include +#include +#include +#include "dist_vars.h" +#include "RNAstruct.h" +#include "treedist.h" +#include "stringdist.h" +#include "utils.h" + + +#define MAXNUM 1000 /* max number of structs for distance matrix */ +#define PRIVATE static +#define PUBLIC + + + +PRIVATE void usage(void); +PRIVATE int parse_input(char *line); + + + +PRIVATE int types = 1; /* number of distance types */ +PRIVATE char ttype[10] = "f"; /* distance types */ +PRIVATE int n = 0; /* number of structures read so far */ + + +int main(int argc, char *argv[]) +{ + int tree_types = 0, ttree; + int string_types = 0, tstr; + char *line=NULL, *xstruc, *cc; + int i, j, tt, type; + int it, is; + float dist; + int comp_to_first = 0; + int max = MAXNUM; + + + edit_backtrack = 0; + + /* reading parameters */ + for (i = 1; i < argc; i++) { + if (argv[i][0] == '-') { + if (argv[i][1] == 'D') { + strncpy(ttype, argv[i]+2, 9); + types = (int)strlen(ttype); + } + else if (argv[i][1] == 'F') + comp_to_first = 1; + else if (argv[i][1] == 'M') { + max = atoi(argv[i+1]) + 10; + i++; + } + else + usage(); + } + else + usage(); + } + + Tree *T[5][max]; + swString *S[5][max]; + char *P[max]; /* structures for base pair distances */ + + /* reading sequences from stdin and calculating distances */ + line = get_line(stdin); + type = parse_input(line); + while (type != 999) { + + while (type == 0) { + if (line != NULL) + free(line); + + line = get_line(stdin); + type = parse_input(line); + } + + tree_types = 0; + string_types = 0; + for(tt = 0; tt < types; tt++) { + + switch(ttype[tt]){ + case 'f' : + case 'F' : + xstruc = expand_Full(line); + if(islower(ttype[tt])) /* tree_edit */ + T[tree_types++][n] = make_tree(xstruc); + if(isupper(ttype[tt])) /* string edit */ + S[string_types++][n] = Make_swString(xstruc); + free(xstruc); + break; + + case 'P': + P[n] = strdup(line); + break; + + case 'h' : + case 'H' : + xstruc = b2HIT(line); + if(islower(ttype[tt])) + T[tree_types++][n] = make_tree(xstruc); + if(isupper(ttype[tt])) + S[string_types++][n] = Make_swString(xstruc); + free(xstruc); + break; + + case 'c' : + case 'C' : + cc = b2C(line); + xstruc = expand_Shapiro(cc); + free(cc); + if(islower(ttype[tt])) + T[tree_types++][n] = make_tree(xstruc); + if(isupper(ttype[tt])) + S[string_types++][n] = Make_swString(xstruc); + free(xstruc); + break; + + case 'w' : + case 'W' : + xstruc = b2Shapiro(line); + if(islower(ttype[tt])) + T[tree_types++][n] = make_tree(xstruc); + if(isupper(ttype[tt])) + S[string_types++][n] = Make_swString(xstruc); + free(xstruc); + break; + + default: + nrerror("Unknown distance type"); + } + } + n++; + + if (n >= 2) { + it = 0; + is = 0; + if (comp_to_first) { + for (i=0; i < types; i++) { + if(islower(ttype[i])) { + dist = tree_edit_distance(T[it][0], T[it][1]); + free_tree(T[it][1]); + it++; + } + else if (ttype[i]=='P') { + dist = (float)bp_distance(P[0], P[1]); + free(P[1]); + } + else /* isupper(ttype[i]) */ { + dist = string_edit_distance(S[is][0], S[is][1]); + free(S[is][1]); + is++; + } + printf("%c: %g \n", ttype[i], dist); + } + n = 1; + } + else { + for (i=0; i < types; i++) { + if(islower(ttype[i])) { + dist = tree_edit_distance(T[it][0], T[it][1]); + free_tree(T[it][0]); + free_tree(T[it][1]); + it++; + } + else if (ttype[i]=='P') { + dist = (float)bp_distance(P[0], P[1]); + free(P[0]); + free(P[1]); + } + else /* isupper(ttype[i]) */ { + dist = string_edit_distance(S[is][0], S[is][1]); + free(S[is][0]); + free(S[is][1]); + is++; + } + printf("%c: %g \n", ttype[i], dist); + } + n = 0; + } + } + fflush(stdout); + + free(line); + line = get_line(stdin); + type = parse_input(line); + } + + if (comp_to_first) { + it = 0; + is = 0; + for (i=0; i < types; i++) { + if(islower(ttype[i])) + free_tree(T[it++][0]); + else if (ttype[i]=='P') + free(P[0]); + else /* isupper(ttype[i]) */ + free(S[is++][1]); + } + } + + return 0; +} + +/*--------------------------------------------------------------------------*/ + +PRIVATE int parse_input(char *line) +{ + int i,o; + + if (line == NULL) + return 999; + + i=o=0; + while( line[i] ){ + switch(line[i]) { + case '(' : + o++; + i++; + break; + case '.' : + i++; + break; + case ')' : + i++; + o--; + if(o<0) return 0; + break; + default: + return 0; + } + } + if (o>0) + return 0; + return 1; +} + +/*--------------------------------------------------------------------------*/ + +PRIVATE void usage(void) +{ + nrerror("usage: RNAmotif_distance [-D[fhwcFHWCP]] [-F] [-M ]"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.c~ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.c~ new file mode 100755 index 000000000..40022eb90 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.c~ @@ -0,0 +1,548 @@ +/* + Distances of Secondary Structures + Walter Fontana, Ivo L Hofacker, Peter F Stadler + Vienna RNA Package +*/ +#include +#include +#include +#include +#include +#include +#include "dist_vars.h" +#include "RNAstruct.h" +#include "treedist.h" +#include "stringdist.h" +#include "utils.h" + +#define MAXNUM 1000 /* max number of structs for distance matrix */ + +#define PUBLIC +#define PRIVATE static +/*@unused@*/ +static char rcsid[] = "$Id: RNAdistance.c,v 1.8 2005/07/24 08:35:15 ivo Exp $"; +PRIVATE void command_line(int argc, char *argv[]); +PRIVATE void usage(void); +PRIVATE int parse_input(char *line); +PRIVATE int check_tree(char *line, char alpha[]); +PRIVATE int check_brackets(char *line); +PRIVATE void print_aligned_lines(FILE *somewhere); + +PRIVATE char ruler[] ="....,....1....,....2....,....3....,....4" +"....,....5....,....6....,....7....,....8"; +PRIVATE int types=1; +PRIVATE int task; +PRIVATE int taxa_list; +PRIVATE char outfile[50], *list_title; + +PRIVATE char ttype[10]="f"; +PRIVATE int n=0; + +int main(int argc, char *argv[]) +{ + char *line=NULL, *xstruc, *cc; + Tree *T[10][MAXNUM]; + int tree_types = 0, ttree; + swString *S[10][MAXNUM]; + char *P[MAXNUM]; /* structures for base pair distances */ + int string_types = 0, tstr; + int i,j, tt, istty, type; + int it, is; + FILE *somewhere=NULL; + + command_line(argc, argv); + + if((outfile[0]=='\0')&&(task==2)&&(edit_backtrack)) + strcpy(outfile,"backtrack.file"); + if(outfile[0]!='\0') somewhere = fopen(outfile,"w"); + if (somewhere==NULL) somewhere = stdout; + istty = isatty(fileno(stdin))&&isatty(fileno(stdout)); + + do { + if ((istty)&&(n==0)) { + printf("\nInput structure; @ to quit\n"); + printf("%s\n", ruler); + } + do { + if (line!=NULL) free(line); + line=get_line(stdin); + } while ((type=parse_input(line))==0); + + if (((type==999)||(type==888))&&(task==2)) { /* do matrices */ + if (taxa_list) + printf("* END of taxa list\n"); + + ttree = 0; tstr = 0; + for (tt=0; tt< types; tt++) { + printf("> %c %d\n", ttype[tt], n); + if(islower(ttype[tt])) { + for (i=1; i1) { + for (it=0, is=0, i=0; i1) { + for (it=0, is=0, i=0; i') { + if (taxa_list) + printf("%d :%s\n", n+1, line+1); + else printf("%s\n", line); + return 0; + } + + cp = strchr(line,' '); + if (cp) *cp='\0'; /* get rid of junk at the end of line */ + + switch (line[0]) { + case '.' : + type = 1; + break; + + case '(' : /* it's a tree */ + i=1; + xx = 0; + type = 4; /* coarse */ + rooted = 0; + while (line[i]) { + if (line[i]=='.'){ + type = 1; /* Full */ + break; + } + if ( (line[i]=='U')||(line[i]=='P') ) { + type = 2; /* FFull */ + xx = 1; + break; + } + if (line[i]=='S') { + type = 3; + xx = 1; + break; /* Shapiro tree */ + } + if ((line[i]!='(')&&(line[i]!=')')) xx = 1; + i++; + } + if(!xx) type =1; + + rooted = (line[strlen(line)-2]=='R'); + break; + case '@' : + return 999; + + default: + return 0; + } + + switch (type) { + case 1: + if(check_brackets(line)) + return 1; + break; + case 2: + if(check_tree(line,"UP") ) { + if(rooted) return 2; + else return -2; + } + break; + case 3: + if(check_tree(line,"HBIMSE") ){ + if(rooted) return -3; + else return -3; + } + break; + case 4: + if(check_tree(line,"HBIM") ){ + if(rooted) return 4; + else return -4; + } + break; + } + return 0; +} + +/*--------------------------------------------------------------------------*/ + + +PRIVATE int check_tree(char *line, char alpha[]) +{ + int n, i, o; + char *pos; + + n = (int) strlen(line); + + if( line[0] != '(' ) return 0; + i=o=1; + while( line[i] ){ + while( line[i] == '(' ){ + o++; + i++; + } + pos=strchr(alpha, (int)line[i]); + if (pos) { + while (isdigit((int) line[++i])); + if (line[i]!=')') return 0; + } + if (line[i]=='R') { + i++; + if ((i!=n-1)||(line[i]!=')')) return 0; + } + if (line[i]==')') { + o--; + if(o< 0) return 0; + if( (i0) return 0; + return 1; +} + +/*--------------------------------------------------------------------------*/ + + +PRIVATE int check_brackets(char *line) +{ + int i,o; + + i=o=0; + while( line[i] ){ + switch(line[i]) { + case '(' : + o++; + i++; + break; + case '.' : + i++; + break; + case ')' : + i++; + o--; + if(o<0) return 0; + break; + default: + return 0; + } + } + if (o>0) return 0; + return 1; +} + +/*--------------------------------------------------------------------------*/ + + +PRIVATE void command_line(int argc, char *argv[]) +{ + int i; + + edit_backtrack = 0; + types=1; ttype[0]='f'; task=1; + + for (i=1; i= argc) outfile[0] = '\0'; + else if (argv[i+1][0]=='-') outfile[0] = '\0'; + else { + i++; + strncpy(outfile,argv[i],49); + } + edit_backtrack = 1; + break; + default: + usage(); + } + } +} + +/*--------------------------------------------------------------------------*/ + +PRIVATE void print_aligned_lines(FILE *somewhere) +{ + if (edit_backtrack) { + fprintf(somewhere, "\n%s\n%s\n", aligned_line[0], aligned_line[1]); + fflush(somewhere); + } +} + +/*--------------------------------------------------------------------------*/ + +PRIVATE void usage(void) +{ + nrerror("usage: RNAdistance [-D[fhwcFHWCP]] [-X[p|m|f|c]] [-S] [-B [file]]"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.o new file mode 100755 index 000000000..aeb26bc48 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAmotif_distance.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNApaln b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNApaln new file mode 100755 index 000000000..2fe0351a0 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNApaln differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNApaln.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNApaln.c new file mode 100755 index 000000000..fe7e2332e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNApaln.c @@ -0,0 +1,341 @@ +/* + Distances of Secondary Structure Ensembles + Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer + Vienna RNA Package +*/ +#include +#include +#include +#include +#include +#include +#include +#include "part_func.h" +#include "fold.h" +#include "fold_vars.h" +#include "profiledist.h" +#include "dist_vars.h" +#include "utils.h" +#include "ProfileAln.h" + +#define PUBLIC +#define PRIVATE static + +#define MAXLENGTH 10000 +#define MAXSEQ 1000 +/*@unused@*/ +static char rcsid[] = "$Id: RNApaln.c,v 1.3 2005/07/24 08:35:15 ivo Exp $"; + +static double gapo=1.5, gape=0.666, seqw=0.5; +static int endgaps=0; + +PRIVATE void command_line(int argc, char *argv[]); +PRIVATE void usage(void); +PRIVATE void print_aligned_lines(FILE *somewhere); + +PRIVATE char task; +PRIVATE char outfile[50]; +PRIVATE char ruler[] ="....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +extern void PS_dot_plot(char *string, char *file); +extern void read_parameter_file(const char fname[]); +extern float profile_aln(const float *T1, const char *seq1, + const float *T2, const char *seq2); +static int noconv = 0; + +int main(int argc, char *argv[]) + +{ + float *T[MAXSEQ]; + char *seq[MAXSEQ]; + int i,j, istty, n=0; + int type, length, taxa_list=0; + float dist; + FILE *somewhere=NULL; + char *structure; + char *line=NULL, fname[20], *list_title=NULL; + + command_line(argc, argv); + + if((outfile[0]=='\0')&&(task=='m')&&(edit_backtrack)) + strcpy(outfile,"backtrack.file"); + if (outfile[0]!='\0') somewhere = fopen(outfile,"w"); + if (somewhere==NULL) somewhere = stdout; + istty = (isatty(fileno(stdout))&&isatty(fileno(stdin))); + + while (1) { + if ((istty)&&(n==0)) { + printf("\nInput sequence; @ to quit\n"); + printf("%s\n", ruler); + } + + type = 0; + do { /* get sequence to fold */ + if (line!=NULL) free(line); + *fname='\0'; + if ((line=get_line(stdin))==NULL) {type = 999; break;} + if (line[0]=='@') type = 999; + if (line[0]=='*') { + if (taxa_list==0) { + if (task=='m') taxa_list=1; + printf("%s\n", line); + type = 0; + } else { + list_title = strdup(line); + type = 888; + } + } + if (line[0]=='>') { + if (sscanf(line,">%12s", fname)!=0) + strcat(fname, "_dp.ps"); + if (taxa_list) + printf("%d : %s\n", n+1, line+1); + else printf("%s\n",line); + type = 0; + } + if (isalpha(line[0])) { + char *cp; + cp =strchr(line,' '); + if (cp) *cp='\0'; + type = 1; + } + } while(type==0); + + if( (task == 'm')&&(type>800) ) { + if (taxa_list) + printf("* END of taxa list\n"); + printf("> p %d (pdist)\n",n); + for (i=1; i %d %d\n",i+1,j+1); + print_aligned_lines(somewhere); + } + printf("\n"); + } + if (type==888) { /* do another distance matrix */ + n = 0; + printf("%s\n", list_title); + free(list_title); + } + } + + if(type>800) { + for (i=0; i1) { + dist = profile_aln(T[1], seq[1], T[0], seq[0]); + printf("%g\n",dist); + print_aligned_lines(somewhere); + free_profile(T[1]); free(seq[1]); + n=1; + } + break; + case 'c' : + if (n>1) { + dist = profile_aln(T[1], seq[1], T[0],seq[0]); + printf("%g\n",dist); + print_aligned_lines(somewhere); + free_profile(T[0]); free(seq[0]); + T[0] = T[1]; seq[0] = seq[1]; + n=1; + } + break; + + case 'm' : + break; + + default : + nrerror("This can't happen."); + } /* END switch task */ + (void) fflush(stdout); + } /* END while */ + if (line !=NULL) free(line); + return 0; +} + +/* ----------------------------------------------------------------- */ + +PRIVATE void command_line(int argc, char *argv[]) +{ + + int i, sym; + char *ns_bases=NULL, *c; + char *ParamFile=NULL; + + task = 'p'; + for (i=1; i= argc) outfile[0] = '\0'; + else if (argv[i+1][0]=='-') outfile[0] = '\0'; + else { + i++; + strncpy(outfile,argv[i],49); + } + edit_backtrack = 1; + break; + case 'P': + if (++i +#include +#include +#include +#include +#include +#include +#include "part_func.h" +#include "fold_vars.h" +#include "profiledist.h" +#include "dist_vars.h" +#include "utils.h" + +#define PUBLIC +#define PRIVATE static + +#define MAXLENGTH 10000 +#define MAXSEQ 1000 +/*@unused@*/ +static char rcsid[] = "$Id: RNApdist.c,v 1.8 2002/11/07 12:19:41 ivo Exp $"; + +PRIVATE void command_line(int argc, char *argv[]); +PRIVATE void usage(void); +PRIVATE void print_aligned_lines(FILE *somewhere); + +PRIVATE char task; +PRIVATE char outfile[50]; +PRIVATE char ruler[] ="....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +extern void PS_dot_plot(char *string, char *file); +extern void read_parameter_file(const char fname[]); +static int noconv = 0; + +int main(int argc, char *argv[]) + +{ + float *T[MAXSEQ]; + int i,j, istty, n=0; + int type, length, taxa_list=0; + float dist; + FILE *somewhere=NULL; + char *structure; + char *line=NULL, fname[20], *list_title=NULL; + + command_line(argc, argv); + + if((outfile[0]=='\0')&&(task=='m')&&(edit_backtrack)) + strcpy(outfile,"backtrack.file"); + if (outfile[0]!='\0') somewhere = fopen(outfile,"w"); + if (somewhere==NULL) somewhere = stdout; + istty = (isatty(fileno(stdout))&&isatty(fileno(stdin))); + + while (1) { + if ((istty)&&(n==0)) { + printf("\nInput sequence; @ to quit\n"); + printf("%s\n", ruler); + } + + type = 0; + do { /* get sequence to fold */ + if (line!=NULL) free(line); + *fname='\0'; + if ((line=get_line(stdin))==NULL) {type = 999; break;} + if (line[0]=='@') type = 999; + if (line[0]=='*') { + if (taxa_list==0) { + if (task=='m') taxa_list=1; + printf("%s\n", line); + type = 0; + } else { + list_title = strdup(line); + type = 888; + } + } + if (line[0]=='>') { + if (sscanf(line,">%12s", fname)!=0) + strcat(fname, "_dp.ps"); + if (taxa_list) + printf("%d : %s\n", n+1, line+1); + else printf("%s\n",line); + type = 0; + } + if (isalpha(line[0])) { + char *cp; + cp =strchr(line,' '); + if (cp) *cp='\0'; + type = 1; + } + } while(type==0); + + if( (task == 'm')&&(type>800) ) { + if (taxa_list) + printf("* END of taxa list\n"); + printf("> p %d (pdist)\n",n); + for (i=1; i %d %d\n",i+1,j+1); + print_aligned_lines(somewhere); + } + printf("\n"); + } + if (type==888) { /* do another distance matrix */ + n = 0; + printf("%s\n", list_title); + free(list_title); + } + } + + if(type>800) { + for (i=0; i1) { + dist = profile_edit_distance(T[1], T[0]); + printf("%g\n",dist); + print_aligned_lines(somewhere); + free_profile(T[1]); + n=1; + } + break; + case 'c' : + if (n>1) { + dist = profile_edit_distance(T[1], T[0]); + printf("%g\n",dist); + print_aligned_lines(somewhere); + free_profile(T[0]); + T[0] = T[1]; + n=1; + } + break; + + case 'm' : + break; + + default : + nrerror("This can't happen."); + } /* END switch task */ + (void) fflush(stdout); + } /* END while */ + if (line !=NULL) free(line); + return 0; +} + +/* ----------------------------------------------------------------- */ + +PRIVATE void command_line(int argc, char *argv[]) +{ + + int i, sym; + char *ns_bases=NULL, *c; + char *ParamFile=NULL; + + task = 'p'; + for (i=1; i= argc) outfile[0] = '\0'; + else if (argv[i+1][0]=='-') outfile[0] = '\0'; + else { + i++; + strncpy(outfile,argv[i],49); + } + edit_backtrack = 1; + break; + case 'P': + if (++i */ +/* + Ineractive Access to folding Routines + + c Ivo L Hofacker + Vienna RNA package +*/ + +#include +#include +#include +#include +#include +#include +#include "fold.h" +#include "part_func.h" +#include "fold_vars.h" +#include "utils.h" +#include "PS_dot.h" + +extern float Lfold(char *string, char *structure, int maxdist); +extern void read_parameter_file(const char fname[]); +extern int pfl_fold(char *sequence, int winSize, float cutoff, struct plist **pl); +extern void init_pf_foldLP(int length); +extern void free_pf_arraysLP(void); + +/*@unused@*/ +static char rcsid[] = "$Id: RNAplfold.c,v 1.2 2006/01/16 09:49:07 ivo Exp $"; + +#define PRIVATE static + +static char scale[] = "....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +PRIVATE void usage(void); + +/*--------------------------------------------------------------------------*/ + +int main(int argc, char *argv[]) +{ + char *string, *line; + char *structure=NULL, *cstruc=NULL; + char fname[30], ffname[20]; + char *ParamFile=NULL; + char *ns_bases=NULL, *c; + int i, length, l, sym,r; + int istty; + int noconv=0; + int maxdist=70; + int winSize; + float cutoff=0.01; + int hit; + plist *pl; + do_backtrack = 1; + string=NULL; + dangles=2; + for (i=1; i')) { + if (*line=='>') + (void) sscanf(line, ">%12s", fname); + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) break; + } + + if ((line ==NULL) || (strcmp(line, "@") == 0)) break; + + string = (char *) space(strlen(line)+1); + (void) sscanf(line,"%s",string); + free(line); + length = (int) strlen(string); + + structure = (char *) space((unsigned) length+1); + + for (l = 0; l < length; l++) { + string[l] = toupper(string[l]); + if (!noconv && string[l] == 'T') string[l] = 'U'; + } + if (istty) + printf("length = %d\n", length); + + /* initialize_fold(length); */ + update_fold_params(); + maxdist=winSize; + if (length= 5) { + pf_scale = -1; + + init_pf_foldLP(length); + + hit=pfl_fold(string, maxdist, cutoff, &pl); + free_pf_arraysLP(); + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_dp.ps"); + } + else strcpy(ffname, "plfold_dp.ps"); + PS_dot_plot_turn(string, pl, ffname, maxdist); + free(pl); + + if (cstruc!=NULL) free(cstruc); + (void) fflush(stdout); + } + free(string); + free(structure); + } while (1); + return 0; +} + +PRIVATE void usage(void) +{ + nrerror("usage:\n" + "RNAplfold [-L span]\n" + " [-T temp] [-4] [-d[0|1|2]] [-noGU] [-noCloseGU]\n" + " [-noLP] [-P paramfile] [-nsp pairs] [-noconv]\n"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplfold.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplfold.o new file mode 100755 index 000000000..890c13b5d Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplfold.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot new file mode 100755 index 000000000..031d426c2 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot.c new file mode 100755 index 000000000..71c9f5daf --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot.c @@ -0,0 +1,127 @@ +/* + Plot RNA structures using different layout algorithms + Last changed Time-stamp: <2003-09-10 13:55:01 ivo> +*/ + +#include +#include +#include +#include +#include +#include +#include "utils.h" +#include "PS_dot.h" + +#define PRIVATE static + +PRIVATE char scale[] = ".........1.........2.........3.........4.........5.........6.........7.........8"; + +PRIVATE void usage(void); + + +/*--------------------------------------------------------------------------*/ + +extern int svg_rna_plot(char *string, char *structure, char *ssfile); + +int main(int argc, char *argv[]) +{ + + char *string=NULL, *line; + char *structure=NULL, *pre=NULL, *post=NULL; + char fname[13], ffname[20]; + int i, r; + float energy; + int istty; + char format[5]="ps"; + + string=NULL; + for (i=1; i')) { + if (*line=='>') + sscanf(line, ">%12s", fname); + printf("%s\n", line); + free(line); + if ((line = get_line(stdin))==NULL) line = "@"; + } + + if (strcmp(line, "@") == 0) break; + + string = (char *) space(strlen(line)+1); + sscanf(line,"%s",string); + free(line); + + if ((line = get_line(stdin))==NULL) break; + structure = (char *) space(strlen(line)+1); + sscanf(line,"%s (%f)", structure, &energy); + free(line); + + if (strlen(string)!=strlen(structure)) + nrerror("sequence and structure have unequal length!"); + + if (fname[0]!='\0') { + strcpy(ffname, fname); + strcat(ffname, "_ss"); + } else + strcpy(ffname, "rna"); + + switch (format[0]) { + case 'p': + strcat(ffname, ".ps"); + PS_rna_plot_a(string, structure, ffname, pre, post); + break; + case 'g': + strcat(ffname, ".gml"); + gmlRNA(string, structure, ffname, 'x'); + break; + case 'x': + strcat(ffname, ".ss"); + xrna_plot(string, structure, ffname); + break; + case 's': + strcat(ffname, ".svg"); + svg_rna_plot(string, structure, ffname); + break; + default: + usage(); + } + fflush(stdout); + free(string); + free(structure); + } while (1); + return 0; +} + +PRIVATE void usage(void) +{ + nrerror("usage: RNAplot [-t 0|1] [-o ps|gml|xrna|svg] [--pre ] [--post ]"); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot.o new file mode 100755 index 000000000..d93f9766e Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAplot.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAstats b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAstats new file mode 100755 index 000000000..d6ad31068 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAstats differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAstats.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAstats.c new file mode 100755 index 000000000..333f54c98 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/Progs/RNAstats.c @@ -0,0 +1,363 @@ +/* + * RNA folding statistics program Based on RNAsubopt. + */ + +#include +#include +#include +#include +#include +#include +#include +#include "part_func.h" +#include "fold.h" +#include "fold_vars.h" +#include "utils.h" +#include "subopt.h" +extern void read_parameter_file(const char fname[]); +extern int st_back; +/* @unused@ */ +static char UNUSED rcsid[] = "$Id: RNAstats.c,v 1.0 2006/01/02 Exp $"; + +#define ENTROPY(X) (X==0 ? 0 : (-X*log2f(X))) + +#define PRIVATE static + +static char scale[] = "....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +extern double print_energy; +PRIVATE void usage(void); +float *bp_entropy(int length); +extern char *pbacktrack(char *sequence); +/*--------------------------------------------------------------------------*/ + +int +main(int argc, char *argv[]) +{ + char *line; + char *sequence; + char *ss = NULL; + char *ParamFile = NULL; + char *ns_bases = NULL, *c; + int i, length, l, sym, r; + double deltaf, deltap = 0; + int delta = 100; + int statType = 1; + int slideOffset = 1; + int slideWindow = 200; + + do_backtrack = 1; + dangles = 2; + + /* Read command line arguments ********************************************/ + + for (i = 1; i < argc; i++) { + if (argv[i][0] == '-') + switch (argv[i][1]) { + case 'T': + if (argv[i][2] != '\0') + usage(); + if (i == argc - 1) + usage(); + r = sscanf(argv[++i], "%lf", &temperature); + if (r != 1) + usage(); + break; + case 'S': + if (argv[i][2] != '\0') + usage(); + if (i == argc - 1) + usage(); + (void) sscanf(argv[++i], "%d", &statType); + break; + case 'o': + if (argv[i][2] != '\0') + usage(); + if (i == argc - 1) + usage(); + (void) sscanf(argv[++i], "%d", &slideOffset); + break; + case 'w': + if (argv[i][2] != '\0') + usage(); + if (i == argc - 1) + usage(); + (void) sscanf(argv[++i], "%d", &slideWindow); + break; + case 'n': + if (strcmp(argv[i], "-noGU") == 0) + noGU = 1; + if (strcmp(argv[i], "-noCloseGU") == 0) + no_closingGU = 1; + if (strcmp(argv[i], "-noLP") == 0) + noLonelyPairs = 1; + if (strcmp(argv[i], "-nsp") == 0) { + if (i == argc - 1) + usage(); + ns_bases = argv[++i]; + } + break; + case '4': + tetra_loop = 0; + break; + case 'd': + dangles = 0; + if (argv[i][2] != '\0') { + r = sscanf(argv[i] + 2, "%d", &dangles); + if (r != 1) + usage(); + } + break; + case 'P': + if (i == argc - 1) + usage(); + ParamFile = argv[++i]; + break; + case 's': + subopt_sorted = 1; + break; + case 'l': + if (strcmp(argv[i], "-logML") == 0) { + logML = 1; + break; + } else + usage(); + break; + case 'e': + if (i >= argc - 1) + usage(); + if (strcmp(argv[i], "-ep") == 0) + r = sscanf(argv[++i], "%lf", &deltap); + else { + r = sscanf(argv[++i], "%lf", &deltaf); + delta = (int) (0.1 + deltaf * 100); + } + if (r != 1) + usage(); + break; + default: + usage(); + } + } + + if (ParamFile != NULL) + read_parameter_file(ParamFile); + + if (ns_bases != NULL) { + nonstandards = space(33); + c = ns_bases; + i = sym = 0; + if (*c == '-') { + sym = 1; + c++; + } + while (*c) { + if (*c != ',') { + nonstandards[i++] = *c++; + nonstandards[i++] = *c; + if ((sym) && (*c != *(c - 1))) { + nonstandards[i++] = *c; + nonstandards[i++] = *(c - 1); + } + } + c++; + } + } + + + /* Main Loop. Process each line as a sequence *****************************/ + + int mergePos = (int)(floor(((float)(slideWindow - slideOffset)) / 2)) + 1; + + do { + + /* Read sequence, make sure it's long enough and allocate memory for structure */ + + if ((line = get_line(stdin)) == NULL) + break; + + if (slideWindow > strlen(line)) + { + fprintf(stderr, "Sequence length (%d) should be at least window-length (%d)", strlen(line), slideWindow); + nrerror ("Quitting."); + } + + /* printf ("Sliding window %d\n", slideWindow); */ + + sequence = (char *) space(strlen(line) + 1); + (void) sscanf(line, "%s", sequence); + free(line); + + length = (int) strlen(sequence); + + for (l = 0; l < length; l++) + sequence[l] = toupper(sequence[l]); + + + /* Some deltap calculations */ + + if (logML != 0 || dangles == 1 || dangles == 3) + if (deltap <= 0) + deltap = delta / 100. + 0.001; + if (deltap > 0) + print_energy = deltap; + + int i, j; + double mfe, kT; + + int startPos; + char rememberBp; + + st_back = 1; + + /* Construct the sub-sequence to be processed, based on the window size + and offset. Then calculate the required statistics for each such sub-sequence */ + + ss = (char *) space((unsigned)(slideWindow + 1)); + + for (startPos = 0; startPos <= (length - slideWindow); startPos += slideOffset) + { + /* Crop the sequence at window size */ + + rememberBp = sequence[startPos + slideWindow]; + sequence[startPos + slideWindow] = 0; + + /* Initial folding of the sequence */ + + mfe = fold((char*)(sequence + startPos), ss); + + kT = (temperature + 273.15) * 1.98717 / 1000.; /* in Kcal */ + pf_scale = exp(-(1.03 * mfe) / kT / length); + + (void) pf_fold((char*)(sequence + startPos), NULL); + + float *bpProfile; + float *bpEntropy; + float basePairedP; + char na; + + /* Use the Make_bp_profile function to calculate the probability of + each bp to be paired. Then either print out this probability + or the entropy of this probability */ + + bpProfile = (float *)Make_bp_profile (slideWindow); + bpEntropy = (float *)bp_entropy (slideWindow); + + /* P[i*3+0] unpaired, P[i*3+1] upstream, P[i*3+2] downstream p */ + + /* First time only -- pad with data before mergePos */ + if (!startPos) + { + for (j = 1; j < mergePos; j++) + { + basePairedP = (1-bpProfile[j*3]); + na = sequence[startPos + j - 1]; + + printf("%d\t%d\tPairness\t%.2f\t%c\n", j, j, basePairedP, na); + printf("%d\t%d\tPairness_Entropy\t%.2f\t%c\n", j, j, ENTROPY(basePairedP) + ENTROPY((1-basePairedP)), na); + printf("%d\t%d\tEntropy\t%.2f\t%c\n", j, j, bpEntropy[j], na); + /* Not printing dG */ + } + } + + /* Always -- print center data */ + for (j = mergePos; j < mergePos + slideOffset; j++) + { + basePairedP = (1-bpProfile[j*3]); + na = sequence[startPos + j - 1]; + + printf("%d\t%d\tPairness\t%.2f\t%c\n", j+startPos, j+startPos, basePairedP, na); + printf("%d\t%d\tPairness_Entropy\t%.2f\t$c\n", j+startPos, j+startPos, ENTROPY(basePairedP) + ENTROPY((1-basePairedP)), na); + printf("%d\t%d\tEntropy\t%.2f\t%c\n", j+startPos, j+startPos, bpEntropy[j], na); + } + + /* Always -- print dG data (but only once) */ + printf("%d\t%d\tdG\t%.2f\n", startPos+mergePos, (startPos+mergePos+slideOffset-1), -mfe); + + /* Last time only -- pad with data after mergePos */ + if (startPos + slideOffset > length - slideWindow) + { + for (j = mergePos + slideOffset; j < slideWindow+1; j++) + { + basePairedP = (1-bpProfile[j*3]); + na = sequence[startPos + j - 1]; + + printf("%d\t%d\tPairness\t%.2f\t%c\n", j+startPos, j+startPos, basePairedP, na); + printf("%d\t%d\tPairness_Entropy\t%.2f\t%c\n", j+startPos, j+startPos, ENTROPY(basePairedP) + ENTROPY((1-basePairedP)), na); + printf("%d\t%d\tEntropy\t%.2f\t%c\n", j+startPos, j+startPos, bpEntropy[j], na); + } + } + + free (bpProfile); + free (bpEntropy); + + /* Restore the bp at the position where we placed the "0" beofre */ + sequence[startPos + slideWindow] = rememberBp; + } + + (void) fflush(stdout); + + free_pf_arrays(); + free(ss); + free(sequence); + + } while (1); + return 0; +} + +/******************************************************************************/ + +float *bp_entropy(int length) +{ + int i,j; + int L=3; + float *P; + float entropy; + + P = (float *) space((length)*sizeof(float)); + + for (i=1; i */ +/* + Ineractive access to suboptimal folding + + c Ivo L Hofacker + Vienna RNA package +*/ +#include +#include +#include +#include +#include +#include +#include +#include "part_func.h" +#include "fold.h" +#include "fold_vars.h" +#include "utils.h" +#include "subopt.h" +extern void read_parameter_file(const char fname[]); +extern int st_back; +/*@unused@*/ +static char UNUSED rcsid[] = "$Id: RNAsubopt.c,v 1.11 2004/08/12 10:59:31 ivo Exp $"; + +#define PRIVATE static + +static char scale[] = "....,....1....,....2....,....3....,....4" + "....,....5....,....6....,....7....,....8"; + +extern double print_energy; +PRIVATE void usage(void); +extern char *pbacktrack(char *sequence); +/*--------------------------------------------------------------------------*/ + +int main(int argc, char *argv[]) +{ + char *line; + char *sequence; + char *structure = NULL; + char fname[21]; + char *ParamFile = NULL; + char *ns_bases = NULL, *c; + int i, length, l, sym, r; + int istty; + double deltaf, deltap=0; + int delta=100; + int n_back = 0; + + do_backtrack = 1; + dangles = 2; + for (i=1; i=argc-1) usage(); + if (strcmp(argv[i],"-ep")==0) + r=sscanf(argv[++i], "%lf", &deltap); + else { + r=sscanf(argv[++i], "%lf", &deltaf); + delta = (int) (0.1+deltaf*100); + } + if (r!=1) usage(); + break; + default: usage(); + } + } + + if (ParamFile != NULL) + read_parameter_file(ParamFile); + + if (ns_bases != NULL) { + nonstandards = space(33); + c=ns_bases; + i=sym=0; + if (*c=='-') { + sym=1; c++; + } + while (*c) { + if (*c!=',') { + nonstandards[i++]=*c++; + nonstandards[i++]=*c; + if ((sym)&&(*c!=*(c-1))) { + nonstandards[i++]=*c; + nonstandards[i++]=*(c-1); + } + } + c++; + } + } + istty = isatty(fileno(stdout))&&isatty(fileno(stdin)); + if ((fold_constrained)&&(istty)) { + printf("Input constraints using the following notation:\n"); + /* printf("| : paired with another base\n"); */ + printf(". : no constraint at all\n"); + printf("x : base must not pair\n"); + } + + do { /* main loop: continue until end of file */ + if (istty) { + printf("\nInput string (upper or lower case); @ to quit\n"); + printf("%s\n", scale); + } + fname[0]='\0'; + if ((line = get_line(stdin))==NULL) break; + + /* skip comment lines and get filenames */ + while ((*line=='*')||(*line=='\0')||(*line=='>')) { + if (*line=='>') + (void) sscanf(line, ">%20s", fname); + free(line); + if ((line = get_line(stdin))==NULL) break;; + } + + if ((line==NULL) || strcmp(line, "@") == 0) break; + + sequence = (char *) space(strlen(line)+1); + (void) sscanf(line,"%s",sequence); + free(line); + length = (int) strlen(sequence); + + structure = (char *) space((unsigned) length+1); + if (fold_constrained) { + char *cstruc; + cstruc = get_line(stdin); + if (cstruc!=NULL) { + strncpy(structure, cstruc, length); + for (i=0; i0) + print_energy = deltap; + + /* first lines of output (suitable for sort +1n) */ + if (fname[0] != '\0') + printf("> %s [%d]\n", fname, delta); + + if (n_back>0) { + int i; + double mfe, kT; + char *ss; + st_back=1; + ss = (char *) space(strlen(sequence)+1); + strncpy(ss, structure, length); + mfe = fold(sequence, ss); + kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */ + pf_scale = exp(-(1.03*mfe)/kT/length); + strncpy(ss, structure, length); + (void) pf_fold(sequence, ss); + init_rand(); + free(ss); + for (i=0; i and change the code as indicated by the comment: + + else if (_Tr::eq(_C, _D)) + {_Chg = true; + _I.rdbuf()->snextc(); // replace snextc with sbumpc + break; } + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/Makefile new file mode 100755 index 000000000..7d062e84a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/Makefile @@ -0,0 +1,577 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# Makefile. 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It is known to compile without +modifications at least under SunOS 8.x, and linux. +Other UN*X flavours should present no problems. +You need a compiler that understands standard C++. +See the INSTALL file for details. + +For more details about RNAforester information see the man page. + +If you're a commercial user and find these programs useful, please consider +supporting further developments with a donation. + +The most recent source code and documentation should always be available on +the web at http://bibiserv.techfak.uni-bielefeld.de/rnaforester + +I appreciate any feedback! Send your comments, suggestions, and questions to +mhoechsm@techfak.uni-bielefeld.de + +Matthias Hoechsmann, June 2004 + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/TODO b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/TODO new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/aclocal.m4 b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/aclocal.m4 new file mode 100755 index 000000000..74de4a198 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/aclocal.m4 @@ -0,0 +1,862 @@ +# generated automatically by aclocal 1.9.5 -*- Autoconf -*- + +# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, +# 2005 Free Software Foundation, Inc. +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +# Copyright (C) 2002, 2003, 2005 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# AM_AUTOMAKE_VERSION(VERSION) +# ---------------------------- +# Automake X.Y traces this macro to ensure aclocal.m4 has been +# generated from the m4 files accompanying Automake X.Y. +AC_DEFUN([AM_AUTOMAKE_VERSION], [am__api_version="1.9"]) + +# AM_SET_CURRENT_AUTOMAKE_VERSION +# ------------------------------- +# Call AM_AUTOMAKE_VERSION so it can be traced. +# This function is AC_REQUIREd by AC_INIT_AUTOMAKE. +AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], + [AM_AUTOMAKE_VERSION([1.9.5])]) + +# AM_AUX_DIR_EXPAND -*- Autoconf -*- + +# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets +# $ac_aux_dir to `$srcdir/foo'. 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We just wanted to have am__tar + # and am__untar set. + test -n "${am_cv_prog_tar_$1}" && break + + # tar/untar a dummy directory, and stop if the command works + rm -rf conftest.dir + mkdir conftest.dir + echo GrepMe > conftest.dir/file + AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar]) + rm -rf conftest.dir + if test -s conftest.tar; then + AM_RUN_LOG([$am__untar /dev/null 2>&1 && break + fi +done +rm -rf conftest.dir + +AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool]) +AC_MSG_RESULT([$am_cv_prog_tar_$1])]) +AC_SUBST([am__tar]) +AC_SUBST([am__untar]) +]) # _AM_PROG_TAR + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.guess b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.guess new file mode 100755 index 000000000..fd30ab031 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.guess @@ -0,0 +1,1354 @@ +#! /bin/sh +# Attempt to guess a canonical system name. +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, +# 2000, 2001, 2002 Free Software Foundation, Inc. + +timestamp='2002-07-23' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + +# Originally written by Per Bothner . +# Please send patches to . Submit a context +# diff and a properly formatted ChangeLog entry. +# +# This script attempts to guess a canonical system name similar to +# config.sub. If it succeeds, it prints the system name on stdout, and +# exits with 0. Otherwise, it exits with 1. +# +# The plan is that this can be called by configure scripts if you +# don't specify an explicit build system type. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] + +Output the configuration name of the system \`$me' is run on. + +Operation modes: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.guess ($timestamp) + +Originally written by Per Bothner. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001 +Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit 0 ;; + --version | -v ) + echo "$version" ; exit 0 ;; + --help | --h* | -h ) + echo "$usage"; exit 0 ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + * ) + break ;; + esac +done + +if test $# != 0; then + echo "$me: too many arguments$help" >&2 + exit 1 +fi + +trap 'exit 1' 1 2 15 + +# CC_FOR_BUILD -- compiler used by this script. Note that the use of a +# compiler to aid in system detection is discouraged as it requires +# temporary files to be created and, as you can see below, it is a +# headache to deal with in a portable fashion. + +# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still +# use `HOST_CC' if defined, but it is deprecated. + +# This shell variable is my proudest work .. or something. --bje + +set_cc_for_build='tmpdir=${TMPDIR-/tmp}/config-guess-$$ ; +(old=`umask` && umask 077 && mkdir $tmpdir && umask $old && unset old) + || (echo "$me: cannot create $tmpdir" >&2 && exit 1) ; +dummy=$tmpdir/dummy ; +files="$dummy.c $dummy.o $dummy.rel $dummy" ; +trap '"'"'rm -f $files; rmdir $tmpdir; exit 1'"'"' 1 2 15 ; +case $CC_FOR_BUILD,$HOST_CC,$CC in + ,,) echo "int x;" > $dummy.c ; + for c in cc gcc c89 c99 ; do + if ($c $dummy.c -c -o $dummy.o) >/dev/null 2>&1 ; then + CC_FOR_BUILD="$c"; break ; + fi ; + done ; + rm -f $files ; + if test x"$CC_FOR_BUILD" = x ; then + CC_FOR_BUILD=no_compiler_found ; + fi + ;; + ,,*) CC_FOR_BUILD=$CC ;; + ,*,*) CC_FOR_BUILD=$HOST_CC ;; +esac ; +unset files' + +# This is needed to find uname on a Pyramid OSx when run in the BSD universe. +# (ghazi@noc.rutgers.edu 1994-08-24) +if (test -f /.attbin/uname) >/dev/null 2>&1 ; then + PATH=$PATH:/.attbin ; export PATH +fi + +UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown +UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown +UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown +UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown + +# Note: order is significant - the case branches are not exclusive. + +case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in + *:NetBSD:*:*) + # NetBSD (nbsd) targets should (where applicable) match one or + # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*, + # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently + # switched to ELF, *-*-netbsd* would select the old + # object file format. This provides both forward + # compatibility and a consistent mechanism for selecting the + # object file format. + # + # Note: NetBSD doesn't particularly care about the vendor + # portion of the name. We always set it to "unknown". + sysctl="sysctl -n hw.machine_arch" + UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \ + /usr/sbin/$sysctl 2>/dev/null || echo unknown)` + case "${UNAME_MACHINE_ARCH}" in + armeb) machine=armeb-unknown ;; + arm*) machine=arm-unknown ;; + sh3el) machine=shl-unknown ;; + sh3eb) machine=sh-unknown ;; + *) machine=${UNAME_MACHINE_ARCH}-unknown ;; + esac + # The Operating System including object format, if it has switched + # to ELF recently, or will in the future. + case "${UNAME_MACHINE_ARCH}" in + arm*|i386|m68k|ns32k|sh3*|sparc|vax) + eval $set_cc_for_build + if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep __ELF__ >/dev/null + then + # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). + # Return netbsd for either. FIX? + os=netbsd + else + os=netbsdelf + fi + ;; + *) + os=netbsd + ;; + esac + # The OS release + release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` + # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: + # contains redundant information, the shorter form: + # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. + echo "${machine}-${os}${release}" + exit 0 ;; + amiga:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + arc:OpenBSD:*:*) + echo mipsel-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + hp300:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + mac68k:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + macppc:OpenBSD:*:*) + echo powerpc-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + mvme68k:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + mvme88k:OpenBSD:*:*) + echo m88k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + mvmeppc:OpenBSD:*:*) + echo powerpc-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + pmax:OpenBSD:*:*) + echo mipsel-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + sgi:OpenBSD:*:*) + echo mipseb-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + sun3:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + wgrisc:OpenBSD:*:*) + echo mipsel-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + *:OpenBSD:*:*) + echo ${UNAME_MACHINE}-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + alpha:OSF1:*:*) + if test $UNAME_RELEASE = "V4.0"; then + UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` + fi + # A Vn.n version is a released version. + # A Tn.n version is a released field test version. + # A Xn.n version is an unreleased experimental baselevel. + # 1.2 uses "1.2" for uname -r. + eval $set_cc_for_build + cat <$dummy.s + .data +\$Lformat: + .byte 37,100,45,37,120,10,0 # "%d-%x\n" + + .text + .globl main + .align 4 + .ent main +main: + .frame \$30,16,\$26,0 + ldgp \$29,0(\$27) + .prologue 1 + .long 0x47e03d80 # implver \$0 + lda \$2,-1 + .long 0x47e20c21 # amask \$2,\$1 + lda \$16,\$Lformat + mov \$0,\$17 + not \$1,\$18 + jsr \$26,printf + ldgp \$29,0(\$26) + mov 0,\$16 + jsr \$26,exit + .end main +EOF + $CC_FOR_BUILD $dummy.s -o $dummy 2>/dev/null + if test "$?" = 0 ; then + case `$dummy` in + 0-0) + UNAME_MACHINE="alpha" + ;; + 1-0) + UNAME_MACHINE="alphaev5" + ;; + 1-1) + UNAME_MACHINE="alphaev56" + ;; + 1-101) + UNAME_MACHINE="alphapca56" + ;; + 2-303) + UNAME_MACHINE="alphaev6" + ;; + 2-307) + UNAME_MACHINE="alphaev67" + ;; + 2-1307) + UNAME_MACHINE="alphaev68" + ;; + 3-1307) + UNAME_MACHINE="alphaev7" + ;; + esac + fi + rm -f $dummy.s $dummy && rmdir $tmpdir + echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[VTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` + exit 0 ;; + Alpha\ *:Windows_NT*:*) + # How do we know it's Interix rather than the generic POSIX subsystem? + # Should we change UNAME_MACHINE based on the output of uname instead + # of the specific Alpha model? + echo alpha-pc-interix + exit 0 ;; + 21064:Windows_NT:50:3) + echo alpha-dec-winnt3.5 + exit 0 ;; + Amiga*:UNIX_System_V:4.0:*) + echo m68k-unknown-sysv4 + exit 0;; + *:[Aa]miga[Oo][Ss]:*:*) + echo ${UNAME_MACHINE}-unknown-amigaos + exit 0 ;; + *:[Mm]orph[Oo][Ss]:*:*) + echo ${UNAME_MACHINE}-unknown-morphos + exit 0 ;; + *:OS/390:*:*) + echo i370-ibm-openedition + exit 0 ;; + arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) + echo arm-acorn-riscix${UNAME_RELEASE} + exit 0;; + SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) + echo hppa1.1-hitachi-hiuxmpp + exit 0;; + Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) + # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. + if test "`(/bin/universe) 2>/dev/null`" = att ; then + echo pyramid-pyramid-sysv3 + else + echo pyramid-pyramid-bsd + fi + exit 0 ;; + NILE*:*:*:dcosx) + echo pyramid-pyramid-svr4 + exit 0 ;; + DRS?6000:UNIX_SV:4.2*:7*) + case `/usr/bin/uname -p` in + sparc) echo sparc-icl-nx7 && exit 0 ;; + esac ;; + sun4H:SunOS:5.*:*) + echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) + echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + i86pc:SunOS:5.*:*) + echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + sun4*:SunOS:6*:*) + # According to config.sub, this is the proper way to canonicalize + # SunOS6. Hard to guess exactly what SunOS6 will be like, but + # it's likely to be more like Solaris than SunOS4. + echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + sun4*:SunOS:*:*) + case "`/usr/bin/arch -k`" in + Series*|S4*) + UNAME_RELEASE=`uname -v` + ;; + esac + # Japanese Language versions have a version number like `4.1.3-JL'. + echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` + exit 0 ;; + sun3*:SunOS:*:*) + echo m68k-sun-sunos${UNAME_RELEASE} + exit 0 ;; + sun*:*:4.2BSD:*) + UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` + test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 + case "`/bin/arch`" in + sun3) + echo m68k-sun-sunos${UNAME_RELEASE} + ;; + sun4) + echo sparc-sun-sunos${UNAME_RELEASE} + ;; + esac + exit 0 ;; + aushp:SunOS:*:*) + echo sparc-auspex-sunos${UNAME_RELEASE} + exit 0 ;; + # The situation for MiNT is a little confusing. The machine name + # can be virtually everything (everything which is not + # "atarist" or "atariste" at least should have a processor + # > m68000). The system name ranges from "MiNT" over "FreeMiNT" + # to the lowercase version "mint" (or "freemint"). Finally + # the system name "TOS" denotes a system which is actually not + # MiNT. But MiNT is downward compatible to TOS, so this should + # be no problem. + atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit 0 ;; + atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit 0 ;; + *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit 0 ;; + milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) + echo m68k-milan-mint${UNAME_RELEASE} + exit 0 ;; + hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) + echo m68k-hades-mint${UNAME_RELEASE} + exit 0 ;; + *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) + echo m68k-unknown-mint${UNAME_RELEASE} + exit 0 ;; + powerpc:machten:*:*) + echo powerpc-apple-machten${UNAME_RELEASE} + exit 0 ;; + RISC*:Mach:*:*) + echo mips-dec-mach_bsd4.3 + exit 0 ;; + RISC*:ULTRIX:*:*) + echo mips-dec-ultrix${UNAME_RELEASE} + exit 0 ;; + VAX*:ULTRIX*:*:*) + echo vax-dec-ultrix${UNAME_RELEASE} + exit 0 ;; + 2020:CLIX:*:* | 2430:CLIX:*:*) + echo clipper-intergraph-clix${UNAME_RELEASE} + exit 0 ;; + mips:*:*:UMIPS | mips:*:*:RISCos) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c +#ifdef __cplusplus +#include /* for printf() prototype */ + int main (int argc, char *argv[]) { +#else + int main (argc, argv) int argc; char *argv[]; { +#endif + #if defined (host_mips) && defined (MIPSEB) + #if defined (SYSTYPE_SYSV) + printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_SVR4) + printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) + printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); + #endif + #endif + exit (-1); + } +EOF + $CC_FOR_BUILD $dummy.c -o $dummy \ + && $dummy `echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` \ + && rm -f $dummy.c $dummy && rmdir $tmpdir && exit 0 + rm -f $dummy.c $dummy && rmdir $tmpdir + echo mips-mips-riscos${UNAME_RELEASE} + exit 0 ;; + Motorola:PowerMAX_OS:*:*) + echo powerpc-motorola-powermax + exit 0 ;; + Night_Hawk:*:*:PowerMAX_OS) + echo powerpc-harris-powermax + exit 0 ;; + Night_Hawk:Power_UNIX:*:*) + echo powerpc-harris-powerunix + exit 0 ;; + m88k:CX/UX:7*:*) + echo m88k-harris-cxux7 + exit 0 ;; + m88k:*:4*:R4*) + echo m88k-motorola-sysv4 + exit 0 ;; + m88k:*:3*:R3*) + echo m88k-motorola-sysv3 + exit 0 ;; + AViiON:dgux:*:*) + # DG/UX returns AViiON for all architectures + UNAME_PROCESSOR=`/usr/bin/uname -p` + if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] + then + if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ + [ ${TARGET_BINARY_INTERFACE}x = x ] + then + echo m88k-dg-dgux${UNAME_RELEASE} + else + echo m88k-dg-dguxbcs${UNAME_RELEASE} + fi + else + echo i586-dg-dgux${UNAME_RELEASE} + fi + exit 0 ;; + M88*:DolphinOS:*:*) # DolphinOS (SVR3) + echo m88k-dolphin-sysv3 + exit 0 ;; + M88*:*:R3*:*) + # Delta 88k system running SVR3 + echo m88k-motorola-sysv3 + exit 0 ;; + XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) + echo m88k-tektronix-sysv3 + exit 0 ;; + Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) + echo m68k-tektronix-bsd + exit 0 ;; + *:IRIX*:*:*) + echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` + exit 0 ;; + ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. + echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id + exit 0 ;; # Note that: echo "'`uname -s`'" gives 'AIX ' + i*86:AIX:*:*) + echo i386-ibm-aix + exit 0 ;; + ia64:AIX:*:*) + if [ -x /usr/bin/oslevel ] ; then + IBM_REV=`/usr/bin/oslevel` + else + IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + fi + echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} + exit 0 ;; + *:AIX:2:3) + if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + + main() + { + if (!__power_pc()) + exit(1); + puts("powerpc-ibm-aix3.2.5"); + exit(0); + } +EOF + $CC_FOR_BUILD $dummy.c -o $dummy && $dummy && rm -f $dummy.c $dummy && rmdir $tmpdir && exit 0 + rm -f $dummy.c $dummy && rmdir $tmpdir + echo rs6000-ibm-aix3.2.5 + elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then + echo rs6000-ibm-aix3.2.4 + else + echo rs6000-ibm-aix3.2 + fi + exit 0 ;; + *:AIX:*:[45]) + IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` + if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then + IBM_ARCH=rs6000 + else + IBM_ARCH=powerpc + fi + if [ -x /usr/bin/oslevel ] ; then + IBM_REV=`/usr/bin/oslevel` + else + IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + fi + echo ${IBM_ARCH}-ibm-aix${IBM_REV} + exit 0 ;; + *:AIX:*:*) + echo rs6000-ibm-aix + exit 0 ;; + ibmrt:4.4BSD:*|romp-ibm:BSD:*) + echo romp-ibm-bsd4.4 + exit 0 ;; + ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and + echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to + exit 0 ;; # report: romp-ibm BSD 4.3 + *:BOSX:*:*) + echo rs6000-bull-bosx + exit 0 ;; + DPX/2?00:B.O.S.:*:*) + echo m68k-bull-sysv3 + exit 0 ;; + 9000/[34]??:4.3bsd:1.*:*) + echo m68k-hp-bsd + exit 0 ;; + hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) + echo m68k-hp-bsd4.4 + exit 0 ;; + 9000/[34678]??:HP-UX:*:*) + HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` + case "${UNAME_MACHINE}" in + 9000/31? ) HP_ARCH=m68000 ;; + 9000/[34]?? ) HP_ARCH=m68k ;; + 9000/[678][0-9][0-9]) + if [ -x /usr/bin/getconf ]; then + sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` + sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` + case "${sc_cpu_version}" in + 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 + 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 + 532) # CPU_PA_RISC2_0 + case "${sc_kernel_bits}" in + 32) HP_ARCH="hppa2.0n" ;; + 64) HP_ARCH="hppa2.0w" ;; + '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 + esac ;; + esac + fi + if [ "${HP_ARCH}" = "" ]; then + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + + #define _HPUX_SOURCE + #include + #include + + int main () + { + #if defined(_SC_KERNEL_BITS) + long bits = sysconf(_SC_KERNEL_BITS); + #endif + long cpu = sysconf (_SC_CPU_VERSION); + + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1"); break; + case CPU_PA_RISC2_0: + #if defined(_SC_KERNEL_BITS) + switch (bits) + { + case 64: puts ("hppa2.0w"); break; + case 32: puts ("hppa2.0n"); break; + default: puts ("hppa2.0"); break; + } break; + #else /* !defined(_SC_KERNEL_BITS) */ + puts ("hppa2.0"); break; + #endif + default: puts ("hppa1.0"); break; + } + exit (0); + } +EOF + (CCOPTS= $CC_FOR_BUILD $dummy.c -o $dummy 2>/dev/null) && HP_ARCH=`$dummy` + if test -z "$HP_ARCH"; then HP_ARCH=hppa; fi + rm -f $dummy.c $dummy && rmdir $tmpdir + fi ;; + esac + echo ${HP_ARCH}-hp-hpux${HPUX_REV} + exit 0 ;; + ia64:HP-UX:*:*) + HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` + echo ia64-hp-hpux${HPUX_REV} + exit 0 ;; + 3050*:HI-UX:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + int + main () + { + long cpu = sysconf (_SC_CPU_VERSION); + /* The order matters, because CPU_IS_HP_MC68K erroneously returns + true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct + results, however. */ + if (CPU_IS_PA_RISC (cpu)) + { + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; + case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; + default: puts ("hppa-hitachi-hiuxwe2"); break; + } + } + else if (CPU_IS_HP_MC68K (cpu)) + puts ("m68k-hitachi-hiuxwe2"); + else puts ("unknown-hitachi-hiuxwe2"); + exit (0); + } +EOF + $CC_FOR_BUILD $dummy.c -o $dummy && $dummy && rm -f $dummy.c $dummy && rmdir $tmpdir && exit 0 + rm -f $dummy.c $dummy && rmdir $tmpdir + echo unknown-hitachi-hiuxwe2 + exit 0 ;; + 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) + echo hppa1.1-hp-bsd + exit 0 ;; + 9000/8??:4.3bsd:*:*) + echo hppa1.0-hp-bsd + exit 0 ;; + *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) + echo hppa1.0-hp-mpeix + exit 0 ;; + hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) + echo hppa1.1-hp-osf + exit 0 ;; + hp8??:OSF1:*:*) + echo hppa1.0-hp-osf + exit 0 ;; + i*86:OSF1:*:*) + if [ -x /usr/sbin/sysversion ] ; then + echo ${UNAME_MACHINE}-unknown-osf1mk + else + echo ${UNAME_MACHINE}-unknown-osf1 + fi + exit 0 ;; + parisc*:Lites*:*:*) + echo hppa1.1-hp-lites + exit 0 ;; + C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) + echo c1-convex-bsd + exit 0 ;; + C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit 0 ;; + C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) + echo c34-convex-bsd + exit 0 ;; + C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) + echo c38-convex-bsd + exit 0 ;; + C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) + echo c4-convex-bsd + exit 0 ;; + CRAY*Y-MP:*:*:*) + echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*[A-Z]90:*:*:*) + echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ + | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ + -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ + -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*TS:*:*:*) + echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*T3D:*:*:*) + echo alpha-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*T3E:*:*:*) + echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*SV1:*:*:*) + echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) + FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` + echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit 0 ;; + i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) + echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} + exit 0 ;; + sparc*:BSD/OS:*:*) + echo sparc-unknown-bsdi${UNAME_RELEASE} + exit 0 ;; + *:BSD/OS:*:*) + echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} + exit 0 ;; + *:FreeBSD:*:*) + # Determine whether the default compiler uses glibc. + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + #if __GLIBC__ >= 2 + LIBC=gnu + #else + LIBC= + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=` + rm -f $dummy.c && rmdir $tmpdir + echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`${LIBC:+-$LIBC} + exit 0 ;; + i*:CYGWIN*:*) + echo ${UNAME_MACHINE}-pc-cygwin + exit 0 ;; + i*:MINGW*:*) + echo ${UNAME_MACHINE}-pc-mingw32 + exit 0 ;; + i*:PW*:*) + echo ${UNAME_MACHINE}-pc-pw32 + exit 0 ;; + x86:Interix*:3*) + echo i386-pc-interix3 + exit 0 ;; + i*:Windows_NT*:* | Pentium*:Windows_NT*:*) + # How do we know it's Interix rather than the generic POSIX subsystem? + # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we + # UNAME_MACHINE based on the output of uname instead of i386? + echo i386-pc-interix + exit 0 ;; + i*:UWIN*:*) + echo ${UNAME_MACHINE}-pc-uwin + exit 0 ;; + p*:CYGWIN*:*) + echo powerpcle-unknown-cygwin + exit 0 ;; + prep*:SunOS:5.*:*) + echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + *:GNU:*:*) + echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` + exit 0 ;; + i*86:Minix:*:*) + echo ${UNAME_MACHINE}-pc-minix + exit 0 ;; + arm*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + ia64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + m68*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + mips:Linux:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #undef CPU + #undef mips + #undef mipsel + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + CPU=mipsel + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + CPU=mips + #else + CPU= + #endif + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=` + rm -f $dummy.c && rmdir $tmpdir + test x"${CPU}" != x && echo "${CPU}-pc-linux-gnu" && exit 0 + ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu + exit 0 ;; + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-gnu + exit 0 ;; + alpha:Linux:*:*) + case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null + if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi + echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + exit 0 ;; + parisc:Linux:*:* | hppa:Linux:*:*) + # Look for CPU level + case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in + PA7*) echo hppa1.1-unknown-linux-gnu ;; + PA8*) echo hppa2.0-unknown-linux-gnu ;; + *) echo hppa-unknown-linux-gnu ;; + esac + exit 0 ;; + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-gnu + exit 0 ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo ${UNAME_MACHINE}-ibm-linux + exit 0 ;; + sh*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + sparc:Linux:*:* | sparc64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + x86_64:Linux:*:*) + echo x86_64-unknown-linux-gnu + exit 0 ;; + i*86:Linux:*:*) + # The BFD linker knows what the default object file format is, so + # first see if it will tell us. cd to the root directory to prevent + # problems with other programs or directories called `ld' in the path. + # Set LC_ALL=C to ensure ld outputs messages in English. + ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ + | sed -ne '/supported targets:/!d + s/[ ][ ]*/ /g + s/.*supported targets: *// + s/ .*// + p'` + case "$ld_supported_targets" in + elf32-i386) + TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" + ;; + a.out-i386-linux) + echo "${UNAME_MACHINE}-pc-linux-gnuaout" + exit 0 ;; + coff-i386) + echo "${UNAME_MACHINE}-pc-linux-gnucoff" + exit 0 ;; + "") + # Either a pre-BFD a.out linker (linux-gnuoldld) or + # one that does not give us useful --help. + echo "${UNAME_MACHINE}-pc-linux-gnuoldld" + exit 0 ;; + esac + # Determine whether the default compiler is a.out or elf + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + #ifdef __ELF__ + # ifdef __GLIBC__ + # if __GLIBC__ >= 2 + LIBC=gnu + # else + LIBC=gnulibc1 + # endif + # else + LIBC=gnulibc1 + # endif + #else + #ifdef __INTEL_COMPILER + LIBC=gnu + #else + LIBC=gnuaout + #endif + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=` + rm -f $dummy.c && rmdir $tmpdir + test x"${LIBC}" != x && echo "${UNAME_MACHINE}-pc-linux-${LIBC}" && exit 0 + test x"${TENTATIVE}" != x && echo "${TENTATIVE}" && exit 0 + ;; + i*86:DYNIX/ptx:4*:*) + # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. + # earlier versions are messed up and put the nodename in both + # sysname and nodename. + echo i386-sequent-sysv4 + exit 0 ;; + i*86:UNIX_SV:4.2MP:2.*) + # Unixware is an offshoot of SVR4, but it has its own version + # number series starting with 2... + # I am not positive that other SVR4 systems won't match this, + # I just have to hope. -- rms. + # Use sysv4.2uw... so that sysv4* matches it. + echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} + exit 0 ;; + i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) + UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` + if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then + echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} + else + echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} + fi + exit 0 ;; + i*86:*:5:[78]*) + case `/bin/uname -X | grep "^Machine"` in + *486*) UNAME_MACHINE=i486 ;; + *Pentium) UNAME_MACHINE=i586 ;; + *Pent*|*Celeron) UNAME_MACHINE=i686 ;; + esac + echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} + exit 0 ;; + i*86:*:3.2:*) + if test -f /usr/options/cb.name; then + UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then + UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` + (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 + (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ + && UNAME_MACHINE=i586 + (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ + && UNAME_MACHINE=i686 + (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ + && UNAME_MACHINE=i686 + echo ${UNAME_MACHINE}-pc-sco$UNAME_REL + else + echo ${UNAME_MACHINE}-pc-sysv32 + fi + exit 0 ;; + i*86:*DOS:*:*) + echo ${UNAME_MACHINE}-pc-msdosdjgpp + exit 0 ;; + pc:*:*:*) + # Left here for compatibility: + # uname -m prints for DJGPP always 'pc', but it prints nothing about + # the processor, so we play safe by assuming i386. + echo i386-pc-msdosdjgpp + exit 0 ;; + Intel:Mach:3*:*) + echo i386-pc-mach3 + exit 0 ;; + paragon:*:*:*) + echo i860-intel-osf1 + exit 0 ;; + i860:*:4.*:*) # i860-SVR4 + if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then + echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 + else # Add other i860-SVR4 vendors below as they are discovered. + echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 + fi + exit 0 ;; + mini*:CTIX:SYS*5:*) + # "miniframe" + echo m68010-convergent-sysv + exit 0 ;; + M68*:*:R3V[567]*:*) + test -r /sysV68 && echo 'm68k-motorola-sysv' && exit 0 ;; + 3[34]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0) + OS_REL='' + test -r /etc/.relid \ + && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && echo i486-ncr-sysv4.3${OS_REL} && exit 0 + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && echo i586-ncr-sysv4.3${OS_REL} && exit 0 ;; + 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && echo i486-ncr-sysv4 && exit 0 ;; + m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) + echo m68k-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + mc68030:UNIX_System_V:4.*:*) + echo m68k-atari-sysv4 + exit 0 ;; + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) + echo i386-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + TSUNAMI:LynxOS:2.*:*) + echo sparc-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + rs6000:LynxOS:2.*:*) + echo rs6000-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) + echo powerpc-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + SM[BE]S:UNIX_SV:*:*) + echo mips-dde-sysv${UNAME_RELEASE} + exit 0 ;; + RM*:ReliantUNIX-*:*:*) + echo mips-sni-sysv4 + exit 0 ;; + RM*:SINIX-*:*:*) + echo mips-sni-sysv4 + exit 0 ;; + *:SINIX-*:*:*) + if uname -p 2>/dev/null >/dev/null ; then + UNAME_MACHINE=`(uname -p) 2>/dev/null` + echo ${UNAME_MACHINE}-sni-sysv4 + else + echo ns32k-sni-sysv + fi + exit 0 ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says + echo i586-unisys-sysv4 + exit 0 ;; + *:UNIX_System_V:4*:FTX*) + # From Gerald Hewes . + # How about differentiating between stratus architectures? -djm + echo hppa1.1-stratus-sysv4 + exit 0 ;; + *:*:*:FTX*) + # From seanf@swdc.stratus.com. + echo i860-stratus-sysv4 + exit 0 ;; + *:VOS:*:*) + # From Paul.Green@stratus.com. + echo hppa1.1-stratus-vos + exit 0 ;; + mc68*:A/UX:*:*) + echo m68k-apple-aux${UNAME_RELEASE} + exit 0 ;; + news*:NEWS-OS:6*:*) + echo mips-sony-newsos6 + exit 0 ;; + R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) + if [ -d /usr/nec ]; then + echo mips-nec-sysv${UNAME_RELEASE} + else + echo mips-unknown-sysv${UNAME_RELEASE} + fi + exit 0 ;; + BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. + echo powerpc-be-beos + exit 0 ;; + BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. + echo powerpc-apple-beos + exit 0 ;; + BePC:BeOS:*:*) # BeOS running on Intel PC compatible. + echo i586-pc-beos + exit 0 ;; + SX-4:SUPER-UX:*:*) + echo sx4-nec-superux${UNAME_RELEASE} + exit 0 ;; + SX-5:SUPER-UX:*:*) + echo sx5-nec-superux${UNAME_RELEASE} + exit 0 ;; + Power*:Rhapsody:*:*) + echo powerpc-apple-rhapsody${UNAME_RELEASE} + exit 0 ;; + *:Rhapsody:*:*) + echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} + exit 0 ;; + *:Darwin:*:*) + echo `uname -p`-apple-darwin${UNAME_RELEASE} + exit 0 ;; + *:procnto*:*:* | *:QNX:[0123456789]*:*) + UNAME_PROCESSOR=`uname -p` + if test "$UNAME_PROCESSOR" = "x86"; then + UNAME_PROCESSOR=i386 + UNAME_MACHINE=pc + fi + echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} + exit 0 ;; + *:QNX:*:4*) + echo i386-pc-qnx + exit 0 ;; + NSR-[GKLNPTVW]:NONSTOP_KERNEL:*:*) + echo nsr-tandem-nsk${UNAME_RELEASE} + exit 0 ;; + *:NonStop-UX:*:*) + echo mips-compaq-nonstopux + exit 0 ;; + BS2000:POSIX*:*:*) + echo bs2000-siemens-sysv + exit 0 ;; + DS/*:UNIX_System_V:*:*) + echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} + exit 0 ;; + *:Plan9:*:*) + # "uname -m" is not consistent, so use $cputype instead. 386 + # is converted to i386 for consistency with other x86 + # operating systems. + if test "$cputype" = "386"; then + UNAME_MACHINE=i386 + else + UNAME_MACHINE="$cputype" + fi + echo ${UNAME_MACHINE}-unknown-plan9 + exit 0 ;; + i*86:OS/2:*:*) + # If we were able to find `uname', then EMX Unix compatibility + # is probably installed. + echo ${UNAME_MACHINE}-pc-os2-emx + exit 0 ;; + *:TOPS-10:*:*) + echo pdp10-unknown-tops10 + exit 0 ;; + *:TENEX:*:*) + echo pdp10-unknown-tenex + exit 0 ;; + KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) + echo pdp10-dec-tops20 + exit 0 ;; + XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) + echo pdp10-xkl-tops20 + exit 0 ;; + *:TOPS-20:*:*) + echo pdp10-unknown-tops20 + exit 0 ;; + *:ITS:*:*) + echo pdp10-unknown-its + exit 0 ;; + i*86:XTS-300:*:STOP) + echo ${UNAME_MACHINE}-unknown-stop + exit 0 ;; + i*86:atheos:*:*) + echo ${UNAME_MACHINE}-unknown-atheos + exit 0 ;; +esac + +#echo '(No uname command or uname output not recognized.)' 1>&2 +#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 + +eval $set_cc_for_build +cat >$dummy.c < +# include +#endif +main () +{ +#if defined (sony) +#if defined (MIPSEB) + /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, + I don't know.... */ + printf ("mips-sony-bsd\n"); exit (0); +#else +#include + printf ("m68k-sony-newsos%s\n", +#ifdef NEWSOS4 + "4" +#else + "" +#endif + ); exit (0); +#endif +#endif + +#if defined (__arm) && defined (__acorn) && defined (__unix) + printf ("arm-acorn-riscix"); exit (0); +#endif + +#if defined (hp300) && !defined (hpux) + printf ("m68k-hp-bsd\n"); exit (0); +#endif + +#if defined (NeXT) +#if !defined (__ARCHITECTURE__) +#define __ARCHITECTURE__ "m68k" +#endif + int version; + version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; + if (version < 4) + printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); + else + printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); + exit (0); +#endif + +#if defined (MULTIMAX) || defined (n16) +#if defined (UMAXV) + printf ("ns32k-encore-sysv\n"); exit (0); +#else +#if defined (CMU) + printf ("ns32k-encore-mach\n"); exit (0); +#else + printf ("ns32k-encore-bsd\n"); exit (0); +#endif +#endif +#endif + +#if defined (__386BSD__) + printf ("i386-pc-bsd\n"); exit (0); +#endif + +#if defined (sequent) +#if defined (i386) + printf ("i386-sequent-dynix\n"); exit (0); +#endif +#if defined (ns32000) + printf ("ns32k-sequent-dynix\n"); exit (0); +#endif +#endif + +#if defined (_SEQUENT_) + struct utsname un; + + uname(&un); + + if (strncmp(un.version, "V2", 2) == 0) { + printf ("i386-sequent-ptx2\n"); exit (0); + } + if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ + printf ("i386-sequent-ptx1\n"); exit (0); + } + printf ("i386-sequent-ptx\n"); exit (0); + +#endif + +#if defined (vax) +# if !defined (ultrix) +# include +# if defined (BSD) +# if BSD == 43 + printf ("vax-dec-bsd4.3\n"); exit (0); +# else +# if BSD == 199006 + printf ("vax-dec-bsd4.3reno\n"); exit (0); +# else + printf ("vax-dec-bsd\n"); exit (0); +# endif +# endif +# else + printf ("vax-dec-bsd\n"); exit (0); +# endif +# else + printf ("vax-dec-ultrix\n"); exit (0); +# endif +#endif + +#if defined (alliant) && defined (i860) + printf ("i860-alliant-bsd\n"); exit (0); +#endif + + exit (1); +} +EOF + +$CC_FOR_BUILD $dummy.c -o $dummy 2>/dev/null && $dummy && rm -f $dummy.c $dummy && rmdir $tmpdir && exit 0 +rm -f $dummy.c $dummy && rmdir $tmpdir + +# Apollos put the system type in the environment. + +test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit 0; } + +# Convex versions that predate uname can use getsysinfo(1) + +if [ -x /usr/convex/getsysinfo ] +then + case `getsysinfo -f cpu_type` in + c1*) + echo c1-convex-bsd + exit 0 ;; + c2*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit 0 ;; + c34*) + echo c34-convex-bsd + exit 0 ;; + c38*) + echo c38-convex-bsd + exit 0 ;; + c4*) + echo c4-convex-bsd + exit 0 ;; + esac +fi + +cat >&2 < in order to provide the needed +information to handle your system. + +config.guess timestamp = $timestamp + +uname -m = `(uname -m) 2>/dev/null || echo unknown` +uname -r = `(uname -r) 2>/dev/null || echo unknown` +uname -s = `(uname -s) 2>/dev/null || echo unknown` +uname -v = `(uname -v) 2>/dev/null || echo unknown` + +/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` +/bin/uname -X = `(/bin/uname -X) 2>/dev/null` + +hostinfo = `(hostinfo) 2>/dev/null` +/bin/universe = `(/bin/universe) 2>/dev/null` +/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` +/bin/arch = `(/bin/arch) 2>/dev/null` +/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` +/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` + +UNAME_MACHINE = ${UNAME_MACHINE} +UNAME_RELEASE = ${UNAME_RELEASE} +UNAME_SYSTEM = ${UNAME_SYSTEM} +UNAME_VERSION = ${UNAME_VERSION} +EOF + +exit 1 + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.h new file mode 100755 index 000000000..2ae6546d3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.h @@ -0,0 +1,74 @@ +/* config.h. Generated by configure. */ +/* config.h.in. Generated from configure.in by autoheader. */ + +/* Define to 1 if you have the header file. */ +#define HAVE_INTTYPES_H 1 + +/* Define to 1 if you have the `g2' library (-lg2). */ +#define HAVE_LIBG2 1 + +/* Define to 1 if you have the `gd' library (-lgd). */ +/* #undef HAVE_LIBGD */ + +/* Define to 1 if you have the `RNA' library (-lRNA). */ +#define HAVE_LIBRNA 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_MEMORY_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STDINT_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STDLIB_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STRINGS_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STRING_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_SYS_STAT_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_SYS_TYPES_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_UNISTD_H 1 + +/* Name of package */ +#define PACKAGE "RNAforester" + +/* Define to the address where bug reports for this package should be sent. */ +#define PACKAGE_BUGREPORT "mhoechsm@techfak.uni-bielefeld.de" + +/* Define to the full name of this package. */ +#define PACKAGE_NAME "RNAforester" + +/* Define to the full name and version of this package. */ +#define PACKAGE_STRING "RNAforester 1.5" + +/* Define to the one symbol short name of this package. */ +#define PACKAGE_TARNAME "RNAforester" + +/* Define to the version of this package. */ +#define PACKAGE_VERSION "1.5" + +/* Define to 1 if you have the ANSI C header files. */ +/* #undef STDC_HEADERS */ + +/* Version number of package */ +#define VERSION "1.5" + +/* Define to empty if `const' does not conform to ANSI C. */ +/* #undef const */ + +/* Define to `__inline__' or `__inline' if that's what the C compiler + calls it, or to nothing if 'inline' is not supported under any name. */ +#ifndef __cplusplus +/* #undef inline */ +#endif + +/* Define to `unsigned' if does not define. */ +/* #undef size_t */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.h.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.h.in new file mode 100755 index 000000000..ab253a9cf --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.h.in @@ -0,0 +1,73 @@ +/* config.h.in. Generated from configure.in by autoheader. */ + +/* Define to 1 if you have the header file. */ +#undef HAVE_INTTYPES_H + +/* Define to 1 if you have the `g2' library (-lg2). */ +#undef HAVE_LIBG2 + +/* Define to 1 if you have the `gd' library (-lgd). */ +#undef HAVE_LIBGD + +/* Define to 1 if you have the `RNA' library (-lRNA). */ +#undef HAVE_LIBRNA + +/* Define to 1 if you have the header file. */ +#undef HAVE_MEMORY_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDINT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDLIB_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRINGS_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRING_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_STAT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_TYPES_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_UNISTD_H + +/* Name of package */ +#undef PACKAGE + +/* Define to the address where bug reports for this package should be sent. */ +#undef PACKAGE_BUGREPORT + +/* Define to the full name of this package. */ +#undef PACKAGE_NAME + +/* Define to the full name and version of this package. */ +#undef PACKAGE_STRING + +/* Define to the one symbol short name of this package. */ +#undef PACKAGE_TARNAME + +/* Define to the version of this package. */ +#undef PACKAGE_VERSION + +/* Define to 1 if you have the ANSI C header files. */ +#undef STDC_HEADERS + +/* Version number of package */ +#undef VERSION + +/* Define to empty if `const' does not conform to ANSI C. */ +#undef const + +/* Define to `__inline__' or `__inline' if that's what the C compiler + calls it, or to nothing if 'inline' is not supported under any name. */ +#ifndef __cplusplus +#undef inline +#endif + +/* Define to `unsigned' if does not define. */ +#undef size_t diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.log b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.log new file mode 100755 index 000000000..6bb87a562 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.log @@ -0,0 +1,675 @@ +This file contains any messages produced by compilers while +running configure, to aid debugging if configure makes a mistake. + +It was created by RNAforester configure 1.5, which was +generated by GNU Autoconf 2.59. Invocation command line was + + $ ./configure --prefix=/usr/local --cache-file=/dev/null --srcdir=. + +## --------- ## +## Platform. ## +## --------- ## + +hostname = mcluster02 +uname -m = x86_64 +uname -r = 2.6.9-34.ELsmp +uname -s = Linux +uname -v = #1 SMP Fri Feb 24 16:56:28 EST 2006 + +/usr/bin/uname -p = unknown +/bin/uname -X = unknown + +/bin/arch = x86_64 +/usr/bin/arch -k = unknown +/usr/convex/getsysinfo = unknown +hostinfo = unknown +/bin/machine = unknown +/usr/bin/oslevel = unknown +/bin/universe = unknown + +PATH: /storage/appl/n1ge6u7/bin/lx24-amd64 +PATH: /opt/sun/n1gc/bin +PATH: /usr/local/bin +PATH: /bin +PATH: /usr/bin +PATH: /opt/c3-4/ +PATH: /usr/X11R6/bin +PATH: /usr/local/bin +PATH: /usr/local/bin/X11R5 +PATH: /usr/local/X11R5/bin +PATH: /usr/X11R6/bin +PATH: /home/rabani/Develop/perl/GeneXPress +PATH: /home/rabani/Develop/perl/Genome +PATH: /home/rabani/Develop/perl/Lib +PATH: /home/rabani/Develop/perl/Parsers +PATH: /home/rabani/Develop/perl/RNA +PATH: /home/rabani/Develop/perl/Sequence +PATH: /home/rabani/Develop/perl/System +PATH: /home/rabani/Develop/perl/Web +PATH: /home/rabani/Develop/perl/Web/DataDir +PATH: /home/rabani/Develop/genie_release64/Programs +PATH: /storage/appl/matlab14.3/bin +PATH: /home/rabani + + +## ----------- ## +## Core tests. ## +## ----------- ## + +configure:1369: checking for a BSD-compatible install +configure:1424: result: /usr/bin/install -c +configure:1435: checking whether build environment is sane +configure:1478: result: yes +configure:1543: checking for gawk +configure:1559: found /bin/gawk +configure:1569: result: gawk +configure:1579: checking whether make sets $(MAKE) +configure:1599: result: yes +configure:1823: checking for g++ +configure:1839: found /usr/bin/g++ +configure:1849: result: g++ +configure:1865: checking for C++ compiler version +configure:1868: g++ --version &5 +g++ (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2) +Copyright (C) 2004 Free Software Foundation, Inc. +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + +configure:1871: $? = 0 +configure:1873: g++ -v &5 +Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.5/specs +Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux +Thread model: posix +gcc version 3.4.5 20051201 (Red Hat 3.4.5-2) +configure:1876: $? = 0 +configure:1878: g++ -V &5 +g++: `-V' option must have argument +configure:1881: $? = 1 +configure:1904: checking for C++ compiler default output file name +configure:1907: g++ conftest.cc >&5 +configure:1910: $? = 0 +configure:1956: result: a.out +configure:1961: checking whether the C++ compiler works +configure:1967: ./a.out +configure:1970: $? = 0 +configure:1987: result: yes +configure:1994: checking whether we are cross compiling +configure:1996: result: no +configure:1999: checking for suffix of executables +configure:2001: g++ -o conftest conftest.cc >&5 +configure:2004: $? = 0 +configure:2029: result: +configure:2035: checking for suffix of object files +configure:2056: g++ -c conftest.cc >&5 +configure:2059: $? = 0 +configure:2081: result: o +configure:2085: checking whether we are using the GNU C++ compiler +configure:2109: g++ -c conftest.cc >&5 +configure:2115: $? = 0 +configure:2119: test -z + || test ! -s conftest.err +configure:2122: $? = 0 +configure:2125: test -s conftest.o +configure:2128: $? = 0 +configure:2141: result: yes +configure:2147: checking whether g++ accepts -g +configure:2168: g++ -c -g conftest.cc >&5 +configure:2174: $? = 0 +configure:2178: test -z + || test ! -s conftest.err +configure:2181: $? = 0 +configure:2184: test -s conftest.o +configure:2187: $? = 0 +configure:2198: result: yes +configure:2240: g++ -c -g -O2 conftest.cc >&5 +configure:2246: $? = 0 +configure:2250: test -z + || test ! -s conftest.err +configure:2253: $? = 0 +configure:2256: test -s conftest.o +configure:2259: $? = 0 +configure:2285: g++ -c -g -O2 conftest.cc >&5 +conftest.cc: In function `int main()': +conftest.cc:15: error: `exit' was not declared in this scope +configure:2291: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "RNAforester" +| #define PACKAGE_TARNAME "RNAforester" +| #define PACKAGE_VERSION "1.5" +| #define PACKAGE_STRING "RNAforester 1.5" +| #define PACKAGE_BUGREPORT "mhoechsm@techfak.uni-bielefeld.de" +| #define PACKAGE "RNAforester" +| #define VERSION "1.5" +| /* end confdefs.h. */ +| +| int +| main () +| { +| exit (42); +| ; +| return 0; +| } +configure:2240: g++ -c -g -O2 conftest.cc >&5 +configure:2246: $? = 0 +configure:2250: test -z + || test ! -s conftest.err +configure:2253: $? = 0 +configure:2256: test -s conftest.o +configure:2259: $? = 0 +configure:2285: g++ -c -g -O2 conftest.cc >&5 +configure:2291: $? = 0 +configure:2295: test -z + || test ! -s conftest.err +configure:2298: $? = 0 +configure:2301: test -s conftest.o +configure:2304: $? = 0 +configure:2338: checking for style of include used by make +configure:2366: result: GNU +configure:2394: checking dependency style of g++ +configure:2484: result: gcc3 +configure:2547: checking for gcc +configure:2563: found /usr/bin/gcc +configure:2573: result: gcc +configure:2817: checking for C compiler version +configure:2820: gcc --version &5 +gcc (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2) +Copyright (C) 2004 Free Software Foundation, Inc. +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + +configure:2823: $? = 0 +configure:2825: gcc -v &5 +Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.5/specs +Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux +Thread model: posix +gcc version 3.4.5 20051201 (Red Hat 3.4.5-2) +configure:2828: $? = 0 +configure:2830: gcc -V &5 +gcc: `-V' option must have argument +configure:2833: $? = 1 +configure:2836: checking whether we are using the GNU C compiler +configure:2860: gcc -c conftest.c >&5 +configure:2866: $? = 0 +configure:2870: test -z + || test ! -s conftest.err +configure:2873: $? = 0 +configure:2876: test -s conftest.o +configure:2879: $? = 0 +configure:2892: result: yes +configure:2898: checking whether gcc accepts -g +configure:2919: gcc -c -g conftest.c >&5 +configure:2925: $? = 0 +configure:2929: test -z + || test ! -s conftest.err +configure:2932: $? = 0 +configure:2935: test -s conftest.o +configure:2938: $? = 0 +configure:2949: result: yes +configure:2966: checking for gcc option to accept ANSI C +configure:3036: gcc -c -g -O2 conftest.c >&5 +configure:3042: $? = 0 +configure:3046: test -z + || test ! -s conftest.err +configure:3049: $? = 0 +configure:3052: test -s conftest.o +configure:3055: $? = 0 +configure:3073: result: none needed +configure:3091: gcc -c -g -O2 conftest.c >&5 +conftest.c:2: error: syntax error before "me" +configure:3097: $? = 1 +configure: failed program was: +| #ifndef __cplusplus +| choke me +| #endif +configure:3232: checking dependency style of gcc +configure:3322: result: gcc3 +configure:3364: result: using (to be built) libRNA.a in ../lib +configure:3376: checking for gdImageLine in -lgd +configure:3406: g++ -o conftest -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ -L../../lib conftest.cc -lgd -lRNA >&5 +/usr/bin/ld: cannot find -lRNA +collect2: ld returned 1 exit status +configure:3412: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "RNAforester" +| #define PACKAGE_TARNAME "RNAforester" +| #define PACKAGE_VERSION "1.5" +| #define PACKAGE_STRING "RNAforester 1.5" +| #define PACKAGE_BUGREPORT "mhoechsm@techfak.uni-bielefeld.de" +| #define PACKAGE "RNAforester" +| #define VERSION "1.5" +| #ifdef __cplusplus +| extern "C" void std::exit (int) throw (); using std::exit; +| #endif +| #define HAVE_LIBRNA 1 +| /* end confdefs.h. */ +| +| /* Override any gcc2 internal prototype to avoid an error. */ +| #ifdef __cplusplus +| extern "C" +| #endif +| /* We use char because int might match the return type of a gcc2 +| builtin and then its argument prototype would still apply. */ +| char gdImageLine (); +| int +| main () +| { +| gdImageLine (); +| ; +| return 0; +| } +configure:3438: result: no +configure:3455: checking how to run the C++ preprocessor +configure:3486: g++ -E -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc +configure:3492: $? = 0 +configure:3524: g++ -E -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc +conftest.cc:15:28: ac_nonexistent.h: No such file or directory +configure:3530: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "RNAforester" +| #define PACKAGE_TARNAME "RNAforester" +| #define PACKAGE_VERSION "1.5" +| #define PACKAGE_STRING "RNAforester 1.5" +| #define PACKAGE_BUGREPORT "mhoechsm@techfak.uni-bielefeld.de" +| #define PACKAGE "RNAforester" +| #define VERSION "1.5" +| #ifdef __cplusplus +| extern "C" void std::exit (int) throw (); using std::exit; +| #endif +| #define HAVE_LIBRNA 1 +| /* end confdefs.h. */ +| #include +configure:3569: result: g++ -E +configure:3593: g++ -E -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc +configure:3599: $? = 0 +configure:3631: g++ -E -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc +conftest.cc:15:28: ac_nonexistent.h: No such file or directory +configure:3637: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "RNAforester" +| #define PACKAGE_TARNAME "RNAforester" +| #define PACKAGE_VERSION "1.5" +| #define PACKAGE_STRING "RNAforester 1.5" +| #define PACKAGE_BUGREPORT "mhoechsm@techfak.uni-bielefeld.de" +| #define PACKAGE "RNAforester" +| #define VERSION "1.5" +| #ifdef __cplusplus +| extern "C" void std::exit (int) throw (); using std::exit; +| #endif +| #define HAVE_LIBRNA 1 +| /* end confdefs.h. */ +| #include +configure:3681: checking for egrep +configure:3691: result: grep -E +configure:3696: checking for ANSI C header files +configure:3721: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3727: $? = 0 +configure:3731: test -z + || test ! -s conftest.err +configure:3734: $? = 0 +configure:3737: test -s conftest.o +configure:3740: $? = 0 +configure:3829: g++ -o conftest -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ -L../../lib conftest.cc -lRNA >&5 +/usr/bin/ld: cannot find -lRNA +collect2: ld returned 1 exit status +configure:3832: $? = 1 +configure: program exited with status 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "RNAforester" +| #define PACKAGE_TARNAME "RNAforester" +| #define PACKAGE_VERSION "1.5" +| #define PACKAGE_STRING "RNAforester 1.5" +| #define PACKAGE_BUGREPORT "mhoechsm@techfak.uni-bielefeld.de" +| #define PACKAGE "RNAforester" +| #define VERSION "1.5" +| #ifdef __cplusplus +| extern "C" void std::exit (int) throw (); using std::exit; +| #endif +| #define HAVE_LIBRNA 1 +| /* end confdefs.h. */ +| #include +| #if ((' ' & 0x0FF) == 0x020) +| # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +| # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +| #else +| # define ISLOWER(c) (('a' <= (c) && (c) <= 'i') || ('j' <= (c) && (c) <= 'r') || ('s' <= (c) && (c) <= 'z')) +| # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +| #endif +| +| #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +| int +| main () +| { +| int i; +| for (i = 0; i < 256; i++) +| if (XOR (islower (i), ISLOWER (i)) +| || toupper (i) != TOUPPER (i)) +| exit(2); +| exit (0); +| } +configure:3852: result: no +configure:3876: checking for sys/types.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3876: checking for sys/stat.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3876: checking for stdlib.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3876: checking for string.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3876: checking for memory.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3876: checking for strings.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3876: checking for inttypes.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3876: checking for stdint.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3876: checking for unistd.h +configure:3892: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3898: $? = 0 +configure:3902: test -z + || test ! -s conftest.err +configure:3905: $? = 0 +configure:3908: test -s conftest.o +configure:3911: $? = 0 +configure:3922: result: yes +configure:3944: checking g2.h usability +configure:3956: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:3962: $? = 0 +configure:3966: test -z + || test ! -s conftest.err +configure:3969: $? = 0 +configure:3972: test -s conftest.o +configure:3975: $? = 0 +configure:3985: result: yes +configure:3989: checking g2.h presence +configure:3999: g++ -E -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc +configure:4005: $? = 0 +configure:4025: result: yes +configure:4060: checking for g2.h +configure:4067: result: yes +configure:4084: checking for an ANSI C-conforming const +configure:4151: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:4157: $? = 0 +configure:4161: test -z + || test ! -s conftest.err +configure:4164: $? = 0 +configure:4167: test -s conftest.o +configure:4170: $? = 0 +configure:4181: result: yes +configure:4191: checking for inline +configure:4212: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:4218: $? = 0 +configure:4222: test -z + || test ! -s conftest.err +configure:4225: $? = 0 +configure:4228: test -s conftest.o +configure:4231: $? = 0 +configure:4243: result: inline +configure:4262: checking for size_t +configure:4286: g++ -c -g -O2 -Ig2-0.70/src/ -Lg2-0.70/ conftest.cc >&5 +configure:4292: $? = 0 +configure:4296: test -z + || test ! -s conftest.err +configure:4299: $? = 0 +configure:4302: test -s conftest.o +configure:4305: $? = 0 +configure:4316: result: yes +configure:4463: creating ./config.status + +## ---------------------- ## +## Running config.status. ## +## ---------------------- ## + +This file was extended by RNAforester config.status 1.5, which was +generated by GNU Autoconf 2.59. Invocation command line was + + CONFIG_FILES = + CONFIG_HEADERS = + CONFIG_LINKS = + CONFIG_COMMANDS = + $ ./config.status + +on mcluster02 + +config.status:698: creating Makefile +config.status:698: creating src/Makefile +config.status:698: creating man/Makefile +config.status:802: creating config.h +config.status:910: config.h is unchanged +config.status:1090: executing depfiles commands +configure:5803: configuring in g2-0.70 +configure:5920: running /bin/sh './configure' --prefix=/usr/local '--prefix=/usr/local' '--cache-file=/dev/null' '--srcdir=.' --cache-file=/dev/null --srcdir=. + +## ---------------- ## +## Cache variables. ## +## ---------------- ## + +ac_cv_c_compiler_gnu=yes +ac_cv_c_const=yes +ac_cv_c_inline=inline +ac_cv_cxx_compiler_gnu=yes +ac_cv_env_CC_set= +ac_cv_env_CC_value= +ac_cv_env_CFLAGS_set= +ac_cv_env_CFLAGS_value= +ac_cv_env_CPPFLAGS_set= +ac_cv_env_CPPFLAGS_value= +ac_cv_env_CXXCPP_set= +ac_cv_env_CXXCPP_value= +ac_cv_env_CXXFLAGS_set= +ac_cv_env_CXXFLAGS_value= +ac_cv_env_CXX_set= +ac_cv_env_CXX_value= +ac_cv_env_LDFLAGS_set= +ac_cv_env_LDFLAGS_value= +ac_cv_env_build_alias_set= +ac_cv_env_build_alias_value= +ac_cv_env_host_alias_set= +ac_cv_env_host_alias_value= +ac_cv_env_target_alias_set= +ac_cv_env_target_alias_value= +ac_cv_exeext= +ac_cv_header_g2_h=yes +ac_cv_header_inttypes_h=yes +ac_cv_header_memory_h=yes +ac_cv_header_stdc=no +ac_cv_header_stdint_h=yes +ac_cv_header_stdlib_h=yes +ac_cv_header_string_h=yes +ac_cv_header_strings_h=yes +ac_cv_header_sys_stat_h=yes +ac_cv_header_sys_types_h=yes +ac_cv_header_unistd_h=yes +ac_cv_lib_gd_gdImageLine=no +ac_cv_objext=o +ac_cv_path_install='/usr/bin/install -c' +ac_cv_prog_AWK=gawk +ac_cv_prog_CXXCPP='g++ -E' +ac_cv_prog_ac_ct_CC=gcc +ac_cv_prog_ac_ct_CXX=g++ +ac_cv_prog_cc_g=yes +ac_cv_prog_cc_stdc= +ac_cv_prog_cxx_g=yes +ac_cv_prog_egrep='grep -E' +ac_cv_prog_make_make_set=yes +ac_cv_type_size_t=yes +am_cv_CC_dependencies_compiler_type=gcc3 +am_cv_CXX_dependencies_compiler_type=gcc3 + +## ----------------- ## +## Output variables. ## +## ----------------- ## + +ACLOCAL='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing --run aclocal-1.9' +AMDEPBACKSLASH='\' +AMDEP_FALSE='#' +AMDEP_TRUE='' +AMTAR='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing --run tar' +AUTOCONF='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing --run autoconf' +AUTOHEADER='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing --run autoheader' +AUTOMAKE='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing --run automake-1.9' +AWK='gawk' +CC='gcc' +CCDEPMODE='depmode=gcc3' +CFLAGS='-g -O2' +CPPFLAGS=' -I../g2-0.70/include/' +CXX='g++' +CXXCPP='g++ -E' +CXXDEPMODE='depmode=gcc3' +CXXFLAGS='-g -O2' +CYGPATH_W='echo' +DEFS='-DHAVE_CONFIG_H' +DEPDIR='.deps' +ECHO_C='' +ECHO_N='-n' +ECHO_T='' +EGREP='grep -E' +EXEEXT='' +INSTALL_DATA='${INSTALL} -m 644' +INSTALL_PROGRAM='${INSTALL}' +INSTALL_SCRIPT='${INSTALL}' +INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s' +LDFLAGS='-L../g2-0.70 -L../../lib ' +LIBOBJS='' +LIBS='-lg2 -lRNA ' +LTLIBOBJS='' +MAKEINFO='${SHELL} /home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing --run makeinfo' +OBJEXT='o' +PACKAGE='RNAforester' +PACKAGE_BUGREPORT='mhoechsm@techfak.uni-bielefeld.de' +PACKAGE_NAME='RNAforester' +PACKAGE_STRING='RNAforester 1.5' +PACKAGE_TARNAME='RNAforester' +PACKAGE_VERSION='1.5' +PATH_SEPARATOR=':' +SET_MAKE='' +SHELL='/bin/sh' +STRIP='' +VERSION='1.5' +ac_ct_CC='gcc' +ac_ct_CXX='g++' +ac_ct_STRIP='' +am__fastdepCC_FALSE='#' +am__fastdepCC_TRUE='' +am__fastdepCXX_FALSE='#' +am__fastdepCXX_TRUE='' +am__include='include' +am__leading_dot='.' +am__quote='' +am__tar='${AMTAR} chof - "$$tardir"' +am__untar='${AMTAR} xf -' +bindir='${exec_prefix}/bin' +build_alias='' +datadir='${prefix}/share' +exec_prefix='${prefix}' +host_alias='' +includedir='${prefix}/include' +infodir='${prefix}/info' +install_sh='/home/rabani/Genie/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/install-sh' +libdir='${exec_prefix}/lib' +libexecdir='${exec_prefix}/libexec' +localstatedir='${prefix}/var' +mandir='${prefix}/man' +mkdir_p='mkdir -p --' +oldincludedir='/usr/include' +prefix='/usr/local' +program_transform_name='s,x,x,' +sbindir='${exec_prefix}/sbin' +sharedstatedir='${prefix}/com' +subdirs=' g2-0.70' +sysconfdir='${prefix}/etc' +target_alias='' + +## ----------- ## +## confdefs.h. ## +## ----------- ## + +#define HAVE_INTTYPES_H 1 +#define HAVE_LIBG2 1 +#define HAVE_LIBRNA 1 +#define HAVE_MEMORY_H 1 +#define HAVE_STDINT_H 1 +#define HAVE_STDLIB_H 1 +#define HAVE_STRINGS_H 1 +#define HAVE_STRING_H 1 +#define HAVE_SYS_STAT_H 1 +#define HAVE_SYS_TYPES_H 1 +#define HAVE_UNISTD_H 1 +#define PACKAGE "RNAforester" +#define PACKAGE_BUGREPORT "mhoechsm@techfak.uni-bielefeld.de" +#define PACKAGE_NAME "RNAforester" +#define PACKAGE_STRING "RNAforester 1.5" +#define PACKAGE_TARNAME "RNAforester" +#define PACKAGE_VERSION "1.5" +#define VERSION "1.5" +#endif +#ifdef __cplusplus +extern "C" void std::exit (int) throw (); using std::exit; + +configure: exit 0 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.status b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.status new file mode 100755 index 000000000..fe67d98ce --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/config.status @@ -0,0 +1,1181 @@ +#! /bin/sh +# Generated by configure. +# Run this file to recreate the current configuration. +# Compiler output produced by configure, useful for debugging +# configure, is in config.log if it exists. + +debug=false +ac_cs_recheck=false +ac_cs_silent=false +SHELL=${CONFIG_SHELL-/bin/sh} +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## + +# Be Bourne compatible +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' +elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then + set -o posix +fi +DUALCASE=1; export DUALCASE # for MKS sh + +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + + +# Work around bugs in pre-3.0 UWIN ksh. +$as_unset ENV MAIL MAILPATH +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +for as_var in \ + LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ + LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ + LC_TELEPHONE LC_TIME +do + if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then + eval $as_var=C; export $as_var + else + $as_unset $as_var + fi +done + +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)$' \| \ + . : '\(.\)' 2>/dev/null || +echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } + /^X\/\(\/\/\)$/{ s//\1/; q; } + /^X\/\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + + +# PATH needs CR, and LINENO needs CR and PATH. +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + echo "#! /bin/sh" >conf$$.sh + echo "exit 0" >>conf$$.sh + chmod +x conf$$.sh + if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then + PATH_SEPARATOR=';' + else + PATH_SEPARATOR=: + fi + rm -f conf$$.sh +fi + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" || { + # Find who we are. Look in the path if we contain no path at all + # relative or not. + case $0 in + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done + + ;; + esac + # We did not find ourselves, most probably we were run as `sh COMMAND' + # in which case we are not to be found in the path. + if test "x$as_myself" = x; then + as_myself=$0 + fi + if test ! -f "$as_myself"; then + { { echo "$as_me:$LINENO: error: cannot find myself; rerun with an absolute path" >&5 +echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2;} + { (exit 1); exit 1; }; } + fi + case $CONFIG_SHELL in + '') + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for as_base in sh bash ksh sh5; do + case $as_dir in + /*) + if ("$as_dir/$as_base" -c ' + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then + $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } + $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } + CONFIG_SHELL=$as_dir/$as_base + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$0" ${1+"$@"} + fi;; + esac + done +done +;; + esac + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line before each line; the second 'sed' does the real + # work. The second script uses 'N' to pair each line-number line + # with the numbered line, and appends trailing '-' during + # substitution so that $LINENO is not a special case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) + sed '=' <$as_myself | + sed ' + N + s,$,-, + : loop + s,^\(['$as_cr_digits']*\)\(.*\)[$]LINENO\([^'$as_cr_alnum'_]\),\1\2\1\3, + t loop + s,-$,, + s,^['$as_cr_digits']*\n,, + ' >$as_me.lineno && + chmod +x $as_me.lineno || + { { echo "$as_me:$LINENO: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&5 +echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2;} + { (exit 1); exit 1; }; } + + # Don't try to exec as it changes $[0], causing all sort of problems + # (the dirname of $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensible to this). + . ./$as_me.lineno + # Exit status is that of the last command. + exit +} + + +case `echo "testing\c"; echo 1,2,3`,`echo -n testing; echo 1,2,3` in + *c*,-n*) ECHO_N= ECHO_C=' +' ECHO_T=' ' ;; + *c*,* ) ECHO_N=-n ECHO_C= ECHO_T= ;; + *) ECHO_N= ECHO_C='\c' ECHO_T= ;; +esac + +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +rm -f conf$$ conf$$.exe conf$$.file +echo >conf$$.file +if ln -s conf$$.file conf$$ 2>/dev/null; then + # We could just check for DJGPP; but this test a) works b) is more generic + # and c) will remain valid once DJGPP supports symlinks (DJGPP 2.04). + if test -f conf$$.exe; then + # Don't use ln at all; we don't have any links + as_ln_s='cp -p' + else + as_ln_s='ln -s' + fi +elif ln conf$$.file conf$$ 2>/dev/null; then + as_ln_s=ln +else + as_ln_s='cp -p' +fi +rm -f conf$$ conf$$.exe conf$$.file + +if mkdir -p . 2>/dev/null; then + as_mkdir_p=: +else + test -d ./-p && rmdir ./-p + as_mkdir_p=false +fi + +as_executable_p="test -f" + +# Sed expression to map a string onto a valid CPP name. +as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" + +# Sed expression to map a string onto a valid variable name. +as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" + + +# IFS +# We need space, tab and new line, in precisely that order. +as_nl=' +' +IFS=" $as_nl" + +# CDPATH. +$as_unset CDPATH + +exec 6>&1 + +# Open the log real soon, to keep \$[0] and so on meaningful, and to +# report actual input values of CONFIG_FILES etc. instead of their +# values after options handling. 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Invocation command line was + + CONFIG_FILES = $CONFIG_FILES + CONFIG_HEADERS = $CONFIG_HEADERS + CONFIG_LINKS = $CONFIG_LINKS + CONFIG_COMMANDS = $CONFIG_COMMANDS + $ $0 $@ + +_CSEOF +echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 +echo >&5 +config_files=" Makefile src/Makefile man/Makefile" +config_headers=" config.h" +config_commands=" depfiles" + +ac_cs_usage="\ +\`$as_me' instantiates files from templates according to the +current configuration. + +Usage: $0 [OPTIONS] [FILE]... + + -h, --help print this help, then exit + -V, --version print version number, then exit + -q, --quiet do not print progress messages + -d, --debug don't remove temporary files + --recheck update $as_me by reconfiguring in the same conditions + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE + +Configuration files: +$config_files + +Configuration headers: +$config_headers + +Configuration commands: +$config_commands + +Report bugs to ." +ac_cs_version="\ +RNAforester config.status 1.5 +configured by ./configure, generated by GNU Autoconf 2.59, + with options \"'--prefix=/usr/local' '--cache-file=/dev/null' '--srcdir=.'\" + +Copyright (C) 2003 Free Software Foundation, Inc. +This config.status script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it." +srcdir=. +INSTALL="/usr/bin/install -c" +# If no file are specified by the user, then we need to provide default +# value. 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Disable this feature. + alias -g '${1+"$@"}'='"$@"' +elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then + set -o posix +fi +DUALCASE=1; export DUALCASE # for MKS sh + +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + + +# Work around bugs in pre-3.0 UWIN ksh. +$as_unset ENV MAIL MAILPATH +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +for as_var in \ + LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ + LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ + LC_TELEPHONE LC_TIME +do + if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then + eval $as_var=C; export $as_var + else + $as_unset $as_var + fi +done + +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)$' \| \ + . : '\(.\)' 2>/dev/null || +echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } + /^X\/\(\/\/\)$/{ s//\1/; q; } + /^X\/\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + + +# PATH needs CR, and LINENO needs CR and PATH. +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + echo "#! /bin/sh" >conf$$.sh + echo "exit 0" >>conf$$.sh + chmod +x conf$$.sh + if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then + PATH_SEPARATOR=';' + else + PATH_SEPARATOR=: + fi + rm -f conf$$.sh +fi + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" || { + # Find who we are. 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See below for descriptions of some of the useful variables. + +Defaults for the options are specified in brackets. + +Configuration: + -h, --help display this help and exit + --help=short display options specific to this package + --help=recursive display the short help of all the included packages + -V, --version display version information and exit + -q, --quiet, --silent do not print \`checking...' messages + --cache-file=FILE cache test results in FILE [disabled] + -C, --config-cache alias for \`--cache-file=config.cache' + -n, --no-create do not create output files + --srcdir=DIR find the sources in DIR [configure dir or \`..'] + +_ACEOF + + cat <<_ACEOF +Installation directories: + --prefix=PREFIX install architecture-independent files in PREFIX + [$ac_default_prefix] + --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX + [PREFIX] + +By default, \`make install' will install all the files in +\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify +an installation prefix other than \`$ac_default_prefix' using \`--prefix', +for instance \`--prefix=\$HOME'. + +For better control, use the options below. + +Fine tuning of the installation directories: + --bindir=DIR user executables [EPREFIX/bin] + --sbindir=DIR system admin executables [EPREFIX/sbin] + --libexecdir=DIR program executables [EPREFIX/libexec] + --datadir=DIR read-only architecture-independent data [PREFIX/share] + --sysconfdir=DIR read-only single-machine data [PREFIX/etc] + --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] + --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --libdir=DIR object code libraries [EPREFIX/lib] + --includedir=DIR C header files [PREFIX/include] + --oldincludedir=DIR C header files for non-gcc [/usr/include] + --infodir=DIR info documentation [PREFIX/info] + --mandir=DIR man documentation [PREFIX/man] +_ACEOF + + cat <<\_ACEOF + +Program names: + --program-prefix=PREFIX prepend PREFIX to installed program names + --program-suffix=SUFFIX append SUFFIX to installed program names + --program-transform-name=PROGRAM run sed PROGRAM on installed program names +_ACEOF +fi + +if test -n "$ac_init_help"; then + case $ac_init_help in + short | recursive ) echo "Configuration of RNAforester 1.5:";; + esac + cat <<\_ACEOF + +Optional Features: + --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no) + --enable-FEATURE[=ARG] include FEATURE [ARG=yes] + --disable-dependency-tracking speeds up one-time build + --enable-dependency-tracking do not reject slow dependency extractors + +Optional Packages: + --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] + --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) +--with-ViennaRNA-lib where to search for libRNA.a + +Some influential environment variables: + CXX C++ compiler command + CXXFLAGS C++ compiler flags + LDFLAGS linker flags, e.g. -L if you have libraries in a + nonstandard directory + CPPFLAGS C/C++ preprocessor flags, e.g. -I if you have + headers in a nonstandard directory + CC C compiler command + CFLAGS C compiler flags + CXXCPP C++ preprocessor + +Use these variables to override the choices made by `configure' or to help +it to find libraries and programs with nonstandard names/locations. + +Report bugs to . +_ACEOF +fi + +if test "$ac_init_help" = "recursive"; then + # If there are subdirs, report their specific --help. + ac_popdir=`pwd` + for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue + test -d $ac_dir || continue + ac_builddir=. + +if test "$ac_dir" != .; then + ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'` + # A "../" for each directory in $ac_dir_suffix. + ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'` +else + ac_dir_suffix= ac_top_builddir= +fi + +case $srcdir in + .) # No --srcdir option. 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Use of quotes ensures accuracy. + *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; + esac + fi +done +if $ac_cache_corrupted; then + { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 +echo "$as_me: error: changes in the environment can compromise the build" >&2;} + { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 +echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} + { (exit 1); exit 1; }; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + + + + + + + + + + + + + + + + + + + + + + + + + + + +am__api_version="1.9" +ac_aux_dir= +for ac_dir in $srcdir $srcdir/.. $srcdir/../..; do + if test -f $ac_dir/install-sh; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install-sh -c" + break + elif test -f $ac_dir/install.sh; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install.sh -c" + break + elif test -f $ac_dir/shtool; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/shtool install -c" + break + fi +done +if test -z "$ac_aux_dir"; then + { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&5 +echo "$as_me: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&2;} + { (exit 1); exit 1; }; } +fi +ac_config_guess="$SHELL $ac_aux_dir/config.guess" +ac_config_sub="$SHELL $ac_aux_dir/config.sub" +ac_configure="$SHELL $ac_aux_dir/configure" # This should be Cygnus configure. + +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 +echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6 +if test -z "$INSTALL"; then +if test "${ac_cv_path_install+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + done + done + ;; +esac +done + + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. We don't cache a + # path for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the path is relative. + INSTALL=$ac_install_sh + fi +fi +echo "$as_me:$LINENO: result: $INSTALL" >&5 +echo "${ECHO_T}$INSTALL" >&6 + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' + +echo "$as_me:$LINENO: checking whether build environment is sane" >&5 +echo $ECHO_N "checking whether build environment is sane... $ECHO_C" >&6 +# Just in case +sleep 1 +echo timestamp > conftest.file +# Do `set' in a subshell so we don't clobber the current shell's +# arguments. Must try -L first in case configure is actually a +# symlink; some systems play weird games with the mod time of symlinks +# (eg FreeBSD returns the mod time of the symlink's containing +# directory). +if ( + set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null` + if test "$*" = "X"; then + # -L didn't work. + set X `ls -t $srcdir/configure conftest.file` + fi + rm -f conftest.file + if test "$*" != "X $srcdir/configure conftest.file" \ + && test "$*" != "X conftest.file $srcdir/configure"; then + + # If neither matched, then we have a broken ls. This can happen + # if, for instance, CONFIG_SHELL is bash and it inherits a + # broken ls alias from the environment. This has actually + # happened. Such a system could not be considered "sane". + { { echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&5 +echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&2;} + { (exit 1); exit 1; }; } + fi + + test "$2" = conftest.file + ) +then + # Ok. + : +else + { { echo "$as_me:$LINENO: error: newly created file is older than distributed files! +Check your system clock" >&5 +echo "$as_me: error: newly created file is older than distributed files! +Check your system clock" >&2;} + { (exit 1); exit 1; }; } +fi +echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 +test "$program_prefix" != NONE && + program_transform_name="s,^,$program_prefix,;$program_transform_name" +# Use a double $ so make ignores it. +test "$program_suffix" != NONE && + program_transform_name="s,\$,$program_suffix,;$program_transform_name" +# Double any \ or $. echo might interpret backslashes. +# By default was `s,x,x', remove it if useless. +cat <<\_ACEOF >conftest.sed +s/[\\$]/&&/g;s/;s,x,x,$// +_ACEOF +program_transform_name=`echo $program_transform_name | sed -f conftest.sed` +rm conftest.sed + +# expand $ac_aux_dir to an absolute path +am_aux_dir=`cd $ac_aux_dir && pwd` + +test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing" +# Use eval to expand $SHELL +if eval "$MISSING --run true"; then + am_missing_run="$MISSING --run " +else + am_missing_run= + { echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5 +echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;} +fi + +if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then + # We used to keeping the `.' as first argument, in order to + # allow $(mkdir_p) to be used without argument. As in + # $(mkdir_p) $(somedir) + # where $(somedir) is conditionally defined. However this is wrong + # for two reasons: + # 1. if the package is installed by a user who cannot write `.' + # make install will fail, + # 2. the above comment should most certainly read + # $(mkdir_p) $(DESTDIR)$(somedir) + # so it does not work when $(somedir) is undefined and + # $(DESTDIR) is not. + # To support the latter case, we have to write + # test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir), + # so the `.' trick is pointless. + mkdir_p='mkdir -p --' +else + # On NextStep and OpenStep, the `mkdir' command does not + # recognize any option. It will interpret all options as + # directories to create, and then abort because `.' already + # exists. + for d in ./-p ./--version; + do + test -d $d && rmdir $d + done + # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists. + if test -f "$ac_aux_dir/mkinstalldirs"; then + mkdir_p='$(mkinstalldirs)' + else + mkdir_p='$(install_sh) -d' + fi +fi + +for ac_prog in gawk mawk nawk awk +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_AWK+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$AWK"; then + ac_cv_prog_AWK="$AWK" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_AWK="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +AWK=$ac_cv_prog_AWK +if test -n "$AWK"; then + echo "$as_me:$LINENO: result: $AWK" >&5 +echo "${ECHO_T}$AWK" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$AWK" && break +done + +echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6 +set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y,:./+-,___p_,'` +if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.make <<\_ACEOF +all: + @echo 'ac_maketemp="$(MAKE)"' +_ACEOF +# GNU make sometimes prints "make[1]: Entering...", which would confuse us. +eval `${MAKE-make} -f conftest.make 2>/dev/null | grep temp=` +if test -n "$ac_maketemp"; then + eval ac_cv_prog_make_${ac_make}_set=yes +else + eval ac_cv_prog_make_${ac_make}_set=no +fi +rm -f conftest.make +fi +if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then + echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + SET_MAKE= +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 + SET_MAKE="MAKE=${MAKE-make}" +fi + +rm -rf .tst 2>/dev/null +mkdir .tst 2>/dev/null +if test -d .tst; then + am__leading_dot=. +else + am__leading_dot=_ +fi +rmdir .tst 2>/dev/null + +# test to see if srcdir already configured +if test "`cd $srcdir && pwd`" != "`pwd`" && + test -f $srcdir/config.status; then + { { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5 +echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;} + { (exit 1); exit 1; }; } +fi + +# test whether we have cygpath +if test -z "$CYGPATH_W"; then + if (cygpath --version) >/dev/null 2>/dev/null; then + CYGPATH_W='cygpath -w' + else + CYGPATH_W=echo + fi +fi + + +# Define the identity of the package. + PACKAGE='RNAforester' + VERSION='1.5' + + +cat >>confdefs.h <<_ACEOF +#define PACKAGE "$PACKAGE" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define VERSION "$VERSION" +_ACEOF + +# Some tools Automake needs. + +ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"} + + +AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"} + + +AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"} + + +AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"} + + +MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"} + +install_sh=${install_sh-"$am_aux_dir/install-sh"} + +# Installed binaries are usually stripped using `strip' when the user +# run `make install-strip'. However `strip' might not be the right +# tool to use in cross-compilation environments, therefore Automake +# will honor the `STRIP' environment variable to overrule this program. +if test "$cross_compiling" != no; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. +set dummy ${ac_tool_prefix}strip; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_STRIP+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$STRIP"; then + ac_cv_prog_STRIP="$STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_STRIP="${ac_tool_prefix}strip" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +STRIP=$ac_cv_prog_STRIP +if test -n "$STRIP"; then + echo "$as_me:$LINENO: result: $STRIP" >&5 +echo "${ECHO_T}$STRIP" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_STRIP"; then + ac_ct_STRIP=$STRIP + # Extract the first word of "strip", so it can be a program name with args. +set dummy strip; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_STRIP"; then + ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_STRIP="strip" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + test -z "$ac_cv_prog_ac_ct_STRIP" && ac_cv_prog_ac_ct_STRIP=":" +fi +fi +ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP +if test -n "$ac_ct_STRIP"; then + echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 +echo "${ECHO_T}$ac_ct_STRIP" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + STRIP=$ac_ct_STRIP +else + STRIP="$ac_cv_prog_STRIP" +fi + +fi +INSTALL_STRIP_PROGRAM="\${SHELL} \$(install_sh) -c -s" + +# We need awk for the "check" target. The system "awk" is bad on +# some platforms. +# Always define AMTAR for backward compatibility. + +AMTAR=${AMTAR-"${am_missing_run}tar"} + +am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' + + + + + + + ac_config_headers="$ac_config_headers config.h" + + +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu +if test -n "$ac_tool_prefix"; then + for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CXX+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CXX"; then + ac_cv_prog_CXX="$CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CXX=$ac_cv_prog_CXX +if test -n "$CXX"; then + echo "$as_me:$LINENO: result: $CXX" >&5 +echo "${ECHO_T}$CXX" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CXX" && break + done +fi +if test -z "$CXX"; then + ac_ct_CXX=$CXX + for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CXX"; then + ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CXX="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CXX=$ac_cv_prog_ac_ct_CXX +if test -n "$ac_ct_CXX"; then + echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 +echo "${ECHO_T}$ac_ct_CXX" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CXX" && break +done +test -n "$ac_ct_CXX" || ac_ct_CXX="g++" + + CXX=$ac_ct_CXX +fi + + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C++ compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files a.out a.exe b.out" +# Try to create an executable without -o first, disregard a.out. +# It will help us diagnose broken compilers, and finding out an intuition +# of exeext. +echo "$as_me:$LINENO: checking for C++ compiler default output file name" >&5 +echo $ECHO_N "checking for C++ compiler default output file name... $ECHO_C" >&6 +ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` +if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 + (eval $ac_link_default) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # Find the output, starting from the most likely. This scheme is +# not robust to junk in `.', hence go to wildcards (a.*) only as a last +# resort. + +# Be careful to initialize this variable, since it used to be cached. +# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. +ac_cv_exeext= +# b.out is created by i960 compilers. +for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out +do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) + ;; + conftest.$ac_ext ) + # This is the source file. + ;; + [ab].out ) + # We found the default executable, but exeext='' is most + # certainly right. + break;; + *.* ) + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + # FIXME: I believe we export ac_cv_exeext for Libtool, + # but it would be cool to find out if it's true. Does anybody + # maintain Libtool? --akim. + export ac_cv_exeext + break;; + * ) + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: C++ compiler cannot create executables +See \`config.log' for more details." >&5 +echo "$as_me: error: C++ compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; } +fi + +ac_exeext=$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_file" >&5 +echo "${ECHO_T}$ac_file" >&6 + +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether the C++ compiler works" >&5 +echo $ECHO_N "checking whether the C++ compiler works... $ECHO_C" >&6 +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. +if test "$cross_compiling" != yes; then + if { ac_try='./$ac_file' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { echo "$as_me:$LINENO: error: cannot run C++ compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot run C++ compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + fi + fi +fi +echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + +rm -f a.out a.exe conftest$ac_cv_exeext b.out +ac_clean_files=$ac_clean_files_save +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 +echo "$as_me:$LINENO: result: $cross_compiling" >&5 +echo "${ECHO_T}$cross_compiling" >&6 + +echo "$as_me:$LINENO: checking for suffix of executables" >&5 +echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + export ac_cv_exeext + break;; + * ) break;; + esac +done +else + { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +echo "${ECHO_T}$ac_cv_exeext" >&6 + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +echo "$as_me:$LINENO: checking for suffix of object files" >&5 +echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 +if test "${ac_cv_objext+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.o conftest.obj +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; + *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest.$ac_cv_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 +echo "${ECHO_T}$ac_cv_objext" >&6 +OBJEXT=$ac_cv_objext +ac_objext=$OBJEXT +echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_cxx_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6 +GXX=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CXXFLAGS=${CXXFLAGS+set} +ac_save_CXXFLAGS=$CXXFLAGS +CXXFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 +echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cxx_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cxx_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cxx_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6 +if test "$ac_test_CXXFLAGS" = set; then + CXXFLAGS=$ac_save_CXXFLAGS +elif test $ac_cv_prog_cxx_g = yes; then + if test "$GXX" = yes; then + CXXFLAGS="-g -O2" + else + CXXFLAGS="-g" + fi +else + if test "$GXX" = yes; then + CXXFLAGS="-O2" + else + CXXFLAGS= + fi +fi +for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +#include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +DEPDIR="${am__leading_dot}deps" + + ac_config_commands="$ac_config_commands depfiles" + + +am_make=${MAKE-make} +cat > confinc << 'END' +am__doit: + @echo done +.PHONY: am__doit +END +# If we don't find an include directive, just comment out the code. +echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5 +echo $ECHO_N "checking for style of include used by $am_make... $ECHO_C" >&6 +am__include="#" +am__quote= +_am_result=none +# First try GNU make style include. +echo "include confinc" > confmf +# We grep out `Entering directory' and `Leaving directory' +# messages which can occur if `w' ends up in MAKEFLAGS. +# In particular we don't look at `^make:' because GNU make might +# be invoked under some other name (usually "gmake"), in which +# case it prints its new name instead of `make'. +if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then + am__include=include + am__quote= + _am_result=GNU +fi +# Now try BSD make style include. +if test "$am__include" = "#"; then + echo '.include "confinc"' > confmf + if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then + am__include=.include + am__quote="\"" + _am_result=BSD + fi +fi + + +echo "$as_me:$LINENO: result: $_am_result" >&5 +echo "${ECHO_T}$_am_result" >&6 +rm -f confinc confmf + +# Check whether --enable-dependency-tracking or --disable-dependency-tracking was given. +if test "${enable_dependency_tracking+set}" = set; then + enableval="$enable_dependency_tracking" + +fi; +if test "x$enable_dependency_tracking" != xno; then + am_depcomp="$ac_aux_dir/depcomp" + AMDEPBACKSLASH='\' +fi + + +if test "x$enable_dependency_tracking" != xno; then + AMDEP_TRUE= + AMDEP_FALSE='#' +else + AMDEP_TRUE='#' + AMDEP_FALSE= +fi + + + + +depcc="$CXX" am_compiler_list= + +echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 +echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6 +if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then + # We make a subdir and do the tests there. Otherwise we can end up + # making bogus files that we don't know about and never remove. For + # instance it was reported that on HP-UX the gcc test will end up + # making a dummy file named `D' -- because `-MD' means `put the output + # in D'. + mkdir conftest.dir + # Copy depcomp to subdir because otherwise we won't find it if we're + # using a relative directory. + cp "$am_depcomp" conftest.dir + cd conftest.dir + # We will build objects and dependencies in a subdirectory because + # it helps to detect inapplicable dependency modes. For instance + # both Tru64's cc and ICC support -MD to output dependencies as a + # side effect of compilation, but ICC will put the dependencies in + # the current directory while Tru64 will put them in the object + # directory. + mkdir sub + + am_cv_CXX_dependencies_compiler_type=none + if test "$am_compiler_list" = ""; then + am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp` + fi + for depmode in $am_compiler_list; do + # Setup a source with many dependencies, because some compilers + # like to wrap large dependency lists on column 80 (with \), and + # we should not choose a depcomp mode which is confused by this. + # + # We need to recreate these files for each test, as the compiler may + # overwrite some of them when testing with obscure command lines. + # This happens at least with the AIX C compiler. + : > sub/conftest.c + for i in 1 2 3 4 5 6; do + echo '#include "conftst'$i'.h"' >> sub/conftest.c + # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with + # Solaris 8's {/usr,}/bin/sh. + touch sub/conftst$i.h + done + echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf + + case $depmode in + nosideeffect) + # after this tag, mechanisms are not by side-effect, so they'll + # only be used when explicitly requested + if test "x$enable_dependency_tracking" = xyes; then + continue + else + break + fi + ;; + none) break ;; + esac + # We check with `-c' and `-o' for the sake of the "dashmstdout" + # mode. It turns out that the SunPro C++ compiler does not properly + # handle `-M -o', and we need to detect this. + if depmode=$depmode \ + source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \ + depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \ + $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \ + >/dev/null 2>conftest.err && + grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 && + grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 && + ${MAKE-make} -s -f confmf > /dev/null 2>&1; then + # icc doesn't choke on unknown options, it will just issue warnings + # or remarks (even with -Werror). So we grep stderr for any message + # that says an option was ignored or not supported. + # When given -MP, icc 7.0 and 7.1 complain thusly: + # icc: Command line warning: ignoring option '-M'; no argument required + # The diagnosis changed in icc 8.0: + # icc: Command line remark: option '-MP' not supported + if (grep 'ignoring option' conftest.err || + grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else + am_cv_CXX_dependencies_compiler_type=$depmode + break + fi + fi + done + + cd .. + rm -rf conftest.dir +else + am_cv_CXX_dependencies_compiler_type=none +fi + +fi +echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5 +echo "${ECHO_T}$am_cv_CXX_dependencies_compiler_type" >&6 +CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type + + + +if + test "x$enable_dependency_tracking" != xno \ + && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then + am__fastdepCXX_TRUE= + am__fastdepCXX_FALSE='#' +else + am__fastdepCXX_TRUE='#' + am__fastdepCXX_FALSE= +fi + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $# != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CC" && break +done + + CC=$ac_ct_CC +fi + +fi + + +test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 +if test "${ac_cv_c_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 +GCC=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +CFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 +echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cc_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 +echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_prog_cc_stdc=no +ac_save_CC=$CC +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std1 is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std1. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +# Don't try gcc -ansi; that turns off useful extensions and +# breaks some systems' header files. +# AIX -qlanglvl=ansi +# Ultrix and OSF/1 -std1 +# HP-UX 10.20 and later -Ae +# HP-UX older versions -Aa -D_HPUX_SOURCE +# SVR4 -Xc -D__EXTENSIONS__ +for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_stdc=$ac_arg +break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext +done +rm -f conftest.$ac_ext conftest.$ac_objext +CC=$ac_save_CC + +fi + +case "x$ac_cv_prog_cc_stdc" in + x|xno) + echo "$as_me:$LINENO: result: none needed" >&5 +echo "${ECHO_T}none needed" >&6 ;; + *) + echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 + CC="$CC $ac_cv_prog_cc_stdc" ;; +esac + +# Some people use a C++ compiler to compile C. Since we use `exit', +# in C++ we need to declare it. In case someone uses the same compiler +# for both compiling C and C++ we need to have the C++ compiler decide +# the declaration of exit, since it's the most demanding environment. +cat >conftest.$ac_ext <<_ACEOF +#ifndef __cplusplus + choke me +#endif +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +#include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +depcc="$CC" am_compiler_list= + +echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 +echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6 +if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then + # We make a subdir and do the tests there. Otherwise we can end up + # making bogus files that we don't know about and never remove. For + # instance it was reported that on HP-UX the gcc test will end up + # making a dummy file named `D' -- because `-MD' means `put the output + # in D'. + mkdir conftest.dir + # Copy depcomp to subdir because otherwise we won't find it if we're + # using a relative directory. + cp "$am_depcomp" conftest.dir + cd conftest.dir + # We will build objects and dependencies in a subdirectory because + # it helps to detect inapplicable dependency modes. For instance + # both Tru64's cc and ICC support -MD to output dependencies as a + # side effect of compilation, but ICC will put the dependencies in + # the current directory while Tru64 will put them in the object + # directory. + mkdir sub + + am_cv_CC_dependencies_compiler_type=none + if test "$am_compiler_list" = ""; then + am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp` + fi + for depmode in $am_compiler_list; do + # Setup a source with many dependencies, because some compilers + # like to wrap large dependency lists on column 80 (with \), and + # we should not choose a depcomp mode which is confused by this. + # + # We need to recreate these files for each test, as the compiler may + # overwrite some of them when testing with obscure command lines. + # This happens at least with the AIX C compiler. + : > sub/conftest.c + for i in 1 2 3 4 5 6; do + echo '#include "conftst'$i'.h"' >> sub/conftest.c + # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with + # Solaris 8's {/usr,}/bin/sh. + touch sub/conftst$i.h + done + echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf + + case $depmode in + nosideeffect) + # after this tag, mechanisms are not by side-effect, so they'll + # only be used when explicitly requested + if test "x$enable_dependency_tracking" = xyes; then + continue + else + break + fi + ;; + none) break ;; + esac + # We check with `-c' and `-o' for the sake of the "dashmstdout" + # mode. It turns out that the SunPro C++ compiler does not properly + # handle `-M -o', and we need to detect this. + if depmode=$depmode \ + source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \ + depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \ + $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \ + >/dev/null 2>conftest.err && + grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 && + grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 && + ${MAKE-make} -s -f confmf > /dev/null 2>&1; then + # icc doesn't choke on unknown options, it will just issue warnings + # or remarks (even with -Werror). So we grep stderr for any message + # that says an option was ignored or not supported. + # When given -MP, icc 7.0 and 7.1 complain thusly: + # icc: Command line warning: ignoring option '-M'; no argument required + # The diagnosis changed in icc 8.0: + # icc: Command line remark: option '-MP' not supported + if (grep 'ignoring option' conftest.err || + grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else + am_cv_CC_dependencies_compiler_type=$depmode + break + fi + fi + done + + cd .. + rm -rf conftest.dir +else + am_cv_CC_dependencies_compiler_type=none +fi + +fi +echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5 +echo "${ECHO_T}$am_cv_CC_dependencies_compiler_type" >&6 +CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type + + + +if + test "x$enable_dependency_tracking" != xno \ + && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then + am__fastdepCC_TRUE= + am__fastdepCC_FALSE='#' +else + am__fastdepCC_TRUE='#' + am__fastdepCC_FALSE= +fi + + +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + + + +# Check whether --with-ViennaRNA-lib or --without-ViennaRNA-lib was given. +if test "${with_ViennaRNA_lib+set}" = set; then + withval="$with_ViennaRNA_lib" + LIBS="$withval/libRNA.a ${LIBS}" && +cat >>confdefs.h <<\_ACEOF +#define HAVE_LIBRNA 1 +_ACEOF + +else + LDFLAGS="-L../../lib ${LDFLAGS}" + if test -r "../lib/fold.c"; then + cat >>confdefs.h <<\_ACEOF +#define HAVE_LIBRNA 1 +_ACEOF + + LIBS="-lRNA ${LIBS}" + echo "$as_me:$LINENO: result: using (to be built) libRNA.a in ../lib" >&5 +echo "${ECHO_T}using (to be built) libRNA.a in ../lib" >&6 + fi + +fi; + +save_CPPFLAGS=$CPPFLAGS +CPPFLAGS="-Ig2-0.70/src/ -Lg2-0.70/ ${CPPFLAGS}" + + + + +echo "$as_me:$LINENO: checking for gdImageLine in -lgd" >&5 +echo $ECHO_N "checking for gdImageLine in -lgd... $ECHO_C" >&6 +if test "${ac_cv_lib_gd_gdImageLine+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lgd $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gdImageLine (); +int +main () +{ +gdImageLine (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_gd_gdImageLine=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_gd_gdImageLine=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_gd_gdImageLine" >&5 +echo "${ECHO_T}$ac_cv_lib_gd_gdImageLine" >&6 +if test $ac_cv_lib_gd_gdImageLine = yes; then + cat >>confdefs.h <<_ACEOF +#define HAVE_LIBGD 1 +_ACEOF + + LIBS="-lgd $LIBS" + +fi + + +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu +echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5 +echo $ECHO_N "checking how to run the C++ preprocessor... $ECHO_C" >&6 +if test -z "$CXXCPP"; then + if test "${ac_cv_prog_CXXCPP+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + # Double quotes because CXXCPP needs to be expanded + for CXXCPP in "$CXX -E" "/lib/cpp" + do + ac_preproc_ok=false +for ac_cxx_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_cxx_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether non-existent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_cxx_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # Broken: success on invalid input. +continue +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + break +fi + + done + ac_cv_prog_CXXCPP=$CXXCPP + +fi + CXXCPP=$ac_cv_prog_CXXCPP +else + ac_cv_prog_CXXCPP=$CXXCPP +fi +echo "$as_me:$LINENO: result: $CXXCPP" >&5 +echo "${ECHO_T}$CXXCPP" >&6 +ac_preproc_ok=false +for ac_cxx_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_cxx_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether non-existent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_cxx_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # Broken: success on invalid input. +continue +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : +else + { { echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check +See \`config.log' for more details." >&5 +echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + +echo "$as_me:$LINENO: checking for egrep" >&5 +echo $ECHO_N "checking for egrep... $ECHO_C" >&6 +if test "${ac_cv_prog_egrep+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if echo a | (grep -E '(a|b)') >/dev/null 2>&1 + then ac_cv_prog_egrep='grep -E' + else ac_cv_prog_egrep='egrep' + fi +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_egrep" >&5 +echo "${ECHO_T}$ac_cv_prog_egrep" >&6 + EGREP=$ac_cv_prog_egrep + + +echo "$as_me:$LINENO: checking for ANSI C header files" >&5 +echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 +if test "${ac_cv_header_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_header_stdc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_header_stdc=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + +if test $ac_cv_header_stdc = yes; then + # SunOS 4.x string.h does not declare mem*, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "memchr" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "free" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. + if test "$cross_compiling" = yes; then + : +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#if ((' ' & 0x0FF) == 0x020) +# define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +#else +# define ISLOWER(c) \ + (('a' <= (c) && (c) <= 'i') \ + || ('j' <= (c) && (c) <= 'r') \ + || ('s' <= (c) && (c) <= 'z')) +# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +#endif + +#define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +int +main () +{ + int i; + for (i = 0; i < 256; i++) + if (XOR (islower (i), ISLOWER (i)) + || toupper (i) != TOUPPER (i)) + exit(2); + exit (0); +} +_ACEOF +rm -f conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: program exited with status $ac_status" >&5 +echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no +fi +rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +fi +fi +echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 +echo "${ECHO_T}$ac_cv_header_stdc" >&6 +if test $ac_cv_header_stdc = yes; then + +cat >>confdefs.h <<\_ACEOF +#define STDC_HEADERS 1 +_ACEOF + +fi + +# On IRIX 5.3, sys/types and inttypes.h are conflicting. + + + + + + + + + +for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ + inttypes.h stdint.h unistd.h +do +as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` +echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + eval "$as_ac_Header=yes" +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +eval "$as_ac_Header=no" +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 +if test `eval echo '${'$as_ac_Header'}'` = yes; then + cat >>confdefs.h <<_ACEOF +#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + +if test "${ac_cv_header_g2_h+set}" = set; then + echo "$as_me:$LINENO: checking for g2.h" >&5 +echo $ECHO_N "checking for g2.h... $ECHO_C" >&6 +if test "${ac_cv_header_g2_h+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +fi +echo "$as_me:$LINENO: result: $ac_cv_header_g2_h" >&5 +echo "${ECHO_T}$ac_cv_header_g2_h" >&6 +else + # Is the header compilable? +echo "$as_me:$LINENO: checking g2.h usability" >&5 +echo $ECHO_N "checking g2.h usability... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_header_compiler=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_header_compiler=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +echo "${ECHO_T}$ac_header_compiler" >&6 + +# Is the header present? +echo "$as_me:$LINENO: checking g2.h presence" >&5 +echo $ECHO_N "checking g2.h presence... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_cxx_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + ac_header_preproc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi +rm -f conftest.err conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +echo "${ECHO_T}$ac_header_preproc" >&6 + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in + yes:no: ) + { echo "$as_me:$LINENO: WARNING: g2.h: accepted by the compiler, rejected by the preprocessor!" >&5 +echo "$as_me: WARNING: g2.h: accepted by the compiler, rejected by the preprocessor!" >&2;} + { echo "$as_me:$LINENO: WARNING: g2.h: proceeding with the compiler's result" >&5 +echo "$as_me: WARNING: g2.h: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { echo "$as_me:$LINENO: WARNING: g2.h: present but cannot be compiled" >&5 +echo "$as_me: WARNING: g2.h: present but cannot be compiled" >&2;} + { echo "$as_me:$LINENO: WARNING: g2.h: check for missing prerequisite headers?" >&5 +echo "$as_me: WARNING: g2.h: check for missing prerequisite headers?" >&2;} + { echo "$as_me:$LINENO: WARNING: g2.h: see the Autoconf documentation" >&5 +echo "$as_me: WARNING: g2.h: see the Autoconf documentation" >&2;} + { echo "$as_me:$LINENO: WARNING: g2.h: section \"Present But Cannot Be Compiled\"" >&5 +echo "$as_me: WARNING: g2.h: section \"Present But Cannot Be Compiled\"" >&2;} + { echo "$as_me:$LINENO: WARNING: g2.h: proceeding with the preprocessor's result" >&5 +echo "$as_me: WARNING: g2.h: proceeding with the preprocessor's result" >&2;} + { echo "$as_me:$LINENO: WARNING: g2.h: in the future, the compiler will take precedence" >&5 +echo "$as_me: WARNING: g2.h: in the future, the compiler will take precedence" >&2;} + ( + cat <<\_ASBOX +## ------------------------------------------------ ## +## Report this to mhoechsm@techfak.uni-bielefeld.de ## +## ------------------------------------------------ ## +_ASBOX + ) | + sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac +echo "$as_me:$LINENO: checking for g2.h" >&5 +echo $ECHO_N "checking for g2.h... $ECHO_C" >&6 +if test "${ac_cv_header_g2_h+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_header_g2_h=$ac_header_preproc +fi +echo "$as_me:$LINENO: result: $ac_cv_header_g2_h" >&5 +echo "${ECHO_T}$ac_cv_header_g2_h" >&6 + +fi +if test $ac_cv_header_g2_h = yes; then + +cat >>confdefs.h <<\_ACEOF +#define HAVE_LIBG2 1 +_ACEOF + +else + { echo "$as_me:$LINENO: WARNING: Compiling without support for graphical output. Install the g2 library that comes with the RNAforester distribution or download the latest version at http://g2.sourceforge.net/" >&5 +echo "$as_me: WARNING: Compiling without support for graphical output. Install the g2 library that comes with the RNAforester distribution or download the latest version at http://g2.sourceforge.net/" >&2;} +fi + + + +echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 +echo $ECHO_N "checking for an ANSI C-conforming const... $ECHO_C" >&6 +if test "${ac_cv_c_const+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +/* FIXME: Include the comments suggested by Paul. */ +#ifndef __cplusplus + /* Ultrix mips cc rejects this. */ + typedef int charset[2]; + const charset x; + /* SunOS 4.1.1 cc rejects this. */ + char const *const *ccp; + char **p; + /* NEC SVR4.0.2 mips cc rejects this. */ + struct point {int x, y;}; + static struct point const zero = {0,0}; + /* AIX XL C 1.02.0.0 rejects this. + It does not let you subtract one const X* pointer from another in + an arm of an if-expression whose if-part is not a constant + expression */ + const char *g = "string"; + ccp = &g + (g ? g-g : 0); + /* HPUX 7.0 cc rejects these. */ + ++ccp; + p = (char**) ccp; + ccp = (char const *const *) p; + { /* SCO 3.2v4 cc rejects this. */ + char *t; + char const *s = 0 ? (char *) 0 : (char const *) 0; + + *t++ = 0; + } + { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ + int x[] = {25, 17}; + const int *foo = &x[0]; + ++foo; + } + { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ + typedef const int *iptr; + iptr p = 0; + ++p; + } + { /* AIX XL C 1.02.0.0 rejects this saying + "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ + struct s { int j; const int *ap[3]; }; + struct s *b; b->j = 5; + } + { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ + const int foo = 10; + } +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_c_const=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_c_const=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5 +echo "${ECHO_T}$ac_cv_c_const" >&6 +if test $ac_cv_c_const = no; then + +cat >>confdefs.h <<\_ACEOF +#define const +_ACEOF + +fi + +echo "$as_me:$LINENO: checking for inline" >&5 +echo $ECHO_N "checking for inline... $ECHO_C" >&6 +if test "${ac_cv_c_inline+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_c_inline=no +for ac_kw in inline __inline__ __inline; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifndef __cplusplus +typedef int foo_t; +static $ac_kw foo_t static_foo () {return 0; } +$ac_kw foo_t foo () {return 0; } +#endif + +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_c_inline=$ac_kw; break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done + +fi +echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5 +echo "${ECHO_T}$ac_cv_c_inline" >&6 + + +case $ac_cv_c_inline in + inline | yes) ;; + *) + case $ac_cv_c_inline in + no) ac_val=;; + *) ac_val=$ac_cv_c_inline;; + esac + cat >>confdefs.h <<_ACEOF +#ifndef __cplusplus +#define inline $ac_val +#endif +_ACEOF + ;; +esac + +echo "$as_me:$LINENO: checking for size_t" >&5 +echo $ECHO_N "checking for size_t... $ECHO_C" >&6 +if test "${ac_cv_type_size_t+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if ((size_t *) 0) + return 0; +if (sizeof (size_t)) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? 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Invocation command line was + + CONFIG_FILES = $CONFIG_FILES + CONFIG_HEADERS = $CONFIG_HEADERS + CONFIG_LINKS = $CONFIG_LINKS + CONFIG_COMMANDS = $CONFIG_COMMANDS + $ $0 $@ + +_CSEOF +echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 +echo >&5 +_ACEOF + +# Files that config.status was made for. +if test -n "$ac_config_files"; then + echo "config_files=\"$ac_config_files\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_headers"; then + echo "config_headers=\"$ac_config_headers\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_links"; then + echo "config_links=\"$ac_config_links\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_commands"; then + echo "config_commands=\"$ac_config_commands\"" >>$CONFIG_STATUS +fi + +cat >>$CONFIG_STATUS <<\_ACEOF + +ac_cs_usage="\ +\`$as_me' instantiates files from templates according to the +current configuration. + +Usage: $0 [OPTIONS] [FILE]... + + -h, --help print this help, then exit + -V, --version print version number, then exit + -q, --quiet do not print progress messages + -d, --debug don't remove temporary files + --recheck update $as_me by reconfiguring in the same conditions + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE + +Configuration files: +$config_files + +Configuration headers: +$config_headers + +Configuration commands: +$config_commands + +Report bugs to ." +_ACEOF + +cat >>$CONFIG_STATUS <<_ACEOF +ac_cs_version="\\ +RNAforester config.status 1.5 +configured by $0, generated by GNU Autoconf 2.59, + with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\" + +Copyright (C) 2003 Free Software Foundation, Inc. +This config.status script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it." +srcdir=$srcdir +INSTALL="$INSTALL" +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF +# If no file are specified by the user, then we need to provide default +# value. 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Make it in the build tree +# simply because there is no reason to put it here, and in addition, +# creating and moving files from /tmp can sometimes cause problems. +# Create a temporary directory, and hook for its removal unless debugging. +$debug || +{ + trap 'exit_status=$?; rm -rf $tmp && exit $exit_status' 0 + trap '{ (exit 1); exit 1; }' 1 2 13 15 +} + +# Create a (secure) tmp directory for tmp files. + +{ + tmp=`(umask 077 && mktemp -d -q "./confstatXXXXXX") 2>/dev/null` && + test -n "$tmp" && test -d "$tmp" +} || +{ + tmp=./confstat$$-$RANDOM + (umask 077 && mkdir $tmp) +} || +{ + echo "$me: cannot create a temporary directory in ." >&2 + { (exit 1); exit 1; } +} + +_ACEOF + +cat >>$CONFIG_STATUS <<_ACEOF + +# +# CONFIG_FILES section. +# + +# No need to generate the scripts if there are no CONFIG_FILES. +# This happens for instance when ./config.status config.h +if test -n "\$CONFIG_FILES"; then + # Protect against being on the right side of a sed subst in config.status. + sed 's/,@/@@/; s/@,/@@/; s/,;t t\$/@;t t/; /@;t t\$/s/[\\\\&,]/\\\\&/g; + s/@@/,@/; s/@@/@,/; s/@;t t\$/,;t t/' >\$tmp/subs.sed <<\\CEOF +s,@SHELL@,$SHELL,;t t +s,@PATH_SEPARATOR@,$PATH_SEPARATOR,;t t +s,@PACKAGE_NAME@,$PACKAGE_NAME,;t t +s,@PACKAGE_TARNAME@,$PACKAGE_TARNAME,;t t +s,@PACKAGE_VERSION@,$PACKAGE_VERSION,;t t +s,@PACKAGE_STRING@,$PACKAGE_STRING,;t t +s,@PACKAGE_BUGREPORT@,$PACKAGE_BUGREPORT,;t t +s,@exec_prefix@,$exec_prefix,;t t +s,@prefix@,$prefix,;t t +s,@program_transform_name@,$program_transform_name,;t t +s,@bindir@,$bindir,;t t +s,@sbindir@,$sbindir,;t t +s,@libexecdir@,$libexecdir,;t t +s,@datadir@,$datadir,;t t +s,@sysconfdir@,$sysconfdir,;t t +s,@sharedstatedir@,$sharedstatedir,;t t +s,@localstatedir@,$localstatedir,;t t +s,@libdir@,$libdir,;t t +s,@includedir@,$includedir,;t t +s,@oldincludedir@,$oldincludedir,;t t +s,@infodir@,$infodir,;t t +s,@mandir@,$mandir,;t t +s,@build_alias@,$build_alias,;t t +s,@host_alias@,$host_alias,;t t +s,@target_alias@,$target_alias,;t t +s,@DEFS@,$DEFS,;t t +s,@ECHO_C@,$ECHO_C,;t t +s,@ECHO_N@,$ECHO_N,;t t +s,@ECHO_T@,$ECHO_T,;t t +s,@LIBS@,$LIBS,;t t +s,@INSTALL_PROGRAM@,$INSTALL_PROGRAM,;t t +s,@INSTALL_SCRIPT@,$INSTALL_SCRIPT,;t t +s,@INSTALL_DATA@,$INSTALL_DATA,;t t +s,@CYGPATH_W@,$CYGPATH_W,;t t +s,@PACKAGE@,$PACKAGE,;t t +s,@VERSION@,$VERSION,;t t +s,@ACLOCAL@,$ACLOCAL,;t t +s,@AUTOCONF@,$AUTOCONF,;t t +s,@AUTOMAKE@,$AUTOMAKE,;t t +s,@AUTOHEADER@,$AUTOHEADER,;t t +s,@MAKEINFO@,$MAKEINFO,;t t +s,@install_sh@,$install_sh,;t t +s,@STRIP@,$STRIP,;t t +s,@ac_ct_STRIP@,$ac_ct_STRIP,;t t +s,@INSTALL_STRIP_PROGRAM@,$INSTALL_STRIP_PROGRAM,;t t +s,@mkdir_p@,$mkdir_p,;t t +s,@AWK@,$AWK,;t t +s,@SET_MAKE@,$SET_MAKE,;t t +s,@am__leading_dot@,$am__leading_dot,;t t +s,@AMTAR@,$AMTAR,;t t +s,@am__tar@,$am__tar,;t t +s,@am__untar@,$am__untar,;t t +s,@CXX@,$CXX,;t t +s,@CXXFLAGS@,$CXXFLAGS,;t t +s,@LDFLAGS@,$LDFLAGS,;t t +s,@CPPFLAGS@,$CPPFLAGS,;t t +s,@ac_ct_CXX@,$ac_ct_CXX,;t t +s,@EXEEXT@,$EXEEXT,;t t +s,@OBJEXT@,$OBJEXT,;t t +s,@DEPDIR@,$DEPDIR,;t t +s,@am__include@,$am__include,;t t +s,@am__quote@,$am__quote,;t t +s,@AMDEP_TRUE@,$AMDEP_TRUE,;t t +s,@AMDEP_FALSE@,$AMDEP_FALSE,;t t +s,@AMDEPBACKSLASH@,$AMDEPBACKSLASH,;t t +s,@CXXDEPMODE@,$CXXDEPMODE,;t t +s,@am__fastdepCXX_TRUE@,$am__fastdepCXX_TRUE,;t t +s,@am__fastdepCXX_FALSE@,$am__fastdepCXX_FALSE,;t t +s,@CC@,$CC,;t t +s,@CFLAGS@,$CFLAGS,;t t +s,@ac_ct_CC@,$ac_ct_CC,;t t +s,@CCDEPMODE@,$CCDEPMODE,;t t +s,@am__fastdepCC_TRUE@,$am__fastdepCC_TRUE,;t t +s,@am__fastdepCC_FALSE@,$am__fastdepCC_FALSE,;t t +s,@CXXCPP@,$CXXCPP,;t t +s,@EGREP@,$EGREP,;t t +s,@subdirs@,$subdirs,;t t +s,@LIBOBJS@,$LIBOBJS,;t t +s,@LTLIBOBJS@,$LTLIBOBJS,;t t +CEOF + +_ACEOF + + cat >>$CONFIG_STATUS <<\_ACEOF + # Split the substitutions into bite-sized pieces for seds with + # small command number limits, like on Digital OSF/1 and HP-UX. + ac_max_sed_lines=48 + ac_sed_frag=1 # Number of current file. + ac_beg=1 # First line for current file. + ac_end=$ac_max_sed_lines # Line after last line for current file. + ac_more_lines=: + ac_sed_cmds= + while $ac_more_lines; do + if test $ac_beg -gt 1; then + sed "1,${ac_beg}d; ${ac_end}q" $tmp/subs.sed >$tmp/subs.frag + else + sed "${ac_end}q" $tmp/subs.sed >$tmp/subs.frag + fi + if test ! 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The first handles `#define' +# templates, and the second `#undef' templates. +# And first: Protect against being on the right side of a sed subst in +# config.status. Protect against being in an unquoted here document +# in config.status. +rm -f conftest.defines conftest.undefs +# Using a here document instead of a string reduces the quoting nightmare. +# Putting comments in sed scripts is not portable. +# +# `end' is used to avoid that the second main sed command (meant for +# 0-ary CPP macros) applies to n-ary macro definitions. +# See the Autoconf documentation for `clear'. +cat >confdef2sed.sed <<\_ACEOF +s/[\\&,]/\\&/g +s,[\\$`],\\&,g +t clear +: clear +s,^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*\)\(([^)]*)\)[ ]*\(.*\)$,${ac_dA}\1${ac_dB}\1\2${ac_dC}\3${ac_dD},gp +t end +s,^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)$,${ac_dA}\1${ac_dB}\1${ac_dC}\2${ac_dD},gp +: end +_ACEOF +# If some macros were called several times there might be several times +# the same #defines, which is useless. Nevertheless, we may not want to +# sort them, since we want the *last* AC-DEFINE to be honored. +uniq confdefs.h | sed -n -f confdef2sed.sed >conftest.defines +sed 's/ac_d/ac_u/g' conftest.defines >conftest.undefs +rm -f confdef2sed.sed + +# This sed command replaces #undef with comments. This is necessary, for +# example, in the case of _POSIX_SOURCE, which is predefined and required +# on some systems where configure will not decide to define it. +cat >>conftest.undefs <<\_ACEOF +s,^[ ]*#[ ]*undef[ ][ ]*[a-zA-Z_][a-zA-Z_0-9]*,/* & */, +_ACEOF + +# Break up conftest.defines because some shells have a limit on the size +# of here documents, and old seds have small limits too (100 cmds). +echo ' # Handle all the #define templates only if necessary.' >>$CONFIG_STATUS +echo ' if grep "^[ ]*#[ ]*define" $tmp/in >/dev/null; then' >>$CONFIG_STATUS +echo ' # If there are no defines, we may have an empty if/fi' >>$CONFIG_STATUS +echo ' :' >>$CONFIG_STATUS +rm -f conftest.tail +while grep . conftest.defines >/dev/null +do + # Write a limited-size here document to $tmp/defines.sed. + echo ' cat >$tmp/defines.sed <>$CONFIG_STATUS + # Speed up: don't consider the non `#define' lines. + echo '/^[ ]*#[ ]*define/!b' >>$CONFIG_STATUS + # Work around the forget-to-reset-the-flag bug. + echo 't clr' >>$CONFIG_STATUS + echo ': clr' >>$CONFIG_STATUS + sed ${ac_max_here_lines}q conftest.defines >>$CONFIG_STATUS + echo 'CEOF + sed -f $tmp/defines.sed $tmp/in >$tmp/out + rm -f $tmp/in + mv $tmp/out $tmp/in +' >>$CONFIG_STATUS + sed 1,${ac_max_here_lines}d conftest.defines >conftest.tail + rm -f conftest.defines + mv conftest.tail conftest.defines +done +rm -f conftest.defines +echo ' fi # grep' >>$CONFIG_STATUS +echo >>$CONFIG_STATUS + +# Break up conftest.undefs because some shells have a limit on the size +# of here documents, and old seds have small limits too (100 cmds). +echo ' # Handle all the #undef templates' >>$CONFIG_STATUS +rm -f conftest.tail +while grep . conftest.undefs >/dev/null +do + # Write a limited-size here document to $tmp/undefs.sed. + echo ' cat >$tmp/undefs.sed <>$CONFIG_STATUS + # Speed up: don't consider the non `#undef' + echo '/^[ ]*#[ ]*undef/!b' >>$CONFIG_STATUS + # Work around the forget-to-reset-the-flag bug. + echo 't clr' >>$CONFIG_STATUS + echo ': clr' >>$CONFIG_STATUS + sed ${ac_max_here_lines}q conftest.undefs >>$CONFIG_STATUS + echo 'CEOF + sed -f $tmp/undefs.sed $tmp/in >$tmp/out + rm -f $tmp/in + mv $tmp/out $tmp/in +' >>$CONFIG_STATUS + sed 1,${ac_max_here_lines}d conftest.undefs >conftest.tail + rm -f conftest.undefs + mv conftest.tail conftest.undefs +done +rm -f conftest.undefs + +cat >>$CONFIG_STATUS <<\_ACEOF + # Let's still pretend it is `configure' which instantiates (i.e., don't + # use $as_me), people would be surprised to read: + # /* config.h. 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We are building in place. + ac_srcdir=. + if test -z "$ac_top_builddir"; then + ac_top_srcdir=. + else + ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` + fi ;; + [\\/]* | ?:[\\/]* ) # Absolute path. + ac_srcdir=$srcdir$ac_dir_suffix; + ac_top_srcdir=$srcdir ;; + *) # Relative path. + ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix + ac_top_srcdir=$ac_top_builddir$srcdir ;; +esac + +# Do not use `cd foo && pwd` to compute absolute paths, because +# the directories may not exist. +case `pwd` in +.) ac_abs_builddir="$ac_dir";; +*) + case "$ac_dir" in + .) ac_abs_builddir=`pwd`;; + [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";; + *) ac_abs_builddir=`pwd`/"$ac_dir";; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_top_builddir=${ac_top_builddir}.;; +*) + case ${ac_top_builddir}. in + .) ac_abs_top_builddir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;; + *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_srcdir=$ac_srcdir;; +*) + case $ac_srcdir in + .) ac_abs_srcdir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;; + *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_top_srcdir=$ac_top_srcdir;; +*) + case $ac_top_srcdir in + .) ac_abs_top_srcdir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;; + *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;; + esac;; +esac + + + cd $ac_dir + + # Check for guested configure; otherwise get Cygnus style configure. + if test -f $ac_srcdir/configure.gnu; then + ac_sub_configure="$SHELL '$ac_srcdir/configure.gnu'" + elif test -f $ac_srcdir/configure; then + ac_sub_configure="$SHELL '$ac_srcdir/configure'" + elif test -f $ac_srcdir/configure.in; then + ac_sub_configure=$ac_configure + else + { echo "$as_me:$LINENO: WARNING: no configuration information is in $ac_dir" >&5 +echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2;} + ac_sub_configure= + fi + + # The recursion is here. + if test -n "$ac_sub_configure"; then + # Make the cache file name correct relative to the subdirectory. + case $cache_file in + [\\/]* | ?:[\\/]* ) ac_sub_cache_file=$cache_file ;; + *) # Relative path. + ac_sub_cache_file=$ac_top_builddir$cache_file ;; + esac + + { echo "$as_me:$LINENO: running $ac_sub_configure $ac_sub_configure_args --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir" >&5 +echo "$as_me: running $ac_sub_configure $ac_sub_configure_args --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir" >&6;} + # The eval makes quoting arguments work. + eval $ac_sub_configure $ac_sub_configure_args \ + --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir || + { { echo "$as_me:$LINENO: error: $ac_sub_configure failed for $ac_dir" >&5 +echo "$as_me: error: $ac_sub_configure failed for $ac_dir" >&2;} + { (exit 1); exit 1; }; } + fi + + cd $ac_popdir + done +fi + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/configure.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/configure.in new file mode 100755 index 000000000..b36bdfc02 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/configure.in @@ -0,0 +1,64 @@ +dnl Process this file with autoconf to produce a configure script. +AC_REVISION($Revision: 1.13 $) +AC_INIT(RNAforester,1.5,mhoechsm@techfak.uni-bielefeld.de,RNAforester) +AC_PREREQ(2.53) +AM_INIT_AUTOMAKE + +dnl create a config.h file (Automake will add -DHAVE_CONFIG_H) +AM_CONFIG_HEADER(config.h) + +dnl Checks for programs. +AC_PROG_CXX +AC_PROG_CC +AC_LANG(C++) + +dnl Checks for libraries. +dnl AC_CHECK_LIB(g2,g2_open_vd,,AC_MSG_WARN(Compiling without support for graphical output. Install the g2 library that comes with the RNAforester distribution or download the latest version at http://g2.sourceforge.net/)) + +AC_ARG_WITH(ViennaRNA-lib, + [--with-ViennaRNA-lib where to search for libRNA.a], + LIBS=["$withval/libRNA.a ${LIBS}"] && AC_DEFINE(HAVE_LIBRNA,1,Define to 1 if you have the `RNA' library (-lRNA).), + LDFLAGS="-L../../lib ${LDFLAGS}" + if test -r "../lib/fold.c"; then + AC_DEFINE(HAVE_LIBRNA) + LIBS=["-lRNA ${LIBS}"] + AC_MSG_RESULT([using (to be built) libRNA.a in ../lib]) + fi + ) +dnl AC_CHECK_LIB(RNA, fold,,AC_MSG_WARN(Vienna RNA library libRNA.a was not found. RNAforester will be compiled without the structure prediction option -p and graphical output)) + +save_CPPFLAGS=$CPPFLAGS +CPPFLAGS=["-Ig2-0.70/src/ -Lg2-0.70/ ${CPPFLAGS}"] + + +AC_CHECK_LIB(gd,gdImageLine,,) + +dnl Checks for header files. +AC_HEADER_STDC +AC_CHECK_HEADER(g2.h,AC_DEFINE(HAVE_LIBG2,1,Define to 1 if you have the `g2' library (-lg2).),AC_MSG_WARN(Compiling without support for graphical output. Install the g2 library that comes with the RNAforester distribution or download the latest version at http://g2.sourceforge.net/)) +dnl AC_CHECK_HEADER(g2_PS.h,,AC_MSG_WARN(Compiling without support for graphical output. Install the g2 library that comes with the RNAforester distribution or download the latest version at http://g2.sourceforge.net/)) + +dnl Checks for typedefs, structures, and compiler characteristics. +AC_C_CONST +AC_C_INLINE +AC_TYPE_SIZE_T + +CPPFLAGS="$save_CPPFLAGS -I../g2-0.70/include/" +LDFLAGS=["-L../g2-0.70 ${LDFLAGS}"] + +if ${HAVE_LIBG2}; then + LIBS=["-lg2 ${LIBS}"] +fi + +AC_SUBST(CXX) +AC_SUBST(CPPFLAGS) +AC_SUBST(LIBS) +AC_SUBST(LDFLAGS) + +dnl Checks for library functions. + +AC_CONFIG_SUBDIRS(g2-0.70) +AC_OUTPUT(Makefile src/Makefile man/Makefile) + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/depcomp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/depcomp new file mode 100755 index 000000000..807b991f4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/depcomp @@ -0,0 +1,423 @@ +#! /bin/sh + +# depcomp - compile a program generating dependencies as side-effects +# Copyright 1999, 2000 Free Software Foundation, Inc. + +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2, or (at your option) +# any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA +# 02111-1307, USA. + +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + +# Originally written by Alexandre Oliva . + +if test -z "$depmode" || test -z "$source" || test -z "$object"; then + echo "depcomp: Variables source, object and depmode must be set" 1>&2 + exit 1 +fi +# `libtool' can also be set to `yes' or `no'. + +if test -z "$depfile"; then + base=`echo "$object" | sed -e 's,^.*/,,' -e 's,\.\([^.]*\)$,.P\1,'` + dir=`echo "$object" | sed 's,/.*$,/,'` + if test "$dir" = "$object"; then + dir= + fi + # FIXME: should be _deps on DOS. + depfile="$dir.deps/$base" +fi + +tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} + +rm -f "$tmpdepfile" + +# Some modes work just like other modes, but use different flags. We +# parameterize here, but still list the modes in the big case below, +# to make depend.m4 easier to write. Note that we *cannot* use a case +# here, because this file can only contain one case statement. +if test "$depmode" = hp; then + # HP compiler uses -M and no extra arg. + gccflag=-M + depmode=gcc +fi + +if test "$depmode" = dashXmstdout; then + # This is just like dashmstdout with a different argument. + dashmflag=-xM + depmode=dashmstdout +fi + +case "$depmode" in +gcc3) +## gcc 3 implements dependency tracking that does exactly what +## we want. Yay! Note: for some reason libtool 1.4 doesn't like +## it if -MD -MP comes after the -MF stuff. Hmm. + "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + mv "$tmpdepfile" "$depfile" + ;; + +gcc) +## There are various ways to get dependency output from gcc. Here's +## why we pick this rather obscure method: +## - Don't want to use -MD because we'd like the dependencies to end +## up in a subdir. Having to rename by hand is ugly. +## (We might end up doing this anyway to support other compilers.) +## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like +## -MM, not -M (despite what the docs say). +## - Using -M directly means running the compiler twice (even worse +## than renaming). + if test -z "$gccflag"; then + gccflag=-MD, + fi + "$@" -Wp,"$gccflag$tmpdepfile" + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + echo "$object : \\" > "$depfile" + alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz +## The second -e expression handles DOS-style file names with drive letters. + sed -e 's/^[^:]*: / /' \ + -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" +## This next piece of magic avoids the `deleted header file' problem. +## The problem is that when a header file which appears in a .P file +## is deleted, the dependency causes make to die (because there is +## typically no way to rebuild the header). We avoid this by adding +## dummy dependencies for each header file. Too bad gcc doesn't do +## this for us directly. + tr ' ' ' +' < "$tmpdepfile" | +## Some versions of gcc put a space before the `:'. On the theory +## that the space means something, we add a space to the output as +## well. +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +hp) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + +sgi) + if test "$libtool" = yes; then + "$@" "-Wp,-MDupdate,$tmpdepfile" + else + "$@" -MDupdate "$tmpdepfile" + fi + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + + if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files + echo "$object : \\" > "$depfile" + + # Clip off the initial element (the dependent). Don't try to be + # clever and replace this with sed code, as IRIX sed won't handle + # lines with more than a fixed number of characters (4096 in + # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines; + # the IRIX cc adds comments like `#:fec' to the end of the + # dependency line. + tr ' ' ' +' < "$tmpdepfile" \ + | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ + tr ' +' ' ' >> $depfile + echo >> $depfile + + # The second pass generates a dummy entry for each header file. + tr ' ' ' +' < "$tmpdepfile" \ + | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ + >> $depfile + else + # The sourcefile does not contain any dependencies, so just + # store a dummy comment line, to avoid errors with the Makefile + # "include basename.Plo" scheme. + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +aix) + # The C for AIX Compiler uses -M and outputs the dependencies + # in a .u file. This file always lives in the current directory. + # Also, the AIX compiler puts `$object:' at the start of each line; + # $object doesn't have directory information. + stripped=`echo "$object" | sed -e 's,^.*/,,' -e 's/\(.*\)\..*$/\1/'` + tmpdepfile="$stripped.u" + outname="$stripped.o" + if test "$libtool" = yes; then + "$@" -Wc,-M + else + "$@" -M + fi + + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + + if test -f "$tmpdepfile"; then + # Each line is of the form `foo.o: dependent.h'. + # Do two passes, one to just change these to + # `$object: dependent.h' and one to simply `dependent.h:'. + sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile" + sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile" + else + # The sourcefile does not contain any dependencies, so just + # store a dummy comment line, to avoid errors with the Makefile + # "include basename.Plo" scheme. + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +tru64) + # The Tru64 compiler uses -MD to generate dependencies as a side + # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'. + # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put + # dependencies in `foo.d' instead, so we check for that too. + # Subdirectories are respected. + dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` + test "x$dir" = "x$object" && dir= + base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` + + if test "$libtool" = yes; then + tmpdepfile1="$dir.libs/$base.lo.d" + tmpdepfile2="$dir.libs/$base.d" + "$@" -Wc,-MD + else + tmpdepfile1="$dir$base.o.d" + tmpdepfile2="$dir$base.d" + "$@" -MD + fi + + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile1" "$tmpdepfile2" + exit $stat + fi + + if test -f "$tmpdepfile1"; then + tmpdepfile="$tmpdepfile1" + else + tmpdepfile="$tmpdepfile2" + fi + if test -f "$tmpdepfile"; then + sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" + # That's a space and a tab in the []. + sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" + else + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +#nosideeffect) + # This comment above is used by automake to tell side-effect + # dependency tracking mechanisms from slower ones. + +dashmstdout) + # Important note: in order to support this mode, a compiler *must* + # always write the proprocessed file to stdout, regardless of -o. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test $1 != '--mode=compile'; do + shift + done + shift + fi + + # Remove `-o $object'. We will use -o /dev/null later, + # however we can't do the remplacement now because + # `-o $object' might simply not be used + IFS=" " + for arg + do + case $arg in + -o) + shift + ;; + $object) + shift + ;; + *) + set fnord "$@" "$arg" + shift # fnord + shift # $arg + ;; + esac + done + + test -z "$dashmflag" && dashmflag=-M + "$@" -o /dev/null $dashmflag | sed 's:^[^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile" + rm -f "$depfile" + cat < "$tmpdepfile" > "$depfile" + tr ' ' ' +' < "$tmpdepfile" | \ +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +dashXmstdout) + # This case only exists to satisfy depend.m4. It is never actually + # run, as this mode is specially recognized in the preamble. + exit 1 + ;; + +makedepend) + "$@" || exit $? + # X makedepend + shift + cleared=no + for arg in "$@"; do + case $cleared in + no) + set ""; shift + cleared=yes ;; + esac + case "$arg" in + -D*|-I*) + set fnord "$@" "$arg"; shift ;; + -*) + ;; + *) + set fnord "$@" "$arg"; shift ;; + esac + done + obj_suffix="`echo $object | sed 's/^.*\././'`" + touch "$tmpdepfile" + ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" + rm -f "$depfile" + cat < "$tmpdepfile" > "$depfile" + sed '1,2d' "$tmpdepfile" | tr ' ' ' +' | \ +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" "$tmpdepfile".bak + ;; + +cpp) + # Important note: in order to support this mode, a compiler *must* + # always write the proprocessed file to stdout. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test $1 != '--mode=compile'; do + shift + done + shift + fi + + # Remove `-o $object'. + IFS=" " + for arg + do + case $arg in + -o) + shift + ;; + $object) + shift + ;; + *) + set fnord "$@" "$arg" + shift # fnord + shift # $arg + ;; + esac + done + + "$@" -E | + sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' | + sed '$ s: \\$::' > "$tmpdepfile" + rm -f "$depfile" + echo "$object : \\" > "$depfile" + cat < "$tmpdepfile" >> "$depfile" + sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +msvisualcpp) + # Important note: in order to support this mode, a compiler *must* + # always write the proprocessed file to stdout, regardless of -o, + # because we must use -o when running libtool. + "$@" || exit $? + IFS=" " + for arg + do + case "$arg" in + "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") + set fnord "$@" + shift + shift + ;; + *) + set fnord "$@" "$arg" + shift + shift + ;; + esac + done + "$@" -E | + sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" + rm -f "$depfile" + echo "$object : \\" > "$depfile" + . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" + echo " " >> "$depfile" + . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +none) + exec "$@" + ;; + +*) + echo "Unknown depmode $depmode" 1>&2 + exit 1 + ;; +esac + +exit 0 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CHANGES b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CHANGES new file mode 100755 index 000000000..37ec91579 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CHANGES @@ -0,0 +1,144 @@ +0.70 +==== +- added support for access to the physical devices low level handles +- added animation demo for Win32 +- improved cygwin compatibility +- improved spline implementation +- improved pixel compatibility between X11 and GD +- fixed X11 window position problem occured with some window managers +- fixed arc and filled arc functions +- fixed memory bug (thanks to Kurihara Satoshi) +- fixed problem with black bar if resource DLL was not compiled +- fixed problem with flickering and background behind text +- bug fix for background color in g2_win32_SetBackground + +0.62 +==== +- PS in place of X11 for demo_cpp + +0.61 +==== +- ANSI C streamlining + +0.60 +==== +- added FIG device +- added win32 mouse support +- added check for dashed lines to g2_test +- bugfixes + +0.51 +==== +- g2_perl improvements (added GD device, added splines, removed GIF, + retested, added simple README) +- added configurable logging +- added some new configuration parameters and slightly changed + configuration naming convention (g2_config.h) +- added doxygen comments for automatic docu generation +- general documentation update + +0.50 +==== +- removed GIF code +- improved fortran port + +0.49a +===== +- number of small fixes +- number of changes :) + +0.42 +==== +-license change to LGPL + +0.41b +===== +-added new Tijs Michels spline implementation +-small fixes in spline package +-added g2_spline_demo.c +-changed LINKDLL into G2L in g2.h +-removed some non ansi parts (e.g. // comments) +-added query pointer for X11 (mouse) + +0.41a +===== +-modified header files for usage with c++ +-modified header files for building Win32 DLL +-added DLL version to Win32 workspace +-added Tijs Michels spline implementation +-small fixes in Makefile.in + +0.40 +==== +- added perl support +- g2_draw_string replaced with g2_string +- added g2_image function +- added g2_control_pd.* files +- g2_device_exist moved to user space (perl) +- added g2_set_line_width support in GIF device +- added prefix to Makefile.in +- updated descrip.mms + +0.30 (23.10.1998) +================ +- finished Win32 implementation +- fixed bug in virtual device section +- minor changes in g2_X11.c (include string.h) +- finished VMS port (descrip.mms files) + +0.23 (09.07.1998) +================= +- finished Fortran interface (tested on Linux and DU) +- added arc and filled_arc emulation +- minor bug fix in g2_ui_control.c (thanks to E.M. (Mark) Palandri) +- finished GIF interface +- added new demo files +- some bug fixes + +0.22 (03.06.1998) +================= +- bugfix in g2_device.c +- minor changes + +0.21 (03.06.1998) +================= +- added g2_ld (last device) concept +- minor changes in make procedures +- back to the normal 'numbering' :-) +- added (very simple) demo0.c + +0.20a (02.06.1998) +================== +- added configure script +- changed file/make structure of g2 project +- changed version numbering (a-alpha, b-beta etc.) + +0.11 (30.04.1998) +================= +- fixed bug in Makefile +- fixed bug with r rescaling (circle, ellipse and arc) in g2_graphic_pd.c +- small fix in g2_X11 +- added g2_us2pds_xxxx in g2_util.c +- minor changes in makefile.i386 and makefile.alpha + +0.10 (24.04.1998) +================= +- major kernel rewrite +- small fixes in X11 part +- removed funix: g2_AllocateBasicColors +- added Fortran interface (alpha) + +0.02 (31.03.1998) +================= +- new funix: g2_Save +- added contrib directory + + +0.01 (19.03.1998) +================= +- created CHANGES file :-) +- some small fixes +- added g2_attach_X11X and changed g2_attach_X11 to be a wrapper to + the new function +- added PostScript interface + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/COPYING b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/COPYING new file mode 100755 index 000000000..b1e3f5a26 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/COPYING @@ -0,0 +1,504 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 2.1, February 1999 + + Copyright (C) 1991, 1999 Free Software Foundation, Inc. + 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +[This is the first released version of the Lesser GPL. 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Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random Hacker. + + , 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Repository new file mode 100755 index 000000000..317b1d1fc --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Entries new file mode 100755 index 000000000..d954ef27f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Entries @@ -0,0 +1,29 @@ +D/autom4te.cache//// +D/CVS//// +D/demo//// +D/doc//// +D/g2_perl//// +D/include//// +D/perl//// +D/src//// +/CHANGES/1.1/Tue Jun 14 21:02:57 2005// +/COPYING/1.1/Tue Apr 17 20:16:38 2001// +/INSTALL/1.1/Mon Mar 29 21:47:11 2004// +/Makefile.in/1.1/Thu Aug 4 12:40:53 2005// +/README/1.1/Sun Feb 29 23:47:46 2004// +/TODO/1.1/Sun Feb 29 23:47:46 2004// +/config.guess/1.1/Mon Jan 18 10:56:51 1999// +/config.sub/1.1/Mon Jan 18 10:56:51 1999// +/configure/1.1/Thu Aug 4 12:41:58 2005// +/configure.in/1.1/Wed Apr 21 03:19:15 2004// +/descrip.mms/1.1/Thu Nov 22 00:14:25 2001// +/g2.dsp/1.1/Sat Apr 17 21:21:11 2004// +/g2.dsw/1.1/Sat Apr 17 21:28:13 2004// +/g2_anim.dsp/1.1/Sat Apr 17 21:16:41 2004// +/g2demo.dsp/1.1/Sat Apr 17 21:21:11 2004// +/g2dll.dsp/1.1/Sat Apr 17 21:28:13 2004// +/g2res.dsp/1.1/Sat Apr 17 21:21:11 2004// +/gd.dsp/1.1/Sun Jun 6 12:50:15 1999// +/install-sh/1.1/Mon Jan 18 10:56:51 1999// +/simple_win32.dsp/1.1/Sat Apr 17 21:28:13 2004// +/Makefile/1.1/Fri Aug 5 10:17:46 2005// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Repository new file mode 100755 index 000000000..0652b4086 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/INSTALL b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/INSTALL new file mode 100755 index 000000000..4fc58ad2b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/INSTALL @@ -0,0 +1,94 @@ +Installation +============ + +LINUX +----- + +Either install RPM packet with binaries, or compile as described in the +UNIX section + +UNIX +---- + +1. Extract package with gzip -dc g2-xxxx.tar.gz | tar xvf - + +2. Run './configure' + +3. Run 'make depend' + +4. Optionally edit src/g2_config.h to fine-tune g2 behavior (only if + you know what are you doing) + +5. Run 'make' + +6. Run 'make install' or copy libg2.a and g2.h, g2_X11.h, g2_gd.h, and + g2_PS.h to the default locations for library and include files. + +7. cd to demo directory and run 'make demo' to compile demo + applications + +8. To rebuild documentation run 'make doc' (html, PS and pdf manual + should be already included into documentation). + + +WINDOWS NT +---------- + +1. Extract package: unzip 'g2-xxxx.zip' + +2. For gd support, please download the binary gd version and place it in a + folder next to g2 using default folder name gdwin32, i.e. it is expected + in ../gdwin32 from the folder this file is residing. + You also will need to create the bgd.lib file using makemsvcimport.bat + +3. MS Visual C++ users can build both library and demos with the supplied + project file: g2.xxx + users of gcc or other commandline based compilers with make support + continue as in Unix example + + +VMS +--- + +Note: VMS is not tested in latest builds. However descrip.mms is a +good starting point. + +1. set default to root of distribution directory + +2. type mms to build g2.olb library + +3. to compile demo files, set defualt to [.demo] and type mms + +4. to install: copy g2.olb and g2.h, g2_X11.h and g2_PS.h to install + directories + + +PNG-SUPPORT +----------- + +g2 needs to be linked to the free available gd library written by +Thomas Boutell in order to create PNG files. g2 is tested with +version 2.0.22 of gd. gd is available at http://www.boutell.com/gd/ and +at numerous mirror sites. Use a ftp search +(e.g. http://ftpsearch.ntnu.no/) and search for "gd1.3.tar.gz" to find +your nearest mirror site. + + +PERL SUPPORT +------------ +1. build g2 library +2. cd to g2_perl and run + perl Makefile.PL + make + make test + + +SHARED LIBRARIES +---------------- +Support for shared libraries is tested on Linux and OSF +(DigitalUnix). To build shared libraries type 'make shared'. If you +want to run demo applications without installed shared libraries, you +should add to LD_LIBRARY_PATH the path to the g2 shared library +(e.g. 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/some/path/to/g2') + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/Makefile new file mode 100755 index 000000000..93b66162d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/Makefile @@ -0,0 +1,149 @@ +# +# +# Makefile for g2 library +# +# + +G2_VERSION = 0.70 + +# +# g2 installation directories +# +LIBDIR = /usr/local/lib +INCDIR = /usr/local/include + + +#LIBDIR = $(HOME)/local/lib +#INCDIR = $(HOME)/local/include + +# +#------------------------ do not edit ------------------------ +# +SHELL = /bin/sh + +CC = gcc +CFLAGS = -I./src -g -O2 -I/usr/X11R6/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_GD=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 +INSTALL = /usr/bin/install -c +INSTALL_DATA = ${INSTALL} -m 644 +FIND = find +MAKEDEPEND = makedepend +AR = ar +ARFLAGS = -cr +RANLIB = ranlib +LD = ld +LDFLAGS = -L/usr/X11R6/lib64 -L/usr/local/lib -lm -lX11 -lgd + + +BASE_DIR = ./src +BASE_SRC = $(BASE_DIR)/g2_device.c $(BASE_DIR)/g2_ui_control.c \ + $(BASE_DIR)/g2_util.c $(BASE_DIR)/g2_fif.c \ + $(BASE_DIR)/g2_virtual_device.c $(BASE_DIR)/g2_physical_device.c \ + $(BASE_DIR)/g2_graphic_pd.c $(BASE_DIR)/g2_control_pd.c \ + $(BASE_DIR)/g2_ui_graphic.c $(BASE_DIR)/g2_ui_virtual_device.c \ + $(BASE_DIR)/g2_ui_device.c $(BASE_DIR)/g2_splines.c +BASE_INS = $(BASE_DIR)/g2.h + + +PS_DIR = ./src/PS +PS_SRC = $(PS_DIR)/g2_PS.c +PS_INS = $(PS_DIR)/g2_PS.h + +FIG_DIR = ./src/FIG +FIG_SRC = $(FIG_DIR)/g2_FIG.c +FIG_INS = $(FIG_DIR)/g2_FIG.h + +X11_DIR = ./src/X11 +X11_SRC = $(X11_DIR)/g2_X11.c +X11_INS = $(X11_DIR)/g2_X11.h + +#WIN32_DIR = ./src/WIN32 +#WIN32_SRC = $(WIN32_DIR)/g2_win32.c $(WIN32_DIR)/g2_win32_thread.c +#WIN32_INS = $(WIN32_DIR)/g2_win32.h + +GD_DIR = ./src/GD +GD_SRC = $(GD_DIR)/g2_gd.c +GD_INS = $(GD_DIR)/g2_gd.h + + +SRC = $(BASE_SRC) $(PS_SRC) $(FIG_SRC) $(X11_SRC) $(WIN32_SRC) $(GD_SRC) +OBJ = $(SRC:.c=.o) + +INS = $(BASE_INS) $(PS_INS) $(FIG_INS) $(X11_INS) $(WIN32_INS) $(GD_INS) + +# +# define some phony targets +# +.PHONY: all shared clean doc release demo + +# +# major rule +# +.c.o: + $(CC) $(CFLAGS) -c $< -o $@ + + +all: libg2.a + test -d ./include || mkdir ./include + cp $(INS) ./include/ + +shared: libg2.so.0.$(G2_VERSION) + @echo + + +libg2.a: $(OBJ) + $(AR) $(ARFLAGS) libg2.a $(OBJ) + test ! -n "$(RANLIB)" || $(RANLIB) $@ + +libg2.so.0.$(G2_VERSION): $(OBJ) + ld -shared -soname libg2.so.0 -o $@ $(OBJ) + +install: libg2.a + test -d $(LIBDIR) || mkdir -p $(LIBDIR) + test -d $(INCDIR) || mkdir -p $(INCDIR) + $(INSTALL_DATA) libg2.a $(LIBDIR) + for IFILE in $(INS); do \ + $(INSTALL_DATA) $$IFILE $(INCDIR); \ + done + +release: clean doc + cp ./doc/latex/refman.ps ./doc/g2_refman.ps + cp ./doc/latex/refman.pdf ./doc/g2_refman.pdf + rm -r ./doc/latex + +doc: + (cd ./doc ; doxygen Doxyfile) + (cd ./doc/latex ; make ps ; make pdf) + + +clean: + -(cd ./demo ; make clean) + -rm -f $(OBJ) + -rm -f libg2.a config.cache config.log Makefile.bak config.status + -rm -f ./include/*.h + -$(FIND) . -name "*~" -exec rm -f {} \; + -(cd ./g2_perl ; make clean) + -rm -f ./g2_perl/test.ps + -rm -f ./g2_perl/test.png + -rm -f ./g2_perl/test.jpg + -rm -f ./g2_perl/test.fig + -rm -f ./g2_perl/Makefile.old + -rm -f ./libg2.so.0.$(G2_VERSION) + -rm -f libg2.$(G2_VERSION).a + -rm -f a.out + -rm -fr doc/html/ doc/latex/ doc/g2_refman.ps doc/g2_refman.pdf + +demo: libg2.a + (cd ./demo ; make) + +depend: + $(MAKEDEPEND) -- $(CFLAGS) -- $(SRC) + @echo + @echo "Run 'make' to build g2 library." + @echo + +distdir: + cp -r * $(distdir) + + +# DO NOT DELETE THIS LINE -- make depend depends on it. + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/Makefile.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/Makefile.in new file mode 100755 index 000000000..025ef5f5b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/Makefile.in @@ -0,0 +1,149 @@ +# +# +# Makefile for g2 library +# +# + +G2_VERSION = 0.70 + +# +# g2 installation directories +# +LIBDIR = @prefix@/lib +INCDIR = @prefix@/include + + +#LIBDIR = $(HOME)/local/lib +#INCDIR = $(HOME)/local/include + +# +#------------------------ do not edit ------------------------ +# +SHELL = /bin/sh + +CC = @CC@ +CFLAGS = -I./src @CFLAGS@ @DEFS@ +INSTALL = @INSTALL@ +INSTALL_DATA = @INSTALL_DATA@ +FIND = @FIND@ +MAKEDEPEND = @MAKEDEPEND@ +AR = ar +ARFLAGS = -cr +RANLIB = @RANLIB@ +LD = ld +LDFLAGS = @LDFLAGS@ + + +BASE_DIR = ./src +BASE_SRC = $(BASE_DIR)/g2_device.c $(BASE_DIR)/g2_ui_control.c \ + $(BASE_DIR)/g2_util.c $(BASE_DIR)/g2_fif.c \ + $(BASE_DIR)/g2_virtual_device.c $(BASE_DIR)/g2_physical_device.c \ + $(BASE_DIR)/g2_graphic_pd.c $(BASE_DIR)/g2_control_pd.c \ + $(BASE_DIR)/g2_ui_graphic.c $(BASE_DIR)/g2_ui_virtual_device.c \ + $(BASE_DIR)/g2_ui_device.c $(BASE_DIR)/g2_splines.c +BASE_INS = $(BASE_DIR)/g2.h + + +@DO_PS@PS_DIR = ./src/PS +@DO_PS@PS_SRC = $(PS_DIR)/g2_PS.c +@DO_PS@PS_INS = $(PS_DIR)/g2_PS.h + +@DO_FIG@FIG_DIR = ./src/FIG +@DO_FIG@FIG_SRC = $(FIG_DIR)/g2_FIG.c +@DO_FIG@FIG_INS = $(FIG_DIR)/g2_FIG.h + +@DO_X11@X11_DIR = ./src/X11 +@DO_X11@X11_SRC = $(X11_DIR)/g2_X11.c +@DO_X11@X11_INS = $(X11_DIR)/g2_X11.h + +@DO_WIN32@WIN32_DIR = ./src/WIN32 +@DO_WIN32@WIN32_SRC = $(WIN32_DIR)/g2_win32.c $(WIN32_DIR)/g2_win32_thread.c +@DO_WIN32@WIN32_INS = $(WIN32_DIR)/g2_win32.h + +@DO_GD@GD_DIR = ./src/GD +@DO_GD@GD_SRC = $(GD_DIR)/g2_gd.c +@DO_GD@GD_INS = $(GD_DIR)/g2_gd.h + + +SRC = $(BASE_SRC) $(PS_SRC) $(FIG_SRC) $(X11_SRC) $(WIN32_SRC) $(GD_SRC) +OBJ = $(SRC:.c=.o) + +INS = $(BASE_INS) $(PS_INS) $(FIG_INS) $(X11_INS) $(WIN32_INS) $(GD_INS) + +# +# define some phony targets +# +.PHONY: all shared clean doc release demo + +# +# major rule +# +.c.o: + $(CC) $(CFLAGS) -c $< -o $@ + + +all: libg2.a + test -d ./include || mkdir ./include + cp $(INS) ./include/ + +shared: libg2.@LD_SHARED_EXT@ + @echo + + +libg2.a: $(OBJ) + $(AR) $(ARFLAGS) libg2.a $(OBJ) + test ! -n "$(RANLIB)" || $(RANLIB) $@ + +libg2.@LD_SHARED_EXT@: $(OBJ) + @LD_SHARED@ @LD_SHARED_FLAGS@ -o $@ $(OBJ) @LD_SHARED_OPT@ + +install: libg2.a + test -d $(LIBDIR) || mkdir -p $(LIBDIR) + test -d $(INCDIR) || mkdir -p $(INCDIR) + $(INSTALL_DATA) libg2.a $(LIBDIR) + for IFILE in $(INS); do \ + $(INSTALL_DATA) $$IFILE $(INCDIR); \ + done + +release: clean doc + cp ./doc/latex/refman.ps ./doc/g2_refman.ps + cp ./doc/latex/refman.pdf ./doc/g2_refman.pdf + rm -r ./doc/latex + +doc: + (cd ./doc ; doxygen Doxyfile) + (cd ./doc/latex ; make ps ; make pdf) + + +clean: + -(cd ./demo ; make clean) + -rm -f $(OBJ) + -rm -f libg2.a config.cache config.log Makefile.bak config.status + -rm -f ./include/*.h + -$(FIND) . -name "*~" -exec rm -f {} \; + -(cd ./g2_perl ; make clean) + -rm -f ./g2_perl/test.ps + -rm -f ./g2_perl/test.png + -rm -f ./g2_perl/test.jpg + -rm -f ./g2_perl/test.fig + -rm -f ./g2_perl/Makefile.old + -rm -f ./libg2.@LD_SHARED_EXT@ + -rm -f libg2.$(G2_VERSION).a + -rm -f a.out + -rm -fr doc/html/ doc/latex/ doc/g2_refman.ps doc/g2_refman.pdf + +demo: libg2.a + (cd ./demo ; make) + +depend: + $(MAKEDEPEND) -- $(CFLAGS) -- $(SRC) + @echo + @echo "Run 'make' to build g2 library." + @echo + +distdir: + cp -r * $(distdir) + + +# DO NOT DELETE THIS LINE -- make depend depends on it. + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/README b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/README new file mode 100755 index 000000000..80f0401cb --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/README @@ -0,0 +1,80 @@ +g2 - graphic library (C) 1999 Lj. Milanovic, H. Wagner + +Version 0.xx + +License Information +=================== + +This library is free software; you can redistribute it and/or +modify it under the terms of the GNU Lesser General Public +License as published by the Free Software Foundation; either +version 2.1 of the License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +Lesser General Public License for more details. + +See INSTALL for information on how to install g2 see the html +documentation in the doc/ subdirectory for a function reference + +What is g2 ? +============ + +Short version (if you are in hurry): + + - 2D graphic library + - Simple to use + - Supports several types of output devices (currently X11, + gd (PNG, JPEG), PostScript) + - Concept allows easy implementation of new device types + - Virtual devices allow to send output simultaneously to several devices + - User definable coordinate system + - Written in ANSI-C + - Tested under Digital Unix, AIX, Linux, VMS and Windows NT + - Fortran interface + +Long version: + +g2 is a simple to use graphics library for 2D graphical applications +written in Ansi-C. This library provides a comprehensive set of +functions for simultaneous generation of graphical output on different +types of devices. Presently, following devices are currently supported +by g2: X11, gd (PNG, JPEG), PostScript (xfig and Win32 are in developement). +One major feature of the g2_library is the concept of virtual devices. An +arbitrary number of physical devices (such as PNG, or X11) can be +grouped to create a so-called virtual device. Commands sent to such a +virtual devices will automatically issued to all attached physical +devices. This allows for example simultaneous output to a PNG file and +a Postscript file. A virtual device in turn can be attached to another +virtual device, allowing to construct trees of devices. Virtual +devices can also be useful when using different user-coordinate +systems. E.g. one X11 window showing an overview of a graphical +output, and a second window showing a zoom of a more detailed area of +the graphic. Drawing in both windows is performed by one single +command to the virtual device. + + + /-------> PNG: g2_attach(id_PNG,... + ----------------------- +g2_plot---> | Virtual device: id |--------> X11: g2_attach(id_X11,... + ----------------------- + \-------> PS: g2_attach(id_PS,... + +If you don't need or like the concept of virtual devices, simply ignore it. + + +CONTACT +======= + +You can contact the authors and contributors by e-mail (/ is @ and - is .): + +Ljubomir Milanovic ljubo/users-sourceforge-net +Horst Wagner wagner/users-sourceforge-net +Tijs Michels (spline implementation) tijs/vimec-nl + +or visit g2 home page on: + +http://g2.sourceforge.net/ + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/TODO b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/TODO new file mode 100755 index 000000000..cf294d193 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/TODO @@ -0,0 +1,8 @@ + +- native g2_image support +- gd: setlinedash +- finish xfig support +- test (and add) Fortran interface on more platforms +- new devices (e.g. PNG, JPG, etc.) +- documentation for developement of new devices + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Repository new file mode 100755 index 000000000..c49a15b09 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/autom4te.cache diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/output.0 b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/output.0 new file mode 100755 index 000000000..de34feaaf --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/output.0 @@ -0,0 +1,6602 @@ +@%:@! /bin/sh +@%:@ Guess values for system-dependent variables and create Makefiles. +@%:@ Generated by GNU Autoconf 2.59. +@%:@ +@%:@ Copyright (C) 2003 Free Software Foundation, Inc. +@%:@ This configure script is free software; the Free Software Foundation +@%:@ gives unlimited permission to copy, distribute and modify it. +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## + +# Be Bourne compatible +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' +elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then + set -o posix +fi +DUALCASE=1; export DUALCASE # for MKS sh + +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + + +# Work around bugs in pre-3.0 UWIN ksh. +$as_unset ENV MAIL MAILPATH +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +for as_var in \ + LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ + LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ + LC_TELEPHONE LC_TIME +do + if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then + eval $as_var=C; export $as_var + else + $as_unset $as_var + fi +done + +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)$' \| \ + . : '\(.\)' 2>/dev/null || +echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } + /^X\/\(\/\/\)$/{ s//\1/; q; } + /^X\/\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + + +# PATH needs CR, and LINENO needs CR and PATH. +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + echo "#! /bin/sh" >conf$$.sh + echo "exit 0" >>conf$$.sh + chmod +x conf$$.sh + if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then + PATH_SEPARATOR=';' + else + PATH_SEPARATOR=: + fi + rm -f conf$$.sh +fi + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" || { + # Find who we are. 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Use of quotes ensures accuracy. + *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; + esac + fi +done +if $ac_cache_corrupted; then + { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 +echo "$as_me: error: changes in the environment can compromise the build" >&2;} + { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 +echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} + { (exit 1); exit 1; }; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + + + + + + + + + + + + + + + + + + + +PRODUCT=g2 + + +# +# check cannonical system name, +# and set options for shared libraries (black magic) +# +ac_aux_dir= +for ac_dir in $srcdir $srcdir/.. $srcdir/../..; do + if test -f $ac_dir/install-sh; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install-sh -c" + break + elif test -f $ac_dir/install.sh; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install.sh -c" + break + elif test -f $ac_dir/shtool; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/shtool install -c" + break + fi +done +if test -z "$ac_aux_dir"; then + { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&5 +echo "$as_me: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&2;} + { (exit 1); exit 1; }; } +fi +ac_config_guess="$SHELL $ac_aux_dir/config.guess" +ac_config_sub="$SHELL $ac_aux_dir/config.sub" +ac_configure="$SHELL $ac_aux_dir/configure" # This should be Cygnus configure. + +# Make sure we can run config.sub. +$ac_config_sub sun4 >/dev/null 2>&1 || + { { echo "$as_me:$LINENO: error: cannot run $ac_config_sub" >&5 +echo "$as_me: error: cannot run $ac_config_sub" >&2;} + { (exit 1); exit 1; }; } + +echo "$as_me:$LINENO: checking build system type" >&5 +echo $ECHO_N "checking build system type... $ECHO_C" >&6 +if test "${ac_cv_build+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_build_alias=$build_alias +test -z "$ac_cv_build_alias" && + ac_cv_build_alias=`$ac_config_guess` +test -z "$ac_cv_build_alias" && + { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5 +echo "$as_me: error: cannot guess build type; you must specify one" >&2;} + { (exit 1); exit 1; }; } +ac_cv_build=`$ac_config_sub $ac_cv_build_alias` || + { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_build_alias failed" >&5 +echo "$as_me: error: $ac_config_sub $ac_cv_build_alias failed" >&2;} + { (exit 1); exit 1; }; } + +fi +echo "$as_me:$LINENO: result: $ac_cv_build" >&5 +echo "${ECHO_T}$ac_cv_build" >&6 +build=$ac_cv_build +build_cpu=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` +build_vendor=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` +build_os=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` + + +echo "$as_me:$LINENO: checking host system type" >&5 +echo $ECHO_N "checking host system type... $ECHO_C" >&6 +if test "${ac_cv_host+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_host_alias=$host_alias +test -z "$ac_cv_host_alias" && + ac_cv_host_alias=$ac_cv_build_alias +ac_cv_host=`$ac_config_sub $ac_cv_host_alias` || + { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_host_alias failed" >&5 +echo "$as_me: error: $ac_config_sub $ac_cv_host_alias failed" >&2;} + { (exit 1); exit 1; }; } + +fi +echo "$as_me:$LINENO: result: $ac_cv_host" >&5 +echo "${ECHO_T}$ac_cv_host" >&6 +host=$ac_cv_host +host_cpu=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` +host_vendor=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` +host_os=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` + + +case "$host" in + *-linux*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-shared -soname libg2.so.0' + LD_SHARED_OPT='' + LD_SHARED_EXT='so.0.$(G2_VERSION)' + cat >>confdefs.h <<\_ACEOF +@%:@define LINUX 1 +_ACEOF +;; + *-aix*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-bM:SRE -bnoentry -bexpall' + LD_SHARED_OPT='$(LDFLAGS) -lc' + LD_SHARED_EXT='so' + cat >>confdefs.h <<\_ACEOF +@%:@define AIX 1 +_ACEOF +;; + *-osf*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-shared' + LD_SHARED_OPT='$(LDFLAGS) -lc' + LD_SHARED_EXT='so' + cat >>confdefs.h <<\_ACEOF +@%:@define OSF 1 +_ACEOF +;; + *) + LD_SHARED_EXT='so' + cat >>confdefs.h <<\_ACEOF +@%:@define UNIX 1 +_ACEOF +;; +esac + + + + + + +# +# check C compiler, preprocesor, etc. +# +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $@%:@ != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CC" && break +done + + CC=$ac_ct_CC +fi + +fi + + +test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files a.out a.exe b.out" +# Try to create an executable without -o first, disregard a.out. +# It will help us diagnose broken compilers, and finding out an intuition +# of exeext. +echo "$as_me:$LINENO: checking for C compiler default output file name" >&5 +echo $ECHO_N "checking for C compiler default output file name... $ECHO_C" >&6 +ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` +if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 + (eval $ac_link_default) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # Find the output, starting from the most likely. This scheme is +# not robust to junk in `.', hence go to wildcards (a.*) only as a last +# resort. + +# Be careful to initialize this variable, since it used to be cached. +# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. +ac_cv_exeext= +# b.out is created by i960 compilers. +for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out +do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) + ;; + conftest.$ac_ext ) + # This is the source file. + ;; + [ab].out ) + # We found the default executable, but exeext='' is most + # certainly right. + break;; + *.* ) + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + # FIXME: I believe we export ac_cv_exeext for Libtool, + # but it would be cool to find out if it's true. Does anybody + # maintain Libtool? --akim. + export ac_cv_exeext + break;; + * ) + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: C compiler cannot create executables +See \`config.log' for more details." >&5 +echo "$as_me: error: C compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; } +fi + +ac_exeext=$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_file" >&5 +echo "${ECHO_T}$ac_file" >&6 + +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether the C compiler works" >&5 +echo $ECHO_N "checking whether the C compiler works... $ECHO_C" >&6 +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. +if test "$cross_compiling" != yes; then + if { ac_try='./$ac_file' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { echo "$as_me:$LINENO: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + fi + fi +fi +echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + +rm -f a.out a.exe conftest$ac_cv_exeext b.out +ac_clean_files=$ac_clean_files_save +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 +echo "$as_me:$LINENO: result: $cross_compiling" >&5 +echo "${ECHO_T}$cross_compiling" >&6 + +echo "$as_me:$LINENO: checking for suffix of executables" >&5 +echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + export ac_cv_exeext + break;; + * ) break;; + esac +done +else + { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +echo "${ECHO_T}$ac_cv_exeext" >&6 + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +echo "$as_me:$LINENO: checking for suffix of object files" >&5 +echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 +if test "${ac_cv_objext+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.o conftest.obj +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; + *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest.$ac_cv_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 +echo "${ECHO_T}$ac_cv_objext" >&6 +OBJEXT=$ac_cv_objext +ac_objext=$OBJEXT +echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 +if test "${ac_cv_c_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 +GCC=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +CFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 +echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cc_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 +echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_prog_cc_stdc=no +ac_save_CC=$CC +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std1 is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std1. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +# Don't try gcc -ansi; that turns off useful extensions and +# breaks some systems' header files. +# AIX -qlanglvl=ansi +# Ultrix and OSF/1 -std1 +# HP-UX 10.20 and later -Ae +# HP-UX older versions -Aa -D_HPUX_SOURCE +# SVR4 -Xc -D__EXTENSIONS__ +for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_stdc=$ac_arg +break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext +done +rm -f conftest.$ac_ext conftest.$ac_objext +CC=$ac_save_CC + +fi + +case "x$ac_cv_prog_cc_stdc" in + x|xno) + echo "$as_me:$LINENO: result: none needed" >&5 +echo "${ECHO_T}none needed" >&6 ;; + *) + echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 + CC="$CC $ac_cv_prog_cc_stdc" ;; +esac + +# Some people use a C++ compiler to compile C. Since we use `exit', +# in C++ we need to declare it. In case someone uses the same compiler +# for both compiling C and C++ we need to have the C++ compiler decide +# the declaration of exit, since it's the most demanding environment. +cat >conftest.$ac_ext <<_ACEOF +@%:@ifndef __cplusplus + choke me +@%:@endif +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +@%:@include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 +echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6 +# On Suns, sometimes $CPP names a directory. +if test -n "$CPP" && test -d "$CPP"; then + CPP= +fi +if test -z "$CPP"; then + if test "${ac_cv_prog_CPP+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + # Double quotes because CPP needs to be expanded + for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" + do + ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +@%:@ifdef __STDC__ +@%:@ include +@%:@else +@%:@ include +@%:@endif + Syntax error +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether non-existent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +@%:@include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # Broken: success on invalid input. +continue +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + break +fi + + done + ac_cv_prog_CPP=$CPP + +fi + CPP=$ac_cv_prog_CPP +else + ac_cv_prog_CPP=$CPP +fi +echo "$as_me:$LINENO: result: $CPP" >&5 +echo "${ECHO_T}$CPP" >&6 +ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +@%:@ifdef __STDC__ +@%:@ include +@%:@else +@%:@ include +@%:@endif + Syntax error +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether non-existent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +@%:@include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # Broken: success on invalid input. +continue +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : +else + { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&5 +echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu +if test -n "$ac_tool_prefix"; then + for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CXX+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CXX"; then + ac_cv_prog_CXX="$CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CXX=$ac_cv_prog_CXX +if test -n "$CXX"; then + echo "$as_me:$LINENO: result: $CXX" >&5 +echo "${ECHO_T}$CXX" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CXX" && break + done +fi +if test -z "$CXX"; then + ac_ct_CXX=$CXX + for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CXX"; then + ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CXX="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CXX=$ac_cv_prog_ac_ct_CXX +if test -n "$ac_ct_CXX"; then + echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 +echo "${ECHO_T}$ac_ct_CXX" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CXX" && break +done +test -n "$ac_ct_CXX" || ac_ct_CXX="g++" + + CXX=$ac_ct_CXX +fi + + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C++ compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_cxx_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6 +GXX=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CXXFLAGS=${CXXFLAGS+set} +ac_save_CXXFLAGS=$CXXFLAGS +CXXFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 +echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cxx_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cxx_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cxx_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6 +if test "$ac_test_CXXFLAGS" = set; then + CXXFLAGS=$ac_save_CXXFLAGS +elif test $ac_cv_prog_cxx_g = yes; then + if test "$GXX" = yes; then + CXXFLAGS="-g -O2" + else + CXXFLAGS="-g" + fi +else + if test "$GXX" = yes; then + CXXFLAGS="-O2" + else + CXXFLAGS= + fi +fi +for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +@%:@include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. +set dummy ${ac_tool_prefix}ranlib; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_RANLIB+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$RANLIB"; then + ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +RANLIB=$ac_cv_prog_RANLIB +if test -n "$RANLIB"; then + echo "$as_me:$LINENO: result: $RANLIB" >&5 +echo "${ECHO_T}$RANLIB" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_RANLIB"; then + ac_ct_RANLIB=$RANLIB + # Extract the first word of "ranlib", so it can be a program name with args. +set dummy ranlib; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_RANLIB"; then + ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_RANLIB="ranlib" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + test -z "$ac_cv_prog_ac_ct_RANLIB" && ac_cv_prog_ac_ct_RANLIB=":" +fi +fi +ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB +if test -n "$ac_ct_RANLIB"; then + echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5 +echo "${ECHO_T}$ac_ct_RANLIB" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + RANLIB=$ac_ct_RANLIB +else + RANLIB="$ac_cv_prog_RANLIB" +fi + +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 +echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6 +if test -z "$INSTALL"; then +if test "${ac_cv_path_install+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + done + done + ;; +esac +done + + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. We don't cache a + # path for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the path is relative. + INSTALL=$ac_install_sh + fi +fi +echo "$as_me:$LINENO: result: $INSTALL" >&5 +echo "${ECHO_T}$INSTALL" >&6 + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' + +# Extract the first word of "find", so it can be a program name with args. +set dummy find; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_FIND+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$FIND"; then + ac_cv_prog_FIND="$FIND" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_FIND="find" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + test -z "$ac_cv_prog_FIND" && ac_cv_prog_FIND=":" +fi +fi +FIND=$ac_cv_prog_FIND +if test -n "$FIND"; then + echo "$as_me:$LINENO: result: $FIND" >&5 +echo "${ECHO_T}$FIND" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +# Extract the first word of "makedepend", so it can be a program name with args. +set dummy makedepend; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_MAKEDEPEND+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$MAKEDEPEND"; then + ac_cv_prog_MAKEDEPEND="$MAKEDEPEND" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_MAKEDEPEND="makedepend" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + test -z "$ac_cv_prog_MAKEDEPEND" && ac_cv_prog_MAKEDEPEND=":" +fi +fi +MAKEDEPEND=$ac_cv_prog_MAKEDEPEND +if test -n "$MAKEDEPEND"; then + echo "$as_me:$LINENO: result: $MAKEDEPEND" >&5 +echo "${ECHO_T}$MAKEDEPEND" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + +echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 +echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6 +if test "${ac_cv_lib_dl_dlopen+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldl $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char dlopen (); +int +main () +{ +dlopen (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_dl_dlopen=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_dl_dlopen=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5 +echo "${ECHO_T}$ac_cv_lib_dl_dlopen" >&6 +if test $ac_cv_lib_dl_dlopen = yes; then + have_dl=yes +else + have_dl=no +fi + + + +# +# Try to locate the X Window System include files and libraries +# and add /usr/local to include and lib path and add -lm (for testing) +# + +echo "$as_me:$LINENO: checking for X" >&5 +echo $ECHO_N "checking for X... $ECHO_C" >&6 + + +# Check whether --with-x or --without-x was given. +if test "${with_x+set}" = set; then + withval="$with_x" + +fi; +# $have_x is `yes', `no', `disabled', or empty when we do not yet know. +if test "x$with_x" = xno; then + # The user explicitly disabled X. + have_x=disabled +else + if test "x$x_includes" != xNONE && test "x$x_libraries" != xNONE; then + # Both variables are already set. + have_x=yes + else + if test "${ac_cv_have_x+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + # One or both of the vars are not set, and there is no cached value. +ac_x_includes=no ac_x_libraries=no +rm -fr conftest.dir +if mkdir conftest.dir; then + cd conftest.dir + # Make sure to not put "make" in the Imakefile rules, since we grep it out. + cat >Imakefile <<'_ACEOF' +acfindx: + @echo 'ac_im_incroot="${INCROOT}"; ac_im_usrlibdir="${USRLIBDIR}"; ac_im_libdir="${LIBDIR}"' +_ACEOF + if (xmkmf) >/dev/null 2>/dev/null && test -f Makefile; then + # GNU make sometimes prints "make[1]: Entering...", which would confuse us. + eval `${MAKE-make} acfindx 2>/dev/null | grep -v make` + # Open Windows xmkmf reportedly sets LIBDIR instead of USRLIBDIR. + for ac_extension in a so sl; do + if test ! -f $ac_im_usrlibdir/libX11.$ac_extension && + test -f $ac_im_libdir/libX11.$ac_extension; then + ac_im_usrlibdir=$ac_im_libdir; break + fi + done + # Screen out bogus values from the imake configuration. They are + # bogus both because they are the default anyway, and because + # using them would break gcc on systems where it needs fixed includes. + case $ac_im_incroot in + /usr/include) ;; + *) test -f "$ac_im_incroot/X11/Xos.h" && ac_x_includes=$ac_im_incroot;; + esac + case $ac_im_usrlibdir in + /usr/lib | /lib) ;; + *) test -d "$ac_im_usrlibdir" && ac_x_libraries=$ac_im_usrlibdir ;; + esac + fi + cd .. + rm -fr conftest.dir +fi + +# Standard set of common directories for X headers. +# Check X11 before X11Rn because it is often a symlink to the current release. +ac_x_header_dirs=' +/usr/X11/include +/usr/X11R6/include +/usr/X11R5/include +/usr/X11R4/include + +/usr/include/X11 +/usr/include/X11R6 +/usr/include/X11R5 +/usr/include/X11R4 + +/usr/local/X11/include +/usr/local/X11R6/include +/usr/local/X11R5/include +/usr/local/X11R4/include + +/usr/local/include/X11 +/usr/local/include/X11R6 +/usr/local/include/X11R5 +/usr/local/include/X11R4 + +/usr/X386/include +/usr/x386/include +/usr/XFree86/include/X11 + +/usr/include +/usr/local/include +/usr/unsupported/include +/usr/athena/include +/usr/local/x11r5/include +/usr/lpp/Xamples/include + +/usr/openwin/include +/usr/openwin/share/include' + +if test "$ac_x_includes" = no; then + # Guess where to find include files, by looking for Intrinsic.h. + # First, try using that file with no special directory specified. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +@%:@include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # We can compile using X headers with no special include directory. +ac_x_includes= +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + for ac_dir in $ac_x_header_dirs; do + if test -r "$ac_dir/X11/Intrinsic.h"; then + ac_x_includes=$ac_dir + break + fi +done +fi +rm -f conftest.err conftest.$ac_ext +fi # $ac_x_includes = no + +if test "$ac_x_libraries" = no; then + # Check for the libraries. + # See if we find them without any special options. + # Don't add to $LIBS permanently. + ac_save_LIBS=$LIBS + LIBS="-lXt $LIBS" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +@%:@include +int +main () +{ +XtMalloc (0) + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + LIBS=$ac_save_LIBS +# We can link X programs with no special library path. +ac_x_libraries= +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +LIBS=$ac_save_LIBS +for ac_dir in `echo "$ac_x_includes $ac_x_header_dirs" | sed s/include/lib/g` +do + # Don't even attempt the hair of trying to link an X program! + for ac_extension in a so sl; do + if test -r $ac_dir/libXt.$ac_extension; then + ac_x_libraries=$ac_dir + break 2 + fi + done +done +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi # $ac_x_libraries = no + +if test "$ac_x_includes" = no || test "$ac_x_libraries" = no; then + # Didn't find X anywhere. Cache the known absence of X. + ac_cv_have_x="have_x=no" +else + # Record where we found X for the cache. + ac_cv_have_x="have_x=yes \ + ac_x_includes=$ac_x_includes ac_x_libraries=$ac_x_libraries" +fi +fi + + fi + eval "$ac_cv_have_x" +fi # $with_x != no + +if test "$have_x" != yes; then + echo "$as_me:$LINENO: result: $have_x" >&5 +echo "${ECHO_T}$have_x" >&6 + no_x=yes +else + # If each of the values was on the command line, it overrides each guess. + test "x$x_includes" = xNONE && x_includes=$ac_x_includes + test "x$x_libraries" = xNONE && x_libraries=$ac_x_libraries + # Update the cache value to reflect the command line values. + ac_cv_have_x="have_x=yes \ + ac_x_includes=$x_includes ac_x_libraries=$x_libraries" + echo "$as_me:$LINENO: result: libraries $x_libraries, headers $x_includes" >&5 +echo "${ECHO_T}libraries $x_libraries, headers $x_includes" >&6 +fi + +if test "$no_x" = yes; then + # Not all programs may use this symbol, but it does not hurt to define it. + +cat >>confdefs.h <<\_ACEOF +@%:@define X_DISPLAY_MISSING 1 +_ACEOF + + X_CFLAGS= X_PRE_LIBS= X_LIBS= X_EXTRA_LIBS= +else + if test -n "$x_includes"; then + X_CFLAGS="$X_CFLAGS -I$x_includes" + fi + + # It would also be nice to do this for all -L options, not just this one. + if test -n "$x_libraries"; then + X_LIBS="$X_LIBS -L$x_libraries" + # For Solaris; some versions of Sun CC require a space after -R and + # others require no space. Words are not sufficient . . . . + case `(uname -sr) 2>/dev/null` in + "SunOS 5"*) + echo "$as_me:$LINENO: checking whether -R must be followed by a space" >&5 +echo $ECHO_N "checking whether -R must be followed by a space... $ECHO_C" >&6 + ac_xsave_LIBS=$LIBS; LIBS="$LIBS -R$x_libraries" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_R_nospace=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_R_nospace=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + if test $ac_R_nospace = yes; then + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 + X_LIBS="$X_LIBS -R$x_libraries" + else + LIBS="$ac_xsave_LIBS -R $x_libraries" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_R_space=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_R_space=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + if test $ac_R_space = yes; then + echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + X_LIBS="$X_LIBS -R $x_libraries" + else + echo "$as_me:$LINENO: result: neither works" >&5 +echo "${ECHO_T}neither works" >&6 + fi + fi + LIBS=$ac_xsave_LIBS + esac + fi + + # Check for system-dependent libraries X programs must link with. + # Do this before checking for the system-independent R6 libraries + # (-lICE), since we may need -lsocket or whatever for X linking. + + if test "$ISC" = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lnsl_s -linet" + else + # Martyn Johnson says this is needed for Ultrix, if the X + # libraries were built with DECnet support. And Karl Berry says + # the Alpha needs dnet_stub (dnet does not exist). + ac_xsave_LIBS="$LIBS"; LIBS="$LIBS $X_LIBS -lX11" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char XOpenDisplay (); +int +main () +{ +XOpenDisplay (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +echo "$as_me:$LINENO: checking for dnet_ntoa in -ldnet" >&5 +echo $ECHO_N "checking for dnet_ntoa in -ldnet... $ECHO_C" >&6 +if test "${ac_cv_lib_dnet_dnet_ntoa+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldnet $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char dnet_ntoa (); +int +main () +{ +dnet_ntoa (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_dnet_dnet_ntoa=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_dnet_dnet_ntoa=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_dnet_dnet_ntoa" >&5 +echo "${ECHO_T}$ac_cv_lib_dnet_dnet_ntoa" >&6 +if test $ac_cv_lib_dnet_dnet_ntoa = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet" +fi + + if test $ac_cv_lib_dnet_dnet_ntoa = no; then + echo "$as_me:$LINENO: checking for dnet_ntoa in -ldnet_stub" >&5 +echo $ECHO_N "checking for dnet_ntoa in -ldnet_stub... $ECHO_C" >&6 +if test "${ac_cv_lib_dnet_stub_dnet_ntoa+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldnet_stub $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char dnet_ntoa (); +int +main () +{ +dnet_ntoa (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_dnet_stub_dnet_ntoa=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_dnet_stub_dnet_ntoa=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_dnet_stub_dnet_ntoa" >&5 +echo "${ECHO_T}$ac_cv_lib_dnet_stub_dnet_ntoa" >&6 +if test $ac_cv_lib_dnet_stub_dnet_ntoa = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet_stub" +fi + + fi +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + LIBS="$ac_xsave_LIBS" + + # msh@cis.ufl.edu says -lnsl (and -lsocket) are needed for his 386/AT, + # to get the SysV transport functions. + # Chad R. Larson says the Pyramis MIS-ES running DC/OSx (SVR4) + # needs -lnsl. + # The nsl library prevents programs from opening the X display + # on Irix 5.2, according to T.E. Dickey. + # The functions gethostbyname, getservbyname, and inet_addr are + # in -lbsd on LynxOS 3.0.1/i386, according to Lars Hecking. + echo "$as_me:$LINENO: checking for gethostbyname" >&5 +echo $ECHO_N "checking for gethostbyname... $ECHO_C" >&6 +if test "${ac_cv_func_gethostbyname+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define gethostbyname to an innocuous variant, in case declares gethostbyname. + For example, HP-UX 11i declares gettimeofday. */ +#define gethostbyname innocuous_gethostbyname + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char gethostbyname (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef gethostbyname + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gethostbyname (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) +choke me +#else +char (*f) () = gethostbyname; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != gethostbyname; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_gethostbyname=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_gethostbyname=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_gethostbyname" >&5 +echo "${ECHO_T}$ac_cv_func_gethostbyname" >&6 + + if test $ac_cv_func_gethostbyname = no; then + echo "$as_me:$LINENO: checking for gethostbyname in -lnsl" >&5 +echo $ECHO_N "checking for gethostbyname in -lnsl... $ECHO_C" >&6 +if test "${ac_cv_lib_nsl_gethostbyname+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lnsl $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gethostbyname (); +int +main () +{ +gethostbyname (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_nsl_gethostbyname=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_nsl_gethostbyname=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_nsl_gethostbyname" >&5 +echo "${ECHO_T}$ac_cv_lib_nsl_gethostbyname" >&6 +if test $ac_cv_lib_nsl_gethostbyname = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lnsl" +fi + + if test $ac_cv_lib_nsl_gethostbyname = no; then + echo "$as_me:$LINENO: checking for gethostbyname in -lbsd" >&5 +echo $ECHO_N "checking for gethostbyname in -lbsd... $ECHO_C" >&6 +if test "${ac_cv_lib_bsd_gethostbyname+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lbsd $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gethostbyname (); +int +main () +{ +gethostbyname (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_bsd_gethostbyname=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_bsd_gethostbyname=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_bsd_gethostbyname" >&5 +echo "${ECHO_T}$ac_cv_lib_bsd_gethostbyname" >&6 +if test $ac_cv_lib_bsd_gethostbyname = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lbsd" +fi + + fi + fi + + # lieder@skyler.mavd.honeywell.com says without -lsocket, + # socket/setsockopt and other routines are undefined under SCO ODT + # 2.0. But -lsocket is broken on IRIX 5.2 (and is not necessary + # on later versions), says Simon Leinen: it contains gethostby* + # variants that don't use the name server (or something). -lsocket + # must be given before -lnsl if both are needed. We assume that + # if connect needs -lnsl, so does gethostbyname. + echo "$as_me:$LINENO: checking for connect" >&5 +echo $ECHO_N "checking for connect... $ECHO_C" >&6 +if test "${ac_cv_func_connect+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define connect to an innocuous variant, in case declares connect. + For example, HP-UX 11i declares gettimeofday. */ +#define connect innocuous_connect + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char connect (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef connect + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char connect (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_connect) || defined (__stub___connect) +choke me +#else +char (*f) () = connect; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != connect; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_connect=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_connect=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_connect" >&5 +echo "${ECHO_T}$ac_cv_func_connect" >&6 + + if test $ac_cv_func_connect = no; then + echo "$as_me:$LINENO: checking for connect in -lsocket" >&5 +echo $ECHO_N "checking for connect in -lsocket... $ECHO_C" >&6 +if test "${ac_cv_lib_socket_connect+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lsocket $X_EXTRA_LIBS $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char connect (); +int +main () +{ +connect (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_socket_connect=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_socket_connect=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_socket_connect" >&5 +echo "${ECHO_T}$ac_cv_lib_socket_connect" >&6 +if test $ac_cv_lib_socket_connect = yes; then + X_EXTRA_LIBS="-lsocket $X_EXTRA_LIBS" +fi + + fi + + # Guillermo Gomez says -lposix is necessary on A/UX. + echo "$as_me:$LINENO: checking for remove" >&5 +echo $ECHO_N "checking for remove... $ECHO_C" >&6 +if test "${ac_cv_func_remove+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define remove to an innocuous variant, in case declares remove. + For example, HP-UX 11i declares gettimeofday. */ +#define remove innocuous_remove + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char remove (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef remove + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char remove (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_remove) || defined (__stub___remove) +choke me +#else +char (*f) () = remove; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != remove; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_remove=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_remove=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_remove" >&5 +echo "${ECHO_T}$ac_cv_func_remove" >&6 + + if test $ac_cv_func_remove = no; then + echo "$as_me:$LINENO: checking for remove in -lposix" >&5 +echo $ECHO_N "checking for remove in -lposix... $ECHO_C" >&6 +if test "${ac_cv_lib_posix_remove+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lposix $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char remove (); +int +main () +{ +remove (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_posix_remove=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_posix_remove=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_posix_remove" >&5 +echo "${ECHO_T}$ac_cv_lib_posix_remove" >&6 +if test $ac_cv_lib_posix_remove = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lposix" +fi + + fi + + # BSDI BSD/OS 2.1 needs -lipc for XOpenDisplay. + echo "$as_me:$LINENO: checking for shmat" >&5 +echo $ECHO_N "checking for shmat... $ECHO_C" >&6 +if test "${ac_cv_func_shmat+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define shmat to an innocuous variant, in case declares shmat. + For example, HP-UX 11i declares gettimeofday. */ +#define shmat innocuous_shmat + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char shmat (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef shmat + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char shmat (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_shmat) || defined (__stub___shmat) +choke me +#else +char (*f) () = shmat; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != shmat; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_shmat=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_shmat=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_shmat" >&5 +echo "${ECHO_T}$ac_cv_func_shmat" >&6 + + if test $ac_cv_func_shmat = no; then + echo "$as_me:$LINENO: checking for shmat in -lipc" >&5 +echo $ECHO_N "checking for shmat in -lipc... $ECHO_C" >&6 +if test "${ac_cv_lib_ipc_shmat+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lipc $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char shmat (); +int +main () +{ +shmat (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_ipc_shmat=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_ipc_shmat=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_ipc_shmat" >&5 +echo "${ECHO_T}$ac_cv_lib_ipc_shmat" >&6 +if test $ac_cv_lib_ipc_shmat = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lipc" +fi + + fi + fi + + # Check for libraries that X11R6 Xt/Xaw programs need. + ac_save_LDFLAGS=$LDFLAGS + test -n "$x_libraries" && LDFLAGS="$LDFLAGS -L$x_libraries" + # SM needs ICE to (dynamically) link under SunOS 4.x (so we have to + # check for ICE first), but we must link in the order -lSM -lICE or + # we get undefined symbols. So assume we have SM if we have ICE. + # These have to be linked with before -lX11, unlike the other + # libraries we check for below, so use a different variable. + # John Interrante, Karl Berry + echo "$as_me:$LINENO: checking for IceConnectionNumber in -lICE" >&5 +echo $ECHO_N "checking for IceConnectionNumber in -lICE... $ECHO_C" >&6 +if test "${ac_cv_lib_ICE_IceConnectionNumber+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lICE $X_EXTRA_LIBS $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char IceConnectionNumber (); +int +main () +{ +IceConnectionNumber (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_ICE_IceConnectionNumber=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_ICE_IceConnectionNumber=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_ICE_IceConnectionNumber" >&5 +echo "${ECHO_T}$ac_cv_lib_ICE_IceConnectionNumber" >&6 +if test $ac_cv_lib_ICE_IceConnectionNumber = yes; then + X_PRE_LIBS="$X_PRE_LIBS -lSM -lICE" +fi + + LDFLAGS=$ac_save_LDFLAGS + +fi + +CFLAGS="$CFLAGS $X_CFLAGS -I/usr/local/include" +LDFLAGS="$LDFLAGS $X_LIBS -L/usr/local/lib" + + +DO_PS='#' +DO_FIG='#' +DO_X11='#' +DO_GD='#' +DO_WIN32='#' + + +# +# check supported devices +# +echo "$as_me:$LINENO: checking for main in -lm" >&5 +echo $ECHO_N "checking for main in -lm... $ECHO_C" >&6 +if test "${ac_cv_lib_m_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lm $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_m_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_m_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_m_main" >&5 +echo "${ECHO_T}$ac_cv_lib_m_main" >&6 +if test $ac_cv_lib_m_main = yes; then + DO_PS='';DO_FIG='';LDFLAGS="$LDFLAGS -lm";cat >>confdefs.h <<\_ACEOF +@%:@define DO_PS 1 +_ACEOF + cat >>confdefs.h <<\_ACEOF +@%:@define DO_FIG 1 +_ACEOF + +else + break +fi + +echo "$as_me:$LINENO: checking for main in -lX11" >&5 +echo $ECHO_N "checking for main in -lX11... $ECHO_C" >&6 +if test "${ac_cv_lib_X11_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lX11 $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_X11_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_X11_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_X11_main" >&5 +echo "${ECHO_T}$ac_cv_lib_X11_main" >&6 +if test $ac_cv_lib_X11_main = yes; then + DO_X11='';LDFLAGS="$LDFLAGS -lX11";cat >>confdefs.h <<\_ACEOF +@%:@define DO_X11 1 +_ACEOF + +fi + +echo "$as_me:$LINENO: checking for main in -lgd" >&5 +echo $ECHO_N "checking for main in -lgd... $ECHO_C" >&6 +if test "${ac_cv_lib_gd_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lgd $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_gd_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_gd_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_gd_main" >&5 +echo "${ECHO_T}$ac_cv_lib_gd_main" >&6 +if test $ac_cv_lib_gd_main = yes; then + have_gd=yes +else + have_gd=no +fi + +if test "$have_gd" = yes +then + LDFLAGS="$LDFLAGS -lgd" + echo "$as_me:$LINENO: checking for gdImagePng" >&5 +echo $ECHO_N "checking for gdImagePng... $ECHO_C" >&6 +if test "${ac_cv_func_gdImagePng+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define gdImagePng to an innocuous variant, in case declares gdImagePng. + For example, HP-UX 11i declares gettimeofday. */ +#define gdImagePng innocuous_gdImagePng + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char gdImagePng (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef gdImagePng + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gdImagePng (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_gdImagePng) || defined (__stub___gdImagePng) +choke me +#else +char (*f) () = gdImagePng; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != gdImagePng; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_gdImagePng=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_gdImagePng=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_gdImagePng" >&5 +echo "${ECHO_T}$ac_cv_func_gdImagePng" >&6 +if test $ac_cv_func_gdImagePng = yes; then + DO_GD='';cat >>confdefs.h <<\_ACEOF +@%:@define DO_GD 1 +_ACEOF + +fi + +fi + +# +# handling cygwin environment (and gd for cygwin == bgd) +# + +case $host_os in + *cygwin* ) CYGWIN=yes;; + * ) CYGWIN=no;; +esac + +if test "$CYGWIN" = yes +then + LDFLAGS="$LDFLAGS -L/lib/w32api" + echo "$as_me:$LINENO: checking for main in -lgdi32" >&5 +echo $ECHO_N "checking for main in -lgdi32... $ECHO_C" >&6 +if test "${ac_cv_lib_gdi32_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lgdi32 $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_gdi32_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_gdi32_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_gdi32_main" >&5 +echo "${ECHO_T}$ac_cv_lib_gdi32_main" >&6 +if test $ac_cv_lib_gdi32_main = yes; then + DO_WIN32='';LDFLAGS="$LDFLAGS -lgdi32";cat >>confdefs.h <<\_ACEOF +@%:@define DO_WIN32 1 +_ACEOF + +fi + + echo "$as_me:$LINENO: checking for main in -lbgd" >&5 +echo $ECHO_N "checking for main in -lbgd... $ECHO_C" >&6 +if test "${ac_cv_lib_bgd_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lbgd $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_bgd_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_bgd_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_bgd_main" >&5 +echo "${ECHO_T}$ac_cv_lib_bgd_main" >&6 +if test $ac_cv_lib_bgd_main = yes; then + have_bgd=yes +else + have_bgd=no +fi + + if test "$have_bgd" = yes + then + LDFLAGS="$LDFLAGS -lbgd" + echo "$as_me:$LINENO: checking for gdImagePng" >&5 +echo $ECHO_N "checking for gdImagePng... $ECHO_C" >&6 +if test "${ac_cv_func_gdImagePng+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define gdImagePng to an innocuous variant, in case declares gdImagePng. + For example, HP-UX 11i declares gettimeofday. */ +#define gdImagePng innocuous_gdImagePng + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char gdImagePng (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef gdImagePng + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gdImagePng (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_gdImagePng) || defined (__stub___gdImagePng) +choke me +#else +char (*f) () = gdImagePng; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != gdImagePng; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_gdImagePng=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_gdImagePng=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_gdImagePng" >&5 +echo "${ECHO_T}$ac_cv_func_gdImagePng" >&6 +if test $ac_cv_func_gdImagePng = yes; then + DO_GD='';cat >>confdefs.h <<\_ACEOF +@%:@define DO_GD 1 +_ACEOF + +fi + + fi +fi + +# +# Declare variables which we want substituted in the Makefile.in's +# + + + + + + +echo "$as_me:$LINENO: checking for egrep" >&5 +echo $ECHO_N "checking for egrep... $ECHO_C" >&6 +if test "${ac_cv_prog_egrep+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if echo a | (grep -E '(a|b)') >/dev/null 2>&1 + then ac_cv_prog_egrep='grep -E' + else ac_cv_prog_egrep='egrep' + fi +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_egrep" >&5 +echo "${ECHO_T}$ac_cv_prog_egrep" >&6 + EGREP=$ac_cv_prog_egrep + + +echo "$as_me:$LINENO: checking for ANSI C header files" >&5 +echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 +if test "${ac_cv_header_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_header_stdc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_header_stdc=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + +if test $ac_cv_header_stdc = yes; then + # SunOS 4.x string.h does not declare mem*, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "memchr" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "free" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. + if test "$cross_compiling" = yes; then + : +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#if ((' ' & 0x0FF) == 0x020) +# define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +#else +# define ISLOWER(c) \ + (('a' <= (c) && (c) <= 'i') \ + || ('j' <= (c) && (c) <= 'r') \ + || ('s' <= (c) && (c) <= 'z')) +# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +#endif + +#define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +int +main () +{ + int i; + for (i = 0; i < 256; i++) + if (XOR (islower (i), ISLOWER (i)) + || toupper (i) != TOUPPER (i)) + exit(2); + exit (0); +} +_ACEOF +rm -f conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: program exited with status $ac_status" >&5 +echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no +fi +rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +fi +fi +echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 +echo "${ECHO_T}$ac_cv_header_stdc" >&6 +if test $ac_cv_header_stdc = yes; then + +cat >>confdefs.h <<\_ACEOF +@%:@define STDC_HEADERS 1 +_ACEOF + +fi + +# On IRIX 5.3, sys/types and inttypes.h are conflicting. + + + + + + + + + +for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ + inttypes.h stdint.h unistd.h +do +as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` +echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +@%:@include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + eval "$as_ac_Header=yes" +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +eval "$as_ac_Header=no" +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 +if test `eval echo '${'$as_ac_Header'}'` = yes; then + cat >>confdefs.h <<_ACEOF +@%:@define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + + +for ac_header in limits.h +do +as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 +else + # Is the header compilable? +echo "$as_me:$LINENO: checking $ac_header usability" >&5 +echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +@%:@include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_header_compiler=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_header_compiler=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +echo "${ECHO_T}$ac_header_compiler" >&6 + +# Is the header present? +echo "$as_me:$LINENO: checking $ac_header presence" >&5 +echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +@%:@include <$ac_header> +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + ac_header_preproc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi +rm -f conftest.err conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +echo "${ECHO_T}$ac_header_preproc" >&6 + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + ( + cat <<\_ASBOX +@%:@@%:@ ------------------------------------------ @%:@@%:@ +@%:@@%:@ Report this to the AC_PACKAGE_NAME lists. @%:@@%:@ +@%:@@%:@ ------------------------------------------ @%:@@%:@ +_ASBOX + ) | + sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac +echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 + +fi +if test `eval echo '${'$as_ac_Header'}'` = yes; then + cat >>confdefs.h <<_ACEOF +@%:@define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + + + +# +# finally create makefiles using Makefile.in +# +echo + ac_config_files="$ac_config_files Makefile demo/Makefile g2_perl/Makefile.PL" +cat >confcache <<\_ACEOF +# This file is a shell script that caches the results of configure +# tests run on this system so they can be shared between configure +# scripts and configure runs, see configure's option --config-cache. +# It is not useful on other systems. If it contains results you don't +# want to keep, you may remove or edit it. +# +# config.status only pays attention to the cache file if you give it +# the --recheck option to rerun configure. +# +# `ac_cv_env_foo' variables (set or unset) will be overridden when +# loading this file, other *unset* `ac_cv_foo' will be assigned the +# following values. + +_ACEOF + +# The following way of writing the cache mishandles newlines in values, +# but we know of no workaround that is simple, portable, and efficient. +# So, don't put newlines in cache variables' values. +# Ultrix sh set writes to stderr and can't be redirected directly, +# and sets the high bit in the cache file unless we assign to the vars. +{ + (set) 2>&1 | + case `(ac_space=' '; set | grep ac_space) 2>&1` in + *ac_space=\ *) + # `set' does not quote correctly, so add quotes (double-quote + # substitution turns \\\\ into \\, and sed turns \\ into \). + sed -n \ + "s/'/'\\\\''/g; + s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" + ;; + *) + # `set' quotes correctly as required by POSIX, so do not add quotes. + sed -n \ + "s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1=\\2/p" + ;; + esac; +} | + sed ' + t clear + : clear + s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/ + t end + /^ac_cv_env/!s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/ + : end' >>confcache +if diff $cache_file confcache >/dev/null 2>&1; then :; else + if test -w $cache_file; then + test "x$cache_file" != "x/dev/null" && echo "updating cache $cache_file" + cat confcache >$cache_file + else + echo "not updating unwritable cache $cache_file" + fi +fi +rm -f confcache + +test "x$prefix" = xNONE && prefix=$ac_default_prefix +# Let make expand exec_prefix. +test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' + +# VPATH may cause trouble with some makes, so we remove $(srcdir), +# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and +# trailing colons and then remove the whole line if VPATH becomes empty +# (actually we leave an empty line to preserve line numbers). +if test "x$srcdir" = x.; then + ac_vpsub='/^[ ]*VPATH[ ]*=/{ +s/:*\$(srcdir):*/:/; +s/:*\${srcdir}:*/:/; +s/:*@srcdir@:*/:/; +s/^\([^=]*=[ ]*\):*/\1/; +s/:*$//; +s/^[^=]*=[ ]*$//; +}' +fi + +# Transform confdefs.h into DEFS. +# Protect against shell expansion while executing Makefile rules. +# Protect against Makefile macro expansion. +# +# If the first sed substitution is executed (which looks for macros that +# take arguments), then we branch to the quote section. Otherwise, +# look for a macro that doesn't take arguments. +cat >confdef2opt.sed <<\_ACEOF +t clear +: clear +s,^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\),-D\1=\2,g +t quote +s,^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\),-D\1=\2,g +t quote +d +: quote +s,[ `~#$^&*(){}\\|;'"<>?],\\&,g +s,\[,\\&,g +s,\],\\&,g +s,\$,$$,g +p +_ACEOF +# We use echo to avoid assuming a particular line-breaking character. +# The extra dot is to prevent the shell from consuming trailing +# line-breaks from the sub-command output. A line-break within +# single-quotes doesn't work because, if this script is created in a +# platform that uses two characters for line-breaks (e.g., DOS), tr +# would break. +ac_LF_and_DOT=`echo; echo .` +DEFS=`sed -n -f confdef2opt.sed confdefs.h | tr "$ac_LF_and_DOT" ' .'` +rm -f confdef2opt.sed + + +ac_libobjs= +ac_ltlibobjs= +for ac_i in : $LIB@&t@OBJS; do test "x$ac_i" = x: && continue + # 1. Remove the extension, and $U if already installed. + ac_i=`echo "$ac_i" | + sed 's/\$U\././;s/\.o$//;s/\.obj$//'` + # 2. Add them. + ac_libobjs="$ac_libobjs $ac_i\$U.$ac_objext" + ac_ltlibobjs="$ac_ltlibobjs $ac_i"'$U.lo' +done +LIB@&t@OBJS=$ac_libobjs + +LTLIBOBJS=$ac_ltlibobjs + + + +: ${CONFIG_STATUS=./config.status} +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files $CONFIG_STATUS" +{ echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5 +echo "$as_me: creating $CONFIG_STATUS" >&6;} +cat >$CONFIG_STATUS <<_ACEOF +#! $SHELL +# Generated by $as_me. +# Run this file to recreate the current configuration. +# Compiler output produced by configure, useful for debugging +# configure, is in config.log if it exists. + +debug=false +ac_cs_recheck=false +ac_cs_silent=false +SHELL=\${CONFIG_SHELL-$SHELL} +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## + +# Be Bourne compatible +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # is contrary to our usage. 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The first 'sed' inserts a + # line-number line before each line; the second 'sed' does the real + # work. The second script uses 'N' to pair each line-number line + # with the numbered line, and appends trailing '-' during + # substitution so that $LINENO is not a special case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # second 'sed' script. Blame Lee E. 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Logging --version etc. is OK. +exec 5>>config.log +{ + echo + sed 'h;s/./-/g;s/^.../@%:@@%:@ /;s/...$/ @%:@@%:@/;p;x;p;x' <<_ASBOX +@%:@@%:@ Running $as_me. @%:@@%:@ +_ASBOX +} >&5 +cat >&5 <<_CSEOF + +This file was extended by $as_me, which was +generated by GNU Autoconf 2.59. Invocation command line was + + CONFIG_FILES = $CONFIG_FILES + CONFIG_HEADERS = $CONFIG_HEADERS + CONFIG_LINKS = $CONFIG_LINKS + CONFIG_COMMANDS = $CONFIG_COMMANDS + $ $0 $@ + +_CSEOF +echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 +echo >&5 +_ACEOF + +# Files that config.status was made for. +if test -n "$ac_config_files"; then + echo "config_files=\"$ac_config_files\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_headers"; then + echo "config_headers=\"$ac_config_headers\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_links"; then + echo "config_links=\"$ac_config_links\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_commands"; then + echo "config_commands=\"$ac_config_commands\"" >>$CONFIG_STATUS +fi + +cat >>$CONFIG_STATUS <<\_ACEOF + +ac_cs_usage="\ +\`$as_me' instantiates files from templates according to the +current configuration. + +Usage: $0 [OPTIONS] [FILE]... + + -h, --help print this help, then exit + -V, --version print version number, then exit + -q, --quiet do not print progress messages + -d, --debug don't remove temporary files + --recheck update $as_me by reconfiguring in the same conditions + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + +Configuration files: +$config_files + +Report bugs to ." +_ACEOF + +cat >>$CONFIG_STATUS <<_ACEOF +ac_cs_version="\\ +config.status +configured by $0, generated by GNU Autoconf 2.59, + with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\" + +Copyright (C) 2003 Free Software Foundation, Inc. +This config.status script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it." +srcdir=$srcdir +INSTALL="$INSTALL" +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF +# If no file are specified by the user, then we need to provide default +# value. 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Set only those that are not. +# We use the long form for the default assignment because of an extremely +# bizarre bug on SunOS 4.1.3. +if $ac_need_defaults; then + test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files +fi + +# Have a temporary directory for convenience. Make it in the build tree +# simply because there is no reason to put it here, and in addition, +# creating and moving files from /tmp can sometimes cause problems. +# Create a temporary directory, and hook for its removal unless debugging. +$debug || +{ + trap 'exit_status=$?; rm -rf $tmp && exit $exit_status' 0 + trap '{ (exit 1); exit 1; }' 1 2 13 15 +} + +# Create a (secure) tmp directory for tmp files. + +{ + tmp=`(umask 077 && mktemp -d -q "./confstatXXXXXX") 2>/dev/null` && + test -n "$tmp" && test -d "$tmp" +} || +{ + tmp=./confstat$$-$RANDOM + (umask 077 && mkdir $tmp) +} || +{ + echo "$me: cannot create a temporary directory in ." >&2 + { (exit 1); exit 1; } +} + +_ACEOF + +cat >>$CONFIG_STATUS <<_ACEOF + +# +# CONFIG_FILES section. +# + +# No need to generate the scripts if there are no CONFIG_FILES. +# This happens for instance when ./config.status config.h +if test -n "\$CONFIG_FILES"; then + # Protect against being on the right side of a sed subst in config.status. + sed 's/,@/@@/; s/@,/@@/; s/,;t t\$/@;t t/; /@;t t\$/s/[\\\\&,]/\\\\&/g; + s/@@/,@/; s/@@/@,/; s/@;t t\$/,;t t/' >\$tmp/subs.sed <<\\CEOF +s,@SHELL@,$SHELL,;t t +s,@PATH_SEPARATOR@,$PATH_SEPARATOR,;t t +s,@PACKAGE_NAME@,$PACKAGE_NAME,;t t +s,@PACKAGE_TARNAME@,$PACKAGE_TARNAME,;t t +s,@PACKAGE_VERSION@,$PACKAGE_VERSION,;t t +s,@PACKAGE_STRING@,$PACKAGE_STRING,;t t +s,@PACKAGE_BUGREPORT@,$PACKAGE_BUGREPORT,;t t +s,@exec_prefix@,$exec_prefix,;t t +s,@prefix@,$prefix,;t t +s,@program_transform_name@,$program_transform_name,;t t +s,@bindir@,$bindir,;t t +s,@sbindir@,$sbindir,;t t +s,@libexecdir@,$libexecdir,;t t +s,@datadir@,$datadir,;t t +s,@sysconfdir@,$sysconfdir,;t t +s,@sharedstatedir@,$sharedstatedir,;t t +s,@localstatedir@,$localstatedir,;t t +s,@libdir@,$libdir,;t t +s,@includedir@,$includedir,;t t +s,@oldincludedir@,$oldincludedir,;t t +s,@infodir@,$infodir,;t t +s,@mandir@,$mandir,;t t +s,@build_alias@,$build_alias,;t t +s,@host_alias@,$host_alias,;t t +s,@target_alias@,$target_alias,;t t +s,@DEFS@,$DEFS,;t t +s,@ECHO_C@,$ECHO_C,;t t +s,@ECHO_N@,$ECHO_N,;t t +s,@ECHO_T@,$ECHO_T,;t t +s,@LIBS@,$LIBS,;t t +s,@build@,$build,;t t +s,@build_cpu@,$build_cpu,;t t +s,@build_vendor@,$build_vendor,;t t +s,@build_os@,$build_os,;t t +s,@host@,$host,;t t +s,@host_cpu@,$host_cpu,;t t +s,@host_vendor@,$host_vendor,;t t +s,@host_os@,$host_os,;t t +s,@LD_SHARED@,$LD_SHARED,;t t +s,@LD_SHARED_FLAGS@,$LD_SHARED_FLAGS,;t t +s,@LD_SHARED_OPT@,$LD_SHARED_OPT,;t t +s,@LD_SHARED_EXT@,$LD_SHARED_EXT,;t t +s,@CC@,$CC,;t t +s,@CFLAGS@,$CFLAGS,;t t +s,@LDFLAGS@,$LDFLAGS,;t t +s,@CPPFLAGS@,$CPPFLAGS,;t t +s,@ac_ct_CC@,$ac_ct_CC,;t t +s,@EXEEXT@,$EXEEXT,;t t +s,@OBJEXT@,$OBJEXT,;t t +s,@CPP@,$CPP,;t t +s,@CXX@,$CXX,;t t +s,@CXXFLAGS@,$CXXFLAGS,;t t +s,@ac_ct_CXX@,$ac_ct_CXX,;t t +s,@RANLIB@,$RANLIB,;t t +s,@ac_ct_RANLIB@,$ac_ct_RANLIB,;t t +s,@INSTALL_PROGRAM@,$INSTALL_PROGRAM,;t t +s,@INSTALL_SCRIPT@,$INSTALL_SCRIPT,;t t +s,@INSTALL_DATA@,$INSTALL_DATA,;t t +s,@FIND@,$FIND,;t t +s,@MAKEDEPEND@,$MAKEDEPEND,;t t +s,@X_CFLAGS@,$X_CFLAGS,;t t +s,@X_PRE_LIBS@,$X_PRE_LIBS,;t t +s,@X_LIBS@,$X_LIBS,;t t +s,@X_EXTRA_LIBS@,$X_EXTRA_LIBS,;t t +s,@DO_PS@,$DO_PS,;t t +s,@DO_FIG@,$DO_FIG,;t t +s,@DO_X11@,$DO_X11,;t t +s,@DO_WIN32@,$DO_WIN32,;t t +s,@DO_GD@,$DO_GD,;t t +s,@EGREP@,$EGREP,;t t +s,@LIB@&t@OBJS@,$LIB@&t@OBJS,;t t +s,@LTLIBOBJS@,$LTLIBOBJS,;t t +CEOF + +_ACEOF + + cat >>$CONFIG_STATUS <<\_ACEOF + # Split the substitutions into bite-sized pieces for seds with + # small command number limits, like on Digital OSF/1 and HP-UX. + ac_max_sed_lines=48 + ac_sed_frag=1 # Number of current file. + ac_beg=1 # First line for current file. + ac_end=$ac_max_sed_lines # Line after last line for current file. + ac_more_lines=: + ac_sed_cmds= + while $ac_more_lines; do + if test $ac_beg -gt 1; then + sed "1,${ac_beg}d; ${ac_end}q" $tmp/subs.sed >$tmp/subs.frag + else + sed "${ac_end}q" $tmp/subs.sed >$tmp/subs.frag + fi + if test ! 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Generated by config.status. */ + if test x"$ac_file" = x-; then + configure_input= + else + configure_input="$ac_file. " + fi + configure_input=$configure_input"Generated from `echo $ac_file_in | + sed 's,.*/,,'` by configure." + + # First look for the input files in the build tree, otherwise in the + # src tree. + ac_file_inputs=`IFS=: + for f in $ac_file_in; do + case $f in + -) echo $tmp/stdin ;; + [\\/$]*) + # Absolute (can't be DOS-style, as IFS=:) + test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + echo "$f";; + *) # Relative + if test -f "$f"; then + # Build tree + echo "$f" + elif test -f "$srcdir/$f"; then + # Source tree + echo "$srcdir/$f" + else + # /dev/null tree + { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + fi;; + esac + done` || { (exit 1); exit 1; } +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF + sed "$ac_vpsub +$extrasub +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF +:t +/@[a-zA-Z_][a-zA-Z_0-9]*@/!b +s,@configure_input@,$configure_input,;t t +s,@srcdir@,$ac_srcdir,;t t +s,@abs_srcdir@,$ac_abs_srcdir,;t t +s,@top_srcdir@,$ac_top_srcdir,;t t +s,@abs_top_srcdir@,$ac_abs_top_srcdir,;t t +s,@builddir@,$ac_builddir,;t t +s,@abs_builddir@,$ac_abs_builddir,;t t +s,@top_builddir@,$ac_top_builddir,;t t +s,@abs_top_builddir@,$ac_abs_top_builddir,;t t +s,@INSTALL@,$ac_INSTALL,;t t +" $ac_file_inputs | (eval "$ac_sed_cmds") >$tmp/out + rm -f $tmp/stdin + if test x"$ac_file" != x-; then + mv $tmp/out $ac_file + else + cat $tmp/out + rm -f $tmp/out + fi + +done +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF + +{ (exit 0); exit 0; } +_ACEOF +chmod +x $CONFIG_STATUS +ac_clean_files=$ac_clean_files_save + + +# configure is writing to config.log, and then calls config.status. +# config.status does its own redirection, appending to config.log. +# Unfortunately, on DOS this fails, as config.log is still kept open +# by configure, so config.status won't be able to write to it; its +# output is simply discarded. So we exec the FD to /dev/null, +# effectively closing config.log, so it can be properly (re)opened and +# appended to by config.status. When coming back to configure, we +# need to make the FD available again. +if test "$no_create" != yes; then + ac_cs_success=: + ac_config_status_args= + test "$silent" = yes && + ac_config_status_args="$ac_config_status_args --quiet" + exec 5>/dev/null + $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false + exec 5>>config.log + # Use ||, not &&, to avoid exiting from the if with $? = 1, which + # would make configure fail if this is the last instruction. + $ac_cs_success || { (exit 1); exit 1; } +fi + + +echo +echo "Supported devices:" +if test "$DO_PS" != "#"; then echo " PostScript"; fi +if test "$DO_FIG" != "#"; then echo " FIG"; fi +if test "$DO_X11" != "#"; then echo " X11"; fi +if test "$DO_WIN32" != "#"; then echo " Win32"; fi +if test "$DO_GD" != "#"; then echo " GD"; fi + +echo +echo "Unsupported devices:" +if test "$DO_PS" = "#"; then echo " PostScript"; fi +if test "$DO_FIG" = "#"; then echo " FIG"; fi +if test "$DO_X11" = "#"; then echo " X11"; fi +if test "$DO_WIN32" = "#"; then echo " Win32"; fi +if test "$DO_GD" = "#"; then echo " GD"; fi + +echo +echo "Run 'make depend' to create dependencies." +echo diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/requests b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/requests new file mode 100755 index 000000000..a9ac0c3d3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/requests @@ -0,0 +1,123 @@ +# This file was generated. +# It contains the lists of macros which have been traced. +# It can be safely removed. + +@request = ( + bless( [ + '0', + 1, + [ + '/usr/share/autoconf' + ], + [ + '/usr/share/autoconf/autoconf/autoconf.m4f', + 'configure.in' + ], + { + '_LT_AC_TAGCONFIG' => 1, + 'm4_pattern_forbid' => 1, + 'AC_CANONICAL_TARGET' => 1, + 'AC_CONFIG_LIBOBJ_DIR' => 1, + 'AC_C_VOLATILE' => 1, + 'AC_TYPE_OFF_T' => 1, + 'AC_FUNC_CLOSEDIR_VOID' => 1, + 'AC_REPLACE_FNMATCH' => 1, + 'AC_DEFUN' => 1, + 'AC_PROG_LIBTOOL' => 1, + 'AC_FUNC_STAT' => 1, + 'AC_FUNC_WAIT3' => 1, + 'AC_HEADER_TIME' => 1, + 'AC_FUNC_LSTAT' => 1, + 'AC_STRUCT_TM' => 1, + 'AM_AUTOMAKE_VERSION' => 1, + 'AC_FUNC_GETMNTENT' => 1, + 'AC_TYPE_MODE_T' => 1, + 'AC_CHECK_HEADERS' => 1, + 'AC_FUNC_STRTOD' => 1, + 'AC_FUNC_STRNLEN' => 1, + 'm4_sinclude' => 1, + 'AC_PROG_CXX' => 1, + 'AC_PATH_X' => 1, + 'AC_FUNC_LSTAT_FOLLOWS_SLASHED_SYMLINK' => 1, + 'AC_PROG_AWK' => 1, + '_m4_warn' => 1, + 'AC_HEADER_STDC' => 1, + 'AC_HEADER_MAJOR' => 1, + 'AC_FUNC_ERROR_AT_LINE' => 1, + 'AC_PROG_GCC_TRADITIONAL' => 1, + 'AC_LIBSOURCE' => 1, + 'AC_FUNC_MBRTOWC' => 1, + 'AC_STRUCT_ST_BLOCKS' => 1, + 'AC_CANONICAL_BUILD' => 1, + 'AC_TYPE_SIGNAL' => 1, + 'AC_TYPE_UID_T' => 1, + 'AC_PROG_MAKE_SET' => 1, + 'AC_CONFIG_AUX_DIR' => 1, + 'm4_pattern_allow' => 1, + 'sinclude' => 1, + 'AC_DEFINE_TRACE_LITERAL' => 1, + 'AC_FUNC_STRERROR_R' => 1, + 'AC_PROG_CC' => 1, + 'AC_FUNC_FORK' => 1, + 'AC_DECL_SYS_SIGLIST' => 1, + 'AU_DEFUN' => 1, + 'AC_FUNC_STRCOLL' => 1, + 'AC_FUNC_VPRINTF' => 1, + 'AC_PROG_YACC' => 1, + 'AC_INIT' => 1, + 'AC_STRUCT_TIMEZONE' => 1, + 'AC_FUNC_CHOWN' => 1, + 'AC_SUBST' => 1, + 'AC_FUNC_ALLOCA' => 1, + 'AC_CANONICAL_HOST' => 1, + 'AC_FUNC_GETPGRP' => 1, + 'AC_PROG_RANLIB' => 1, + 'AM_INIT_AUTOMAKE' => 1, + 'AC_FUNC_SETPGRP' => 1, + 'AC_CONFIG_SUBDIRS' => 1, + 'AC_FUNC_MMAP' => 1, + 'AC_FUNC_REALLOC' => 1, + 'AC_TYPE_SIZE_T' => 1, + 'AC_CONFIG_LINKS' => 1, + 'AC_CHECK_TYPES' => 1, + 'LT_SUPPORTED_TAG' => 1, + 'AC_CHECK_MEMBERS' => 1, + 'AM_MAINTAINER_MODE' => 1, + 'AC_DEFUN_ONCE' => 1, + 'AC_FUNC_UTIME_NULL' => 1, + 'AC_FUNC_SELECT_ARGTYPES' => 1, + 'AC_HEADER_STAT' => 1, + 'AC_FUNC_STRFTIME' => 1, + 'AC_PROG_CPP' => 1, + 'AC_C_INLINE' => 1, + 'AM_ENABLE_MULTILIB' => 1, + 'AC_PROG_LEX' => 1, + 'AC_C_CONST' => 1, + 'AC_TYPE_PID_T' => 1, + 'AC_CONFIG_FILES' => 1, + 'include' => 1, + 'AC_FUNC_SETVBUF_REVERSED' => 1, + 'AC_PROG_INSTALL' => 1, + 'AM_GNU_GETTEXT' => 1, + 'AC_FUNC_OBSTACK' => 1, + 'AC_CHECK_LIB' => 1, + 'AC_FUNC_MALLOC' => 1, + 'AC_FUNC_GETGROUPS' => 1, + 'AC_FUNC_GETLOADAVG' => 1, + 'AH_OUTPUT' => 1, + 'AC_FUNC_FSEEKO' => 1, + 'AM_PROG_CC_C_O' => 1, + 'AC_FUNC_MKTIME' => 1, + 'AC_CANONICAL_SYSTEM' => 1, + 'AM_CONDITIONAL' => 1, + 'AC_CONFIG_HEADERS' => 1, + 'AC_HEADER_SYS_WAIT' => 1, + 'AC_PROG_LN_S' => 1, + 'AC_FUNC_MEMCMP' => 1, + 'm4_include' => 1, + 'AC_HEADER_DIRENT' => 1, + 'AC_CHECK_FUNCS' => 1 + } + ], 'Autom4te::Request' ) + ); + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/traces.0 b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/traces.0 new file mode 100755 index 000000000..6a5c04d11 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/autom4te.cache/traces.0 @@ -0,0 +1,191 @@ +m4trace:configure.in:5: -1- 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[have_dl=no]) +m4trace:configure.in:61: -1- AC_PATH_X +m4trace:configure.in:61: -1- AC_DEFINE_TRACE_LITERAL([X_DISPLAY_MISSING]) +m4trace:configure.in:61: -1- AH_OUTPUT([X_DISPLAY_MISSING], [/* Define to 1 if the X Window System is missing or not being used. */ +#undef X_DISPLAY_MISSING]) +m4trace:configure.in:61: -1- AC_CHECK_LIB([dnet], [dnet_ntoa], [X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet"]) +m4trace:configure.in:61: -1- AC_CHECK_LIB([dnet_stub], [dnet_ntoa], [X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet_stub"]) +m4trace:configure.in:61: -1- AC_CHECK_LIB([nsl], [gethostbyname], [X_EXTRA_LIBS="$X_EXTRA_LIBS -lnsl"]) +m4trace:configure.in:61: -1- AC_CHECK_LIB([bsd], [gethostbyname], [X_EXTRA_LIBS="$X_EXTRA_LIBS -lbsd"]) +m4trace:configure.in:61: -1- AC_CHECK_LIB([socket], [connect], [X_EXTRA_LIBS="-lsocket $X_EXTRA_LIBS"], [], [$X_EXTRA_LIBS]) +m4trace:configure.in:61: -1- AC_CHECK_LIB([posix], [remove], [X_EXTRA_LIBS="$X_EXTRA_LIBS -lposix"]) +m4trace:configure.in:61: -1- AC_CHECK_LIB([ipc], 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AC_CHECK_LIB([gd], [main], [have_gd=yes], [have_gd=no]) +m4trace:configure.in:82: -2- AC_DEFINE_TRACE_LITERAL([DO_GD]) +m4trace:configure.in:88: -1- _m4_warn([obsolete], [The macro `AC_CYGWIN' is obsolete. +You should run autoupdate.], [autoconf/specific.m4:363: AC_CYGWIN is expanded from... +configure.in:88: the top level]) +m4trace:configure.in:88: -1- AC_CANONICAL_HOST +m4trace:configure.in:88: -1- _m4_warn([syntax], [AC_CANONICAL_HOST invoked multiple times], [autoconf/specific.m4:363: AC_CYGWIN is expanded from... +configure.in:88: the top level]) +m4trace:configure.in:88: -1- _m4_warn([obsolete], [AC_CYGWIN is obsolete: use AC_CANONICAL_HOST and $host_os], [autoconf/specific.m4:363: AC_CYGWIN is expanded from... +configure.in:88: the top level]) +m4trace:configure.in:92: -2- AC_DEFINE_TRACE_LITERAL([DO_WIN32]) +m4trace:configure.in:92: -1- AC_CHECK_LIB([gdi32], [main], [DO_WIN32='';LDFLAGS="$LDFLAGS -lgdi32";cat >>confdefs.h <<\_ACEOF +@%:@define DO_WIN32 1 +_ACEOF +]) +m4trace:configure.in:93: -1- AC_CHECK_LIB([bgd], [main], [have_bgd=yes], [have_bgd=no]) +m4trace:configure.in:97: -2- AC_DEFINE_TRACE_LITERAL([DO_GD]) +m4trace:configure.in:104: -1- AC_SUBST([DO_PS]) +m4trace:configure.in:105: -1- AC_SUBST([DO_FIG]) +m4trace:configure.in:106: -1- AC_SUBST([DO_X11]) +m4trace:configure.in:107: -1- AC_SUBST([DO_WIN32]) +m4trace:configure.in:108: -1- AC_SUBST([DO_GD]) +m4trace:configure.in:110: -1- AC_HEADER_STDC +m4trace:configure.in:110: -1- AC_SUBST([EGREP]) +m4trace:configure.in:110: -1- AC_DEFINE_TRACE_LITERAL([STDC_HEADERS]) +m4trace:configure.in:110: -1- AH_OUTPUT([STDC_HEADERS], [/* Define to 1 if you have the ANSI C header files. */ +#undef STDC_HEADERS]) +m4trace:configure.in:111: -1- AC_CHECK_HEADERS([limits.h]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_LIMITS_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_LIMITS_H]) +m4trace:configure.in:111: -1- AC_CHECK_HEADERS([sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ + inttypes.h stdint.h unistd.h], [], [], [$ac_includes_default]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_SYS_TYPES_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_TYPES_H]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_SYS_STAT_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_STAT_H]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_STDLIB_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_STDLIB_H]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_STRING_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_STRING_H]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_MEMORY_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_MEMORY_H]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_STRINGS_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_STRINGS_H]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_INTTYPES_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_INTTYPES_H]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_STDINT_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_STDINT_H]) +m4trace:configure.in:111: -1- AH_OUTPUT([HAVE_UNISTD_H], [/* Define to 1 if you have the header file. */ +#undef HAVE_UNISTD_H]) +m4trace:configure.in:119: -1- AC_CONFIG_FILES([Makefile demo/Makefile g2_perl/Makefile.PL]) +m4trace:configure.in:119: -1- _m4_warn([obsolete], [AC_OUTPUT should be used without arguments. +You should run autoupdate.], []) +m4trace:configure.in:119: -1- AC_SUBST([LIB@&t@OBJS], [$ac_libobjs]) +m4trace:configure.in:119: -1- AC_SUBST([LTLIBOBJS], [$ac_ltlibobjs]) diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.guess b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.guess new file mode 100755 index 000000000..6be7a693c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.guess @@ -0,0 +1,1450 @@ +#! /bin/sh +# Attempt to guess a canonical system name. +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, +# 2000, 2001, 2002, 2003, 2004 Free Software Foundation, Inc. + +timestamp='2004-08-11' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + +# Originally written by Per Bothner . +# Please send patches to . Submit a context +# diff and a properly formatted ChangeLog entry. +# +# This script attempts to guess a canonical system name similar to +# config.sub. If it succeeds, it prints the system name on stdout, and +# exits with 0. Otherwise, it exits with 1. +# +# The plan is that this can be called by configure scripts if you +# don't specify an explicit build system type. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] + +Output the configuration name of the system \`$me' is run on. + +Operation modes: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.guess ($timestamp) + +Originally written by Per Bothner. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004 +Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit 0 ;; + --version | -v ) + echo "$version" ; exit 0 ;; + --help | --h* | -h ) + echo "$usage"; exit 0 ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + * ) + break ;; + esac +done + +if test $# != 0; then + echo "$me: too many arguments$help" >&2 + exit 1 +fi + +trap 'exit 1' 1 2 15 + +# CC_FOR_BUILD -- compiler used by this script. Note that the use of a +# compiler to aid in system detection is discouraged as it requires +# temporary files to be created and, as you can see below, it is a +# headache to deal with in a portable fashion. + +# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still +# use `HOST_CC' if defined, but it is deprecated. + +# Portable tmp directory creation inspired by the Autoconf team. + +set_cc_for_build=' +trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ; +trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ; +: ${TMPDIR=/tmp} ; + { tmp=`(umask 077 && mktemp -d -q "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } || + { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } || + { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } || + { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ; +dummy=$tmp/dummy ; +tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ; +case $CC_FOR_BUILD,$HOST_CC,$CC in + ,,) echo "int x;" > $dummy.c ; + for c in cc gcc c89 c99 ; do + if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then + CC_FOR_BUILD="$c"; break ; + fi ; + done ; + if test x"$CC_FOR_BUILD" = x ; then + CC_FOR_BUILD=no_compiler_found ; + fi + ;; + ,,*) CC_FOR_BUILD=$CC ;; + ,*,*) CC_FOR_BUILD=$HOST_CC ;; +esac ;' + +# This is needed to find uname on a Pyramid OSx when run in the BSD universe. +# (ghazi@noc.rutgers.edu 1994-08-24) +if (test -f /.attbin/uname) >/dev/null 2>&1 ; then + PATH=$PATH:/.attbin ; export PATH +fi + +UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown +UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown +UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown +UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown + +# Note: order is significant - the case branches are not exclusive. + +case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in + *:NetBSD:*:*) + # NetBSD (nbsd) targets should (where applicable) match one or + # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*, + # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently + # switched to ELF, *-*-netbsd* would select the old + # object file format. This provides both forward + # compatibility and a consistent mechanism for selecting the + # object file format. + # + # Note: NetBSD doesn't particularly care about the vendor + # portion of the name. We always set it to "unknown". + sysctl="sysctl -n hw.machine_arch" + UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \ + /usr/sbin/$sysctl 2>/dev/null || echo unknown)` + case "${UNAME_MACHINE_ARCH}" in + armeb) machine=armeb-unknown ;; + arm*) machine=arm-unknown ;; + sh3el) machine=shl-unknown ;; + sh3eb) machine=sh-unknown ;; + *) machine=${UNAME_MACHINE_ARCH}-unknown ;; + esac + # The Operating System including object format, if it has switched + # to ELF recently, or will in the future. + case "${UNAME_MACHINE_ARCH}" in + arm*|i386|m68k|ns32k|sh3*|sparc|vax) + eval $set_cc_for_build + if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep __ELF__ >/dev/null + then + # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). + # Return netbsd for either. FIX? + os=netbsd + else + os=netbsdelf + fi + ;; + *) + os=netbsd + ;; + esac + # The OS release + # Debian GNU/NetBSD machines have a different userland, and + # thus, need a distinct triplet. However, they do not need + # kernel version information, so it can be replaced with a + # suitable tag, in the style of linux-gnu. + case "${UNAME_VERSION}" in + Debian*) + release='-gnu' + ;; + *) + release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` + ;; + esac + # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: + # contains redundant information, the shorter form: + # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. + echo "${machine}-${os}${release}" + exit 0 ;; + amd64:OpenBSD:*:*) + echo x86_64-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + amiga:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + arc:OpenBSD:*:*) + echo mipsel-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + cats:OpenBSD:*:*) + echo arm-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + hp300:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + luna88k:OpenBSD:*:*) + echo m88k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + mac68k:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + macppc:OpenBSD:*:*) + echo powerpc-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + mvme68k:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + mvme88k:OpenBSD:*:*) + echo m88k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + mvmeppc:OpenBSD:*:*) + echo powerpc-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + pmax:OpenBSD:*:*) + echo mipsel-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + sgi:OpenBSD:*:*) + echo mipseb-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + sun3:OpenBSD:*:*) + echo m68k-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + wgrisc:OpenBSD:*:*) + echo mipsel-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + *:OpenBSD:*:*) + echo ${UNAME_MACHINE}-unknown-openbsd${UNAME_RELEASE} + exit 0 ;; + *:ekkoBSD:*:*) + echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE} + exit 0 ;; + macppc:MirBSD:*:*) + echo powerppc-unknown-mirbsd${UNAME_RELEASE} + exit 0 ;; + *:MirBSD:*:*) + echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE} + exit 0 ;; + alpha:OSF1:*:*) + case $UNAME_RELEASE in + *4.0) + UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` + ;; + *5.*) + UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'` + ;; + esac + # According to Compaq, /usr/sbin/psrinfo has been available on + # OSF/1 and Tru64 systems produced since 1995. I hope that + # covers most systems running today. This code pipes the CPU + # types through head -n 1, so we only detect the type of CPU 0. + ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` + case "$ALPHA_CPU_TYPE" in + "EV4 (21064)") + UNAME_MACHINE="alpha" ;; + "EV4.5 (21064)") + UNAME_MACHINE="alpha" ;; + "LCA4 (21066/21068)") + UNAME_MACHINE="alpha" ;; + "EV5 (21164)") + UNAME_MACHINE="alphaev5" ;; + "EV5.6 (21164A)") + UNAME_MACHINE="alphaev56" ;; + "EV5.6 (21164PC)") + UNAME_MACHINE="alphapca56" ;; + "EV5.7 (21164PC)") + UNAME_MACHINE="alphapca57" ;; + "EV6 (21264)") + UNAME_MACHINE="alphaev6" ;; + "EV6.7 (21264A)") + UNAME_MACHINE="alphaev67" ;; + "EV6.8CB (21264C)") + UNAME_MACHINE="alphaev68" ;; + "EV6.8AL (21264B)") + UNAME_MACHINE="alphaev68" ;; + "EV6.8CX (21264D)") + UNAME_MACHINE="alphaev68" ;; + "EV6.9A (21264/EV69A)") + UNAME_MACHINE="alphaev69" ;; + "EV7 (21364)") + UNAME_MACHINE="alphaev7" ;; + "EV7.9 (21364A)") + UNAME_MACHINE="alphaev79" ;; + esac + # A Pn.n version is a patched version. + # A Vn.n version is a released version. + # A Tn.n version is a released field test version. + # A Xn.n version is an unreleased experimental baselevel. + # 1.2 uses "1.2" for uname -r. + echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` + exit 0 ;; + Alpha\ *:Windows_NT*:*) + # How do we know it's Interix rather than the generic POSIX subsystem? + # Should we change UNAME_MACHINE based on the output of uname instead + # of the specific Alpha model? + echo alpha-pc-interix + exit 0 ;; + 21064:Windows_NT:50:3) + echo alpha-dec-winnt3.5 + exit 0 ;; + Amiga*:UNIX_System_V:4.0:*) + echo m68k-unknown-sysv4 + exit 0;; + *:[Aa]miga[Oo][Ss]:*:*) + echo ${UNAME_MACHINE}-unknown-amigaos + exit 0 ;; + *:[Mm]orph[Oo][Ss]:*:*) + echo ${UNAME_MACHINE}-unknown-morphos + exit 0 ;; + *:OS/390:*:*) + echo i370-ibm-openedition + exit 0 ;; + *:OS400:*:*) + echo powerpc-ibm-os400 + exit 0 ;; + arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) + echo arm-acorn-riscix${UNAME_RELEASE} + exit 0;; + SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) + echo hppa1.1-hitachi-hiuxmpp + exit 0;; + Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) + # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. + if test "`(/bin/universe) 2>/dev/null`" = att ; then + echo pyramid-pyramid-sysv3 + else + echo pyramid-pyramid-bsd + fi + exit 0 ;; + NILE*:*:*:dcosx) + echo pyramid-pyramid-svr4 + exit 0 ;; + DRS?6000:unix:4.0:6*) + echo sparc-icl-nx6 + exit 0 ;; + DRS?6000:UNIX_SV:4.2*:7*) + case `/usr/bin/uname -p` in + sparc) echo sparc-icl-nx7 && exit 0 ;; + esac ;; + sun4H:SunOS:5.*:*) + echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) + echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + i86pc:SunOS:5.*:*) + echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + sun4*:SunOS:6*:*) + # According to config.sub, this is the proper way to canonicalize + # SunOS6. Hard to guess exactly what SunOS6 will be like, but + # it's likely to be more like Solaris than SunOS4. + echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + sun4*:SunOS:*:*) + case "`/usr/bin/arch -k`" in + Series*|S4*) + UNAME_RELEASE=`uname -v` + ;; + esac + # Japanese Language versions have a version number like `4.1.3-JL'. + echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` + exit 0 ;; + sun3*:SunOS:*:*) + echo m68k-sun-sunos${UNAME_RELEASE} + exit 0 ;; + sun*:*:4.2BSD:*) + UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` + test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 + case "`/bin/arch`" in + sun3) + echo m68k-sun-sunos${UNAME_RELEASE} + ;; + sun4) + echo sparc-sun-sunos${UNAME_RELEASE} + ;; + esac + exit 0 ;; + aushp:SunOS:*:*) + echo sparc-auspex-sunos${UNAME_RELEASE} + exit 0 ;; + # The situation for MiNT is a little confusing. The machine name + # can be virtually everything (everything which is not + # "atarist" or "atariste" at least should have a processor + # > m68000). The system name ranges from "MiNT" over "FreeMiNT" + # to the lowercase version "mint" (or "freemint"). Finally + # the system name "TOS" denotes a system which is actually not + # MiNT. But MiNT is downward compatible to TOS, so this should + # be no problem. + atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit 0 ;; + atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit 0 ;; + *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit 0 ;; + milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) + echo m68k-milan-mint${UNAME_RELEASE} + exit 0 ;; + hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) + echo m68k-hades-mint${UNAME_RELEASE} + exit 0 ;; + *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) + echo m68k-unknown-mint${UNAME_RELEASE} + exit 0 ;; + m68k:machten:*:*) + echo m68k-apple-machten${UNAME_RELEASE} + exit 0 ;; + powerpc:machten:*:*) + echo powerpc-apple-machten${UNAME_RELEASE} + exit 0 ;; + RISC*:Mach:*:*) + echo mips-dec-mach_bsd4.3 + exit 0 ;; + RISC*:ULTRIX:*:*) + echo mips-dec-ultrix${UNAME_RELEASE} + exit 0 ;; + VAX*:ULTRIX*:*:*) + echo vax-dec-ultrix${UNAME_RELEASE} + exit 0 ;; + 2020:CLIX:*:* | 2430:CLIX:*:*) + echo clipper-intergraph-clix${UNAME_RELEASE} + exit 0 ;; + mips:*:*:UMIPS | mips:*:*:RISCos) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c +#ifdef __cplusplus +#include /* for printf() prototype */ + int main (int argc, char *argv[]) { +#else + int main (argc, argv) int argc; char *argv[]; { +#endif + #if defined (host_mips) && defined (MIPSEB) + #if defined (SYSTYPE_SYSV) + printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_SVR4) + printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) + printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); + #endif + #endif + exit (-1); + } +EOF + $CC_FOR_BUILD -o $dummy $dummy.c \ + && $dummy `echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` \ + && exit 0 + echo mips-mips-riscos${UNAME_RELEASE} + exit 0 ;; + Motorola:PowerMAX_OS:*:*) + echo powerpc-motorola-powermax + exit 0 ;; + Motorola:*:4.3:PL8-*) + echo powerpc-harris-powermax + exit 0 ;; + Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) + echo powerpc-harris-powermax + exit 0 ;; + Night_Hawk:Power_UNIX:*:*) + echo powerpc-harris-powerunix + exit 0 ;; + m88k:CX/UX:7*:*) + echo m88k-harris-cxux7 + exit 0 ;; + m88k:*:4*:R4*) + echo m88k-motorola-sysv4 + exit 0 ;; + m88k:*:3*:R3*) + echo m88k-motorola-sysv3 + exit 0 ;; + AViiON:dgux:*:*) + # DG/UX returns AViiON for all architectures + UNAME_PROCESSOR=`/usr/bin/uname -p` + if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] + then + if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ + [ ${TARGET_BINARY_INTERFACE}x = x ] + then + echo m88k-dg-dgux${UNAME_RELEASE} + else + echo m88k-dg-dguxbcs${UNAME_RELEASE} + fi + else + echo i586-dg-dgux${UNAME_RELEASE} + fi + exit 0 ;; + M88*:DolphinOS:*:*) # DolphinOS (SVR3) + echo m88k-dolphin-sysv3 + exit 0 ;; + M88*:*:R3*:*) + # Delta 88k system running SVR3 + echo m88k-motorola-sysv3 + exit 0 ;; + XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) + echo m88k-tektronix-sysv3 + exit 0 ;; + Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) + echo m68k-tektronix-bsd + exit 0 ;; + *:IRIX*:*:*) + echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` + exit 0 ;; + ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. + echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id + exit 0 ;; # Note that: echo "'`uname -s`'" gives 'AIX ' + i*86:AIX:*:*) + echo i386-ibm-aix + exit 0 ;; + ia64:AIX:*:*) + if [ -x /usr/bin/oslevel ] ; then + IBM_REV=`/usr/bin/oslevel` + else + IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + fi + echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} + exit 0 ;; + *:AIX:2:3) + if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + + main() + { + if (!__power_pc()) + exit(1); + puts("powerpc-ibm-aix3.2.5"); + exit(0); + } +EOF + $CC_FOR_BUILD -o $dummy $dummy.c && $dummy && exit 0 + echo rs6000-ibm-aix3.2.5 + elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then + echo rs6000-ibm-aix3.2.4 + else + echo rs6000-ibm-aix3.2 + fi + exit 0 ;; + *:AIX:*:[45]) + IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` + if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then + IBM_ARCH=rs6000 + else + IBM_ARCH=powerpc + fi + if [ -x /usr/bin/oslevel ] ; then + IBM_REV=`/usr/bin/oslevel` + else + IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + fi + echo ${IBM_ARCH}-ibm-aix${IBM_REV} + exit 0 ;; + *:AIX:*:*) + echo rs6000-ibm-aix + exit 0 ;; + ibmrt:4.4BSD:*|romp-ibm:BSD:*) + echo romp-ibm-bsd4.4 + exit 0 ;; + ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and + echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to + exit 0 ;; # report: romp-ibm BSD 4.3 + *:BOSX:*:*) + echo rs6000-bull-bosx + exit 0 ;; + DPX/2?00:B.O.S.:*:*) + echo m68k-bull-sysv3 + exit 0 ;; + 9000/[34]??:4.3bsd:1.*:*) + echo m68k-hp-bsd + exit 0 ;; + hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) + echo m68k-hp-bsd4.4 + exit 0 ;; + 9000/[34678]??:HP-UX:*:*) + HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` + case "${UNAME_MACHINE}" in + 9000/31? ) HP_ARCH=m68000 ;; + 9000/[34]?? ) HP_ARCH=m68k ;; + 9000/[678][0-9][0-9]) + if [ -x /usr/bin/getconf ]; then + sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` + sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` + case "${sc_cpu_version}" in + 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 + 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 + 532) # CPU_PA_RISC2_0 + case "${sc_kernel_bits}" in + 32) HP_ARCH="hppa2.0n" ;; + 64) HP_ARCH="hppa2.0w" ;; + '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 + esac ;; + esac + fi + if [ "${HP_ARCH}" = "" ]; then + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + + #define _HPUX_SOURCE + #include + #include + + int main () + { + #if defined(_SC_KERNEL_BITS) + long bits = sysconf(_SC_KERNEL_BITS); + #endif + long cpu = sysconf (_SC_CPU_VERSION); + + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1"); break; + case CPU_PA_RISC2_0: + #if defined(_SC_KERNEL_BITS) + switch (bits) + { + case 64: puts ("hppa2.0w"); break; + case 32: puts ("hppa2.0n"); break; + default: puts ("hppa2.0"); break; + } break; + #else /* !defined(_SC_KERNEL_BITS) */ + puts ("hppa2.0"); break; + #endif + default: puts ("hppa1.0"); break; + } + exit (0); + } +EOF + (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` + test -z "$HP_ARCH" && HP_ARCH=hppa + fi ;; + esac + if [ ${HP_ARCH} = "hppa2.0w" ] + then + # avoid double evaluation of $set_cc_for_build + test -n "$CC_FOR_BUILD" || eval $set_cc_for_build + if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E -) | grep __LP64__ >/dev/null + then + HP_ARCH="hppa2.0w" + else + HP_ARCH="hppa64" + fi + fi + echo ${HP_ARCH}-hp-hpux${HPUX_REV} + exit 0 ;; + ia64:HP-UX:*:*) + HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` + echo ia64-hp-hpux${HPUX_REV} + exit 0 ;; + 3050*:HI-UX:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + int + main () + { + long cpu = sysconf (_SC_CPU_VERSION); + /* The order matters, because CPU_IS_HP_MC68K erroneously returns + true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct + results, however. */ + if (CPU_IS_PA_RISC (cpu)) + { + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; + case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; + default: puts ("hppa-hitachi-hiuxwe2"); break; + } + } + else if (CPU_IS_HP_MC68K (cpu)) + puts ("m68k-hitachi-hiuxwe2"); + else puts ("unknown-hitachi-hiuxwe2"); + exit (0); + } +EOF + $CC_FOR_BUILD -o $dummy $dummy.c && $dummy && exit 0 + echo unknown-hitachi-hiuxwe2 + exit 0 ;; + 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) + echo hppa1.1-hp-bsd + exit 0 ;; + 9000/8??:4.3bsd:*:*) + echo hppa1.0-hp-bsd + exit 0 ;; + *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) + echo hppa1.0-hp-mpeix + exit 0 ;; + hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) + echo hppa1.1-hp-osf + exit 0 ;; + hp8??:OSF1:*:*) + echo hppa1.0-hp-osf + exit 0 ;; + i*86:OSF1:*:*) + if [ -x /usr/sbin/sysversion ] ; then + echo ${UNAME_MACHINE}-unknown-osf1mk + else + echo ${UNAME_MACHINE}-unknown-osf1 + fi + exit 0 ;; + parisc*:Lites*:*:*) + echo hppa1.1-hp-lites + exit 0 ;; + C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) + echo c1-convex-bsd + exit 0 ;; + C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit 0 ;; + C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) + echo c34-convex-bsd + exit 0 ;; + C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) + echo c38-convex-bsd + exit 0 ;; + C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) + echo c4-convex-bsd + exit 0 ;; + CRAY*Y-MP:*:*:*) + echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*[A-Z]90:*:*:*) + echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ + | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ + -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ + -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*TS:*:*:*) + echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*T3E:*:*:*) + echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + CRAY*SV1:*:*:*) + echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + *:UNICOS/mp:*:*) + echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit 0 ;; + F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) + FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` + echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit 0 ;; + 5000:UNIX_System_V:4.*:*) + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` + echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit 0 ;; + i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) + echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} + exit 0 ;; + sparc*:BSD/OS:*:*) + echo sparc-unknown-bsdi${UNAME_RELEASE} + exit 0 ;; + *:BSD/OS:*:*) + echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} + exit 0 ;; + *:FreeBSD:*:*) + echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` + exit 0 ;; + i*:CYGWIN*:*) + echo ${UNAME_MACHINE}-pc-cygwin + exit 0 ;; + i*:MINGW*:*) + echo ${UNAME_MACHINE}-pc-mingw32 + exit 0 ;; + i*:PW*:*) + echo ${UNAME_MACHINE}-pc-pw32 + exit 0 ;; + x86:Interix*:[34]*) + echo i586-pc-interix${UNAME_RELEASE}|sed -e 's/\..*//' + exit 0 ;; + [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) + echo i${UNAME_MACHINE}-pc-mks + exit 0 ;; + i*:Windows_NT*:* | Pentium*:Windows_NT*:*) + # How do we know it's Interix rather than the generic POSIX subsystem? + # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we + # UNAME_MACHINE based on the output of uname instead of i386? + echo i586-pc-interix + exit 0 ;; + i*:UWIN*:*) + echo ${UNAME_MACHINE}-pc-uwin + exit 0 ;; + p*:CYGWIN*:*) + echo powerpcle-unknown-cygwin + exit 0 ;; + prep*:SunOS:5.*:*) + echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit 0 ;; + *:GNU:*:*) + # the GNU system + echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` + exit 0 ;; + *:GNU/*:*:*) + # other systems with GNU libc and userland + echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu + exit 0 ;; + i*86:Minix:*:*) + echo ${UNAME_MACHINE}-pc-minix + exit 0 ;; + arm*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + cris:Linux:*:*) + echo cris-axis-linux-gnu + exit 0 ;; + ia64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + m32r*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + m68*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + mips:Linux:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #undef CPU + #undef mips + #undef mipsel + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + CPU=mipsel + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + CPU=mips + #else + CPU= + #endif + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=` + test x"${CPU}" != x && echo "${CPU}-unknown-linux-gnu" && exit 0 + ;; + mips64:Linux:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #undef CPU + #undef mips64 + #undef mips64el + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + CPU=mips64el + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + CPU=mips64 + #else + CPU= + #endif + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=` + test x"${CPU}" != x && echo "${CPU}-unknown-linux-gnu" && exit 0 + ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu + exit 0 ;; + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-gnu + exit 0 ;; + alpha:Linux:*:*) + case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null + if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi + echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + exit 0 ;; + parisc:Linux:*:* | hppa:Linux:*:*) + # Look for CPU level + case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in + PA7*) echo hppa1.1-unknown-linux-gnu ;; + PA8*) echo hppa2.0-unknown-linux-gnu ;; + *) echo hppa-unknown-linux-gnu ;; + esac + exit 0 ;; + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-gnu + exit 0 ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo ${UNAME_MACHINE}-ibm-linux + exit 0 ;; + sh64*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + sh*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + sparc:Linux:*:* | sparc64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit 0 ;; + x86_64:Linux:*:*) + echo x86_64-unknown-linux-gnu + exit 0 ;; + i*86:Linux:*:*) + # The BFD linker knows what the default object file format is, so + # first see if it will tell us. cd to the root directory to prevent + # problems with other programs or directories called `ld' in the path. + # Set LC_ALL=C to ensure ld outputs messages in English. + ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ + | sed -ne '/supported targets:/!d + s/[ ][ ]*/ /g + s/.*supported targets: *// + s/ .*// + p'` + case "$ld_supported_targets" in + elf32-i386) + TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" + ;; + a.out-i386-linux) + echo "${UNAME_MACHINE}-pc-linux-gnuaout" + exit 0 ;; + coff-i386) + echo "${UNAME_MACHINE}-pc-linux-gnucoff" + exit 0 ;; + "") + # Either a pre-BFD a.out linker (linux-gnuoldld) or + # one that does not give us useful --help. + echo "${UNAME_MACHINE}-pc-linux-gnuoldld" + exit 0 ;; + esac + # Determine whether the default compiler is a.out or elf + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + #ifdef __ELF__ + # ifdef __GLIBC__ + # if __GLIBC__ >= 2 + LIBC=gnu + # else + LIBC=gnulibc1 + # endif + # else + LIBC=gnulibc1 + # endif + #else + #ifdef __INTEL_COMPILER + LIBC=gnu + #else + LIBC=gnuaout + #endif + #endif + #ifdef __dietlibc__ + LIBC=dietlibc + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=` + test x"${LIBC}" != x && echo "${UNAME_MACHINE}-pc-linux-${LIBC}" && exit 0 + test x"${TENTATIVE}" != x && echo "${TENTATIVE}" && exit 0 + ;; + i*86:DYNIX/ptx:4*:*) + # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. + # earlier versions are messed up and put the nodename in both + # sysname and nodename. + echo i386-sequent-sysv4 + exit 0 ;; + i*86:UNIX_SV:4.2MP:2.*) + # Unixware is an offshoot of SVR4, but it has its own version + # number series starting with 2... + # I am not positive that other SVR4 systems won't match this, + # I just have to hope. -- rms. + # Use sysv4.2uw... so that sysv4* matches it. + echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} + exit 0 ;; + i*86:OS/2:*:*) + # If we were able to find `uname', then EMX Unix compatibility + # is probably installed. + echo ${UNAME_MACHINE}-pc-os2-emx + exit 0 ;; + i*86:XTS-300:*:STOP) + echo ${UNAME_MACHINE}-unknown-stop + exit 0 ;; + i*86:atheos:*:*) + echo ${UNAME_MACHINE}-unknown-atheos + exit 0 ;; + i*86:syllable:*:*) + echo ${UNAME_MACHINE}-pc-syllable + exit 0 ;; + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) + echo i386-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + i*86:*DOS:*:*) + echo ${UNAME_MACHINE}-pc-msdosdjgpp + exit 0 ;; + i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) + UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` + if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then + echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} + else + echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} + fi + exit 0 ;; + i*86:*:5:[78]*) + case `/bin/uname -X | grep "^Machine"` in + *486*) UNAME_MACHINE=i486 ;; + *Pentium) UNAME_MACHINE=i586 ;; + *Pent*|*Celeron) UNAME_MACHINE=i686 ;; + esac + echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} + exit 0 ;; + i*86:*:3.2:*) + if test -f /usr/options/cb.name; then + UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then + UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` + (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 + (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ + && UNAME_MACHINE=i586 + (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ + && UNAME_MACHINE=i686 + (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ + && UNAME_MACHINE=i686 + echo ${UNAME_MACHINE}-pc-sco$UNAME_REL + else + echo ${UNAME_MACHINE}-pc-sysv32 + fi + exit 0 ;; + pc:*:*:*) + # Left here for compatibility: + # uname -m prints for DJGPP always 'pc', but it prints nothing about + # the processor, so we play safe by assuming i386. + echo i386-pc-msdosdjgpp + exit 0 ;; + Intel:Mach:3*:*) + echo i386-pc-mach3 + exit 0 ;; + paragon:*:*:*) + echo i860-intel-osf1 + exit 0 ;; + i860:*:4.*:*) # i860-SVR4 + if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then + echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 + else # Add other i860-SVR4 vendors below as they are discovered. + echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 + fi + exit 0 ;; + mini*:CTIX:SYS*5:*) + # "miniframe" + echo m68010-convergent-sysv + exit 0 ;; + mc68k:UNIX:SYSTEM5:3.51m) + echo m68k-convergent-sysv + exit 0 ;; + M680?0:D-NIX:5.3:*) + echo m68k-diab-dnix + exit 0 ;; + M68*:*:R3V[5678]*:*) + test -r /sysV68 && echo 'm68k-motorola-sysv' && exit 0 ;; + 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) + OS_REL='' + test -r /etc/.relid \ + && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && echo i486-ncr-sysv4.3${OS_REL} && exit 0 + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && echo i586-ncr-sysv4.3${OS_REL} && exit 0 ;; + 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && echo i486-ncr-sysv4 && exit 0 ;; + m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) + echo m68k-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + mc68030:UNIX_System_V:4.*:*) + echo m68k-atari-sysv4 + exit 0 ;; + TSUNAMI:LynxOS:2.*:*) + echo sparc-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + rs6000:LynxOS:2.*:*) + echo rs6000-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) + echo powerpc-unknown-lynxos${UNAME_RELEASE} + exit 0 ;; + SM[BE]S:UNIX_SV:*:*) + echo mips-dde-sysv${UNAME_RELEASE} + exit 0 ;; + RM*:ReliantUNIX-*:*:*) + echo mips-sni-sysv4 + exit 0 ;; + RM*:SINIX-*:*:*) + echo mips-sni-sysv4 + exit 0 ;; + *:SINIX-*:*:*) + if uname -p 2>/dev/null >/dev/null ; then + UNAME_MACHINE=`(uname -p) 2>/dev/null` + echo ${UNAME_MACHINE}-sni-sysv4 + else + echo ns32k-sni-sysv + fi + exit 0 ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says + echo i586-unisys-sysv4 + exit 0 ;; + *:UNIX_System_V:4*:FTX*) + # From Gerald Hewes . + # How about differentiating between stratus architectures? -djm + echo hppa1.1-stratus-sysv4 + exit 0 ;; + *:*:*:FTX*) + # From seanf@swdc.stratus.com. + echo i860-stratus-sysv4 + exit 0 ;; + *:VOS:*:*) + # From Paul.Green@stratus.com. + echo hppa1.1-stratus-vos + exit 0 ;; + mc68*:A/UX:*:*) + echo m68k-apple-aux${UNAME_RELEASE} + exit 0 ;; + news*:NEWS-OS:6*:*) + echo mips-sony-newsos6 + exit 0 ;; + R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) + if [ -d /usr/nec ]; then + echo mips-nec-sysv${UNAME_RELEASE} + else + echo mips-unknown-sysv${UNAME_RELEASE} + fi + exit 0 ;; + BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. + echo powerpc-be-beos + exit 0 ;; + BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. + echo powerpc-apple-beos + exit 0 ;; + BePC:BeOS:*:*) # BeOS running on Intel PC compatible. + echo i586-pc-beos + exit 0 ;; + SX-4:SUPER-UX:*:*) + echo sx4-nec-superux${UNAME_RELEASE} + exit 0 ;; + SX-5:SUPER-UX:*:*) + echo sx5-nec-superux${UNAME_RELEASE} + exit 0 ;; + SX-6:SUPER-UX:*:*) + echo sx6-nec-superux${UNAME_RELEASE} + exit 0 ;; + Power*:Rhapsody:*:*) + echo powerpc-apple-rhapsody${UNAME_RELEASE} + exit 0 ;; + *:Rhapsody:*:*) + echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} + exit 0 ;; + *:Darwin:*:*) + UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown + case $UNAME_PROCESSOR in + *86) UNAME_PROCESSOR=i686 ;; + unknown) UNAME_PROCESSOR=powerpc ;; + esac + echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} + exit 0 ;; + *:procnto*:*:* | *:QNX:[0123456789]*:*) + UNAME_PROCESSOR=`uname -p` + if test "$UNAME_PROCESSOR" = "x86"; then + UNAME_PROCESSOR=i386 + UNAME_MACHINE=pc + fi + echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} + exit 0 ;; + *:QNX:*:4*) + echo i386-pc-qnx + exit 0 ;; + NSR-?:NONSTOP_KERNEL:*:*) + echo nsr-tandem-nsk${UNAME_RELEASE} + exit 0 ;; + *:NonStop-UX:*:*) + echo mips-compaq-nonstopux + exit 0 ;; + BS2000:POSIX*:*:*) + echo bs2000-siemens-sysv + exit 0 ;; + DS/*:UNIX_System_V:*:*) + echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} + exit 0 ;; + *:Plan9:*:*) + # "uname -m" is not consistent, so use $cputype instead. 386 + # is converted to i386 for consistency with other x86 + # operating systems. + if test "$cputype" = "386"; then + UNAME_MACHINE=i386 + else + UNAME_MACHINE="$cputype" + fi + echo ${UNAME_MACHINE}-unknown-plan9 + exit 0 ;; + *:TOPS-10:*:*) + echo pdp10-unknown-tops10 + exit 0 ;; + *:TENEX:*:*) + echo pdp10-unknown-tenex + exit 0 ;; + KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) + echo pdp10-dec-tops20 + exit 0 ;; + XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) + echo pdp10-xkl-tops20 + exit 0 ;; + *:TOPS-20:*:*) + echo pdp10-unknown-tops20 + exit 0 ;; + *:ITS:*:*) + echo pdp10-unknown-its + exit 0 ;; + SEI:*:*:SEIUX) + echo mips-sei-seiux${UNAME_RELEASE} + exit 0 ;; + *:DragonFly:*:*) + echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` + exit 0 ;; + *:*VMS:*:*) + UNAME_MACHINE=`(uname -p) 2>/dev/null` + case "${UNAME_MACHINE}" in + A*) echo alpha-dec-vms && exit 0 ;; + I*) echo ia64-dec-vms && exit 0 ;; + V*) echo vax-dec-vms && exit 0 ;; + esac +esac + +#echo '(No uname command or uname output not recognized.)' 1>&2 +#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 + +eval $set_cc_for_build +cat >$dummy.c < +# include +#endif +main () +{ +#if defined (sony) +#if defined (MIPSEB) + /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, + I don't know.... */ + printf ("mips-sony-bsd\n"); exit (0); +#else +#include + printf ("m68k-sony-newsos%s\n", +#ifdef NEWSOS4 + "4" +#else + "" +#endif + ); exit (0); +#endif +#endif + +#if defined (__arm) && defined (__acorn) && defined (__unix) + printf ("arm-acorn-riscix"); exit (0); +#endif + +#if defined (hp300) && !defined (hpux) + printf ("m68k-hp-bsd\n"); exit (0); +#endif + +#if defined (NeXT) +#if !defined (__ARCHITECTURE__) +#define __ARCHITECTURE__ "m68k" +#endif + int version; + version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; + if (version < 4) + printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); + else + printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); + exit (0); +#endif + +#if defined (MULTIMAX) || defined (n16) +#if defined (UMAXV) + printf ("ns32k-encore-sysv\n"); exit (0); +#else +#if defined (CMU) + printf ("ns32k-encore-mach\n"); exit (0); +#else + printf ("ns32k-encore-bsd\n"); exit (0); +#endif +#endif +#endif + +#if defined (__386BSD__) + printf ("i386-pc-bsd\n"); exit (0); +#endif + +#if defined (sequent) +#if defined (i386) + printf ("i386-sequent-dynix\n"); exit (0); +#endif +#if defined (ns32000) + printf ("ns32k-sequent-dynix\n"); exit (0); +#endif +#endif + +#if defined (_SEQUENT_) + struct utsname un; + + uname(&un); + + if (strncmp(un.version, "V2", 2) == 0) { + printf ("i386-sequent-ptx2\n"); exit (0); + } + if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ + printf ("i386-sequent-ptx1\n"); exit (0); + } + printf ("i386-sequent-ptx\n"); exit (0); + +#endif + +#if defined (vax) +# if !defined (ultrix) +# include +# if defined (BSD) +# if BSD == 43 + printf ("vax-dec-bsd4.3\n"); exit (0); +# else +# if BSD == 199006 + printf ("vax-dec-bsd4.3reno\n"); exit (0); +# else + printf ("vax-dec-bsd\n"); exit (0); +# endif +# endif +# else + printf ("vax-dec-bsd\n"); exit (0); +# endif +# else + printf ("vax-dec-ultrix\n"); exit (0); +# endif +#endif + +#if defined (alliant) && defined (i860) + printf ("i860-alliant-bsd\n"); exit (0); +#endif + + exit (1); +} +EOF + +$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && $dummy && exit 0 + +# Apollos put the system type in the environment. + +test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit 0; } + +# Convex versions that predate uname can use getsysinfo(1) + +if [ -x /usr/convex/getsysinfo ] +then + case `getsysinfo -f cpu_type` in + c1*) + echo c1-convex-bsd + exit 0 ;; + c2*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit 0 ;; + c34*) + echo c34-convex-bsd + exit 0 ;; + c38*) + echo c38-convex-bsd + exit 0 ;; + c4*) + echo c4-convex-bsd + exit 0 ;; + esac +fi + +cat >&2 < in order to provide the needed +information to handle your system. + +config.guess timestamp = $timestamp + +uname -m = `(uname -m) 2>/dev/null || echo unknown` +uname -r = `(uname -r) 2>/dev/null || echo unknown` +uname -s = `(uname -s) 2>/dev/null || echo unknown` +uname -v = `(uname -v) 2>/dev/null || echo unknown` + +/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` +/bin/uname -X = `(/bin/uname -X) 2>/dev/null` + +hostinfo = `(hostinfo) 2>/dev/null` +/bin/universe = `(/bin/universe) 2>/dev/null` +/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` +/bin/arch = `(/bin/arch) 2>/dev/null` +/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` +/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` + +UNAME_MACHINE = ${UNAME_MACHINE} +UNAME_RELEASE = ${UNAME_RELEASE} +UNAME_SYSTEM = ${UNAME_SYSTEM} +UNAME_VERSION = ${UNAME_VERSION} +EOF + +exit 1 + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.log b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.log new file mode 100755 index 000000000..239d398b1 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.log @@ -0,0 +1,664 @@ +This file contains any messages produced by compilers while +running configure, to aid debugging if configure makes a mistake. + +It was created by configure, which was +generated by GNU Autoconf 2.59. Invocation command line was + + $ ./configure --prefix=/usr/local --prefix=/usr/local --cache-file=/dev/null --srcdir=. --cache-file=/dev/null --srcdir=. + +## --------- ## +## Platform. ## +## --------- ## + +hostname = mcluster02 +uname -m = x86_64 +uname -r = 2.6.9-34.ELsmp +uname -s = Linux +uname -v = #1 SMP Fri Feb 24 16:56:28 EST 2006 + +/usr/bin/uname -p = unknown +/bin/uname -X = unknown + +/bin/arch = x86_64 +/usr/bin/arch -k = unknown +/usr/convex/getsysinfo = unknown +hostinfo = unknown +/bin/machine = unknown +/usr/bin/oslevel = unknown +/bin/universe = unknown + +PATH: /storage/appl/n1ge6u7/bin/lx24-amd64 +PATH: /opt/sun/n1gc/bin +PATH: /usr/local/bin +PATH: /bin +PATH: /usr/bin +PATH: /opt/c3-4/ +PATH: /usr/X11R6/bin +PATH: /usr/local/bin +PATH: /usr/local/bin/X11R5 +PATH: /usr/local/X11R5/bin +PATH: /usr/X11R6/bin +PATH: /home/rabani/Develop/perl/GeneXPress +PATH: /home/rabani/Develop/perl/Genome +PATH: /home/rabani/Develop/perl/Lib +PATH: /home/rabani/Develop/perl/Parsers +PATH: /home/rabani/Develop/perl/RNA +PATH: /home/rabani/Develop/perl/Sequence +PATH: /home/rabani/Develop/perl/System +PATH: /home/rabani/Develop/perl/Web +PATH: /home/rabani/Develop/perl/Web/DataDir +PATH: /home/rabani/Develop/genie_release64/Programs +PATH: /storage/appl/matlab14.3/bin +PATH: /home/rabani + + +## ----------- ## +## Core tests. ## +## ----------- ## + +configure:1349: checking build system type +configure:1367: result: x86_64-unknown-linux-gnu +configure:1375: checking host system type +configure:1389: result: x86_64-unknown-linux-gnu +configure:1487: checking for gcc +configure:1503: found /usr/bin/gcc +configure:1513: result: gcc +configure:1757: checking for C compiler version +configure:1760: gcc --version &5 +gcc (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2) +Copyright (C) 2004 Free Software Foundation, Inc. +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + +configure:1763: $? = 0 +configure:1765: gcc -v &5 +Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.5/specs +Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux +Thread model: posix +gcc version 3.4.5 20051201 (Red Hat 3.4.5-2) +configure:1768: $? = 0 +configure:1770: gcc -V &5 +gcc: `-V' option must have argument +configure:1773: $? = 1 +configure:1796: checking for C compiler default output file name +configure:1799: gcc conftest.c >&5 +configure:1802: $? = 0 +configure:1848: result: a.out +configure:1853: checking whether the C compiler works +configure:1859: ./a.out +configure:1862: $? = 0 +configure:1879: result: yes +configure:1886: checking whether we are cross compiling +configure:1888: result: no +configure:1891: checking for suffix of executables +configure:1893: gcc -o conftest conftest.c >&5 +configure:1896: $? = 0 +configure:1921: result: +configure:1927: checking for suffix of object files +configure:1948: gcc -c conftest.c >&5 +configure:1951: $? = 0 +configure:1973: result: o +configure:1977: checking whether we are using the GNU C compiler +configure:2001: gcc -c conftest.c >&5 +configure:2007: $? = 0 +configure:2011: test -z + || test ! -s conftest.err +configure:2014: $? = 0 +configure:2017: test -s conftest.o +configure:2020: $? = 0 +configure:2033: result: yes +configure:2039: checking whether gcc accepts -g +configure:2060: gcc -c -g conftest.c >&5 +configure:2066: $? = 0 +configure:2070: test -z + || test ! -s conftest.err +configure:2073: $? = 0 +configure:2076: test -s conftest.o +configure:2079: $? = 0 +configure:2090: result: yes +configure:2107: checking for gcc option to accept ANSI C +configure:2177: gcc -c -g -O2 conftest.c >&5 +configure:2183: $? = 0 +configure:2187: test -z + || test ! -s conftest.err +configure:2190: $? = 0 +configure:2193: test -s conftest.o +configure:2196: $? = 0 +configure:2214: result: none needed +configure:2232: gcc -c -g -O2 conftest.c >&5 +conftest.c:2: error: syntax error before "me" +configure:2238: $? = 1 +configure: failed program was: +| #ifndef __cplusplus +| choke me +| #endif +configure:2376: checking how to run the C preprocessor +configure:2411: gcc -E conftest.c +configure:2417: $? = 0 +configure:2449: gcc -E conftest.c +conftest.c:10:28: ac_nonexistent.h: No such file or directory +configure:2455: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "" +| #define PACKAGE_TARNAME "" +| #define PACKAGE_VERSION "" +| #define PACKAGE_STRING "" +| #define PACKAGE_BUGREPORT "" +| #define LINUX 1 +| /* end confdefs.h. */ +| #include +configure:2494: result: gcc -E +configure:2518: gcc -E conftest.c +configure:2524: $? = 0 +configure:2556: gcc -E conftest.c +conftest.c:10:28: ac_nonexistent.h: No such file or directory +configure:2562: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "" +| #define PACKAGE_TARNAME "" +| #define PACKAGE_VERSION "" +| #define PACKAGE_STRING "" +| #define PACKAGE_BUGREPORT "" +| #define LINUX 1 +| /* end confdefs.h. */ +| #include +configure:2657: checking for g++ +configure:2673: found /usr/bin/g++ +configure:2683: result: g++ +configure:2699: checking for C++ compiler version +configure:2702: g++ --version &5 +g++ (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2) +Copyright (C) 2004 Free Software Foundation, Inc. +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + +configure:2705: $? = 0 +configure:2707: g++ -v &5 +Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.5/specs +Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux +Thread model: posix +gcc version 3.4.5 20051201 (Red Hat 3.4.5-2) +configure:2710: $? = 0 +configure:2712: g++ -V &5 +g++: `-V' option must have argument +configure:2715: $? = 1 +configure:2718: checking whether we are using the GNU C++ compiler +configure:2742: g++ -c conftest.cc >&5 +configure:2748: $? = 0 +configure:2752: test -z + || test ! -s conftest.err +configure:2755: $? = 0 +configure:2758: test -s conftest.o +configure:2761: $? = 0 +configure:2774: result: yes +configure:2780: checking whether g++ accepts -g +configure:2801: g++ -c -g conftest.cc >&5 +configure:2807: $? = 0 +configure:2811: test -z + || test ! -s conftest.err +configure:2814: $? = 0 +configure:2817: test -s conftest.o +configure:2820: $? = 0 +configure:2831: result: yes +configure:2873: g++ -c -g -O2 conftest.cc >&5 +configure:2879: $? = 0 +configure:2883: test -z + || test ! -s conftest.err +configure:2886: $? = 0 +configure:2889: test -s conftest.o +configure:2892: $? = 0 +configure:2918: g++ -c -g -O2 conftest.cc >&5 +conftest.cc: In function `int main()': +conftest.cc:14: error: `exit' was not declared in this scope +configure:2924: $? = 1 +configure: failed program was: +| /* confdefs.h. */ +| +| #define PACKAGE_NAME "" +| #define PACKAGE_TARNAME "" +| #define PACKAGE_VERSION "" +| #define PACKAGE_STRING "" +| #define PACKAGE_BUGREPORT "" +| #define LINUX 1 +| /* end confdefs.h. */ +| +| int +| main () +| { +| exit (42); +| ; +| return 0; +| } +configure:2873: g++ -c -g -O2 conftest.cc >&5 +configure:2879: $? = 0 +configure:2883: test -z + || test ! -s conftest.err +configure:2886: $? = 0 +configure:2889: test -s conftest.o +configure:2892: $? = 0 +configure:2918: g++ -c -g -O2 conftest.cc >&5 +configure:2924: $? = 0 +configure:2928: test -z + || test ! -s conftest.err +configure:2931: $? = 0 +configure:2934: test -s conftest.o +configure:2937: $? = 0 +configure:3001: checking for ranlib +configure:3017: found /usr/bin/ranlib +configure:3028: result: ranlib +configure:3053: checking for a BSD-compatible install +configure:3108: result: /usr/bin/install -c +configure:3121: checking for find +configure:3137: found /usr/bin/find +configure:3148: result: find +configure:3157: checking for makedepend +configure:3173: found /usr/X11R6/bin/makedepend +configure:3184: result: makedepend +configure:3192: checking for dlopen in -ldl +configure:3222: gcc -o conftest -g -O2 conftest.c -ldl >&5 +configure:3228: $? = 0 +configure:3232: test -z + || test ! -s conftest.err +configure:3235: $? = 0 +configure:3238: test -s conftest +configure:3241: $? = 0 +configure:3254: result: yes +configure:3269: checking for X +configure:3499: result: libraries /usr/X11R6/lib64, headers /usr/X11R6/include +configure:3671: gcc -o conftest -g -O2 conftest.c -L/usr/X11R6/lib64 -lX11 >&5 +configure:3677: $? = 0 +configure:3681: test -z + || test ! -s conftest.err +configure:3684: $? = 0 +configure:3687: test -s conftest +configure:3690: $? = 0 +configure:3848: checking for gethostbyname +configure:3905: gcc -o conftest -g -O2 conftest.c >&5 +configure:3911: $? = 0 +configure:3915: test -z + || test ! -s conftest.err +configure:3918: $? = 0 +configure:3921: test -s conftest +configure:3924: $? = 0 +configure:3936: result: yes +configure:4087: checking for connect +configure:4144: gcc -o conftest -g -O2 conftest.c >&5 +configure:4150: $? = 0 +configure:4154: test -z + || test ! -s conftest.err +configure:4157: $? = 0 +configure:4160: test -s conftest +configure:4163: $? = 0 +configure:4175: result: yes +configure:4250: checking for remove +configure:4307: gcc -o conftest -g -O2 conftest.c >&5 +configure:4313: $? = 0 +configure:4317: test -z + || test ! -s conftest.err +configure:4320: $? = 0 +configure:4323: test -s conftest +configure:4326: $? = 0 +configure:4338: result: yes +configure:4413: checking for shmat +configure:4470: gcc -o conftest -g -O2 conftest.c >&5 +configure:4476: $? = 0 +configure:4480: test -z + || test ! -s conftest.err +configure:4483: $? = 0 +configure:4486: test -s conftest +configure:4489: $? = 0 +configure:4501: result: yes +configure:4585: checking for IceConnectionNumber in -lICE +configure:4615: gcc -o conftest -g -O2 -L/usr/X11R6/lib64 conftest.c -lICE >&5 +configure:4621: $? = 0 +configure:4625: test -z + || test ! -s conftest.err +configure:4628: $? = 0 +configure:4631: test -s conftest +configure:4634: $? = 0 +configure:4647: result: yes +configure:4671: checking for main in -lm +configure:4695: gcc -o conftest -g -O2 -I/usr/X11R6/include -I/usr/local/include -L/usr/X11R6/lib64 -L/usr/local/lib conftest.c -lm >&5 +configure:4701: $? = 0 +configure:4705: test -z + || test ! -s conftest.err +configure:4708: $? = 0 +configure:4711: test -s conftest +configure:4714: $? = 0 +configure:4727: result: yes +configure:4741: checking for main in -lX11 +configure:4765: gcc -o conftest -g -O2 -I/usr/X11R6/include -I/usr/local/include -L/usr/X11R6/lib64 -L/usr/local/lib -lm conftest.c -lX11 >&5 +configure:4771: $? = 0 +configure:4775: test -z + || test ! -s conftest.err +configure:4778: $? = 0 +configure:4781: test -s conftest +configure:4784: $? = 0 +configure:4797: result: yes +configure:4806: checking for main in -lgd +configure:4830: gcc -o conftest -g -O2 -I/usr/X11R6/include -I/usr/local/include -L/usr/X11R6/lib64 -L/usr/local/lib -lm -lX11 conftest.c -lgd >&5 +configure:4836: $? = 0 +configure:4840: test -z + || test ! -s conftest.err +configure:4843: $? = 0 +configure:4846: test -s conftest +configure:4849: $? = 0 +configure:4862: result: yes +configure:4873: checking for gdImagePng +configure:4930: gcc -o conftest -g -O2 -I/usr/X11R6/include -I/usr/local/include -L/usr/X11R6/lib64 -L/usr/local/lib -lm -lX11 -lgd conftest.c >&5 +configure:4936: $? = 0 +configure:4940: test -z + || test ! -s conftest.err +configure:4943: $? = 0 +configure:4946: test -s conftest +configure:4949: $? = 0 +configure:4961: result: yes +configure:5225: checking for egrep +configure:5235: result: grep -E +configure:5240: checking for ANSI C header files +configure:5265: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5271: $? = 0 +configure:5275: test -z + || test ! -s conftest.err +configure:5278: $? = 0 +configure:5281: test -s conftest.o +configure:5284: $? = 0 +configure:5373: gcc -o conftest -g -O2 -I/usr/X11R6/include -I/usr/local/include -L/usr/X11R6/lib64 -L/usr/local/lib -lm -lX11 -lgd conftest.c >&5 +configure:5376: $? = 0 +configure:5378: ./conftest +configure:5381: $? = 0 +configure:5396: result: yes +configure:5420: checking for sys/types.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5420: checking for sys/stat.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5420: checking for stdlib.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5420: checking for string.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5420: checking for memory.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5420: checking for strings.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5420: checking for inttypes.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5420: checking for stdint.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5420: checking for unistd.h +configure:5436: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5442: $? = 0 +configure:5446: test -z + || test ! -s conftest.err +configure:5449: $? = 0 +configure:5452: test -s conftest.o +configure:5455: $? = 0 +configure:5466: result: yes +configure:5492: checking limits.h usability +configure:5504: gcc -c -g -O2 -I/usr/X11R6/include -I/usr/local/include conftest.c >&5 +configure:5510: $? = 0 +configure:5514: test -z + || test ! -s conftest.err +configure:5517: $? = 0 +configure:5520: test -s conftest.o +configure:5523: $? = 0 +configure:5533: result: yes +configure:5537: checking limits.h presence +configure:5547: gcc -E conftest.c +configure:5553: $? = 0 +configure:5573: result: yes +configure:5608: checking for limits.h +configure:5615: result: yes +configure:5762: creating ./config.status + +## ---------------------- ## +## Running config.status. ## +## ---------------------- ## + +This file was extended by config.status, which was +generated by GNU Autoconf 2.59. Invocation command line was + + CONFIG_FILES = + CONFIG_HEADERS = + CONFIG_LINKS = + CONFIG_COMMANDS = + $ ./config.status + +on mcluster02 + +config.status:671: creating Makefile +config.status:671: creating demo/Makefile +config.status:671: creating g2_perl/Makefile.PL + +## ---------------- ## +## Cache variables. ## +## ---------------- ## + +ac_cv_build=x86_64-unknown-linux-gnu +ac_cv_build_alias=x86_64-unknown-linux-gnu +ac_cv_c_compiler_gnu=yes +ac_cv_cxx_compiler_gnu=yes +ac_cv_env_CC_set= +ac_cv_env_CC_value= +ac_cv_env_CFLAGS_set= +ac_cv_env_CFLAGS_value= +ac_cv_env_CPPFLAGS_set= +ac_cv_env_CPPFLAGS_value= +ac_cv_env_CPP_set= +ac_cv_env_CPP_value= +ac_cv_env_CXXFLAGS_set= +ac_cv_env_CXXFLAGS_value= +ac_cv_env_CXX_set= +ac_cv_env_CXX_value= +ac_cv_env_LDFLAGS_set= +ac_cv_env_LDFLAGS_value= +ac_cv_env_build_alias_set= +ac_cv_env_build_alias_value= +ac_cv_env_host_alias_set= +ac_cv_env_host_alias_value= +ac_cv_env_target_alias_set= +ac_cv_env_target_alias_value= +ac_cv_exeext= +ac_cv_func_connect=yes +ac_cv_func_gdImagePng=yes +ac_cv_func_gethostbyname=yes +ac_cv_func_remove=yes +ac_cv_func_shmat=yes +ac_cv_have_x='have_x=yes ac_x_includes=/usr/X11R6/include ac_x_libraries=/usr/X11R6/lib64' +ac_cv_header_inttypes_h=yes +ac_cv_header_limits_h=yes +ac_cv_header_memory_h=yes +ac_cv_header_stdc=yes +ac_cv_header_stdint_h=yes +ac_cv_header_stdlib_h=yes +ac_cv_header_string_h=yes +ac_cv_header_strings_h=yes +ac_cv_header_sys_stat_h=yes +ac_cv_header_sys_types_h=yes +ac_cv_header_unistd_h=yes +ac_cv_host=x86_64-unknown-linux-gnu +ac_cv_host_alias=x86_64-unknown-linux-gnu +ac_cv_lib_ICE_IceConnectionNumber=yes +ac_cv_lib_X11_main=yes +ac_cv_lib_dl_dlopen=yes +ac_cv_lib_gd_main=yes +ac_cv_lib_m_main=yes +ac_cv_objext=o +ac_cv_path_install='/usr/bin/install -c' +ac_cv_prog_CPP='gcc -E' +ac_cv_prog_FIND=find +ac_cv_prog_MAKEDEPEND=makedepend +ac_cv_prog_ac_ct_CC=gcc +ac_cv_prog_ac_ct_CXX=g++ +ac_cv_prog_ac_ct_RANLIB=ranlib +ac_cv_prog_cc_g=yes +ac_cv_prog_cc_stdc= +ac_cv_prog_cxx_g=yes +ac_cv_prog_egrep='grep -E' + +## ----------------- ## +## Output variables. ## +## ----------------- ## + +CC='gcc' +CFLAGS='-g -O2 -I/usr/X11R6/include -I/usr/local/include' +CPP='gcc -E' +CPPFLAGS='' +CXX='g++' +CXXFLAGS='-g -O2' +DEFS='-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_GD=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 ' +DO_FIG='' +DO_GD='' +DO_PS='' +DO_WIN32='#' +DO_X11='' +ECHO_C='' +ECHO_N='-n' +ECHO_T='' +EGREP='grep -E' +EXEEXT='' +FIND='find' +INSTALL_DATA='${INSTALL} -m 644' +INSTALL_PROGRAM='${INSTALL}' +INSTALL_SCRIPT='${INSTALL}' +LDFLAGS=' -L/usr/X11R6/lib64 -L/usr/local/lib -lm -lX11 -lgd' +LD_SHARED='ld' +LD_SHARED_EXT='so.0.$(G2_VERSION)' +LD_SHARED_FLAGS='-shared -soname libg2.so.0' +LD_SHARED_OPT='' +LIBOBJS='' +LIBS='' +LTLIBOBJS='' +MAKEDEPEND='makedepend' +OBJEXT='o' +PACKAGE_BUGREPORT='' +PACKAGE_NAME='' +PACKAGE_STRING='' +PACKAGE_TARNAME='' +PACKAGE_VERSION='' +PATH_SEPARATOR=':' +RANLIB='ranlib' +SHELL='/bin/sh' +X_CFLAGS=' -I/usr/X11R6/include' +X_EXTRA_LIBS='' +X_LIBS=' -L/usr/X11R6/lib64' +X_PRE_LIBS=' -lSM -lICE' +ac_ct_CC='gcc' +ac_ct_CXX='g++' +ac_ct_RANLIB='ranlib' +bindir='${exec_prefix}/bin' +build='x86_64-unknown-linux-gnu' +build_alias='' +build_cpu='x86_64' +build_os='linux-gnu' +build_vendor='unknown' +datadir='${prefix}/share' +exec_prefix='${prefix}' +host='x86_64-unknown-linux-gnu' +host_alias='' +host_cpu='x86_64' +host_os='linux-gnu' +host_vendor='unknown' +includedir='${prefix}/include' +infodir='${prefix}/info' +libdir='${exec_prefix}/lib' +libexecdir='${exec_prefix}/libexec' +localstatedir='${prefix}/var' +mandir='${prefix}/man' +oldincludedir='/usr/include' +prefix='/usr/local' +program_transform_name='s,x,x,' +sbindir='${exec_prefix}/sbin' +sharedstatedir='${prefix}/com' +sysconfdir='${prefix}/etc' +target_alias='' + +## ----------- ## +## confdefs.h. ## +## ----------- ## + +#define DO_FIG 1 +#define DO_GD 1 +#define DO_PS 1 +#define DO_X11 1 +#define HAVE_INTTYPES_H 1 +#define HAVE_LIMITS_H 1 +#define HAVE_MEMORY_H 1 +#define HAVE_STDINT_H 1 +#define HAVE_STDLIB_H 1 +#define HAVE_STRINGS_H 1 +#define HAVE_STRING_H 1 +#define HAVE_SYS_STAT_H 1 +#define HAVE_SYS_TYPES_H 1 +#define HAVE_UNISTD_H 1 +#define LINUX 1 +#define PACKAGE_BUGREPORT "" +#define PACKAGE_NAME "" +#define PACKAGE_STRING "" +#define PACKAGE_TARNAME "" +#define PACKAGE_VERSION "" +#define STDC_HEADERS 1 +#endif +#ifdef __cplusplus +extern "C" void std::exit (int) throw (); using std::exit; + +configure: exit 0 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.status b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.status new file mode 100755 index 000000000..6bd9c1033 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/config.status @@ -0,0 +1,745 @@ +#! /bin/sh +# Generated by configure. +# Run this file to recreate the current configuration. +# Compiler output produced by configure, useful for debugging +# configure, is in config.log if it exists. + +debug=false +ac_cs_recheck=false +ac_cs_silent=false +SHELL=${CONFIG_SHELL-/bin/sh} +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## + +# Be Bourne compatible +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' +elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then + set -o posix +fi +DUALCASE=1; export DUALCASE # for MKS sh + +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + + +# Work around bugs in pre-3.0 UWIN ksh. +$as_unset ENV MAIL MAILPATH +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +for as_var in \ + LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ + LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ + LC_TELEPHONE LC_TIME +do + if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then + eval $as_var=C; export $as_var + else + $as_unset $as_var + fi +done + +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)$' \| \ + . : '\(.\)' 2>/dev/null || +echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } + /^X\/\(\/\/\)$/{ s//\1/; q; } + /^X\/\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + + +# PATH needs CR, and LINENO needs CR and PATH. +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + echo "#! /bin/sh" >conf$$.sh + echo "exit 0" >>conf$$.sh + chmod +x conf$$.sh + if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then + PATH_SEPARATOR=';' + else + PATH_SEPARATOR=: + fi + rm -f conf$$.sh +fi + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" || { + # Find who we are. Look in the path if we contain no path at all + # relative or not. + case $0 in + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done + + ;; + esac + # We did not find ourselves, most probably we were run as `sh COMMAND' + # in which case we are not to be found in the path. + if test "x$as_myself" = x; then + as_myself=$0 + fi + if test ! -f "$as_myself"; then + { { echo "$as_me:$LINENO: error: cannot find myself; rerun with an absolute path" >&5 +echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2;} + { (exit 1); exit 1; }; } + fi + case $CONFIG_SHELL in + '') + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for as_base in sh bash ksh sh5; do + case $as_dir in + /*) + if ("$as_dir/$as_base" -c ' + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then + $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } + $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } + CONFIG_SHELL=$as_dir/$as_base + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$0" ${1+"$@"} + fi;; + esac + done +done +;; + esac + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line before each line; the second 'sed' does the real + # work. The second script uses 'N' to pair each line-number line + # with the numbered line, and appends trailing '-' during + # substitution so that $LINENO is not a special case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) + sed '=' <$as_myself | + sed ' + N + s,$,-, + : loop + s,^\(['$as_cr_digits']*\)\(.*\)[$]LINENO\([^'$as_cr_alnum'_]\),\1\2\1\3, + t loop + s,-$,, + s,^['$as_cr_digits']*\n,, + ' >$as_me.lineno && + chmod +x $as_me.lineno || + { { echo "$as_me:$LINENO: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&5 +echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2;} + { (exit 1); exit 1; }; } + + # Don't try to exec as it changes $[0], causing all sort of problems + # (the dirname of $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensible to this). + . ./$as_me.lineno + # Exit status is that of the last command. + exit +} + + +case `echo "testing\c"; echo 1,2,3`,`echo -n testing; echo 1,2,3` in + *c*,-n*) ECHO_N= ECHO_C=' +' ECHO_T=' ' ;; + *c*,* ) ECHO_N=-n ECHO_C= ECHO_T= ;; + *) ECHO_N= ECHO_C='\c' ECHO_T= ;; +esac + +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +rm -f conf$$ conf$$.exe conf$$.file +echo >conf$$.file +if ln -s conf$$.file conf$$ 2>/dev/null; then + # We could just check for DJGPP; but this test a) works b) is more generic + # and c) will remain valid once DJGPP supports symlinks (DJGPP 2.04). + if test -f conf$$.exe; then + # Don't use ln at all; we don't have any links + as_ln_s='cp -p' + else + as_ln_s='ln -s' + fi +elif ln conf$$.file conf$$ 2>/dev/null; then + as_ln_s=ln +else + as_ln_s='cp -p' +fi +rm -f conf$$ conf$$.exe conf$$.file + +if mkdir -p . 2>/dev/null; then + as_mkdir_p=: +else + test -d ./-p && rmdir ./-p + as_mkdir_p=false +fi + +as_executable_p="test -f" + +# Sed expression to map a string onto a valid CPP name. +as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" + +# Sed expression to map a string onto a valid variable name. +as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" + + +# IFS +# We need space, tab and new line, in precisely that order. +as_nl=' +' +IFS=" $as_nl" + +# CDPATH. +$as_unset CDPATH + +exec 6>&1 + +# Open the log real soon, to keep \$[0] and so on meaningful, and to +# report actual input values of CONFIG_FILES etc. instead of their +# values after options handling. Logging --version etc. is OK. +exec 5>>config.log +{ + echo + sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX +## Running $as_me. ## +_ASBOX +} >&5 +cat >&5 <<_CSEOF + +This file was extended by $as_me, which was +generated by GNU Autoconf 2.59. Invocation command line was + + CONFIG_FILES = $CONFIG_FILES + CONFIG_HEADERS = $CONFIG_HEADERS + CONFIG_LINKS = $CONFIG_LINKS + CONFIG_COMMANDS = $CONFIG_COMMANDS + $ $0 $@ + +_CSEOF +echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 +echo >&5 +config_files=" Makefile demo/Makefile g2_perl/Makefile.PL" + +ac_cs_usage="\ +\`$as_me' instantiates files from templates according to the +current configuration. + +Usage: $0 [OPTIONS] [FILE]... + + -h, --help print this help, then exit + -V, --version print version number, then exit + -q, --quiet do not print progress messages + -d, --debug don't remove temporary files + --recheck update $as_me by reconfiguring in the same conditions + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + +Configuration files: +$config_files + +Report bugs to ." +ac_cs_version="\ +config.status +configured by ./configure, generated by GNU Autoconf 2.59, + with options \"'--prefix=/usr/local' '--cache-file=/dev/null' '--srcdir=.'\" + +Copyright (C) 2003 Free Software Foundation, Inc. +This config.status script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it." +srcdir=. +INSTALL="/usr/bin/install -c" +# If no file are specified by the user, then we need to provide default +# value. By we need to know if files were specified by the user. +ac_need_defaults=: +while test $# != 0 +do + case $1 in + --*=*) + ac_option=`expr "x$1" : 'x\([^=]*\)='` + ac_optarg=`expr "x$1" : 'x[^=]*=\(.*\)'` + ac_shift=: + ;; + -*) + ac_option=$1 + ac_optarg=$2 + ac_shift=shift + ;; + *) # This is not an option, so the user has probably given explicit + # arguments. + ac_option=$1 + ac_need_defaults=false;; + esac + + case $ac_option in + # Handling of the options. + -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r) + ac_cs_recheck=: ;; + --version | --vers* | -V ) + echo "$ac_cs_version"; exit 0 ;; + --he | --h) + # Conflict between --help and --header + { { echo "$as_me:$LINENO: error: ambiguous option: $1 +Try \`$0 --help' for more information." >&5 +echo "$as_me: error: ambiguous option: $1 +Try \`$0 --help' for more information." >&2;} + { (exit 1); exit 1; }; };; + --help | --hel | -h ) + echo "$ac_cs_usage"; exit 0 ;; + --debug | --d* | -d ) + debug=: ;; + --file | --fil | --fi | --f ) + $ac_shift + CONFIG_FILES="$CONFIG_FILES $ac_optarg" + ac_need_defaults=false;; + --header | --heade | --head | --hea ) + $ac_shift + CONFIG_HEADERS="$CONFIG_HEADERS $ac_optarg" + ac_need_defaults=false;; + -q | -quiet | --quiet | --quie | --qui | --qu | --q \ + | -silent | --silent | --silen | --sile | --sil | --si | --s) + ac_cs_silent=: ;; + + # This is an error. + -*) { { echo "$as_me:$LINENO: error: unrecognized option: $1 +Try \`$0 --help' for more information." >&5 +echo "$as_me: error: unrecognized option: $1 +Try \`$0 --help' for more information." >&2;} + { (exit 1); exit 1; }; } ;; + + *) ac_config_targets="$ac_config_targets $1" ;; + + esac + shift +done + +ac_configure_extra_args= + +if $ac_cs_silent; then + exec 6>/dev/null + ac_configure_extra_args="$ac_configure_extra_args --silent" +fi + +if $ac_cs_recheck; then + echo "running /bin/sh ./configure " '--prefix=/usr/local' '--cache-file=/dev/null' '--srcdir=.' $ac_configure_extra_args " --no-create --no-recursion" >&6 + exec /bin/sh ./configure '--prefix=/usr/local' '--cache-file=/dev/null' '--srcdir=.' $ac_configure_extra_args --no-create --no-recursion +fi + +for ac_config_target in $ac_config_targets +do + case "$ac_config_target" in + # Handling of arguments. + "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;; + "demo/Makefile" ) CONFIG_FILES="$CONFIG_FILES demo/Makefile" ;; + "g2_perl/Makefile.PL" ) CONFIG_FILES="$CONFIG_FILES g2_perl/Makefile.PL" ;; + *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 +echo "$as_me: error: invalid argument: $ac_config_target" >&2;} + { (exit 1); exit 1; }; };; + esac +done + +# If the user did not use the arguments to specify the items to instantiate, +# then the envvar interface is used. Set only those that are not. +# We use the long form for the default assignment because of an extremely +# bizarre bug on SunOS 4.1.3. +if $ac_need_defaults; then + test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files +fi + +# Have a temporary directory for convenience. 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It does not imply ALL GNU software can. +# +# This file is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place - Suite 330, +# Boston, MA 02111-1307, USA. + +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + +# Please send patches to . Submit a context +# diff and a properly formatted ChangeLog entry. +# +# Configuration subroutine to validate and canonicalize a configuration type. +# Supply the specified configuration type as an argument. +# If it is invalid, we print an error message on stderr and exit with code 1. +# Otherwise, we print the canonical config type on stdout and succeed. + +# This file is supposed to be the same for all GNU packages +# and recognize all the CPU types, system types and aliases +# that are meaningful with *any* GNU software. +# Each package is responsible for reporting which valid configurations +# it does not support. The user should be able to distinguish +# a failure to support a valid configuration from a meaningless +# configuration. + +# The goal of this file is to map all the various variations of a given +# machine specification into a single specification in the form: +# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM +# or in some cases, the newer four-part form: +# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM +# It is wrong to echo any other type of specification. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] CPU-MFR-OPSYS + $0 [OPTION] ALIAS + +Canonicalize a configuration name. + +Operation modes: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.sub ($timestamp) + +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004 +Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit 0 ;; + --version | -v ) + echo "$version" ; exit 0 ;; + --help | --h* | -h ) + echo "$usage"; exit 0 ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" + exit 1 ;; + + *local*) + # First pass through any local machine types. + echo $1 + exit 0;; + + * ) + break ;; + esac +done + +case $# in + 0) echo "$me: missing argument$help" >&2 + exit 1;; + 1) ;; + *) echo "$me: too many arguments$help" >&2 + exit 1;; +esac + +# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). +# Here we must recognize all the valid KERNEL-OS combinations. +maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` +case $maybe_os in + nto-qnx* | linux-gnu* | linux-dietlibc | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | \ + kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | storm-chaos* | os2-emx* | rtmk-nova*) + os=-$maybe_os + basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` + ;; + *) + basic_machine=`echo $1 | sed 's/-[^-]*$//'` + if [ $basic_machine != $1 ] + then os=`echo $1 | sed 's/.*-/-/'` + else os=; fi + ;; +esac + +### Let's recognize common machines as not being operating systems so +### that things like config.sub decstation-3100 work. We also +### recognize some manufacturers as not being operating systems, so we +### can provide default operating systems below. +case $os in + -sun*os*) + # Prevent following clause from handling this invalid input. + ;; + -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ + -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ + -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ + -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ + -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ + -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ + -apple | -axis | -knuth | -cray) + os= + basic_machine=$1 + ;; + -sim | -cisco | -oki | -wec | -winbond) + os= + basic_machine=$1 + ;; + -scout) + ;; + -wrs) + os=-vxworks + basic_machine=$1 + ;; + -chorusos*) + os=-chorusos + basic_machine=$1 + ;; + -chorusrdb) + os=-chorusrdb + basic_machine=$1 + ;; + -hiux*) + os=-hiuxwe2 + ;; + -sco5) + os=-sco3.2v5 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco4) + os=-sco3.2v4 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco3.2.[4-9]*) + os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco3.2v[4-9]*) + # Don't forget version if it is 3.2v4 or newer. + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco*) + os=-sco3.2v2 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -udk*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -isc) + os=-isc2.2 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -clix*) + basic_machine=clipper-intergraph + ;; + -isc*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -lynx*) + os=-lynxos + ;; + -ptx*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` + ;; + -windowsnt*) + os=`echo $os | sed -e 's/windowsnt/winnt/'` + ;; + -psos*) + os=-psos + ;; + -mint | -mint[0-9]*) + basic_machine=m68k-atari + os=-mint + ;; +esac + +# Decode aliases for certain CPU-COMPANY combinations. +case $basic_machine in + # Recognize the basic CPU types without company name. + # Some are omitted here because they have special meanings below. + 1750a | 580 \ + | a29k \ + | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ + | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ + | am33_2.0 \ + | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr \ + | c4x | clipper \ + | d10v | d30v | dlx | dsp16xx \ + | fr30 | frv \ + | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ + | i370 | i860 | i960 | ia64 \ + | ip2k | iq2000 \ + | m32r | m32rle | m68000 | m68k | m88k | mcore \ + | mips | mipsbe | mipseb | mipsel | mipsle \ + | mips16 \ + | mips64 | mips64el \ + | mips64vr | mips64vrel \ + | mips64orion | mips64orionel \ + | mips64vr4100 | mips64vr4100el \ + | mips64vr4300 | mips64vr4300el \ + | mips64vr5000 | mips64vr5000el \ + | mipsisa32 | mipsisa32el \ + | mipsisa32r2 | mipsisa32r2el \ + | mipsisa64 | mipsisa64el \ + | mipsisa64r2 | mipsisa64r2el \ + | mipsisa64sb1 | mipsisa64sb1el \ + | mipsisa64sr71k | mipsisa64sr71kel \ + | mipstx39 | mipstx39el \ + | mn10200 | mn10300 \ + | msp430 \ + | ns16k | ns32k \ + | openrisc | or32 \ + | pdp10 | pdp11 | pj | pjl \ + | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ + | pyramid \ + | sh | sh[1234] | sh[23]e | sh[34]eb | shbe | shle | sh[1234]le | sh3ele \ + | sh64 | sh64le \ + | sparc | sparc64 | sparc86x | sparclet | sparclite | sparcv8 | sparcv9 | sparcv9b \ + | strongarm \ + | tahoe | thumb | tic4x | tic80 | tron \ + | v850 | v850e \ + | we32k \ + | x86 | xscale | xstormy16 | xtensa \ + | z8k) + basic_machine=$basic_machine-unknown + ;; + m6811 | m68hc11 | m6812 | m68hc12) + # Motorola 68HC11/12. + basic_machine=$basic_machine-unknown + os=-none + ;; + m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) + ;; + + # We use `pc' rather than `unknown' + # because (1) that's what they normally are, and + # (2) the word "unknown" tends to confuse beginning users. + i*86 | x86_64) + basic_machine=$basic_machine-pc + ;; + # Object if more than one company name word. + *-*-*) + echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 + exit 1 + ;; + # Recognize the basic CPU types with company name. + 580-* \ + | a29k-* \ + | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ + | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ + | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ + | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ + | avr-* \ + | bs2000-* \ + | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ + | clipper-* | craynv-* | cydra-* \ + | d10v-* | d30v-* | dlx-* \ + | elxsi-* \ + | f30[01]-* | f700-* | fr30-* | frv-* | fx80-* \ + | h8300-* | h8500-* \ + | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ + | i*86-* | i860-* | i960-* | ia64-* \ + | ip2k-* | iq2000-* \ + | m32r-* | m32rle-* \ + | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ + | m88110-* | m88k-* | mcore-* \ + | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ + | mips16-* \ + | mips64-* | mips64el-* \ + | mips64vr-* | mips64vrel-* \ + | mips64orion-* | mips64orionel-* \ + | mips64vr4100-* | mips64vr4100el-* \ + | mips64vr4300-* | mips64vr4300el-* \ + | mips64vr5000-* | mips64vr5000el-* \ + | mipsisa32-* | mipsisa32el-* \ + | mipsisa32r2-* | mipsisa32r2el-* \ + | mipsisa64-* | mipsisa64el-* \ + | mipsisa64r2-* | mipsisa64r2el-* \ + | mipsisa64sb1-* | mipsisa64sb1el-* \ + | mipsisa64sr71k-* | mipsisa64sr71kel-* \ + | mipstx39-* | mipstx39el-* \ + | mmix-* \ + | msp430-* \ + | none-* | np1-* | ns16k-* | ns32k-* \ + | orion-* \ + | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ + | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ + | pyramid-* \ + | romp-* | rs6000-* \ + | sh-* | sh[1234]-* | sh[23]e-* | sh[34]eb-* | shbe-* \ + | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ + | sparc-* | sparc64-* | sparc86x-* | sparclet-* | sparclite-* \ + | sparcv8-* | sparcv9-* | sparcv9b-* | strongarm-* | sv1-* | sx?-* \ + | tahoe-* | thumb-* \ + | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ + | tron-* \ + | v850-* | v850e-* | vax-* \ + | we32k-* \ + | x86-* | x86_64-* | xps100-* | xscale-* | xstormy16-* \ + | xtensa-* \ + | ymp-* \ + | z8k-*) + ;; + # Recognize the various machine names and aliases which stand + # for a CPU type and a company and sometimes even an OS. + 386bsd) + basic_machine=i386-unknown + os=-bsd + ;; + 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) + basic_machine=m68000-att + ;; + 3b*) + basic_machine=we32k-att + ;; + a29khif) + basic_machine=a29k-amd + os=-udi + ;; + abacus) + basic_machine=abacus-unknown + ;; + adobe68k) + basic_machine=m68010-adobe + os=-scout + ;; + alliant | fx80) + basic_machine=fx80-alliant + ;; + altos | altos3068) + basic_machine=m68k-altos + ;; + am29k) + basic_machine=a29k-none + os=-bsd + ;; + amd64) + basic_machine=x86_64-pc + ;; + amd64-*) + basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + amdahl) + basic_machine=580-amdahl + os=-sysv + ;; + amiga | amiga-*) + basic_machine=m68k-unknown + ;; + amigaos | amigados) + basic_machine=m68k-unknown + os=-amigaos + ;; + amigaunix | amix) + basic_machine=m68k-unknown + os=-sysv4 + ;; + apollo68) + basic_machine=m68k-apollo + os=-sysv + ;; + apollo68bsd) + basic_machine=m68k-apollo + os=-bsd + ;; + aux) + basic_machine=m68k-apple + os=-aux + ;; + balance) + basic_machine=ns32k-sequent + os=-dynix + ;; + c90) + basic_machine=c90-cray + os=-unicos + ;; + convex-c1) + basic_machine=c1-convex + os=-bsd + ;; + convex-c2) + basic_machine=c2-convex + os=-bsd + ;; + convex-c32) + basic_machine=c32-convex + os=-bsd + ;; + convex-c34) + basic_machine=c34-convex + os=-bsd + ;; + convex-c38) + basic_machine=c38-convex + os=-bsd + ;; + cray | j90) + basic_machine=j90-cray + os=-unicos + ;; + craynv) + basic_machine=craynv-cray + os=-unicosmp + ;; + cr16c) + basic_machine=cr16c-unknown + os=-elf + ;; + crds | unos) + basic_machine=m68k-crds + ;; + cris | cris-* | etrax*) + basic_machine=cris-axis + ;; + crx) + basic_machine=crx-unknown + os=-elf + ;; + da30 | da30-*) + basic_machine=m68k-da30 + ;; + decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) + basic_machine=mips-dec + ;; + decsystem10* | dec10*) + basic_machine=pdp10-dec + os=-tops10 + ;; + decsystem20* | dec20*) + basic_machine=pdp10-dec + os=-tops20 + ;; + delta | 3300 | motorola-3300 | motorola-delta \ + | 3300-motorola | delta-motorola) + basic_machine=m68k-motorola + ;; + delta88) + basic_machine=m88k-motorola + os=-sysv3 + ;; + dpx20 | dpx20-*) + basic_machine=rs6000-bull + os=-bosx + ;; + dpx2* | dpx2*-bull) + basic_machine=m68k-bull + os=-sysv3 + ;; + ebmon29k) + basic_machine=a29k-amd + os=-ebmon + ;; + elxsi) + basic_machine=elxsi-elxsi + os=-bsd + ;; + encore | umax | mmax) + basic_machine=ns32k-encore + ;; + es1800 | OSE68k | ose68k | ose | OSE) + basic_machine=m68k-ericsson + os=-ose + ;; + fx2800) + basic_machine=i860-alliant + ;; + genix) + basic_machine=ns32k-ns + ;; + gmicro) + basic_machine=tron-gmicro + os=-sysv + ;; + go32) + basic_machine=i386-pc + os=-go32 + ;; + h3050r* | hiux*) + basic_machine=hppa1.1-hitachi + os=-hiuxwe2 + ;; + h8300hms) + basic_machine=h8300-hitachi + os=-hms + ;; + h8300xray) + basic_machine=h8300-hitachi + os=-xray + ;; + h8500hms) + basic_machine=h8500-hitachi + os=-hms + ;; + harris) + basic_machine=m88k-harris + os=-sysv3 + ;; + hp300-*) + basic_machine=m68k-hp + ;; + hp300bsd) + basic_machine=m68k-hp + os=-bsd + ;; + hp300hpux) + basic_machine=m68k-hp + os=-hpux + ;; + hp3k9[0-9][0-9] | hp9[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hp9k2[0-9][0-9] | hp9k31[0-9]) + basic_machine=m68000-hp + ;; + hp9k3[2-9][0-9]) + basic_machine=m68k-hp + ;; + hp9k6[0-9][0-9] | hp6[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hp9k7[0-79][0-9] | hp7[0-79][0-9]) + basic_machine=hppa1.1-hp + ;; + hp9k78[0-9] | hp78[0-9]) + # FIXME: really hppa2.0-hp + basic_machine=hppa1.1-hp + ;; + hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) + # FIXME: really hppa2.0-hp + basic_machine=hppa1.1-hp + ;; + hp9k8[0-9][13679] | hp8[0-9][13679]) + basic_machine=hppa1.1-hp + ;; + hp9k8[0-9][0-9] | hp8[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hppa-next) + os=-nextstep3 + ;; + hppaosf) + basic_machine=hppa1.1-hp + os=-osf + ;; + hppro) + basic_machine=hppa1.1-hp + os=-proelf + ;; + i370-ibm* | ibm*) + basic_machine=i370-ibm + ;; +# I'm not sure what "Sysv32" means. Should this be sysv3.2? + i*86v32) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv32 + ;; + i*86v4*) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv4 + ;; + i*86v) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv + ;; + i*86sol2) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-solaris2 + ;; + i386mach) + basic_machine=i386-mach + os=-mach + ;; + i386-vsta | vsta) + basic_machine=i386-unknown + os=-vsta + ;; + iris | iris4d) + basic_machine=mips-sgi + case $os in + -irix*) + ;; + *) + os=-irix4 + ;; + esac + ;; + isi68 | isi) + basic_machine=m68k-isi + os=-sysv + ;; + m88k-omron*) + basic_machine=m88k-omron + ;; + magnum | m3230) + basic_machine=mips-mips + os=-sysv + ;; + merlin) + basic_machine=ns32k-utek + os=-sysv + ;; + mingw32) + basic_machine=i386-pc + os=-mingw32 + ;; + miniframe) + basic_machine=m68000-convergent + ;; + *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) + basic_machine=m68k-atari + os=-mint + ;; + mips3*-*) + basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` + ;; + mips3*) + basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown + ;; + monitor) + basic_machine=m68k-rom68k + os=-coff + ;; + morphos) + basic_machine=powerpc-unknown + os=-morphos + ;; + msdos) + basic_machine=i386-pc + os=-msdos + ;; + mvs) + basic_machine=i370-ibm + os=-mvs + ;; + ncr3000) + basic_machine=i486-ncr + os=-sysv4 + ;; + netbsd386) + basic_machine=i386-unknown + os=-netbsd + ;; + netwinder) + basic_machine=armv4l-rebel + os=-linux + ;; + news | news700 | news800 | news900) + basic_machine=m68k-sony + os=-newsos + ;; + news1000) + basic_machine=m68030-sony + os=-newsos + ;; + news-3600 | risc-news) + basic_machine=mips-sony + os=-newsos + ;; + necv70) + basic_machine=v70-nec + os=-sysv + ;; + next | m*-next ) + basic_machine=m68k-next + case $os in + -nextstep* ) + ;; + -ns2*) + os=-nextstep2 + ;; + *) + os=-nextstep3 + ;; + esac + ;; + nh3000) + basic_machine=m68k-harris + os=-cxux + ;; + nh[45]000) + basic_machine=m88k-harris + os=-cxux + ;; + nindy960) + basic_machine=i960-intel + os=-nindy + ;; + mon960) + basic_machine=i960-intel + os=-mon960 + ;; + nonstopux) + basic_machine=mips-compaq + os=-nonstopux + ;; + np1) + basic_machine=np1-gould + ;; + nsr-tandem) + basic_machine=nsr-tandem + ;; + op50n-* | op60c-*) + basic_machine=hppa1.1-oki + os=-proelf + ;; + or32 | or32-*) + basic_machine=or32-unknown + os=-coff + ;; + os400) + basic_machine=powerpc-ibm + os=-os400 + ;; + OSE68000 | ose68000) + basic_machine=m68000-ericsson + os=-ose + ;; + os68k) + basic_machine=m68k-none + os=-os68k + ;; + pa-hitachi) + basic_machine=hppa1.1-hitachi + os=-hiuxwe2 + ;; + paragon) + basic_machine=i860-intel + os=-osf + ;; + pbd) + basic_machine=sparc-tti + ;; + pbb) + basic_machine=m68k-tti + ;; + pc532 | pc532-*) + basic_machine=ns32k-pc532 + ;; + pentium | p5 | k5 | k6 | nexgen | viac3) + basic_machine=i586-pc + ;; + pentiumpro | p6 | 6x86 | athlon | athlon_*) + basic_machine=i686-pc + ;; + pentiumii | pentium2 | pentiumiii | pentium3) + basic_machine=i686-pc + ;; + pentium4) + basic_machine=i786-pc + ;; + pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) + basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentiumpro-* | p6-* | 6x86-* | athlon-*) + basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) + basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentium4-*) + basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pn) + basic_machine=pn-gould + ;; + power) basic_machine=power-ibm + ;; + ppc) basic_machine=powerpc-unknown + ;; + ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppcle | powerpclittle | ppc-le | powerpc-little) + basic_machine=powerpcle-unknown + ;; + ppcle-* | powerpclittle-*) + basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppc64) basic_machine=powerpc64-unknown + ;; + ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppc64le | powerpc64little | ppc64-le | powerpc64-little) + basic_machine=powerpc64le-unknown + ;; + ppc64le-* | powerpc64little-*) + basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ps2) + basic_machine=i386-ibm + ;; + pw32) + basic_machine=i586-unknown + os=-pw32 + ;; + rom68k) + basic_machine=m68k-rom68k + os=-coff + ;; + rm[46]00) + basic_machine=mips-siemens + ;; + rtpc | rtpc-*) + basic_machine=romp-ibm + ;; + s390 | s390-*) + basic_machine=s390-ibm + ;; + s390x | s390x-*) + basic_machine=s390x-ibm + ;; + sa29200) + basic_machine=a29k-amd + os=-udi + ;; + sb1) + basic_machine=mipsisa64sb1-unknown + ;; + sb1el) + basic_machine=mipsisa64sb1el-unknown + ;; + sei) + basic_machine=mips-sei + os=-seiux + ;; + sequent) + basic_machine=i386-sequent + ;; + sh) + basic_machine=sh-hitachi + os=-hms + ;; + sh64) + basic_machine=sh64-unknown + ;; + sparclite-wrs | simso-wrs) + basic_machine=sparclite-wrs + os=-vxworks + ;; + sps7) + basic_machine=m68k-bull + os=-sysv2 + ;; + spur) + basic_machine=spur-unknown + ;; + st2000) + basic_machine=m68k-tandem + ;; + stratus) + basic_machine=i860-stratus + os=-sysv4 + ;; + sun2) + basic_machine=m68000-sun + ;; + sun2os3) + basic_machine=m68000-sun + os=-sunos3 + ;; + sun2os4) + basic_machine=m68000-sun + os=-sunos4 + ;; + sun3os3) + basic_machine=m68k-sun + os=-sunos3 + ;; + sun3os4) + basic_machine=m68k-sun + os=-sunos4 + ;; + sun4os3) + basic_machine=sparc-sun + os=-sunos3 + ;; + sun4os4) + basic_machine=sparc-sun + os=-sunos4 + ;; + sun4sol2) + basic_machine=sparc-sun + os=-solaris2 + ;; + sun3 | sun3-*) + basic_machine=m68k-sun + ;; + sun4) + basic_machine=sparc-sun + ;; + sun386 | sun386i | roadrunner) + basic_machine=i386-sun + ;; + sv1) + basic_machine=sv1-cray + os=-unicos + ;; + symmetry) + basic_machine=i386-sequent + os=-dynix + ;; + t3e) + basic_machine=alphaev5-cray + os=-unicos + ;; + t90) + basic_machine=t90-cray + os=-unicos + ;; + tic54x | c54x*) + basic_machine=tic54x-unknown + os=-coff + ;; + tic55x | c55x*) + basic_machine=tic55x-unknown + os=-coff + ;; + tic6x | c6x*) + basic_machine=tic6x-unknown + os=-coff + ;; + tx39) + basic_machine=mipstx39-unknown + ;; + tx39el) + basic_machine=mipstx39el-unknown + ;; + toad1) + basic_machine=pdp10-xkl + os=-tops20 + ;; + tower | tower-32) + basic_machine=m68k-ncr + ;; + tpf) + basic_machine=s390x-ibm + os=-tpf + ;; + udi29k) + basic_machine=a29k-amd + os=-udi + ;; + ultra3) + basic_machine=a29k-nyu + os=-sym1 + ;; + v810 | necv810) + basic_machine=v810-nec + os=-none + ;; + vaxv) + basic_machine=vax-dec + os=-sysv + ;; + vms) + basic_machine=vax-dec + os=-vms + ;; + vpp*|vx|vx-*) + basic_machine=f301-fujitsu + ;; + vxworks960) + basic_machine=i960-wrs + os=-vxworks + ;; + vxworks68) + basic_machine=m68k-wrs + os=-vxworks + ;; + vxworks29k) + basic_machine=a29k-wrs + os=-vxworks + ;; + w65*) + basic_machine=w65-wdc + os=-none + ;; + w89k-*) + basic_machine=hppa1.1-winbond + os=-proelf + ;; + xps | xps100) + basic_machine=xps100-honeywell + ;; + ymp) + basic_machine=ymp-cray + os=-unicos + ;; + z8k-*-coff) + basic_machine=z8k-unknown + os=-sim + ;; + none) + basic_machine=none-none + os=-none + ;; + +# Here we handle the default manufacturer of certain CPU types. It is in +# some cases the only manufacturer, in others, it is the most popular. + w89k) + basic_machine=hppa1.1-winbond + ;; + op50n) + basic_machine=hppa1.1-oki + ;; + op60c) + basic_machine=hppa1.1-oki + ;; + romp) + basic_machine=romp-ibm + ;; + mmix) + basic_machine=mmix-knuth + ;; + rs6000) + basic_machine=rs6000-ibm + ;; + vax) + basic_machine=vax-dec + ;; + pdp10) + # there are many clones, so DEC is not a safe bet + basic_machine=pdp10-unknown + ;; + pdp11) + basic_machine=pdp11-dec + ;; + we32k) + basic_machine=we32k-att + ;; + sh3 | sh4 | sh[34]eb | sh[1234]le | sh[23]ele) + basic_machine=sh-unknown + ;; + sh64) + basic_machine=sh64-unknown + ;; + sparc | sparcv8 | sparcv9 | sparcv9b) + basic_machine=sparc-sun + ;; + cydra) + basic_machine=cydra-cydrome + ;; + orion) + basic_machine=orion-highlevel + ;; + orion105) + basic_machine=clipper-highlevel + ;; + mac | mpw | mac-mpw) + basic_machine=m68k-apple + ;; + pmac | pmac-mpw) + basic_machine=powerpc-apple + ;; + *-unknown) + # Make sure to match an already-canonicalized machine name. + ;; + *) + echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 + exit 1 + ;; +esac + +# Here we canonicalize certain aliases for manufacturers. +case $basic_machine in + *-digital*) + basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'` + ;; + *-commodore*) + basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'` + ;; + *) + ;; +esac + +# Decode manufacturer-specific aliases for certain operating systems. + +if [ x"$os" != x"" ] +then +case $os in + # First match some system type aliases + # that might get confused with valid system types. + # -solaris* is a basic system type, with this one exception. + -solaris1 | -solaris1.*) + os=`echo $os | sed -e 's|solaris1|sunos4|'` + ;; + -solaris) + os=-solaris2 + ;; + -svr4*) + os=-sysv4 + ;; + -unixware*) + os=-sysv4.2uw + ;; + -gnu/linux*) + os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'` + ;; + # First accept the basic system types. + # The portable systems comes first. + # Each alternative MUST END IN A *, to match a version number. + # -sysv* is not here because it comes later, after sysvr4. + -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ + | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\ + | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ + | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ + | -aos* \ + | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ + | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ + | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* | -openbsd* \ + | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \ + | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ + | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ + | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ + | -chorusos* | -chorusrdb* \ + | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ + | -mingw32* | -linux-gnu* | -linux-uclibc* | -uxpv* | -beos* | -mpeix* | -udk* \ + | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \ + | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \ + | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \ + | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \ + | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \ + | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly*) + # Remember, each alternative MUST END IN *, to match a version number. + ;; + -qnx*) + case $basic_machine in + x86-* | i*86-*) + ;; + *) + os=-nto$os + ;; + esac + ;; + -nto-qnx*) + ;; + -nto*) + os=`echo $os | sed -e 's|nto|nto-qnx|'` + ;; + -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \ + | -windows* | -osx | -abug | -netware* | -os9* | -beos* \ + | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*) + ;; + -mac*) + os=`echo $os | sed -e 's|mac|macos|'` + ;; + -linux-dietlibc) + os=-linux-dietlibc + ;; + -linux*) + os=`echo $os | sed -e 's|linux|linux-gnu|'` + ;; + -sunos5*) + os=`echo $os | sed -e 's|sunos5|solaris2|'` + ;; + -sunos6*) + os=`echo $os | sed -e 's|sunos6|solaris3|'` + ;; + -opened*) + os=-openedition + ;; + -os400*) + os=-os400 + ;; + -wince*) + os=-wince + ;; + -osfrose*) + os=-osfrose + ;; + -osf*) + os=-osf + ;; + -utek*) + os=-bsd + ;; + -dynix*) + os=-bsd + ;; + -acis*) + os=-aos + ;; + -atheos*) + os=-atheos + ;; + -syllable*) + os=-syllable + ;; + -386bsd) + os=-bsd + ;; + -ctix* | -uts*) + os=-sysv + ;; + -nova*) + os=-rtmk-nova + ;; + -ns2 ) + os=-nextstep2 + ;; + -nsk*) + os=-nsk + ;; + # Preserve the version number of sinix5. + -sinix5.*) + os=`echo $os | sed -e 's|sinix|sysv|'` + ;; + -sinix*) + os=-sysv4 + ;; + -tpf*) + os=-tpf + ;; + -triton*) + os=-sysv3 + ;; + -oss*) + os=-sysv3 + ;; + -svr4) + os=-sysv4 + ;; + -svr3) + os=-sysv3 + ;; + -sysvr4) + os=-sysv4 + ;; + # This must come after -sysvr4. + -sysv*) + ;; + -ose*) + os=-ose + ;; + -es1800*) + os=-ose + ;; + -xenix) + os=-xenix + ;; + -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) + os=-mint + ;; + -aros*) + os=-aros + ;; + -kaos*) + os=-kaos + ;; + -none) + ;; + *) + # Get rid of the `-' at the beginning of $os. + os=`echo $os | sed 's/[^-]*-//'` + echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2 + exit 1 + ;; +esac +else + +# Here we handle the default operating systems that come with various machines. +# The value should be what the vendor currently ships out the door with their +# machine or put another way, the most popular os provided with the machine. + +# Note that if you're going to try to match "-MANUFACTURER" here (say, +# "-sun"), then you have to tell the case statement up towards the top +# that MANUFACTURER isn't an operating system. Otherwise, code above +# will signal an error saying that MANUFACTURER isn't an operating +# system, and we'll never get to this point. + +case $basic_machine in + *-acorn) + os=-riscix1.2 + ;; + arm*-rebel) + os=-linux + ;; + arm*-semi) + os=-aout + ;; + c4x-* | tic4x-*) + os=-coff + ;; + # This must come before the *-dec entry. + pdp10-*) + os=-tops20 + ;; + pdp11-*) + os=-none + ;; + *-dec | vax-*) + os=-ultrix4.2 + ;; + m68*-apollo) + os=-domain + ;; + i386-sun) + os=-sunos4.0.2 + ;; + m68000-sun) + os=-sunos3 + # This also exists in the configure program, but was not the + # default. + # os=-sunos4 + ;; + m68*-cisco) + os=-aout + ;; + mips*-cisco) + os=-elf + ;; + mips*-*) + os=-elf + ;; + or32-*) + os=-coff + ;; + *-tti) # must be before sparc entry or we get the wrong os. + os=-sysv3 + ;; + sparc-* | *-sun) + os=-sunos4.1.1 + ;; + *-be) + os=-beos + ;; + *-ibm) + os=-aix + ;; + *-knuth) + os=-mmixware + ;; + *-wec) + os=-proelf + ;; + *-winbond) + os=-proelf + ;; + *-oki) + os=-proelf + ;; + *-hp) + os=-hpux + ;; + *-hitachi) + os=-hiux + ;; + i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent) + os=-sysv + ;; + *-cbm) + os=-amigaos + ;; + *-dg) + os=-dgux + ;; + *-dolphin) + os=-sysv3 + ;; + m68k-ccur) + os=-rtu + ;; + m88k-omron*) + os=-luna + ;; + *-next ) + os=-nextstep + ;; + *-sequent) + os=-ptx + ;; + *-crds) + os=-unos + ;; + *-ns) + os=-genix + ;; + i370-*) + os=-mvs + ;; + *-next) + os=-nextstep3 + ;; + *-gould) + os=-sysv + ;; + *-highlevel) + os=-bsd + ;; + *-encore) + os=-bsd + ;; + *-sgi) + os=-irix + ;; + *-siemens) + os=-sysv4 + ;; + *-masscomp) + os=-rtu + ;; + f30[01]-fujitsu | f700-fujitsu) + os=-uxpv + ;; + *-rom68k) + os=-coff + ;; + *-*bug) + os=-coff + ;; + *-apple) + os=-macos + ;; + *-atari*) + os=-mint + ;; + *) + os=-none + ;; +esac +fi + +# Here we handle the case where we know the os, and the CPU type, but not the +# manufacturer. We pick the logical manufacturer. +vendor=unknown +case $basic_machine in + *-unknown) + case $os in + -riscix*) + vendor=acorn + ;; + -sunos*) + vendor=sun + ;; + -aix*) + vendor=ibm + ;; + -beos*) + vendor=be + ;; + -hpux*) + vendor=hp + ;; + -mpeix*) + vendor=hp + ;; + -hiux*) + vendor=hitachi + ;; + -unos*) + vendor=crds + ;; + -dgux*) + vendor=dg + ;; + -luna*) + vendor=omron + ;; + -genix*) + vendor=ns + ;; + -mvs* | -opened*) + vendor=ibm + ;; + -os400*) + vendor=ibm + ;; + -ptx*) + vendor=sequent + ;; + -tpf*) + vendor=ibm + ;; + -vxsim* | -vxworks* | -windiss*) + vendor=wrs + ;; + -aux*) + vendor=apple + ;; + -hms*) + vendor=hitachi + ;; + -mpw* | -macos*) + vendor=apple + ;; + -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) + vendor=atari + ;; + -vos*) + vendor=stratus + ;; + esac + basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"` + ;; +esac + +echo $basic_machine$os +exit 0 + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/configure b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/configure new file mode 100755 index 000000000..fd4d1d5bf --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/configure @@ -0,0 +1,6602 @@ +#! /bin/sh +# Guess values for system-dependent variables and create Makefiles. +# Generated by GNU Autoconf 2.59. +# +# Copyright (C) 2003 Free Software Foundation, Inc. +# This configure script is free software; the Free Software Foundation +# gives unlimited permission to copy, distribute and modify it. +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## + +# Be Bourne compatible +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' +elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then + set -o posix +fi +DUALCASE=1; export DUALCASE # for MKS sh + +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + + +# Work around bugs in pre-3.0 UWIN ksh. +$as_unset ENV MAIL MAILPATH +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +for as_var in \ + LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ + LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ + LC_TELEPHONE LC_TIME +do + if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then + eval $as_var=C; export $as_var + else + $as_unset $as_var + fi +done + +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1; then + as_expr=expr +else + as_expr=false +fi + +if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)$' \| \ + . : '\(.\)' 2>/dev/null || +echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } + /^X\/\(\/\/\)$/{ s//\1/; q; } + /^X\/\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + + +# PATH needs CR, and LINENO needs CR and PATH. +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + echo "#! /bin/sh" >conf$$.sh + echo "exit 0" >>conf$$.sh + chmod +x conf$$.sh + if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then + PATH_SEPARATOR=';' + else + PATH_SEPARATOR=: + fi + rm -f conf$$.sh +fi + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" || { + # Find who we are. Look in the path if we contain no path at all + # relative or not. + case $0 in + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done + + ;; + esac + # We did not find ourselves, most probably we were run as `sh COMMAND' + # in which case we are not to be found in the path. + if test "x$as_myself" = x; then + as_myself=$0 + fi + if test ! -f "$as_myself"; then + { echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2 + { (exit 1); exit 1; }; } + fi + case $CONFIG_SHELL in + '') + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for as_base in sh bash ksh sh5; do + case $as_dir in + /*) + if ("$as_dir/$as_base" -c ' + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then + $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } + $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } + CONFIG_SHELL=$as_dir/$as_base + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$0" ${1+"$@"} + fi;; + esac + done +done +;; + esac + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. 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See below for descriptions of some of the useful variables. + +Defaults for the options are specified in brackets. + +Configuration: + -h, --help display this help and exit + --help=short display options specific to this package + --help=recursive display the short help of all the included packages + -V, --version display version information and exit + -q, --quiet, --silent do not print \`checking...' messages + --cache-file=FILE cache test results in FILE [disabled] + -C, --config-cache alias for \`--cache-file=config.cache' + -n, --no-create do not create output files + --srcdir=DIR find the sources in DIR [configure dir or \`..'] + +_ACEOF + + cat <<_ACEOF +Installation directories: + --prefix=PREFIX install architecture-independent files in PREFIX + [$ac_default_prefix] + --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX + [PREFIX] + +By default, \`make install' will install all the files in +\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify +an installation prefix other than \`$ac_default_prefix' using \`--prefix', +for instance \`--prefix=\$HOME'. + +For better control, use the options below. + +Fine tuning of the installation directories: + --bindir=DIR user executables [EPREFIX/bin] + --sbindir=DIR system admin executables [EPREFIX/sbin] + --libexecdir=DIR program executables [EPREFIX/libexec] + --datadir=DIR read-only architecture-independent data [PREFIX/share] + --sysconfdir=DIR read-only single-machine data [PREFIX/etc] + --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] + --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --libdir=DIR object code libraries [EPREFIX/lib] + --includedir=DIR C header files [PREFIX/include] + --oldincludedir=DIR C header files for non-gcc [/usr/include] + --infodir=DIR info documentation [PREFIX/info] + --mandir=DIR man documentation [PREFIX/man] +_ACEOF + + cat <<\_ACEOF + +X features: + --x-includes=DIR X include files are in DIR + --x-libraries=DIR X library files are in DIR + +System types: + --build=BUILD configure for building on BUILD [guessed] + --host=HOST cross-compile to build programs to run on HOST [BUILD] +_ACEOF +fi + +if test -n "$ac_init_help"; then + + cat <<\_ACEOF + +Optional Packages: + --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] + --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) + --with-x use the X Window System + +Some influential environment variables: + CC C compiler command + CFLAGS C compiler flags + LDFLAGS linker flags, e.g. -L if you have libraries in a + nonstandard directory + CPPFLAGS C/C++ preprocessor flags, e.g. -I if you have + headers in a nonstandard directory + CPP C preprocessor + CXX C++ compiler command + CXXFLAGS C++ compiler flags + +Use these variables to override the choices made by `configure' or to help +it to find libraries and programs with nonstandard names/locations. + +_ACEOF +fi + +if test "$ac_init_help" = "recursive"; then + # If there are subdirs, report their specific --help. + ac_popdir=`pwd` + for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue + test -d $ac_dir || continue + ac_builddir=. + +if test "$ac_dir" != .; then + ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'` + # A "../" for each directory in $ac_dir_suffix. + ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'` +else + ac_dir_suffix= ac_top_builddir= +fi + +case $srcdir in + .) # No --srcdir option. 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"$ac_site_file" + fi +done + +if test -r "$cache_file"; then + # Some versions of bash will fail to source /dev/null (special + # files actually), so we avoid doing that. + if test -f "$cache_file"; then + { echo "$as_me:$LINENO: loading cache $cache_file" >&5 +echo "$as_me: loading cache $cache_file" >&6;} + case $cache_file in + [\\/]* | ?:[\\/]* ) . $cache_file;; + *) . ./$cache_file;; + esac + fi +else + { echo "$as_me:$LINENO: creating cache $cache_file" >&5 +echo "$as_me: creating cache $cache_file" >&6;} + >$cache_file +fi + +# Check that the precious variables saved in the cache have kept the same +# value. +ac_cache_corrupted=false +for ac_var in `(set) 2>&1 | + sed -n 's/^ac_env_\([a-zA-Z_0-9]*\)_set=.*/\1/p'`; do + eval ac_old_set=\$ac_cv_env_${ac_var}_set + eval ac_new_set=\$ac_env_${ac_var}_set + eval ac_old_val="\$ac_cv_env_${ac_var}_value" + eval ac_new_val="\$ac_env_${ac_var}_value" + case $ac_old_set,$ac_new_set in + set,) + { echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 +echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} + ac_cache_corrupted=: ;; + ,set) + { echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5 +echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} + ac_cache_corrupted=: ;; + ,);; + *) + if test "x$ac_old_val" != "x$ac_new_val"; then + { echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5 +echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} + { echo "$as_me:$LINENO: former value: $ac_old_val" >&5 +echo "$as_me: former value: $ac_old_val" >&2;} + { echo "$as_me:$LINENO: current value: $ac_new_val" >&5 +echo "$as_me: current value: $ac_new_val" >&2;} + ac_cache_corrupted=: + fi;; + esac + # Pass precious variables to config.status. + if test "$ac_new_set" = set; then + case $ac_new_val in + *" "*|*" "*|*[\[\]\~\#\$\^\&\*\(\)\{\}\\\|\;\<\>\?\"\']*) + ac_arg=$ac_var=`echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; + *) ac_arg=$ac_var=$ac_new_val ;; + esac + case " $ac_configure_args " in + *" '$ac_arg' "*) ;; # Avoid dups. 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then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install-sh -c" + break + elif test -f $ac_dir/install.sh; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install.sh -c" + break + elif test -f $ac_dir/shtool; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/shtool install -c" + break + fi +done +if test -z "$ac_aux_dir"; then + { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&5 +echo "$as_me: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&2;} + { (exit 1); exit 1; }; } +fi +ac_config_guess="$SHELL $ac_aux_dir/config.guess" +ac_config_sub="$SHELL $ac_aux_dir/config.sub" +ac_configure="$SHELL $ac_aux_dir/configure" # This should be Cygnus configure. + +# Make sure we can run config.sub. +$ac_config_sub sun4 >/dev/null 2>&1 || + { { echo "$as_me:$LINENO: error: cannot run $ac_config_sub" >&5 +echo "$as_me: error: cannot run $ac_config_sub" >&2;} + { (exit 1); exit 1; }; } + +echo "$as_me:$LINENO: checking build system type" >&5 +echo $ECHO_N "checking build system type... $ECHO_C" >&6 +if test "${ac_cv_build+set}" = set; 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then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_host_alias=$host_alias +test -z "$ac_cv_host_alias" && + ac_cv_host_alias=$ac_cv_build_alias +ac_cv_host=`$ac_config_sub $ac_cv_host_alias` || + { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_host_alias failed" >&5 +echo "$as_me: error: $ac_config_sub $ac_cv_host_alias failed" >&2;} + { (exit 1); exit 1; }; } + +fi +echo "$as_me:$LINENO: result: $ac_cv_host" >&5 +echo "${ECHO_T}$ac_cv_host" >&6 +host=$ac_cv_host +host_cpu=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` +host_vendor=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` +host_os=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` + + +case "$host" in + *-linux*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-shared -soname libg2.so.0' + LD_SHARED_OPT='' + LD_SHARED_EXT='so.0.$(G2_VERSION)' + cat >>confdefs.h <<\_ACEOF +#define LINUX 1 +_ACEOF +;; + *-aix*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-bM:SRE -bnoentry -bexpall' + LD_SHARED_OPT='$(LDFLAGS) -lc' + LD_SHARED_EXT='so' + cat >>confdefs.h <<\_ACEOF +#define AIX 1 +_ACEOF +;; + *-osf*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-shared' + LD_SHARED_OPT='$(LDFLAGS) -lc' + LD_SHARED_EXT='so' + cat >>confdefs.h <<\_ACEOF +#define OSF 1 +_ACEOF +;; + *) + LD_SHARED_EXT='so' + cat >>confdefs.h <<\_ACEOF +#define UNIX 1 +_ACEOF +;; +esac + + + + + + +# +# check C compiler, preprocesor, etc. +# +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $# != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CC" && break +done + + CC=$ac_ct_CC +fi + +fi + + +test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files a.out a.exe b.out" +# Try to create an executable without -o first, disregard a.out. +# It will help us diagnose broken compilers, and finding out an intuition +# of exeext. +echo "$as_me:$LINENO: checking for C compiler default output file name" >&5 +echo $ECHO_N "checking for C compiler default output file name... $ECHO_C" >&6 +ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` +if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 + (eval $ac_link_default) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # Find the output, starting from the most likely. This scheme is +# not robust to junk in `.', hence go to wildcards (a.*) only as a last +# resort. + +# Be careful to initialize this variable, since it used to be cached. +# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. +ac_cv_exeext= +# b.out is created by i960 compilers. +for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out +do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) + ;; + conftest.$ac_ext ) + # This is the source file. + ;; + [ab].out ) + # We found the default executable, but exeext='' is most + # certainly right. + break;; + *.* ) + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + # FIXME: I believe we export ac_cv_exeext for Libtool, + # but it would be cool to find out if it's true. Does anybody + # maintain Libtool? --akim. + export ac_cv_exeext + break;; + * ) + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: C compiler cannot create executables +See \`config.log' for more details." >&5 +echo "$as_me: error: C compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; } +fi + +ac_exeext=$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_file" >&5 +echo "${ECHO_T}$ac_file" >&6 + +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether the C compiler works" >&5 +echo $ECHO_N "checking whether the C compiler works... $ECHO_C" >&6 +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. +if test "$cross_compiling" != yes; then + if { ac_try='./$ac_file' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { echo "$as_me:$LINENO: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + fi + fi +fi +echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + +rm -f a.out a.exe conftest$ac_cv_exeext b.out +ac_clean_files=$ac_clean_files_save +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 +echo "$as_me:$LINENO: result: $cross_compiling" >&5 +echo "${ECHO_T}$cross_compiling" >&6 + +echo "$as_me:$LINENO: checking for suffix of executables" >&5 +echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + export ac_cv_exeext + break;; + * ) break;; + esac +done +else + { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +echo "${ECHO_T}$ac_cv_exeext" >&6 + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +echo "$as_me:$LINENO: checking for suffix of object files" >&5 +echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 +if test "${ac_cv_objext+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.o conftest.obj +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; + *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest.$ac_cv_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 +echo "${ECHO_T}$ac_cv_objext" >&6 +OBJEXT=$ac_cv_objext +ac_objext=$OBJEXT +echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 +if test "${ac_cv_c_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 +GCC=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +CFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 +echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cc_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 +echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_prog_cc_stdc=no +ac_save_CC=$CC +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std1 is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std1. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +# Don't try gcc -ansi; that turns off useful extensions and +# breaks some systems' header files. +# AIX -qlanglvl=ansi +# Ultrix and OSF/1 -std1 +# HP-UX 10.20 and later -Ae +# HP-UX older versions -Aa -D_HPUX_SOURCE +# SVR4 -Xc -D__EXTENSIONS__ +for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_stdc=$ac_arg +break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext +done +rm -f conftest.$ac_ext conftest.$ac_objext +CC=$ac_save_CC + +fi + +case "x$ac_cv_prog_cc_stdc" in + x|xno) + echo "$as_me:$LINENO: result: none needed" >&5 +echo "${ECHO_T}none needed" >&6 ;; + *) + echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 + CC="$CC $ac_cv_prog_cc_stdc" ;; +esac + +# Some people use a C++ compiler to compile C. Since we use `exit', +# in C++ we need to declare it. In case someone uses the same compiler +# for both compiling C and C++ we need to have the C++ compiler decide +# the declaration of exit, since it's the most demanding environment. +cat >conftest.$ac_ext <<_ACEOF +#ifndef __cplusplus + choke me +#endif +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +#include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 +echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6 +# On Suns, sometimes $CPP names a directory. +if test -n "$CPP" && test -d "$CPP"; then + CPP= +fi +if test -z "$CPP"; then + if test "${ac_cv_prog_CPP+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + # Double quotes because CPP needs to be expanded + for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" + do + ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether non-existent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # Broken: success on invalid input. +continue +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + break +fi + + done + ac_cv_prog_CPP=$CPP + +fi + CPP=$ac_cv_prog_CPP +else + ac_cv_prog_CPP=$CPP +fi +echo "$as_me:$LINENO: result: $CPP" >&5 +echo "${ECHO_T}$CPP" >&6 +ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether non-existent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # Broken: success on invalid input. +continue +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : +else + { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&5 +echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu +if test -n "$ac_tool_prefix"; then + for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CXX+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CXX"; then + ac_cv_prog_CXX="$CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CXX=$ac_cv_prog_CXX +if test -n "$CXX"; then + echo "$as_me:$LINENO: result: $CXX" >&5 +echo "${ECHO_T}$CXX" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CXX" && break + done +fi +if test -z "$CXX"; then + ac_ct_CXX=$CXX + for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CXX"; then + ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CXX="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CXX=$ac_cv_prog_ac_ct_CXX +if test -n "$ac_ct_CXX"; then + echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 +echo "${ECHO_T}$ac_ct_CXX" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CXX" && break +done +test -n "$ac_ct_CXX" || ac_ct_CXX="g++" + + CXX=$ac_ct_CXX +fi + + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C++ compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_cxx_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6 +GXX=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CXXFLAGS=${CXXFLAGS+set} +ac_save_CXXFLAGS=$CXXFLAGS +CXXFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 +echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cxx_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cxx_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cxx_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6 +if test "$ac_test_CXXFLAGS" = set; then + CXXFLAGS=$ac_save_CXXFLAGS +elif test $ac_cv_prog_cxx_g = yes; then + if test "$GXX" = yes; then + CXXFLAGS="-g -O2" + else + CXXFLAGS="-g" + fi +else + if test "$GXX" = yes; then + CXXFLAGS="-O2" + else + CXXFLAGS= + fi +fi +for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +#include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. +set dummy ${ac_tool_prefix}ranlib; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_RANLIB+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$RANLIB"; then + ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +RANLIB=$ac_cv_prog_RANLIB +if test -n "$RANLIB"; then + echo "$as_me:$LINENO: result: $RANLIB" >&5 +echo "${ECHO_T}$RANLIB" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_RANLIB"; then + ac_ct_RANLIB=$RANLIB + # Extract the first word of "ranlib", so it can be a program name with args. +set dummy ranlib; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_RANLIB"; then + ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_RANLIB="ranlib" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + test -z "$ac_cv_prog_ac_ct_RANLIB" && ac_cv_prog_ac_ct_RANLIB=":" +fi +fi +ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB +if test -n "$ac_ct_RANLIB"; then + echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5 +echo "${ECHO_T}$ac_ct_RANLIB" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + RANLIB=$ac_ct_RANLIB +else + RANLIB="$ac_cv_prog_RANLIB" +fi + +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 +echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6 +if test -z "$INSTALL"; then +if test "${ac_cv_path_install+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + done + done + ;; +esac +done + + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. We don't cache a + # path for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the path is relative. + INSTALL=$ac_install_sh + fi +fi +echo "$as_me:$LINENO: result: $INSTALL" >&5 +echo "${ECHO_T}$INSTALL" >&6 + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' + +# Extract the first word of "find", so it can be a program name with args. +set dummy find; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_FIND+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$FIND"; then + ac_cv_prog_FIND="$FIND" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_FIND="find" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + test -z "$ac_cv_prog_FIND" && ac_cv_prog_FIND=":" +fi +fi +FIND=$ac_cv_prog_FIND +if test -n "$FIND"; then + echo "$as_me:$LINENO: result: $FIND" >&5 +echo "${ECHO_T}$FIND" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +# Extract the first word of "makedepend", so it can be a program name with args. +set dummy makedepend; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_MAKEDEPEND+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$MAKEDEPEND"; then + ac_cv_prog_MAKEDEPEND="$MAKEDEPEND" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_MAKEDEPEND="makedepend" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + test -z "$ac_cv_prog_MAKEDEPEND" && ac_cv_prog_MAKEDEPEND=":" +fi +fi +MAKEDEPEND=$ac_cv_prog_MAKEDEPEND +if test -n "$MAKEDEPEND"; then + echo "$as_me:$LINENO: result: $MAKEDEPEND" >&5 +echo "${ECHO_T}$MAKEDEPEND" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + +echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 +echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6 +if test "${ac_cv_lib_dl_dlopen+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldl $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char dlopen (); +int +main () +{ +dlopen (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_dl_dlopen=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_dl_dlopen=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5 +echo "${ECHO_T}$ac_cv_lib_dl_dlopen" >&6 +if test $ac_cv_lib_dl_dlopen = yes; then + have_dl=yes +else + have_dl=no +fi + + + +# +# Try to locate the X Window System include files and libraries +# and add /usr/local to include and lib path and add -lm (for testing) +# + +echo "$as_me:$LINENO: checking for X" >&5 +echo $ECHO_N "checking for X... $ECHO_C" >&6 + + +# Check whether --with-x or --without-x was given. +if test "${with_x+set}" = set; then + withval="$with_x" + +fi; +# $have_x is `yes', `no', `disabled', or empty when we do not yet know. +if test "x$with_x" = xno; then + # The user explicitly disabled X. + have_x=disabled +else + if test "x$x_includes" != xNONE && test "x$x_libraries" != xNONE; then + # Both variables are already set. + have_x=yes + else + if test "${ac_cv_have_x+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + # One or both of the vars are not set, and there is no cached value. +ac_x_includes=no ac_x_libraries=no +rm -fr conftest.dir +if mkdir conftest.dir; then + cd conftest.dir + # Make sure to not put "make" in the Imakefile rules, since we grep it out. + cat >Imakefile <<'_ACEOF' +acfindx: + @echo 'ac_im_incroot="${INCROOT}"; ac_im_usrlibdir="${USRLIBDIR}"; ac_im_libdir="${LIBDIR}"' +_ACEOF + if (xmkmf) >/dev/null 2>/dev/null && test -f Makefile; then + # GNU make sometimes prints "make[1]: Entering...", which would confuse us. + eval `${MAKE-make} acfindx 2>/dev/null | grep -v make` + # Open Windows xmkmf reportedly sets LIBDIR instead of USRLIBDIR. + for ac_extension in a so sl; do + if test ! -f $ac_im_usrlibdir/libX11.$ac_extension && + test -f $ac_im_libdir/libX11.$ac_extension; then + ac_im_usrlibdir=$ac_im_libdir; break + fi + done + # Screen out bogus values from the imake configuration. They are + # bogus both because they are the default anyway, and because + # using them would break gcc on systems where it needs fixed includes. + case $ac_im_incroot in + /usr/include) ;; + *) test -f "$ac_im_incroot/X11/Xos.h" && ac_x_includes=$ac_im_incroot;; + esac + case $ac_im_usrlibdir in + /usr/lib | /lib) ;; + *) test -d "$ac_im_usrlibdir" && ac_x_libraries=$ac_im_usrlibdir ;; + esac + fi + cd .. + rm -fr conftest.dir +fi + +# Standard set of common directories for X headers. +# Check X11 before X11Rn because it is often a symlink to the current release. +ac_x_header_dirs=' +/usr/X11/include +/usr/X11R6/include +/usr/X11R5/include +/usr/X11R4/include + +/usr/include/X11 +/usr/include/X11R6 +/usr/include/X11R5 +/usr/include/X11R4 + +/usr/local/X11/include +/usr/local/X11R6/include +/usr/local/X11R5/include +/usr/local/X11R4/include + +/usr/local/include/X11 +/usr/local/include/X11R6 +/usr/local/include/X11R5 +/usr/local/include/X11R4 + +/usr/X386/include +/usr/x386/include +/usr/XFree86/include/X11 + +/usr/include +/usr/local/include +/usr/unsupported/include +/usr/athena/include +/usr/local/x11r5/include +/usr/lpp/Xamples/include + +/usr/openwin/include +/usr/openwin/share/include' + +if test "$ac_x_includes" = no; then + # Guess where to find include files, by looking for Intrinsic.h. + # First, try using that file with no special directory specified. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + # We can compile using X headers with no special include directory. +ac_x_includes= +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + for ac_dir in $ac_x_header_dirs; do + if test -r "$ac_dir/X11/Intrinsic.h"; then + ac_x_includes=$ac_dir + break + fi +done +fi +rm -f conftest.err conftest.$ac_ext +fi # $ac_x_includes = no + +if test "$ac_x_libraries" = no; then + # Check for the libraries. + # See if we find them without any special options. + # Don't add to $LIBS permanently. + ac_save_LIBS=$LIBS + LIBS="-lXt $LIBS" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +int +main () +{ +XtMalloc (0) + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + LIBS=$ac_save_LIBS +# We can link X programs with no special library path. +ac_x_libraries= +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +LIBS=$ac_save_LIBS +for ac_dir in `echo "$ac_x_includes $ac_x_header_dirs" | sed s/include/lib/g` +do + # Don't even attempt the hair of trying to link an X program! + for ac_extension in a so sl; do + if test -r $ac_dir/libXt.$ac_extension; then + ac_x_libraries=$ac_dir + break 2 + fi + done +done +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi # $ac_x_libraries = no + +if test "$ac_x_includes" = no || test "$ac_x_libraries" = no; then + # Didn't find X anywhere. Cache the known absence of X. + ac_cv_have_x="have_x=no" +else + # Record where we found X for the cache. + ac_cv_have_x="have_x=yes \ + ac_x_includes=$ac_x_includes ac_x_libraries=$ac_x_libraries" +fi +fi + + fi + eval "$ac_cv_have_x" +fi # $with_x != no + +if test "$have_x" != yes; then + echo "$as_me:$LINENO: result: $have_x" >&5 +echo "${ECHO_T}$have_x" >&6 + no_x=yes +else + # If each of the values was on the command line, it overrides each guess. + test "x$x_includes" = xNONE && x_includes=$ac_x_includes + test "x$x_libraries" = xNONE && x_libraries=$ac_x_libraries + # Update the cache value to reflect the command line values. + ac_cv_have_x="have_x=yes \ + ac_x_includes=$x_includes ac_x_libraries=$x_libraries" + echo "$as_me:$LINENO: result: libraries $x_libraries, headers $x_includes" >&5 +echo "${ECHO_T}libraries $x_libraries, headers $x_includes" >&6 +fi + +if test "$no_x" = yes; then + # Not all programs may use this symbol, but it does not hurt to define it. + +cat >>confdefs.h <<\_ACEOF +#define X_DISPLAY_MISSING 1 +_ACEOF + + X_CFLAGS= X_PRE_LIBS= X_LIBS= X_EXTRA_LIBS= +else + if test -n "$x_includes"; then + X_CFLAGS="$X_CFLAGS -I$x_includes" + fi + + # It would also be nice to do this for all -L options, not just this one. + if test -n "$x_libraries"; then + X_LIBS="$X_LIBS -L$x_libraries" + # For Solaris; some versions of Sun CC require a space after -R and + # others require no space. Words are not sufficient . . . . + case `(uname -sr) 2>/dev/null` in + "SunOS 5"*) + echo "$as_me:$LINENO: checking whether -R must be followed by a space" >&5 +echo $ECHO_N "checking whether -R must be followed by a space... $ECHO_C" >&6 + ac_xsave_LIBS=$LIBS; LIBS="$LIBS -R$x_libraries" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_R_nospace=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_R_nospace=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + if test $ac_R_nospace = yes; then + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 + X_LIBS="$X_LIBS -R$x_libraries" + else + LIBS="$ac_xsave_LIBS -R $x_libraries" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_R_space=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_R_space=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + if test $ac_R_space = yes; then + echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + X_LIBS="$X_LIBS -R $x_libraries" + else + echo "$as_me:$LINENO: result: neither works" >&5 +echo "${ECHO_T}neither works" >&6 + fi + fi + LIBS=$ac_xsave_LIBS + esac + fi + + # Check for system-dependent libraries X programs must link with. + # Do this before checking for the system-independent R6 libraries + # (-lICE), since we may need -lsocket or whatever for X linking. + + if test "$ISC" = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lnsl_s -linet" + else + # Martyn Johnson says this is needed for Ultrix, if the X + # libraries were built with DECnet support. And Karl Berry says + # the Alpha needs dnet_stub (dnet does not exist). + ac_xsave_LIBS="$LIBS"; LIBS="$LIBS $X_LIBS -lX11" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char XOpenDisplay (); +int +main () +{ +XOpenDisplay (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +echo "$as_me:$LINENO: checking for dnet_ntoa in -ldnet" >&5 +echo $ECHO_N "checking for dnet_ntoa in -ldnet... $ECHO_C" >&6 +if test "${ac_cv_lib_dnet_dnet_ntoa+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldnet $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char dnet_ntoa (); +int +main () +{ +dnet_ntoa (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_dnet_dnet_ntoa=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_dnet_dnet_ntoa=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_dnet_dnet_ntoa" >&5 +echo "${ECHO_T}$ac_cv_lib_dnet_dnet_ntoa" >&6 +if test $ac_cv_lib_dnet_dnet_ntoa = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet" +fi + + if test $ac_cv_lib_dnet_dnet_ntoa = no; then + echo "$as_me:$LINENO: checking for dnet_ntoa in -ldnet_stub" >&5 +echo $ECHO_N "checking for dnet_ntoa in -ldnet_stub... $ECHO_C" >&6 +if test "${ac_cv_lib_dnet_stub_dnet_ntoa+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldnet_stub $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char dnet_ntoa (); +int +main () +{ +dnet_ntoa (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_dnet_stub_dnet_ntoa=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_dnet_stub_dnet_ntoa=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_dnet_stub_dnet_ntoa" >&5 +echo "${ECHO_T}$ac_cv_lib_dnet_stub_dnet_ntoa" >&6 +if test $ac_cv_lib_dnet_stub_dnet_ntoa = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet_stub" +fi + + fi +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + LIBS="$ac_xsave_LIBS" + + # msh@cis.ufl.edu says -lnsl (and -lsocket) are needed for his 386/AT, + # to get the SysV transport functions. + # Chad R. Larson says the Pyramis MIS-ES running DC/OSx (SVR4) + # needs -lnsl. + # The nsl library prevents programs from opening the X display + # on Irix 5.2, according to T.E. Dickey. + # The functions gethostbyname, getservbyname, and inet_addr are + # in -lbsd on LynxOS 3.0.1/i386, according to Lars Hecking. + echo "$as_me:$LINENO: checking for gethostbyname" >&5 +echo $ECHO_N "checking for gethostbyname... $ECHO_C" >&6 +if test "${ac_cv_func_gethostbyname+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define gethostbyname to an innocuous variant, in case declares gethostbyname. + For example, HP-UX 11i declares gettimeofday. */ +#define gethostbyname innocuous_gethostbyname + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char gethostbyname (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef gethostbyname + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gethostbyname (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) +choke me +#else +char (*f) () = gethostbyname; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != gethostbyname; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_gethostbyname=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_gethostbyname=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_gethostbyname" >&5 +echo "${ECHO_T}$ac_cv_func_gethostbyname" >&6 + + if test $ac_cv_func_gethostbyname = no; then + echo "$as_me:$LINENO: checking for gethostbyname in -lnsl" >&5 +echo $ECHO_N "checking for gethostbyname in -lnsl... $ECHO_C" >&6 +if test "${ac_cv_lib_nsl_gethostbyname+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lnsl $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gethostbyname (); +int +main () +{ +gethostbyname (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_nsl_gethostbyname=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_nsl_gethostbyname=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_nsl_gethostbyname" >&5 +echo "${ECHO_T}$ac_cv_lib_nsl_gethostbyname" >&6 +if test $ac_cv_lib_nsl_gethostbyname = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lnsl" +fi + + if test $ac_cv_lib_nsl_gethostbyname = no; then + echo "$as_me:$LINENO: checking for gethostbyname in -lbsd" >&5 +echo $ECHO_N "checking for gethostbyname in -lbsd... $ECHO_C" >&6 +if test "${ac_cv_lib_bsd_gethostbyname+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lbsd $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gethostbyname (); +int +main () +{ +gethostbyname (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_bsd_gethostbyname=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_bsd_gethostbyname=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_bsd_gethostbyname" >&5 +echo "${ECHO_T}$ac_cv_lib_bsd_gethostbyname" >&6 +if test $ac_cv_lib_bsd_gethostbyname = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lbsd" +fi + + fi + fi + + # lieder@skyler.mavd.honeywell.com says without -lsocket, + # socket/setsockopt and other routines are undefined under SCO ODT + # 2.0. But -lsocket is broken on IRIX 5.2 (and is not necessary + # on later versions), says Simon Leinen: it contains gethostby* + # variants that don't use the name server (or something). -lsocket + # must be given before -lnsl if both are needed. We assume that + # if connect needs -lnsl, so does gethostbyname. + echo "$as_me:$LINENO: checking for connect" >&5 +echo $ECHO_N "checking for connect... $ECHO_C" >&6 +if test "${ac_cv_func_connect+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define connect to an innocuous variant, in case declares connect. + For example, HP-UX 11i declares gettimeofday. */ +#define connect innocuous_connect + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char connect (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef connect + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char connect (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_connect) || defined (__stub___connect) +choke me +#else +char (*f) () = connect; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != connect; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_connect=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_connect=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_connect" >&5 +echo "${ECHO_T}$ac_cv_func_connect" >&6 + + if test $ac_cv_func_connect = no; then + echo "$as_me:$LINENO: checking for connect in -lsocket" >&5 +echo $ECHO_N "checking for connect in -lsocket... $ECHO_C" >&6 +if test "${ac_cv_lib_socket_connect+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lsocket $X_EXTRA_LIBS $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char connect (); +int +main () +{ +connect (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_socket_connect=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_socket_connect=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_socket_connect" >&5 +echo "${ECHO_T}$ac_cv_lib_socket_connect" >&6 +if test $ac_cv_lib_socket_connect = yes; then + X_EXTRA_LIBS="-lsocket $X_EXTRA_LIBS" +fi + + fi + + # Guillermo Gomez says -lposix is necessary on A/UX. + echo "$as_me:$LINENO: checking for remove" >&5 +echo $ECHO_N "checking for remove... $ECHO_C" >&6 +if test "${ac_cv_func_remove+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define remove to an innocuous variant, in case declares remove. + For example, HP-UX 11i declares gettimeofday. */ +#define remove innocuous_remove + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char remove (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef remove + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char remove (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_remove) || defined (__stub___remove) +choke me +#else +char (*f) () = remove; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != remove; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_remove=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_remove=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_remove" >&5 +echo "${ECHO_T}$ac_cv_func_remove" >&6 + + if test $ac_cv_func_remove = no; then + echo "$as_me:$LINENO: checking for remove in -lposix" >&5 +echo $ECHO_N "checking for remove in -lposix... $ECHO_C" >&6 +if test "${ac_cv_lib_posix_remove+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lposix $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char remove (); +int +main () +{ +remove (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_posix_remove=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_posix_remove=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_posix_remove" >&5 +echo "${ECHO_T}$ac_cv_lib_posix_remove" >&6 +if test $ac_cv_lib_posix_remove = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lposix" +fi + + fi + + # BSDI BSD/OS 2.1 needs -lipc for XOpenDisplay. + echo "$as_me:$LINENO: checking for shmat" >&5 +echo $ECHO_N "checking for shmat... $ECHO_C" >&6 +if test "${ac_cv_func_shmat+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define shmat to an innocuous variant, in case declares shmat. + For example, HP-UX 11i declares gettimeofday. */ +#define shmat innocuous_shmat + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char shmat (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef shmat + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char shmat (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_shmat) || defined (__stub___shmat) +choke me +#else +char (*f) () = shmat; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != shmat; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_shmat=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_shmat=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_shmat" >&5 +echo "${ECHO_T}$ac_cv_func_shmat" >&6 + + if test $ac_cv_func_shmat = no; then + echo "$as_me:$LINENO: checking for shmat in -lipc" >&5 +echo $ECHO_N "checking for shmat in -lipc... $ECHO_C" >&6 +if test "${ac_cv_lib_ipc_shmat+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lipc $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char shmat (); +int +main () +{ +shmat (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_ipc_shmat=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_ipc_shmat=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_ipc_shmat" >&5 +echo "${ECHO_T}$ac_cv_lib_ipc_shmat" >&6 +if test $ac_cv_lib_ipc_shmat = yes; then + X_EXTRA_LIBS="$X_EXTRA_LIBS -lipc" +fi + + fi + fi + + # Check for libraries that X11R6 Xt/Xaw programs need. + ac_save_LDFLAGS=$LDFLAGS + test -n "$x_libraries" && LDFLAGS="$LDFLAGS -L$x_libraries" + # SM needs ICE to (dynamically) link under SunOS 4.x (so we have to + # check for ICE first), but we must link in the order -lSM -lICE or + # we get undefined symbols. So assume we have SM if we have ICE. + # These have to be linked with before -lX11, unlike the other + # libraries we check for below, so use a different variable. + # John Interrante, Karl Berry + echo "$as_me:$LINENO: checking for IceConnectionNumber in -lICE" >&5 +echo $ECHO_N "checking for IceConnectionNumber in -lICE... $ECHO_C" >&6 +if test "${ac_cv_lib_ICE_IceConnectionNumber+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lICE $X_EXTRA_LIBS $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char IceConnectionNumber (); +int +main () +{ +IceConnectionNumber (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_ICE_IceConnectionNumber=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_ICE_IceConnectionNumber=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_ICE_IceConnectionNumber" >&5 +echo "${ECHO_T}$ac_cv_lib_ICE_IceConnectionNumber" >&6 +if test $ac_cv_lib_ICE_IceConnectionNumber = yes; then + X_PRE_LIBS="$X_PRE_LIBS -lSM -lICE" +fi + + LDFLAGS=$ac_save_LDFLAGS + +fi + +CFLAGS="$CFLAGS $X_CFLAGS -I/usr/local/include" +LDFLAGS="$LDFLAGS $X_LIBS -L/usr/local/lib" + + +DO_PS='#' +DO_FIG='#' +DO_X11='#' +DO_GD='#' +DO_WIN32='#' + + +# +# check supported devices +# +echo "$as_me:$LINENO: checking for main in -lm" >&5 +echo $ECHO_N "checking for main in -lm... $ECHO_C" >&6 +if test "${ac_cv_lib_m_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lm $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_m_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_m_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_m_main" >&5 +echo "${ECHO_T}$ac_cv_lib_m_main" >&6 +if test $ac_cv_lib_m_main = yes; then + DO_PS='';DO_FIG='';LDFLAGS="$LDFLAGS -lm";cat >>confdefs.h <<\_ACEOF +#define DO_PS 1 +_ACEOF + cat >>confdefs.h <<\_ACEOF +#define DO_FIG 1 +_ACEOF + +else + break +fi + +echo "$as_me:$LINENO: checking for main in -lX11" >&5 +echo $ECHO_N "checking for main in -lX11... $ECHO_C" >&6 +if test "${ac_cv_lib_X11_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lX11 $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_X11_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_X11_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_X11_main" >&5 +echo "${ECHO_T}$ac_cv_lib_X11_main" >&6 +if test $ac_cv_lib_X11_main = yes; then + DO_X11='';LDFLAGS="$LDFLAGS -lX11";cat >>confdefs.h <<\_ACEOF +#define DO_X11 1 +_ACEOF + +fi + +echo "$as_me:$LINENO: checking for main in -lgd" >&5 +echo $ECHO_N "checking for main in -lgd... $ECHO_C" >&6 +if test "${ac_cv_lib_gd_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lgd $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_gd_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_gd_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_gd_main" >&5 +echo "${ECHO_T}$ac_cv_lib_gd_main" >&6 +if test $ac_cv_lib_gd_main = yes; then + have_gd=yes +else + have_gd=no +fi + +if test "$have_gd" = yes +then + LDFLAGS="$LDFLAGS -lgd" + echo "$as_me:$LINENO: checking for gdImagePng" >&5 +echo $ECHO_N "checking for gdImagePng... $ECHO_C" >&6 +if test "${ac_cv_func_gdImagePng+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define gdImagePng to an innocuous variant, in case declares gdImagePng. + For example, HP-UX 11i declares gettimeofday. */ +#define gdImagePng innocuous_gdImagePng + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char gdImagePng (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef gdImagePng + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gdImagePng (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_gdImagePng) || defined (__stub___gdImagePng) +choke me +#else +char (*f) () = gdImagePng; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != gdImagePng; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_gdImagePng=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_gdImagePng=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_gdImagePng" >&5 +echo "${ECHO_T}$ac_cv_func_gdImagePng" >&6 +if test $ac_cv_func_gdImagePng = yes; then + DO_GD='';cat >>confdefs.h <<\_ACEOF +#define DO_GD 1 +_ACEOF + +fi + +fi + +# +# handling cygwin environment (and gd for cygwin == bgd) +# + +case $host_os in + *cygwin* ) CYGWIN=yes;; + * ) CYGWIN=no;; +esac + +if test "$CYGWIN" = yes +then + LDFLAGS="$LDFLAGS -L/lib/w32api" + echo "$as_me:$LINENO: checking for main in -lgdi32" >&5 +echo $ECHO_N "checking for main in -lgdi32... $ECHO_C" >&6 +if test "${ac_cv_lib_gdi32_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lgdi32 $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_gdi32_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_gdi32_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_gdi32_main" >&5 +echo "${ECHO_T}$ac_cv_lib_gdi32_main" >&6 +if test $ac_cv_lib_gdi32_main = yes; then + DO_WIN32='';LDFLAGS="$LDFLAGS -lgdi32";cat >>confdefs.h <<\_ACEOF +#define DO_WIN32 1 +_ACEOF + +fi + + echo "$as_me:$LINENO: checking for main in -lbgd" >&5 +echo $ECHO_N "checking for main in -lbgd... $ECHO_C" >&6 +if test "${ac_cv_lib_bgd_main+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lbgd $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + + +int +main () +{ +main (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_bgd_main=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_bgd_main=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_bgd_main" >&5 +echo "${ECHO_T}$ac_cv_lib_bgd_main" >&6 +if test $ac_cv_lib_bgd_main = yes; then + have_bgd=yes +else + have_bgd=no +fi + + if test "$have_bgd" = yes + then + LDFLAGS="$LDFLAGS -lbgd" + echo "$as_me:$LINENO: checking for gdImagePng" >&5 +echo $ECHO_N "checking for gdImagePng... $ECHO_C" >&6 +if test "${ac_cv_func_gdImagePng+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define gdImagePng to an innocuous variant, in case declares gdImagePng. + For example, HP-UX 11i declares gettimeofday. */ +#define gdImagePng innocuous_gdImagePng + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char gdImagePng (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef gdImagePng + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +{ +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char gdImagePng (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined (__stub_gdImagePng) || defined (__stub___gdImagePng) +choke me +#else +char (*f) () = gdImagePng; +#endif +#ifdef __cplusplus +} +#endif + +int +main () +{ +return f != gdImagePng; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_func_gdImagePng=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_func_gdImagePng=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_func_gdImagePng" >&5 +echo "${ECHO_T}$ac_cv_func_gdImagePng" >&6 +if test $ac_cv_func_gdImagePng = yes; then + DO_GD='';cat >>confdefs.h <<\_ACEOF +#define DO_GD 1 +_ACEOF + +fi + + fi +fi + +# +# Declare variables which we want substituted in the Makefile.in's +# + + + + + + +echo "$as_me:$LINENO: checking for egrep" >&5 +echo $ECHO_N "checking for egrep... $ECHO_C" >&6 +if test "${ac_cv_prog_egrep+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if echo a | (grep -E '(a|b)') >/dev/null 2>&1 + then ac_cv_prog_egrep='grep -E' + else ac_cv_prog_egrep='egrep' + fi +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_egrep" >&5 +echo "${ECHO_T}$ac_cv_prog_egrep" >&6 + EGREP=$ac_cv_prog_egrep + + +echo "$as_me:$LINENO: checking for ANSI C header files" >&5 +echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 +if test "${ac_cv_header_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_header_stdc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_header_stdc=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + +if test $ac_cv_header_stdc = yes; then + # SunOS 4.x string.h does not declare mem*, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "memchr" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "free" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. + if test "$cross_compiling" = yes; then + : +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#if ((' ' & 0x0FF) == 0x020) +# define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +#else +# define ISLOWER(c) \ + (('a' <= (c) && (c) <= 'i') \ + || ('j' <= (c) && (c) <= 'r') \ + || ('s' <= (c) && (c) <= 'z')) +# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +#endif + +#define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +int +main () +{ + int i; + for (i = 0; i < 256; i++) + if (XOR (islower (i), ISLOWER (i)) + || toupper (i) != TOUPPER (i)) + exit(2); + exit (0); +} +_ACEOF +rm -f conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: program exited with status $ac_status" >&5 +echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no +fi +rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +fi +fi +echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 +echo "${ECHO_T}$ac_cv_header_stdc" >&6 +if test $ac_cv_header_stdc = yes; then + +cat >>confdefs.h <<\_ACEOF +#define STDC_HEADERS 1 +_ACEOF + +fi + +# On IRIX 5.3, sys/types and inttypes.h are conflicting. + + + + + + + + + +for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ + inttypes.h stdint.h unistd.h +do +as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` +echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + eval "$as_ac_Header=yes" +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +eval "$as_ac_Header=no" +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 +if test `eval echo '${'$as_ac_Header'}'` = yes; then + cat >>confdefs.h <<_ACEOF +#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + + +for ac_header in limits.h +do +as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 +else + # Is the header compilable? +echo "$as_me:$LINENO: checking $ac_header usability" >&5 +echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_header_compiler=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_header_compiler=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +echo "${ECHO_T}$ac_header_compiler" >&6 + +# Is the header present? +echo "$as_me:$LINENO: checking $ac_header presence" >&5 +echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include <$ac_header> +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_c_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_c_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + ac_header_preproc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi +rm -f conftest.err conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +echo "${ECHO_T}$ac_header_preproc" >&6 + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + ( + cat <<\_ASBOX +## ------------------------------------------ ## +## Report this to the AC_PACKAGE_NAME lists. ## +## ------------------------------------------ ## +_ASBOX + ) | + sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac +echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 + +fi +if test `eval echo '${'$as_ac_Header'}'` = yes; then + cat >>confdefs.h <<_ACEOF +#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + + + +# +# finally create makefiles using Makefile.in +# +echo + ac_config_files="$ac_config_files Makefile demo/Makefile g2_perl/Makefile.PL" +cat >confcache <<\_ACEOF +# This file is a shell script that caches the results of configure +# tests run on this system so they can be shared between configure +# scripts and configure runs, see configure's option --config-cache. +# It is not useful on other systems. If it contains results you don't +# want to keep, you may remove or edit it. +# +# config.status only pays attention to the cache file if you give it +# the --recheck option to rerun configure. +# +# `ac_cv_env_foo' variables (set or unset) will be overridden when +# loading this file, other *unset* `ac_cv_foo' will be assigned the +# following values. + +_ACEOF + +# The following way of writing the cache mishandles newlines in values, +# but we know of no workaround that is simple, portable, and efficient. +# So, don't put newlines in cache variables' values. +# Ultrix sh set writes to stderr and can't be redirected directly, +# and sets the high bit in the cache file unless we assign to the vars. +{ + (set) 2>&1 | + case `(ac_space=' '; set | grep ac_space) 2>&1` in + *ac_space=\ *) + # `set' does not quote correctly, so add quotes (double-quote + # substitution turns \\\\ into \\, and sed turns \\ into \). + sed -n \ + "s/'/'\\\\''/g; + s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" + ;; + *) + # `set' quotes correctly as required by POSIX, so do not add quotes. + sed -n \ + "s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1=\\2/p" + ;; + esac; +} | + sed ' + t clear + : clear + s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/ + t end + /^ac_cv_env/!s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/ + : end' >>confcache +if diff $cache_file confcache >/dev/null 2>&1; then :; else + if test -w $cache_file; then + test "x$cache_file" != "x/dev/null" && echo "updating cache $cache_file" + cat confcache >$cache_file + else + echo "not updating unwritable cache $cache_file" + fi +fi +rm -f confcache + +test "x$prefix" = xNONE && prefix=$ac_default_prefix +# Let make expand exec_prefix. +test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' + +# VPATH may cause trouble with some makes, so we remove $(srcdir), +# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and +# trailing colons and then remove the whole line if VPATH becomes empty +# (actually we leave an empty line to preserve line numbers). +if test "x$srcdir" = x.; then + ac_vpsub='/^[ ]*VPATH[ ]*=/{ +s/:*\$(srcdir):*/:/; +s/:*\${srcdir}:*/:/; +s/:*@srcdir@:*/:/; +s/^\([^=]*=[ ]*\):*/\1/; +s/:*$//; +s/^[^=]*=[ ]*$//; +}' +fi + +# Transform confdefs.h into DEFS. +# Protect against shell expansion while executing Makefile rules. +# Protect against Makefile macro expansion. +# +# If the first sed substitution is executed (which looks for macros that +# take arguments), then we branch to the quote section. Otherwise, +# look for a macro that doesn't take arguments. +cat >confdef2opt.sed <<\_ACEOF +t clear +: clear +s,^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\),-D\1=\2,g +t quote +s,^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\),-D\1=\2,g +t quote +d +: quote +s,[ `~#$^&*(){}\\|;'"<>?],\\&,g +s,\[,\\&,g +s,\],\\&,g +s,\$,$$,g +p +_ACEOF +# We use echo to avoid assuming a particular line-breaking character. +# The extra dot is to prevent the shell from consuming trailing +# line-breaks from the sub-command output. A line-break within +# single-quotes doesn't work because, if this script is created in a +# platform that uses two characters for line-breaks (e.g., DOS), tr +# would break. +ac_LF_and_DOT=`echo; echo .` +DEFS=`sed -n -f confdef2opt.sed confdefs.h | tr "$ac_LF_and_DOT" ' .'` +rm -f confdef2opt.sed + + +ac_libobjs= +ac_ltlibobjs= +for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue + # 1. Remove the extension, and $U if already installed. + ac_i=`echo "$ac_i" | + sed 's/\$U\././;s/\.o$//;s/\.obj$//'` + # 2. Add them. + ac_libobjs="$ac_libobjs $ac_i\$U.$ac_objext" + ac_ltlibobjs="$ac_ltlibobjs $ac_i"'$U.lo' +done +LIBOBJS=$ac_libobjs + +LTLIBOBJS=$ac_ltlibobjs + + + +: ${CONFIG_STATUS=./config.status} +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files $CONFIG_STATUS" +{ echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5 +echo "$as_me: creating $CONFIG_STATUS" >&6;} +cat >$CONFIG_STATUS <<_ACEOF +#! $SHELL +# Generated by $as_me. +# Run this file to recreate the current configuration. +# Compiler output produced by configure, useful for debugging +# configure, is in config.log if it exists. + +debug=false +ac_cs_recheck=false +ac_cs_silent=false +SHELL=\${CONFIG_SHELL-$SHELL} +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## + +# Be Bourne compatible +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # is contrary to our usage. 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Look in the path if we contain no path at all + # relative or not. + case $0 in + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done + + ;; + esac + # We did not find ourselves, most probably we were run as `sh COMMAND' + # in which case we are not to be found in the path. + if test "x$as_myself" = x; then + as_myself=$0 + fi + if test ! -f "$as_myself"; then + { { echo "$as_me:$LINENO: error: cannot find myself; rerun with an absolute path" >&5 +echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2;} + { (exit 1); exit 1; }; } + fi + case $CONFIG_SHELL in + '') + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for as_base in sh bash ksh sh5; do + case $as_dir in + /*) + if ("$as_dir/$as_base" -c ' + as_lineno_1=$LINENO + as_lineno_2=$LINENO + as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then + $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } + $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } + CONFIG_SHELL=$as_dir/$as_base + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$0" ${1+"$@"} + fi;; + esac + done +done +;; + esac + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line before each line; the second 'sed' does the real + # work. The second script uses 'N' to pair each line-number line + # with the numbered line, and appends trailing '-' during + # substitution so that $LINENO is not a special case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # second 'sed' script. Blame Lee E. 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Invocation command line was + + CONFIG_FILES = $CONFIG_FILES + CONFIG_HEADERS = $CONFIG_HEADERS + CONFIG_LINKS = $CONFIG_LINKS + CONFIG_COMMANDS = $CONFIG_COMMANDS + $ $0 $@ + +_CSEOF +echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 +echo >&5 +_ACEOF + +# Files that config.status was made for. +if test -n "$ac_config_files"; then + echo "config_files=\"$ac_config_files\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_headers"; then + echo "config_headers=\"$ac_config_headers\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_links"; then + echo "config_links=\"$ac_config_links\"" >>$CONFIG_STATUS +fi + +if test -n "$ac_config_commands"; then + echo "config_commands=\"$ac_config_commands\"" >>$CONFIG_STATUS +fi + +cat >>$CONFIG_STATUS <<\_ACEOF + +ac_cs_usage="\ +\`$as_me' instantiates files from templates according to the +current configuration. + +Usage: $0 [OPTIONS] [FILE]... + + -h, --help print this help, then exit + -V, --version print version number, then exit + -q, --quiet do not print progress messages + -d, --debug don't remove temporary files + --recheck update $as_me by reconfiguring in the same conditions + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + +Configuration files: +$config_files + +Report bugs to ." +_ACEOF + +cat >>$CONFIG_STATUS <<_ACEOF +ac_cs_version="\\ +config.status +configured by $0, generated by GNU Autoconf 2.59, + with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\" + +Copyright (C) 2003 Free Software Foundation, Inc. +This config.status script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it." +srcdir=$srcdir +INSTALL="$INSTALL" +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF +# If no file are specified by the user, then we need to provide default +# value. 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Make it in the build tree +# simply because there is no reason to put it here, and in addition, +# creating and moving files from /tmp can sometimes cause problems. +# Create a temporary directory, and hook for its removal unless debugging. +$debug || +{ + trap 'exit_status=$?; rm -rf $tmp && exit $exit_status' 0 + trap '{ (exit 1); exit 1; }' 1 2 13 15 +} + +# Create a (secure) tmp directory for tmp files. + +{ + tmp=`(umask 077 && mktemp -d -q "./confstatXXXXXX") 2>/dev/null` && + test -n "$tmp" && test -d "$tmp" +} || +{ + tmp=./confstat$$-$RANDOM + (umask 077 && mkdir $tmp) +} || +{ + echo "$me: cannot create a temporary directory in ." >&2 + { (exit 1); exit 1; } +} + +_ACEOF + +cat >>$CONFIG_STATUS <<_ACEOF + +# +# CONFIG_FILES section. +# + +# No need to generate the scripts if there are no CONFIG_FILES. +# This happens for instance when ./config.status config.h +if test -n "\$CONFIG_FILES"; then + # Protect against being on the right side of a sed subst in config.status. + sed 's/,@/@@/; s/@,/@@/; s/,;t t\$/@;t t/; /@;t t\$/s/[\\\\&,]/\\\\&/g; + s/@@/,@/; s/@@/@,/; s/@;t t\$/,;t t/' >\$tmp/subs.sed <<\\CEOF +s,@SHELL@,$SHELL,;t t +s,@PATH_SEPARATOR@,$PATH_SEPARATOR,;t t +s,@PACKAGE_NAME@,$PACKAGE_NAME,;t t +s,@PACKAGE_TARNAME@,$PACKAGE_TARNAME,;t t +s,@PACKAGE_VERSION@,$PACKAGE_VERSION,;t t +s,@PACKAGE_STRING@,$PACKAGE_STRING,;t t +s,@PACKAGE_BUGREPORT@,$PACKAGE_BUGREPORT,;t t +s,@exec_prefix@,$exec_prefix,;t t +s,@prefix@,$prefix,;t t +s,@program_transform_name@,$program_transform_name,;t t +s,@bindir@,$bindir,;t t +s,@sbindir@,$sbindir,;t t +s,@libexecdir@,$libexecdir,;t t +s,@datadir@,$datadir,;t t +s,@sysconfdir@,$sysconfdir,;t t +s,@sharedstatedir@,$sharedstatedir,;t t +s,@localstatedir@,$localstatedir,;t t +s,@libdir@,$libdir,;t t +s,@includedir@,$includedir,;t t +s,@oldincludedir@,$oldincludedir,;t t +s,@infodir@,$infodir,;t t +s,@mandir@,$mandir,;t t +s,@build_alias@,$build_alias,;t t +s,@host_alias@,$host_alias,;t t +s,@target_alias@,$target_alias,;t t +s,@DEFS@,$DEFS,;t t +s,@ECHO_C@,$ECHO_C,;t t +s,@ECHO_N@,$ECHO_N,;t t +s,@ECHO_T@,$ECHO_T,;t t +s,@LIBS@,$LIBS,;t t +s,@build@,$build,;t t +s,@build_cpu@,$build_cpu,;t t +s,@build_vendor@,$build_vendor,;t t +s,@build_os@,$build_os,;t t +s,@host@,$host,;t t +s,@host_cpu@,$host_cpu,;t t +s,@host_vendor@,$host_vendor,;t t +s,@host_os@,$host_os,;t t +s,@LD_SHARED@,$LD_SHARED,;t t +s,@LD_SHARED_FLAGS@,$LD_SHARED_FLAGS,;t t +s,@LD_SHARED_OPT@,$LD_SHARED_OPT,;t t +s,@LD_SHARED_EXT@,$LD_SHARED_EXT,;t t +s,@CC@,$CC,;t t +s,@CFLAGS@,$CFLAGS,;t t +s,@LDFLAGS@,$LDFLAGS,;t t +s,@CPPFLAGS@,$CPPFLAGS,;t t +s,@ac_ct_CC@,$ac_ct_CC,;t t +s,@EXEEXT@,$EXEEXT,;t t +s,@OBJEXT@,$OBJEXT,;t t +s,@CPP@,$CPP,;t t +s,@CXX@,$CXX,;t t +s,@CXXFLAGS@,$CXXFLAGS,;t t +s,@ac_ct_CXX@,$ac_ct_CXX,;t t +s,@RANLIB@,$RANLIB,;t t +s,@ac_ct_RANLIB@,$ac_ct_RANLIB,;t t +s,@INSTALL_PROGRAM@,$INSTALL_PROGRAM,;t t +s,@INSTALL_SCRIPT@,$INSTALL_SCRIPT,;t t +s,@INSTALL_DATA@,$INSTALL_DATA,;t t +s,@FIND@,$FIND,;t t +s,@MAKEDEPEND@,$MAKEDEPEND,;t t +s,@X_CFLAGS@,$X_CFLAGS,;t t +s,@X_PRE_LIBS@,$X_PRE_LIBS,;t t +s,@X_LIBS@,$X_LIBS,;t t +s,@X_EXTRA_LIBS@,$X_EXTRA_LIBS,;t t +s,@DO_PS@,$DO_PS,;t t +s,@DO_FIG@,$DO_FIG,;t t +s,@DO_X11@,$DO_X11,;t t +s,@DO_WIN32@,$DO_WIN32,;t t +s,@DO_GD@,$DO_GD,;t t +s,@EGREP@,$EGREP,;t t +s,@LIBOBJS@,$LIBOBJS,;t t +s,@LTLIBOBJS@,$LTLIBOBJS,;t t +CEOF + +_ACEOF + + cat >>$CONFIG_STATUS <<\_ACEOF + # Split the substitutions into bite-sized pieces for seds with + # small command number limits, like on Digital OSF/1 and HP-UX. + ac_max_sed_lines=48 + ac_sed_frag=1 # Number of current file. + ac_beg=1 # First line for current file. + ac_end=$ac_max_sed_lines # Line after last line for current file. + ac_more_lines=: + ac_sed_cmds= + while $ac_more_lines; do + if test $ac_beg -gt 1; then + sed "1,${ac_beg}d; ${ac_end}q" $tmp/subs.sed >$tmp/subs.frag + else + sed "${ac_end}q" $tmp/subs.sed >$tmp/subs.frag + fi + if test ! -s $tmp/subs.frag; then + ac_more_lines=false + else + # The purpose of the label and of the branching condition is to + # speed up the sed processing (if there are no `@' at all, there + # is no need to browse any of the substitutions). + # These are the two extra sed commands mentioned above. + (echo ':t + /@[a-zA-Z_][a-zA-Z_0-9]*@/!b' && cat $tmp/subs.frag) >$tmp/subs-$ac_sed_frag.sed + if test -z "$ac_sed_cmds"; then + ac_sed_cmds="sed -f $tmp/subs-$ac_sed_frag.sed" + else + ac_sed_cmds="$ac_sed_cmds | sed -f $tmp/subs-$ac_sed_frag.sed" + fi + ac_sed_frag=`expr $ac_sed_frag + 1` + ac_beg=$ac_end + ac_end=`expr $ac_end + $ac_max_sed_lines` + fi + done + if test -z "$ac_sed_cmds"; then + ac_sed_cmds=cat + fi +fi # test -n "$CONFIG_FILES" + +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF +for ac_file in : $CONFIG_FILES; do test "x$ac_file" = x: && continue + # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in". + case $ac_file in + - | *:- | *:-:* ) # input from stdin + cat >$tmp/stdin + ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;; + *:* ) ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;; + * ) ac_file_in=$ac_file.in ;; + esac + + # Compute @srcdir@, @top_srcdir@, and @INSTALL@ for subdirectories. + ac_dir=`(dirname "$ac_file") 2>/dev/null || +$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$ac_file" : 'X\(//\)[^/]' \| \ + X"$ac_file" : 'X\(//\)$' \| \ + X"$ac_file" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$ac_file" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + { if $as_mkdir_p; then + mkdir -p "$ac_dir" + else + as_dir="$ac_dir" + as_dirs= + while test ! -d "$as_dir"; do + as_dirs="$as_dir $as_dirs" + as_dir=`(dirname "$as_dir") 2>/dev/null || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + done + test ! -n "$as_dirs" || mkdir $as_dirs + fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5 +echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;} + { (exit 1); exit 1; }; }; } + + ac_builddir=. + +if test "$ac_dir" != .; then + ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'` + # A "../" for each directory in $ac_dir_suffix. + ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'` +else + ac_dir_suffix= ac_top_builddir= +fi + +case $srcdir in + .) # No --srcdir option. We are building in place. + ac_srcdir=. + if test -z "$ac_top_builddir"; then + ac_top_srcdir=. + else + ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` + fi ;; + [\\/]* | ?:[\\/]* ) # Absolute path. + ac_srcdir=$srcdir$ac_dir_suffix; + ac_top_srcdir=$srcdir ;; + *) # Relative path. + ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix + ac_top_srcdir=$ac_top_builddir$srcdir ;; +esac + +# Do not use `cd foo && pwd` to compute absolute paths, because +# the directories may not exist. +case `pwd` in +.) ac_abs_builddir="$ac_dir";; +*) + case "$ac_dir" in + .) ac_abs_builddir=`pwd`;; + [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";; + *) ac_abs_builddir=`pwd`/"$ac_dir";; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_top_builddir=${ac_top_builddir}.;; +*) + case ${ac_top_builddir}. in + .) ac_abs_top_builddir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;; + *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_srcdir=$ac_srcdir;; +*) + case $ac_srcdir in + .) ac_abs_srcdir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;; + *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;; + esac;; +esac +case $ac_abs_builddir in +.) ac_abs_top_srcdir=$ac_top_srcdir;; +*) + case $ac_top_srcdir in + .) ac_abs_top_srcdir=$ac_abs_builddir;; + [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;; + *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;; + esac;; +esac + + + case $INSTALL in + [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;; + *) ac_INSTALL=$ac_top_builddir$INSTALL ;; + esac + + if test x"$ac_file" != x-; then + { echo "$as_me:$LINENO: creating $ac_file" >&5 +echo "$as_me: creating $ac_file" >&6;} + rm -f "$ac_file" + fi + # Let's still pretend it is `configure' which instantiates (i.e., don't + # use $as_me), people would be surprised to read: + # /* config.h. Generated by config.status. */ + if test x"$ac_file" = x-; then + configure_input= + else + configure_input="$ac_file. " + fi + configure_input=$configure_input"Generated from `echo $ac_file_in | + sed 's,.*/,,'` by configure." + + # First look for the input files in the build tree, otherwise in the + # src tree. + ac_file_inputs=`IFS=: + for f in $ac_file_in; do + case $f in + -) echo $tmp/stdin ;; + [\\/$]*) + # Absolute (can't be DOS-style, as IFS=:) + test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + echo "$f";; + *) # Relative + if test -f "$f"; then + # Build tree + echo "$f" + elif test -f "$srcdir/$f"; then + # Source tree + echo "$srcdir/$f" + else + # /dev/null tree + { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + fi;; + esac + done` || { (exit 1); exit 1; } +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF + sed "$ac_vpsub +$extrasub +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF +:t +/@[a-zA-Z_][a-zA-Z_0-9]*@/!b +s,@configure_input@,$configure_input,;t t +s,@srcdir@,$ac_srcdir,;t t +s,@abs_srcdir@,$ac_abs_srcdir,;t t +s,@top_srcdir@,$ac_top_srcdir,;t t +s,@abs_top_srcdir@,$ac_abs_top_srcdir,;t t +s,@builddir@,$ac_builddir,;t t +s,@abs_builddir@,$ac_abs_builddir,;t t +s,@top_builddir@,$ac_top_builddir,;t t +s,@abs_top_builddir@,$ac_abs_top_builddir,;t t +s,@INSTALL@,$ac_INSTALL,;t t +" $ac_file_inputs | (eval "$ac_sed_cmds") >$tmp/out + rm -f $tmp/stdin + if test x"$ac_file" != x-; then + mv $tmp/out $ac_file + else + cat $tmp/out + rm -f $tmp/out + fi + +done +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF + +{ (exit 0); exit 0; } +_ACEOF +chmod +x $CONFIG_STATUS +ac_clean_files=$ac_clean_files_save + + +# configure is writing to config.log, and then calls config.status. +# config.status does its own redirection, appending to config.log. +# Unfortunately, on DOS this fails, as config.log is still kept open +# by configure, so config.status won't be able to write to it; its +# output is simply discarded. So we exec the FD to /dev/null, +# effectively closing config.log, so it can be properly (re)opened and +# appended to by config.status. When coming back to configure, we +# need to make the FD available again. +if test "$no_create" != yes; then + ac_cs_success=: + ac_config_status_args= + test "$silent" = yes && + ac_config_status_args="$ac_config_status_args --quiet" + exec 5>/dev/null + $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false + exec 5>>config.log + # Use ||, not &&, to avoid exiting from the if with $? = 1, which + # would make configure fail if this is the last instruction. + $ac_cs_success || { (exit 1); exit 1; } +fi + + +echo +echo "Supported devices:" +if test "$DO_PS" != "#"; then echo " PostScript"; fi +if test "$DO_FIG" != "#"; then echo " FIG"; fi +if test "$DO_X11" != "#"; then echo " X11"; fi +if test "$DO_WIN32" != "#"; then echo " Win32"; fi +if test "$DO_GD" != "#"; then echo " GD"; fi + +echo +echo "Unsupported devices:" +if test "$DO_PS" = "#"; then echo " PostScript"; fi +if test "$DO_FIG" = "#"; then echo " FIG"; fi +if test "$DO_X11" = "#"; then echo " X11"; fi +if test "$DO_WIN32" = "#"; then echo " Win32"; fi +if test "$DO_GD" = "#"; then echo " GD"; fi + +echo +echo "Run 'make depend' to create dependencies." +echo diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/configure.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/configure.in new file mode 100755 index 000000000..f750225bb --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/configure.in @@ -0,0 +1,139 @@ + +# +# Check for one project file +# +AC_INIT(src/g2_device.c) + +PRODUCT=g2 + + +# +# check cannonical system name, +# and set options for shared libraries (black magic) +# +AC_CANONICAL_HOST +case "$host" in + *-linux*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-shared -soname libg2.so.0' + LD_SHARED_OPT='' + LD_SHARED_EXT='so.0.$(G2_VERSION)' + AC_DEFINE(LINUX);; + *-aix*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-bM:SRE -bnoentry -bexpall' + LD_SHARED_OPT='$(LDFLAGS) -lc' + LD_SHARED_EXT='so' + AC_DEFINE(AIX);; + *-osf*) + LD_SHARED='ld' + LD_SHARED_FLAGS='-shared' + LD_SHARED_OPT='$(LDFLAGS) -lc' + LD_SHARED_EXT='so' + AC_DEFINE(OSF);; + *) + LD_SHARED_EXT='so' + AC_DEFINE(UNIX);; +esac + +AC_SUBST(LD_SHARED) +AC_SUBST(LD_SHARED_FLAGS) +AC_SUBST(LD_SHARED_OPT) +AC_SUBST(LD_SHARED_EXT) + +# +# check C compiler, preprocesor, etc. +# +AC_PROG_CC +AC_PROG_CPP +AC_PROG_CXX +AC_PROG_RANLIB +AC_PROG_INSTALL +AC_CHECK_PROG(FIND, find, find, :) +AC_CHECK_PROG(MAKEDEPEND, makedepend, makedepend, :) +AC_CHECK_LIB(dl, dlopen, have_dl=yes, have_dl=no) + + +# +# Try to locate the X Window System include files and libraries +# and add /usr/local to include and lib path and add -lm (for testing) +# +AC_PATH_XTRA +CFLAGS="$CFLAGS $X_CFLAGS -I/usr/local/include" +LDFLAGS="$LDFLAGS $X_LIBS -L/usr/local/lib" + + +DO_PS='#' +DO_FIG='#' +DO_X11='#' +DO_GD='#' +DO_WIN32='#' + + +# +# check supported devices +# +AC_CHECK_LIB(m,main,DO_PS='';DO_FIG='';LDFLAGS="$LDFLAGS -lm";AC_DEFINE(DO_PS) AC_DEFINE(DO_FIG),break) +AC_CHECK_LIB(X11, main, DO_X11='';LDFLAGS="$LDFLAGS -lX11";AC_DEFINE(DO_X11)) +AC_CHECK_LIB(gd, main, have_gd=yes, have_gd=no) +if test "$have_gd" = yes +then + LDFLAGS="$LDFLAGS -lgd" + AC_CHECK_FUNC(gdImagePng, DO_GD='';AC_DEFINE(DO_GD)) +fi + +# +# handling cygwin environment (and gd for cygwin == bgd) +# +AC_CYGWIN +if test "$CYGWIN" = yes +then + LDFLAGS="$LDFLAGS -L/lib/w32api" + AC_CHECK_LIB(gdi32, main, DO_WIN32='';LDFLAGS="$LDFLAGS -lgdi32";AC_DEFINE(DO_WIN32)) + AC_CHECK_LIB(bgd, main, have_bgd=yes, have_bgd=no) + if test "$have_bgd" = yes + then + LDFLAGS="$LDFLAGS -lbgd" + AC_CHECK_FUNC(gdImagePng, DO_GD='';AC_DEFINE(DO_GD)) + fi +fi + +# +# Declare variables which we want substituted in the Makefile.in's +# +AC_SUBST(DO_PS) +AC_SUBST(DO_FIG) +AC_SUBST(DO_X11) +AC_SUBST(DO_WIN32) +AC_SUBST(DO_GD) + +AC_HEADER_STDC +AC_CHECK_HEADERS(limits.h) + + + +# +# finally create makefiles using Makefile.in +# +echo +AC_OUTPUT(Makefile demo/Makefile g2_perl/Makefile.PL) + +echo +echo "Supported devices:" +if test "$DO_PS" != "#"; then echo " PostScript"; fi +if test "$DO_FIG" != "#"; then echo " FIG"; fi +if test "$DO_X11" != "#"; then echo " X11"; fi +if test "$DO_WIN32" != "#"; then echo " Win32"; fi +if test "$DO_GD" != "#"; then echo " GD"; fi + +echo +echo "Unsupported devices:" +if test "$DO_PS" = "#"; then echo " PostScript"; fi +if test "$DO_FIG" = "#"; then echo " FIG"; fi +if test "$DO_X11" = "#"; then echo " X11"; fi +if test "$DO_WIN32" = "#"; then echo " Win32"; fi +if test "$DO_GD" = "#"; then echo " GD"; fi + +echo +echo "Run 'make depend' to create dependencies." +echo diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Repository new file mode 100755 index 000000000..c5ef7f818 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/demo/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Entries new file mode 100755 index 000000000..b75535d9a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Entries @@ -0,0 +1,21 @@ +D/CVS//// +/Makefile.in/1.1/Tue Jun 14 20:44:20 2005// +/demo_cpp.cpp/1.1/Tue Apr 20 20:18:09 2004// +/demo_f.f/1.1/Tue Apr 17 20:16:38 2001// +/descrip.mms/1.1/Thu Nov 22 00:15:59 2001// +/g2_anim.c/1.1/Fri Apr 16 01:20:04 2004// +/g2_arc.c/1.1/Tue Feb 22 22:16:18 2005// +/g2_splines_demo.c/1.1/Sun Feb 29 23:47:46 2004// +/g2_test.c/1.1/Sat Apr 3 22:57:15 2004// +/g2_test.f/1.1/Thu Mar 4 23:13:36 2004// +/handles.c/1.1/Tue Jun 14 20:44:20 2005// +/penguin.c/1.1/Mon Jan 18 10:56:51 1999// +/penguin.inc/1.1/Thu Mar 4 23:13:36 2004// +/pointer.c/1.1/Tue Apr 17 20:16:38 2001// +/simple_FIG.c/1.1/Thu Apr 1 22:29:34 2004// +/simple_PS.c/1.1/Tue Apr 17 20:16:38 2001// +/simple_X11.c/1.1/Tue Apr 17 20:16:38 2001// +/simple_gd.c/1.1/Tue Apr 17 20:16:38 2001// +/simple_win32.c/1.1/Tue Sep 3 04:10:23 2002// +/xlink.opt/1.1/Mon Jan 18 10:56:51 1999// +/Makefile/1.1/Fri Aug 5 10:17:46 2005// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Repository new file mode 100755 index 000000000..6762ec27d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/demo diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/Makefile new file mode 100755 index 000000000..334e4c8eb --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/Makefile @@ -0,0 +1,87 @@ +# +# +# Makefile for g2_library (demo) +# +# + + +CC = gcc +CXX = g++ +##Linux +F77 = g77 +CPP = /lib/cpp + +##OSF +#F77 = f77 +#F77_FLAGS=-i8 + +##AIX +#F77 = xlf +#CPP = /usr/ccs/lib/cpp + +##IRIX +#F77 = f77 -n32 +#CPP = /lib/cpp -P -DFORTRAN + +CFLAGS = -I../src -I../src/X11 -I../src/PS -I../src/Win32 -I../src/GD -I../src/FIG -g -O2 -I/usr/X11R6/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_GD=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 +CXXFLAGS = -I../src -I../src/X11 -I../src/PS -I../src/Win32 -I../src/GD/ -I../src/FIG -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_GD=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 +LDFLAGS = -L.. -lg2 -L/usr/X11R6/lib64 -L/usr/local/lib -lm -lX11 -lgd + +DEMO_PS = simple_PS +DEMO_FIG = simple_FIG +DEMO_X11 = simple_X11 pointer handles +DEMO_GD = simple_gd +#DEMO_WIN32 = simple_win32 + + +DEMO = g2_test g2_arc g2_splines_demo demo_cpp $(DEMO_PS) $(DEMO_FIG) $(DEMO_X11) $(DEMO_GD) $(DEMO_WIN32) + +all: $(DEMO) + +demo: $(DEMO) + + +g2_test: g2_test.c + $(CC) $(CFLAGS) g2_test.c $(LDFLAGS) -o $@ + +g2_arc: g2_arc.c + $(CC) $(CFLAGS) g2_arc.c $(LDFLAGS) -o $@ + +g2_splines_demo: g2_splines_demo.c + $(CC) $(CFLAGS) g2_splines_demo.c $(LDFLAGS) -o $@ + +simple_PS: simple_PS.c + $(CC) $(CFLAGS) simple_PS.c $(LDFLAGS) -o $@ + +simple_FIG: simple_FIG.c + $(CC) $(CFLAGS) simple_FIG.c $(LDFLAGS) -o $@ + +simple_X11: simple_X11.c + $(CC) $(CFLAGS) simple_X11.c $(LDFLAGS) -o $@ + +simple_win32: simple_win32.c + $(CC) $(CFLAGS) simple_win32.c $(LDFLAGS) -lkernel32 -lgdi32 -luser32 -lcomdlg32 -o $@ + +pointer: pointer.c + $(CC) $(CFLAGS) pointer.c $(LDFLAGS) -o $@ + +handles: handles.c + $(CC) $(CFLAGS) handles.c $(LDFLAGS) -o $@ + +simple_gd: simple_gd.c + $(CC) $(CFLAGS) simple_gd.c $(LDFLAGS) -o $@ + +demo_cpp: demo_cpp.cpp + $(CXX) $(CXXFLAGS) demo_cpp.cpp $(LDFLAGS) -o $@ + +demo_f: demo_f.f + $(F77) $(F77_FLAGS) demo_f.f $(LDFLAGS) -o $@ + +g2testf: g2_test.f + $(CPP) -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_GD=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -E g2_test.f > g2testf.f + $(F77) g2testf.f $(LDFLAGS) -o g2testf + +clean: + -rm $(DEMO) g2testf g2testf.f demo_f *~ core *.ps *.fig *.eps *.png *.jpg *.fig.bak + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/Makefile.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/Makefile.in new file mode 100755 index 000000000..8a57d8d37 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/Makefile.in @@ -0,0 +1,87 @@ +# +# +# Makefile for g2_library (demo) +# +# + + +CC = @CC@ +CXX = @CXX@ +##Linux +F77 = g77 +CPP = /lib/cpp + +##OSF +#F77 = f77 +#F77_FLAGS=-i8 + +##AIX +#F77 = xlf +#CPP = /usr/ccs/lib/cpp + +##IRIX +#F77 = f77 -n32 +#CPP = /lib/cpp -P -DFORTRAN + +CFLAGS = -I../src -I../src/X11 -I../src/PS -I../src/Win32 -I../src/GD -I../src/FIG @CFLAGS@ @DEFS@ +CXXFLAGS = -I../src -I../src/X11 -I../src/PS -I../src/Win32 -I../src/GD/ -I../src/FIG @CXXFLAGS@ @DEFS@ +LDFLAGS = -L.. -lg2 @LDFLAGS@ + +@DO_PS@DEMO_PS = simple_PS +@DO_FIG@DEMO_FIG = simple_FIG +@DO_X11@DEMO_X11 = simple_X11 pointer handles +@DO_GD@DEMO_GD = simple_gd +@DO_WIN32@DEMO_WIN32 = simple_win32 + + +DEMO = g2_test g2_arc g2_splines_demo demo_cpp $(DEMO_PS) $(DEMO_FIG) $(DEMO_X11) $(DEMO_GD) $(DEMO_WIN32) + +all: $(DEMO) + +demo: $(DEMO) + + +g2_test: g2_test.c + $(CC) $(CFLAGS) g2_test.c $(LDFLAGS) -o $@ + +g2_arc: g2_arc.c + $(CC) $(CFLAGS) g2_arc.c $(LDFLAGS) -o $@ + +g2_splines_demo: g2_splines_demo.c + $(CC) $(CFLAGS) g2_splines_demo.c $(LDFLAGS) -o $@ + +simple_PS: simple_PS.c + $(CC) $(CFLAGS) simple_PS.c $(LDFLAGS) -o $@ + +simple_FIG: simple_FIG.c + $(CC) $(CFLAGS) simple_FIG.c $(LDFLAGS) -o $@ + +simple_X11: simple_X11.c + $(CC) $(CFLAGS) simple_X11.c $(LDFLAGS) -o $@ + +simple_win32: simple_win32.c + $(CC) $(CFLAGS) simple_win32.c $(LDFLAGS) -lkernel32 -lgdi32 -luser32 -lcomdlg32 -o $@ + +pointer: pointer.c + $(CC) $(CFLAGS) pointer.c $(LDFLAGS) -o $@ + +handles: handles.c + $(CC) $(CFLAGS) handles.c $(LDFLAGS) -o $@ + +simple_gd: simple_gd.c + $(CC) $(CFLAGS) simple_gd.c $(LDFLAGS) -o $@ + +demo_cpp: demo_cpp.cpp + $(CXX) $(CXXFLAGS) demo_cpp.cpp $(LDFLAGS) -o $@ + +demo_f: demo_f.f + $(F77) $(F77_FLAGS) demo_f.f $(LDFLAGS) -o $@ + +g2testf: g2_test.f + $(CPP) @DEFS@ -E g2_test.f > g2testf.f + $(F77) g2testf.f $(LDFLAGS) -o g2testf + +clean: + -rm $(DEMO) g2testf g2testf.f demo_f *~ core *.ps *.fig *.eps *.png *.jpg *.fig.bak + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/demo_cpp.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/demo_cpp.cpp new file mode 100755 index 000000000..c78480a4e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/demo_cpp.cpp @@ -0,0 +1,40 @@ +#include +#include +#include +#include + +/* A very simple example to demonstrate g2 in a C++ environment */ + + +class Circle +{ +public: + Circle(int d, double x, double y, double r) + : _d(d), _x(x), _y(y), _r(r) + { + g2_circle(d, x, y, r); + g2_flush(d); + } + + void Fill() + { + g2_filled_circle(_d, _x, _y, _r); + g2_flush(_d); + } +private: + int _d; + double _x, _y, _r; +}; + + +int main(int argc, char *argv[]) +{ + int d; + d=g2_open_PS("demo_cpp.ps", g2_A4, g2_PS_port); + Circle c(d, 150, 150, 25); + c.Fill(); + Circle c2(d, 150, 175, 25); + g2_close(d); + std::cout << "demo_cpp.ps generated\n"; + return 0; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/demo_f.f b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/demo_f.f new file mode 100755 index 000000000..599826b0f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/demo_f.f @@ -0,0 +1,59 @@ +c +c Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +c This file is part of the g2 library +c +c This library is free software; you can redistribute it and/or +c modify it under the terms of the GNU Lesser General Public +c License as published by the Free Software Foundation; either +c version 2.1 of the License, or (at your option) any later version. +c +c This library is distributed in the hope that it will be useful, +c but WITHOUT ANY WARRANTY; without even the implied warranty of +c MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +c Lesser General Public License for more details. +c +c You should have received a copy of the GNU Lesser General Public +c License along with this library; if not, write to the Free Software +c Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +c + real demo_f + real a, b + real d, d1, d2 + real color + + d=g2_open_vd() + write (6,*) d + d1=g2_open_X11(100.0, 100.0) + write (6,*) d1 + d2=g2_open_PS('demo_f.ps', 4.0, 1.0) + write (6,*) d2 + + call g2_attach(d, d1) + call g2_attach(d, d2) + + call g2_plot(d, 50.0, 50.0) + call g2_arc(d, 50.0, 50.0, 30.0, 20.0, 45.0, 180.0) + + color=g2_ink(d1, 1.0, 0.0, 0.0) + call g2_pen(d1, color) + write (6,*) color + call g2_string(d1, 15.0, 75.0, 'TEST (Window)') + + color=g2_ink(d2, 0.0, 1.0, 0.0) + call g2_pen(d2, color) + write (6,*) color + call g2_string(d2, 15.0, 75.0, 'TEST (File)') + + call g2_pen(d, 1.0) + call g2_circle(d, 20.0, 20.0, 10.0) + call g2_string(d, 20.0, 20.0, 'All devices!') + call g2_flush(d) + + call g2_close(d2) + + read (*,*) a + + stop + end + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/descrip.mms b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/descrip.mms new file mode 100755 index 000000000..d89ac9b08 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/descrip.mms @@ -0,0 +1,57 @@ +! +! VMS descrip.mms for g2 demos +! + +! +! Change these pointers to the correct location of libGD,libpng, etc +! +GD_LIBS = [.-.-.-.GD-1_8_4]libgd.olb/lib,[.-.-.-.lpng120]libpng.olb/lib,[.-.-.-.ZLIB]libz.olb/lib,[.-.-.-.JPEG-6B]libjpeg.olb/lib + +.IFDEF debug +CC_FLAGS = /noopt/debug/nolist/warnings \ + /include_directory=([-.src],[-.src.X11],[-.src.PS],[-.src.GD]) \ + /define=(DO_PS, DO_X11, DO_GD) +LINK_FLAGS = +.ELSE +CC_FLAGS = /nolist/warnings \ + /include_directory=([-.src],[-.src.X11],[-.src.PS],[-.src.GD]) \ + /define=(DO_PS, DO_X11, DO_GD) +LINK_FLAGS = +.ENDIF + +! +! Rules +! +.c.obj : ; cc $(CC_FLAGS)/obj=$(mms$target) $(mms$source) + + +! +! exe files +! +all : g2_test.exe, simple_X11.exe, simple_PS.exe + @ write sys$output "Demo files compiled." + + +g2_test.exe : g2_test.obj + link $(LINK_FLAGS)/exe=g2_test.exe g2_test.obj, \ + [-]g2.olb/lib, []xlink.opt/opt, $(GD_LIBS) + +simple_X11.exe : simple_X11.obj + link $(LINK_FLAGS)/exe=simple_X11.exe simple_X11.obj, \ + [-]g2.olb/lib, []xlink.opt/opt + +simple_PS.exe : simple_PS.obj + link $(LINK_FLAGS)/exe=simple_PS.exe simple_PS.obj, [-]g2.olb/lib + + + +clean : + delete *.exe;* , *.obj;* , *.olb;* + + +! +! Dependencies +! +g2_test.obj : g2_test.c +simple_X11.obj : simple_X11.c +simple_PS.obj : simple_PS.c diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_anim.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_anim.c new file mode 100755 index 000000000..5116f119d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_anim.c @@ -0,0 +1,60 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include + + +#define N 300 +#define W 400 +#define H 400 + +int main() +{ + int d; + int x[N]; + int y[N]; + int c[N]; + int i,t; + + d=g2_open_win32(W, H, "simple_animation", 0); + g2_set_auto_flush(d,0); + + for (i=0;i +#include + +#ifdef DO_PS +#include +#endif +#ifdef DO_FIG +#include +#endif +#ifdef DO_X11 +#include +#endif +#ifdef DO_GD +#include +#endif +#ifdef DO_WIN32 +#include +#endif +#ifdef DO_WMF32 +#include +#endif + +#define maxdev 10 + +int main() +{ + int i, j; + int d, dev[maxdev]={-1, -1, -1, -1, -1,-1, -1, -1, -1, -1}; + int ndev=0; + char str[256]; + double y; + + printf("\nG2_VERSION %s\n", G2_VERSION); + + d=g2_open_vd(); /* open virtual device */ + + printf("Adding.."); + +#ifdef DO_PS + printf("..PS"); + dev[ndev]=g2_open_PS("g2_arc.ps", g2_A4, g2_PS_land); + g2_attach(d, dev[ndev]); + ndev++; + + printf("..EPSF"); + dev[ndev]=g2_open_EPSF("g2_arc.eps"); + g2_attach(d, dev[ndev]); + ndev++; + printf("..EPSF_CLIP"); + dev[ndev]=g2_open_EPSF_CLIP("g2_arc_clip.eps",400,400); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_FIG + printf("..FIG"); + dev[ndev]=g2_open_FIG("g2_arc.fig"); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_X11 + printf("..X11"); + dev[ndev]=g2_open_X11(400,400); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_GD + printf("..GD(png)"); + dev[ndev]=g2_open_gd("g2_arc.png", 400, 400,g2_gd_png); + g2_attach(d, dev[ndev]); + ndev++; + printf("..GD(jpeg)"); + dev[ndev]=g2_open_gd("g2_arc.jpg", 400, 400,g2_gd_jpeg); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_WIN32 + printf("..WIN32"); + dev[ndev]=g2_open_win32(400, 400,"g2_arc",0); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_WMF32 + printf("..WMF32"); + dev[ndev]=g2_open_win32(775, 575,"g2_arc.emf",1); + g2_attach(d, dev[ndev]); + ndev++; +#endif + g2_set_auto_flush(d,0); + + printf("\n"); + + g2_string(d,10, 50,"90,90"); + g2_string(d,10,100,"90,360"); + g2_string(d,10,150,"90,0"); + g2_string(d,10,200,"360,90"); + g2_string(d,10,250,"-45,45"); + g2_string(d,10,300,"-45,-315"); + g2_string(d,10,350,"-495,-405"); + + g2_arc(d, 100, 50, 45, 25, 90, 90); + g2_arc(d, 100, 100, 45, 25, 90, 360); + g2_arc(d, 100, 150, 45, 25, 90, 0); + g2_arc(d, 100, 200, 45, 25, 360, 90); + g2_arc(d, 100, 250, 45, 25, -45, 45); + g2_arc(d, 100, 300, 45, 25, -45, -315); + g2_arc(d, 100, 350, 45, 25, -495, -405); + + g2_filled_arc(d, 100, 50, 40, 20, 90, 90); + g2_filled_arc(d, 100, 100, 40, 20, 90, 360); + g2_filled_arc(d, 100, 150, 40, 20, 90, 0); + g2_filled_arc(d, 100, 200, 40, 20, 360, 90); + g2_filled_arc(d, 100, 250, 40, 20, -45, 45); + g2_filled_arc(d, 100, 300, 40, 20, -45, -315); + g2_filled_arc(d, 100, 350, 40, 20, -495, -405); + + + + g2_string(d,320, 50,"0,0"); + g2_string(d,320,100,"360,90"); + g2_string(d,320,150,"0,90"); + g2_string(d,320,200,"90,360"); + g2_string(d,320,250,"45,-45"); + g2_string(d,320,300,"-315,-45"); + g2_string(d,320,350,"-405,-495"); + + g2_arc(d, 250, 50, 45, 25, 0, 0); + g2_arc(d, 250, 100, 45, 25, 360, 90); + g2_arc(d, 250, 150, 45, 25, 0, 90); + g2_arc(d, 250, 200, 45, 25, 90, 360); + g2_arc(d, 250, 250, 45, 25, 45, -45); + g2_arc(d, 250, 300, 45, 25, -315, -45); + g2_arc(d, 250, 350, 45, 25, -405, -495); + + g2_filled_arc(d, 250, 50, 40, 20, 90, 90); + g2_filled_arc(d, 250, 100, 40, 20, 360, 90); + g2_filled_arc(d, 250, 150, 40, 20, 0, 90); + g2_filled_arc(d, 250, 200, 40, 20, 90, 360); + g2_filled_arc(d, 250, 250, 40, 20, 45, -45); + g2_filled_arc(d, 250, 300, 40, 20, -315, -45); + g2_filled_arc(d, 250, 350, 40, 20, -405, -495); + + g2_flush(d); + printf("\nDone.\n[Enter]\n"); + getchar(); + g2_close(d); + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_splines_demo.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_splines_demo.c new file mode 100755 index 000000000..d02b152b7 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_splines_demo.c @@ -0,0 +1,143 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +/* + * g2_splines_demo.c + * 06/16/99 + */ + +#include + +#include +#ifdef DO_PS +#include +#endif +#ifdef DO_X11 +#include +#endif +#ifdef DO_GD +#include +#endif +#ifdef DO_WIN32 +#include +#endif +#ifdef DO_WMF32 +#include +#endif + + + +#define n 14 +#define o 60 +#define tn 0.6 + +#define X11 0 +#define PS 1 +#define GD 2 + +int otp=X11; + +int id=-1 ; /* default output device */ + + +void curves() +{ + int i; + double points[(2*n)]; + double dy[n] = { 10., 280., 140., 200., 60., 120., 380., + 500., 480., 400., 220., 180., 260., 340.}; + + for (i = 0; i < n; i++) { + points[(i+i)] = (i*o)+20.; /* from 20 to 800 (20+(13*60)) */ + points[(i+i+1)] = dy[i]; + } + g2_pen(id, 1); + g2_poly_line(id, n, points); + g2_pen(id, 3); + g2_spline(id, n, points, o); + g2_pen(id, 7); + g2_b_spline(id, n, points, o); + g2_pen(id, 10); + g2_raspln(id, n, points, tn); + g2_pen(id, 19); + g2_para_3(id, n, points); + g2_pen(id, 22); + g2_para_5(id, n, points); +} + +void axes() +{ + g2_line(id, 5, 300, 810, 300); + g2_line(id, 400, 5, 400, 560); +} + +void draw() +{ + g2_rectangle(id, 5, 5, 810, 560); /* window: 815 x 565 */ + axes(); + curves(); +} + +int main(int argc, char *argv[]) +{ + int dev[5]={-1, -1, -1, -1, -1}; + + id=g2_open_vd(); /* open virtual device */ + + printf("\nAdding.."); + +#ifdef DO_PS + printf("..PS"); + dev[0]=g2_open_PS("g2_splines_demo.ps", g2_A4, g2_PS_land); + g2_attach(id, dev[0]); +#endif +#ifdef DO_X11 + printf("..X11"); + dev[1]=g2_open_X11(850, 600); + g2_attach(id, dev[1]); +#endif +#ifdef DO_GD + printf("..GD"); + dev[2]=g2_open_gd("g2_splines_demo.png", 850, 600, g2_gd_png); + g2_attach(id, dev[2]); +#endif +#ifdef DO_WIN32 + printf("..WIN32"); + dev[3]=g2_open_win32(850, 600,"g2_splines_demo",0); + g2_set_auto_flush(dev[3],0); + g2_attach(id, dev[3]); +#endif +#ifdef DO_WMF32 + printf("..WMF32"); + dev[4]=g2_open_win32(850, 600,"g2_splines_demo.emf",1); + g2_set_auto_flush(dev[3],0); + g2_attach(id, dev[4]); +#endif + + g2_set_auto_flush(id,0); + g2_set_coordinate_system(id, 12, 15, 1., 1.); + + draw(); + g2_flush(id); + if (otp==X11) { + printf("\nDone.\n[Enter]\n"); + getchar(); + } + g2_close(id); + return 0; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_test.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_test.c new file mode 100755 index 000000000..850eda679 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_test.c @@ -0,0 +1,254 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ + +#include +#include + +#ifdef DO_PS +#include +#endif +#ifdef DO_FIG +#include +#endif +#ifdef DO_X11 +#include +#endif +#ifdef DO_GD +#include +#endif +#ifdef DO_WIN32 +#include +#endif +#ifdef DO_WMF32 +#include +#endif + +#define maxdev 10 + +int main() +{ + int i, j; + int d, dev[maxdev]={-1, -1, -1, -1, -1,-1, -1, -1, -1, -1}; + int ndev=0; + char str[256]; + double pts[10]; + double y; +#include "penguin.c" + + printf("\nG2_VERSION %s\n", G2_VERSION); + + d=g2_open_vd(); /* open virtual device */ + + printf("Adding.."); + +#ifdef DO_PS + printf("..PS"); + dev[ndev]=g2_open_PS("g2_test.ps", g2_A4, g2_PS_land); + g2_attach(d, dev[ndev]); + ndev++; + + printf("..EPSF"); + dev[ndev]=g2_open_EPSF("g2_test.eps"); + g2_attach(d, dev[ndev]); + ndev++; + printf("..EPSF_CLIP"); + dev[ndev]=g2_open_EPSF_CLIP("g2_test_clip.eps",200,200); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_FIG + printf("..FIG"); + dev[ndev]=g2_open_FIG("g2_test.fig"); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_X11 + printf("..X11"); + dev[ndev]=g2_open_X11(775, 575); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_GD + printf("..GD(png)"); + dev[ndev]=g2_open_gd("g2_test.png", 775, 575,g2_gd_png); + g2_attach(d, dev[ndev]); + ndev++; + printf("..GD(jpeg)"); + dev[ndev]=g2_open_gd("g2_test.jpg", 775, 575,g2_gd_jpeg); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_WIN32 + printf("..WIN32"); + dev[ndev]=g2_open_win32(775, 575,"g2_test",0); + g2_attach(d, dev[ndev]); + ndev++; +#endif +#ifdef DO_WMF32 + printf("..WMF32"); + dev[ndev]=g2_open_win32(775, 575,"g2_test.emf",1); + g2_attach(d, dev[ndev]); + ndev++; +#endif + g2_set_auto_flush(d,0); + + printf("\n"); + + /* g2_set_coordinate_system(d, 775, 575, -0.75, -1.0); */ + + for(i=0;i<27;i++) { + g2_pen(d, i); + g2_filled_circle(d, i*20+10, 10, 10); + g2_pen(d, 1); + g2_circle(d, i*20+10, 10, 10); + sprintf(str, "%d", i); + g2_string(d, i*20+7, 21, str); + } + + for(j=0;j=0) + for(i=0;i<=64;i++) { + g2_move(dev[j], 2*i+575, 5); + g2_pen(dev[j], g2_ink(dev[j], i/64., 0, 0)); + g2_line_r(dev[j], 0, 20); + g2_pen(dev[j], g2_ink(dev[j], 0, i/64., 0)); + g2_line_r(dev[j], 10, 20); + g2_pen(dev[j], g2_ink(dev[j], 0, 0, i/64.)); + g2_line_r(dev[j], -10, 20); + } + + g2_pen(d, 1); + g2_line(d, 200, 50, 350, 50); + g2_line(d, 200, 48, 350, 48); + g2_line(d, 200, 46, 350, 46); + g2_line(d, 200, 46, 200, 75); + g2_line(d, 198, 46, 198, 75); + g2_line(d, 196, 46, 196, 75); + g2_string(d, 200, 50, "012abcABC#())(\\-+~*!$%&"); + + g2_pen(d, 1); + for(i=1;i<25;i++) { + g2_line(d, 15, i*20+50, 15, i*20+50+i); + g2_set_font_size(d, 12); + sprintf(str, "%2d:", i); + g2_string(d, 20, i*20+50, str); + g2_set_font_size(d, i); + g2_string(d, 40, i*20+50, "hello, world"); + } + + g2_plot(d, 150, 70); + g2_line(d, 147, 68, 153, 68); + + y=100; + g2_line(d, 120, y, 170, y+50); + g2_triangle(d, 150, y, 250, y, 200, y+50); + g2_rectangle(d, 300, y, 400, y+50); + g2_circle(d, 450, y+25, 25); + g2_ellipse(d, 550, y+25, 45, 25); + g2_arc(d, 650, y+25, 25, 45, 90, 360); + + pts[0]=4; + pts[1]=4; + g2_set_dash(d, 2, pts); + g2_line(d, 120+5, y, 170+5, y+50); + g2_triangle(d, 150+10, y+4, 250-10, y+4, 200, y+50-5); + g2_rectangle(d, 305, y+5, 395, y+50-5); + g2_circle(d, 450, y+25, 20); + g2_ellipse(d, 550, y+25, 40, 20); + g2_arc(d, 650, y+25, 20, 40, 90, 360); + g2_set_dash(d, 0, NULL); + + y=200; + g2_filled_triangle(d, 150, y, 250, y, 200, y+50); + g2_filled_rectangle(d, 300, y, 400, y+50); + g2_filled_circle(d, 450, y+25, 25); + g2_filled_ellipse(d, 550, y+25, 45, 25); + g2_filled_arc(d, 650, y+25, 25, 45, 90, 360); + + + y=300; + pts[0]=150; pts[1]=y; + pts[2]=175; pts[3]=y+100; + pts[4]=200; pts[5]=y; + pts[6]=225; pts[7]=y+100; + pts[8]=250; pts[9]=y; + g2_poly_line(d, 5, pts); + g2_pen(d, 19); + g2_b_spline(d, 5, pts, 20); + g2_pen(d, 1); + + pts[0]=300; pts[1]=y; + pts[2]=350; pts[3]=y; + pts[4]=375; pts[5]=y+50; + pts[6]=325; pts[7]=y+90; + pts[8]=275; pts[9]=y+50; + g2_polygon(d, 5, pts); + + pts[0]=450; pts[1]=y; + pts[2]=500; pts[3]=y; + pts[4]=525; pts[5]=y+50; + pts[6]=475; pts[7]=y+90; + pts[8]=425; pts[9]=y+50; + g2_filled_polygon(d, 5, pts); + + + g2_image(d, 55., 50., 53, 62, penguin); + g2_image(d, 75., 130., 53, 62, penguin); + g2_pen(d, 1); + + g2_line(d, 225, 448, 200+19*25, 448); + for(i=1;i<20;i++) { + g2_pen(d,i+1); + g2_set_line_width(d, i); + g2_move(d, 200+i*25, 450); + g2_line_to(d, 200+i*25, 550); + } + g2_pen(d,1); + + g2_set_line_width(d, 5); + for(i=1;i<10;i++) { + pts[0]=1*i; + pts[1]=2*i; + pts[2]=3*i; + g2_set_dash(d, 3, pts); + g2_line(d, 550, 300+i*8, 750, 350+i*8); + } + + g2_set_dash(d, 0, NULL); + g2_set_line_width(d, 4); + g2_arc(d, 740, 180, 25, 100, -45+15, -45-15); + g2_arc(d, 740, 180, 20, 95, -45-15, -45+15); + g2_filled_arc(d, 740, 180, 12, 50, -45+15, -45-15); + + g2_set_line_width(d, 1); + g2_circle(d, 400, 400, 20); + g2_ellipse(d, 400, 400, 25, 25); + g2_arc(d, 400, 400, 30, 30, 0, 360); + + g2_flush(d); + printf("\nDone.\n[Enter]\n"); + getchar(); + g2_close(d); + return 0; +} + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_test.f b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_test.f new file mode 100755 index 000000000..b15712c74 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/g2_test.f @@ -0,0 +1,210 @@ +c +c Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +c This file is part of the g2 library +c +c This library is free software; you can redistribute it and/or +c modify it under the terms of the GNU Lesser General Public +c License as published by the Free Software Foundation; either +c version 2.1 of the License, or (at your option) any later version. +c +c This library is distributed in the hope that it will be useful, +c but WITHOUT ANY WARRANTY; without even the implied warranty of +c MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +c Lesser General Public License for more details. +c +c You should have received a copy of the GNU Lesser General Public +c License along with this library; if not, write to the Free Software +c Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +c + +c +c This file will be processed by cpp, the outpu g2testf.f is feeded into fortran compiler +c See Makefile for details. +c + +c program main +c implicit none + integer ndev, i, j + real d, c, dev(0:10) + character str*256 + real pts(0:10) + real y + include 'penguin.inc' +c integer image(64) +c data image/ +c & 0, 0, 2, 2, 2, 2, 0, 0, +c & 0, 2, 0, 0, 0, 0, 2, 0, +c & 2, 0, 3, 0, 0, 3, 0, 2, +c & 2, 0, 0, 0, 0, 0, 0, 2, +c & 2, 3, 0, 0, 0, 0, 3, 2, +c & 2, 0, 3, 3, 3, 3, 0, 2, +c & 0, 2, 0, 0, 0, 0, 2, 0, +c & 0, 0, 2, 2, 2, 2, 0, 0 / +c /*open virtual device */ + d=g2_open_vd() + print*,"Adding.. VD=", d + ndev = 1 + +#ifdef DO_PS + dev(ndev)=g2_open_ps('g2testf.ps', 4., 0.) + print*,"..PS=",dev(ndev) + call g2_attach(d, dev(ndev)) + ndev = ndev + 1 +#endif +#ifdef DO_X11 + dev(ndev)=g2_open_x11(775., 575.) + print*,"..X11=",dev(ndev) + call g2_attach(d,dev(ndev)) + ndev = ndev + 1 +#endif +#ifdef DO_GD + str='g2testf.png' + str(12:12)=char(0) + dev(ndev)=g2_open_gd(str, 775., 575., 0.) + print*,"..GD=",dev(ndev) + call g2_attach(d,dev(ndev)) + ndev = ndev + 1 +#endif + call g2_set_auto_flush(d,0.) + +c call g2_set_coordinate_system(d, 775., 575., -0.75, -1.0) + + do i=0,27 + call g2_pen(d, float(i)) + call g2_filled_circle(d, float(i*20+10), 10., 10.) + call g2_pen(d, 1.) + call g2_circle(d, float(i*20+10), 10., 10.) + write(str(1:4),'(i3,a1)') i,char(0) + call g2_string(d, float(i*20+7), 21., str(1:4)) + enddo + + do j=1,ndev + if(dev(j).gt.0) then + do i=0,64 + call g2_move(dev(j), float(2*i+575), 5.) + c = g2_ink(dev(j), float(i)/64., 0., 0.) + call g2_pen(dev(j), c) + call g2_line_r(dev(j), 0., 20.) + c = g2_ink(dev(j), 0., float(i)/64., 0.) + call g2_pen(dev(j), c ) + call g2_line_r(dev(j), 10., 20.) + c = g2_ink(dev(j), 0., 0., float(i)/64.) + call g2_pen(dev(j), c) + call g2_line_r(dev(j), -10., 20.) + enddo + endif + enddo + call g2_pen(d, 1.) + call g2_line(d, 200., 50., 350., 50.) + call g2_line(d, 200., 48., 350., 48.) + call g2_line(d, 200., 46., 350., 46.) + call g2_line(d, 200., 46., 200., 75.) + call g2_line(d, 198., 46., 198., 75.) + call g2_line(d, 196., 46., 196., 75.) + str="012abcABC#())(\\-+~*!$%&"//char(0) + call g2_string(d, 200., 50., str) + + call g2_pen(d, 1.) + do i=1,25 + call g2_line(d, 15., float(i*20+50), 15., float(i*20+50+i)) + call g2_set_font_size(d, 12.) + write(str(1:3),'(i2,a1)') i,char(0) + call g2_string(d, 20., float(i*20+50), str) + call g2_set_font_size(d, float(i)) + str='Hello, world!'//char(0) + call g2_string(d, 40., float(i*20+50), str) + enddo + + + call g2_plot(d, 150., 70.) + call g2_line(d, 147., 68., 153., 68.) + + y=100. + call g2_line(d, 100., y, 150., y+50.) + call g2_triangle(d, 150., y, 250., y, 200., y+50.) + call g2_rectangle(d, 300., y, 400., y+50.) + call g2_circle(d, 450., y+25., 25.) + call g2_ellipse(d, 550., y+25., 45., 25.) + call g2_arc(d, 650., y+25., 25., 45., 90., 360.) + + y=200. + call g2_filled_triangle(d, 150., y, 250., y, 200., y+50.) + call g2_filled_rectangle(d, 300., y, 400., y+50.) + call g2_filled_circle(d, 450., y+25., 25.) + call g2_filled_ellipse(d, 550., y+25., 45., 25.) + call g2_filled_arc(d, 650., y+25., 25., 45., 90., 360.) + + + y=300. + pts(0)=150. + pts(1)=y + pts(2)=175. + pts(3)=y+100. + pts(4)=200. + pts(5)=y + pts(6)=225. + pts(7)=y+100. + pts(8)=250. + pts(9)=y + call g2_poly_line(d, 5., pts) + call g2_pen(d, 19.) + call g2_b_spline(d, 5., pts, 20.) + call g2_pen(d, 1.) + + pts(0)=300. + pts(1)=y + pts(2)=350. + pts(3)=y + pts(4)=375. + pts(5)=y+50. + pts(6)=325. + pts(7)=y+90. + pts(8)=275. + pts(9)=y+50. + call g2_polygon(d, 5., pts) + + pts(0)=450. + pts(1)=y + pts(2)=500. + pts(3)=y + pts(4)=525. + pts(5)=y+50. + pts(6)=475. + pts(7)=y+90. + pts(8)=425. + pts(9)=y+50. + call g2_filled_polygon(d, 5, pts) + + call g2_image(d, 55., 50., 53., 62., penguin) + call g2_image(d, 75., 130., 53., 62., penguin) + call g2_pen(d, 1.) + + call g2_line(d, 225., 448., float(200+19*25), 448.) + do i=1,20 + call g2_pen(d,float(i+1)) + call g2_set_line_width(d, float(i)) + call g2_move(d, float(200+i*25), 450.) + call g2_line_to(d, float(200+i*25), 550.) + enddo + call g2_pen(d,1.) + + call g2_set_line_width(d, 5.) + do i=1,10 + pts(0)=float(1*i) + pts(1)=float(2*i) + pts(2)=float(3*i) + call g2_set_dash(d, 3., pts) + call g2_line(d, 550., float(300+i*8), 750., float(350+i*8)) + enddo + + call g2_set_dash(d, 0., pts) + call g2_set_line_width(d, 5.) + call g2_arc(d, 740., 180., 25., 100., -45.+15., -45.-15.) + call g2_filled_arc(d, 740., 180., 12., 50., -45.+15., -45.-15.) +c---------------------------------------------------------- + call g2_flush(d) + print*,"Done...(Enter)" + read(*,'(a)') str + call g2_close(d) + end +c #eof# diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/handles.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/handles.c new file mode 100755 index 000000000..5bc5d53f3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/handles.c @@ -0,0 +1,58 @@ +/***************************************************************************** +** Copyright (C) 1998-2005 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include +#include + +#include + +int main() +{ + int d1, d2; + void *handles[G2_PD_HANDLES_SIZE]; + Display *display; + Drawable *drawable; + GC *gc; + + + d1=g2_open_X11(100, 100); + g2_line(d1, 10, 10, 90, 90); + + g2_get_pd_handles(d1, handles); + display = handles[0]; + drawable = handles[5]; + gc = handles[4]; + + printf("%p %p %p\n", display, drawable, gc); + + XDrawString(display, *drawable, *gc, + 10,10, "OK", 2); + + g2_flush(d1); + + d2=g2_open_PS("handles.ps", g2_A4, g2_PS_port); + g2_get_pd_handles(d2, handles); + printf("%p %p %p\n", handles[0], handles[1], handles[2]); + + + getchar(); + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/penguin.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/penguin.c new file mode 100755 index 000000000..6b5a1f45e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/penguin.c @@ -0,0 +1,63 @@ +static int penguin[53*62] = +{00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,01,01,01,01,01,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00, +00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,01,01,01,01,01,01,01,01,01,01,01,01,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00, +00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,01,01,01,01,01,01,01,01,01,01,01,01,01,01,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00, 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+00,01,01,25,25,25,25,25,25,25,25,25,25,25,25,25,25,25,25,01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,25,25,25,25,25,25,25,25,01,01,00,00,00,00,00,00,00, +00,00,01,01,01,01,25,25,25,25,25,25,25,25,25,25,25,25,25,01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,25,25,25,25,25,25,25,01,01,00,00,00,00,00,00,00,00, +00,00,00,00,00,00,00,00,01,01,01,01,25,25,25,25,25,25,01,01,01,00,00,00,00,00,00,00,00,00,00,00,00,00,01,01,01,25,25,25,25,01,01,01,00,00,00,00,00,00,00,00,00, +00,00,00,00,00,00,00,00,00,00,01,01,01,01,25,25,25,01,01,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,01,01,01,01,01,01,01,01,01,00,00,00,00,00,00,00,00,00,00, +00,00,00,00,00,00,00,00,00,00,00,00,00,00,01,01,01,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,01,01,01,01,01,00,00,00,00,00,00,00,00,00,00,00,00}; diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/penguin.inc b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/penguin.inc new file mode 100755 index 000000000..52495e331 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/penguin.inc @@ -0,0 +1,64 @@ + real penguin(1:53,1:62) + data ((penguin(i,j),i=1,53),j=1,62)/ + & 23*0,5*1,25*0, + & 20*0,12*1,21*0, + & 19*0,14*1,20*0, + & 19*0,11*1,1*0,3*1,19*0, + & 18*0,12*1,2*0,2*1,19*0, + & 18*0,17*1,18*0, + & 17*0,19*1,17*0, + & 17*0,19*1,17*0, + & 17*0,19*1,17*0, + & 17*0,3*1,1*0,6*1,3*0,6*1,17*0, + & 17*0,2*1,4*0,3*1,6*0,4*1,17*0, + & 17*0,2*1,1*0,1*1,2*0,2*1,3*0,2*1,2*0,4*1,17*0, + & 17*0,5*1,1*0,2*1,2*0,3*1,2*0,4*1,17*0, + & 17*0,5*1,1*0,3*1,1*0,3*1,2*0,4*1,17*0, + & 17*0,3*1,1*0,7*25,2*1,2*0,4*1,17*0, + & 17*0,4*1,9*25,6*1,17*0, + & 17*0,2*1,13*25,4*1,17*0, + & 18*0,1*1,13*25,4*1,17*0, + & 18*0,2*1,8*25,2*1,2*25,5*1,16*0, + & 18*0,3*1,3*25,2*1,4*25,1*0,3*1,2*0,2*1,15*0, + & 18*0,6*1,4*25,2*1,2*0,2*1,2*0,3*1,14*0, + & 17*0,2*1,2*0,2*1,1*25,4*1,4*0,7*1,14*0, + & 17*0,2*1,2*0,5*1,6*0,7*1,14*0, + & 16*0,3*1,3*0,2*1,9*0,7*1,13*0, + & 15*0,3*1,16*0,7*1,12*0, + & 14*0,3*1,17*0,8*1,11*0, + & 14*0,3*1,17*0,8*1,11*0, + & 14*0,3*1,17*0,3*1,1*0,5*1,10*0, + & 12*0,5*1,18*0,9*1,9*0, + & 12*0,5*1,19*0,3*1,1*0,4*1,9*0, + & 11*0,2*1,1*0,2*1,20*0,9*1,8*0, + & 11*0,5*1,20*0,4*1,1*0,4*1,8*0, + & 11*0,4*1,22*0,8*1,8*0, + & 10*0,4*1,23*0,9*1,7*0, + & 10*0,4*1,24*0,3*1,1*0,5*1,6*0, + & 10*0,4*1,24*0,3*1,1*0,5*1,6*0, + & 9*0,5*1,24*0,3*1,1*0,5*1,6*0, + & 8*0,2*1,1*0,2*1,25*0,3*1,1*0,5*1,6*0, + & 8*0,2*1,1*0,2*1,25*0,3*1,1*0,5*1,6*0, + & 8*0,5*1,25*0,3*1,1*0,5*1,6*0, + & 7*0,6*1,25*0,9*1,6*0, + & 7*0,4*1,1*0,1*1,26*0,8*1,6*0, + & 7*0,5*1,26*0,9*1,6*0, + & 7*0,4*25,2*1,23*0,11*1,6*0, + & 7*0,5*25,2*1,22*0,2*25,8*1,1*25,6*0, + & 6*0,1*1,6*25,3*1,19*0,1*1,3*25,6*1,3*25,5*0, + & 6*0,1*1,7*25,3*1,18*0,1*1,3*25,5*1,3*25,1*1,5*0, + & 5*0,1*1,8*25,3*1,18*0,1*1,4*25,3*1,4*25,1*1,5*0, + & 1*0,13*25,5*1,16*0,1*1,11*25,2*1,4*0, + & 1*1,14*25,5*1,15*0,1*1,11*25,3*1,3*0, + & 1*0,16*25,4*1,14*0,1*1,12*25,3*1,2*0, + & 1*0,1*1,15*25,4*1,14*0,1*1,14*25,2*1,1*0, + & 1*0,1*1,15*25,2*1,14*0,1*1,1*0,1*1,16*25,1*1, + & 1*0,1*1,16*25,1*1,13*0,2*1,1*0,1*1,16*25,1*1, + & 1*0,1*1,17*25,1*1,1*0,1*1,8*0,4*1,1*0,1*1,14*25,2*1,1*0, + & 1*1,18*25,15*1,1*0,1*1,13*25,1*1,3*0, + & 1*1,18*25,17*1,9*25,3*1,5*0, + & 1*0,2*1,16*25,17*1,8*25,2*1,7*0, + & 2*0,4*1,13*25,17*1,7*25,2*1,8*0, + & 8*0,4*1,6*25,3*1,13*0,3*1,4*25,3*1,9*0, + & 10*0,4*1,3*25,2*1,15*0,9*1,10*0, + & 14*0,3*1,19*0,5*1,12*0/ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/pointer.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/pointer.c new file mode 100755 index 000000000..48968a879 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/pointer.c @@ -0,0 +1,46 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include + +int main() +{ + int d; + double x, y; + unsigned int button; + + d=g2_open_X11(100, 50); + + g2_set_coordinate_system(d, 50, 25, 50., 25.); + + g2_line(d, -1, 0, 1, 0); + g2_line(d, 0, -1, 0, 1); + + printf("Press to start\n"); + getchar(); + + for(;;) { + g2_query_pointer(d, &x, &y, &button); + printf("%f %f 0x%04x\n", x, y, button); + } + + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_FIG.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_FIG.c new file mode 100755 index 000000000..74da920ff --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_FIG.c @@ -0,0 +1,30 @@ +/***************************************************************************** +** Copyright (C) 1998-2004 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include + +int main() +{ + int d; + d=g2_open_FIG("simple.fig"); + g2_line(d, 10, 10, 90, 90); + g2_close(d); + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_PS.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_PS.c new file mode 100755 index 000000000..29af9014f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_PS.c @@ -0,0 +1,30 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include + +int main() +{ + int d; + d=g2_open_PS("simple.ps", g2_A4, g2_PS_port); + g2_line(d, 10, 10, 90, 90); + g2_close(d); + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_X11.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_X11.c new file mode 100755 index 000000000..c26860927 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_X11.c @@ -0,0 +1,31 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include + +int main() +{ + int d; + d=g2_open_X11(100, 100); + g2_line(d, 10, 10, 90, 90); + getchar(); + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_gd.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_gd.c new file mode 100755 index 000000000..4871aee6d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_gd.c @@ -0,0 +1,31 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include + +int main() +{ + int d; + + d=g2_open_gd("simple.png", 100, 100, g2_gd_png); + g2_line(d, 10, 10, 90, 90); + g2_close(d); + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_win32.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_win32.c new file mode 100755 index 000000000..8dee671c1 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/simple_win32.c @@ -0,0 +1,31 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include + +int main() +{ + int d; + d=g2_open_win32(100, 100, "simple_win32", 0); + g2_line(d, 10, 10, 90, 90); + getchar(); + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/xlink.opt b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/xlink.opt new file mode 100755 index 000000000..6bc5bd482 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/demo/xlink.opt @@ -0,0 +1 @@ +sys$share:decw$xlibshr/share diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/descrip.mms b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/descrip.mms new file mode 100755 index 000000000..e5cc36013 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/descrip.mms @@ -0,0 +1,71 @@ +! +! VMS descrip.mms for g2 +! +GD_INCLUDE = [.-.-.GD-1_8_4] + + +.IFDEF debug +CC_FLAGS = /noopt/debug/nolist/warnings/include_directory=("./src",$(GD_INCLUDE)) \ + /define=(DO_PS, DO_X11, DO_GD) +.ELSE +CC_FLAGS = /nolist/warnings/include_directory=("./src",$(GD_INCLUDE)) \ + /define=(DO_PS, DO_X11, DO_GD) +.ENDIF + +! +! Object files +! +OBJ = [.src]g2_device.obj, [.src]g2_fif.obj, [.src]g2_graphic_pd.obj, \ + [.src]g2_physical_device.obj, [.src]g2_ui_control.obj, \ + [.src]g2_ui_device.obj, [.src]g2_ui_graphic.obj, \ + [.src]g2_ui_virtual_device.obj, [.src]g2_util.obj, \ + [.src]g2_virtual_device.obj, [.src]g2_control_pd.obj, \ + [.src]g2_splines.obj +OBJ_X11 = [.src.X11]g2_X11.obj +OBJ_PS = [.src.PS]g2_PS.obj +OBJ_GD = [.src.GD]g2_GD.obj + +HEADERS = [.src]g2.h, [.src]g2_config.h, [.src]g2_device.h, \ + [.src]g2_funix.h, [.src]g2_graphic_pd.h, \ + [.src]g2_physical_device.h, [.src]g2_util.h, \ + [.src]g2_virtual_device.h, [.src]g2_control_pd.h +HEADERS_X11 = [.src.X11]g2_X11.h, [.src.X11]g2_X11_P.h, \ + [.src.X11]g2_X11_funix.h +HEADERS_PS = [.src.PS]g2_PS.h, [.src.PS]g2_PS_P.h, \ + [.src.PS]g2_PS_definitions.h, [.src.PS]g2_PS_funix.h +HEADERS_GD = [.src.GD]g2_GD.h, [.src.GD]g2_GD_P.h, [.src.GD]g2_GD_funix.h +! +! Rules +! +.c.obj : ; cc $(CC_FLAGS)/obj=$(mms$target) $(mms$source) + + +all : g2.olb + @ write sys$output "Done." + +g2.olb : $(OBJ) $(OBJ_X11) $(OBJ_PS) $(OBJ_GD) + library/create g2.olb $(OBJ), $(OBJ_X11), $(OBJ_PS), $(OBJ_GD) + +clean : + delete [...]*.exe;* , [...]*.obj;* , [...]*.olb;* + + +! +! Dependencies +! +[.src]g2_device.obj : [.src]g2_device.c $(HEADERS) +[.src]g2_fif.obj : [.src]g2_fif.c $(HEADERS) +[.src]g2_graphic_pd.obj : [.src]g2_graphic_pd.c $(HEADERS) +[.src]g2_physical_device.obj : [.src]g2_physical_device.c $(HEADERS) +[.src]g2_ui_control.obj : [.src]g2_ui_control.c $(HEADERS) +[.src]g2_ui_device.obj : [.src]g2_ui_device.c $(HEADERS) +[.src]g2_ui_graphic.obj : [.src]g2_ui_graphic.c $(HEADERS) +[.src]g2_ui_virtual_device.obj : [.src]g2_ui_virtual_device.c $(HEADERS) +[.src]g2_util.obj : [.src]g2_util.c $(HEADERS) +[.src]g2_virtual_device.obj : [.src]g2_virtual_device.c $(HEADERS) +[.src]g2_splines.obj : [.src]g2_splines.c $(HEADERS) + +[.X11]g2_X11.obj : [.src.X11]g2_X11.c $(HEADERS) $(HEADERS_X11) +[.PS]g2_PS.obj : [.src.PS]g2_PS.c $(HEADERS) $(HEADERS_PS) +[.GD]g2_GD.obj : [.src.GD]g2_GD.c $(HEADERS) $(HEADERS_GD) + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Repository new file mode 100755 index 000000000..e05ed8916 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/doc/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Entries new file mode 100755 index 000000000..36fcdcd81 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Entries @@ -0,0 +1,3 @@ +D/CVS//// +/Doxyfile/1.1/Tue Jun 14 21:14:27 2005// +/g2_main.dox/1.1/Mon Apr 5 21:40:53 2004// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Repository new file mode 100755 index 000000000..908db64f0 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/doc diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/Doxyfile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/Doxyfile new file mode 100755 index 000000000..a9d6e6a92 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/Doxyfile @@ -0,0 +1,1117 @@ +# Doxyfile 1.3.6 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = g2 + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = 0.7x + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, +# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Japanese-en +# (Japanese with English messages), Korean, Korean-en, Norwegian, Polish, Portuguese, +# Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian. + +OUTPUT_LANGUAGE = English + +# This tag can be used to specify the encoding used in the generated output. +# The encoding is not always determined by the language that is chosen, +# but also whether or not the output is meant for Windows or non-Windows users. +# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES +# forces the Windows encoding (this is the default for the Windows binary), +# whereas setting the tag to NO uses a Unix-style encoding (the default for +# all platforms other than Windows). + +USE_WINDOWS_ENCODING = NO + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is used +# as the annotated text. Otherwise, the brief description is used as-is. If left +# blank, the following values are used ("$name" is automatically replaced with the +# name of the entity): "The $name class" "The $name widget" "The $name file" +# "is" "provides" "specifies" "contains" "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all inherited +# members of a class in the documentation of that class as if those members were +# ordinary class members. Constructors, destructors and assignment operators of +# the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = NO + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. It is allowed to use relative paths in the argument list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like the Qt-style comments (thus requiring an +# explicit @brief command for a brief description. + +JAVADOC_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the DETAILS_AT_TOP tag is set to YES then Doxygen +# will output the detailed description near the top, like JavaDoc. +# If set to NO, the detailed description appears after the member +# documentation. + +DETAILS_AT_TOP = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 8 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = YES + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java sources +# only. Doxygen will then generate output that is more tailored for Java. +# For instance, namespaces will be presented as packages, qualified scopes +# will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = YES + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = ../src/ . + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx *.hpp +# *.h++ *.idl *.odl *.cs *.php *.php3 *.inc + +FILE_PATTERNS = *.c *.h *.dox + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = ../src/g2_fif.c g2_fif.h + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or directories +# that are symbolic links (a Unix filesystem feature) are excluded from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. + +EXCLUDE_PATTERNS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. + +INPUT_FILTER = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES (the default) +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES (the default) +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = YES + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = NO + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be +# generated containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, +# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are +# probably better off using the HTML help feature. + +GENERATE_TREEVIEW = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = YES + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = NO + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = NO + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. This is useful +# if you want to understand what is going on. On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_PREDEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse the +# parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base or +# super classes. Setting the tag to NO turns the diagrams off. Note that this +# option is superseded by the HAVE_DOT option below. This is only a fallback. It is +# recommended to install and use dot, since it yields more powerful graphs. + +CLASS_DIAGRAMS = YES + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = NO + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will +# generate a call dependency graph for every global function or class method. +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable call graphs for selected +# functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + +DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found on the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width +# (in pixels) of the graphs generated by dot. If a graph becomes larger than +# this value, doxygen will try to truncate the graph, so that it fits within +# the specified constraint. Beware that most browsers cannot cope with very +# large images. + +MAX_DOT_GRAPH_WIDTH = 1024 + +# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height +# (in pixels) of the graphs generated by dot. If a graph becomes larger than +# this value, doxygen will try to truncate the graph, so that it fits within +# the specified constraint. Beware that most browsers cannot cope with very +# large images. + +MAX_DOT_GRAPH_HEIGHT = 1024 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes that +# lay further from the root node will be omitted. Note that setting this option to +# 1 or 2 may greatly reduce the computation time needed for large code bases. Also +# note that a graph may be further truncated if the graph's image dimensions are +# not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH and MAX_DOT_GRAPH_HEIGHT). +# If 0 is used for the depth value (the default), the graph is not depth-constrained. + +MAX_DOT_GRAPH_DEPTH = 0 + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to the search engine +#--------------------------------------------------------------------------- + +# The SEARCHENGINE tag specifies whether or not a search engine should be +# used. If set to NO the values of all tags below this one will be ignored. + +SEARCHENGINE = NO diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/g2_main.dox b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/g2_main.dox new file mode 100755 index 000000000..332a24875 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/doc/g2_main.dox @@ -0,0 +1,356 @@ + +/* this file is used mainly to hold some general g2 doxygen +documentation in the doxygen format */ + + +/* define some main groups */ + +/** + * \defgroup interface g2 User Interface + */ + +/** + * \ingroup interface + * \defgroup physdev g2 Physical devices + * + * g2 physical devices are drivers for different output + * formats. + * + */ + + + +/** \mainpage + + +\section licence License Notice + +This library is free software; you can redistribute it and/or modify +it under the terms of the GNU Lesser General Public License as +published by the Free Software Foundation; either version 2.1 of the +License, or (at your option) any later version. This library is +distributed in the hope that it will be useful, but WITHOUT ANY +WARRANTY; without even the implied warranty of MERCHANTABILITY or +FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public +License for more details. You should have received a copy of the GNU +Lesser General Public License along with this library; if not, write +to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, +Boston, MA 02111-1307 USA * + +Copyright (C) 1998-2004 Ljubomir Milanovic & Horst Wagner. + + +\section introduction Introduction + +\subsection what What is g2 ? + +\subsubsection short Short version (if you are in hurry) + + - 2D graphic library + - Simple to use + - Supports several types of output devices (currently X11, + PostScript, devices supported by gd http://www.boutell.com/gd/ + (PNG, JPEG), FIG (http://www.xfig.org) and MS Windows windows) + - Concept allows easy implementation of new device types + - Virtual devices allow to send output simultaneously to several devices + - User definable coordinate system + - Written in ANSI-C + - Tested under Digital Unix, AIX, Linux, VMS and Windows NT + - Perl support + - Fortran interface + +\subsubsection long Long version + +g2 is a simple to use graphics library for 2D graphical applications +written in Ansi-C. This library provides a comprehensive set of +functions for simultaneous generation of graphical output on different +types of devices. Presently, following devices are currently supported +by g2: X11, gd (PNG and JPEG), PostScript and FIG (xfig). +One major feature of the g2_library is the concept of virtual devices. +An arbitrary number of physical devices (such as PostScript, or X11) can +be grouped to create a so-called virtual device. Commands sent to such a +virtual devices will automatically issued to all attached physical +devices. This allows for example simultaneous output to a PNG file and a +Postscript file. A virtual device in turn can be attached to another +virtual device, allowing to construct trees of devices. +Virtual devices can also be useful when using different user-coordinate +systems. E.g. one X11 window showing an overview of a graphical output, +and a second window showing a zoom of a more detailed area of the +graphic. Drawing in both windows is performed by one single command to +the virtual device. + +\code + /-------> PNG: g2_attach(id_PNG,.. + ----------------------- +g2_plot---> | Virtual device: id |--------> X11: g2_attach(id_X11,... + ----------------------- + \-------> PS: g2_attach(id_PS,... +\endcode + +If you don't need or like the concept of virtual devices, simply ignore it. + + + +\section getting Getting Started + +\subsection preinstallation Preinstallation tasks: + + * PNG and JPEG support + + g2 uses the gd library by Thomas Boutell to generate PNG files. This + package is freeware (however not GPL) and can be downloaded at + http://www.boutell.com/gd/. + Linux users might prefer to install a pre-compiled gd rpm package + which should be available at your local RedHat mirrorsite. + NT users should install the gd source package in a subdirectory + named "gd" which should be located in the same directory as the g2 + subdirectory (but not in the g2 directory itself). Otherwise file + locations for gd must be modified in the g2 project workspace. + Unix and VMS users will have to build and install gd according to + the instructions found in the gd distribution. + + +\subsection installation Installation + + +LINUX + + -# Either install RPM packet with binaries, or compile as described + in the UNIX section + +UNIX + + -# Extract package with gzip -dc g2-xxxx.tar.gz | tar xvf - + -# Run './configure' + -# Optionally run 'make depend' + -# Run 'make' + -# Run 'make install' or copy libg2.a and g2.h, g2_X11.h, g2_gd.h, + anf g2_PS.h to the default locations for library and include files. + -# Optional: cd to demo directory and run 'make demo' to compile demo applications + +WINDOWS NT + + -# Extract package using either the .tar.gz or the .zip distribution + -# MS Visual C++ users can build both library and demos with the + supplied project file: g2.dsw (To obtain an icon and use menu + functions you must also build the g2res project in g2.dsw) + -# users of gcc or other commandline based compilers with make + support continue as in Unix example + -# It is also possible to compile g2 on winNT/95 using the free + cygwin32 library and a X-windows library for windows. + Theoretically it should be possible to support both X-windows and + native NT/95 windows at the same time. + +PERL (old instructions) + + -# Change to directory g2_perl + -# Perform following steps + -# perl Makefile.PL + -# make + -# make test + -# make install + -# See the \ref perl "Perl interface" section for more information + -# swig is also supported, more details are comming ... + +VMS + + -# Try to extract either the tar.gz or the zip distribution (whatever + is easier for you) + -# type mms to compile library (descrip.mms file is suplied) + -# run mms in demo directory to compile demo applications + + +\subsection simple A simple example + +The following example is a minimal application. It draws a rectangle in +a postscript file. + +\code +#include +#include + +main() +{ + int id; + id = g2_open_PS("rect.ps", g2_A4, g2_PS_land); + g2_rectangle(id, 20, 20, 150, 150); + g2_close(id); +} +\endcode + +- Always include . Additionally include header files for all +types of devices you want to use. +- Open devices using g2_open_XY functions. The open function +returns a device id of type int, which you need to refer to the device. +- Call g2_close() to close device. +- Consider turning off auto flush (g2_set_auto_flush()) for improved performance. + + +You want to draw a PNG file instead of a PostScript file ? + +replace the PS header file with + +\code +#include +\endcode + +and replace the g2_open_PS function call with + +\code +id = g2_open_gd("rect.png", 300, 200, g2_gd_png); +\endcode + +You want to draw to a PNG file and a PostScript file with one plot +command ? + +Here we use the concept of virtual devices. Open a PNG and PostScript +device, then open a virtual device and attach both the PNG and +PostScript device to the virtual device. Plot commands to the virtual +device will be issued to both PNG and PostScript device. You can attach +and detatch further devices at any time. + +\code +#include +#include +#include + +main() +{ + int id_PS,id_PNG,id; + + id_PS = g2_open_PS("rect.ps", g2_A4, g2_PS_land); + id_PNG = g2_open_gd("rect.png", 300, 200, g2_gd_png); + id = g2_open_vd(); + + g2_attach(id, id_PS); + g2_attach(id, id_PNG); + + g2_rectangle(id, 20, 20, 150, 150); + g2_circle(id, 50, 60, 100); + + g2_close(id); +} +\endcode + +Note: closing a virtual device automatically closes all attached devices. + + +\subsubsection more More examples + +More examples showing the usage of different user coordinate systems, +multiple virtual devices, etc. can be found in the distribution (demo +directory). + + +\subsection fortran Fortran interface + +The Fortran interface for g2 is currently tested for Linux and Digital +Unix/OSF. Function names for Fortran are the same as in C, however +following differences exist: + + * all variables including device IDs are of type REAL + * void functions are implemented as subroutines and must be called + with CALL + * constants defined by #define in C (e.g. g2_A4) do not work. Get + corresponding values from the apropriate header files. + +A short Fortran example: + +\code + program demo + real d,color + d=g2_open_PS('demo_f.ps', 4.0, 1.0) + call g2_plot(d, 50.0, 50.0) + call g2_string(d, 25.0, 75.0, 'TEST ') + color=g2_ink(d, 1.0, 0.0, 0.0) + write (6,*) color + call g2_pen(d, color) + call g2_circle(d, 20.0, 20.0, 10.0) + call g2_flush(d) + call g2_close(d) + stop + end +\endcode + +\subsection perl Perl interface (old info) + +The perl interface for g2 is currently tested for Linux and Digital +Unix/OSF. Function names in perl are the same as in C, however the +device itself is implemented object orientated, i.e. the device argument +is ommited in all functions. +E.g., following simple perl script: + +\code +use G2; + +$d = newX11 G2::Device(100,100); +$d->circle(10, 10, 20); +$d->string(20, 40, "Hello World"); + +print "\nDone.\n[Enter]\n"; +getc(STDIN); + +$d->close() +\endcode + +The creator functions are newX11, newGIF, newPS, etc. and accept the +same arguments as the open functions in the C version. +See the perl documentation (perldoc G2) for more details and the test.pl +script for a more extensive example. + +\section Contact + +You can contact the authors and contributors by e-mail (/ is @ and - is .): + +- Ljubomir Milanovic: ljubo/users-sourceforge-net +- Horst Wagner: wagner/users-sourceforge-net +- Tijs Michels (spline implementation): tijs/vimec-nl + +or visit g2 home page on: http://g2.sourceforge.net/ + +*/ + + + +/** \page paper PS paper sizes + + +\subsection paper PostScript paper sizes + +\code +g2 Name Name Size(Pt) +-------------------------------------------------------- +g2_A0 A0 2384 x 3370 +g2_A1 A1 1684 x 2384 +g2_A2 A2 1191 x 1684 +g2_A3 A3 842 x 1191 +g2_A4 A4 595 x 842 +g2_A5 A5 420 x 595 +g2_A6 A6 297 x 420 +g2_A7 A7 210 x 297 +g2_A8 A8 148 x 210 +g2_A9 A9 105 x 148 +g2_B0 B0 2920 x 4127 +g2_B1 B1 2064 x 2920 +g2_B2 B2 1460 x 2064 +g2_B3 B3 1032 x 1460 +g2_B4 B4 729 x 1032 +g2_B5 B5 516 x 729 +g2_B6 B6 363 x 516 +g2_B7 B7 258 x 363 +g2_B8 B8 181 x 258 +g2_B9 B9 127 x 181 +g2_B10 B10 91 x 127 +g2_Comm_10_Envelope Comm #10 Envelope 297 x 684 +g2_C5_Envelope C5 Envelope 461 x 648 +g2_DL_Envelope DL Envelope 312 x 624 +g2_Folio Folio 595 x 935 +g2_Executive Executive 522 x 756 +g2_Letter Letter 612 x 792 +g2_Legal Legal 612 x 1008 +g2_Ledger Ledger 1224 x 792 +g2_Tabloid Tabloid 792 x 1224 +\endcode + + +*/ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2.dsp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2.dsp new file mode 100755 index 000000000..f8c3c46db --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2.dsp @@ -0,0 +1,152 @@ +# Microsoft Developer Studio Project File - Name="g2" - Package Owner=<4> +# Microsoft Developer Studio Generated Build File, Format Version 6.00 +# ** DO NOT EDIT ** + +# TARGTYPE "Win32 (x86) Static Library" 0x0104 + +CFG=g2 - Win32 Debug +!MESSAGE This is not a valid makefile. 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To build this project using NMAKE, +!MESSAGE use the Export Makefile command and run +!MESSAGE +!MESSAGE NMAKE /f "g2_anim.mak". +!MESSAGE +!MESSAGE You can specify a configuration when running NMAKE +!MESSAGE by defining the macro CFG on the command line. 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Win32 Release" +# Name "g2_anim - Win32 Debug" +# Begin Group "Source Files" + +# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat" +# Begin Source File + +SOURCE=.\demo\g2_anim.c +# End Source File +# End Group +# Begin Group "Header Files" + +# PROP Default_Filter "h;hpp;hxx;hm;inl" +# End Group +# Begin Group "Resource Files" + +# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe" +# End Group +# End Target +# End Project diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Repository new file mode 100755 index 000000000..774fb0d0d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/g2_perl/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Entries new file mode 100755 index 000000000..3e1d03e59 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Entries @@ -0,0 +1,10 @@ +D/CVS//// +/Changes/1.1/Mon Jan 18 10:56:52 1999// +/G2.pm/1.1/Mon Apr 5 21:40:53 2004// +/G2.xs/1.1/Fri Jan 21 00:53:49 2005// +/MANIFEST/1.1/Mon Jan 18 10:56:52 1999// +/Makefile.PL.in/1.1/Mon Apr 5 21:40:53 2004// +/README/1.1/Wed Mar 10 22:23:58 2004// +/test.pl/1.1/Tue Apr 20 02:23:32 2004// +/typemap/1.1/Mon Jan 18 10:56:52 1999// +/Makefile.PL/1.1/Fri Aug 5 10:17:47 2005// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Repository new file mode 100755 index 000000000..652510514 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/g2_perl diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Changes b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Changes new file mode 100755 index 000000000..d0b1f0a1a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Changes @@ -0,0 +1,5 @@ +Revision history for Perl extension G2. + +0.01 Wed Nov 11 17:34:43 1998 + - original version; created by h2xs 1.18 + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/G2.pm b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/G2.pm new file mode 100755 index 000000000..fd7e511aa --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/G2.pm @@ -0,0 +1,361 @@ +package G2; + +use strict; +use Carp; +use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $AUTOLOAD); + +require Exporter; +require DynaLoader; +require AutoLoader; +use strict; + +@ISA = qw(Exporter DynaLoader); +# Items to export into callers namespace by default. Note: do not export +# names by default without a very good reason. Use EXPORT_OK instead. +# Do not simply export all your public functions/methods/constants. +@EXPORT = qw( + G2LD + G2_H + G2_VERSION +); +$VERSION = '0.01'; + +sub AUTOLOAD { + # This AUTOLOAD is used to 'autoload' constants from the constant() + # XS function. If a constant is not found then control is passed + # to the AUTOLOAD in AutoLoader. + + my $constname; + ($constname = $AUTOLOAD) =~ s/.*:://; + my $val = constant($constname, @_ ? $_[0] : 0); + if ($! != 0) { + if ($! =~ /Invalid/) { + $AutoLoader::AUTOLOAD = $AUTOLOAD; + goto &AutoLoader::AUTOLOAD; + } + else { + croak "Your vendor has not defined G2 macro $constname"; + } + } + eval "sub $AUTOLOAD { $val }"; + goto &$AUTOLOAD; +} + +bootstrap G2 $VERSION; + +# Preloaded methods go here. + +# Autoload methods go after =cut, and are processed by the autosplit program. + +1; +__END__ +# Below is the stub of documentation for your module. You better edit it! + +=head1 NAME + +G2 - A simple graphics library ported to Perl. + +=head1 SYNOPSIS + + use G2; + + $dev1 = newX11 G2::Device(775, 575); + $dev2 = newGD G2::Device("test.png",600,200); + + $dev1->rectangle(20,20,150,150); + $dev1->circle(100,150,60); + + $dev2->circle(100,150,60); + $dev2->string(100,50,"A circle in a PNG file"); + +=head1 DESCRIPTION + +g2 is a simple to use graphics library for 2D graphical applications. +This library provides a comprehensive set of functions for +simultaneous generation of graphical output on different types of devices. +Presently, following devices are currently supported by g2: X11, PNG, +PostScript (xfig is in developement). +One major feature of the g2_library is the concept of virtual devices. An +arbitrary number of physical devices (such as PNG, or X11) can be grouped to +create a so-called virtual device. Commands sent to such a virtual devices +will automatically issued to all attached physical devices. This allows for +example simultaneous output to a PNG file and a Postscript file. A virtual +device in turn can be attached to another virtual device, allowing to +construct trees of devices. +Virtual devices can also be useful when using different user-coordinate +systems. E.g. one X11 window showing an overview of a graphical output, and +a second window showing a zoom of a more detailed area of the graphic. +Drawing in both windows is performed by one single command to the virtual +device. +Please see g2 documentation (C interface) for up to date version. + +=head1 Exported constants + + G2LD + G2_H + G2_VERSION + + +=head1 Exported functions + +=head2 Creating new devices + +=over 5 + +=item C + +C I + +opens an X11 window with width and height of X11 window given in pixels. +returns : a new X11 device. + +=item C + +C I + +opens a new PostScript device. +file_name: name of PostScript file +paper: Paper size (e.g. g2_A4, g2_Letter). See +PostScript paper sizes for a full list of supported sizes. +orientation: paper orientation. Either g2_PS_land for +landscape or g2_PS_port for portrait +returns : a new PostScript device. + +=item C + +C I + +open a new GD device +width,height: width and height of the image in pixels +filename: name of the output file. +type: file type, 0-jpeg, 1-png +returns : a new GD device + +=item C + +C I + +Create a new Virtual Device. An arbitrary number of physical devices +(such as PNG, or X11) can be grouped to +create a so-called virtual device. Commands sent to such a virtual devices +will automatically issued to all attached physical devices. This allows for +example simultaneous output to a PNG file and a Postscript file. A virtual +device in turn can be attached to another virtual device, allowing to +construct trees of devices. +Virtual devices can also be useful when using different user-coordinate +systems. E.g. one X11 window showing an overview of a graphical output, and +a second window showing a zoom of a more detailed area of the graphic. +Drawing in both windows is performed by one single command to the virtual +device. + +=head2 Device Functions + +=item C<> + +C I + +=item C<> + +C I + +=item C<> + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=head2 Drawing Functions + + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + +=item C + +C I + Draw an ellipse on device dev + x,y: center point + r1,r2: x and y radius + +=item C + +C I + Draw a filled ellipse on device dev + x,y: center point + r1,r2: x and y radius + +=item C + +C I + +Draw an arc with center point at (x,y), x and y radius given by +r1,r2 and starting and ending angle in radians a1,a2 + +=item C + +C I + Draw a filled arc on device dev + x,y: center point + r1,r2: x and y radius + a1,a2: starting and ending angle in radians + +=item C + +C I + +=item C<> + +C I + +=item C<> + +C I + +=head1 AUTHORS + +Horst Wagner (wagner/users-sourceforge.net) and Ljubomir Milanovic (ljubo/users-sourceforge-net) + +=head1 COPYRIGHT + +Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +This file is part of the g2 library + +This library is free software; you can redistribute it and/or +modify it under the terms of the GNU Lesser General Public +License as published by the Free Software Foundation; either +version 2.1 of the License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +Lesser General Public License for more details. + +You should have received a copy of the GNU Lesser General Public +License along with this library; if not, write to the Free Software +Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +=cut diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/G2.xs b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/G2.xs new file mode 100755 index 000000000..5f4d55fd3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/G2.xs @@ -0,0 +1,922 @@ +#ifdef __cplusplus +extern "C" { +#endif +#include "EXTERN.h" +#include "perl.h" +#include "XSUB.h" + +#ifdef __cplusplus +} +#endif + +#include +#include + +#ifdef DO_PS +#include +#endif /* DO_PS */ + +#ifdef DO_FIG +#include +#endif /* DO_FIG */ + +#ifdef DO_X11 +#include +#endif /* DO_X11 */ + +#ifdef DO_GD +#include +#endif /* DO_GD */ + +#ifdef DO_WIN32 +#include +#endif /* DO_WIN32 */ + + +static int +not_here(s) +char *s; +{ + croak("%s not implemented on this architecture", s); + return -1; +} + +static double +constant(name, arg) +char *name; +int arg; +{ + errno = 0; + switch (*name) { + case 'A': + break; + case 'B': + break; + case 'C': + break; + case 'D': + break; + case 'E': + break; + case 'F': + break; + case 'G': + if (strEQ(name, "G2LD")) +#ifdef G2LD + return G2LD; +#else + goto not_there; +#endif + if (strEQ(name, "G2_H")) +#ifdef G2_H + return G2_H; +#else + goto not_there; +#endif + if (strEQ(name, "G2_VERSION")) +#ifdef G2_VERSION + return atof(G2_VERSION); +#else + goto not_there; +#endif + break; + case 'H': + break; + case 'I': + break; + case 'J': + break; + case 'K': + break; + case 'L': + break; + case 'M': + break; + case 'N': + break; + case 'O': + break; + case 'P': + break; + case 'Q': + break; + case 'R': + break; + case 'S': + break; + case 'T': + break; + case 'U': + break; + case 'V': + break; + case 'W': + break; + case 'X': + break; + case 'Y': + break; + case 'Z': + break; + } + errno = EINVAL; + return 0; + +not_there: + errno = ENOENT; + return 0; +} + +typedef int* DevType; +typedef DevType G2__Device; + + +MODULE = G2 PACKAGE = G2 + + +double +constant(name,arg) + char * name + int arg + +MODULE = G2 PACKAGE = G2::Device PREFIX = g2_ + +#ifdef DO_X11 + +G2::Device +g2_newX11(packname="G2::Device", width=100,height=100) + char * packname + int width + int height + PROTOTYPE: $;$$ + CODE: + { + DevType theDevice; + theDevice = (int *)malloc(sizeof(int)); + *theDevice = g2_open_X11(width, height); + RETVAL = theDevice; + } + OUTPUT: + RETVAL + +#endif /* DO_X11 */ + + +#ifdef DO_WIN32 + +G2::Device +g2_newWin32(packname="G2::Device", width=100,height=100,filename="Win32 window",type=0) + char * packname + int width + int height + char * filename + int type + PROTOTYPE: $;$$ + CODE: + { + DevType theDevice; + theDevice = (int *)malloc(sizeof(int)); + *theDevice = g2_open_win32(width, height, filename, type); + RETVAL = theDevice; + } + OUTPUT: + RETVAL + +#endif /* DO_WIN32 */ + +#ifdef DO_GD + +G2::Device +g2_newGD(packname="G2::Device", filename="g2.png", width=100, height=100, type=1) + char * packname + char * filename + int width + int height + int type + PROTOTYPE: $;$$$ + CODE: + { + DevType theDevice; + theDevice = (int *)malloc(sizeof(int)); + *theDevice = g2_open_gd(filename, width, height, type); + RETVAL = theDevice; + } + OUTPUT: + RETVAL + +#endif /* DO_GD */ + +#ifdef DO_PS + +G2::Device +g2_newPS(packname="G2::Device", filename="g2.ps", paper=1,orientation=1) + char * packname + char * filename + int paper + int orientation + PROTOTYPE: $;$$$ + CODE: + { + DevType theDevice; + theDevice = (int *)malloc(sizeof(int)); + *theDevice = g2_open_PS(filename, paper, orientation); + RETVAL = theDevice; + } + OUTPUT: + RETVAL + +G2::Device +g2_newEPSF(packname="G2::Device", filename="g2.eps") + char * packname + char * filename + PROTOTYPE: $;$$$ + CODE: + { + DevType theDevice; + theDevice = (int *)malloc(sizeof(int)); + *theDevice = g2_open_EPSF(filename); + RETVAL = theDevice; + } + OUTPUT: + RETVAL + +G2::Device +g2_newEPSF_CLIP(packname="G2::Device", filename="g2.eps",width=100,height=100) + char * packname + char * filename + long width + long height + PROTOTYPE: $;$$$ + CODE: + { + DevType theDevice; + theDevice = (int *)malloc(sizeof(int)); + *theDevice = g2_open_EPSF_CLIP(filename,width,height); + RETVAL = theDevice; + } + OUTPUT: + RETVAL + +#endif /* DO_PS */ + +#ifdef DO_FIG + +G2::Device +g2_newFIG(packname="G2::Device", filename="g2.fig") + char * packname + char * filename + PROTOTYPE: $;$$$ + CODE: + { + DevType theDevice; + theDevice = (int *)malloc(sizeof(int)); + *theDevice = g2_open_FIG(filename); + RETVAL = theDevice; + } + OUTPUT: + RETVAL + +#endif /* DO_FIG */ + + +G2::Device +g2_newvd(packname="G2::Device") + char * packname + PROTOTYPE: $; + CODE: + { + DevType theDevice; + theDevice = (int *)malloc(sizeof(int)); + *theDevice = g2_open_vd(); + RETVAL = theDevice; + } + OUTPUT: + RETVAL + + +void +g2_DESTROY(dev) + G2::Device dev + PROTOTYPE: $ + CODE: + { + if(g2_device_exist(*dev)) { + g2_close(*dev); + } + free(dev); + } + + +void +g2_attach(vd_dev, dev) + G2::Device vd_dev + G2::Device dev + PROTOTYPE: $ + CODE: + { + g2_attach(*vd_dev, *dev); + } + +void +g2_detach(vd_dev, dev) + G2::Device vd_dev + G2::Device dev + PROTOTYPE: $ + CODE: + { + g2_detach(*vd_dev, *dev); + } + +void +g2_close(dev) + G2::Device dev + PROTOTYPE: + CODE: + { + g2_close(*dev); + } + +void +g2_set_auto_flush(dev, on_off) + G2::Device dev + int on_off + PROTOTYPE: $ + CODE: + { + g2_set_auto_flush(*dev, on_off); + } + +void +g2_flush(dev) + G2::Device dev + PROTOTYPE: + CODE: + { + g2_flush(*dev); + } + +void +g2_save(dev) + G2::Device dev + PROTOTYPE: + CODE: + { + g2_save(*dev); + } + +void +g2_set_coordinate_system(dev, x_origin, y_origin, x_mul, y_mul) + G2::Device dev + double x_origin + double y_origin + double x_mul + double y_mul + PROTOTYPE: $$$$ + CODE: + { + g2_set_coordinate_system(*dev, x_origin, y_origin, x_mul, y_mul); + } + + +int +g2_ink(pd_dev, red, green, blue) + G2::Device pd_dev + double red + double green + double blue + PROTOTYPE: $$$ + CODE: + { + RETVAL = g2_ink(*pd_dev, red, green, blue); + } + OUTPUT: + RETVAL + +void +g2_pen(dev, color) + G2::Device dev + int color + PROTOTYPE: $ + CODE: + { + g2_pen(*dev, color); + } + + +void +g2_set_dash(dev, N, dashes=NULL) + G2::Device dev + int N + double * dashes + PROTOTYPE: $ + CODE: + { + g2_set_dash(*dev, N, dashes); + free(dashes); + } + +void +g2_set_font_size(dev, size) + G2::Device dev + double size + PROTOTYPE: $ + CODE: + { + g2_set_font_size(*dev, size); + } + +void +g2_set_line_width(dev, w) + G2::Device dev + double w + PROTOTYPE: $ + CODE: + { + g2_set_line_width(*dev, w); + } + +void +g2_clear_palette(dev) + G2::Device dev + PROTOTYPE: + CODE: + { + g2_clear_palette(*dev); + } + +void +g2_reset_palette(dev) + G2::Device dev + PROTOTYPE: + CODE: + { + g2_reset_palette(*dev); + } + +void +g2_allocate_basic_colors(dev) + G2::Device dev + PROTOTYPE: + CODE: + { + g2_allocate_basic_colors(*dev); + } + +void +g2_clear(dev) + G2::Device dev + PROTOTYPE: + CODE: + { + g2_clear(*dev); + } + +void +g2_set_background(dev, color) + G2::Device dev + int color + PROTOTYPE: $ + CODE: + { + g2_set_background(*dev, color); + } + +void +g2_move(dev, x, y) + G2::Device dev + double x + double y + PROTOTYPE: $$ + CODE: + { + g2_move(*dev, x, y); + } + +void +g2_move_r(dev, dx, dy) + G2::Device dev + double dx + double dy + PROTOTYPE: $$ + CODE: + { + g2_move_r(*dev, dx, dy); + } + +void +g2_plot(dev, x, y) + G2::Device dev + double x + double y + PROTOTYPE: $$ + CODE: + { + g2_plot(*dev, x, y); + } + +void +g2_plot_r(dev, dx, dy) + G2::Device dev + double dx + double dy + PROTOTYPE: $$ + CODE: + { + g2_plot_r(*dev, dx, dy); + } + + + +void +g2_line(dev, x1, y1, x2, y2) + G2::Device dev + double x1 + double y1 + double x2 + double y2 + + PROTOTYPE: $$$$ + CODE: + { + g2_line(*dev, x1, y1, x2, y2); + } + +void +g2_line_r(dev, dx, dy) + G2::Device dev + double dx + double dy + PROTOTYPE: $$ + CODE: + { + g2_line_r(*dev, dx, dy); + } + +void +g2_line_to(dev, x, y) + G2::Device dev + double x + double y + PROTOTYPE: $$ + CODE: + { + g2_line_to(*dev, x, y); + } + +void +g2_poly_line(dev, N_pt, points) + G2::Device dev + int N_pt + double * points + PROTOTYPE: $$ + CODE: + { + g2_poly_line(*dev, N_pt, points); + free(points); + } + +void +g2_triangle(dev, x1, y1, x2, y2, x3, y3) + G2::Device dev + double x1 + double y1 + double x2 + double y2 + double x3 + double y3 + PROTOTYPE: $$$$$$$ + CODE: + { + g2_triangle(*dev, x1, y1, x2, y2, x3, y3); + } + + +void +g2_filled_triangle(dev, x1, y1, x2, y2, x3, y3) + G2::Device dev + double x1 + double y1 + double x2 + double y2 + double x3 + double y3 + PROTOTYPE: $$$$$$$ + CODE: + { + g2_filled_triangle(*dev, x1, y1, x2, y2, x3, y3); + } + +void +g2_rectangle(dev, x1, y1, x2, y2) + G2::Device dev + double x1 + double y1 + double x2 + double y2 + PROTOTYPE: $$$$ + CODE: + { + g2_rectangle(*dev, x1, y1, x2, y2); + } + + +void +g2_filled_rectangle(dev, x1, y1, x2, y2) + G2::Device dev + double x1 + double y1 + double x2 + double y2 + PROTOTYPE: $$$$ + CODE: + { + g2_filled_rectangle(*dev, x1, y1, x2, y2); + } + +void +g2_polygon(dev, N_pt, points) + G2::Device dev + int N_pt + double * points + PROTOTYPE: $$ + CODE: + { + g2_polygon(*dev, N_pt, points); + free(points); + } + +void +g2_filled_polygon(dev, N_pt, points) + G2::Device dev + int N_pt + double * points + PROTOTYPE: $$ + CODE: + { + g2_filled_polygon(*dev, N_pt, points); + free(points); + } + +void +g2_circle(dev, x, y, r) + G2::Device dev + double x + double y + double r + PROTOTYPE: $$$ + CODE: + { + g2_circle(*dev, x, y, r); + } + +void +g2_filled_circle(dev, x, y, r) + G2::Device dev + double x + double y + double r + PROTOTYPE: $$$ + CODE: + { + g2_filled_circle(*dev, x, y, r); + } + +void +g2_ellipse(dev, x, y, r1, r2) + G2::Device dev + double x + double y + double r1 + double r2 + PROTOTYPE: $$$$ + CODE: + { + g2_ellipse(*dev, x, y, r1, r2); + } + +void +g2_filled_ellipse(dev, x, y, r1, r2) + G2::Device dev + double x + double y + double r1 + double r2 + PROTOTYPE: $$$$ + CODE: + { + g2_filled_ellipse(*dev, x, y, r1, r2); + } + +void +g2_arc(dev, x, y, r1, r2, a1, a2) + G2::Device dev + double x + double y + double r1 + double r2 + double a1 + double a2 + PROTOTYPE: $$$$$$ + CODE: + { + g2_arc(*dev, x, y, r1, r2, a1, a2); + } + +void +g2_filled_arc(dev, x, y, r1, r2, a1, a2) + G2::Device dev + double x + double y + double r1 + double r2 + double a1 + double a2 + PROTOTYPE: $$$$$$ + CODE: + { + g2_filled_arc(*dev, x, y, r1, r2, a1, a2); + } + +void +g2_string(dev, x, y, text) + G2::Device dev + double x + double y + char * text + PROTOTYPE: $$$ + CODE: + { + g2_string(*dev, x, y, text); + } + +void +g2_set_QP(dev, d, shape) + G2::Device dev + double d + enum QPshape shape + PROTOTYPE: $$ + CODE: + { + g2_set_QP(*dev, d, shape); + } + +void +g2_plot_QP(dev, x, y) + G2::Device dev + double x + double y + PROTOTYPE: $$ + CODE: + { + g2_plot_QP(*dev, x, y); + } + +void +g2_query_pointer(dev) + G2::Device dev + PROTOTYPE: $$ + CODE: + { + double x, y; + unsigned int button; + g2_query_pointer(*dev, &x, &y, &button); + } + + + + + +void +g2_spline(dev, N_pt, points, o) + G2::Device dev + int N_pt + double * points + int o + PROTOTYPE: $$ + CODE: + { + g2_spline(*dev, N_pt, points, o); + free(points); + } + + +void +g2_b_spline(dev, N_pt, points, o) + G2::Device dev + int N_pt + double * points + int o + PROTOTYPE: $$ + CODE: + { + g2_b_spline(*dev, N_pt, points, o); + free(points); + } + + +void +g2_raspln(dev, N_pt, points, tn) + G2::Device dev + int N_pt + double * points + double tn + PROTOTYPE: $$ + CODE: + { + g2_raspln(*dev, N_pt, points, tn); + free(points); + } + + +void +g2_para_3(dev, N_pt, points) + G2::Device dev + int N_pt + double * points + PROTOTYPE: $$ + CODE: + { + g2_para_3(*dev, N_pt, points); + free(points); + } + + +void +g2_para_5(dev, N_pt, points) + G2::Device dev + int N_pt + double * points + PROTOTYPE: $$ + CODE: + { + g2_para_5(*dev, N_pt, points); + free(points); + } + + +void +g2_filled_spline(dev, N_pt, points, o) + G2::Device dev + int N_pt + double * points + int o + PROTOTYPE: $$ + CODE: + { + g2_filled_spline(*dev, N_pt, points, o); + free(points); + } + + +void +g2_filled_b_spline(dev, N_pt, points, o) + G2::Device dev + int N_pt + double * points + int o + PROTOTYPE: $$ + CODE: + { + g2_filled_b_spline(*dev, N_pt, points, o); + free(points); + } + + +void +g2_filled_raspln(dev, N_pt, points, tn) + G2::Device dev + int N_pt + double * points + double tn + PROTOTYPE: $$ + CODE: + { + g2_filled_raspln(*dev, N_pt, points, tn); + free(points); + } + + +void +g2_filled_para_3(dev, N_pt, points) + G2::Device dev + int N_pt + double * points + PROTOTYPE: $$ + CODE: + { + g2_filled_para_3(*dev, N_pt, points); + free(points); + } + + +void +g2_filled_para_5(dev, N_pt, points) + G2::Device dev + int N_pt + double * points + PROTOTYPE: $$ + CODE: + { + g2_filled_para_5(*dev, N_pt, points); + free(points); + } diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/MANIFEST b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/MANIFEST new file mode 100755 index 000000000..3e434f1a4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/MANIFEST @@ -0,0 +1,7 @@ +Changes +G2.pm +G2.xs +MANIFEST +Makefile.PL +test.pl +typemap diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Makefile.PL b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Makefile.PL new file mode 100755 index 000000000..e870d2a44 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Makefile.PL @@ -0,0 +1,10 @@ +use ExtUtils::MakeMaker; +# See lib/ExtUtils/MakeMaker.pm for details of how to influence +# the contents of the Makefile that is written. +WriteMakefile( + 'NAME' => 'G2', + 'VERSION_FROM' => 'G2.pm', # finds $VERSION + 'LIBS' => ['-L./.. -lg2 -L/usr/X11R6/lib64 -L/usr/local/lib -lm -lX11 -lgd'], # e.g., '-lm' + 'DEFINE' => '-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_GD=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 ', # e.g., '-DHAVE_SOMETHING' + 'INC' => '-I./../include', # e.g., '-I/usr/local/include' +); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Makefile.PL.in b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Makefile.PL.in new file mode 100755 index 000000000..14c5a6346 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/Makefile.PL.in @@ -0,0 +1,10 @@ +use ExtUtils::MakeMaker; +# See lib/ExtUtils/MakeMaker.pm for details of how to influence +# the contents of the Makefile that is written. +WriteMakefile( + 'NAME' => 'G2', + 'VERSION_FROM' => 'G2.pm', # finds $VERSION + 'LIBS' => ['-L./.. -lg2 @LDFLAGS@'], # e.g., '-lm' + 'DEFINE' => '@DEFS@', # e.g., '-DHAVE_SOMETHING' + 'INC' => '-I./../include', # e.g., '-I/usr/local/include' +); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/README b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/README new file mode 100755 index 000000000..fbde50c75 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/README @@ -0,0 +1,11 @@ + +To build g2 perl module: + +perl Makefile.PL +make + +Inspect test.pl and comment out unsupported devices. + +make test +make install + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/test.pl b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/test.pl new file mode 100755 index 000000000..8a6304a4b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/test.pl @@ -0,0 +1,213 @@ +# Before `make install' is performed this script should be runnable with +# `make test'. After `make install' it should work as `perl test.pl' + +######################### We start with some black magic to print on failure. + +# Change 1..1 below to 1..last_test_to_print . +# (It may become useful if the test is moved to ./t subdirectory.) + +BEGIN { $| = 1; print "1..1\n"; } +END {print "not ok 1\n" unless $loaded;} +use G2; + +$loaded = 1; +print "ok 1\n"; + +######################### End of black magic. + +# Insert your test code below (better if it prints "ok 13" +# (correspondingly "not ok 13") depending on the success of chunk 13 +# of the test code): + +$d = newvd G2::Device(); + +#PS +if ($d->can(newPS)) + { + $dev[0] = newPS G2::Device("test.ps", 4, 0); + $d->attach($dev[0]); + } +else + { + print "Not supported: PS\n"; + } + + +#FIG +if ($d->can(newFIG)) + { + $dev[1] = newFIG G2::Device("test.fig"); + $d->attach($dev[1]); +} +else + { + print "Not supported: FIG\n"; + } + + +#X11 +if ($d->can(newX11)) + { + $dev[2] = newX11 G2::Device(775, 575); + $d->attach($dev[2]); + } +else + { + print "Not supported: X11\n"; + } + + +#Win32 +if ($d->can(newWin32)) + { + $dev[2] = newWin32 G2::Device(775, 575); + $d->attach($dev[2]); + } +else + { + print "Not supported: Win32\n"; + } + +#GD +if ($d->can(newGD)) + { + $dev[3] = newGD G2::Device("test.png", 775, 575, 1); + $d->attach($dev[3]); + } +else + { + print "Not supported: GD\n"; + } + +$d->set_auto_flush(0); + +for($i=0;$i<27;$i++) { + $d->pen($i); + $d->filled_circle($i*20+10, 10, 10); + $d->pen(1); + $d->circle($i*20+10, 10, 10); + $str = sprintf("%d", $i); + $d->string($i*20+7, 21, $str); + } + +for($j=0;$j<$#dev;$j++) + { + if($dev[$j] > 0) + { + for($i=0;$i<=64;$i++) { + $dev[$j]->move( 2*$i+575, 5); + $dev[$j]->pen($dev[$j]->ink($i/64., 0, 0)); + $dev[$j]->line_r(0, 20); + $dev[$j]->pen($dev[$j]->ink(0, $i/64., 0)); + $dev[$j]->line_r(10, 20); + $dev[$j]->pen($dev[$j]->ink(0, 0, $i/64.)); + $dev[$j]->line_r(-10, 20); + } + } + } + + $d->pen(1); + $d->line(200, 50, 350, 50); + $d->line(200, 48, 350, 48); + $d->line(200, 46, 350, 46); + $d->line(200, 46, 200, 75); + $d->line(198, 46, 198, 75); + $d->line(196, 46, 196, 75); + $d->string(200, 50, "012abcABC#())(\\-+~*!$%&"); + $d->pen(1); + for($i=1;$i<25;$i++) { + $d->line(15, $i*20+50, 15, $i*20+50+$i); + $d->set_font_size(12); + $str = sprintf("%2d:", $i); + $d->string(20, $i*20+50, $str); + $d->set_font_size($i); + $d->string(40, $i*20+50, "hello, world"); + } + + $d->plot(150, 70); + $d->line(147, 68, 153, 68); + + $y=100; + $d->line(120, $y, 170, $y+50); + $d->triangle(150, $y, 250, $y, 200, $y+50); + $d->rectangle(300, $y, 400, $y+50); + $d->circle(450, $y+25, 25); + $d->ellipse(550, $y+25, 45, 25); + $d->arc(650, $y+25, 25, 45, 90, 360); + + $pts[0]=4; + $pts[1]=4; + $d->set_dash(2, \@pts); + $d->line(120+5, $y, 170+5, $y+50); + $d->triangle(150+10, $y+4, 250-10, $y+4, 200, $y+50-5); + $d->rectangle(305, $y+5, 395, $y+50-5); + $d->circle(450, $y+25, 20); + $d->ellipse(550, $y+25, 40, 20); + $d->arc(650, $y+25, 20, 40, 90, 360); + $d->set_dash(0); + + $y=200; + $d->filled_triangle(150, $y, 250, $y, 200, $y+50); + $d->filled_rectangle(300, $y, 400, $y+50); + $d->filled_circle(450, $y+25, 25); + $d->filled_ellipse(550, $y+25, 45, 25); + $d->filled_arc(650, $y+25, 25, 45, 90, 360); + + $y=300.; + $pts[0]=150.; $pts[1]=$y; + $pts[2]=175.; $pts[3]=$y+100.; + $pts[4]=200.; $pts[5]=$y; + $pts[6]=225.; $pts[7]=$y+100.; + $pts[8]=250.; $pts[9]=$y; + $d->poly_line(5, \@pts); + $d->pen(19); + $d->b_spline(5, \@pts, 20); + $d->pen(1); + + $pts[0]=300; $pts[1]=$y; + $pts[2]=350; $pts[3]=$y; + $pts[4]=375; $pts[5]=$y+50; + $pts[6]=325; $pts[7]=$y+90; + $pts[8]=275; $pts[9]=$y+50; + $d->polygon(5, \@pts); + + $pts[0]=450; $pts[1]=$y; + $pts[2]=500; $pts[3]=$y; + $pts[4]=525; $pts[5]=$y+50; + $pts[6]=475; $pts[7]=$y+90; + $pts[8]=425; $pts[9]=$y+50; + $d->filled_polygon(5, \@pts); + + + $d->line(225, 448, 200+19*25, 448); + for($i=1;$i<20;$i++) { + $d->pen($i+1); + $d->set_line_width($i); + $d->move(200+$i*25, 450); + $d->line_to(200+$i*25, 550); + } + $d->pen(1); + + $d->set_line_width(5); + for($i=1;$i<10;$i++) { + $pts[0]=1*$i; + $pts[1]=2*$i; + $pts[2]=3*$i; + $d->set_dash(3, \@pts); + $d->line(550, 300+$i*8, 750, 350+$i*8); + } + + $d->set_dash(0); + $d->set_line_width(5); + $d->arc(740, 180, 25, 100, -45+15, -45-15); + $d->filled_arc(740, 180, 12, 50, -45+15, -45-15); + + $d->set_line_width(1); + $d->circle(400, 400, 20); + $d->ellipse(400, 400, 25, 25); + $d->arc(400, 400, 30, 30, 0, 360); + + $d->flush; + print "\nDone.\n[Enter]\n"; + getc(STDIN); + $d->close(); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/typemap b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/typemap new file mode 100755 index 000000000..837edca5c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2_perl/typemap @@ -0,0 +1,28 @@ +enum QPshape T_PTROBJ +G2::Device T_PTROBJ +double * T_dbl_array + +INPUT +T_dbl_array + { + AV *tempav; + I32 len; + int i; + SV **tv; + if (!SvROK($arg)) { + croak(\"$arg is not a reference.\"); + } + if (SvTYPE(SvRV($arg)) != SVt_PVAV) { + croak(\"$arg is not an array.\"); + } + tempav = (AV*)SvRV($arg); + len = av_len(tempav)+1; + $var = (double *) malloc(len*sizeof(double)); + for (i=0;i +# Microsoft Developer Studio Generated Build File, Format Version 6.00 +# ** DO NOT EDIT ** + +# TARGTYPE "Win32 (x86) Console Application" 0x0103 + +CFG=g2demo - Win32 Debug +!MESSAGE This is not a valid makefile. To build this project using NMAKE, +!MESSAGE use the Export Makefile command and run +!MESSAGE +!MESSAGE NMAKE /f "g2demo.mak". +!MESSAGE +!MESSAGE You can specify a configuration when running NMAKE +!MESSAGE by defining the macro CFG on the command line. For example: +!MESSAGE +!MESSAGE NMAKE /f "g2demo.mak" CFG="g2demo - Win32 Debug" +!MESSAGE +!MESSAGE Possible choices for configuration are: +!MESSAGE +!MESSAGE "g2demo - Win32 Release" (based on "Win32 (x86) Console Application") +!MESSAGE "g2demo - Win32 Debug" (based on "Win32 (x86) Console Application") +!MESSAGE + +# Begin Project +# PROP AllowPerConfigDependencies 0 +# PROP Scc_ProjName "" +# PROP Scc_LocalPath "" +CPP=cl.exe +RSC=rc.exe + +!IF "$(CFG)" == "g2demo - Win32 Release" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 0 +# PROP BASE Output_Dir "Release" +# PROP BASE Intermediate_Dir "Release" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 0 +# PROP Output_Dir "Release" +# PROP Intermediate_Dir "Release" +# PROP Ignore_Export_Lib 0 +# PROP Target_Dir "" +# ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c +# ADD CPP /nologo /MD /W3 /GX /O2 /I "src/GIF" /I "./src" /I "src" /I "src/PS" /I "src/WIN32" /I "src/GD" /I "src/FIG" /D "NDEBUG" /D "G2DLL" /D "DO_GIF" /D "_CONSOLE" /D "_MBCS" /D "WIN32" /D "DO_PS" /D "DO_FIG" /D "DO_WIN32" /D "DO_WMF32" /D "DO_EPSF" /YX /FD /c +# ADD BASE RSC /l 0x409 /d "NDEBUG" +# ADD RSC /l 0x409 /d "NDEBUG" +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LINK32=link.exe +# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386 +# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386 /libpath:"./Release" +# SUBTRACT LINK32 /verbose + +!ELSEIF "$(CFG)" == "g2demo - Win32 Debug" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 1 +# PROP BASE Output_Dir "g2demo__" +# PROP BASE Intermediate_Dir "g2demo__" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 1 +# PROP Output_Dir "Debug" +# PROP Intermediate_Dir "Debug" +# PROP Ignore_Export_Lib 0 +# PROP Target_Dir "" +# ADD BASE CPP /nologo /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c +# ADD CPP /nologo /MD /W3 /Gm /GX /ZI /Od /I "src/gd" /I "./src" /I "src" /I "src/PS" /I "src/WIN32" /I "src/GD" /I "src/FIG" /D "_DEBUG" /D "DO_GD" /D "DO_EPSF_CLIP" /D "_CONSOLE" /D "_MBCS" /D "WIN32" /D "DO_PS" /D "DO_FIG" /D "DO_WIN32" /D "DO_WMF32" /D "DO_EPSF" /FR /YX /FD /c +# ADD BASE RSC /l 0x409 /d "_DEBUG" +# ADD RSC /l 0x409 /fo"g2_win32.res" /d "_DEBUG" +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LINK32=link.exe +# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept +# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /incremental:no /debug /machine:I386 /pdbtype:sept /libpath:"./Debug" /libpath:"../gd" + +!ENDIF + +# Begin Target + +# Name "g2demo - Win32 Release" +# Name "g2demo - Win32 Debug" +# Begin Source File + +SOURCE=.\demo\g2_test.c +# End Source File +# Begin Source File + +SOURCE=..\gdwin32\bgd.lib +# End Source File +# End Target +# End Project diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2dll.dsp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2dll.dsp new file mode 100755 index 000000000..b3009e649 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2dll.dsp @@ -0,0 +1,161 @@ +# Microsoft Developer Studio Project File - Name="g2dll" - Package Owner=<4> +# Microsoft Developer Studio Generated Build File, Format Version 6.00 +# ** DO NOT EDIT ** + +# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102 + +CFG=g2dll - Win32 Debug +!MESSAGE This is not a valid makefile. To build this project using NMAKE, +!MESSAGE use the Export Makefile command and run +!MESSAGE +!MESSAGE NMAKE /f "g2dll.mak". +!MESSAGE +!MESSAGE You can specify a configuration when running NMAKE +!MESSAGE by defining the macro CFG on the command line. For example: +!MESSAGE +!MESSAGE NMAKE /f "g2dll.mak" CFG="g2dll - Win32 Debug" +!MESSAGE +!MESSAGE Possible choices for configuration are: +!MESSAGE +!MESSAGE "g2dll - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library") +!MESSAGE "g2dll - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library") +!MESSAGE + +# Begin Project +# PROP AllowPerConfigDependencies 0 +# PROP Scc_ProjName "" +# PROP Scc_LocalPath "" +CPP=cl.exe +MTL=midl.exe +RSC=rc.exe + +!IF "$(CFG)" == "g2dll - Win32 Release" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 0 +# PROP BASE Output_Dir "Release" +# PROP BASE Intermediate_Dir "Release" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 0 +# PROP Output_Dir "Release" +# PROP Intermediate_Dir "Release" +# PROP Target_Dir "" +# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "G2DLL_EXPORTS" /YX /FD /c +# ADD CPP /nologo /MT /W3 /GX /O2 /I "../gd" /I "./src" /I "../src" /D "NDEBUG" /D "MAKEDLL" /D "G2DLL" /D "WIN32" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "G2DLL_EXPORTS" /YX /FD /c +# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /win32 +# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /win32 +# ADD BASE RSC /l 0x409 /d "NDEBUG" +# ADD RSC /l 0x409 /d "NDEBUG" +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LINK32=link.exe +# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /dll /machine:I386 +# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /dll /machine:I386 + +!ELSEIF "$(CFG)" == "g2dll - Win32 Debug" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 1 +# PROP BASE Output_Dir "g2dll___Win32_Debug" +# PROP BASE Intermediate_Dir "g2dll___Win32_Debug" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 1 +# PROP Output_Dir "Debug" +# PROP Intermediate_Dir "Debug" +# PROP Target_Dir "" +# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "G2DLL_EXPORTS" /YX /FD /GZ /c +# ADD CPP /nologo /MD /W3 /Gm /GX /ZI /Od /I "../gd" /I "./src" /I "../src" /D "_DEBUG" /D "MAKEDLL" /D "G2DLL" /D "WIN32" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "G2DLL_EXPORTS" /YX /FD /GZ /c +# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32 +# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32 +# ADD BASE RSC /l 0x409 /d "_DEBUG" +# ADD RSC /l 0x409 /d "_DEBUG" +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LINK32=link.exe +# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /dll /debug /machine:I386 /pdbtype:sept +# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /dll /debug /machine:I386 /pdbtype:sept + +!ENDIF + +# Begin Target + +# Name "g2dll - Win32 Release" +# Name "g2dll - Win32 Debug" +# Begin Group "Source Files" + +# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat" +# Begin Source File + +SOURCE=.\src\g2_control_pd.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_device.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_fif.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_graphic_pd.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_physical_device.c +# End Source File +# Begin Source File + +SOURCE=.\src\PS\g2_PS.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_splines.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_ui_control.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_ui_device.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_ui_graphic.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_ui_virtual_device.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_util.c +# End Source File +# Begin Source File + +SOURCE=.\src\g2_virtual_device.c +# End Source File +# Begin Source File + +SOURCE=.\src\Win32\g2_win32.c +# End Source File +# Begin Source File + +SOURCE=.\src\Win32\g2_win32_thread.c +# End Source File +# End Group +# Begin Group "Header Files" + +# PROP Default_Filter "h;hpp;hxx;hm;inl" +# End Group +# Begin Group "Resource Files" + +# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe" +# End Group +# End Target +# End Project diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2res.dsp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2res.dsp new file mode 100755 index 000000000..ee971c2fa --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/g2res.dsp @@ -0,0 +1,101 @@ +# Microsoft Developer Studio Project File - Name="g2res" - Package Owner=<4> +# Microsoft Developer Studio Generated Build File, Format Version 6.00 +# ** DO NOT EDIT ** + +# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102 + +CFG=g2res - Win32 Debug +!MESSAGE This is not a valid makefile. To build this project using NMAKE, +!MESSAGE use the Export Makefile command and run +!MESSAGE +!MESSAGE NMAKE /f "g2res.mak". +!MESSAGE +!MESSAGE You can specify a configuration when running NMAKE +!MESSAGE by defining the macro CFG on the command line. For example: +!MESSAGE +!MESSAGE NMAKE /f "g2res.mak" CFG="g2res - Win32 Debug" +!MESSAGE +!MESSAGE Possible choices for configuration are: +!MESSAGE +!MESSAGE "g2res - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library") +!MESSAGE "g2res - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library") +!MESSAGE + +# Begin Project +# PROP AllowPerConfigDependencies 0 +# PROP Scc_ProjName "" +# PROP Scc_LocalPath "" +CPP=cl.exe +MTL=midl.exe +RSC=rc.exe + +!IF "$(CFG)" == "g2res - Win32 Release" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 0 +# PROP BASE Output_Dir "g2res__0" +# PROP BASE Intermediate_Dir "g2res__0" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 0 +# PROP Output_Dir "Release" +# PROP Intermediate_Dir "Release" +# PROP Target_Dir "" +# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c +# ADD CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c +# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /o "NUL" /win32 +# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /o "NUL" /win32 +# ADD BASE RSC /l 0x409 /d "NDEBUG" +# ADD RSC /l 0x409 /d "NDEBUG" +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LINK32=link.exe +# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /machine:I386 +# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /machine:I386 + +!ELSEIF "$(CFG)" == "g2res - Win32 Debug" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 1 +# PROP BASE Output_Dir "g2res__1" +# PROP BASE Intermediate_Dir "g2res__1" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 1 +# PROP Output_Dir "Debug" +# PROP Intermediate_Dir "Debug" +# PROP Target_Dir "" +# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c +# ADD CPP /nologo /MD /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c +# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /o "NUL" /win32 +# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /o "NUL" /win32 +# ADD BASE RSC /l 0x409 /d "_DEBUG" +# ADD RSC /l 0x409 /d "_DEBUG" +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LINK32=link.exe +# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /debug /machine:I386 /pdbtype:sept +# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /debug /machine:I386 /pdbtype:sept + +!ENDIF + +# Begin Target + +# Name "g2res - Win32 Release" +# Name "g2res - Win32 Debug" +# Begin Source File + +SOURCE=.\src\Win32\g2_Win32.ico +# End Source File +# Begin Source File + +SOURCE=.\src\Win32\g2_win32.rc +# End Source File +# Begin Source File + +SOURCE=.\src\Win32\g2res.c +# End Source File +# End Target +# End Project diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/gd.dsp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/gd.dsp new file mode 100755 index 000000000..a4b3abec8 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/gd.dsp @@ -0,0 +1,108 @@ +# Microsoft Developer Studio Project File - Name="gd" - Package Owner=<4> +# Microsoft Developer Studio Generated Build File, Format Version 6.00 +# ** DO NOT EDIT ** + +# TARGTYPE "Win32 (x86) Static Library" 0x0104 + +CFG=gd - Win32 Debug +!MESSAGE This is not a valid makefile. To build this project using NMAKE, +!MESSAGE use the Export Makefile command and run +!MESSAGE +!MESSAGE NMAKE /f "gd.mak". +!MESSAGE +!MESSAGE You can specify a configuration when running NMAKE +!MESSAGE by defining the macro CFG on the command line. For example: +!MESSAGE +!MESSAGE NMAKE /f "gd.mak" CFG="gd - Win32 Debug" +!MESSAGE +!MESSAGE Possible choices for configuration are: +!MESSAGE +!MESSAGE "gd - Win32 Release" (based on "Win32 (x86) Static Library") +!MESSAGE "gd - Win32 Debug" (based on "Win32 (x86) Static Library") +!MESSAGE + +# Begin Project +# PROP AllowPerConfigDependencies 0 +# PROP Scc_ProjName "" +# PROP Scc_LocalPath "" +CPP=cl.exe +RSC=rc.exe + +!IF "$(CFG)" == "gd - Win32 Release" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 0 +# PROP BASE Output_Dir "Release" +# PROP BASE Intermediate_Dir "Release" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 0 +# PROP Output_Dir "Release" +# PROP Intermediate_Dir "Release" +# PROP Target_Dir "" +# ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c +# ADD CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c +# ADD BASE RSC /l 0x409 +# ADD RSC /l 0x409 +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LIB32=link.exe -lib +# ADD BASE LIB32 /nologo +# ADD LIB32 /nologo + +!ELSEIF "$(CFG)" == "gd - Win32 Debug" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 1 +# PROP BASE Output_Dir "gd___Win" +# PROP BASE Intermediate_Dir "gd___Win" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 1 +# PROP Output_Dir "Debug" +# PROP Intermediate_Dir "Debug" +# PROP Target_Dir "" +# ADD BASE CPP /nologo /W3 /GX /Z7 /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c +# ADD CPP /nologo /W3 /GX /Z7 /Od /I "../../../gd1.3" /I "./src" /I "../src" /D "_WINDOWS" /D "WIN32" /D "_DEBUG" /YX /FD /c +# ADD BASE RSC /l 0x409 +# ADD RSC /l 0x409 +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LIB32=link.exe -lib +# ADD BASE LIB32 /nologo +# ADD LIB32 /nologo + +!ENDIF + +# Begin Target + +# Name "gd - Win32 Release" +# Name "gd - Win32 Debug" +# Begin Source File + +SOURCE=..\gd\gd.c +# End Source File +# Begin Source File + +SOURCE=..\gd\gdfontg.c +# End Source File +# Begin Source File + +SOURCE=..\gd\gdfontl.c +# End Source File +# Begin Source File + +SOURCE=..\gd\gdfontmb.c +# End Source File +# Begin Source File + +SOURCE=..\gd\gdfonts.c +# End Source File +# Begin Source File + +SOURCE=..\gd\gdfontt.c +# End Source File +# End Target +# End Project diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Repository new file mode 100755 index 000000000..7a693e0b2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/include diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2.h new file mode 100755 index 000000000..e16a92293 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2.h @@ -0,0 +1,200 @@ +/***************************************************************************** +** Copyright (C) 1998-2005 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_H +#define _G2_H + + +/* g2 version */ +#define G2_VERSION "0.70" + + +#if defined(__cplusplus) +extern "C" +{ +#endif + +/* Common Library header for DLL and application */ +#ifdef WIN32 +#ifdef G2DLL +#ifdef MAKEDLL +/* Create DLL */ +#pragma message( "Building DLL library") +#define G2L __declspec( dllexport) +#else +/* Use DLL */ +#define G2L __declspec( dllimport) +#endif +#else +/* Use static win32 */ +#define G2L +#endif +#else +/* Use non-win32 */ +#define G2L +#endif + + +#define G2LD g2_ld() + +#if defined(SWIG) +#if defined(DO_X11) +%include "X11/g2_X11.h" +#endif +#if defined(DO_PS) +%include "PS/g2_PS.h" +#endif +#if defined(DO_GD) +%include "GD/g2_gd.h" +#endif +#if defined(DO_WIN32) +%include "WIN32/g2_win32.h" +#endif + +%module g2 + +%include typemaps.i + +%{ +#include "g2.h" +#if defined(DO_X11) +#include "g2_X11.h" +#endif +#if defined(DO_PS) +#include "g2_PS.h" +#endif +#if defined(DO_GD) +#include "g2_gd.h" +#endif +#if defined(DO_WIN32) +#include "WIN32/g2_win32.h" +#endif +%} + +#endif +/* end SWIG */ + + +enum QPshape { + QPrect, /**< rectangular quasi pixel */ + QPcirc /**< circle as a quasi pixel */ +}; + +/* compatibility with old versions */ +#define g2_draw_string(dev, x, y, text) g2_string((dev), (x), (y), (text)) + + + +G2L int g2_open_vd(void); +G2L void g2_attach(int vd_dev, int dev); +G2L void g2_detach(int vd_dev, int dev); + +G2L void g2_close(int dev); +G2L void g2_set_auto_flush(int dev, int on_off); +G2L void g2_flush(int dev); +G2L void g2_save(int dev); +G2L void g2_set_coordinate_system(int dev, double x_origin, double y_origin, + double x_mul, double y_mul); + +G2L int g2_ld(); +G2L void g2_set_ld(int dev); + +G2L int g2_ink(int pd_dev, double red, double green, double blue); +G2L void g2_pen(int dev, int color); +G2L void g2_set_dash(int dev, int N, double *dashes); +G2L void g2_set_font_size(int dev, double size); +G2L void g2_set_line_width(int dev, double w); +G2L void g2_clear_palette(int dev); +G2L void g2_reset_palette(int dev); +G2L void g2_allocate_basic_colors(int dev); + +G2L void g2_clear(int dev); +G2L void g2_set_background(int dev, int color); + +G2L void g2_move(int dev, double x, double y); +G2L void g2_move_r(int dev, double dx, double dy); + +G2L void g2_plot(int dev, double x, double y); +G2L void g2_plot_r(int dev, double dx, double dy); +G2L void g2_line(int dev, double x1, double y1, double x2, double y2); +G2L void g2_line_r(int dev, double dx, double dy); +G2L void g2_line_to(int dev, double x, double y); +G2L void g2_poly_line(int dev, int N_pt, double *points); +G2L void g2_triangle(int dev, double x1, double y1, + double x2, double y2, + double x3, double y3); +G2L void g2_filled_triangle(int dev, double x1, double y1, + double x2, double y2, + double x3, double y3); +G2L void g2_rectangle(int dev, double x1, double y1, double x2, double y2); +G2L void g2_filled_rectangle(int dev, + double x1, double y1, double x2, double y2); +G2L void g2_polygon(int dev, int N_pt, double *points); +G2L void g2_filled_polygon(int dev, int N_pt, double *points); +G2L void g2_circle(int dev, double x, double y, double r); +G2L void g2_filled_circle(int dev, double x, double y, double r); +G2L void g2_ellipse(int dev, double x, double y, double r1, double r2); +G2L void g2_filled_ellipse(int dev, double x, double y, double r1, double r2); +G2L void g2_arc(int dev, + double x, double y, + double r1, double r2, + double a1, double a2); +G2L void g2_filled_arc(int dev, double x, double y, + double r1, double r2, + double a1, double a2); +G2L void g2_string(int dev, double x, double y, const char *text); +G2L void g2_image(int dev, + double x, double y, int x_size, int y_size, int *pens); + +G2L void g2_set_QP(int dev, double d, enum QPshape shape); +G2L void g2_plot_QP(int dev, double x, double y); +#if !defined(SWIG) +G2L void g2_query_pointer(int dev, double *x, double *y, unsigned int *button); +#else +extern void g2_query_pointer(int dev, double *OUTPUT,double *OUTPUT,unsigned int *OUTPUT); +#endif + + + /* Tijs Michels */ + /* 06/16/99 */ + +G2L void g2_spline(int id, int n, double *points, int o); +G2L void g2_b_spline(int id, int n, double *points, int o); +G2L void g2_raspln(int id, int n, double *points, double tn); +G2L void g2_para_3(int id, int n, double *points); +G2L void g2_para_5(int id, int n, double *points); +G2L void g2_filled_spline(int id, int n, double *points, int o); +G2L void g2_filled_b_spline(int id, int n, double *points, int o); +G2L void g2_filled_raspln(int id, int n, double *points, double tn); +G2L void g2_filled_para_3(int id, int n, double *points); +G2L void g2_filled_para_5(int id, int n, double *points); + + +/** Actualy private function, but... **/ +G2L int g2_device_exist(int dix); + +/** Use only if you know what are you doing **/ +#define G2_PD_HANDLES_SIZE 32 +G2L void g2_get_pd_handles(int pd, void *handles[G2_PD_HANDLES_SIZE]); + + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + +#endif /* _G2_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2_FIG.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2_FIG.h new file mode 100755 index 000000000..908d8f384 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2_FIG.h @@ -0,0 +1,54 @@ +/***************************************************************************** +** Copyright (C) 1998-2004 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_FIG_H +#define _G2_FIG_H + +#if defined(__cplusplus) +extern "C" +{ +#endif + + +/* Common Library header for DLL and application */ +#ifdef WIN32 +#ifdef G2DLL +#ifdef MAKEDLL +/* Create DLL */ +#define G2L __declspec( dllexport) +#else +/* Use DLL */ +#define G2L __declspec( dllimport) +#endif +#else +/* Use static win32 */ +#define G2L +#endif +#else +/* Use non-win32 */ +#define G2L +#endif + +G2L int g2_open_FIG(const char *file_name); + + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + +#endif /* _G2_FIG_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2_PS.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2_PS.h new file mode 100755 index 000000000..88eb918c9 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/include/g2_PS.h @@ -0,0 +1,118 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_PS_H +#define _G2_PS_H + +#if defined(__cplusplus) +extern "C" +{ +#endif + +/** + * g2 paper type. + * + * \ingroup PS + */ +enum g2_PS_paper { /* Name Size(Pt) */ + g2_A0, /**< A0 2384 x 3370 */ + g2_A1, /**< A1 1684 x 2384 */ + g2_A2, /**< A2 1191 x 1684 */ + g2_A3, /**< A3 842 x 1191 */ + g2_A4, /**< A4 595 x 842 */ + g2_A5, /**< A5 420 x 595 */ + g2_A6, /**< A6 297 x 420 */ + g2_A7, /**< A7 210 x 297 */ + g2_A8, /**< A8 148 x 210 */ + g2_A9, /**< A9 105 x 148 */ + g2_B0, /**< B0 2920 x 4127 */ + g2_B1, /**< B1 2064 x 2920 */ + g2_B2, /**< B2 1460 x 2064 */ + g2_B3, /**< B3 1032 x 1460 */ + g2_B4, /**< B4 729 x 1032 */ + g2_B5, /**< B5 516 x 729 */ + g2_B6, /**< B6 363 x 516 */ + g2_B7, /**< B7 258 x 363 */ + g2_B8, /**< B8 181 x 258 */ + g2_B9, /**< B9 127 x 181 */ + g2_B10, /**< B10 91 x 127 */ + g2_Comm_10_Envelope, /**< Comm #10 Envelope 297 x 684 */ + g2_C5_Envelope, /**< C5 Envelope 461 x 648 */ + g2_DL_Envelope, /**< DL Envelope 312 x 624 */ + g2_Folio, /**< Folio 595 x 935 */ + g2_Executive, /**< Executive 522 x 756 */ + g2_Letter, /**< Letter 612 x 792 */ + g2_Legal, /**< Legal 612 x 1008 */ + g2_Ledger, /**< Ledger 1224 x 792 */ + g2_Tabloid /**< Tabloid 792 x 1224 */ +}; + + +/** + * g2 paper orientation. + * + * \ingroup PS + */ +enum g2_PS_orientation { + g2_PS_land, /**< landscape */ + g2_PS_port /**< portrait */ +}; + +/* + * g2 Format + */ +enum g2_PS_format { + g2_PS_PostScript, /* PostScript */ + g2_PS_EPSF, /* EPSF format */ + g2_PS_EPSF_CLIP /* EPSF format with predefined Bounding Box*/ +}; + +/* Common Library header for DLL and application */ +#ifdef WIN32 +#ifdef G2DLL +#ifdef MAKEDLL +/* Create DLL */ +#define G2L __declspec( dllexport) +#else +/* Use DLL */ +#define G2L __declspec( dllimport) +#endif +#else +/* Use static win32 */ +#define G2L +#endif +#else +/* Use non-win32 */ +#define G2L +#endif + + +G2L int g2_open_PS(const char *file_name, + enum g2_PS_paper paper, + enum g2_PS_orientation orientation); + +G2L int g2_open_EPSF(const char *file_name); + +G2L int g2_open_EPSF_CLIP(const char *file_name, + long width, long height); + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + +#endif /* _G2_PS_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/install-sh b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/install-sh new file mode 100755 index 000000000..58719246f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/install-sh @@ -0,0 +1,238 @@ +#! /bin/sh +# +# install - install a program, script, or datafile +# This comes from X11R5. +# +# Calling this script install-sh is preferred over install.sh, to prevent +# `make' implicit rules from creating a file called install from it +# when there is no Makefile. +# +# This script is compatible with the BSD install script, but was written +# from scratch. +# + + +# set DOITPROG to echo to test this script + +# Don't use :- since 4.3BSD and earlier shells don't like it. +doit="${DOITPROG-}" + + +# put in absolute paths if you don't have them in your path; or use env. vars. + +mvprog="${MVPROG-mv}" +cpprog="${CPPROG-cp}" +chmodprog="${CHMODPROG-chmod}" +chownprog="${CHOWNPROG-chown}" +chgrpprog="${CHGRPPROG-chgrp}" +stripprog="${STRIPPROG-strip}" +rmprog="${RMPROG-rm}" +mkdirprog="${MKDIRPROG-mkdir}" + +transformbasename="" +transform_arg="" +instcmd="$mvprog" +chmodcmd="$chmodprog 0755" +chowncmd="" +chgrpcmd="" +stripcmd="" +rmcmd="$rmprog -f" +mvcmd="$mvprog" +src="" +dst="" +dir_arg="" + +while [ x"$1" != x ]; do + case $1 in + -c) instcmd="$cpprog" + shift + continue;; + + -d) dir_arg=true + shift + continue;; + + -m) chmodcmd="$chmodprog $2" + shift + shift + continue;; + + -o) chowncmd="$chownprog $2" + shift + shift + continue;; + + -g) chgrpcmd="$chgrpprog $2" + shift + shift + continue;; + + -s) stripcmd="$stripprog" + shift + continue;; + + -t=*) transformarg=`echo $1 | sed 's/-t=//'` + shift + continue;; + + -b=*) transformbasename=`echo $1 | sed 's/-b=//'` + shift + continue;; + + *) if [ x"$src" = x ] + then + src=$1 + else + # this colon is to work around a 386BSD /bin/sh bug + : + dst=$1 + fi + shift + continue;; + esac +done + +if [ x"$src" = x ] +then + echo "install: no input file specified" + exit 1 +else + true +fi + +if [ x"$dir_arg" != x ]; then + dst=$src + src="" + + if [ -d $dst ]; then + instcmd=: + else + instcmd=mkdir + fi +else + +# Waiting for this to be detected by the "$instcmd $src $dsttmp" command +# might cause directories to be created, which would be especially bad +# if $src (and thus $dsttmp) contains '*'. + + if [ -f $src -o -d $src ] + then + true + else + echo "install: $src does not exist" + exit 1 + fi + + if [ x"$dst" = x ] + then + echo "install: no destination specified" + exit 1 + else + true + fi + +# If destination is a directory, append the input filename; if your system +# does not like double slashes in filenames, you may need to add some logic + + if [ -d $dst ] + then + dst="$dst"/`basename $src` + else + true + fi +fi + +## this sed command emulates the dirname command +dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'` + +# Make sure that the destination directory exists. +# this part is taken from Noah Friedman's mkinstalldirs script + +# Skip lots of stat calls in the usual case. +if [ ! -d "$dstdir" ]; then +defaultIFS=' +' +IFS="${IFS-${defaultIFS}}" + +oIFS="${IFS}" +# Some sh's can't handle IFS=/ for some reason. +IFS='%' +set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'` +IFS="${oIFS}" + +pathcomp='' + +while [ $# -ne 0 ] ; do + pathcomp="${pathcomp}${1}" + shift + + if [ ! -d "${pathcomp}" ] ; + then + $mkdirprog "${pathcomp}" + else + true + fi + + pathcomp="${pathcomp}/" +done +fi + +if [ x"$dir_arg" != x ] +then + $doit $instcmd $dst && + + if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi && + if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi && + if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi && + if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi +else + +# If we're going to rename the final executable, determine the name now. + + if [ x"$transformarg" = x ] + then + dstfile=`basename $dst` + else + dstfile=`basename $dst $transformbasename | + sed $transformarg`$transformbasename + fi + +# don't allow the sed command to completely eliminate the filename + + if [ x"$dstfile" = x ] + then + dstfile=`basename $dst` + else + true + fi + +# Make a temp file name in the proper directory. + + dsttmp=$dstdir/#inst.$$# + +# Move or copy the file name to the temp name + + $doit $instcmd $src $dsttmp && + + trap "rm -f ${dsttmp}" 0 && + +# and set any options; do chmod last to preserve setuid bits + +# If any of these fail, we abort the whole thing. If we want to +# ignore errors from any of these, just make sure not to ignore +# errors from the above "$doit $instcmd $src $dsttmp" command. + + if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi && + if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi && + if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi && + if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi && + +# Now rename the file to the real destination. + + $doit $rmcmd -f $dstdir/$dstfile && + $doit $mvcmd $dsttmp $dstdir/$dstfile + +fi && + + +exit 0 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/libg2.a b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/libg2.a new file mode 100755 index 000000000..788bbddda Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/libg2.a differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Repository new file mode 100755 index 000000000..b54d25adb --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/perl/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Entries new file mode 100755 index 000000000..4cb30fa71 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Entries @@ -0,0 +1,5 @@ +D/CVS//// +/Makefile.PL/1.1/Sun Aug 11 03:10:43 2002// +/README.perl/1.1/Tue Sep 3 03:11:00 2002// +/g2.pm/1.1/Wed Feb 27 02:04:40 2002// +/g2_wrap.c/1.1/Thu Aug 4 13:08:39 2005// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Repository new file mode 100755 index 000000000..58d7bedc3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/perl diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/Makefile.PL b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/Makefile.PL new file mode 100755 index 000000000..f2cdeb282 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/Makefile.PL @@ -0,0 +1,58 @@ +use ExtUtils::MakeMaker qw(prompt WriteMakefile); + +# =====> PATHS: CHECK AND ADJUST <===== +my @INC = qw(-I../src -I../src/win32 -I../src/PS -I../src/GD); +my @LIBPATH = qw(-L../Debug -L../../gd-1.8.4); +my @LIBS = qw(-lg2); + +# FEATURE FLAGS +warn "\nPlease choose the features that match how g2 was built:\n"; + +my $PS = lc prompt('Build PostScript support?','y') eq 'y'; +my $GD = lc prompt('Build gd (Bitmap) support?','y') eq 'y'; +my $WIN32 = lc prompt('Build Win32 support?','y') eq 'y'; +my $X11 = lc prompt('Build X11 support?','y') eq 'y'; + +warn "\nIf you experience compile problems, please check the \@INC, \@LIBPATH and \@LIBS\n", + "arrays defined in Makefile.PL and manually adjust, if necessary.\n\n"; + +#### no user-serviceable parts below ##### + +push @LIBS,'-lgd' if $GD; +push @LIBS, '-lm' unless $^O eq 'MSWin32'; + +# FreeBSD 3.3 with libgd built from ports croaks if -lXpm is specified +if ($^O ne 'freebsd' && $^O ne 'MSWin32') { + push @LIBS,'-lX11','-lXpm' if $XPM; +} + +my $CAPI = defined $ExtUtils::MakeMaker::CAPI_support ? 'TRUE' : 'FALSE'; +my $DEFINES = ''; +$DEFINES .= ' -DDO_PS' if $PS; +$DEFINES .= ' -DDO_GD' if $GD; +$DEFINES .= ' -DDO_WIN32' if $WIN32; +$DEFINES .= ' -DDO_X11' if $X11; + +WriteMakefile( + 'NAME' => 'g2', + 'VERSION_FROM' => 'g2.pm', + 'dist' => {'COMPRESS'=>'gzip -9f', 'SUFFIX' => 'gz', + 'ZIP'=>'/usr/bin/zip','ZIPFLAGS'=>'-rl'}, + 'OBJECT' => 'g2_wrap.o', + 'OPTIMIZE' => '-g', + 'LIBS' => [join(' ',$ENV{'G2_LIBS'},@LIBPATH,@LIBS)], + 'INC' => join(' ',$ENV{'G2_INC'},@INC), + 'AUTHOR' => 'Horst Wagner', + 'ABSTRACT' => 'Perl interface to g2 Graphics Library', + 'CAPI' => $CAPI, + 'DEFINE' => $DEFINES, +); + +sub MY::postamble { + my $postamble = <<'END'; +html: g2.pm + pod2html --outfile=g2.html g2.pm +END + $postamble; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/README.perl b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/README.perl new file mode 100755 index 000000000..049a36ea8 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/README.perl @@ -0,0 +1,18 @@ +Howto build perl library + +perl Makefile.PL +swig -perl5 -o g2_wrap.c -I../src -DDO_PS -DDO_GD ../src/g2.h +"c:\Program Files\SWIG-1.3.13\swig" -perl5 -o g2_wrap.c -I../src -DDO_PS -DDO_GD -DDO_WIN32 ../src/g2.h +nmake +nmake install + +To make ActiveState PPD: + +tar cvf g2.tar blib +gzip --best g2.tar +nmake ppd +copy tar.gz file into subdir x86 +You have to edit the resulting PPD file and add the location of the package archive into . The location is relative to the PPD file. +To install do: +ppm install g2.ppd + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/g2.pm b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/g2.pm new file mode 100755 index 000000000..f58269c63 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/g2.pm @@ -0,0 +1,10 @@ +# This file was automatically generated by SWIG +package g2; +require Exporter; +require DynaLoader; +@ISA = qw(Exporter DynaLoader); +package g2; +bootstrap g2; +package g2; +@EXPORT = qw( ); +1; diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/g2_wrap.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/g2_wrap.c new file mode 100755 index 000000000..67cdff36e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/perl/g2_wrap.c @@ -0,0 +1,2172 @@ +/* ---------------------------------------------------------------------------- + * This file was automatically generated by SWIG (http://www.swig.org). + * Version 1.3.13u-20020617-2210 + * + * This file is not intended to be easily readable and contains a number of + * coding conventions designed to improve portability and efficiency. Do not make + * changes to this file unless you know what you are doing--modify the SWIG + * interface file instead. + * ----------------------------------------------------------------------------- */ + +/*********************************************************************** + * common.swg + * + * This file contains generic SWIG runtime support for pointer + * type checking as well as a few commonly used macros to control + * external linkage. + * + * Author : David Beazley (beazley@cs.uchicago.edu) + * + * Copyright (c) 1999-2000, The University of Chicago + * + * This file may be freely redistributed without license or fee provided + * this copyright message remains intact. + ************************************************************************/ + +#include + +#if defined(_WIN32) || defined(__WIN32__) +# if defined(_MSC_VER) +# if defined(STATIC_LINKED) +# define SWIGEXPORT(a) a +# define SWIGIMPORT(a) extern a +# else +# define SWIGEXPORT(a) __declspec(dllexport) a +# define SWIGIMPORT(a) extern a +# endif +# else +# if defined(__BORLANDC__) +# define SWIGEXPORT(a) a _export +# define SWIGIMPORT(a) a _export +# else +# define SWIGEXPORT(a) a +# define SWIGIMPORT(a) a +# endif +# endif +#else +# define SWIGEXPORT(a) a +# define SWIGIMPORT(a) a +#endif + +#ifdef SWIG_GLOBAL +#define SWIGRUNTIME(a) SWIGEXPORT(a) +#else +#define SWIGRUNTIME(a) static a +#endif + +#ifdef __cplusplus +extern "C" { +#endif + +typedef void *(*swig_converter_func)(void *); +typedef struct swig_type_info *(*swig_dycast_func)(void **); + +typedef struct swig_type_info { + const char *name; + swig_converter_func converter; + const char *str; + swig_dycast_func dcast; + struct swig_type_info *next; + struct swig_type_info *prev; + void *clientdata; +} swig_type_info; + +#ifdef SWIG_NOINCLUDE + +SWIGIMPORT(swig_type_info *) SWIG_TypeRegister(swig_type_info *); +SWIGIMPORT(swig_type_info *) SWIG_TypeCheck(char *c, swig_type_info *); +SWIGIMPORT(void *) SWIG_TypeCast(swig_type_info *, void *); +SWIGIMPORT(swig_type_info *) SWIG_TypeDynamicCast(swig_type_info *, void **); +SWIGIMPORT(swig_type_info *) SWIG_TypeQuery(const char *); +SWIGIMPORT(void) SWIG_TypeClientData(swig_type_info *, void *); + +#else + +static swig_type_info *swig_type_list = 0; + +/* Register a type mapping with the type-checking */ +SWIGRUNTIME(swig_type_info *) +SWIG_TypeRegister(swig_type_info *ti) +{ + swig_type_info *tc, *head, *ret, *next; + /* Check to see if this type has already been registered */ + tc = swig_type_list; + while (tc) { + if (strcmp(tc->name, ti->name) == 0) { + /* Already exists in the table. Just add additional types to the list */ + head = tc; + next = tc->next; + goto l1; + } + tc = tc->prev; + } + head = ti; + next = 0; + + /* Place in list */ + ti->prev = swig_type_list; + swig_type_list = ti; + + /* Build linked lists */ + l1: + ret = head; + tc = ti + 1; + /* Patch up the rest of the links */ + while (tc->name) { + head->next = tc; + tc->prev = head; + head = tc; + tc++; + } + head->next = next; + return ret; +} + +/* Check the typename */ +SWIGRUNTIME(swig_type_info *) +SWIG_TypeCheck(char *c, swig_type_info *ty) +{ + swig_type_info *s; + if (!ty) return 0; /* Void pointer */ + s = ty->next; /* First element always just a name */ + while (s) { + if (strcmp(s->name,c) == 0) { + if (s == ty->next) return s; + /* Move s to the top of the linked list */ + s->prev->next = s->next; + if (s->next) { + s->next->prev = s->prev; + } + /* Insert s as second element in the list */ + s->next = ty->next; + if (ty->next) ty->next->prev = s; + ty->next = s; + return s; + } + s = s->next; + } + return 0; +} + +/* Cast a pointer up an inheritance hierarchy */ +SWIGRUNTIME(void *) +SWIG_TypeCast(swig_type_info *ty, void *ptr) +{ + if ((!ty) || (!ty->converter)) return ptr; + return (*ty->converter)(ptr); +} + +/* Dynamic pointer casting. Down an inheritance hierarchy */ +SWIGRUNTIME(swig_type_info *) +SWIG_TypeDynamicCast(swig_type_info *ty, void **ptr) +{ + swig_type_info *lastty = ty; + if (!ty || !ty->dcast) return ty; + while (ty && (ty->dcast)) { + ty = (*ty->dcast)(ptr); + if (ty) lastty = ty; + } + return lastty; +} + +/* Search for a swig_type_info structure */ +SWIGRUNTIME(swig_type_info *) +SWIG_TypeQuery(const char *name) { + swig_type_info *ty = swig_type_list; + while (ty) { + if (ty->str && (strcmp(name,ty->str) == 0)) return ty; + if (ty->name && (strcmp(name,ty->name) == 0)) return ty; + ty = ty->prev; + } + return 0; +} + +/* Set the clientdata field for a type */ +SWIGRUNTIME(void) +SWIG_TypeClientData(swig_type_info *ti, void *clientdata) { + swig_type_info *tc, *equiv; + if (ti->clientdata) return; + ti->clientdata = clientdata; + equiv = ti->next; + while (equiv) { + if (!equiv->converter) { + tc = swig_type_list; + while (tc) { + if ((strcmp(tc->name, equiv->name) == 0)) + SWIG_TypeClientData(tc,clientdata); + tc = tc->prev; + } + } + equiv = equiv->next; + } +} +#endif + +#ifdef __cplusplus +} + +#endif + +/* ----------------------------------------------------------------------------- + * perl5.swg + * + * Perl5 runtime library + * $Header: /homes/mhoechsm/cvsroot/RNAforester/g2-0.70/perl/g2_wrap.c,v 1.1 2005/08/04 13:08:39 mhoechsm Exp $ + * ----------------------------------------------------------------------------- */ + +#define SWIGPERL +#define SWIGPERL5 +#ifdef __cplusplus +/* Needed on some windows machines---since MS plays funny + games with the header files under C++ */ +#include +#include +extern "C" { +#endif +#include "EXTERN.h" +#include "perl.h" +#include "XSUB.h" + +/* Get rid of free and malloc defined by perl */ +#undef free +#undef malloc + +#ifndef pTHX_ +#define pTHX_ +#endif + +#include +#ifdef __cplusplus +} +#endif + +/* Note: SwigMagicFuncHack is a typedef used to get the C++ + compiler to just shut up already */ + +#ifdef PERL_OBJECT +#define MAGIC_PPERL CPerlObj *pPerl = (CPerlObj *) this; +typedef int (CPerlObj::*SwigMagicFunc)(SV *, MAGIC *); + +#ifdef __cplusplus +extern "C" { +#endif +typedef int (CPerlObj::*SwigMagicFuncHack)(SV *, MAGIC *); +#ifdef __cplusplus +} +#endif + +#define SWIG_MAGIC(a,b) (SV *a, MAGIC *b) +#define SWIGCLASS_STATIC +#else +#define MAGIC_PPERL +#define SWIGCLASS_STATIC static +#ifndef MULTIPLICITY +#define SWIG_MAGIC(a,b) (SV *a, MAGIC *b) +typedef int (*SwigMagicFunc)(SV *, MAGIC *); + +#ifdef __cplusplus +extern "C" { +#endif +typedef int (*SwigMagicFuncHack)(SV *, MAGIC *); +#ifdef __cplusplus +} +#endif + + +#else +#define SWIG_MAGIC(a,b) (struct interpreter *interp, SV *a, MAGIC *b) +typedef int (*SwigMagicFunc)(struct interpreter *, SV *, MAGIC *); +#ifdef __cplusplus +extern "C" { +#endif +typedef int (*SwigMagicFuncHack)(struct interpreter *, SV *, MAGIC *); +#ifdef __cplusplus +} +#endif + +#endif +#endif + +#if defined(WIN32) && defined(PERL_OBJECT) && !defined(PerlIO_exportFILE) +#define PerlIO_exportFILE(fh,fl) (FILE*)(fh) +#endif + +/* Modifications for newer Perl 5.005 releases */ + +#if !defined(PERL_REVISION) || ((PERL_REVISION >= 5) && ((PERL_VERSION < 5) || ((PERL_VERSION == 5) && (PERL_SUBVERSION < 50)))) +#ifndef PL_sv_yes +#define PL_sv_yes sv_yes +#endif +#ifndef PL_sv_undef +#define PL_sv_undef sv_undef +#endif +#ifndef PL_na +#define PL_na na +#endif +#endif + +#include + +#ifdef __cplusplus +extern "C" { +#endif + +#ifdef SWIG_NOINCLUDE + +#ifndef PERL_OBJECT +extern int SWIG_ConvertPtr(SV *, void **, swig_type_info *, int flags); +extern void SWIG_MakePtr(SV *, void *, swig_type_info *, int flags); +#else +extern int _SWIG_ConvertPtr(CPerlObj *, SV *, void **, swig_type_info *,int flags); +extern void _SWIG_MakePtr(CPerlObj *, SV *, void *, swig_type_info *, int flags); +#define SWIG_ConvertPtr(a,b,c,d) _SWIG_ConvertPtr(pPerl,a,b,c,d) +#define SWIG_MakePtr(a,b,c,d) _SWIG_MakePtr(pPerl,a,b,c,d) +#endif + +#else + +/* Function for getting a pointer value */ + +#ifndef PERL_OBJECT +SWIGRUNTIME(int) +SWIG_ConvertPtr(SV *sv, void **ptr, swig_type_info *_t, int flags) +#else +#define SWIG_ConvertPtr(a,b,c,d) _SWIG_ConvertPtr(pPerl,a,b,c,d) +SWIGRUNTIME(int) +_SWIG_ConvertPtr(CPerlObj *pPerl, SV *sv, void **ptr, swig_type_info *_t, int flags) +#endif +{ + char *_c; + swig_type_info *tc; + IV tmp; + + /* If magical, apply more magic */ + if (SvGMAGICAL(sv)) + mg_get(sv); + + /* Check to see if this is an object */ + if (sv_isobject(sv)) { + SV *tsv = (SV*) SvRV(sv); + if ((SvTYPE(tsv) == SVt_PVHV)) { + MAGIC *mg; + if (SvMAGICAL(tsv)) { + mg = mg_find(tsv,'P'); + if (mg) { + SV *rsv = mg->mg_obj; + if (sv_isobject(rsv)) { + tmp = SvIV((SV*)SvRV(rsv)); + } + } + } else { + return -1; + } + } else { + tmp = SvIV((SV*)SvRV(sv)); + } + if (!_t) { + *(ptr) = (void *) tmp; + return 0; + } + } else if (! SvOK(sv)) { /* Check for undef */ + *(ptr) = (void *) 0; + return 0; + } else if (SvTYPE(sv) == SVt_RV) { /* Check for NULL pointer */ + *(ptr) = (void *) 0; + if (!SvROK(sv)) + return 0; + else + return -1; + } else { /* Don't know what it is */ + *(ptr) = (void *) 0; + return -1; + } + if (_t) { + /* Now see if the types match */ + _c = HvNAME(SvSTASH(SvRV(sv))); + tc = SWIG_TypeCheck(_c,_t); + if (!tc) { + *ptr = (void *) tmp; + return -1; + } + *ptr = SWIG_TypeCast(tc,(void *)tmp); + return 0; + } + *ptr = (void *) tmp; + return 0; +} +#ifndef PERL_OBJECT +SWIGRUNTIME(void) +SWIG_MakePtr(SV *sv, void *ptr, swig_type_info *t,int flags) +#else +#define SWIG_MakePtr(a,b,c,d) _SWIG_MakePtr(pPerl,a,b,c,d) +SWIGRUNTIME(void) +_SWIG_MakePtr(CPerlObj *pPerl, SV *sv, void *ptr, swig_type_info *t, int flags) +#endif +{ + sv_setref_pv(sv, (char *) t->name, ptr); +} + +#endif + +typedef XS(SwigPerlWrapper); +typedef SwigPerlWrapper *SwigPerlWrapperPtr; + +/* Structure for command table */ +typedef struct { + const char *name; + SwigPerlWrapperPtr wrapper; +} swig_command_info; + +/* Information for constant table */ + +#define SWIG_INT 1 +#define SWIG_FLOAT 2 +#define SWIG_STRING 3 +#define SWIG_POINTER 4 +#define SWIG_BINARY 5 + +/* Constant information structure */ +typedef struct swig_constant_info { + int type; + const char *name; + long lvalue; + double dvalue; + void *pvalue; + swig_type_info **ptype; +} swig_constant_info; + +#ifdef __cplusplus +} +#endif + +/* Structure for variable table */ +typedef struct { + const char *name; + SwigMagicFunc set; + SwigMagicFunc get; + swig_type_info **type; +} swig_variable_info; + +/* Magic variable code */ +#ifndef PERL_OBJECT +#define swig_create_magic(s,a,b,c) _swig_create_magic(s,a,b,c) + #ifndef MULTIPLICITY + static void _swig_create_magic(SV *sv, char *name, int (*set)(SV *, MAGIC *), int \ +(*get)(SV *,MAGIC *)) { + #else + static void _swig_create_magic(SV *sv, char *name, int (*set)(struct interpreter*,\ + SV *, MAGIC *), int (*get)(struct interpreter*, SV *,MAGIC *)) { + #endif +#else +#define swig_create_magic(s,a,b,c) _swig_create_magic(pPerl,s,a,b,c) +static void _swig_create_magic(CPerlObj *pPerl, SV *sv, const char *name, int (CPerlObj::*set)(SV *, MAGIC *), int (CPerlObj::*get)(SV *, MAGIC *)) { +#endif + MAGIC *mg; + sv_magic(sv,sv,'U',(char *) name,strlen(name)); + mg = mg_find(sv,'U'); + mg->mg_virtual = (MGVTBL *) malloc(sizeof(MGVTBL)); + mg->mg_virtual->svt_get = (SwigMagicFuncHack) get; + mg->mg_virtual->svt_set = (SwigMagicFuncHack) set; + mg->mg_virtual->svt_len = 0; + mg->mg_virtual->svt_clear = 0; + mg->mg_virtual->svt_free = 0; +} + + + + + + + +/* -------- TYPES TABLE (BEGIN) -------- */ + +#define SWIGTYPE_p_double swig_types[0] +#define SWIGTYPE_p_int swig_types[1] +static swig_type_info *swig_types[3]; + +/* -------- TYPES TABLE (END) -------- */ + +#define SWIG_init boot_g2 + +#define SWIG_name "g2::boot_g2" +#define SWIG_prefix "g2::" + +#ifdef __cplusplus +extern "C" +#endif +#ifndef PERL_OBJECT +#ifndef MULTIPLICITY +SWIGEXPORT(void) SWIG_init (CV* cv); +#else +SWIGEXPORT(void) SWIG_init (pTHXo_ CV* cv); +#endif +#else +SWIGEXPORT(void) SWIG_init (CV *cv, CPerlObj *); +#endif + + +#include "g2.h" +#if defined(DO_X11) +#include "g2_X11.h" +#endif +#if defined(DO_PS) +#include "g2_PS.h" +#endif +#if defined(DO_GD) +#include "g2_gd.h" +#endif +#if defined(DO_WIN32) +#include "WIN32/g2_win32.h" +#endif + +extern void g2_query_pointer(int,double *,double *,unsigned int *); +#ifdef PERL_OBJECT +#define MAGIC_CLASS _wrap_g2_var:: +class _wrap_g2_var : public CPerlObj { +public: +#else +#define MAGIC_CLASS +#endif +SWIGCLASS_STATIC int swig_magic_readonly(pTHX_ SV *sv, MAGIC *mg) { + MAGIC_PPERL + sv = sv; mg = mg; + croak("Value is read-only."); + return 0; +} + + +#ifdef PERL_OBJECT +}; +#endif + +#ifdef __cplusplus +extern "C" { +#endif +XS(_wrap_g2_open_PS) { + char *arg1 ; + int arg2 ; + int arg3 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_open_PS(file_name,paper,orientation);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + arg2 = (int) SvIV(ST(1)); + arg3 = (int) SvIV(ST(2)); + result = (int)g2_open_PS((char const *)arg1,(enum g2_PS_paper)arg2,(enum g2_PS_orientation)arg3); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + +XS(_wrap_g2_open_EPSF) { + char *arg1 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_open_EPSF(file_name);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + result = (int)g2_open_EPSF((char const *)arg1); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + +XS(_wrap_g2_open_EPSF_CLIP) { + char *arg1 ; + long arg2 ; + long arg3 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_open_EPSF_CLIP(file_name,width,height);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + arg2 = (long) SvIV(ST(1)); + arg3 = (long) SvIV(ST(2)); + result = (int)g2_open_EPSF_CLIP((char const *)arg1,arg2,arg3); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + +XS(_wrap_g2_open_gd) { + char *arg1 ; + int arg2 ; + int arg3 ; + int arg4 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_open_gd(filename,width,height,gd_type);"); + } + if (!SvOK((SV*) ST(0))) arg1 = 0; + else arg1 = (char *) SvPV(ST(0), PL_na); + arg2 = (int) SvIV(ST(1)); + arg3 = (int) SvIV(ST(2)); + arg4 = (int) SvIV(ST(3)); + result = (int)g2_open_gd((char const *)arg1,arg2,arg3,(enum g2_gd_type)arg4); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + +XS(_wrap_g2_open_win32) { + int arg1 ; + int arg2 ; + char *arg3 ; + int arg4 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_open_win32(width,height,filename,type);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + if (!SvOK((SV*) ST(2))) arg3 = 0; + else arg3 = (char *) SvPV(ST(2), PL_na); + arg4 = (int) SvIV(ST(3)); + result = (int)g2_open_win32(arg1,arg2,(char const *)arg3,arg4); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + +XS(_wrap_g2_open_vd) { + int result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + croak("Usage: g2_open_vd();"); + } + result = (int)g2_open_vd(); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + +XS(_wrap_g2_attach) { + int arg1 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + croak("Usage: g2_attach(vd_dev,dev);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + g2_attach(arg1,arg2); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_detach) { + int arg1 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + croak("Usage: g2_detach(vd_dev,dev);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + g2_detach(arg1,arg2); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_close) { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_close(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_close(arg1); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_set_auto_flush) { + int arg1 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + croak("Usage: g2_set_auto_flush(dev,on_off);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + g2_set_auto_flush(arg1,arg2); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_flush) { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_flush(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_flush(arg1); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_save) { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_save(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_save(arg1); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_set_coordinate_system) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + int argvi = 0; + dXSARGS; + + if ((items < 5) || (items > 5)) { + croak("Usage: g2_set_coordinate_system(dev,x_origin,y_origin,x_mul,y_mul);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + g2_set_coordinate_system(arg1,arg2,arg3,arg4,arg5); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_ld) { + int result; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + croak("Usage: g2_ld();"); + } + result = (int)g2_ld(); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + +XS(_wrap_g2_set_ld) { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_set_ld(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_set_ld(arg1); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_ink) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_ink(pd_dev,red,green,blue);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + result = (int)g2_ink(arg1,arg2,arg3,arg4); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + +XS(_wrap_g2_pen) { + int arg1 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + croak("Usage: g2_pen(dev,color);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + g2_pen(arg1,arg2); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_set_dash) { + int arg1 ; + int arg2 ; + double *arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_set_dash(dev,N,dashes);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_set_dash. Expected %s", SWIGTYPE_p_double->name); + } + } + g2_set_dash(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_set_font_size) { + int arg1 ; + double arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + croak("Usage: g2_set_font_size(dev,size);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + g2_set_font_size(arg1,arg2); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_set_line_width) { + int arg1 ; + double arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + croak("Usage: g2_set_line_width(dev,w);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + g2_set_line_width(arg1,arg2); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_clear_palette) { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_clear_palette(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_clear_palette(arg1); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_reset_palette) { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_reset_palette(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_reset_palette(arg1); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_allocate_basic_colors) { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_allocate_basic_colors(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_allocate_basic_colors(arg1); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_clear) { + int arg1 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_clear(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_clear(arg1); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_set_background) { + int arg1 ; + int arg2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + croak("Usage: g2_set_background(dev,color);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + g2_set_background(arg1,arg2); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_move) { + int arg1 ; + double arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_move(dev,x,y);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + g2_move(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_move_r) { + int arg1 ; + double arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_move_r(dev,dx,dy);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + g2_move_r(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_plot) { + int arg1 ; + double arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_plot(dev,x,y);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + g2_plot(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_plot_r) { + int arg1 ; + double arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_plot_r(dev,dx,dy);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + g2_plot_r(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_line) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + int argvi = 0; + dXSARGS; + + if ((items < 5) || (items > 5)) { + croak("Usage: g2_line(dev,x1,y1,x2,y2);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + g2_line(arg1,arg2,arg3,arg4,arg5); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_line_r) { + int arg1 ; + double arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_line_r(dev,dx,dy);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + g2_line_r(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_line_to) { + int arg1 ; + double arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_line_to(dev,x,y);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + g2_line_to(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_poly_line) { + int arg1 ; + int arg2 ; + double *arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_poly_line(dev,N_pt,points);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_poly_line. Expected %s", SWIGTYPE_p_double->name); + } + } + g2_poly_line(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_triangle) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + double arg6 ; + double arg7 ; + int argvi = 0; + dXSARGS; + + if ((items < 7) || (items > 7)) { + croak("Usage: g2_triangle(dev,x1,y1,x2,y2,x3,y3);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + arg6 = (double) SvNV(ST(5)); + + arg7 = (double) SvNV(ST(6)); + + g2_triangle(arg1,arg2,arg3,arg4,arg5,arg6,arg7); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_triangle) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + double arg6 ; + double arg7 ; + int argvi = 0; + dXSARGS; + + if ((items < 7) || (items > 7)) { + croak("Usage: g2_filled_triangle(dev,x1,y1,x2,y2,x3,y3);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + arg6 = (double) SvNV(ST(5)); + + arg7 = (double) SvNV(ST(6)); + + g2_filled_triangle(arg1,arg2,arg3,arg4,arg5,arg6,arg7); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_rectangle) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + int argvi = 0; + dXSARGS; + + if ((items < 5) || (items > 5)) { + croak("Usage: g2_rectangle(dev,x1,y1,x2,y2);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + g2_rectangle(arg1,arg2,arg3,arg4,arg5); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_rectangle) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + int argvi = 0; + dXSARGS; + + if ((items < 5) || (items > 5)) { + croak("Usage: g2_filled_rectangle(dev,x1,y1,x2,y2);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + g2_filled_rectangle(arg1,arg2,arg3,arg4,arg5); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_polygon) { + int arg1 ; + int arg2 ; + double *arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_polygon(dev,N_pt,points);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_polygon. Expected %s", SWIGTYPE_p_double->name); + } + } + g2_polygon(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_polygon) { + int arg1 ; + int arg2 ; + double *arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_filled_polygon(dev,N_pt,points);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_filled_polygon. Expected %s", SWIGTYPE_p_double->name); + } + } + g2_filled_polygon(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_circle) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_circle(dev,x,y,r);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + g2_circle(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_circle) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_filled_circle(dev,x,y,r);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + g2_filled_circle(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_ellipse) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + int argvi = 0; + dXSARGS; + + if ((items < 5) || (items > 5)) { + croak("Usage: g2_ellipse(dev,x,y,r1,r2);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + g2_ellipse(arg1,arg2,arg3,arg4,arg5); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_ellipse) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + int argvi = 0; + dXSARGS; + + if ((items < 5) || (items > 5)) { + croak("Usage: g2_filled_ellipse(dev,x,y,r1,r2);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + g2_filled_ellipse(arg1,arg2,arg3,arg4,arg5); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_arc) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + double arg6 ; + double arg7 ; + int argvi = 0; + dXSARGS; + + if ((items < 7) || (items > 7)) { + croak("Usage: g2_arc(dev,x,y,r1,r2,a1,a2);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + arg6 = (double) SvNV(ST(5)); + + arg7 = (double) SvNV(ST(6)); + + g2_arc(arg1,arg2,arg3,arg4,arg5,arg6,arg7); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_arc) { + int arg1 ; + double arg2 ; + double arg3 ; + double arg4 ; + double arg5 ; + double arg6 ; + double arg7 ; + int argvi = 0; + dXSARGS; + + if ((items < 7) || (items > 7)) { + croak("Usage: g2_filled_arc(dev,x,y,r1,r2,a1,a2);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (double) SvNV(ST(3)); + + arg5 = (double) SvNV(ST(4)); + + arg6 = (double) SvNV(ST(5)); + + arg7 = (double) SvNV(ST(6)); + + g2_filled_arc(arg1,arg2,arg3,arg4,arg5,arg6,arg7); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_string) { + int arg1 ; + double arg2 ; + double arg3 ; + char *arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_string(dev,x,y,text);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + if (!SvOK((SV*) ST(3))) arg4 = 0; + else arg4 = (char *) SvPV(ST(3), PL_na); + g2_string(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_image) { + int arg1 ; + double arg2 ; + double arg3 ; + int arg4 ; + int arg5 ; + int *arg6 ; + int argvi = 0; + dXSARGS; + + if ((items < 6) || (items > 6)) { + croak("Usage: g2_image(dev,x,y,x_size,y_size,pens);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + arg4 = (int) SvIV(ST(3)); + arg5 = (int) SvIV(ST(4)); + { + if (SWIG_ConvertPtr(ST(5), (void **) &arg6, SWIGTYPE_p_int,0) < 0) { + croak("Type error in argument 6 of g2_image. Expected %s", SWIGTYPE_p_int->name); + } + } + g2_image(arg1,arg2,arg3,arg4,arg5,arg6); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_set_QP) { + int arg1 ; + double arg2 ; + int arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_set_QP(dev,d,shape);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (int) SvIV(ST(2)); + g2_set_QP(arg1,arg2,(enum QPshape)arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_plot_QP) { + int arg1 ; + double arg2 ; + double arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_plot_QP(dev,x,y);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (double) SvNV(ST(1)); + + arg3 = (double) SvNV(ST(2)); + + g2_plot_QP(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_query_pointer) { + int arg1 ; + double *arg2 ; + double *arg3 ; + unsigned int *arg4 ; + double temp2 ; + double temp3 ; + unsigned int temp4 ; + int argvi = 0; + dXSARGS; + + { + arg2 = &temp2; + } + { + arg3 = &temp3; + } + { + arg4 = &temp4; + } + if ((items < 1) || (items > 1)) { + croak("Usage: g2_query_pointer(dev);"); + } + arg1 = (int) SvIV(ST(0)); + g2_query_pointer(arg1,arg2,arg3,arg4); + + + { + if (argvi >= items) { + EXTEND(sp,1); + } + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi),(double) *(arg2)); + argvi++; + } + { + if (argvi >= items) { + EXTEND(sp,1); + } + ST(argvi) = sv_newmortal(); + sv_setnv(ST(argvi),(double) *(arg3)); + argvi++; + } + { + if (argvi >= items) { + EXTEND(sp,1); + } + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi),(IV) *(arg4)); + argvi++; + } + XSRETURN(argvi); +} + + +XS(_wrap_g2_spline) { + int arg1 ; + int arg2 ; + double *arg3 ; + int arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_spline(id,n,points,o);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_spline. Expected %s", SWIGTYPE_p_double->name); + } + } + arg4 = (int) SvIV(ST(3)); + g2_spline(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_b_spline) { + int arg1 ; + int arg2 ; + double *arg3 ; + int arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_b_spline(id,n,points,o);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_b_spline. Expected %s", SWIGTYPE_p_double->name); + } + } + arg4 = (int) SvIV(ST(3)); + g2_b_spline(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_raspln) { + int arg1 ; + int arg2 ; + double *arg3 ; + double arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_raspln(id,n,points,tn);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_raspln. Expected %s", SWIGTYPE_p_double->name); + } + } + arg4 = (double) SvNV(ST(3)); + + g2_raspln(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_para_3) { + int arg1 ; + int arg2 ; + double *arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_para_3(id,n,points);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_para_3. Expected %s", SWIGTYPE_p_double->name); + } + } + g2_para_3(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_para_5) { + int arg1 ; + int arg2 ; + double *arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_para_5(id,n,points);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_para_5. Expected %s", SWIGTYPE_p_double->name); + } + } + g2_para_5(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_spline) { + int arg1 ; + int arg2 ; + double *arg3 ; + int arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_filled_spline(id,n,points,o);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_filled_spline. Expected %s", SWIGTYPE_p_double->name); + } + } + arg4 = (int) SvIV(ST(3)); + g2_filled_spline(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_b_spline) { + int arg1 ; + int arg2 ; + double *arg3 ; + int arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_filled_b_spline(id,n,points,o);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_filled_b_spline. Expected %s", SWIGTYPE_p_double->name); + } + } + arg4 = (int) SvIV(ST(3)); + g2_filled_b_spline(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_raspln) { + int arg1 ; + int arg2 ; + double *arg3 ; + double arg4 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + croak("Usage: g2_filled_raspln(id,n,points,tn);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_filled_raspln. Expected %s", SWIGTYPE_p_double->name); + } + } + arg4 = (double) SvNV(ST(3)); + + g2_filled_raspln(arg1,arg2,arg3,arg4); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_para_3) { + int arg1 ; + int arg2 ; + double *arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_filled_para_3(id,n,points);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_filled_para_3. Expected %s", SWIGTYPE_p_double->name); + } + } + g2_filled_para_3(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_filled_para_5) { + int arg1 ; + int arg2 ; + double *arg3 ; + int argvi = 0; + dXSARGS; + + if ((items < 3) || (items > 3)) { + croak("Usage: g2_filled_para_5(id,n,points);"); + } + arg1 = (int) SvIV(ST(0)); + arg2 = (int) SvIV(ST(1)); + { + if (SWIG_ConvertPtr(ST(2), (void **) &arg3, SWIGTYPE_p_double,0) < 0) { + croak("Type error in argument 3 of g2_filled_para_5. Expected %s", SWIGTYPE_p_double->name); + } + } + g2_filled_para_5(arg1,arg2,arg3); + + + XSRETURN(argvi); +} + + +XS(_wrap_g2_device_exist) { + int arg1 ; + int result; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + croak("Usage: g2_device_exist(dix);"); + } + arg1 = (int) SvIV(ST(0)); + result = (int)g2_device_exist(arg1); + + ST(argvi) = sv_newmortal(); + sv_setiv(ST(argvi++), (IV) result); + XSRETURN(argvi); +} + + + +/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */ + +static swig_type_info _swigt__p_double[] = {{"_p_double", 0, "double *"},{"_p_double"},{0}}; +static swig_type_info _swigt__p_int[] = {{"_p_int", 0, "int *"},{"_p_int"},{0}}; + +static swig_type_info *swig_types_initial[] = { +_swigt__p_double, +_swigt__p_int, +0 +}; + + +/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (END) -------- */ + +static swig_constant_info swig_constants[] = { +{ SWIG_STRING, (char *) SWIG_prefix "G2_VERSION", 0, 0, (void *)"0.41a", 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A0", (long) g2_A0, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A1", (long) g2_A1, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A2", (long) g2_A2, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A3", (long) g2_A3, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A4", (long) g2_A4, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A5", (long) g2_A5, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A6", (long) g2_A6, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A7", (long) g2_A7, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A8", (long) g2_A8, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_A9", (long) g2_A9, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B0", (long) g2_B0, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B1", (long) g2_B1, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B2", (long) g2_B2, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B3", (long) g2_B3, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B4", (long) g2_B4, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B5", (long) g2_B5, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B6", (long) g2_B6, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B7", (long) g2_B7, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B8", (long) g2_B8, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B9", (long) g2_B9, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_B10", (long) g2_B10, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_Comm_10_Envelope", (long) g2_Comm_10_Envelope, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_C5_Envelope", (long) g2_C5_Envelope, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_DL_Envelope", (long) g2_DL_Envelope, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_Folio", (long) g2_Folio, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_Executive", (long) g2_Executive, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_Letter", (long) g2_Letter, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_Legal", (long) g2_Legal, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_Ledger", (long) g2_Ledger, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_Tabloid", (long) g2_Tabloid, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_PS_land", (long) g2_PS_land, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_PS_port", (long) g2_PS_port, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_PS_PostScript", (long) g2_PS_PostScript, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_PS_EPSF", (long) g2_PS_EPSF, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_PS_EPSF_CLIP", (long) g2_PS_EPSF_CLIP, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_gd_jpeg", (long) g2_gd_jpeg, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_gd_png", (long) g2_gd_png, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_win32", (long) g2_win32, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "g2_wmf32", (long) g2_wmf32, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "QPrect", (long) QPrect, 0, 0, 0}, +{ SWIG_INT, (char *) SWIG_prefix "QPcirc", (long) QPcirc, 0, 0, 0}, +{0} +}; +#ifdef __cplusplus +} +#endif +static swig_variable_info swig_variables[] = { +{0} +}; +static swig_command_info swig_commands[] = { +{"g2::g2_open_PS", _wrap_g2_open_PS}, +{"g2::g2_open_EPSF", _wrap_g2_open_EPSF}, +{"g2::g2_open_EPSF_CLIP", _wrap_g2_open_EPSF_CLIP}, +{"g2::g2_open_gd", _wrap_g2_open_gd}, +{"g2::g2_open_win32", _wrap_g2_open_win32}, +{"g2::g2_open_vd", _wrap_g2_open_vd}, +{"g2::g2_attach", _wrap_g2_attach}, +{"g2::g2_detach", _wrap_g2_detach}, +{"g2::g2_close", _wrap_g2_close}, +{"g2::g2_set_auto_flush", _wrap_g2_set_auto_flush}, +{"g2::g2_flush", _wrap_g2_flush}, +{"g2::g2_save", _wrap_g2_save}, +{"g2::g2_set_coordinate_system", _wrap_g2_set_coordinate_system}, +{"g2::g2_ld", _wrap_g2_ld}, +{"g2::g2_set_ld", _wrap_g2_set_ld}, +{"g2::g2_ink", _wrap_g2_ink}, +{"g2::g2_pen", _wrap_g2_pen}, +{"g2::g2_set_dash", _wrap_g2_set_dash}, +{"g2::g2_set_font_size", _wrap_g2_set_font_size}, +{"g2::g2_set_line_width", _wrap_g2_set_line_width}, +{"g2::g2_clear_palette", _wrap_g2_clear_palette}, +{"g2::g2_reset_palette", _wrap_g2_reset_palette}, +{"g2::g2_allocate_basic_colors", _wrap_g2_allocate_basic_colors}, +{"g2::g2_clear", _wrap_g2_clear}, +{"g2::g2_set_background", _wrap_g2_set_background}, +{"g2::g2_move", _wrap_g2_move}, +{"g2::g2_move_r", _wrap_g2_move_r}, +{"g2::g2_plot", _wrap_g2_plot}, +{"g2::g2_plot_r", _wrap_g2_plot_r}, +{"g2::g2_line", _wrap_g2_line}, +{"g2::g2_line_r", _wrap_g2_line_r}, +{"g2::g2_line_to", _wrap_g2_line_to}, +{"g2::g2_poly_line", _wrap_g2_poly_line}, +{"g2::g2_triangle", _wrap_g2_triangle}, +{"g2::g2_filled_triangle", _wrap_g2_filled_triangle}, +{"g2::g2_rectangle", _wrap_g2_rectangle}, +{"g2::g2_filled_rectangle", _wrap_g2_filled_rectangle}, +{"g2::g2_polygon", _wrap_g2_polygon}, +{"g2::g2_filled_polygon", _wrap_g2_filled_polygon}, +{"g2::g2_circle", _wrap_g2_circle}, +{"g2::g2_filled_circle", _wrap_g2_filled_circle}, +{"g2::g2_ellipse", _wrap_g2_ellipse}, +{"g2::g2_filled_ellipse", _wrap_g2_filled_ellipse}, +{"g2::g2_arc", _wrap_g2_arc}, +{"g2::g2_filled_arc", _wrap_g2_filled_arc}, +{"g2::g2_string", _wrap_g2_string}, +{"g2::g2_image", _wrap_g2_image}, +{"g2::g2_set_QP", _wrap_g2_set_QP}, +{"g2::g2_plot_QP", _wrap_g2_plot_QP}, +{"g2::g2_query_pointer", _wrap_g2_query_pointer}, +{"g2::g2_spline", _wrap_g2_spline}, +{"g2::g2_b_spline", _wrap_g2_b_spline}, +{"g2::g2_raspln", _wrap_g2_raspln}, +{"g2::g2_para_3", _wrap_g2_para_3}, +{"g2::g2_para_5", _wrap_g2_para_5}, +{"g2::g2_filled_spline", _wrap_g2_filled_spline}, +{"g2::g2_filled_b_spline", _wrap_g2_filled_b_spline}, +{"g2::g2_filled_raspln", _wrap_g2_filled_raspln}, +{"g2::g2_filled_para_3", _wrap_g2_filled_para_3}, +{"g2::g2_filled_para_5", _wrap_g2_filled_para_5}, +{"g2::g2_device_exist", _wrap_g2_device_exist}, +{0,0} +}; + +#ifdef __cplusplus +extern "C" +#endif + +XS(SWIG_init) { + dXSARGS; + int i; + for (i = 0; swig_types_initial[i]; i++) { + swig_types[i] = SWIG_TypeRegister(swig_types_initial[i]); + } + + /* Install commands */ + for (i = 0; swig_commands[i].name; i++) { + newXS((char*) swig_commands[i].name,swig_commands[i].wrapper, (char*)__FILE__); + } + + /* Install variables */ + for (i = 0; swig_variables[i].name; i++) { + SV *sv; + sv = perl_get_sv((char*) swig_variables[i].name, TRUE | 0x2); + if (swig_variables[i].type) { + SWIG_MakePtr(sv,(void *)1, *swig_variables[i].type,0); + }else { + sv_setiv(sv,(IV) 0); + } + swig_create_magic(sv, (char *) swig_variables[i].name, swig_variables[i].set, swig_variables[i].get); + } + + /* Install constant */ + for (i = 0; swig_constants[i].type; i++) { + SV *sv; + sv = perl_get_sv((char*)swig_constants[i].name, TRUE | 0x2); + switch(swig_constants[i].type) { + case SWIG_INT: + sv_setiv(sv, (IV) swig_constants[i].lvalue); + break; + case SWIG_FLOAT: + sv_setnv(sv, (double) swig_constants[i].dvalue); + break; + case SWIG_STRING: + sv_setpv(sv, (char *) swig_constants[i].pvalue); + break; + case SWIG_POINTER: + SWIG_MakePtr(sv, swig_constants[i].pvalue, *(swig_constants[i].ptype),0); + break; + case SWIG_BINARY: + /* obj = SWIG_NewPackedObj(swig_constants[i].pvalue, swig_constants[i].lvalue, *(swig_constants[i].ptype)); */ + break; + default: + break; + } + SvREADONLY_on(sv); + } + + ST(0) = &PL_sv_yes; + XSRETURN(1); +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/simple_win32.dsp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/simple_win32.dsp new file mode 100755 index 000000000..fae2d33cb --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/simple_win32.dsp @@ -0,0 +1,101 @@ +# Microsoft Developer Studio Project File - Name="simple_win32" - Package Owner=<4> +# Microsoft Developer Studio Generated Build File, Format Version 6.00 +# ** DO NOT EDIT ** + +# TARGTYPE "Win32 (x86) Console Application" 0x0103 + +CFG=simple_win32 - Win32 Debug +!MESSAGE This is not a valid makefile. To build this project using NMAKE, +!MESSAGE use the Export Makefile command and run +!MESSAGE +!MESSAGE NMAKE /f "simple_win32.mak". +!MESSAGE +!MESSAGE You can specify a configuration when running NMAKE +!MESSAGE by defining the macro CFG on the command line. For example: +!MESSAGE +!MESSAGE NMAKE /f "simple_win32.mak" CFG="simple_win32 - Win32 Debug" +!MESSAGE +!MESSAGE Possible choices for configuration are: +!MESSAGE +!MESSAGE "simple_win32 - Win32 Release" (based on "Win32 (x86) Console Application") +!MESSAGE "simple_win32 - Win32 Debug" (based on "Win32 (x86) Console Application") +!MESSAGE + +# Begin Project +# PROP AllowPerConfigDependencies 0 +# PROP Scc_ProjName "" +# PROP Scc_LocalPath "" +CPP=cl.exe +RSC=rc.exe + +!IF "$(CFG)" == "simple_win32 - Win32 Release" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 0 +# PROP BASE Output_Dir "Release" +# PROP BASE Intermediate_Dir "Release" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 0 +# PROP Output_Dir "Release" +# PROP Intermediate_Dir "Release" +# PROP Target_Dir "" +# ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c +# ADD CPP /nologo /W3 /GX /O2 /I "src/gd" /I "./src" /I "src" /I "src/PS" /I "src/WIN32" /I "src/GD" /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c +# ADD BASE RSC /l 0x409 /d "NDEBUG" +# ADD RSC /l 0x409 /d "NDEBUG" +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LINK32=link.exe +# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386 +# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386 + +!ELSEIF "$(CFG)" == "simple_win32 - Win32 Debug" + +# PROP BASE Use_MFC 0 +# PROP BASE Use_Debug_Libraries 1 +# PROP BASE Output_Dir "simple_win32___Win32_Debug" +# PROP BASE Intermediate_Dir "simple_win32___Win32_Debug" +# PROP BASE Target_Dir "" +# PROP Use_MFC 0 +# PROP Use_Debug_Libraries 1 +# PROP Output_Dir "Debug" +# PROP Intermediate_Dir "Debug" +# PROP Ignore_Export_Lib 0 +# PROP Target_Dir "" +# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /GZ /c +# ADD CPP /nologo /W3 /Gm /GX /ZI /Od /I "src/gd" /I "./src" /I "src" /I "src/PS" /I "src/WIN32" /I "src/GD" /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /GZ /c +# ADD BASE RSC /l 0x409 /d "_DEBUG" +# ADD RSC /l 0x409 /d "_DEBUG" +BSC32=bscmake.exe +# ADD BASE BSC32 /nologo +# ADD BSC32 /nologo +LINK32=link.exe +# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept +# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept + +!ENDIF + +# Begin Target + +# Name "simple_win32 - Win32 Release" +# Name "simple_win32 - Win32 Debug" +# Begin Group "Source Files" + +# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat" +# Begin Source File + +SOURCE=.\demo\simple_win32.c +# End Source File +# End Group +# Begin Group "Header Files" + +# PROP Default_Filter "h;hpp;hxx;hm;inl" +# End Group +# Begin Group "Resource Files" + +# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe" +# End Group +# End Target +# End Project diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Repository new file mode 100755 index 000000000..1b465e887 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Entries new file mode 100755 index 000000000..8a0902d7b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Entries @@ -0,0 +1,27 @@ +D/CVS//// +D/FIG//// +D/GD//// +D/PS//// +D/Win32//// +D/X11//// +/g2.h/1.1/Tue Jun 14 20:44:20 2005// +/g2_config.h/1.1/Thu Mar 11 23:08:59 2004// +/g2_control_pd.c/1.1/Tue Jun 14 20:44:20 2005// +/g2_control_pd.h/1.1/Tue Jun 14 20:44:20 2005// +/g2_device.c/1.1/Tue Apr 17 20:16:38 2001// +/g2_device.h/1.1/Tue Apr 17 20:16:38 2001// +/g2_fif.c/1.1/Wed Apr 7 22:27:44 2004// +/g2_funix.h/1.1/Tue Jun 14 20:44:20 2005// +/g2_graphic_pd.c/1.1/Tue Feb 22 21:44:46 2005// +/g2_graphic_pd.h/1.1/Thu Feb 26 23:50:24 2004// +/g2_physical_device.c/1.1/Tue Apr 17 20:16:38 2001// +/g2_physical_device.h/1.1/Tue Apr 17 20:16:38 2001// +/g2_splines.c/1.1/Tue Feb 22 21:41:40 2005// +/g2_ui_control.c/1.1/Tue Jun 14 20:44:20 2005// +/g2_ui_device.c/1.1/Tue Mar 23 00:20:27 2004// +/g2_ui_graphic.c/1.1/Tue Mar 23 23:50:40 2004// +/g2_ui_virtual_device.c/1.1/Tue Mar 23 00:20:27 2004// +/g2_util.c/1.1/Wed Apr 7 21:51:25 2004// +/g2_util.h/1.1/Thu Mar 11 23:01:03 2004// +/g2_virtual_device.c/1.1/Tue Apr 17 20:16:38 2001// +/g2_virtual_device.h/1.1/Tue Apr 17 20:16:38 2001// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Repository new file mode 100755 index 000000000..7d4eeb98a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Repository new file mode 100755 index 000000000..d9e68a82a --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/FIG/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Entries new file mode 100755 index 000000000..0e5e0f9ef --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Entries @@ -0,0 +1,5 @@ +D/CVS//// +/g2_FIG.c/1.1/Mon Apr 5 21:40:53 2004// +/g2_FIG.h/1.1/Thu Apr 1 22:29:34 2004// +/g2_FIG_P.h/1.1/Sat Apr 3 23:26:57 2004// +/g2_FIG_funix.h/1.1/Sat Apr 3 22:58:26 2004// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Repository new file mode 100755 index 000000000..1a7809ed8 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/FIG diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.c new file mode 100755 index 000000000..157073881 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.c @@ -0,0 +1,486 @@ +/***************************************************************************** +** Copyright (C) 1998-2004 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include +#include +#include +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_util.h" +#include "g2_config.h" + +#include "g2_FIG.h" +#include "g2_FIG_P.h" +#include "g2_FIG_funix.h" + +#ifndef PI +#define PI 3.14159265358979323846 +#endif /* PI */ + +static int N_FIG=0; +static g2_FIG_device *g2_FIG_dev=NULL; + +/** + * \ingroup physdev + * \defgroup FIG FIG + * + * FIG devices generate output in the FIG 3.2 format. For more details + * about FIG format and xfig application please visit http://www.xfig.org . + * + * \note FIG is a vector-oriented (as oposed to pixel-oriented) format. + * Therefore ::g2_image function and splines are not optimally supported. + */ + + +/** + * + * Create a FIG device. g2 uses A4 paper size (landscape orientation) as default. + * + * \param file_name fig file name + * + * \return physical device id + * + * \ingroup FIG + */ +G2L int g2_open_FIG(const char *file_name) +{ + g2_FIG_device *figout=NULL; + int pid=-1, i; + int vid; + FILE *fp; + + if((fp=fopen(file_name, "w"))==NULL) { + g2_log(Error, "g2_attach_PS: Error! Can not open file '%s'\n", + file_name); + return -1; + } + + if(g2_FIG_dev==NULL) { + g2_FIG_dev=g2_malloc(sizeof(g2_FIG_device)); + N_FIG=1; /* first FIG device */ + figout=&g2_FIG_dev[N_FIG-1]; + pid=0; + } else { + for(i=0;ifp=fp; + figout->pen_color=1; + figout->thickness=-1; + figout->font_size=-1; + figout->N_inks=0; + + /* write file header (incl. color placeholder) */ + g2_FIG_write_file_header(figout); + + /* g2 settings callbacks */ + g2_allocate_basic_colors(vid); + g2_pen(vid, 1); + g2_set_line_width(vid, 1); + g2_set_dash(vid, 0, NULL); + g2_set_font_size(vid, 12); + + return vid; +} + + + +/* + * + * Write header for fig file + * + */ +int g2_FIG_write_file_header(g2_FIG_device *fig) +{ + int i; + + fprintf(fig->fp, "#FIG 3.2\n"); + fprintf(fig->fp, "#Creator: g2 %s\n", G2_VERSION); + + fprintf(fig->fp, "Landscape\n"); + fprintf(fig->fp, "Flush Left\n"); + fprintf(fig->fp, "Metric\n"); + fprintf(fig->fp, "A4\n"); + fprintf(fig->fp, "100\n"); + fprintf(fig->fp, "Single\n"); + fprintf(fig->fp, "-2\n"); + fprintf(fig->fp, "1200 2\n"); + + /* write placeholder for all colors */ + fgetpos(fig->fp, &(fig->color_file_pos)); + for(i=0;i<512;i++) + fprintf(fig->fp, "0 %3d #%02x%02x%02x\n",32+i, 0xff, 0xff, 0xff); + + return 0; +} + + +/* + * + * Delete FIG device + * + */ +int g2_FIG_delete(int pid, void *pdp) +{ + int i; + g2_FIG_device *fig=&g2_FIG_dev[pid]; + + /* now write all defined colors to the reserved place */ + fsetpos(fig->fp, &(fig->color_file_pos)); + for(i=0;iN_inks;i++) { + fprintf(fig->fp, "0 %3d #%02x%02x%02x\n", + 32+i, + (int)fig->inks[i].red, + (int)fig->inks[i].green, + (int)fig->inks[i].blue); + } + + fclose(fig->fp); + fig->fp=NULL; /* free place */ + return 0; +} + + + +int g2_FIG_ink(int pid, void *pdp, + double red, double green, double blue) +{ + /* the fig pen space is betwen 32 and 543, total of 512 colors, + in g2 implementation from 0000 to 0777. + On the other hand ink space is between #000000 and #ffffff. */ + + g2_FIG_device *fig=&g2_FIG_dev[pid]; + + if(fig->N_inks>=512) + return -1; + + fig->inks[fig->N_inks].red = red*0xff; + fig->inks[fig->N_inks].green = green*0xff; + fig->inks[fig->N_inks].blue = blue*0xff; + + return fig->N_inks++; +} + + + +int g2_FIG_pen(int pid, void *pdp, int color) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + + if(color>=fig->N_inks) { + return -1; + } + + fig->pen_color = 32+color; + + return 0; +} + + + +int g2_FIG_set_background(int pid, void *pdp, int color) +{ + return -1; +} + + + +int g2_FIG_clear_palette(int pid, void *pdp) +{ + return -1; +} + + + +int g2_FIG_set_line_width(int pid, void *pdp, int w) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + fig->thickness = w*80./1200.; + return 0; +} + + + +int g2_FIG_set_dash(int pid, void *pdp, int N, int *data) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + int black, white; + + if(N==0 || data==NULL) { + fig->line_style=0; + fig->style_val=-1; + return 0; + } + if(N<2) { + return -1; + } + black = data[0]*80./1200.; /* FIG format has no sofistificated dash concept */ + white = data[1]*80./1200.; /* we will do out best */ + if(black<4) { + fig->line_style = 2; + } else { + fig->line_style = 1; + } + fig->style_val = white; + return 0; +} + + + +int g2_FIG_set_font_size(int pid, void *pdp, int size) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + fig->font_size = size*72./1200.; + return 0; +} + + + +int g2_FIG_clear(int pid, void *pdp) +{ + return -1; +} + + + +int g2_FIG_flush(int pid, void *pdp) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + fflush(fig->fp); + return 0; +} + + + +int g2_FIG_plot(int pid, void *pdp, int x, int y) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + fprintf(fig->fp, "2 1 0 %d %d -1 1 1 -1 -1 1 0 -1 0 0 2\n", + 1, fig->pen_color); + fprintf(fig->fp, " %d %d\n %d %d\n", x, y, x+1, y); + return 0; +} + + + +int g2_FIG_line(int pid, void *pdp, int x1, int y1, int x2, int y2) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + fprintf(fig->fp, "2 1 %d %d %d -1 1 1 -1 %d 1 0 -1 0 0 2\n", + fig->line_style, fig->thickness, fig->pen_color, fig->style_val); + fprintf(fig->fp, " %d %d\n %d %d\n", x1, y1, x2, y2); + return 0; +} + + + +int g2_FIG_poly_line(int pid, void *pdp, int N, int *points) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + int i; + + fprintf(fig->fp,"2 1 %d %d %d -1 1 1 -1 %d 1 0 -1 0 0 %d\n", + fig->line_style, fig->thickness, fig->pen_color, fig->style_val, N); + for(i=0;i<2*N;i+=2) { + fprintf(fig->fp, " %d %d\n", points[i], points[i+1]); + } + return 0; +} + + + +int g2_FIG_polygon(int pid, void *pdp, int N, int *points) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + int i; + + if(N<2) { + return -1; + } + + fprintf(fig->fp,"2 3 %d %d %d -1 1 1 -1 %d 1 0 -1 0 0 %d\n", + fig->line_style, fig->thickness, fig->pen_color, fig->style_val, N+1); + for(i=0;i<2*N;i+=2) { + fprintf(fig->fp, " %d %d\n", points[i], points[i+1]); + } + fprintf(fig->fp, " %d %d\n", points[0], points[1]); + return 0; +} + + + +int g2_FIG_filled_polygon(int pid, void *pdp, int N, int *points) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + int i; + + if(N<2) { + return -1; + } + + fprintf(fig->fp,"2 3 %d %d %d %d 1 1 20 %d 1 0 -1 0 0 %d\n", + fig->line_style, fig->thickness, fig->pen_color, fig->pen_color, + fig->style_val, N+1); + for(i=0;i<2*N;i+=2) { + fprintf(fig->fp, " %d %d\n", points[i], points[i+1]); + } + fprintf(fig->fp, " %d %d\n", points[0], points[1]); + return 0; +} + + +int g2_FIG_arc(int pid, void *pdp, + int x, int y, + int r1, int r2, + double a1, double a2) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + double a0, d; + double a0_rad, da_rad; + int N, i; + + a0=fmod(a1, 360.) + (a1<0? 360:0); /* map a1 to [0, 360) */ + d=a2>a1? a2-a1:a2-a1+360; + + N=3+d/18; + + a0_rad = a0*2.*PI/360.; + da_rad = d*2.*PI/360./(N-1); + + fprintf(fig->fp, "3 2 %d %d %d -1 1 -1-1 %d 0 0 0 %d\n", + fig->line_style, fig->thickness, fig->pen_color, fig->style_val, N); + for(i=0;ifp, " %d %d\n", + (int)(x+r1*cos(a0_rad+i*da_rad)), + (int)(y-r2*sin(a0_rad+i*da_rad))); + } + fprintf(fig->fp, " -1"); + for(i=1;ifp, " -1"); + } + fprintf(fig->fp, " -1\n"); + + return 0; +} + + +int g2_FIG_filled_arc(int pid, void *pdp, + int x, int y, + int r1, int r2, + double a1, double a2) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + double a0, d; + double a0_rad, da_rad; + int N, i; + + a0=fmod(a1, 360.) + (a1<0? 360:0); /* map a1 to [0, 360) */ + d=a2>a1? a2-a1:a2-a1+360; + + N=3+d/18; + + a0_rad = a0*2.*PI/360.; + da_rad = d*2.*PI/360./(N-1); + + fprintf(fig->fp, "3 2 %d %d %d %d 1 -1 20 %d 0 0 0 %d\n", + fig->line_style, fig->thickness, fig->pen_color, fig->pen_color, + fig->style_val, N+2); + for(i=0;ifp, " %d %d\n", + (int)(x+r1*cos(a0_rad+i*da_rad)), (int)(y-r2*sin(a0_rad+i*da_rad))); + } + fprintf(fig->fp, " %d %d\n", x, y); + fprintf(fig->fp, " %d %d\n", + (int)(x+r1*cos(a0_rad+0*da_rad)), + (int)(y-r2*sin(a0_rad+0*da_rad))); + fprintf(fig->fp, " 0"); + for(i=1;ifp, " -1"); + } + fprintf(fig->fp, " 0 0 0\n"); + + return 0; +} + + +int g2_FIG_ellipse(int pid, void *pdp, + int x, int y, + int r1, int r2) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + fprintf(fig->fp,"1 1 %d %d %d -1 1 -1 -1 %d 1 0.0 %d %d %d %d %d %d %d %d\n", + fig->line_style, fig->thickness, fig->pen_color, fig->style_val, + x, y, r1, r2, x, y, x+r1, y+r2); + + return 0; +} + + +int g2_FIG_filled_ellipse(int pid, void *pdp, + int x, int y, + int r1, int r2) +{ + g2_FIG_device *fig=&g2_FIG_dev[pid]; + fprintf(fig->fp,"1 1 %d %d %d %d 1 -1 20 %d 1 0.0 %d %d %d %d %d %d %d %d\n", + fig->line_style, fig->thickness, fig->pen_color, fig->pen_color, fig->style_val, + x, y, r1, r2, x, y, x+r1, y+r2); + + return 0; +} + + +int g2_FIG_draw_string(int pid, void *pdp, + int x, int y, const char *text) +{ + const char *c; + g2_FIG_device *fig=&g2_FIG_dev[pid]; + if(fig->font_size<=0) + return 0; + fprintf(fig->fp,"4 0 %d 1 -1 0 %d 0 5 %d %d %d %d ", + fig->pen_color, fig->font_size, fig->font_size, fig->font_size*strlen(text), x, y); + for(c=text;*c;c++) { + if(*c=='\\') + fputc('\\', fig->fp); /* escape \\ */ + fputc(*c, fig->fp); + } + fprintf(fig->fp,"\\001\n"); + return 0; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.h new file mode 100755 index 000000000..908d8f384 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.h @@ -0,0 +1,54 @@ +/***************************************************************************** +** Copyright (C) 1998-2004 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_FIG_H +#define _G2_FIG_H + +#if defined(__cplusplus) +extern "C" +{ +#endif + + +/* Common Library header for DLL and application */ +#ifdef WIN32 +#ifdef G2DLL +#ifdef MAKEDLL +/* Create DLL */ +#define G2L __declspec( dllexport) +#else +/* Use DLL */ +#define G2L __declspec( dllimport) +#endif +#else +/* Use static win32 */ +#define G2L +#endif +#else +/* Use non-win32 */ +#define G2L +#endif + +G2L int g2_open_FIG(const char *file_name); + + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + +#endif /* _G2_FIG_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.o new file mode 100755 index 000000000..73279fc8e Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG_P.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG_P.h new file mode 100755 index 000000000..c1d15bc9d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG_P.h @@ -0,0 +1,82 @@ +/***************************************************************************** +** This is part of the g2 library +** Copyright (C) 1998 Ljubomir Milanovic & Horst Wagner +** +** This program is free software; you can redistribute it and/or modify +** it under the terms of the GNU General Public License (version 2) as +** published by the Free Software Foundation. +** +** This program is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +** GNU General Public License for more details. +** +** You should have received a copy of the GNU General Public License +** along with this program; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_FIG_P_H +#define _G2_FIG_P_H + +#include "g2_FIG.h" + +#include + +typedef struct _g2_FIG_inks { + unsigned char red; + unsigned char green; + unsigned char blue; +} g2_FIG_inks; + +typedef struct _g2_FIG_device { + FILE *fp; /* output file pointer */ + int pen_color; /* current pen */ + int thickness; /* line thickness */ + int font_size; /* font size */ + int line_style; /* line style according to fig format */ + int style_val; /* line style value acc. to fig format */ + + g2_FIG_inks inks[512]; /* 512 user defined colors */ + int N_inks; /* number of allocated colors */ + fpos_t color_file_pos; /* file position of colors, ftell */ +} g2_FIG_device; + + + +int g2_FIG_write_file_header(g2_FIG_device *figd); +int g2_FIG_delete(int pid, void *pdp); +int g2_FIG_ink(int pid, void *pdp, + double red, double green, double blue); +int g2_FIG_pen(int pid, void *pdp, int color); +int g2_FIG_set_background(int pid, void *pdp, int color); +int g2_FIG_reset_palette(int pid, void *pdp); +int g2_FIG_clear_palette(int pid, void *pdp); +int g2_FIG_set_line_width(int pid, void *pdp, int w); +int g2_FIG_set_dash(int pid, void *pdp, int N, int *data); +int g2_FIG_set_font_size(int pid, void *pdp, int size); +int g2_FIG_clear(int pid, void *pdp); +int g2_FIG_flush(int pid, void *pdp); +int g2_FIG_plot(int pid, void *pdp, int x, int y); +int g2_FIG_line(int pid, void *pdp, int x1, int y1, int x2, int y2); +int g2_FIG_poly_line(int pid, void *pdp, int N, int *points); +int g2_FIG_polygon(int pid, void *pdp, int N, int *points); +int g2_FIG_filled_polygon(int pid, void *pdp, int N, int *points); +int g2_FIG_arc(int pid, void *pdp, + int x, int y, + int r1, int r2, + double a1, double a2); +int g2_FIG_filled_arc(int pid, void *pdp, + int x, int y, + int r1, int r2, + double a1, double a2); +int g2_FIG_ellipse(int pid, void *pdp, + int x, int y, + int r1, int r2); +int g2_FIG_filled_ellipse(int pid, void *pdp, + int x, int y, + int r1, int r2); +int g2_FIG_draw_string(int pid, void *pdp, + int x, int y, const char *text); + +#endif /* _G2_FIG_P_H */ + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG_funix.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG_funix.h new file mode 100755 index 000000000..ac0ddfa30 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/FIG/g2_FIG_funix.h @@ -0,0 +1,56 @@ +/***************************************************************************** +** Copyright (C) 1998-2004 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_FIG_FUNIX_H +#define _G2_FIG_FUNIX_H + +#include "g2_FIG_P.h" +#include "g2_physical_device.h" + +const g2_funix_fun g2_FIG_funix[] = { + { g2_Delete, g2_FIG_delete }, + { g2_Ink, g2_FIG_ink }, + { g2_Pen, g2_FIG_pen }, + { g2_SetBackground, NULL }, + { g2_ClearPalette, NULL }, + { g2_SetLineWidth, g2_FIG_set_line_width }, + { g2_SetDash, g2_FIG_set_dash }, + { g2_SetFontSize, g2_FIG_set_font_size }, + { g2_Clear, g2_FIG_clear }, + { g2_Flush, g2_FIG_flush }, + { g2_Save, g2_FIG_flush }, + { g2_Plot, g2_FIG_plot }, + { g2_Line, g2_FIG_line }, + { g2_PolyLine, g2_FIG_poly_line }, + { g2_Polygon, g2_FIG_polygon }, + { g2_FilledPolygon, g2_FIG_filled_polygon }, + { g2_Rectangle, NULL }, + { g2_FilledRectangle, NULL }, + { g2_Triangle, NULL }, + { g2_FilledTriangle, NULL }, + { g2_Arc, g2_FIG_arc }, + { g2_FilledArc, g2_FIG_filled_arc }, + { g2_Ellipse, g2_FIG_ellipse }, + { g2_FilledEllipse, g2_FIG_filled_ellipse }, + { g2_Circle, NULL }, + { g2_FilledCircle, NULL }, + { g2_String, g2_FIG_draw_string }, + { g2_FUNIX_NULL, NULL } }; + + +#endif /* _G2_FIG_FUNIX_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Repository new file mode 100755 index 000000000..df74fdf87 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/GD/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Entries new file mode 100755 index 000000000..b1d20dce6 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Entries @@ -0,0 +1,5 @@ +D/CVS//// +/g2_gd.c/1.1/Tue Feb 22 03:51:05 2005// +/g2_gd.h/1.1/Tue Mar 23 23:50:40 2004// +/g2_gd_P.h/1.1/Thu Feb 26 23:50:24 2004// +/g2_gd_funix.h/1.1/Tue Feb 22 03:51:06 2005// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Repository new file mode 100755 index 000000000..9d8874e48 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/GD diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd.c new file mode 100755 index 000000000..2bb23703d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd.c @@ -0,0 +1,348 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ + +#include +#include +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_util.h" +#include "g2_config.h" + +#include "g2_gd_P.h" +#include "g2_gd.h" + +#define PDP ((struct g2_gd_STRUCT *)pdp) + +#include "g2_gd_funix.h" + +#ifndef PI +#define PI 3.14159265358979323846 +#endif /* PI */ + + +/** + * \ingroup physdev + * \defgroup GD GD + */ + + +/** + * + * Create a GD device. + * + * \param filename output file name + * \param width width + * \param height height + * \param gd_type file type, see ::g2_gd_type + * + * \return physical device id + * + * \ingroup GD + */ +int g2_open_gd(const char *filename, int width, int height, enum g2_gd_type gd_type) +{ + int pid=-1; + g2_gd_STRUCT *pdp; + + pdp = (g2_gd_STRUCT *)malloc(sizeof(g2_gd_STRUCT)); + + pdp->width = width; + pdp->height = height; + pdp->gd_type = gd_type; + pdp->im = gdImageCreate(width,height); + pdp->f = fopen(filename,"wb"); + pdp->NoOfInks = 0; + pdp->BackCol = 0; + + pid = g2_register_physical_device(pid, pdp, + g2_IntCoor, g2_gd_funix, + 1.0, -1.0, + 0.0, height-1); + + g2_gd_Clear(pid,pdp); + g2_set_line_width(pid, 0.0); + g2_set_font_size(pid, 12.0); + g2_allocate_basic_colors(pid); + g2_pen(pid, 1); + + return pid; +} + + + +int g2_gd_Alloc_Basic(int pid, void *pdp) + { + int icol; + for (icol=0;icol<32;icol++) + gdImageColorAllocate(PDP->im,g2_Basic_Colors[icol][0]/256,g2_Basic_Colors[icol][1]/256,g2_Basic_Colors[icol][2]/256); + PDP->NoOfInks = 32; + return 0; + } + + +int g2_gd_Clear(int pid, void *pdp) + { + gdImageFilledRectangle(PDP->im, 0, 0, PDP->width, PDP->height, PDP->BackCol); + return 0; + } + +int g2_gd_Save(int pid, void *pdp) + { + if (PDP->gd_type == g2_gd_png) + gdImagePng(PDP->im,PDP->f); + else if (PDP->gd_type == g2_gd_jpeg) + gdImageJpeg(PDP->im,PDP->f,-1); + fflush(PDP->f); + rewind(PDP->f); + return 0; + } + +int g2_gd_Delete(int pid, void *pdp) + { + g2_gd_Save(pid,pdp); + fclose(PDP->f); + gdImageDestroy(PDP->im); + free(PDP); + return 0; + } + +int g2_gd_Flush(int pid, void *pdp) + { + return 0; + } + +int g2_gd_Pen(int pid, void *pdp, int color) + { + PDP->CurCol = color; + return 0; + } + +int g2_gd_Ink(int pid, void *pdp, double red, double green, double blue) + { + if(PDP->NoOfInks == 256) + return -1; + else + PDP->NoOfInks++; + return gdImageColorAllocate(PDP->im,(int)(255*red),(int)(255*green),(int)(255*blue)); + } + +int g2_gd_ClearPalette(int pid, void *pdp) + { + int i; + for (i=0;iNoOfInks;i++) + gdImageColorDeallocate(PDP->im,i); + PDP->NoOfInks = 0; + return 0; + } + +int g2_gd_ResetPalette(int pid, void *pdp) + { + g2_gd_ClearPalette(pid,pdp); + g2_gd_Alloc_Basic(pid,pdp); + return 0; + } + +int g2_gd_SetBackground(int pid, void *pdp, int color) + { + PDP->BackCol = color; + return 0; + } + +int g2_gd_SetLineWidth(int pid, void *pdp, int w) + { + PDP->LineWidth = w; + return 0; + } +/* { + if (PDP->brush != NULL) + { + gdImageDestroy(PDP->brush); + } + PDP->brush = gdImageCreate(w,w); + gdImageColorTransparent(PDP->brush,0); + gdImageColorAllocate(PDP->brush,0,0,0); + gdImageColorAllocate(PDP->brush, + gdImageRed(PDP->im,PDP->CurCol), + gdImageGreen(PDP->im,PDP->CurCol), + gdImageBlue(PDP->im,PDP->CurCol)); + gdImageArc(PDP->brush, w/2, w/2, w/2,w/2, 0, 360, 1); + gdImageFill(PDP->brush,w/2,w/2,1); + gdImageSetBrush(PDP->im, PDP->brush); + PDP->OldCol = PDP->CurCol; + PDP->CurCol = gdBrushed; + } + else + { + PDP->CurCol = PDP->OldCol; + } + return 0; + } +*/ + +int g2_gd_SetDash(int pid, void *pdp, int n, char *data) + { + return 0; + } + +int g2_gd_SetDashX(int pid, void *pdp, int N, double *dashes) + { + return 0; + } + +int g2_gd_SetFontSize(int pid, void *pdp, int size) + { + if (size <=10) + PDP->FontSize = gdFontTiny; + else if (size <=12) + PDP->FontSize = gdFontSmall; + else if (size <=13) + PDP->FontSize = gdFontMediumBold; + else if (size <=15) + PDP->FontSize = gdFontLarge; + else + PDP->FontSize = gdFontGiant; + return 0; + } + +int g2_gd_Plot(int pid, void *pdp, int x, int y) + { + gdImageSetPixel(PDP->im, x, y, PDP->CurCol); + return 0; + } + +int g2_gd_Line(int pid, void *pdp, int x1, int y1, int x2, int y2) + { + if (PDP->LineWidth <= 1) + gdImageLine(PDP->im, x1, y1, x2, y2, PDP->CurCol); + else + { + float dx,dy,l; + gdPoint points[4]; + dx = -(float)(y2-y1); + dy = (float)(x2-x1); + l = (float)(PDP->LineWidth/sqrt(dy*dy+dx*dx)/2.); + dx = dx*l; + dy = dy*l; + points[0].x = (int)(x1+dx); + points[0].y = (int)(y1+dy); + points[1].x = (int)(x1-dx); + points[1].y = (int)(y1-dy); + points[2].x = (int)(x2-dx); + points[2].y = (int)(y2-dy); + points[3].x = (int)(x2+dx); + points[3].y = (int)(y2+dy); + gdImageFilledPolygon(PDP->im,points,4,PDP->CurCol); + } + return 0; + } + +int g2_gd_PolyLine(int pid, void *pdp, int N, int *points) + { + return 0; + } + +int g2_gd_Triangle(int pid, void *pdp, int x1, int y1, + int x2, int y2, + int x3, int y3) + { + return 0; + } + +int g2_gd_FilledTriangle(int pid, void *pdp, int x1, int y1, + int x2, int y2, + int x3, int y3) + { + return 0; + } + +int g2_gd_Rectangle(int pid, void *pdp, int x, int y, int x2, int y2) + { + gdImageRectangle(PDP->im, x, y, x2, y2, PDP->CurCol); + return 0; + } + +int g2_gd_FilledRectangle(int pid, void *pdp, int x, int y, int x2, int y2) + { + gdImageFilledRectangle(PDP->im, x, y, x2, y2, PDP->CurCol); + return 0; + } + +int g2_gd_Polygon(int pid, void *pdp, int N, int *points) + { + return 0; + } + +int g2_gd_FilledPolygon(int pid, void *pdp, int N, int *points) + { + gdPoint *GIFPolygon; + int i; + GIFPolygon = (gdPoint *)malloc(N*sizeof(gdPoint)); + for (i=0;iim,GIFPolygon,N,PDP->CurCol); + free(GIFPolygon); + return 0; + } + +int g2_gd_Circle(int pid, void *pdp, int x, int y, int r) + { + gdImageArc(PDP->im, (int)x, (int)y, (int)r, (int)r, 0, 360, PDP->CurCol); + return 0; + } + +int g2_gd_FilledCircle(int pid, void *pdp, int x, int y, int r) + { + return 0; + } + +int g2_gd_Ellipse(int pid, void *pdp, int x, int y, int r1, int r2) + { + return 0; + } + +int g2_gd_FilledEllipse(int pid, void *pdp, int x, int y, int r1, int r2) + { + return 0; + } + +int g2_gd_Arc(int pid, void *pdp, int x, int y, int r1, int r2, double a1, double a2) + { + gdImageArc(PDP->im,x,y,2*r1,2*r2,dtoi(a1),dtoi(a2),PDP->CurCol); + return 0; + } + +int g2_gd_FilledArc(int pid, void *pdp, int x, int y, + int r1, int r2, + double a1, double a2) + { + return 0; + } + +int g2_gd_DrawString(int pid, void *pdp, int x, int y, const char *text) + { + + gdImageString(PDP->im,PDP->FontSize,x,y+2-PDP->FontSize->h,(unsigned char *)text,PDP->CurCol); + return 0; + } + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd.h new file mode 100755 index 000000000..d9588a792 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd.h @@ -0,0 +1,67 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +/* This is g2_GIF.h */ +#ifndef _G2_GD_H +#define _G2_GD_H + +#if defined(__cplusplus) +extern "C" +{ +#endif + +#include + +/* Common Library header for DLL and application */ +#ifdef WIN32 +#ifdef G2DLL +#ifdef MAKEDLL +/* Create DLL */ +#define G2L __declspec( dllexport) +#else +/* Use DLL */ +#define G2L __declspec( dllimport) +#endif +#else +/* Use static win32 */ +#define G2L +#endif +#else +/* Use non-win32 */ +#define G2L +#endif + +/** + * g2 gd bitmap types + * + * \ingroup GD + */ +enum g2_gd_type { + g2_gd_jpeg = 0, /**< jpeg */ + g2_gd_png = 1 /**< png */ +}; + + +G2L int g2_open_gd(const char *filename, int width, int height,enum g2_gd_type gd_type); + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + + +#endif /* _G2_GD_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd_P.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd_P.h new file mode 100755 index 000000000..95e56c7c4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd_P.h @@ -0,0 +1,118 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _g2_GD_P_H +#define _g2_GD_P_H + +#include +#include +#include +#include +#include +#include +#include "g2_config.h" +#include "g2_gd.h" + + static unsigned short g2_Basic_Colors[32][3] = { + {65535,65535,65535},{0,0,0}, + {44461,55512,59110},{0,65535,65535},{0,0,65535}, + {0,0,32896},{61166,33410,61166}, + {65535,0,65535},{41120,8224,61680},{65535,49344,52171}, + {61680,59110,35980},{32639,65535,54484}, + {39064,64507,39064},{0,65535,0},{12850,52685,12850}, + {39578,52685,12850},{44461,65535,12079},{65535,65535,0}, + {65535,55255,0},{61166,56797,33410},{56026,42405,8224},{47288,34438,2827}, + {42405,10794,10794},{53970,26985,7710}, + {52685,34181,16191},{65535,32639,20560}, + {61680,32896,32896},{64250,32896,29298}, + {65535,35980,0},{65535,42405,0},{65535,17733,0}, + {65535,0,0}}; + + +typedef struct g2_gd_STRUCT { + int height; + int width; + FILE *f; + gdImagePtr im; + gdImagePtr brush; + int LineWidth; + int NoOfInks; + int Inks[256]; + int CurCol; + int OldCol; + int BackCol; + gdFontPtr FontSize; + enum g2_gd_type gd_type; + } g2_gd_STRUCT; + + + +int g2_gd_init_gd(int pid, void *pdp, int vid, int width,int height); +int g2_gd_init_gdX(int pid, void *pdp, + int width, int height, + int xposition, int yposition, + char *windowname, char *iconname, + char *icondata, int iconwidth, int iconheight); +int g2_gd_Delete(int pid, void *pdp); +int g2_gd_Clear(int pid, void *pdp); +int g2_gd_Flush(int pid, void *pdp); +int g2_gd_Ink(int pid, void *pdp, + double red, double green, double blue); +int g2_gd_ClearPalette(int pid, void *pdp); +int g2_gd_ResetPalette(int pid, void *pdp); +int g2_gd_SetBackground(int pid, void *pdp, int color); +int g2_gd_Pen(int pid, void *pdp, int color); +int g2_gd_Paper(int pid, void *pdp, int color); +int g2_gd_SetLineWidth(int pid, void *pdp, int w); +int g2_gd_SetDash(int pid, void *pdp, int n, char *data); +int g2_gd_SetFontSize(int pid, void *pdp, int size); +int g2_gd_Plot(int pid, void *pdp, int x, int y); +int g2_gd_Line(int pid, void *pdp, int x1, int y1, int x2, int y2); +int g2_gd_PolyLine(int pid, void *pdp, int N, int *p); +int g2_gd_Polygon(int pid, void *pdp, int N, int *p); +int g2_gd_FilledPolygon(int pid, void *pdp, int N, int *p); +int g2_gd_Triangle(int pid, void *pdp, + int x1, int y1, + int x2, int y2, + int x3, int y3); +int g2_gd_FilledTriangle(int pid, void *pdp, int x1, int y1, + int x2, int y2, + int x3, int y3); +int g2_gd_Rectangle(int pid, void *pdp, int x1, int y1, int x2, int y2); +int g2_gd_FilledRectangle(int pid, void *pdp, + int x1, int y1, int x2, int y2); +int g2_gd_Circle(int pid, void *pdp, int x, int y, int r); +int g2_gd_FilledCircle(int pid, void *pdp, int x, int y, int r); +int g2_gd_Arc(int pid, void *pdp, int x, int y, + int r1, int r2, double a1, double a2); +int g2_gd_FilledArc(int pid, void *pdp, int x, int y, + int r1, int r2, double a1, double a2); +int g2_gd_Ellipse(int pid, void *pdp, int x, int y, int r1, int r2); +int g2_gd_FilledEllipse(int pid, void *pdp, int x, int y, int r1, int r2); +int g2_gd_DrawString(int pid, void *pdp, int x, int y, const char *text); + +int g2_gd_AllocateBasicColors(int pid, void *pdp); + + + +#endif /* _g2_GD_P_H */ + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd_funix.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd_funix.h new file mode 100755 index 000000000..1ba0692de --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/GD/g2_gd_funix.h @@ -0,0 +1,54 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _g2_GD_TOKEN_FUN_H +#define _g2_GD_TOKEN_FUN_H + + +#include "g2_virtual_device.h" +#include "g2_gd_P.h" + +const g2_funix_fun g2_gd_funix[] = + {{g2_Delete,g2_gd_Delete}, + {g2_Ink, g2_gd_Ink}, + {g2_Pen,g2_gd_Pen}, + {g2_SetBackground,g2_gd_SetBackground}, + {g2_ClearPalette,g2_gd_ClearPalette}, + {g2_SetLineWidth,g2_gd_SetLineWidth}, + /* {g2_SetDash,g2_gd_SetDash}, */ + {g2_SetFontSize,g2_gd_SetFontSize}, + {g2_Clear,g2_gd_Clear}, + {g2_Flush,g2_gd_Flush}, + {g2_Plot,g2_gd_Plot}, + {g2_Line,g2_gd_Line}, + /* {g2_PolyLine,g2_gd_PolyLine}, */ + {g2_Rectangle,g2_gd_Rectangle}, + {g2_FilledRectangle,g2_gd_FilledRectangle}, + /* {g2_Polygon,g2_gd_Polygon}, */ + {g2_FilledPolygon,g2_gd_FilledPolygon}, + /* {g2_Circle,g2_gd_Circle}, */ + /* {g2_FilledCircle,g2_gd_FilledCircle}, */ + /* {g2_Ellipse,g2_gd_Ellipse}, */ + /* {g2_FilledEllipse,g2_gd_FilledEllipse}, */ + /* {g2_Arc,g2_gd_Arc}, */ + /* {g2_FilledArc,g2_gd_FilledArc}, */ + {g2_String,g2_gd_DrawString}, + {g2_FUNIX_NULL, NULL}}; + + +#endif /* _g2_GD_TOKEN_FUN_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Repository new file mode 100755 index 000000000..9642f1622 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/PS/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Entries new file mode 100755 index 000000000..430df523e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Entries @@ -0,0 +1,6 @@ +D/CVS//// +/g2_PS.c/1.1/Tue Feb 22 21:34:22 2005// +/g2_PS.h/1.1/Tue Mar 23 23:50:40 2004// +/g2_PS_P.h/1.1/Sun Feb 29 23:47:46 2004// +/g2_PS_definitions.h/1.1/Tue Apr 17 20:16:38 2001// +/g2_PS_funix.h/1.1/Tue Apr 17 20:16:38 2001// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Repository new file mode 100755 index 000000000..75622b0a7 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/PS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.c new file mode 100755 index 000000000..2e3388ea3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.c @@ -0,0 +1,624 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include +#include +#include +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_util.h" +#include "g2_config.h" + +#include "g2_PS.h" +#include "g2_PS_P.h" +#include "g2_PS_funix.h" +#include "g2_PS_definitions.h" + +static int N_PS=0; +static g2_PS_device *g2_PS_dev=NULL; + +/** + * \ingroup physdev + * \defgroup PS PostScript + */ + + +/* + * + * Attach generic PS device + * + */ +G2L int g2_open_PS_generic(const char *file_name, + enum g2_PS_paper paper, + enum g2_PS_orientation orientation, + enum g2_PS_format format, + long width, + long height) +{ + g2_PS_device *psout=NULL; + int pid=-1, i; + int vid; + FILE *fp; + + if((fp=fopen(file_name, "w"))==NULL) { + fprintf(stderr, "g2_attach_PS: Error! Can not open file '%s'\n", + file_name); + return -1; + } + + if(g2_PS_dev==NULL) { + g2_PS_dev=g2_malloc(sizeof(g2_PS_device)); + N_PS=1; /* first PS device */ + psout=&g2_PS_dev[N_PS-1]; + pid=0; + } else { + for(i=0;ifp=fp; /* init PostScript structures */ + psout->paper=paper; + psout->orient=orientation; + psout->format=format; + psout->width=width; + psout->height=height; + psout->inks=NULL; + psout->N_ink=0; + psout->pen=0; + psout->page_counter=0; + psout->bbox = 0; + + g2_PS_write_file_header(psout); + + g2_PS_set_line_width(pid, NULL, 0.0); + g2_PS_set_font_size(pid, NULL, 12.0); + + /* g2 settings */ + g2_allocate_basic_colors(vid); + g2_pen(vid, 1); + + return vid; +} + + +/** + * + * Create a PS device. + * + * \param file_name postscript file name + * \param paper paper type, see ::g2_PS_paper and \ref appendix Appendix + * \param orientation paper orientation, see ::g2_PS_orientation + * + * \return physical device id + * + * \ingroup PS + */ +G2L int g2_open_PS(const char *file_name, + enum g2_PS_paper paper, + enum g2_PS_orientation orientation) +{ + return g2_open_PS_generic(file_name,paper,orientation,g2_PS_PostScript,0,0); +} + + +/** + * + * Create an encapsulated PS device. + * + * \param file_name postscript file name + * + * \return physical device id + * + * \ingroup PS + */ +G2L int g2_open_EPSF(const char *file_name) +{ + return g2_open_PS_generic(file_name,0,0,g2_PS_EPSF,0,0); +} + + +/** + * + * Create an encapsulated PS device with clipping. + * + * \param file_name postscript file name + * \param width clipping region width + * \param height clipping region height + * + * \return physical device id + * + * \ingroup PS + */ +G2L int g2_open_EPSF_CLIP(const char *file_name, + long width, long height) +{ + return g2_open_PS_generic(file_name,0,0,g2_PS_EPSF_CLIP,width,height); +} + +/* + * + * Write header for postscript file + * + */ +int g2_PS_write_file_header(g2_PS_device *ps) +{ + int i; + if (ps->format == g2_PS_PostScript) + { + fprintf(ps->fp,"%%!PS-Adobe-2.0\n"); + switch(ps->orient) + { + case g2_PS_land: + fprintf(ps->fp,"%%%%Orientation: Landscape\n"); + break; + case g2_PS_port: + fprintf(ps->fp,"%%%%Orientation: Portrait\n"); + break; + } + } + else if (ps->format == g2_PS_EPSF_CLIP) + { + fprintf(ps->fp,"%%!PS-Adobe-3.0 EPSF-2.0\n"); + fprintf(ps->fp,"%%%%BoundingBox: 0 0 %ld %ld\n",ps->width,ps->height); + } + else if (ps->format == g2_PS_EPSF) + { + fprintf(ps->fp,"%%!PS-Adobe-3.0 EPSF-2.0\n"); + fprintf(ps->fp,"%%%%BoundingBox: (atend)\n"); + } + + fprintf(ps->fp,"%%%%Creator: g2 %s\n", G2_VERSION); + fprintf(ps->fp, "%%%%EndComments\n"); + + if (ps->format == g2_PS_EPSF_CLIP) + { + fprintf(ps->fp,"0 0 moveto\n"); + fprintf(ps->fp,"0 %ld rlineto\n",ps->height); + fprintf(ps->fp,"%ld 0 rlineto\n",ps->width); + fprintf(ps->fp,"0 %ld rlineto\n",-ps->height); + fprintf(ps->fp,"closepath\n"); + fprintf(ps->fp,"clip\n"); + } + + for(i=0;g2_PS_operators[i]!=NULL;i++) + fputs(g2_PS_operators[i], ps->fp); + + fprintf(ps->fp,"newpath\n"); + if((ps->orient==g2_PS_land) && (ps->format == g2_PS_PostScript)) + fprintf(ps->fp,"%d 0 translate 90 rotate\n", + g2_PS_paper_size[ps->paper][0]); + + fputs("%%PageTrailer\n%%Page: 1 1\n", ps->fp); + + return 0; +} + +/* + * + * Add circle at (x,y) of dimension size to bounding box + * + */ +void g2_PS_bbox_add(g2_PS_device *ps,double x,double y,double size) + { + if (ps->bbox == 0) /* bbox is empty */ + { + ps->x1=x-size; + ps->x2=x+size; + ps->y1=y-size; + ps->y2=y+size; + ps->bbox=1; + return; + } + + if (ps->x1 > x-size) + ps->x1=x-size; + else if (ps->x2 < x+size) + ps->x2=x+size; + + if (ps->y1 > y-size) + ps->y1=y-size; + else if (ps->y2 < y+size) + ps->y2=y+size; + return; + } + +/* + * + * Delete PS device + * + */ +int g2_PS_delete(int pid, void *pdp) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"\nshowpage\n"); + fprintf(ps->fp,"%%%%PageTrailer\n"); + fprintf(ps->fp,"%%%%EndPage\n"); + fprintf(ps->fp,"%%%%Trailer\n"); + if (ps->format == g2_PS_EPSF) + { + fprintf(ps->fp,"%%%%BoundingBox: %d %d %d %d\n", + (int)floor(ps->x1),(int)floor(ps->y1), + (int)ceil(ps->x2),(int)ceil(ps->y2)); + } + fprintf(ps->fp,"%%%%EOF\n"); + fclose(ps->fp); + free(ps->inks); + + ps->fp=NULL; /* free place */ + + return 0; +} + + + +int g2_PS_ink(int pid, void *pdp, + double red, double green, double blue) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + ps->N_ink++; + if(ps->inks==NULL) + ps->inks=(g2_PS_inks *)g2_malloc(ps->N_ink* + sizeof(g2_PS_inks)); + else + ps->inks=(g2_PS_inks *)g2_realloc((void *)ps->inks, + ps->N_ink* + sizeof(g2_PS_inks)); + + ps->inks[ps->N_ink-1].r=red; + ps->inks[ps->N_ink-1].g=green; + ps->inks[ps->N_ink-1].b=blue; + + return ps->N_ink-1; +} + + + +int g2_PS_pen(int pid, void *pdp, int color) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + if(color>=ps->N_ink || color<0) + return -1; + fprintf(ps->fp,"%.4g %.4g %.4g setrgbcolor\n", + (double)ps->inks[color].r, + (double)ps->inks[color].g, + (double)ps->inks[color].b); + ps->pen=color; + return 0; +} + + + +int g2_PS_set_background(int pid, void *pdp, int color) +{ + return 0; +} + + + +int g2_PS_clear_palette(int pid, void *pdp) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + free((void *)ps->inks); + ps->N_ink=0; + ps->inks=NULL; + return 0; +} + + + +int g2_PS_set_line_width(int pid, void *pdp, double w) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"%.4g setlinewidth\n", w); + ps->w = w; + return 0; +} + + + +int g2_PS_set_dash(int pid, void *pdp, int N, double *data) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + int i; + fprintf(ps->fp, "[ "); + for(i=0;i0.0) + fprintf(ps->fp, "%.4g ", data[i]); + fprintf(ps->fp, "] 0 setdash\n"); + return 0; +} + + + +int g2_PS_set_font_size(int pid, void *pdp, double size) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + if(size<=0.0) + return -1; + fprintf(ps->fp,"%s findfont %.4g scalefont setfont\n", g2_PSFont, size); + ps->size = size; + return 0; +} + + + +int g2_PS_clear(int pid, void *pdp) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp, "gsave showpage\n"); + fprintf(ps->fp, "%%%%PageTrailer\n%%%%EndPage\n"); + fprintf(ps->fp, "%%%%Page: %d %d\ngrestore newpath\n", + ps->page_counter+1, ps->page_counter+1); + ps->page_counter++; + return 0; +} + + + +int g2_PS_flush(int pid, void *pdp) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fflush(ps->fp); + return 0; +} + + + +int g2_PS_plot(int pid, void *pdp, double x, double y) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"%.4g %.4g P\n", x, y); + g2_PS_bbox_add(ps,x,y,1); + return 0; +} + + + +int g2_PS_line(int pid, void *pdp, double x1, double y1, double x2, double y2) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"%.4g %.4g M %.4g %.4g L St\n", + x1, y1, x2, y2); + g2_PS_bbox_add(ps,x1,y1,ps->w); + g2_PS_bbox_add(ps,x2,y2,ps->w); + return 0; +} + + + +int g2_PS_poly_line(int pid, void *pdp, int N, double *points) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + int i; + fprintf(ps->fp,"%.4g %.4g M\n", points[0], points[1]); + g2_PS_bbox_add(ps,points[0], points[1],ps->w); + for(i=2;i<2*N;i+=2) + { + fprintf(ps->fp, "%.4g %.4g L\n", points[i], points[i+1]); + g2_PS_bbox_add(ps,points[i], points[i+1],ps->w); + } + fprintf(ps->fp, "St\n"); + return 0; +} + + + +int g2_PS_polygon(int pid, void *pdp, int N, double *points) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + int i; + fprintf(ps->fp,"%.4g %.4g M\n",points[0], points[1]); + g2_PS_bbox_add(ps,points[0], points[1],ps->w); + for(i=2;i<2*N;i+=2) + { + fprintf(ps->fp, "%.4g %.4g L\n", points[i], points[i+1]); + g2_PS_bbox_add(ps,points[i], points[i+1],ps->w); + } + fprintf(ps->fp, "%.4g %.4g L St\n", points[0], points[1]); + return 0; +} + + + +int g2_PS_filled_polygon(int pid, void *pdp, int N, double *points) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + int i; + fprintf(ps->fp,"newpath %.4g %.4g M\n",points[0], points[1]); + g2_PS_bbox_add(ps,points[0], points[1],ps->w); + for(i=2;i<2*N;i+=2) + { + fprintf(ps->fp, "%.4g %.4g L\n", points[i], points[i+1]); + g2_PS_bbox_add(ps,points[i], points[i+1],ps->w); + } + fprintf(ps->fp, "%.4g %.4g L fill St\n", points[0], points[1]); + return 0; +} + + + +int g2_PS_rectangle(int pid, void *pdp, + double x1, double y1, double x2, double y2) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"%.4g %.4g %.4g %.4g R\n", + x2, y2, x1, y1); + g2_PS_bbox_add(ps,x1,y1,ps->w); + g2_PS_bbox_add(ps,x2,y2,ps->w); + return 0; +} + + + +int g2_PS_filled_rectangle(int pid, void *pdp, + double x1, double y1, double x2, double y2) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"%.4g %.4g %.4g %.4g FR\n", + x2, y2, x1, y1); + g2_PS_bbox_add(ps,x1,y1,ps->w); + g2_PS_bbox_add(ps,x2,y2,ps->w); + return 0; +} + + + +int g2_PS_triangle(int pid, void *pdp, + double x1, double y1, + double x2, double y2, + double x3, double y3) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"%.4g %.4g %.4g %.4g %.4g %.4g T\n", + x1,y1,x2,y2,x3,y3); + g2_PS_bbox_add(ps,x1,y1,ps->w); + g2_PS_bbox_add(ps,x2,y2,ps->w); + g2_PS_bbox_add(ps,x3,y3,ps->w); + return 0; +} + + +int g2_PS_filled_triangle(int pid, void *pdp, + double x1, double y1, + double x2, double y2, + double x3, double y3) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"%.4g %.4g %.4g %.4g %.4g %.4g FT\n", + x1,y1,x2,y2,x3,y3); + g2_PS_bbox_add(ps,x1,y1,ps->w); + g2_PS_bbox_add(ps,x2,y2,ps->w); + g2_PS_bbox_add(ps,x3,y3,ps->w); + return 0; +} + + + +int g2_PS_arc(int pid, void *pdp, + double x, double y, + double r1, double r2, + double a1, double a2) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + if(a1==a2) { + a1=0; + a2=360; + } + fprintf(ps->fp,"%.4g %.4g %.4g %.4g %.4g %.4g A\n", + a1, a2, r1, r2, x, y); + g2_PS_bbox_add(ps,x+r1,y+r2,ps->w); + g2_PS_bbox_add(ps,x-r1,y-r2,ps->w); + return 0; +} + + + +int g2_PS_filled_arc(int pid, void *pdp, + double x, double y, + double r1, double r2, + double a1, double a2) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + if(a1==a2) { + a1=0; + a2=360; + } + fprintf(ps->fp,"%.4g %.4g %.4g %.4g %.4g %.4g FA\n", + a1, a2, r1, r2, x, y); + g2_PS_bbox_add(ps,x+r1,y+r2,ps->w); + g2_PS_bbox_add(ps,x-r1,y-r2,ps->w); + return 0; +} + + + +int g2_PS_ellipse(int pid, void *pdp, + double x, double y, + double r1, double r2) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"0 360 %.4g %.4g %.4g %.4g A\n", + r1, r2, x, y); + g2_PS_bbox_add(ps,x+r1,y+r2,ps->w); + g2_PS_bbox_add(ps,x-r1,y-r2,ps->w); + return 0; +} + + + + +int g2_PS_filled_ellipse(int pid, void *pdp, + double x, double y, + double r1, double r2) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fprintf(ps->fp,"0 360 %.4g %.4g %.4g %.4g FA\n", + r1, r2, x, y); + g2_PS_bbox_add(ps,x+r1,y+r2,ps->w); + g2_PS_bbox_add(ps,x-r1,y-r2,ps->w); + return 0; +} + + + +int g2_PS_draw_string(int pid, void *pdp, + double x, double y, const char *text) +{ + g2_PS_device *ps=&g2_PS_dev[pid]; + fputc('(', ps->fp); + for(;*text!='\0';text++) + switch(*text) { + case '(': + fputs("\\(", ps->fp); + break; + case ')': + fputs("\\)", ps->fp); + break; + case '\\': + fputs("\\\\", ps->fp); + break; + default: + fputc(*text, ps->fp); + break; + } + fprintf(ps->fp,") %.4g %.4g S\n", x, y); + g2_PS_bbox_add(ps,x,y,ps->size); + g2_PS_bbox_add(ps,x+ps->size*strlen(text),y,ps->size); + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.h new file mode 100755 index 000000000..88eb918c9 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.h @@ -0,0 +1,118 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_PS_H +#define _G2_PS_H + +#if defined(__cplusplus) +extern "C" +{ +#endif + +/** + * g2 paper type. + * + * \ingroup PS + */ +enum g2_PS_paper { /* Name Size(Pt) */ + g2_A0, /**< A0 2384 x 3370 */ + g2_A1, /**< A1 1684 x 2384 */ + g2_A2, /**< A2 1191 x 1684 */ + g2_A3, /**< A3 842 x 1191 */ + g2_A4, /**< A4 595 x 842 */ + g2_A5, /**< A5 420 x 595 */ + g2_A6, /**< A6 297 x 420 */ + g2_A7, /**< A7 210 x 297 */ + g2_A8, /**< A8 148 x 210 */ + g2_A9, /**< A9 105 x 148 */ + g2_B0, /**< B0 2920 x 4127 */ + g2_B1, /**< B1 2064 x 2920 */ + g2_B2, /**< B2 1460 x 2064 */ + g2_B3, /**< B3 1032 x 1460 */ + g2_B4, /**< B4 729 x 1032 */ + g2_B5, /**< B5 516 x 729 */ + g2_B6, /**< B6 363 x 516 */ + g2_B7, /**< B7 258 x 363 */ + g2_B8, /**< B8 181 x 258 */ + g2_B9, /**< B9 127 x 181 */ + g2_B10, /**< B10 91 x 127 */ + g2_Comm_10_Envelope, /**< Comm #10 Envelope 297 x 684 */ + g2_C5_Envelope, /**< C5 Envelope 461 x 648 */ + g2_DL_Envelope, /**< DL Envelope 312 x 624 */ + g2_Folio, /**< Folio 595 x 935 */ + g2_Executive, /**< Executive 522 x 756 */ + g2_Letter, /**< Letter 612 x 792 */ + g2_Legal, /**< Legal 612 x 1008 */ + g2_Ledger, /**< Ledger 1224 x 792 */ + g2_Tabloid /**< Tabloid 792 x 1224 */ +}; + + +/** + * g2 paper orientation. + * + * \ingroup PS + */ +enum g2_PS_orientation { + g2_PS_land, /**< landscape */ + g2_PS_port /**< portrait */ +}; + +/* + * g2 Format + */ +enum g2_PS_format { + g2_PS_PostScript, /* PostScript */ + g2_PS_EPSF, /* EPSF format */ + g2_PS_EPSF_CLIP /* EPSF format with predefined Bounding Box*/ +}; + +/* Common Library header for DLL and application */ +#ifdef WIN32 +#ifdef G2DLL +#ifdef MAKEDLL +/* Create DLL */ +#define G2L __declspec( dllexport) +#else +/* Use DLL */ +#define G2L __declspec( dllimport) +#endif +#else +/* Use static win32 */ +#define G2L +#endif +#else +/* Use non-win32 */ +#define G2L +#endif + + +G2L int g2_open_PS(const char *file_name, + enum g2_PS_paper paper, + enum g2_PS_orientation orientation); + +G2L int g2_open_EPSF(const char *file_name); + +G2L int g2_open_EPSF_CLIP(const char *file_name, + long width, long height); + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + +#endif /* _G2_PS_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.o new file mode 100755 index 000000000..b49f126a5 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_P.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_P.h new file mode 100755 index 000000000..b68493b1e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_P.h @@ -0,0 +1,99 @@ +/***************************************************************************** +** This is part of the g2 library +** Copyright (C) 1998 Ljubomir Milanovic & Horst Wagner +** +** This program is free software; you can redistribute it and/or modify +** it under the terms of the GNU General Public License (version 2) as +** published by the Free Software Foundation. +** +** This program is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +** GNU General Public License for more details. +** +** You should have received a copy of the GNU General Public License +** along with this program; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_PS_P_H +#define _G2_PS_P_H + +#include "g2_PS.h" + + +typedef struct _g2_PS_inks { + double r; /* red [0:1] */ + double g; /* green [0:1] */ + double b; /* blue [0:1] */ +} g2_PS_inks; + + + +typedef struct _g2_PS_device { + FILE *fp; /* output file pointer */ + enum g2_PS_paper paper; /* paper type */ + enum g2_PS_orientation orient; /* page orientation */ + enum g2_PS_format format; /* PS or EPSF format */ + long width,height; /* width and height for EPSF */ + double x1,y1,x2,y2; /* min. Bounding Box */ + int bbox; /* Bounding Box empty flag */ + double w,size; /* line width/font size (required for Bbox) */ + + g2_PS_inks *inks; /* allocated colors */ + int N_ink; /* number of allocated colors*/ + int pen; /* current pen */ + int page_counter; /* page counter ( Clear() ) */ +} g2_PS_device; + + + +void g2_PS_bbox_add(g2_PS_device *ps,double x,double y,double size); +int g2_PS_write_file_header(g2_PS_device *psd); +int g2_PS_delete(int pid, void *pdp); +int g2_PS_ink(int pid, void *pdp, + double red, double green, double blue); +int g2_PS_pen(int pid, void *pdp, int color); +int g2_PS_set_background(int pid, void *pdp, int color); +int g2_PS_reset_palette(int pid, void *pdp); +int g2_PS_clear_palette(int pid, void *pdp); +int g2_PS_set_line_width(int pid, void *pdp, double w); +int g2_PS_set_dash(int pid, void *pdp, int N, double *data); +int g2_PS_set_font_size(int pid, void *pdp, double size); +int g2_PS_clear(int pid, void *pdp); +int g2_PS_flush(int pid, void *pdp); +int g2_PS_plot(int pid, void *pdp, double x, double y); +int g2_PS_line(int pid, void *pdp, double x1, double y1, double x2, double y2); +int g2_PS_poly_line(int pid, void *pdp, int N, double *points); +int g2_PS_polygon(int pid, void *pdp, int N, double *points); +int g2_PS_filled_polygon(int pid, void *pdp, int N, double *points); +int g2_PS_rectangle(int pid, void *pdp, + double x1, double y1, double x2, double y2); +int g2_PS_filled_rectangle(int pid, void *pdp, + double x1, double y1, double x2, double y2); +int g2_PS_triangle(int pid, void *pdp, + double x1, double y1, + double x2, double y2, + double x3, double y3); +int g2_PS_filled_triangle(int pid, void *pdp, + double x1, double y1, + double x2, double y2, + double x3, double y3); +int g2_PS_arc(int pid, void *pdp, + double x, double y, + double r1, double r2, + double a1, double a2); +int g2_PS_filled_arc(int pid, void *pdp, + double x, double y, + double r1, double r2, + double a1, double a2); +int g2_PS_ellipse(int pid, void *pdp, + double x, double y, + double r1, double r2); +int g2_PS_filled_ellipse(int pid, void *pdp, + double x, double y, + double r1, double r2); +int g2_PS_draw_string(int pid, void *pdp, + double x, double y, const char *text); + +#endif /* _G2_PS_P_H */ + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_definitions.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_definitions.h new file mode 100755 index 000000000..b0b1e4151 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_definitions.h @@ -0,0 +1,104 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ + +/* + * + * Sizes for paper defined in g2_PS.h + * Size is in 1/72 inch (=0.351mm) + */ +static int g2_PS_paper_size[][2]={ + { 2384, 3370 }, /* g2_A0 - A0 */ + { 1684, 2384 }, /* g2_A1 - A1 */ + { 1191, 1684 }, /* g2_A2 - A2 */ + { 842, 1191 }, /* g2_A3 - A3 */ + { 595, 842 }, /* g2_A4 - A4 */ + { 420, 595 }, /* g2_A5 - A5 */ + { 297, 420 }, /* g2_A6 - A6 */ + { 210, 297 }, /* g2_A7 - A7 */ + { 148, 210 }, /* g2_A8 - A8 */ + { 105, 148 }, /* g2_A9 - A9 */ + { 2920, 4127 }, /* g2_B0 - B0 */ + { 2064, 2920 }, /* g2_B1 - B1 */ + { 1460, 2064 }, /* g2_B2 - B2 */ + { 1032, 1460 }, /* g2_B3 - B3 */ + { 729, 1032 }, /* g2_B4 - B4 */ + { 516, 729 }, /* g2_B5 - B5 */ + { 363, 516 }, /* g2_B6 - B6 */ + { 258, 363 }, /* g2_B7 - B7 */ + { 181, 258 }, /* g2_B8 - B8 */ + { 127, 181 }, /* g2_B9 - B9 */ + { 91, 127 }, /* g2_B10 - B10 */ + { 297, 684 }, /* g2_Comm_10_Envelope - Comm #10 Envelope */ + { 461, 648 }, /* g2_C5_Envelope - C5 Envelope */ + { 312, 624 }, /* g2_DL_Envelope - DL Envelope */ + { 595, 935 }, /* g2_Folio - Folio */ + { 522, 756 }, /* g2_Executive - Executive */ + { 612, 792 }, /* g2_Letter - Letter */ + { 612, 1008 }, /* g2_Legal - Legal */ + { 1224, 792 }, /* g2_Ledger - Ledger */ + { 792, 1224 } /* g2_Tabloid - Tabloid */ +}; + + +/* + * + * PS operators + * + */ +char *g2_PS_operators[]={ + " /L { lineto } def", /* lineto */ + " /St { stroke } def", /* stroke */ + " /M { moveto } def", /* moveto */ + " /P {", /* plot */ + " gsave newpath [] 0 setdash 1 setlinecap 0 setlinewidth", + " 0.2 sub exch 0.2 sub exch moveto 0.4 0.4 rlineto", + " stroke grestore} def", + " /T {", /* triangle */ + " newpath", + " moveto lineto lineto", + " closepath stroke} def", + " /FT {", /* filled triangle */ + " newpath", + " moveto lineto lineto", + " closepath fill} def", + " /R {", /* rectangle */ + " newpath", + " 3 index 1 index 6 4 roll 5 index 1 index", + " moveto lineto lineto lineto closepath stroke} def", + " /FR {", /* filled rectangle */ + " newpath", + " 3 index 1 index 6 4 roll 5 index 1 index", + " moveto lineto lineto lineto closepath fill} def", + " /A {", /* arc */ + " gsave /g2_old_matrix matrix currentmatrix def newpath", + " translate scale 0 0 1 5 3 roll arc", + " g2_old_matrix setmatrix stroke grestore } def", + " /FA {", /* filled arc */ + " gsave /g2_old_matrix matrix currentmatrix def newpath", + " translate scale 0 0 moveto 0 0 1 5 3 roll arc closepath", + " g2_old_matrix setmatrix fill grestore } def", + " /S {", /* draw string */ + " gsave newpath", + " translate 0 0 moveto show", + " stroke grestore} def", + "\n", + NULL +}; + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_funix.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_funix.h new file mode 100755 index 000000000..a43cb43b3 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/PS/g2_PS_funix.h @@ -0,0 +1,56 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_PS_FUNIX_H +#define _G2_PS_FUNIX_H + +#include "g2_PS_P.h" +#include "g2_physical_device.h" + +const g2_funix_fun g2_PS_funix[] = { + { g2_Delete, g2_PS_delete }, + { g2_Ink, g2_PS_ink }, + { g2_Pen, g2_PS_pen }, + { g2_SetBackground, g2_PS_set_background }, + { g2_ClearPalette, g2_PS_clear_palette }, + { g2_SetLineWidth, g2_PS_set_line_width }, + { g2_SetDash, g2_PS_set_dash }, + { g2_SetFontSize, g2_PS_set_font_size }, + { g2_Clear, g2_PS_clear }, + { g2_Flush, g2_PS_flush }, + { g2_Save, g2_PS_flush }, + { g2_Plot, g2_PS_plot }, + { g2_Line, g2_PS_line }, + { g2_PolyLine, g2_PS_poly_line }, + { g2_Polygon, g2_PS_polygon }, + { g2_FilledPolygon, g2_PS_filled_polygon }, + { g2_Rectangle, g2_PS_rectangle }, + { g2_FilledRectangle, g2_PS_filled_rectangle }, + { g2_Triangle, g2_PS_triangle }, + { g2_FilledTriangle, g2_PS_filled_triangle }, + { g2_Arc, g2_PS_arc }, + { g2_FilledArc, g2_PS_filled_arc }, + { g2_Ellipse, g2_PS_ellipse }, + { g2_FilledEllipse, g2_PS_filled_ellipse }, + { g2_Circle, NULL }, + { g2_FilledCircle, NULL }, + { g2_String, g2_PS_draw_string }, + { g2_FUNIX_NULL, NULL } }; + + +#endif /* _G2_PS_FUNIX_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Repository new file mode 100755 index 000000000..8644ef8a4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/Win32/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Entries new file mode 100755 index 000000000..0a45d5246 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Entries @@ -0,0 +1,10 @@ +D/CVS//// +/g2_Win32.ico/1.1/Mon Jan 18 10:56:52 1999// +/g2_win32.c/1.1/Sun Jan 23 20:02:59 2005// +/g2_win32.h/1.1/Tue Mar 23 23:50:40 2004// +/g2_win32.rc/1.1/Wed Feb 3 16:18:04 1999// +/g2_win32_P.h/1.1/Sat Apr 17 21:37:55 2004// +/g2_win32_funix.h/1.1/Tue Mar 30 03:56:45 2004// +/g2_win32_thread.c/1.1/Mon Nov 15 04:09:46 2004// +/g2res.c/1.1/Mon Jan 18 10:56:52 1999// +/resource.h/1.1/Mon Jan 18 10:56:52 1999// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Repository new file mode 100755 index 000000000..9106b6201 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/Win32 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_Win32.ico b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_Win32.ico new file mode 100755 index 000000000..ba2f28844 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_Win32.ico differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.c new file mode 100755 index 000000000..78b876005 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.c @@ -0,0 +1,671 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ + +#include +#include +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_util.h" +#include "g2_config.h" + +#include "g2_win32.h" +#include "g2_win32_P.h" +#include "g2_win32_funix.h" + +#include "resource.h" + +/* Global Definitions */ +int g2_win32_registered = FALSE; +HINSTANCE g2res_DLL; /* Instance of the resource DLL */ + +#define PDP ((struct g2_win32_STRUCT *)pdp) + +#ifndef PI +#define PI 3.14159265358979323846 +#endif /* PI */ + +#define sgn(x) (x>0?1:x?-1:0) + +/* someday their might be a DLL version of g2 */ +#ifdef G2DLL +BOOL WINAPI DllMain( HANDLE hModule, DWORD fdwreason, LPVOID lpReserved ) +{ + switch(fdwreason) { + case DLL_PROCESS_ATTACH: + // The DLL is being mapped into process's address space + // Do any required initialization on a per application basis, return FALSE if failed + MessageBox(NULL, "DLL Process Attach", "DLL Message 1", MB_OK); + break; + case DLL_THREAD_ATTACH: + // A thread is created. Do any required initialization on a per thread basis + MessageBox(NULL, "DLL Thread Attach", "DLL Message 1", MB_OK); + break; + case DLL_THREAD_DETACH: + // Thread exits with cleanup + MessageBox(NULL, "DLL Thread Detach", "DLL Message 1", MB_OK); + break; + case DLL_PROCESS_DETACH: + // The DLL unmapped from process's address space. Do necessary cleanup + MessageBox(NULL, "DLL Process Detach", "DLL Message 1", MB_OK); + break; + default: + MessageBox(NULL, "DLL default", "DLL Message 1", MB_OK); + + } + return TRUE; +} +#endif + + +g2_win32_SetPen(int pid, void *pdp) + { + HGDIOBJ oldpen; + LOGBRUSH logBrush ; + logBrush.lbStyle = PS_SOLID; + logBrush.lbColor = PDP->Inks[PDP->Pen]; + logBrush.lbHatch = 0 ; + + oldpen = PDP->hPen; + PDP->hPen = ExtCreatePen (logBrush.lbStyle | PS_GEOMETRIC | + PS_ENDCAP_FLAT | PS_JOIN_BEVEL | (PDP->PenStyle > 0)*PS_USERSTYLE, + PDP->PenWidth, &logBrush, + PDP->PenStyle , PDP->PenDash) ; + if (PDP->hPen != NULL) + { + SelectObject(PDP->hMemDC,PDP->hPen); +/* if (PDP->type == g2_win32)*/ + DeleteObject(oldpen); + } + else + { + errhandler("Pen",NULL); + PDP->hPen = oldpen; + } + + oldpen = PDP->hNullPen; + PDP->hNullPen = CreatePen(PS_SOLID,1,PDP->Inks[PDP->Pen]); + if (PDP->hNullPen != NULL) + { +/* if (PDP->type == g2_win32)*/ + DeleteObject(oldpen); + } + else + { + errhandler("Pen",NULL); + PDP->hNullPen = oldpen; + } + + return 0; + } + + +int g2_win32_Cleanup(int pid, void *pdp) + { + struct g2_win32_STRUCT *thispdp; + + thispdp = pdp; + g2_win32_ClearPalette(pid,pdp); + if (PDP->hBrush != NULL) DeleteObject(PDP->hBrush); + if (PDP->hPen != NULL) DeleteObject(PDP->hPen); + if (PDP->hNullPen != NULL) DeleteObject(PDP->hPen); + if (PDP->hFont != NULL) DeleteObject(PDP->hFont); + if (PDP->hBitmap != NULL) DeleteObject(PDP->hBitmap); + if (PDP->hMemDC != NULL) DeleteDC(PDP->hMemDC); + if (PDP->PenDash != NULL) free(PDP->PenDash); + free(thispdp); + return 0; + } + + + +int g2_win32_Delete(int pid, void *pdp) + { + switch(PDP->type) + { + case g2_win32: + SendMessage(PDP->hwndThreadWindow,WM_CLOSE,(WPARAM)NULL,(LPARAM)NULL); + break; + case g2_wmf32: + { + CloseEnhMetaFile(PDP->hMemDC); + g2_win32_Cleanup(pid,pdp); + break; + } + } + return 0; + } + + +int g2_win32_Clear(int pid, void *pdp) + { + int OldPen; + + OldPen = PDP->Pen; + g2_win32_Pen(pid,pdp,PDP->BkColor); + g2_win32_FilledRectangle(pid,pdp,0,0,PDP->nWidth,PDP->nHeight); + g2_win32_Pen(pid,pdp,OldPen); + return 0; + } + +int g2_win32_Flush(int pid, void *pdp) + { + InvalidateRect(PDP->hwndThreadWindow, (RECT *)NULL, TRUE); + return 0; + } + +int g2_win32_Pen(int pid, void *pdp, int color) + { + struct tagLOGBRUSH logbrush; + HGDIOBJ oldbrush; + + if(color>=PDP->NoOfInks || color<0) + { + fprintf(stderr,"g2_WIN32: Ink %d not defined\n",color); + return -1; + } + + PDP->Pen = color; + PDP->PenColor = PDP->Inks[color]; + g2_win32_SetPen(pid,pdp); + + logbrush.lbStyle = BS_SOLID; + logbrush.lbColor = PDP->PenColor; + oldbrush = PDP->hBrush; + PDP->hBrush = CreateBrushIndirect(&logbrush); + if (PDP->hBrush == NULL) + { + errhandler("Pen (CreateBrush)",NULL); + PDP->hBrush = oldbrush; + } + else +/* if (PDP->type == g2_win32)*/ + DeleteObject(oldbrush); + return 0; + } + +int g2_win32_Ink(int pid, void *pdp, double red, double green, double blue) + { + BYTE rc,gc,bc; + + rc = (BYTE)((int)(red*255)); + gc = (BYTE)((int)(green*255)); + bc = (BYTE)((int)(blue*255)); + + PDP->NoOfInks++; + + if(PDP->Inks==NULL) + PDP->Inks=(COLORREF *)malloc(PDP->NoOfInks*sizeof(COLORREF)); + else + PDP->Inks=(COLORREF *)realloc((void *)PDP->Inks,PDP->NoOfInks*sizeof(COLORREF)); + + if(PDP->Inks==NULL) + { + fputs("g2: not enough memory\n",stderr); + return -1; + } + + PDP->Inks[PDP->NoOfInks-1]=RGB(rc,gc,bc); + return PDP->NoOfInks-1; + } + + +int g2_win32_ClearPalette(int pid, void *pdp) + { + if (PDP->Inks != NULL) + free(PDP->Inks); + PDP->Inks = NULL; + PDP->NoOfInks = 0; + return 0; + } + + +int g2_win32_SetBackground(int pid, void *pdp, int color) + { + PDP->BkColor = color; + SetBkColor(PDP->hMemDC,PDP->BkColor); + return 0; + } + +int g2_win32_SetLineWidth(int pid, void *pdp, int w) + { + PDP->PenWidth = w; + g2_win32_SetPen(pid,pdp); + return 0; + } + +int g2_win32_SetDash(int pid, void *pdp, int n, int *data) + { + if (PDP->PenDash != NULL) + free(PDP->PenDash); + PDP->PenDash = NULL; + PDP->PenStyle = n; + if (n > 0) + { + int i; + PDP->PenDash = (DWORD *)malloc(n*sizeof(DWORD)); + for (i=0;iPenDash[i] = data[i]; + } + g2_win32_SetPen(pid,pdp); + return 0; + } + + +int g2_win32_SetFontSize(int pid, void *pdp, int size) + { + //static LOGFONT lf = {10,0,0,0,0,0,0,0,0,0,0,0,0,"Arial\0"}; + HGDIOBJ oldfont; + + oldfont = PDP->hFont; + //lf.lfHeight = size; + //PDP->hFont = CreateFontIndirect(&lf); + PDP->hFont = CreateFont(-size, 0, 0, 0, FW_NORMAL, 0, 0, 0, 0, OUT_TT_ONLY_PRECIS , 0, PROOF_QUALITY,0, "Times New Roman\0"); + if (PDP->hFont == NULL) + { + errhandler("Font (CreateFont)",NULL); + PDP->hFont = oldfont; + } + else + { + SelectObject(PDP->hMemDC,PDP->hFont); + if (oldfont != NULL)// && PDP->type == g2_win32) + DeleteObject(oldfont); + } + return 0; + } + +int g2_win32_Plot(int pid, void *pdp, int x, int y) + { + return SetPixel(PDP->hMemDC,x,y,PDP->PenColor); + } + +int g2_win32_Line(int pid, void *pdp, int x1, int y1, int x2, int y2) + { + MoveToEx(PDP->hMemDC,x1,y1,NULL); + LineTo(PDP->hMemDC,x2,y2); + SetPixel(PDP->hMemDC,x1,y1,PDP->PenColor); + SetPixel(PDP->hMemDC,x2,y2,PDP->PenColor); + // specifically draw end points since windows does not include one endpoint + return 0; + } + +int g2_win32_PolyLine(int pid, void *pdp, int N, int *points) + { + POINT *PointList; + int i; + + PointList = (POINT *)malloc(N*sizeof(POINT)); + if (PointList == NULL) + { + fprintf(stderr,"g2_win32: not enough memory !\n"); + return -1; + } + for (i=0;ihMemDC,PointList,N); + free(PointList); + return 0; + } + + + +int g2_win32_Rectangle(int pid, void *pdp, int x, int y, int x2, int y2) + { + SelectObject(PDP->hMemDC,GetStockObject(NULL_BRUSH)); + Rectangle(PDP->hMemDC,x,y,x2+1,y2+1); // add one since windows excludes lower right point + return 0; + } + +int g2_win32_FilledRectangle(int pid, void *pdp, int x1, int y1, int x2, int y2) + { + SelectObject(PDP->hMemDC,PDP->hBrush); + SelectObject(PDP->hMemDC,PDP->hNullPen); + return Rectangle(PDP->hMemDC,x1,y1,x2+1,y2+1); // add one since windows excludes lower right point + SelectObject(PDP->hMemDC,PDP->hPen); + return 0; + } + +int g2_win32_Polygon(int pid, void *pdp, int N, int *points) + { + POINT *PointList; + int i; + PointList = (POINT *)malloc(N*sizeof(POINT)); + if (PointList == NULL) + { + fprintf(stderr,"g2: not enough memory !\n"); + return -1; + } + for (i=0;ihMemDC,GetStockObject(NULL_BRUSH)); + Polygon(PDP->hMemDC,PointList,N); + free(PointList); + return 0; + } + +int g2_win32_FilledPolygon(int pid, void *pdp, int N, int *points) + { + POINT *PointList; + int i; + PointList = (POINT *)malloc(N*sizeof(POINT)); + if (PointList == NULL) + { + fprintf(stderr,"g2: not enough memory !\n"); + return -1; + } + for (i=0;ihMemDC,PDP->hBrush); + SelectObject(PDP->hMemDC,PDP->hNullPen); + Polygon(PDP->hMemDC,PointList,N); + SelectObject(PDP->hMemDC,PDP->hPen); + free(PointList); + return 0; + } + +int g2_win32_Ellipse(int pid, void *pdp, int x, int y, int r1, int r2) + { + SelectObject(PDP->hMemDC,GetStockObject(NULL_BRUSH)); + return Ellipse(PDP->hMemDC,x-r1,y-r2,x+r1+1,y+r2+1); // add one since windows is end exclusive + } + +int g2_win32_FilledEllipse(int pid, void *pdp, int x, int y, int r1, int r2) + { + SelectObject(PDP->hMemDC,PDP->hBrush); + SelectObject(PDP->hMemDC,PDP->hNullPen); + return Ellipse(PDP->hMemDC,x-r1,y-r2,x+r1+1,y+r2+1); // add one since windows is end exclusive + SelectObject(PDP->hMemDC,PDP->hPen); + return 0; + } + +int g2_win32_Arc(int pid, void *pdp, int x, int y, int r1, int r2, double a1, double a2) + { + a1 *= PI/180.; + a2 *= PI/180.; + SelectObject(PDP->hMemDC,GetStockObject(NULL_BRUSH)); + if (PDP->type == g2_win32) + return Arc(PDP->hMemDC,x-r1,y-r2,x+r1,y+r2,dtoi(x+r1*cos(a1)),dtoi(y-r2*sin(a1)),dtoi(x+r1*cos(a2)),dtoi(y-r2*sin(a2))); + else + return Arc(PDP->hMemDC,x-r1,y-r2,x+r1,y+r2,dtoi(x+r1*cos(a2)),dtoi(y-r2*sin(a2)),dtoi(x+r1*cos(a1)),dtoi(y-r2*sin(a1))); + } + +int g2_win32_FilledArc(int pid, void *pdp, int x, int y, int r1, int r2, double a1, double a2) + { + a1 *= PI/180.; + a2 *= PI/180.; + SelectObject(PDP->hMemDC,PDP->hBrush); + SelectObject(PDP->hMemDC,PDP->hNullPen); + if (PDP->type == g2_win32) + Pie(PDP->hMemDC,x-r1,y-r2,x+r1,y+r2,dtoi(x+r1*cos(a1)),dtoi(y-r2*sin(a1)),dtoi(x+r1*cos(a2)),dtoi(y-r2*sin(a2))); + else + Pie(PDP->hMemDC,x-r1,y-r2,x+r1,y+r2,dtoi(x+r1*cos(a2)),dtoi(y-r2*sin(a2)),dtoi(x+r1*cos(a1)),dtoi(y-r2*sin(a1))); + SelectObject(PDP->hMemDC,PDP->hPen); + return 0; + } + +int g2_win32_DrawString(int pid, void *pdp, int x, int y, const char *text) + { + SetTextColor(PDP->hMemDC,PDP->PenColor); + SetBkMode(PDP->hMemDC,TRANSPARENT); + return TextOut(PDP->hMemDC,x,y,text,strlen(text)); + } + +int g2_win32_QueryPointer(int pid, void *pdp, int *x, int *y, unsigned int *button) +// +// Thanks to input by Martin stéphane +// + { + POINT point; + + GetCursorPos(&point); + + ScreenToClient(PDP->hwndThreadWindow,&point); + + *y=point.y; + *x=point.x; + *button=0; + + if (PDP->hwndThreadWindow != GetForegroundWindow()) + return; // return if our window does not have the focus + + if (GetKeyState(VK_LBUTTON)<0) + *button=*button+256; + + if (GetKeyState(VK_MBUTTON)<0) + *button=*button+512; + + if (GetKeyState(VK_RBUTTON)<0) + *button=*button+1024; + + return 0; + } + +void errhandler(LPSTR errtxt,HWND hwnd) +{ + LPVOID lpMessageBuffer; + char szError[255]; + DWORD LastError; + + LastError = GetLastError(); + + FormatMessage(FORMAT_MESSAGE_ALLOCATE_BUFFER |FORMAT_MESSAGE_FROM_SYSTEM, + NULL,LastError,MAKELANGID(LANG_NEUTRAL, SUBLANG_DEFAULT), //The user default language + (LPTSTR) &lpMessageBuffer,0,NULL ); + + sprintf(szError,"Error in %s\n Error code %d : %s\n" ,errtxt,LastError,lpMessageBuffer); + MessageBox(hwnd,szError,"error",MB_OK); + + LocalFree( lpMessageBuffer ); +} + + +int InitApplication() +{ + WNDCLASS wc; + + // Fill in window class structure with parameters that describe the + // main window. + + g2res_DLL = LoadLibrary("g2res.dll"); + + if (g2res_DLL == NULL) + printf("Warning: Could not load g2 resource DLL\n Menu and Icon are disabled\n"); + + + wc.style = CS_HREDRAW | CS_VREDRAW; // Class style(s). + wc.lpfnWndProc = g2_WndProc; // Function to retrieve messages for windows of this class. + wc.cbClsExtra = 0; // No per-class extra data. + wc.cbWndExtra = 0; // No per-window extra data. + wc.hInstance = 0; // Application that owns the class. + wc.hIcon = NULL; + if (g2res_DLL != NULL) + { + wc.hIcon = LoadIcon(g2res_DLL, MAKEINTRESOURCE(IDI_ICON1)); + if (wc.hIcon == NULL) + errhandler("Error in LoadIcon",NULL); + } + wc.hCursor = LoadCursor(NULL, IDC_ARROW); + wc.hbrBackground = NULL; + wc.lpszMenuName = "G2WIN32"; + wc.lpszClassName = "g2Window"; // Name used in call to CreateWindow. + + /* Register the window class and return success/failure code. */ + + + if(!RegisterClass(&wc)) + { + errhandler("RegisterClass",NULL); + return FALSE; + } + g2_win32_registered = TRUE; + return TRUE; +} + + +/** + * \ingroup physdev + * \defgroup win32 MS Windows + */ + +/** + * + * Create a Windows device. + * + * \param width window width + * \param height window height + * \param title window title + * \param type window type, see ::g2_win32_type + * + * \return physical device id + * + * \ingroup win32 + */ +int g2_open_win32(int width, int height, const char *title, int type) + { + int pid=0,vid; + long ThreadID; + + g2_win32_STRUCT *pdp; + + pdp = (g2_win32_STRUCT *)malloc(sizeof(g2_win32_STRUCT)); + + PDP->type = type; + PDP->NoOfInks = 0; + PDP->Inks = NULL; + PDP->PenStyle = 0; + PDP->PenWidth = 1; + PDP->PenColor = RGB(1,1,1); + PDP->PenDash = NULL; + PDP->nWidth = width; + PDP->nHeight = height; + PDP->messageloop = 0; + PDP->hFont = NULL; + + switch(type) { + case g2_win32: + { + if(g2_win32_registered == FALSE) + InitApplication(); + + PDP->x = 1; + PDP->y = 1; + if (title != NULL) + PDP->title = title; + else + PDP->title = "g2 Window"; + PDP->hThread = CreateThread(NULL, 0, + (LPTHREAD_START_ROUTINE)g2_StartThread, + (LPVOID)(pdp), + 0, + (LPDWORD) &ThreadID ); + + if (PDP->hThread == NULL) + fprintf(stderr,"g2_win32: Thread could not be started\n"); + + SetThreadPriority(PDP->hThread,THREAD_PRIORITY_ABOVE_NORMAL); + //Wait till window is created by Thread + while( PDP->messageloop == 0) + Sleep(10); + break; + } + case g2_wmf32 : + { + DWORD dwInchesX; + DWORD dwInchesY; + DWORD dwDPI = 72; + RECT Rect = { 0, 0, 0, 0 }; + TCHAR szDesc[] = "Created by g2\0\0"; + HDC hScreenDC; + float PixelsX, PixelsY, MMX, MMY; + + dwInchesX = PDP->nWidth/72; + dwInchesY = PDP->nHeight/72; + // dwInchesX x dwInchesY in .01mm units + SetRect( &Rect, 0, 0,dwInchesX*2540, dwInchesY*2540 ); + + // Get a Reference DC + hScreenDC = GetDC( NULL ); + + // Get the physical characteristics of the reference DC + PixelsX = (float)GetDeviceCaps( hScreenDC, HORZRES ); + PixelsY = (float)GetDeviceCaps( hScreenDC, VERTRES ); + MMX = (float)GetDeviceCaps( hScreenDC, HORZSIZE ); + MMY = (float)GetDeviceCaps( hScreenDC, VERTSIZE ); + + // Create the Metafile + PDP->hMemDC = CreateEnhMetaFile(hScreenDC, title, &Rect, szDesc); + //tstDC = CreateEnhMetaFile(hScreenDC, "test.emf", &Rect, szDesc); + + // Release the reference DC + ReleaseDC( NULL, hScreenDC ); + // Anisotropic mapping mode + SetMapMode( PDP->hMemDC, MM_ANISOTROPIC ); + // Set the Windows extent + SetWindowExtEx( PDP->hMemDC, dwInchesX*dwDPI, dwInchesY*dwDPI, NULL ); + + // Set the viewport extent to reflect + // dwInchesX" x dwInchesY" in device units + SetViewportExtEx( PDP->hMemDC, + (int)((float)dwInchesX*25.4f*PixelsX/MMX), + (int)((float)dwInchesY*25.4f*PixelsY/MMY), + NULL ); +// printf("viewport: %d %d\n",(int)((float)dwInchesX*25.4f*PixelsX/MMX), +// (int)((float)dwInchesY*25.4f*PixelsY/MMY)); + // create the device context +// PDP->hMemDC = CreateMetaFile(NULL) ; + +// PDP->hMemDC = CreateEnhMetaFile( (HDC)NULL, title, &WmfRect, "Created by g2"); +// PDP->hMemDC = CreateMetaFile(title); +// SetMapMode(PDP->hMemDC,MM_LOMETRIC ); +// SetWindowExtEx(PDP->hMemDC,width,height,NULL); +// SetViewportExtEx(PDP->hMemDC,width*1000,height*1000,NULL); + if (PDP->hMemDC == NULL) errhandler("Could not Create Metafile !\n",NULL); + SetArcDirection(PDP->hMemDC,AD_CLOCKWISE); + break; + } + default: + return height; + } + SetTextAlign(PDP->hMemDC,TA_BOTTOM | TA_LEFT); + vid = g2_register_physical_device(pid, pdp, + g2_IntCoor, g2_win32_funix, + 1.0, -1.0, + 0.0, height-1); + + g2_allocate_basic_colors(vid); + g2_pen(vid,1); + g2_set_background(vid, 0); + g2_set_font_size(vid, 10); + g2_clear(vid); + + return vid; + } + +#undef PDP diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.h new file mode 100755 index 000000000..b35a05d37 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.h @@ -0,0 +1,68 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +/* This is g2_win32.h */ +#ifndef _G2_WIN32_H +#define _G2_WIN32_H + +#if defined(__cplusplus) +extern "C" +{ +#endif + +#include + +// Common Library header for DLL and application +#ifdef WIN32 +#ifdef G2DLL +#ifdef MAKEDLL +/* Create DLL */ +#define LINKDLL __declspec( dllexport) +#else +/* Use DLL */ +#define LINKDLL __declspec( dllimport) +#endif +#else +/* Use static win32 */ +#define LINKDLL +#endif +#else +/* Use non-win32 */ +#define LINKDLL +#endif + +/** + * Window type + * + * \ingroup win32 + */ +enum g2_win32_type { + g2_win32, /**< regular window */ + g2_wmf32 /**< windows meta file */ +}; + + +LINKDLL int g2_open_win32(int width, int height, const char *filename,int type); + + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + + +#endif /* _G2_WIN32_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.rc b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.rc new file mode 100755 index 000000000..ffa58aa59 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32.rc @@ -0,0 +1,167 @@ +//Microsoft Developer Studio generated resource script. +// +#include "resource.h" + +#define APSTUDIO_READONLY_SYMBOLS +///////////////////////////////////////////////////////////////////////////// +// +// Generated from the TEXTINCLUDE 2 resource. +// +#include "afxres.h" + +///////////////////////////////////////////////////////////////////////////// +#undef APSTUDIO_READONLY_SYMBOLS + +///////////////////////////////////////////////////////////////////////////// +// English (U.S.) resources + +#if !defined(AFX_RESOURCE_DLL) || defined(AFX_TARG_ENU) +#ifdef _WIN32 +LANGUAGE LANG_ENGLISH, SUBLANG_ENGLISH_US +#pragma code_page(1252) +#endif //_WIN32 + +///////////////////////////////////////////////////////////////////////////// +// +// Icon +// + +// Icon with lowest ID value placed first to ensure application icon +// remains consistent on all systems. +IDI_ICON1 ICON DISCARDABLE "g2_Win32.ico" + +///////////////////////////////////////////////////////////////////////////// +// +// DESIGNINFO +// + +#ifdef APSTUDIO_INVOKED +GUIDELINES DESIGNINFO DISCARDABLE +BEGIN + "ABOUTBOX", DIALOG + BEGIN + LEFTMARGIN, 7 + RIGHTMARGIN, 156 + TOPMARGIN, 7 + BOTTOMMARGIN, 91 + END +END +#endif // APSTUDIO_INVOKED + + +#ifndef _MAC +///////////////////////////////////////////////////////////////////////////// +// +// Version +// + +VS_VERSION_INFO VERSIONINFO + FILEVERSION 1,0,0,1 + PRODUCTVERSION 1,0,0,1 + FILEFLAGSMASK 0x3fL +#ifdef _DEBUG + FILEFLAGS 0x1L +#else + FILEFLAGS 0x0L +#endif + FILEOS 0x40004L + FILETYPE 0x2L + FILESUBTYPE 0x0L +BEGIN + BLOCK "StringFileInfo" + BEGIN + BLOCK "040904b0" + BEGIN + VALUE "CompanyName", "\0" + VALUE "FileDescription", "g2_win32\0" + VALUE "FileVersion", "1, 0, 0, 1\0" + VALUE "InternalName", "g2_win32\0" + VALUE "LegalCopyright", "Copyright © 1996-1998\0" + VALUE "OriginalFilename", "g2_win32\0" + VALUE "ProductName", "g2_win32\0" + VALUE "ProductVersion", "1, 0, 0, 1\0" + END + END + BLOCK "VarFileInfo" + BEGIN + VALUE "Translation", 0x409, 1200 + END +END + +#endif // !_MAC + + +///////////////////////////////////////////////////////////////////////////// +// +// Dialog +// + +ABOUTBOX DIALOG DISCARDABLE 0, 0, 163, 98 +STYLE DS_MODALFRAME | WS_POPUP | WS_CAPTION | WS_SYSMENU +CAPTION "About g2" +FONT 8, "MS Sans Serif" +BEGIN + DEFPUSHBUTTON "OK",IDOK,55,71,50,14 + CTEXT "g2 version 0.40\n\n (c) 1998-1999\n Ljubomir Milanovic\nHorst Wagner", + IDC_STATIC,27,7,105,55 + ICON IDI_ICON1,IDC_STATIC,9,9,20,20 +END + + +#ifdef APSTUDIO_INVOKED +///////////////////////////////////////////////////////////////////////////// +// +// TEXTINCLUDE +// + +1 TEXTINCLUDE DISCARDABLE +BEGIN + "resource.h\0" +END + +2 TEXTINCLUDE DISCARDABLE +BEGIN + "#include ""afxres.h""\r\n" + "\0" +END + +3 TEXTINCLUDE DISCARDABLE +BEGIN + "\r\n" + "\0" +END + +#endif // APSTUDIO_INVOKED + + +///////////////////////////////////////////////////////////////////////////// +// +// Menu +// + +G2WIN32 MENU DISCARDABLE +BEGIN + POPUP "File" + BEGIN + MENUITEM "Copy", ID_FILE_COPY + MENUITEM "Close", ID_FILE_CLOS + MENUITEM SEPARATOR + MENUITEM "About", ID_FILE_ABOUT + END +END + +#endif // English (U.S.) resources +///////////////////////////////////////////////////////////////////////////// + + + +#ifndef APSTUDIO_INVOKED +///////////////////////////////////////////////////////////////////////////// +// +// Generated from the TEXTINCLUDE 3 resource. +// + + +///////////////////////////////////////////////////////////////////////////// +#endif // not APSTUDIO_INVOKED + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_P.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_P.h new file mode 100755 index 000000000..83d3437e4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_P.h @@ -0,0 +1,119 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ + +#ifndef G2_WIN32_P_H +#define G2_WIN32_P_H + +#include "windows.h" +#include + +extern HMENU hmenu; +extern HANDLE ghModule; +extern HINSTANCE g2res_DLL; + +typedef struct g2_win32_STRUCT { + HANDLE hThread; + HWND hwndThreadWindow; + HANDLE hinst; + HBITMAP hBitmap; + HDC hMemDC; + HPEN hPen; + HPEN hNullPen; + HBRUSH hBrush; + HFONT hFont; + int nWidth; + int nHeight; + int x; + int y; + int NoOfInks; + int PenWidth; + int PenStyle; + DWORD *PenDash; + int Pen; + int BkColor; + COLORREF PenColor; + COLORREF *Inks; + char *title; + int type; + int messageloop; + } g2_win32_STRUCT; + + +BOOL SaveBitmapAs(HWND hWnd,struct XPGTHREADINFO *pThreadInfo); +LRESULT CALLBACK g2_WndProc(HWND hWnd, UINT message, WPARAM wParam, LPARAM lParam); +long WINAPI g2_StartThread(struct g2_win32_STRUCT *pdp); +void errhandler(LPSTR errtxt,HWND hwnd); + + +int g2_win32_init_win32(int pid, void *pdp, int vid, int width,int height); +int g2_win32_init_win32X(int pid, void *pdp, + int width, int height, + int xposition, int yposition, + char *windowname, char *iconname, + char *icondata, int iconwidth, int iconheight); +int g2_win32_Delete(int pid, void *pdp); +int g2_win32_Clear(int pid, void *pdp); +int g2_win32_Flush(int pid, void *pdp); +int g2_win32_Ink(int pid, void *pdp, + double red, double green, double blue); +int g2_win32_ClearPalette(int pid, void *pdp); +int g2_win32_ResetPalette(int pid, void *pdp); +int g2_win32_SetBackground(int pid, void *pdp, int color); +int g2_win32_Pen(int pid, void *pdp, int color); +int g2_win32_Paper(int pid, void *pdp, int color); +int g2_win32_SetLineWidth(int pid, void *pdp, int w); +int g2_win32_SetDash(int pid, void *pdp, int n, int *data); +int g2_win32_SetFontSize(int pid, void *pdp, int size); +int g2_win32_Plot(int pid, void *pdp, int x, int y); +int g2_win32_Line(int pid, void *pdp, int x1, int y1, int x2, int y2); +int g2_win32_PolyLine(int pid, void *pdp, int N, int *p); +int g2_win32_Polygon(int pid, void *pdp, int N, int *p); +int g2_win32_FilledPolygon(int pid, void *pdp, int N, int *p); +int g2_win32_Triangle(int pid, void *pdp, + int x1, int y1, + int x2, int y2, + int x3, int y3); +int g2_win32_FilledTriangle(int pid, void *pdp, int x1, int y1, + int x2, int y2, + int x3, int y3); +int g2_win32_Rectangle(int pid, void *pdp, int x1, int y1, int x2, int y2); +int g2_win32_FilledRectangle(int pid, void *pdp, + int x1, int y1, int x2, int y2); +int g2_win32_Circle(int pid, void *pdp, int x, int y, int r); +int g2_win32_FilledCircle(int pid, void *pdp, int x, int y, int r); +int g2_win32_Arc(int pid, void *pdp, int x, int y, + int r1, int r2, double a1, double a2); +int g2_win32_FilledArc(int pid, void *pdp, int x, int y, + int r1, int r2, double a1, double a2); +int g2_win32_Ellipse(int pid, void *pdp, int x, int y, int r1, int r2); +int g2_win32_FilledEllipse(int pid, void *pdp, int x, int y, int r1, int r2); +int g2_win32_DrawString(int pid, void *pdp, int x, int y, const char *text); +int g2_win32_QueryPointer(int pid, void *pdp, int *x, int *y, unsigned int *button); + +int g2_win32_AllocateBasicColors(int pid, void *pdp); + +int g2_win32_Cleanup(int pid, void *pdp); + + +#endif /* g2_win32_P_H */ + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_funix.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_funix.h new file mode 100755 index 000000000..84593b940 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_funix.h @@ -0,0 +1,56 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef G2_WIN32_FUNIX_H +#define G2_WIN32_FUNIX_H + +#include "g2_win32_P.h" +#include "g2_physical_device.h" + +const g2_funix_fun g2_win32_funix[] = { + { g2_Delete, g2_win32_Delete }, + { g2_Ink, g2_win32_Ink }, + { g2_Pen, g2_win32_Pen }, + { g2_SetBackground, g2_win32_SetBackground }, + { g2_ClearPalette, g2_win32_ClearPalette }, + { g2_SetLineWidth, g2_win32_SetLineWidth }, + { g2_SetDash, g2_win32_SetDash }, + { g2_SetFontSize, g2_win32_SetFontSize }, + { g2_Clear, g2_win32_Clear }, + { g2_Flush, g2_win32_Flush }, + { g2_Save, g2_win32_Flush }, + { g2_Plot, g2_win32_Plot }, + { g2_Line, g2_win32_Line }, + { g2_PolyLine, g2_win32_PolyLine }, + { g2_Polygon, g2_win32_Polygon }, + { g2_FilledPolygon, g2_win32_FilledPolygon }, + { g2_Rectangle, g2_win32_Rectangle }, + { g2_FilledRectangle, g2_win32_FilledRectangle }, + { g2_Arc, g2_win32_Arc }, + { g2_FilledArc, g2_win32_FilledArc }, + { g2_Ellipse, g2_win32_Ellipse }, + { g2_FilledEllipse, g2_win32_FilledEllipse }, + { g2_Circle, NULL }, + { g2_FilledCircle, NULL }, + { g2_String, g2_win32_DrawString }, + { g2_QueryPointer, g2_win32_QueryPointer }, + { g2_FUNIX_NULL, NULL } }; + + +#endif /* G2_WIN32_FUNIX_H */ + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_thread.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_thread.c new file mode 100755 index 000000000..7c3153691 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2_win32_thread.c @@ -0,0 +1,213 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ + +#include +#include +#include +#include +#include + +#include "g2_win32_P.h" + +#include "resource.h" + + + +int WINAPI About(HWND hDlg,UINT message, WPARAM wParam,LPARAM lParam) +{ + switch (message){ + case WM_INITDIALOG: + return TRUE; + + case WM_COMMAND: + if (wParam == IDOK) + EndDialog(hDlg,wParam); + break; + } + + return FALSE; +} + + + +LRESULT CALLBACK g2_WndProc(HWND hWnd, UINT message, WPARAM wParam, LPARAM lParam) +{ + PAINTSTRUCT ps; + HDC hDC; + RECT Rect; + struct g2_win32_STRUCT *pdp; + + pdp = (struct g2_win32_STRUCT *)GetWindowLong(hWnd, GWL_USERDATA); + switch (message) { + + case WM_PAINT: + if (pdp == NULL) break; + if (pdp->hBitmap == NULL) break; + +// printf("Received WM_PAINT\n"); + + hDC = BeginPaint (hWnd, &ps); + GetClientRect(hWnd,&Rect); + BitBlt( hDC, Rect.left, Rect.top, Rect.right - Rect.left, + Rect.bottom - Rect.top, pdp->hMemDC, 0, 0, SRCCOPY ); + EndPaint (hWnd, &ps); + return 0L; + + case WM_DESTROY: + +// printf("Received WM_DESTROY\n"); + g2_win32_Cleanup(0,pdp); + ExitThread(0); + return 0L; + + case WM_COMMAND: + switch(LOWORD(wParam)){ + + case ID_FILE_COPY: + if (OpenClipboard(hWnd)) + { + HBITMAP hBitmap; + + EmptyClipboard(); + + if (pdp->hBitmap) + { + if (hBitmap = CopyImage(pdp->hBitmap,IMAGE_BITMAP, + 0,0,LR_COPYRETURNORG)); + SetClipboardData(CF_BITMAP, hBitmap); + } + CloseClipboard(); + } + return 0L; + + case ID_FILE_ABOUT: + if(DialogBox(g2res_DLL,"ABOUTBOX",hWnd,(DLGPROC)About) == -1) + errhandler("Failed to create Dialogbox",NULL); + return 0L; + + case ID_FILE_CLOS: + g2_win32_Delete(0,pdp); + return 0L; + + default: + return (DefWindowProc(hWnd, message, wParam, lParam)); + } + + default: + return (DefWindowProc(hWnd, message, wParam, lParam)); + } +/* we should never get here */ +return -1; +} + +long WINAPI g2_StartThread(struct g2_win32_STRUCT *pdp) +{ +RECT Rect; +HWND hWnd; +MSG msg; +HDC hDC; +HMENU hmenu; +DWORD style; +RECT frame; + +hmenu = NULL; +if (g2res_DLL != NULL) + { + hmenu = LoadMenu(g2res_DLL,"G2WIN32"); + if (hmenu == NULL) errhandler("Load menu failed",NULL); + } + +style = WS_POPUPWINDOW |WS_OVERLAPPED | WS_CAPTION | WS_MINIMIZEBOX; +frame.left = 0; +frame.top = 0; +frame.right = pdp->nWidth; +frame.bottom = pdp->nHeight - ((hmenu==NULL)?GetSystemMetrics(SM_CYMENU):0); + +AdjustWindowRect(&frame,style,1); + +/* Save the instance handle in static variable, which will be used in */ +/* many subsequence calls from this application to Windows. */ + + /* Create a main window for this application instance. */ +pdp->hinst = GetModuleHandle(NULL); + +hWnd = CreateWindow( + "g2Window", // See RegisterClass() call. + pdp->title, // Text for window title bar. + style, + pdp->x, pdp->y, + frame.right - frame.left, // width + frame.bottom - frame.top, // height + NULL, // Overlapped windows have no parent. + hmenu, // Use the window class menu. + 0, // This instance owns this window. + NULL // Pointer not needed. + ); + + // If window could not be created, return "failure" + +if (!hWnd) + { + errhandler("CreateWindow",NULL); + return (FALSE); // return failure :(( + } + +#define WIDTH(x) (x.right-x.left+1) // Macro to get rect width +#define HEIGHT(x) (x.bottom-x.top+1) // Macro to get rect height + +// How big is the window? +GetClientRect( hWnd, &Rect ); + +// Need a DC +hDC = GetDC( hWnd ); +SetBkColor(hDC,RGB(255,255,255)); +// Create a bitmap big enough to hold the window's image +pdp->hBitmap = CreateCompatibleBitmap( hDC, WIDTH(Rect), HEIGHT(Rect) ); +// printf("memdc size: %d %d\n",WIDTH(Rect),HEIGHT(Rect)); +// Create MemDC +pdp->hMemDC = CreateCompatibleDC(hDC); +SelectObject( pdp->hMemDC, pdp->hBitmap ); +// clean up +ReleaseDC( hWnd, hDC ); +#undef WIDTH +#undef HEIGHT + + + +SetWindowLong(hWnd, GWL_USERDATA, (long)pdp); + + pdp->hwndThreadWindow = hWnd; + // Make the window visible; update its client area; and return "success" + ShowWindow(hWnd, SW_SHOWDEFAULT); // Show the window + UpdateWindow(hWnd); // Sends WM_PAINT message + //printf("pdp->messageloop ->= 1;\n"); + pdp->messageloop = 1; + //printf("pdp->messageloop = 1;\n"); + + while (GetMessage(&msg, NULL, 0, 0)) { + TranslateMessage(&msg); + DispatchMessage(&msg); + } + + + return (TRUE); // Returns success :) +} + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2res.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2res.c new file mode 100755 index 000000000..b729ff7fc --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/g2res.c @@ -0,0 +1,7 @@ +#include + + +BOOL WINAPI DllMain( HINSTANCE hInstance, DWORD dwReason, LPVOID lpv) +{ + return 1; +} \ No newline at end of file diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/resource.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/resource.h new file mode 100755 index 000000000..ff8f985b7 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/Win32/resource.h @@ -0,0 +1,21 @@ +//{{NO_DEPENDENCIES}} +// Microsoft Developer Studio generated include file. +// Used by g2_win32.rc +// +#define IDI_ICON1 101 +#define IDD_DIALOG1 104 +#define ID_FILE_SAVEASBMP 40002 +#define ID_FILE_COPY 40003 +#define ID_FILE_ABOUT 40005 +#define ID_FILE_CLOS 40006 + +// Next default values for new objects +// +#ifdef APSTUDIO_INVOKED +#ifndef APSTUDIO_READONLY_SYMBOLS +#define _APS_NEXT_RESOURCE_VALUE 107 +#define _APS_NEXT_COMMAND_VALUE 40007 +#define _APS_NEXT_CONTROL_VALUE 1000 +#define _APS_NEXT_SYMED_VALUE 101 +#endif +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Entries new file mode 100755 index 000000000..178481050 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Entries @@ -0,0 +1 @@ +D diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Repository new file mode 100755 index 000000000..d0f451824 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/X11/CVS diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Entries b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Entries new file mode 100755 index 000000000..b6003b5d5 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Entries @@ -0,0 +1,6 @@ +D/CVS//// +/g2.xpm/1.1/Mon Jan 18 10:56:52 1999// +/g2_X11.c/1.1/Tue Jun 14 20:44:20 2005// +/g2_X11.h/1.1/Tue Apr 17 20:16:38 2001// +/g2_X11_P.h/1.1/Tue Jun 14 20:44:21 2005// +/g2_X11_funix.h/1.1/Tue Jun 14 20:44:21 2005// diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Repository b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Repository new file mode 100755 index 000000000..724d8ea4e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Repository @@ -0,0 +1 @@ +RNAforester/g2-0.70/src/X11 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Root b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Root new file mode 100755 index 000000000..9c9d467ed --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Root @@ -0,0 +1 @@ +mhoechsm@porta.techfak.uni-bielefeld.de:/homes/mhoechsm/cvsroot diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Template b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/CVS/Template new file mode 100755 index 000000000..e69de29bb diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2.xpm b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2.xpm new file mode 100755 index 000000000..339c0fefa --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2.xpm @@ -0,0 +1,180 @@ +/* XPM */ +static char * g2_xpm[] = { +"40 40 137 2", +" c none", +". c #6B1214", +"+ c #6E1314", +"@ c #891C18", +"# c #8F1E19", +"$ c #821A17", +"% c #841A17", +"& c #BD2D1E", +"* c #EC3C24", +"= c #C22F1F", +"- c #7D1816", +"; c #851A17", +"> c #731515", +", c #BC2C1E", +"' c #B1291D", +") c #8D1D18", +"! c #721415", +"~ c #942019", +"{ c #A0231B", +"] c #C93120", +"^ c #6A1214", +"/ c #6D1314", +"( c #771616", +"_ c #8A1C18", +": c #A5251B", +"< c #C12E1F", +"[ c #D53522", +"} c #9E231B", +"| c #6F1315", +"1 c #681114", +"2 c #7A1716", +"3 c #831A17", +"4 c #7F1817", +"5 c #911E19", +"6 c #AA271C", +"7 c #C73020", +"8 c #E03823", +"9 c #E73B24", +"0 c #D23421", +"a c #B42A1D", +"b c #962019", +"c c #7E1817", +"d c #711415", +"e c #9B221A", +"f c #7F1917", +"g c #AF281D", +"h c #CA3120", +"i c #DD3722", +"j c #E13923", +"k c #D73522", +"l c #C42F1F", +"m c #AE281D", +"n c #9D221A", +"o c #931F19", +"p c #8E1E19", +"q c #861B18", +"r c #751515", +"s c #B52A1D", +"t c #881B18", +"u c #6C1214", +"v c #761615", +"w c #AD281C", +"x c #D83622", +"y c #D03321", +"z c #C83120", +"A c #C22E1F", +"B c #BD2D1F", +"C c #A9261C", +"D c #A4251B", +"E c #DB3722", +"F c #851B17", +"G c #A3241B", +"H c #E43A23", +"I c #B32A1D", +"J c #9C221A", +"K c #9E231A", +"L c #D33421", +"M c #901E19", +"N c #A7261C", +"O c #C02E1F", +"P c #AC271C", +"Q c #8E1D18", +"R c #761515", +"S c #691114", +"T c #8B1C18", +"U c #761616", +"V c #B82B1E", +"W c #871B18", +"X c #671114", +"Y c #8C1D18", +"Z c #7B1716", +"` c #861B17", +" . c #881C18", +".. c #801917", +"+. c #A6251C", +"@. c #CB3120", +"#. c #DC3722", +"$. c #791716", +"%. c #9A221A", +"&. c #BA2C1E", +"*. c #98211A", +"=. c #B2291D", +"-. c #99211A", +";. c #B62B1E", +">. c #D13421", +",. c #D53521", +"'. c #CE3321", +"). c #952019", +"!. c #EB3C24", +"~. c #E83B24", +"{. c #DE3823", +"]. c #9F231B", +"^. c #BB2C1E", +"/. c #CF3321", +"(. c #C32F1F", +"_. c #7C1816", +":. c #7E1816", +"<. c #DA3622", +"[. c #E63A24", +"}. c #EA3C24", +"|. c #B0281D", +"1. c #D63522", +"2. c #E23923", +"3. c #E53A23", +"4. c #AB271C", +"5. c #D93622", +"6. c #811917", +"7. c #97211A", +"8. c #7C1716", +"9. c #741515", +"0. c #A8261C", +"a. c #A2241B", +"b. c #D43421", +"c. c #D43521", +"d. c #CC3220", +"e. c #E93B24", +"f. c #BC2D1E", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" . + @ ", +" # $ % & * = - ", +" ; > , ' ", +" ) ! ~ ", +" { ] ", +" . ^ / ( _ : < [ & } $ | 1 ^ 2 ", +" _ 3 4 $ 5 6 7 8 * 9 0 a b c d . . ^ $ 7 ", +" e @ f 3 ~ g h i j k l m n o p ) _ q % r s ", +" t ! u v # w x y z l A B s C D E ", +" ^ | F G H E h I J K D L ", +" 3 M N O P Q R u S S . T U ", +" } 6 a ^ / f V W X Y 6 5 Z ( u ", +" ` .Y ..M G +.{ @.#.x [ C u 2 ", +" / $.# $ .Y ", +" f %.&. . | $. ", +" *.' = v @ +. ", +" g &.&.=. $ -.;.>. ", +" ,.,.0 y '. ).' 7 >. ", +" !.!.~.{.] $ ].^./.k k ", +" ~.E (.: T _.:.# C l <.[.!.!.}. ", +" 7 |.].e G a 7 1.{.j 2.3.9 9 ", +" ].K G 4.' a ;.&.(. #.j 5. ", +" 6.% ) }.8 ] ", +" >.;.e ", +" G _ ( u ", +" 7.t 8.R 9.> ", +" f o +.' I m 0.D G a.].). ", +" 7 b.5.x 1.[ 1.c.d.^.a. ", +" * e.9 9 }.* [.1.f. ", +" ", +" ", +" ", +" "}; diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11.c new file mode 100755 index 000000000..d2f14f276 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11.c @@ -0,0 +1,797 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include +#include +#include +#include +#include +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_util.h" +#include "g2_X11_P.h" +#include "g2_X11.h" +#include "g2_X11_funix.h" +#include "g2_config.h" + + +static int N_X11=0; +static g2_X11_device *g2_X11_dev=NULL; + +/** + * \ingroup physdev + * \defgroup X11 X11 + */ + + +/** + * + * Open a simple X11 window (physical device device). + * + * \param width window width + * \param height window height + * \return physical device id + * + * \ingroup X11 + */ +int g2_open_X11(int width, int height) +{ + return g2_open_X11X(width, height, + 10, 10, + NULL, NULL, + NULL, -1, -1); +} + + + +/** + * + * Open a X11 window (physical device device). If \a icon_width or \a + * icon_height is smaller than 0, the \a icon_data is interpreted as a + * file name. + * + * \param width window width + * \param height window height + * \param x x position on screen + * \param y y position on screen + * \param window_name hint for window manager + * \param icon_name hint for window manager + * \param icon_data icon bitmap (\a icon_width * \a icon_height bits) or file name containing bitmap + * (if \a icon_width <= 0 or \a icon_height <= 0) + * \param icon_width icon width + * \param icon_height icon height + * \return physical device id + * + * \ingroup X11 + */ +int g2_open_X11X(int width, int height, + int x, int y, + char *window_name, char *icon_name, + char *icon_data, int icon_width, int icon_height) +{ + g2_X11_device *xout=NULL; + int pid=-1, i; + char name[32]; + int vid; + + if(g2_X11_dev==NULL) { + g2_X11_dev=g2_malloc(sizeof(g2_X11_device)); + N_X11=1; /* first X11 device */ + xout=&g2_X11_dev[N_X11-1]; + pid=0; + } else { + for(i=0;iwidth=width; /* set window size */ + xout->height=height; + + xout->NofInks=0; /* reset inks */ + xout->inks=NULL; + + vid = g2_register_physical_device(pid, NULL, + g2_IntCoor, g2_X11_funix, + 1.0, -1.0, + 0.0, height-1); + + sprintf(name, "g2: %d", vid); /* set window and icon names */ + if(window_name==NULL) + window_name=name; + if(icon_name==NULL) + icon_name=name; + + g2_X11_init_X11X(pid, width, height, + x, y, + window_name, icon_name, + icon_data, icon_width, icon_height); + + + /* g2 calls */ + g2_allocate_basic_colors(vid); + g2_set_background(vid, 0); + g2_pen(vid, 1); + + return vid; +} + + + + +/* + * + * Extended version of the InitX11 + * + */ +int g2_X11_init_X11X(int pid, int width, int height, + int xposition, int yposition, + char *window_name, char *icon_name, + char *icon_data, + unsigned int icon_width, unsigned int icon_height) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + Window root; + XSetWindowAttributes wattr; + XEvent event; + Pixmap iconPixmap; + XSizeHints sizehints; + int xhot, yhot, rv; + XColor w_scr, w_exa, r_scr, r_exa; + XClassHint class_hint; + + if((xout->display=XOpenDisplay(NULL))==NULL) { + g2_log(Error, "g2: can't open display\n"); + exit(-1); + } + + + xout->root=RootWindow(xout->display, DefaultScreen(xout->display)); + root=xout->root; + + wattr.event_mask=ExposureMask; + xout->window=XCreateWindow(xout->display, root, + xposition, yposition, + width, height, + 0, + CopyFromParent, InputOutput, CopyFromParent, + CWEventMask, + &wattr); + + xout->gc=XCreateGC(xout->display, xout->window, + 0lu, NULL); + + xout->colormap=DefaultColormap(xout->display, + DefaultScreen(xout->display)); + + XAllocNamedColor(xout->display, xout->colormap, + "red", &r_scr, &r_exa); + XAllocNamedColor(xout->display, xout->colormap, + "white", &w_scr, &w_exa); + + + + if(icon_data!=NULL) { + if(icon_width<=0 || icon_height<=0) { /* read icon from file */ + rv=XReadBitmapFile(xout->display, xout->window, + icon_data, &icon_width, &icon_height, + &iconPixmap, &xhot, &yhot); + } else { /* icon is bitmap */ + iconPixmap=XCreatePixmapFromBitmapData(xout->display, + xout->window, + icon_data, + icon_width, icon_height, + 1ul, 0ul, 1); + rv=BitmapSuccess; + } + switch(rv) { + case BitmapOpenFailed: + fputs("g2(OpenXX): bitmap file open failed\n",stderr); + break; + case BitmapFileInvalid: + fputs("g2(OpenXX): bitmap file invalid\n",stderr); + break; + case BitmapNoMemory: + fputs("g2(OpenXX): no enough memeory for bitmap\n",stderr); + break; + } + } else { /* no icon data avail. */ + unsigned char bitmapData[] = { + 0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00, + 0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00, + 0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00, + 0x00,0x00,0x00,0x00,0x00,0x80,0x03,0x00,0x00,0x00,0xe0, + 0x0d,0x00,0x00,0x00,0x60,0x0c,0x00,0x00,0x00,0x20,0x18, + 0x00,0x00,0x00,0x00,0x10,0x00,0xf8,0xe3,0x07,0x08,0x00, + 0xfe,0xfa,0x07,0x0c,0x00,0xbf,0x6e,0x07,0x06,0x80,0x0f, + 0xf5,0x00,0x01,0x80,0x05,0x34,0x80,0x09,0xc0,0x03,0x78, + 0xe0,0x18,0x80,0x00,0x70,0xe0,0x1e,0xc0,0x01,0x70,0x70, + 0x1b,0xc0,0x01,0x50,0x00,0x00,0xc0,0x01,0x70,0x00,0x00, + 0xc0,0x00,0x70,0x00,0x00,0x40,0x03,0x38,0x00,0x00,0x80, + 0x05,0x50,0x00,0x00,0x80,0x0a,0x6e,0x00,0x00,0x00,0xfe, + 0x37,0x00,0x00,0x00,0x6a,0x59,0x00,0x00,0x00,0xbc,0x57, + 0x00,0x00,0x00,0xe0,0x50,0x00,0x00,0x00,0x00,0x60,0x00, + 0x00,0x00,0x00,0x78,0x00,0x00,0x00,0x00,0x7e,0x00,0x00, + 0x00,0x7c,0x2b,0x00,0x00,0x00,0xa4,0x1d,0x00,0x00,0x00, + 0xb8,0x06,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00, + 0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00, + 0x00,0x00}; + iconPixmap=XCreatePixmapFromBitmapData(xout->display, xout->window, + (char*)bitmapData, + 40u, 40u, + w_scr.pixel, r_scr.pixel, + 1ul); + } + + sizehints.x = xposition; + sizehints.y = yposition; + sizehints.min_width = width; + sizehints.max_width = width; + sizehints.min_height = height; + sizehints.max_height = height; + sizehints.flags = PPosition | PMinSize | PMaxSize; + XSetStandardProperties(xout->display, xout->window, + window_name, icon_name, iconPixmap, + (char **)NULL, 0, &sizehints); + + class_hint.res_name = "g2"; + class_hint.res_class = "G2"; + XSetClassHint(xout->display, xout->window, &class_hint); + + + XMapRaised(xout->display, xout->window); + + /* XSetWindowBackground(xout->display, xout->window, w_scr.pixel); */ + XClearWindow(xout->display,xout->window); + + g2_X11_paper(pid, NULL, 0); + g2_X11_set_font_size(pid, NULL, 12); + /* wait expose event */ + /* (no back. store) */ + while(!XCheckWindowEvent(xout->display,xout->window, + ExposureMask,&event)) + ; + + + wattr.event_mask=NoEventMask; /* set NoEventMask */ + wattr.backing_store=Always; /* set backing store */ + XChangeWindowAttributes(xout->display, xout->window, + CWEventMask|CWBackingStore, + &wattr); + + xout->dest = xout->window; + + xout->backing_pixmap = None; + + if(XDoesBackingStore(XDefaultScreenOfDisplay(xout->display))!=Always) { + if(g2_EmulateBackingStore) { + g2_log(Warning, "g2: Warning! Backing store is not available. Allocating pixmap instead.\n"); + + xout->backing_pixmap = XCreatePixmap(xout->display, xout->window, + xout->width, xout->height, + DefaultDepth(xout->display, DefaultScreen(xout->display))); + XSetWindowBackgroundPixmap(xout->display, xout->window, + xout->backing_pixmap); + + XSetForeground (xout->display, xout->gc, w_scr.pixel); + + XFillRectangle(xout->display, xout->backing_pixmap, xout->gc, + 0, 0, xout->width, xout->height); + xout->dest = xout->backing_pixmap; + } else { + g2_log(Warning, "g2: Warning! Backing store is not available.\n"); + } + } + + XFlush(xout->display); + return 0; +} + + + + +int g2_X11_delete(int pid, void *pdp) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XUnmapWindow(xout->display, xout->window); + if (xout->backing_pixmap != None) + XFreePixmap(xout->display,xout->backing_pixmap); + XDestroyWindow(xout->display, xout->window); + XDestroyWindow(xout->display, xout->root); + XFreeGC(xout->display, xout->gc); + XFreeColormap(xout->display, xout->colormap); + XCloseDisplay(xout->display); + if(xout->inks!=NULL) + g2_free(xout->inks); + xout->width=xout->height=0; + xout->display=NULL; + return 0; +} + + + +int g2_X11_clear(int pid, void *pdp) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + + if (xout->backing_pixmap == None) { + XClearWindow(xout->display,xout->window); + } else { + XSetForeground (xout->display, xout->gc, + xout->background); + XFillRectangle(xout->display, xout->dest, xout->gc, + 0, 0, xout->width, xout->height); + } + g2_X11_flush(pid, pdp); + return 0; +} + + + +int g2_X11_flush(int pid, void *pdp) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + if( xout->backing_pixmap != None ) { + XCopyArea(xout->display, xout->dest, xout->window, xout->gc, + 0, 0, xout->width, xout->height, 0, 0); + } + XFlush(xout->display); + return 0; +} + + + +int g2_X11_ink(int pid, void *pdp, + double red, double green, double blue) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XColor color; + + color.flags=DoRed|DoGreen|DoBlue; + color.red = (int)(red * USHRT_MAX); + color.green = (int)(green * USHRT_MAX); + color.blue = (int)(blue * USHRT_MAX); + if(XAllocColor(xout->display,xout->colormap,&color)) { + xout->NofInks++; + if(xout->inks==NULL) + xout->inks= + (unsigned long *)g2_malloc(xout->NofInks*sizeof(unsigned long)); + else + xout->inks= + (unsigned long *)g2_realloc((void *)xout->inks, + xout->NofInks*sizeof(unsigned long)); + if(xout->inks==NULL) { + fputs("g2: not enough memory\n",stderr); + return -1; + } + xout->inks[xout->NofInks-1]=color.pixel; + return xout->NofInks-1; + } else { + fputs("g2: color is not available\n",stderr); + return -1; + } +} + + +int g2_X11_clear_palette(int pid, void *pdp) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XFreeColors(xout->display,xout->colormap, + xout->inks,xout->NofInks,0x0ul); + xout->NofInks=0; + if(xout->inks!=NULL) + free(xout->inks); + xout->inks=NULL; + return 0; +} + + +int g2_X11_set_background(int pid, void *pdp, int color) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + if(color>=xout->NofInks || color<0) + return -1; + if (xout->backing_pixmap == None) + { + XSetWindowBackground(xout->display,xout->dest, + xout->inks[color]); + } + else + { + xout->background = xout->inks[color]; + } + g2_X11_clear(pid,pdp); + return 0; +} + + +int g2_X11_pen(int pid, void *pdp, int color) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + if(color>=xout->NofInks || color<0) + return -1; + XSetForeground(xout->display, xout->gc, xout->inks[color]); + return 0; +} + + + +int g2_X11_paper(int pid, void *pdp, int color) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + if(color>=xout->NofInks || color<0) + return -1; + XSetBackground(xout->display, xout->gc, xout->inks[color]); + return 0; +} + + +int g2_X11_set_line_width(int pid, void *pdp, int w) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XGCValues val; + + val.line_width=w; + XChangeGC(xout->display, xout->gc, GCLineWidth, &val); + return 0; +} + + +int g2_X11_set_dash(int pid, void *pdp, int n, int *data) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XGCValues val; + int i; + + if(n<=0 || data==NULL) { + val.line_style=LineSolid; + XChangeGC(xout->display, xout->gc, GCLineStyle,&val); + } else { + char *ch_data; + ch_data=g2_malloc(n*sizeof(char)); + val.line_style=LineOnOffDash; + for(i=0;i0) + ch_data[i]=(char)data[i]; + else + ch_data[i]=1; + XChangeGC(xout->display, xout->gc, GCLineStyle, &val); + XSetDashes(xout->display, xout->gc, 0, ch_data, n); + g2_free(ch_data); + } + return 0; +} + + +int g2_X11_set_font_size(int pid, void *pdp, int size) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XFontStruct *fnt_str; + char font_name[256]; + int sizei, d, n; + + sizei=dtoi(size); + + if(sizei<=0) + sizei=1; /* set to smallest size */ + + for(n=1;n<32;n++) { + d=((n&0x01)? -1:1)*(n>>1); + sprintf(font_name, g2_X11Font, sizei+d); + fnt_str=XLoadQueryFont(xout->display, font_name); + if(fnt_str==NULL) { + if(!d) + fprintf(stderr,"g2: can not load font: '%s'\n",font_name); + } else { + XSetFont(xout->display,xout->gc,fnt_str->fid); + if(d) + fprintf(stderr,"g2: using '%s' instead\n",font_name); + return 0; + } + } + fprintf(stderr, "g2: are you sure about %d point size\n", size); + return -1; +} + + +int g2_X11_plot(int pid, void *pdp, int x, int y) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XDrawPoint(xout->display, xout->dest, xout->gc, + x, y); + return 0; +} + + +int g2_X11_line(int pid, void *pdp, int x1, int y1, int x2, int y2) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XDrawLine(xout->display,xout->dest,xout->gc, + x1, y1, x2, y2); + return 0; +} + + +int g2_X11_poly_line(int pid, void *pdp, int N, int *p) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XPoint *points; + int i; + points=g2_malloc(N*sizeof(XPoint)); + for(i=0;idisplay,xout->dest,xout->gc, + points, N, + CoordModeOrigin); + g2_free(points); + return 0; +} + + +int g2_X11_polygon(int pid, void *pdp, int N, int *p) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XPoint *points; + int i; + points=g2_malloc((N+1)*sizeof(XPoint)); + for(i=0;idisplay,xout->dest,xout->gc, + points, N+1, + CoordModeOrigin); + g2_free(points); + return 0; +} + + +int g2_X11_filled_polygon(int pid, void *pdp, int N, int *p) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XPoint *points; + int i; + points=g2_malloc((N+1)*sizeof(XPoint)); + for(i=0;idisplay,xout->dest,xout->gc, + points, N+1, + Complex, CoordModeOrigin); + g2_free(points); + return 0; +} + + +int g2_X11_triangle(int pid, void *pdp, + int x1, int y1, + int x2, int y2, + int x3, int y3) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XPoint points[4]; + points[0].x=x1; points[0].y=y1; + points[1].x=x2; points[1].y=y2; + points[2].x=x3; points[2].y=y3; + points[3].x=x1; points[3].y=y1; + XDrawLines(xout->display,xout->dest,xout->gc, + points, 4, CoordModeOrigin); + return 0; +} + + +int g2_X11_filled_triangle(int pid, void *pdp, + int x1, int y1, + int x2, int y2, + int x3, int y3) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XPoint points[4]; + points[0].x=x1; points[0].y=y1; + points[1].x=x2; points[1].y=y2; + points[2].x=x3; points[2].y=y3; + points[3].x=x1; points[3].y=y1; + XFillPolygon(xout->display,xout->dest,xout->gc, + points, 4, Convex, CoordModeOrigin); + return 0; +} + + +int g2_X11_rectangle(int pid, void *pdp, int x1, int y1, int x2, int y2) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XDrawRectangle(xout->display,xout->dest,xout->gc, + x1, y1, x2-x1, y2-y1); + return 0; +} + + + +int g2_X11_filled_rectangle(int pid, void *pdp, int x1, int y1, int x2, int y2) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XDrawRectangle(xout->display,xout->dest,xout->gc, + x1, y1, x2-x1, y2-y1); + XFillRectangle(xout->display,xout->dest,xout->gc, + x1, y1, x2-x1, y2-y1); + return 0; +} + + +int g2_X11_arc(int pid, void *pdp, int x, int y, + int r1, int r2, double a1, double a2) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + double a0, d; + + a0=fmod(a1, 360.) + (a1<0? 360:0); /* map a1 to [0, 360) */ + d=a2>a1? a2-a1:a2-a1+360; + + XDrawArc(xout->display,xout->dest,xout->gc, + x-r1, y-r2, + r1*2, r2*2, + (int)(a0*64.), (int)(d*64.)); + return 0; +} + + +int g2_X11_filled_arc(int pid, void *pdp, int x, int y, + int r1, int r2, double a1, double a2) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + double a0, d; + + a0=fmod(a1, 360.) + (a1<0? 360:0); /* map a1 to [0, 360) */ + d=a2>a1? a2-a1:a2-a1+360; + + XDrawArc(xout->display,xout->dest,xout->gc, + x-r1, y-r2, + r1*2, r2*2, + (int)(a0*64.), (int)(d*64.)); + XFillArc(xout->display,xout->dest,xout->gc, + x-r1, y-r2, + r1*2, r2*2, + (int)(a0*64.), (int)(d*64.)); + return 0; +} + + +int g2_X11_ellipse(int pid, void *pdp, int x, int y, int r1, int r2) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XDrawArc(xout->display,xout->dest,xout->gc, + x-r1, y-r2, + r1*2, r2*2, + 0,360*64); + return 0; +} + + +int g2_X11_filled_ellipse(int pid, void *pdp, int x, int y, int r1, int r2) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XDrawArc(xout->display,xout->dest,xout->gc, + x-r1, y-r2, + r1*2, r2*2, + 0,360*64); + XFillArc(xout->display,xout->dest,xout->gc, + x-r1, y-r2, + r1*2, r2*2, + 0,360*64); + XFlush(xout->display); + return 0; +} + + +int g2_X11_draw_string(int pid, void *pdp, int x, int y, const char *text) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XDrawString(xout->display,xout->dest,xout->gc, + x, y, text, strlen(text)); + return 0; +} + + +int g2_X11_image(int pid, void *pdp, + int x, int y, int width, int height, int *pen_array) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + XImage *image=NULL; + Screen *screen; + unsigned long *ink_array; + int i; + + ink_array=malloc(sizeof(unsigned long)*width*height); + for(i=0;iinks[pen_array[i]]; + + screen=DefaultScreenOfDisplay(xout->display); + image=XCreateImage(xout->display, + DefaultVisualOfScreen(screen), + DefaultDepthOfScreen(screen), + ZPixmap, + 0, /* offset */ + (char *)ink_array, + width, height, + sizeof(unsigned long)*8, /* bitmap pad */ + 0); /* bytes per line */ + /* XInitImage(image); problems with AIX ?!! */ + XPutImage(xout->display, xout->dest, xout->gc, + image, + 0, 0, + x, y, width, height); + + XDestroyImage(image); + free(ink_array); + return 0; +} + + +int g2_X11_query_pointer(int pid, void *pdp, + int *x, int *y, unsigned int *button) +{ + Bool rv; + g2_X11_device *xout=&g2_X11_dev[pid]; + Window root, child; + int rx, ry; + + rv = XQueryPointer(xout->display, xout->window, + &root, &child, &rx, &ry, + x, y, button); + + if(rv) + return 0; + else + return 1; +} + + + +int g2_X11_get_pd_handles(int pid, void *pdp, void *handles[G2_PD_HANDLES_SIZE]) +{ + g2_X11_device *xout=&g2_X11_dev[pid]; + + handles[0]=xout->display; + handles[1]=&xout->window; + handles[2]=&xout->root; + handles[3]=&xout->colormap; + handles[4]=&xout->gc; + handles[5]=&xout->dest; + return 0; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11.h new file mode 100755 index 000000000..4db6bf949 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11.h @@ -0,0 +1,45 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_X11_H +#define _G2_X11_H + +#if defined(__cplusplus) +extern "C" +{ +#endif + + +int g2_open_X11(int width, int height); + +int g2_open_X11X(int width, int height, + int x, int y, + char *window_name, char *icon_name, + char *icon_data, + int icon_width, int icon_height); + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + +#endif /* _G2_X11_H */ + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11_P.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11_P.h new file mode 100755 index 000000000..9c9f3ccba --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11_P.h @@ -0,0 +1,94 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_X11_P_H +#define _G2_X11_P_H + +#include + +#include "g2.h" + +typedef struct { + Display *display; + Window window; + Window root; + Colormap colormap; + GC gc; + Drawable dest; + Pixmap backing_pixmap; + + + unsigned long *inks; /* allocated colors*/ + int NofInks; /* N of allocated colors */ + int width; /* window dimensions */ + int height; + int background; +} g2_X11_device; + + +int g2_X11_init_X11X(int pid, int width, int height, + int xposition, int yposition, + char *window_name, char *icon_name, + char *icon_data, + unsigned int icon_width, unsigned int icon_height); +int g2_X11_delete(int pid, void *pdp); +int g2_X11_clear(int pid, void *pdp); +int g2_X11_flush(int pid, void *pdp); +int g2_X11_ink(int pid, void *pdp, + double red, double green, double blue); +int g2_X11_clear_palette(int pid, void *pdp); +int g2_X11_reset_palette(int pid, void *pdp); +int g2_X11_set_background(int pid, void *pdp, int color); +int g2_X11_pen(int pid, void *pdp, int color); +int g2_X11_paper(int pid, void *pdp, int color); +int g2_X11_set_line_width(int pid, void *pdp, int w); +int g2_X11_set_dash(int pid, void *pdp, int n, int *data); +int g2_X11_set_font_size(int pid, void *pdp, int size); +int g2_X11_plot(int pid, void *pdp, int x, int y); +int g2_X11_line(int pid, void *pdp, int x1, int y1, int x2, int y2); +int g2_X11_poly_line(int pid, void *pdp, int N, int *p); +int g2_X11_polygon(int pid, void *pdp, int N, int *p); +int g2_X11_filled_polygon(int pid, void *pdp, int N, int *p); +int g2_X11_triangle(int pid, void *pdp, + int x1, int y1, + int x2, int y2, + int x3, int y3); +int g2_X11_filled_triangle(int pid, void *pdp, int x1, int y1, + int x2, int y2, + int x3, int y3); +int g2_X11_rectangle(int pid, void *pdp, int x1, int y1, int x2, int y2); +int g2_X11_filled_rectangle(int pid, void *pdp, + int x1, int y1, int x2, int y2); +int g2_X11_arc(int pid, void *pdp, int x, int y, + int r1, int r2, double a1, double a2); +int g2_X11_filled_arc(int pid, void *pdp, int x, int y, + int r1, int r2, double a1, double a2); +int g2_X11_ellipse(int pid, void *pdp, int x, int y, int r1, int r2); +int g2_X11_filled_ellipse(int pid, void *pdp, int x, int y, int r1, int r2); +int g2_X11_draw_string(int pid, void *pdp, int x, int y, const char *text); +int g2_X11_image(int pid, void *pdp, + int x, int y, int width, int height, int *pen_array); +int g2_X11_query_pointer(int pid, void *pdp, + int *x, int *y, unsigned int *button); +int g2_X11_get_pd_handles(int pid, void *pdp, void *handles[G2_PD_HANDLES_SIZE]); +#endif /* _G2_X11_P_H */ + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11_funix.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11_funix.h new file mode 100755 index 000000000..66f9b1fe2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/X11/g2_X11_funix.h @@ -0,0 +1,60 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_X11_FUNIX_H +#define _G2_X11_FUNIX_H + +#include "g2_X11_P.h" +#include "g2_physical_device.h" + + +const g2_funix_fun g2_X11_funix[] = { + { g2_Delete, g2_X11_delete }, + { g2_Ink, g2_X11_ink }, + { g2_Pen, g2_X11_pen }, + { g2_SetBackground, g2_X11_set_background }, + { g2_ClearPalette, g2_X11_clear_palette }, + { g2_SetLineWidth, g2_X11_set_line_width }, + { g2_SetDash, g2_X11_set_dash }, + { g2_SetFontSize, g2_X11_set_font_size }, + { g2_Clear, g2_X11_clear }, + { g2_Flush, g2_X11_flush }, + { g2_Save, g2_X11_flush }, + { g2_Plot, g2_X11_plot }, + { g2_Line, g2_X11_line }, + { g2_PolyLine, g2_X11_poly_line }, + { g2_Polygon, g2_X11_polygon }, + { g2_FilledPolygon, g2_X11_filled_polygon }, + { g2_Rectangle, g2_X11_rectangle }, + { g2_FilledRectangle, g2_X11_filled_rectangle }, + { g2_Triangle, g2_X11_triangle }, + { g2_FilledTriangle, g2_X11_filled_triangle }, + { g2_Arc, g2_X11_arc }, + { g2_FilledArc, g2_X11_filled_arc }, + { g2_Ellipse, g2_X11_ellipse }, + { g2_FilledEllipse, g2_X11_filled_ellipse }, + { g2_Circle, NULL }, + { g2_FilledCircle, NULL }, + { g2_String, g2_X11_draw_string }, + { g2_Image, NULL }, + { g2_QueryPointer, g2_X11_query_pointer }, + { g2_GetPDHandles, g2_X11_get_pd_handles }, + { g2_FUNIX_NULL, NULL } }; + + +#endif /* _G2_X11_FUNIX_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2.h new file mode 100755 index 000000000..e16a92293 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2.h @@ -0,0 +1,200 @@ +/***************************************************************************** +** Copyright (C) 1998-2005 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_H +#define _G2_H + + +/* g2 version */ +#define G2_VERSION "0.70" + + +#if defined(__cplusplus) +extern "C" +{ +#endif + +/* Common Library header for DLL and application */ +#ifdef WIN32 +#ifdef G2DLL +#ifdef MAKEDLL +/* Create DLL */ +#pragma message( "Building DLL library") +#define G2L __declspec( dllexport) +#else +/* Use DLL */ +#define G2L __declspec( dllimport) +#endif +#else +/* Use static win32 */ +#define G2L +#endif +#else +/* Use non-win32 */ +#define G2L +#endif + + +#define G2LD g2_ld() + +#if defined(SWIG) +#if defined(DO_X11) +%include "X11/g2_X11.h" +#endif +#if defined(DO_PS) +%include "PS/g2_PS.h" +#endif +#if defined(DO_GD) +%include "GD/g2_gd.h" +#endif +#if defined(DO_WIN32) +%include "WIN32/g2_win32.h" +#endif + +%module g2 + +%include typemaps.i + +%{ +#include "g2.h" +#if defined(DO_X11) +#include "g2_X11.h" +#endif +#if defined(DO_PS) +#include "g2_PS.h" +#endif +#if defined(DO_GD) +#include "g2_gd.h" +#endif +#if defined(DO_WIN32) +#include "WIN32/g2_win32.h" +#endif +%} + +#endif +/* end SWIG */ + + +enum QPshape { + QPrect, /**< rectangular quasi pixel */ + QPcirc /**< circle as a quasi pixel */ +}; + +/* compatibility with old versions */ +#define g2_draw_string(dev, x, y, text) g2_string((dev), (x), (y), (text)) + + + +G2L int g2_open_vd(void); +G2L void g2_attach(int vd_dev, int dev); +G2L void g2_detach(int vd_dev, int dev); + +G2L void g2_close(int dev); +G2L void g2_set_auto_flush(int dev, int on_off); +G2L void g2_flush(int dev); +G2L void g2_save(int dev); +G2L void g2_set_coordinate_system(int dev, double x_origin, double y_origin, + double x_mul, double y_mul); + +G2L int g2_ld(); +G2L void g2_set_ld(int dev); + +G2L int g2_ink(int pd_dev, double red, double green, double blue); +G2L void g2_pen(int dev, int color); +G2L void g2_set_dash(int dev, int N, double *dashes); +G2L void g2_set_font_size(int dev, double size); +G2L void g2_set_line_width(int dev, double w); +G2L void g2_clear_palette(int dev); +G2L void g2_reset_palette(int dev); +G2L void g2_allocate_basic_colors(int dev); + +G2L void g2_clear(int dev); +G2L void g2_set_background(int dev, int color); + +G2L void g2_move(int dev, double x, double y); +G2L void g2_move_r(int dev, double dx, double dy); + +G2L void g2_plot(int dev, double x, double y); +G2L void g2_plot_r(int dev, double dx, double dy); +G2L void g2_line(int dev, double x1, double y1, double x2, double y2); +G2L void g2_line_r(int dev, double dx, double dy); +G2L void g2_line_to(int dev, double x, double y); +G2L void g2_poly_line(int dev, int N_pt, double *points); +G2L void g2_triangle(int dev, double x1, double y1, + double x2, double y2, + double x3, double y3); +G2L void g2_filled_triangle(int dev, double x1, double y1, + double x2, double y2, + double x3, double y3); +G2L void g2_rectangle(int dev, double x1, double y1, double x2, double y2); +G2L void g2_filled_rectangle(int dev, + double x1, double y1, double x2, double y2); +G2L void g2_polygon(int dev, int N_pt, double *points); +G2L void g2_filled_polygon(int dev, int N_pt, double *points); +G2L void g2_circle(int dev, double x, double y, double r); +G2L void g2_filled_circle(int dev, double x, double y, double r); +G2L void g2_ellipse(int dev, double x, double y, double r1, double r2); +G2L void g2_filled_ellipse(int dev, double x, double y, double r1, double r2); +G2L void g2_arc(int dev, + double x, double y, + double r1, double r2, + double a1, double a2); +G2L void g2_filled_arc(int dev, double x, double y, + double r1, double r2, + double a1, double a2); +G2L void g2_string(int dev, double x, double y, const char *text); +G2L void g2_image(int dev, + double x, double y, int x_size, int y_size, int *pens); + +G2L void g2_set_QP(int dev, double d, enum QPshape shape); +G2L void g2_plot_QP(int dev, double x, double y); +#if !defined(SWIG) +G2L void g2_query_pointer(int dev, double *x, double *y, unsigned int *button); +#else +extern void g2_query_pointer(int dev, double *OUTPUT,double *OUTPUT,unsigned int *OUTPUT); +#endif + + + /* Tijs Michels */ + /* 06/16/99 */ + +G2L void g2_spline(int id, int n, double *points, int o); +G2L void g2_b_spline(int id, int n, double *points, int o); +G2L void g2_raspln(int id, int n, double *points, double tn); +G2L void g2_para_3(int id, int n, double *points); +G2L void g2_para_5(int id, int n, double *points); +G2L void g2_filled_spline(int id, int n, double *points, int o); +G2L void g2_filled_b_spline(int id, int n, double *points, int o); +G2L void g2_filled_raspln(int id, int n, double *points, double tn); +G2L void g2_filled_para_3(int id, int n, double *points); +G2L void g2_filled_para_5(int id, int n, double *points); + + +/** Actualy private function, but... **/ +G2L int g2_device_exist(int dix); + +/** Use only if you know what are you doing **/ +#define G2_PD_HANDLES_SIZE 32 +G2L void g2_get_pd_handles(int pd, void *handles[G2_PD_HANDLES_SIZE]); + + +#if defined(__cplusplus) +} /* end extern "C" */ +#endif + +#endif /* _G2_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_config.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_config.h new file mode 100755 index 000000000..f5607f0cc --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_config.h @@ -0,0 +1,42 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_CONFIG_H +#define _G2_CONFIG_H + +/* + * + * Some g2 defines + * + * Default behaviour is usually ok for most cases + * + */ + +/* g2 warnings are printed to stderr, larger 0=quiet, 1=errors, 2=warnings, 3=verbose, 4=debug */ +#define g2_LogLevel 1 + +/* set to 0 to disable backing store emulation */ +#define g2_EmulateBackingStore 1 + +/* X11 font, note %d for font size */ +#define g2_X11Font "-*-times-medium-r-normal--%d-*-*-*-*-*-*-*" + +/* PostScript font */ +#define g2_PSFont "/Times-Roman" + +#endif /* _G2_CONFIG_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.c new file mode 100755 index 000000000..7c04d2c8b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.c @@ -0,0 +1,314 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_physical_device.h" +#include "g2_util.h" +#include "g2_funix.h" + + + +/* + * + * Flush output + * + */ +void g2_flush_pd(g2_physical_device *pd) +{ + if(pd->ff[g2_Flush].fun!=NULL) { + pd->ff[g2_Flush].fun(pd->pid, pd->pdp); + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Save output + * + */ +void g2_save_pd(g2_physical_device *pd) +{ + if(pd->ff[g2_Save].fun!=NULL) { + pd->ff[g2_Save].fun(pd->pid, pd->pdp); + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Clear device + * + */ +void g2_clear_pd(g2_physical_device *pd) +{ + if(pd->ff[g2_Clear].fun!=NULL) { + pd->ff[g2_Clear].fun(pd->pid, pd->pdp); + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Set pen + * + */ +void g2_pen_pd(g2_physical_device *pd, int color) +{ + if(pd->ff[g2_Pen].fun!=NULL) { + pd->ff[g2_Pen].fun(pd->pid, pd->pdp, color); + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Set background color + * + */ +void g2_set_background_pd(g2_physical_device *pd, int color) +{ + if(pd->ff[g2_SetBackground].fun!=NULL) { + pd->ff[g2_SetBackground].fun(pd->pid, pd->pdp, color); + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Set ink + * + */ +int g2_ink_pd(g2_physical_device *pd, double red, double green, double blue) +{ + int rv=-1; + + if(pd->ff[g2_Ink].fun!=NULL) { + rv=pd->ff[g2_Ink].fun(pd->pid, pd->pdp, + red, green, blue); + } else { + /* emulate ... with .... */ + } + return rv; +} + + + + +/* + * + * Clear palette + * + */ +void g2_clear_palette_pd(g2_physical_device *pd) +{ + if(pd->ff[g2_ClearPalette].fun!=NULL) { + pd->ff[g2_ClearPalette].fun(pd->pid, pd->pdp); + } else { + /* emulate ... with .... */ + } +} + + +/* + * + * Allocate basic colors + * + */ +void g2_allocate_basic_colors_pd(g2_physical_device *pd) +{ + double ct[3]={0.0, 0.5, 1.0}; + int r, g, b; + + if(pd->ff[g2_Ink].fun!=NULL) { + pd->ff[g2_Ink].fun(pd->pid, pd->pdp, /* white */ + 1.0, 1.0, 1.0); + pd->ff[g2_Ink].fun(pd->pid, pd->pdp, /* black */ + 0.0, 0.0, 0.0); + for(r=0;r<3;r++) + for(g=0;g<3;g++) + for(b=0;b<3;b++) + if((r==2 && g==2 && b==2) || + (r==0 && g==0 && b==0)) + continue; + else + pd->ff[g2_Ink].fun(pd->pid, pd->pdp, + ct[r], ct[g], ct[b]); + } +} + + +/* + * + * Set font size + * + */ +void g2_set_font_size_pd(g2_physical_device *pd, double size) +{ + int is; + double ds; + + if(pd->ff[g2_SetFontSize].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + is=dtoi(size*fabs(pd->a22)); /* to pd coordinates */ + pd->ff[g2_SetFontSize].fun(pd->pid, pd->pdp, is); + break; + case g2_DoubleCoor: + ds=size*fabs(pd->a22); /* to pd coordinates */ + pd->ff[g2_SetFontSize].fun(pd->pid, pd->pdp, ds); + break; + } + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Set line width + * + */ +void g2_set_line_width_pd(g2_physical_device *pd, double w) +{ + int iw; + double dw; + + if(pd->ff[g2_SetLineWidth].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + iw=dtoi(w*fabs(pd->a22)); /* to pd coordinates */ + pd->ff[g2_SetLineWidth].fun(pd->pid, pd->pdp, iw); + break; + case g2_DoubleCoor: + dw=w*fabs(pd->a22); /* to pd coordinates */ + pd->ff[g2_SetLineWidth].fun(pd->pid, pd->pdp, dw); + break; + } + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Set dash + * + */ +void g2_set_dash_pd(g2_physical_device *pd, int N, double *dashes) +{ + int j; + double *dd=NULL; + int *id=NULL; + + if(pd->ff[g2_SetDash].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + if(dashes!=NULL) { + id=g2_malloc(N*sizeof(int)); + for(j=0;ja22)); + pd->ff[g2_SetDash].fun(pd->pid, pd->pdp, N, id); + g2_free(id); + } else + pd->ff[g2_SetDash].fun(pd->pid, pd->pdp, 0, NULL); + break; + case g2_DoubleCoor: + if(dashes!=NULL) { + dd=g2_malloc(N*sizeof(double)); + for(j=0;ja22); + pd->ff[g2_SetDash].fun(pd->pid, pd->pdp, N, dd); + g2_free(dd); + break; + } else + pd->ff[g2_SetDash].fun(pd->pid, pd->pdp, 0, NULL); + } + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Query pointer position and button state + * + */ +void g2_query_pointer_pd(g2_physical_device *pd, + double *x, double *y, unsigned int *button) +{ + int ix, iy; + double dx, dy; + + if(pd->ff[g2_QueryPointer].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + pd->ff[g2_QueryPointer].fun(pd->pid, pd->pdp, + &ix, &iy, button); + g2_pdc2uc(pd, ix, iy, x, y); + break; + case g2_DoubleCoor: + pd->ff[g2_QueryPointer].fun(pd->pid, pd->pdp, + &dx, &dy, button); + g2_pdc2uc(pd, dx, dy, x, y); + break; + } + } else { + /* no emulation for query pointer */ + } +} + + +/* + * + * Get low level handles + * + */ +void g2_get_pd_handles_pd(g2_physical_device *pd, void *handles[G2_PD_HANDLES_SIZE]) +{ + if(pd->ff[g2_GetPDHandles].fun!=NULL) { + pd->ff[g2_GetPDHandles].fun(pd->pid, pd->pdp, handles); + } else { + /* no emulation for low level handles */ + } +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.h new file mode 100755 index 000000000..dd27053f6 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.h @@ -0,0 +1,39 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_CONTROL_PD_H +#define _G2_CONTROL_PD_H + +#include "g2_physical_device.h" + +void g2_flush_pd(g2_physical_device *pd); +void g2_save_pd(g2_physical_device *pd); +void g2_clear_pd(g2_physical_device *pd); +void g2_pen_pd(g2_physical_device *pd, int color); +void g2_set_background_pd(g2_physical_device *pd, int color); +int g2_ink_pd(g2_physical_device *pd, double red, double green, double blue); +void g2_clear_palette_pd(g2_physical_device *pd); +void g2_allocate_basic_colors_pd(g2_physical_device *pd); +void g2_set_font_size_pd(g2_physical_device *pd, double size); +void g2_set_line_width_pd(g2_physical_device *pd, double w); +void g2_set_dash_pd(g2_physical_device *pd, int N, double *dashes); +void g2_query_pointer_pd(g2_physical_device *pd, + double *x, double *y, unsigned int *button); +void g2_get_pd_handles_pd(g2_physical_device *pd, void *handles[G2_PD_HANDLES_SIZE]); + +#endif /* _G2_CONTROL_PD_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.o new file mode 100755 index 000000000..e88605c56 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_control_pd.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_device.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_device.c new file mode 100755 index 000000000..8b870387c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_device.c @@ -0,0 +1,206 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_physical_device.h" +#include "g2_virtual_device.h" +#include "g2_util.h" + +int __g2_last_device=-1; /* last acces. device (ld) */ + + +static int g2_dev_size=0; /* size of devices array */ +static g2_device *g2_dev=NULL; /* devices array */ + +static int g2_get_free_device(); +static void g2_init_device(int dix); + + +/* + * + * Register physical device + * + */ +int g2_register_physical_device(int pid, + void *pdp, + g2_coor ct, + const g2_funix_fun *ff, + double a11, double a22, + double b1, double b2) +{ + int dix; + + dix=g2_get_free_device(); + g2_init_device(dix); + g2_dev[dix].t=g2_PD; + g2_dev[dix].d.pd=g2_create_physical_device(pid, pdp, + ct, ff, + a11, a22, + b1, b2); + + __g2_last_device=dix; + return dix; +} + + + +/* + * + * Register virtual device + * + */ +int g2_register_virtual_device() +{ + int dix; + + dix=g2_get_free_device(); + g2_init_device(dix); + g2_dev[dix].t=g2_VD; + g2_dev[dix].d.vd=g2_create_virtual_device(); + + return dix; +} + + +/* + * + * Init device + * + */ +void g2_init_device(int dix) +{ + g2_dev[dix].t=g2_ILLEGAL; + g2_dev[dix].dix=dix; + g2_dev[dix].x=0.0; /* set cursor */ + g2_dev[dix].y=0.0; + g2_dev[dix].auto_flush=1; /* set auto flush */ + g2_dev[dix].QPd=1.0; /* Quasi pixel spec. */ + g2_dev[dix].QPshape=QPrect; +} + +/* + * + * Return pointer to device dix + * + */ +g2_device *g2_get_device_pointer(int dix) +{ + if(dix<0 || dix>=g2_dev_size) + return NULL; + if(g2_dev[dix].t==g2_NDEV) + return NULL; + + return &g2_dev[dix]; +} + + +/* + * + * Return device type + * + */ +g2_device_type g2_get_device_type(int dix) +{ + if(dix<0 || dix>=g2_dev_size) + return g2_ILLEGAL; + return g2_dev[dix].t; +} + + +/* + * + * 1 if device exist otherwise 0 + * + */ +int g2_device_exist(int dix) +{ + if(dix<0 || dix>=g2_dev_size || + g2_dev[dix].t==g2_ILLEGAL || g2_dev[dix].t==g2_NDEV) + return 0; + return 1; +} + + +/* + * + * Destroy device + * + */ +void g2_destroy_device(int dix) +{ + int i; + + for(i=0;i +#include +#include "g2.h" +#include "g2_util.h" + +/* + * + * g2 Fortran Interface + * + */ +#ifdef LINUX +#define FIF(funame) funame ## __ +#else +#define FIF(funame) funame ## _ +#endif + +#define F_REAL float /* everything is float (real) !!!!!!!!!!!!!! */ +#define F_CHAR char /* only char is char */ +#define F_CHAR_LENGTH int /* and char length is integer (it is automatically supplied */ + + +/**********************************************************/ + +#ifdef DO_PS + +#include "PS/g2_PS.h" + + + + + +F_REAL FIF(g2_open_ps)(F_CHAR *text, F_REAL *paper, F_REAL *orientation, + F_CHAR_LENGTH length) +{ + char *str; + int rv; + + str=g2_malloc((length+1)*sizeof(char)); + strncpy(str, text, length); + str[length]='\0'; + rv=g2_open_PS(str, dtoi(*paper), dtoi(*orientation)); + g2_free(str); + + return (F_REAL)rv; +} + +#endif /* DO_PS */ + +/**********************************************************/ + +#ifdef DO_X11 + +#include "X11/g2_X11.h" + +F_REAL FIF(g2_open_x11)(F_REAL *width, F_REAL *height) +{ + return (F_REAL)g2_open_X11(*width, *height); +} + +/* g2_open_x11x is missing */ + +#endif /* DO_X11 */ + +/**********************************************************/ + +#ifdef DO_GD + +#include "GD/g2_gd.h" + +F_REAL FIF(g2_open_gd)(F_CHAR *text, F_REAL *width, F_REAL *height, F_REAL *gd_type, + F_CHAR_LENGTH length) +{ + char *str; + int rv; + + str=g2_malloc((length+1)*sizeof(char)); + strncpy(str, text, length); + str[length]='\0'; + + rv=g2_open_gd(str, *width, *height, *gd_type); + + g2_free(str); + + return (F_REAL)rv; +} + +#endif /* DO_GD */ + +/**********************************************************/ + + +F_REAL FIF(g2_open_vd)(void) +{ + return (F_REAL)g2_open_vd(); +} + + +void FIF(g2_attach)(F_REAL *vd_dev, F_REAL *dev) +{ + g2_attach(dtoi(*vd_dev), dtoi(*dev)); +} + + +void FIF(g2_detach)(F_REAL *vd_dev, F_REAL *dev) +{ + g2_detach(dtoi(*vd_dev), dtoi(*dev)); +} + + + +void FIF(g2_close)(F_REAL *dev) +{ + g2_close(dtoi(*dev)); +} + + +void FIF(g2_set_auto_flush)(F_REAL *dev, F_REAL *on_off) +{ + g2_set_auto_flush(dtoi(*dev), dtoi(*on_off)); +} + + +void FIF(g2_set_coordinate_system)(F_REAL *dev, + F_REAL *x_origin, F_REAL *y_origin, + F_REAL *x_mul, F_REAL *y_mul) +{ + g2_set_coordinate_system(dtoi(*dev), + *x_origin, *y_origin, + *x_mul, *y_mul); +} + + +F_REAL FIF(g2_ld)(void) +{ + return (F_REAL)g2_ld(); +} + + +void FIF(g2_set_ld)(F_REAL *dev) +{ + g2_set_ld(dtoi(*dev)); +} + + + +void FIF(g2_flush)(F_REAL *dev) +{ + g2_flush(dtoi(*dev)); +} + + +void FIF(g2_save)(F_REAL *dev) +{ + g2_save(dtoi(*dev)); +} + + + + +void FIF(g2_arc)(F_REAL *dev, F_REAL *x, F_REAL *y, + F_REAL *r1, F_REAL *r2, F_REAL *a1, F_REAL *a2) +{ + g2_arc(dtoi(*dev), *x, *y, *r1, *r2, *a1, *a2); +} + + +void FIF(g2_circle)(F_REAL *dev, F_REAL *x, F_REAL *y, F_REAL *r) +{ + g2_circle(dtoi(*dev), *x, *y, *r); +} + + +void FIF(g2_clear)(F_REAL *dev) +{ + g2_clear(dtoi(*dev)); +} + + +void FIF(g2_clear_palette)(F_REAL *dev) +{ + g2_clear_palette(dtoi(*dev)); +} + + +void FIF(g2_string)(F_REAL *dev, F_REAL *x, F_REAL *y, F_CHAR *text, + F_CHAR_LENGTH length) +{ + char *str; + str=g2_malloc((length+1)*sizeof(char)); + strncpy(str, text, length); + str[length]='\0'; + g2_string(dtoi(*dev), *x, *y, str); + g2_free(str); +} + + +void FIF(g2_ellipse)(F_REAL *dev, F_REAL *x, F_REAL *y, F_REAL *r1, F_REAL *r2) +{ + g2_ellipse(dtoi(*dev), *x, *y, *r1, *r2); +} + + +void FIF(g2_filled_arc)(F_REAL *dev, F_REAL *x, F_REAL *y, + F_REAL *r1, F_REAL *r2, + F_REAL *a1, F_REAL *a2) +{ + g2_filled_arc(dtoi(*dev), *x, *y, *r1, *r2, *a1, *a2); +} + + +void FIF(g2_filled_circle)(F_REAL *dev, F_REAL *x, F_REAL *y, F_REAL *r) +{ + g2_filled_circle(dtoi(*dev), *x, *y, *r); +} + + +void FIF(g2_filled_ellipse)(F_REAL *dev, F_REAL *x, F_REAL *y, F_REAL *r1, F_REAL *r2) +{ + g2_filled_ellipse(dtoi(*dev), *x, *y, *r1, *r2); +} + + +void FIF(g2_filled_triangle)(F_REAL *dev, F_REAL *x1, F_REAL *y1, + F_REAL *x2, F_REAL *y2, + F_REAL *x3, F_REAL *y3) +{ + g2_filled_triangle(dtoi(*dev), *x1, *y1, *x2, *y2, *x3, *y3); +} + + +F_REAL FIF(g2_ink)(F_REAL *dev, F_REAL *red, F_REAL *green, F_REAL *blue) +{ + return (F_REAL)g2_ink(dtoi(*dev), *red, *green, *blue); +} + + +void FIF(g2_line)(F_REAL *dev, F_REAL *x1, F_REAL *y1, F_REAL *x2, F_REAL *y2) +{ + g2_line(dtoi(*dev), *x1, *y1, *x2, *y2); +} + + +void FIF(g2_poly_line)(F_REAL *dev, F_REAL *N_pt, F_REAL *points) +{ + double *d; + d=g2_floatp2doublep(points, dtoi(*N_pt)*2); + g2_poly_line(dtoi(*dev), dtoi(*N_pt), d); + g2_free(d); +} + + +void FIF(g2_polygon)(F_REAL *dev, F_REAL *N_pt, F_REAL *points) +{ + double *d; + d=g2_floatp2doublep(points, dtoi(*N_pt)*2); + g2_polygon(dtoi(*dev), dtoi(*N_pt), d); + g2_free(d); +} + + +void FIF(g2_filled_polygon)(F_REAL *dev, F_REAL *N_pt, F_REAL *points) +{ + double *d; + d=g2_floatp2doublep(points, dtoi(*N_pt)*2); + g2_filled_polygon(dtoi(*dev), dtoi(*N_pt), d); + g2_free(d); +} + + +void FIF(g2_line_r)(F_REAL *dev, F_REAL *dx, F_REAL *dy) +{ + g2_line_r(dtoi(*dev), *dx, *dy); +} + + +void FIF(g2_line_to)(F_REAL *dev, F_REAL *x, F_REAL *y) +{ + g2_line_to(dtoi(*dev), *x, *y); +} + + +void FIF(g2_move)(F_REAL *dev, F_REAL *x, F_REAL *y) +{ + g2_move(dtoi(*dev), *x, *y); +} + + +void FIF(g2_move_r)(F_REAL *dev, F_REAL *dx, F_REAL *dy) +{ + g2_move_r(dtoi(*dev), *dx, *dy); +} + + +void FIF(g2_pen)(F_REAL *dev, F_REAL *color) +{ + g2_pen(dtoi(*dev), dtoi(*color)); +} + + +void FIF(g2_plot)(F_REAL *dev, F_REAL *x, F_REAL *y) +{ + g2_plot(dtoi(*dev), *x, *y); +} + + +void FIF(g2_plot_r)(F_REAL *dev, F_REAL *dx, F_REAL *dy) +{ + g2_plot_r(dtoi(*dev), *dx, *dy); +} + + +void FIF(g2_rectangle)(F_REAL *dev, + F_REAL *x1, F_REAL *y1, + F_REAL *x2, F_REAL *y2) +{ + g2_rectangle(dtoi(*dev), *x1, *y1, *x2, *y2); +} + + +void FIF(g2_filled_rectangle)(F_REAL *dev, + F_REAL *x1, F_REAL *y1, + F_REAL *x2, F_REAL *y2) +{ + g2_filled_rectangle(dtoi(*dev), *x1, *y1, *x2, *y2); +} + + +void FIF(g2_reset_palette)(F_REAL *dev) +{ + g2_reset_palette(dtoi(*dev)); +} + + +void FIF(g2_set_background)(F_REAL *dev, F_REAL *color) +{ + g2_set_background(dtoi(*dev), dtoi(*color)); +} + + +void FIF(g2_set_dash)(F_REAL *dev, F_REAL *N, F_REAL *dashes) +{ + double *d; + d=g2_floatp2doublep(dashes, dtoi(*N)); + g2_set_dash(dtoi(*dev), dtoi(*N), d); + g2_free(d); +} + + +void FIF(g2_set_font_size)(F_REAL *dev, F_REAL *size) +{ + g2_set_font_size(dtoi(*dev), *size); +} + + +void FIF(g2_set_line_width)(F_REAL *dev, F_REAL *w) +{ + g2_set_line_width(dtoi(*dev), *w); +} + + +void FIF(g2_triangle)(F_REAL *dev, F_REAL *x1, F_REAL *y1, + F_REAL *x2, F_REAL *y2, + F_REAL *x3, F_REAL *y3) +{ + g2_triangle(dtoi(*dev), *x1, *y1, *x2, *y2, *x3, *y3); +} + + +void FIF(g2_set_qp)(F_REAL *dev, F_REAL *d, F_REAL *shape) +{ + g2_set_QP(dtoi(*dev), *d, dtoi(*shape)); +} + + +void FIF(g2_plot_qp)(F_REAL *dev, F_REAL *x, F_REAL *y) +{ + g2_plot_QP(dtoi(*dev), *x, *y); +} + + +/* thanks to Yuri Sbitnev for contributing the g2_image code for FORTRAN */ +void FIF(g2_image)(F_REAL *dev, F_REAL *x, F_REAL *y, F_REAL *x_size, F_REAL *y_size, + F_REAL *pens) +{ + int i, j, xs, ys; + int *mypens; + xs=dtoi(*x_size); + ys=dtoi(*y_size); + mypens=(int *) g2_malloc(xs*ys*sizeof(int)); + for(j=0;j=0), <0 if error */ + + g2_Pen, /* set pen */ + /* ... = (int)pen */ + + g2_SetBackground, /* set background */ + /* ... = (int)pen */ + + g2_ClearPalette, /* reset color pallete to default values */ + /* ... = */ + /* for list of default colors (0,31) see later */ + + g2_SetLineWidth, /* set line width (line, rectangle, ...) */ + /* ... = (double)line width */ + + g2_SetDash, /* set line dash */ + /* ... = (int)number of descr., (double*) bw list */ + + g2_SetFontSize, /* set font size */ + /* ... = (double)font size */ + + g2_Clear, /* clear screen(X11), print page(PostScript), ... */ + /* ... = */ + + g2_Flush, /* update output */ + /* X11: Flush, PostScript: fflush, ... */ + + g2_Save, /* save output to device (e.g. file) */ + /* X11: Flush, etc. */ + + g2_Plot, /* plot point */ + /* ... = (double)x, (double)y */ + + g2_Line, /* draw line */ + /* ... = (double)x1, (double)y1, + (double)x2, (double)y2 */ + + g2_PolyLine, /* draw poly line */ + /* ... = (int)N, + (double*)dp + dp[0]=x1, dp[1]=y1, + ... + dp[2*N-2]=xN, dp[2*N-1]=yN */ + + g2_Polygon, /* draw polygon */ + /* ... = (int)N, + (double*)dp + dp[0]=x1, dp[1]=y1, + ... + dp[2*N-2]=xN, dp[2*N-1]=yN */ + + g2_FilledPolygon, /* draw filled polygon */ + /* ... = (int)N, + (double*)dp + dp[0]=x1, dp[1]=y1, + ... + dp[2*N-2]=xN, dp[2*N-1]=yN */ + + g2_Rectangle, /* draw rectangle */ + /* ... = (double)x1, (double)y1, + (double)x2, (double)y2 */ + + g2_FilledRectangle, /* draw filled rectangle */ + /* ... = (double)x1, (double)x1, + (double)x2, (double)y2 */ + + g2_Triangle, /* draw triangle (should be faster as lines) */ + /* ... = (double)x1, (double)y1, + (double)x2, (double)y2, + (double)x3, (double)y3 */ + + g2_FilledTriangle, /* draw filled triangle */ + /* ... = (double)x1, (double)y1, + (double)x2, (double)y2, + (double)x3, (double)y3 */ + + g2_Arc, /* draw arc */ + /* ... = (double)x, (double)y, + (double)r1, (double)r2, + (double)a1, (double)a2 */ + + g2_FilledArc, /* draw filled arc */ + /* ... = (double)x, (double)y, + (double)r1, (double)r2, + (double)a1, (double)a2 */ + + g2_Ellipse, /* draw ellipse */ + /* ... = (double)x, (double)y, + (double)r1, (double)r2 */ + + g2_FilledEllipse, /* draw filled ellipse */ + /* ... = (double)x, (double)y, + (double)r1, (double)r2 */ + + g2_Circle, /* draw circle */ + /* ... = (double)x, (double)y, + (double)r */ + + g2_FilledCircle, /* draw filled circle */ + /* ... = (double)x, (double)y, + (double)r */ + + g2_String, /* draw string */ + /* ... = (double)x, (double)y, (const char*)string */ + + g2_Image, /* draw (pen) image */ + /* ... = (double)x, (double)y, + (int)x_size, (int)y_size, (int*)pen_array */ + + g2_QueryPointer, /* query pointer position (mouse) */ + /* ... = (double)*x, (double)*y, + (unsigned int)*button */ + g2_GetPDHandles /* get pointers to low level handles */ + /* ... = void *handles[G2_MAX_NUMBER_PD_HANDLES] */ +} g2_funix; + + +#endif /* _G2_FUNIX_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_graphic_pd.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_graphic_pd.c new file mode 100755 index 000000000..db4a6f855 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_graphic_pd.c @@ -0,0 +1,684 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include + +#include "g2_funix.h" +#include "g2_virtual_device.h" +#include "g2_graphic_pd.h" +#include "g2_control_pd.h" +#include "g2_util.h" + +#ifndef PI +#define PI 3.14159265358979323846 +#endif /* PI */ + + +/* + * + * Plot (physical device) + * + */ +void g2_plot_pd(g2_physical_device *pd, double x, double y) +{ + int ix, iy; + double dx, dy; + + if(pd->ff[g2_Plot].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + pd->ff[g2_Plot].fun(pd->pid, pd->pdp, + ix, iy); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + pd->ff[g2_Plot].fun(pd->pid, pd->pdp, + dx, dy); + break; + } + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Draw line (low_level) + * + */ +void g2_line_pd(g2_physical_device *pd, + double x1, double y1, double x2, double y2) +{ + int ix1, iy1, ix2, iy2; + double dx1, dy1, dx2, dy2; + + if(pd->ff[g2_Line].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x1, y1, &ix1, &iy1); + g2_uc2pdc_int(pd, x2, y2, &ix2, &iy2); + pd->ff[g2_Line].fun(pd->pid, pd->pdp, + ix1, iy1, ix2, iy2); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x1, y1, &dx1, &dy1); + g2_uc2pdc_double(pd, x2, y2, &dx2, &dy2); + pd->ff[g2_Line].fun(pd->pid, pd->pdp, + dx1, dy1, dx2, dy2); + break; + } + } else { + /* emulate ... with .... */ + } +} + + + +/* + * + * Draw poly line (physical device) + * + */ +void g2_poly_line_pd(g2_physical_device *pd, + int N, double *points) +{ + int i; + int *ipt; + double *dpt; + + if(pd->ff[g2_PolyLine].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + ipt=g2_malloc(2*N*sizeof(int)); + for(i=0;i<2*N;i+=2) + g2_uc2pdc_int(pd, points[i+0], points[i+1], ipt+i, ipt+i+1); + pd->ff[g2_PolyLine].fun(pd->pid, pd->pdp, + N, ipt); + free(ipt); + break; + case g2_DoubleCoor: + dpt=g2_malloc(2*N*sizeof(double)); + for(i=0;i<2*N;i+=2) + g2_uc2pdc_double(pd, + points[i+0], points[i+1], + dpt+i, dpt+i+1); + pd->ff[g2_PolyLine].fun(pd->pid, pd->pdp, + N, dpt); + free(dpt); + break; + } + } else { + for (i=0;iff[g2_Triangle].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x1, y1, &ix1, &iy1); + g2_uc2pdc_int(pd, x2, y2, &ix2, &iy2); + g2_uc2pdc_int(pd, x3, y3, &ix3, &iy3); + pd->ff[g2_Triangle].fun(pd->pid, pd->pdp, + ix1, iy1, + ix2, iy2, + ix3, iy3); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x1, y1, &dx1, &dy1); + g2_uc2pdc_double(pd, x2, y2, &dx2, &dy2); + g2_uc2pdc_double(pd, x3, y3, &dx3, &dy3); + pd->ff[g2_Triangle].fun(pd->pid, pd->pdp, + dx1, dy1, + dx2, dy2, + dx3, dy3); + } + } else { + g2_line_pd(pd, x1, y1, x2, y2); /* emulate triangle with lines */ + g2_line_pd(pd, x2, y2, x3, y3); + g2_line_pd(pd, x3, y3, x1, y1); + } +} + + + +/* + * + * Filled triangle (physical device) + * + */ +void g2_filled_triangle_pd(g2_physical_device *pd, + double x1, double y1, + double x2, double y2, + double x3, double y3) +{ + int ix1, iy1, ix2, iy2, ix3, iy3; + double dx1, dy1, dx2, dy2, dx3, dy3; + + if(pd->ff[g2_FilledTriangle].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x1, y1, &ix1, &iy1); + g2_uc2pdc_int(pd, x2, y2, &ix2, &iy2); + g2_uc2pdc_int(pd, x3, y3, &ix3, &iy3); + pd->ff[g2_FilledTriangle].fun(pd->pid, pd->pdp, + ix1, iy1, + ix2, iy2, + ix3, iy3); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x1, y1, &dx1, &dy1); + g2_uc2pdc_double(pd, x2, y2, &dx2, &dy2); + g2_uc2pdc_double(pd, x3, y3, &dx3, &dy3); + pd->ff[g2_FilledTriangle].fun(pd->pid, pd->pdp, + dx1, dy1, + dx2, dy2, + dx3, dy3); + } + } else { + double Triangle[6]; /* emulate FilledTriangle with FilledPolygon */ + Triangle[0] = x1; + Triangle[1] = y1; + Triangle[2] = x2; + Triangle[3] = y2; + Triangle[4] = x3; + Triangle[5] = y3; + g2_filled_polygon_pd(pd, 3, Triangle); + } +} + + + +/* + * + * Rectangle (physical device) + * + */ +void g2_rectangle_pd(g2_physical_device *pd, + double x1, double y1, double x2, double y2) +{ + int ix1, iy1, ix2, iy2; + double dx1, dy1, dx2, dy2; + + if(pd->ff[g2_Rectangle].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x1, y1, &ix1, &iy1); + g2_uc2pdc_int(pd, x2, y2, &ix2, &iy2); + g2_sort2_i(&ix1, &ix2); + g2_sort2_i(&iy1, &iy2); + pd->ff[g2_Rectangle].fun(pd->pid, pd->pdp, + ix1, iy1, ix2, iy2); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x1, y1, &dx1, &dy1); + g2_uc2pdc_double(pd, x2, y2, &dx2, &dy2); + g2_sort2_d(&dx1, &dx2); + g2_sort2_d(&dy1, &dy2); + pd->ff[g2_Rectangle].fun(pd->pid, pd->pdp, + dx1, dy1, dx2, dy2); + break; + } + } else { + g2_line_pd(pd, x1, y1, x1, y2); /* emulate rectangle with lines */ + g2_line_pd(pd, x1, y1, x2, y1); + g2_line_pd(pd, x2, y1, x2, y2); + g2_line_pd(pd, x1, y2, x2, y2); + } +} + + + +/* + * + * Filled rectangle (physical device) + * + */ +void g2_filled_rectangle_pd(g2_physical_device *pd, + double x1, double y1, double x2, double y2) +{ + int ix1, iy1, ix2, iy2; + double dx1, dy1, dx2, dy2; + + if(pd->ff[g2_FilledRectangle].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x1, y1, &ix1, &iy1); + g2_uc2pdc_int(pd, x2, y2, &ix2, &iy2); + g2_sort2_i(&ix1, &ix2); + g2_sort2_i(&iy1, &iy2); + pd->ff[g2_FilledRectangle].fun(pd->pid, pd->pdp, + ix1, iy1, ix2, iy2); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x1, y1, &dx1, &dy1); + g2_uc2pdc_double(pd, x2, y2, &dx2, &dy2); + g2_sort2_d(&dx1, &dx2); + g2_sort2_d(&dy1, &dy2); + pd->ff[g2_FilledRectangle].fun(pd->pid, pd->pdp, + dx1, dy1, dx2, dy2); + break; + } + } else { + double Rectangle[8]; /* emulate FilledRectangle with FilledPolygon */ + Rectangle[0] = x1; + Rectangle[1] = y1; + Rectangle[2] = x2; + Rectangle[3] = y1; + Rectangle[4] = x2; + Rectangle[5] = y2; + Rectangle[6] = x1; + Rectangle[7] = y2; + g2_filled_polygon_pd(pd,4,Rectangle); + } +} + + + +/* + * + * Polygon (physical device) + * + */ +void g2_polygon_pd(g2_physical_device *pd, + int N, double *points) +{ + int i; + int *ipt; + double *dpt; + + if(pd->ff[g2_Polygon].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + ipt=g2_malloc(2*N*sizeof(int)); + for(i=0;i<2*N;i+=2) + g2_uc2pdc_int(pd, points[i+0], points[i+1], ipt+i, ipt+i+1); + pd->ff[g2_Polygon].fun(pd->pid, pd->pdp, + N, ipt); + free(ipt); + break; + case g2_DoubleCoor: + dpt=g2_malloc(2*N*sizeof(double)); + for(i=0;i<2*N;i+=2) + g2_uc2pdc_double(pd, + points[i+0], points[i+1], dpt+i, dpt+i+1); + pd->ff[g2_Polygon].fun(pd->pid, pd->pdp, + N, dpt); + free(dpt); + break; + } + } else { + for (i=0;iff[g2_FilledPolygon].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + ipt=g2_malloc(2*N*sizeof(int)); + for(i=0;i<2*N;i+=2) + g2_uc2pdc_int(pd, points[i+0], points[i+1], ipt+i, ipt+i+1); + pd->ff[g2_FilledPolygon].fun(pd->pid, pd->pdp, + N, ipt); + free(ipt); + break; + case g2_DoubleCoor: + dpt=g2_malloc(2*N*sizeof(double)); + for(i=0;i<2*N;i+=2) + g2_uc2pdc_double(pd, + points[i+0], points[i+1], dpt+i, dpt+i+1); + pd->ff[g2_FilledPolygon].fun(pd->pid, pd->pdp, + N, dpt); + free(dpt); + break; + } + } else { + /* emulate filled polygon with .... */ + } +} + + + +/* + * + * Ellipse (physical device) + * + */ +void g2_ellipse_pd(g2_physical_device *pd, + double x, double y, double r1, double r2) +{ + int ix, iy, ir1, ir2; + double dx, dy, dr1, dr2; + + if(pd->ff[g2_Ellipse].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + g2_us2pds_int(pd, r1, r2, &ir1, &ir2); + pd->ff[g2_Ellipse].fun(pd->pid, pd->pdp, + ix, iy, ir1, ir2); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + g2_us2pds_double(pd, r1, r2, &dr1, &dr2); + pd->ff[g2_Ellipse].fun(pd->pid, pd->pdp, + dx, dy, dr1, dr2); + break; + } + } else { + g2_arc_pd(pd, x, y, r1, r2, 0., 360.); /* emulate ellipse with arc */ + } +} + + + +/* + * + * Filled ellipse (physical device) + * + */ +void g2_filled_ellipse_pd(g2_physical_device *pd, + double x, double y, double r1, double r2) +{ + int ix, iy, ir1, ir2; + double dx, dy, dr1, dr2; + + if(pd->ff[g2_FilledEllipse].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + g2_us2pds_int(pd, r1, r2, &ir1, &ir2); + pd->ff[g2_FilledEllipse].fun(pd->pid, pd->pdp, + ix, iy, ir1, ir2); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + g2_us2pds_double(pd, r1, r2, &dr1, &dr2); + pd->ff[g2_FilledEllipse].fun(pd->pid, pd->pdp, + dx, dy, dr1, dr2); + break; + } + } else { + g2_filled_arc_pd(pd, /* emulate filledellipse with filled arc */ + x, y, + r1, r2, + 0., 360.); + } +} + + + +/* + * + * Circle (physical device) + * + */ +void g2_circle_pd(g2_physical_device *pd, + double x, double y, double r) +{ + int ix, iy, ir; + double dx, dy, dr; + + if(pd->ff[g2_Circle].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + g2_us2pds_int(pd, r, 0, &ir, NULL); + pd->ff[g2_Circle].fun(pd->pid, pd->pdp, + ix, iy, ir); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + g2_us2pds_double(pd, r, 0, &dr, NULL); + pd->ff[g2_Circle].fun(pd->pid, pd->pdp, + dx, dy, dr); + break; + } + } else { + g2_ellipse_pd(pd, x, y, r, r); /* emulate circle with ellipse */ + } +} + + + +/* + * + * Filled circle (physical device) + * + */ +void g2_filled_circle_pd(g2_physical_device *pd, + double x, double y, double r) +{ + int ix, iy, ir; + double dx, dy, dr; + + if(pd->ff[g2_FilledCircle].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + g2_us2pds_int(pd, r, 0, &ir, NULL); + pd->ff[g2_FilledCircle].fun(pd->pid, pd->pdp, + ix, iy, ir); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + g2_us2pds_double(pd, r, 0, &dr, NULL); + pd->ff[g2_FilledCircle].fun(pd->pid, pd->pdp, + dx, dy, dr); + break; + } + } else { + g2_filled_ellipse_pd(pd, x, y, r, r); /* emulate */ + } +} + + + +/* + * + * Arc (physical device) + * + */ +void g2_arc_pd(g2_physical_device *pd, + double x, double y, double r1, double r2, double a1, double a2) +{ + int ix, iy, ir1, ir2; + double dx, dy, dr1, dr2; + + if(pd->ff[g2_Arc].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + g2_us2pds_int(pd, r1, r2, &ir1, &ir2); + pd->ff[g2_Arc].fun(pd->pid, pd->pdp, + ix, iy, ir1, ir2, a1, a2); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + g2_us2pds_double(pd, r1, r2, &dr1, &dr2); + pd->ff[g2_Arc].fun(pd->pid, pd->pdp, + dx, dy, dr1, dr2, a1, a2); + break; + } + } else { + double a, da, *pt; /* emulate arc */ + int N, i; + N=(a2==a1)?360:(int)fabs(a2-a1)+8; + a=a1*2.*PI/360.; + da=((a2>a1)? (a2-a1):360.-(a1-a2))*2.*PI/360./(N-1); + pt=g2_malloc(2*N*sizeof(double)); + for(i=0;iff[g2_FilledArc].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + g2_us2pds_int(pd, r1, r2, &ir1, &ir2); + pd->ff[g2_FilledArc].fun(pd->pid, pd->pdp, + ix, iy, ir1, ir2, a1, a2); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + g2_us2pds_double(pd, r1, r2, &dr1, &dr2); + pd->ff[g2_FilledArc].fun(pd->pid, pd->pdp, + dx, dy, dr1, dr2, a1, a2); + break; + } + } else { + double a, da, *pt; /* emulate filled arc */ + int N, i; + N=(a2==a1)?360:(int)fabs(a2-a1)+8; + a=a1*2.*PI/360.; + da=((a2>a1)? (a2-a1):360.-(a1-a2))*2.*PI/360./(N-1); + pt=g2_malloc(2*(N+2)*sizeof(double)); + pt[0]=x; + pt[1]=y; + for(i=0;iff[g2_String].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + pd->ff[g2_String].fun(pd->pid, pd->pdp, + ix, iy, text); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + pd->ff[g2_String].fun(pd->pid, pd->pdp, + dx, dy, text); + break; + } + } else { + /* emulate ... with .... */ + } +} + + + +void g2_image_pd(g2_physical_device *pd, + double x, double y, int x_size, int y_size, int *pens) +{ + int ix, iy; + double dx, dy; + + if(pd->ff[g2_Image].fun!=NULL) { + switch(pd->coor_type) { + case g2_IntCoor: + g2_uc2pdc_int(pd, x, y, &ix, &iy); + pd->ff[g2_Image].fun(pd->pid, pd->pdp, + ix, iy, x_size, y_size, pens); + break; + case g2_DoubleCoor: + g2_uc2pdc_double(pd, x, y, &dx, &dy); + pd->ff[g2_Image].fun(pd->pid, pd->pdp, + dx, dy, x_size, y_size, pens); + break; + } + } else { + for(ix=0;ix +#include +#include "g2_physical_device.h" +#include "g2_funix.h" +#include "g2_util.h" + + +g2_physical_device *g2_create_physical_device(int pid, + void *pdp, + g2_coor ct, + const g2_funix_fun *ff, + double a11, double a22, + double b1, double b2) +{ + g2_physical_device *rd; + int i, j; + + rd=g2_malloc(sizeof(g2_physical_device)); + + rd->pid=pid; /* physical device id (handled by driver) */ + rd->pdp=pdp; /* pointer to something */ + rd->coor_type=ct; /* coord. type */ + rd->a11=a11; /* device->physical device transformation */ + rd->a22=a22; + rd->b1=b1; + rd->b2=b2; + + rd->x_origin=0.0; /* User coordinates specification */ + rd->y_origin=0.0; + rd->x_mul=1.0; + rd->y_mul=1.0; + + rd->ff=g2_malloc(G2_N_FUNIX*sizeof(g2_funix_fun)); + + for(i=0;iff[i].fx=i; + rd->ff[i].fun=NULL; + for(j=0;ff[j].fx!=g2_FUNIX_NULL;j++) + if(ff[j].fx==i) { + rd->ff[i].fun = ff[j].fun; + break; + } + } + + return rd; +} + + +/* + * + * Destroy physical device + * + */ +void g2_destroy_physical_device(g2_physical_device *pd) +{ + g2_free(pd->ff); + g2_free(pd); +} + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_physical_device.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_physical_device.h new file mode 100755 index 000000000..d25d58eae --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_physical_device.h @@ -0,0 +1,61 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_PHYSICAL_DEVICE_H +#define _G2_PHYSICAL_DEVICE_H + +#include "g2.h" +#include "g2_funix.h" + + +typedef enum _g2_coor { /* coord. type */ + g2_IntCoor, g2_DoubleCoor +} g2_coor; + + +typedef struct _g2_funix_fun { /* funix--function paar */ + g2_funix fx; /* function index */ + int (*fun)(); /* pointer to function */ +} g2_funix_fun; + + +typedef struct _g2_physical_device { + int pid; /* physical device id */ + void *pdp; /* pointer to something in phys. dev. */ + g2_coor coor_type; /* coordinate type */ + g2_funix_fun *ff; /* list of funix-function pairs */ + double a11, a22; /* coordinate transformation (ud->pd) */ + double b1, b2; /* Ar + B */ + + double x_origin; /* User coordinates specification */ + double y_origin; + double x_mul; + double y_mul; +} g2_physical_device; + + + +g2_physical_device *g2_create_physical_device(int pid, + void *pdp, + g2_coor ct, + const g2_funix_fun *ff, + double a11, double a22, + double b1, double b2); +void g2_destroy_physical_device(g2_physical_device *pd); + +#endif /* _G2_PHYSICAL_DEVICE_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_physical_device.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_physical_device.o new file mode 100755 index 000000000..a4cc2a04f Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_physical_device.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_splines.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_splines.c new file mode 100755 index 000000000..1e7b345e5 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_splines.c @@ -0,0 +1,880 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +/* + * g2_splines.c + * Tijs Michels + * tijs@vimec.nl + * 06/16/99 + */ + +#include +#include +#include "g2.h" +#include "g2_util.h" + +static void g2_split(int n, const double *points, double *x, double *y); +static void g2_c_spline(int n, const double *points, int m, double *sxy); +static void g2_c_b_spline(int n, const double *points, int m, double *sxy); +static void g2_c_raspln(int n, const double *points, double tn, double *sxy); +static void g2_c_newton(int n, const double *c1, const double *c2, int o, const double *xv, double *yv); +static void g2_c_para_3(int n, const double *points, double *sxy); +static void g2_c_para_5(int n, const double *points, double *sxy); + +void g2_split(int n, const double *points, double *x, double *y) +{ + int i; + for (i = 0; i < n; i++) { + x[i] = points[i+i]; + y[i] = points[i+i+1]; + } +} + +#define eps 1.e-12 + +void g2_c_spline(int n, const double *points, int m, double *sxy) + +/* + * FUNCTIONAL DESCRIPTION: + * + * Compute a curve of m points (sx[j],sy[j]) + * -- j being a positive integer < m -- + * passing through the n data points (x[i],y[i]) + * -- i being a positive integer < n -- + * supplied by the user. + * The procedure to determine sy[j] involves + * Young's method of successive over-relaxation. + * + * FORMAL ARGUMENTS: + * + * n number of data points + * points data points (x[i],y[i]) + * m number of interpolated points; m = (n-1)*o+1 + * for o curve points for every data point + * sxy interpolated points (sx[j],sy[j]) + * + * IMPLICIT INPUTS: NONE + * IMPLICIT OUTPUTS: NONE + * SIDE EFFECTS: NONE + * + * REFERENCES: + * + * 1. Ralston and Wilf, Mathematical Methods for Digital Computers, + * Vol. II, John Wiley and Sons, New York 1967, pp. 156-158. + * 2. Greville, T.N.E., Ed., Proceedings of An Advanced Seminar + * Conducted by the Mathematics Research Center, U.S. Army, + * University of Wisconsin, Madison. October 7-9, 1968. Theory + * and Applications of Spline Functions, Academic Press, + * New York / London 1969, pp. 156-167. + * + * AUTHORS: + * + * Josef Heinen 04/06/88 + * Tijs Michels 06/16/99 + */ + +{ + int i, j; + double *x, *y, *g, *h; + double k, u, delta_g; + + if (n < 3) { + fputs("\nERROR calling function \"g2_c_spline\":\n" + "number of data points input should be at least three\n", stderr); + return; + } + if ((m-1)%(n-1)) { + fputs("\nWARNING from function \"g2_c_spline\":\n" + "number of curve points output for every data point input " + "is not an integer\n", stderr); + } + + x = (double *) g2_malloc(n*4*sizeof(double)); + y = x + n; + g = y + n; + h = g + n; /* for the constant copy of g */ + g2_split(n, points, x, y); + + n--; /* last value index */ + k = x[0]; /* look up once */ + u = (x[n] - k) / (m - 1); /* calculate step outside loop */ + for (j = 0; j < m; j++) sxy[j+j] = j * u + k; /* x-coordinates */ + + for (i = 1; i < n; i++) { + g[i] = 2. * ((y[i+1] - y[i]) / (x[i+1] - x[i]) - + (y[i] - y[i-1]) / (x[i] - x[i-1])) + / (x[i+1] - x[i-1]); /* whereas g[i] will later be changed repeatedly */ + h[i] = 1.5 * g[i]; /* copy h[i] of g[i] will remain constant */ + } + + k = 0.; + + do { + for (u = 0., i = 1; i < n; i++) { + delta_g = .5 * (x[i] - x[i-1]) / (x[i+1] - x[i-1]); + delta_g = (h[i] - + g[i] - + g[i-1] * delta_g - /* 8. - 4 * sqrt(3.) */ + g[i+1] * (.5 - delta_g)) * 1.0717967697244907832; + g[i] += delta_g; + + if (fabs(delta_g) > u) u = fabs(delta_g); + } /* On loop termination u holds the largest delta_g. */ + + if (k == 0.) k = u * eps; + /* Only executed once, at the end of pass one. So k preserves + * the largest delta_g of pass one, multiplied by eps. + */ + } while (u > k); + + m += m, i = 1, j = 0; + do { + u = sxy[j++]; /* x-coordinate */ + + while (x[i] < u) i++; + + if (--i > n) i = n; + + k = (u - x[i]) / (x[i+1] - x[i]); /* calculate outside loop */ + sxy[j++] = y[i] + + (y[i+1] - y[i]) * k + + (u - x[i]) * (u - x[i+1]) * + ((2. - k) * g[i] + + (1. + k) * g[i+1]) / 6.; /* y-coordinate */ + } while (j < m); + g2_free(x); +} + +void g2_spline(int id, int n, double *points, int o) + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + * o number of interpolated points per data point + * + * Given an array of n data points {x[1], y[1], ... x[n], y[n]} plot a + * spline curve on device id with o interpolated points per data point. + * So the larger o, the more fluent the curve. + */ + +{ + int m; + double *sxy; + + m = (n-1)*o+1; + sxy = (double*)g2_malloc(m*2*sizeof(double)); + + g2_c_spline(n, points, m, sxy); + g2_poly_line(id, m, sxy); + + g2_free(sxy); +} + +void g2_filled_spline(int id, int n, double *points, int o) + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + * o number of interpolated points per data point + */ + +{ + int m; + double *sxy; + + m = (n-1)*o+1; + sxy = (double*)g2_malloc((m+1)*2*sizeof(double)); + + g2_c_spline(n, points, m, sxy); + sxy[m+m] = points[n+n-2]; + sxy[m+m+1] = points[1]; + g2_filled_polygon(id, m+1, sxy); + g2_free(sxy); +} + +void g2_c_b_spline(int n, const double *points, int m, double *sxy) + +/* + * g2_c_b_spline takes n input points. It uses parameter t + * to compute sx(t) and sy(t) respectively + */ + +{ + int i, j; + double *x, *y; + double t, bl1, bl2, bl3, bl4; + double interval, xi_3, yi_3, xi, yi; + + if (n < 3) { + fputs("\nERROR calling function \"g2_c_b_spline\":\n" + "number of data points input should be at least three\n", stderr); + return; + } + x = (double *) g2_malloc(n*2*sizeof(double)); + y = x + n; + g2_split(n, points, x, y); + + m--; /* last value index */ + n--; /* last value index */ + interval = (double)n / m; + + for (m += m, i = 2, j = 0; i <= n+1; i++) { + if (i == 2) { + xi_3 = 2 * x[0] - x[1]; + yi_3 = 2 * y[0] - y[1]; + } else { + xi_3 = x[i-3]; + yi_3 = y[i-3]; + } + if (i == n+1) { + xi = 2 * x[n] - x[n-1]; + yi = 2 * y[n] - y[n-1]; + } else { + xi = x[i]; + yi = y[i]; + } + + t = fmod(j * interval, 1.); + + while (t < 1. && j < m) { + bl1 = (1. - t); + bl2 = t * t; /* t^2 */ + bl4 = t * bl2; /* t^3 */ + bl3 = bl4 - bl2; + + bl1 = bl1 * bl1 * bl1; + bl2 = 3. * (bl3 - bl2) + 4.; + bl3 = 3. * ( t - bl3) + 1.; + + sxy[j++] = (bl1 * xi_3 + bl2 * x[i-2] + bl3 * x[i-1] + bl4 * xi) / 6.; /* x-coordinate */ + sxy[j++] = (bl1 * yi_3 + bl2 * y[i-2] + bl3 * y[i-1] + bl4 * yi) / 6.; /* y-coordinate */ + + t += interval; + } + } + sxy[m] = x[n]; + sxy[m+1] = y[n]; + g2_free(x); +} + +void g2_b_spline(int id, int n, double *points, int o) + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + * o number of interpolated points per data point + */ + +{ + int m; + double *sxy; + + m = (n-1)*o+1; + sxy = (double*)g2_malloc(m*2*sizeof(double)); + + g2_c_b_spline(n, points, m, sxy); + g2_poly_line(id, m, sxy); + + g2_free(sxy); +} + +void g2_filled_b_spline(int id, int n, double *points, int o) + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + * o number of interpolated points per data point + */ + +{ + int m; + double *sxy; + + m = (n-1)*o+1; + sxy = (double*)g2_malloc((m+1)*2*sizeof(double)); + + g2_c_b_spline(n, points, m, sxy); + sxy[m+m] = points[n+n-2]; + sxy[m+m+1] = points[1]; + g2_filled_polygon(id, m+1, sxy); + + g2_free(sxy); +} + +/* + * FUNCTION g2_c_raspln + * + * FUNCTIONAL DESCRIPTION: + * + * This function draws a piecewise cubic polynomial through + * the specified data points. The (n-1) cubic polynomials are + * basically parametric cubic Hermite polynomials through the + * n specified data points with tangent values at the data + * points determined by a weighted average of the slopes of + * the secant lines. A tension parameter "tn" is provided to + * adjust the length of the tangent vector at the data points. + * This allows the "roundness" of the curve to be adjusted. + * For further information and references on this technique see: + * + * D. Kochanek and R. Bartels, Interpolating Splines With Local + * Tension, Continuity and Bias Control, Computer Graphics, + * 18(1984)3. + * + * AUTHORS: + * + * Dennis Mikkelson distributed in GPLOT Jan 7, 1988 F77 + * Tijs Michels t.michels@vimec.nl Jun 7, 1999 C + * + * FORMAL ARGUMENTS: + * + * n number of data points, n > 2 + * points double array holding the x and y-coords of the data points + * tn double parameter in [0.0, 2.0]. When tn = 0.0, + * the curve through the data points is very rounded. + * As tn increases the curve is gradually pulled tighter. + * When tn = 2.0, the curve is essentially a polyline + * through the given data points. + * sxy double array holding the coords of the spline curve + * + * IMPLICIT INPUTS: NONE + * IMPLICIT OUTPUTS: NONE + * SIDE EFFECTS: NONE + */ + +#define nb 40 +/* + * Number of straight connecting lines of which each polynomial consists. + * So between one data point and the next, (nb-1) points are placed. + */ + +void g2_c_raspln(int n, const double *points, double tn, double *sxy) +{ + int i, j; + double *x, *y; + double bias, tnFactor, tangentL1, tangentL2; + double D1x, D1y, D2x, D2y, t1x, t1y, t2x, t2y; + double h1[nb+1]; /* Values of the Hermite basis functions */ + double h2[nb+1]; /* at nb+1 evenly spaced points in [0,1] */ + double h3[nb+1]; + double h4[nb+1]; + + x = (double *) g2_malloc(n*2*sizeof(double)); + y = x + n; + g2_split(n, points, x, y); + +/* + * First, store the values of the Hermite basis functions in a table h[ ] + * so no time is wasted recalculating them + */ + for (i = 0; i < nb+1; i++) { + double t, tt, ttt; + t = (double) i / nb; + tt = t * t; + ttt = t * tt; + h1[i] = 2. * ttt - 3. * tt + 1.; + h2[i] = -2. * ttt + 3. * tt; + h3[i] = ttt - 2. * tt + t; + h4[i] = ttt - tt; + } + +/* + * Set local tnFactor based on input parameter tn + */ + if (tn <= 0.) { + tnFactor = 2.; + fputs("g2_c_raspln: Using Tension Factor 0.0: very rounded", stderr); + } + else if (tn >= 2.) { + tnFactor = 0.; + fputs("g2_c_raspln: Using Tension Factor 2.0: not rounded at all", stderr); + } + else tnFactor = 2. - tn; + + D1x = D1y = 0.; /* first point has no preceding point */ + for (j = 0; j < n - 2; j++) { + t1x = x[j+1] - x[j]; + t1y = y[j+1] - y[j]; + t2x = x[j+2] - x[j+1]; + t2y = y[j+2] - y[j+1]; + tangentL1 = t1x * t1x + t1y * t1y; + tangentL2 = t2x * t2x + t2y * t2y; + if (tangentL1 + tangentL2 == 0) bias = .5; + else bias = tangentL2 / (tangentL1 + tangentL2); + D2x = tnFactor * (bias * t1x + (1 - bias) * t2x); + D2y = tnFactor * (bias * t1y + (1 - bias) * t2y); + for (i = 0; i < nb; i++) { + sxy[2 * nb * j + i + i] = + h1[i] * x[j] + h2[i] * x[j+1] + h3[i] * D1x + h4[i] * D2x; + sxy[2 * nb * j + i + i + 1] = + h1[i] * y[j] + h2[i] * y[j+1] + h3[i] * D1y + h4[i] * D2y; + } + D1x = D2x; /* store as preceding point in */ + D1y = D2y; /* the next pass */ + } + +/* + * Do the last subinterval as a special case since no point follows the + * last point + */ + for (i = 0; i < nb+1; i++) { + sxy[2 * nb * (n-2) + i + i] = + h1[i] * x[n-2] + h2[i] * x[n-1] + h3[i] * D1x; + sxy[2 * nb * (n-2) + i + i + 1] = + h1[i] * y[n-2] + h2[i] * y[n-1] + h3[i] * D1y; + } + g2_free(x); +} + +void g2_raspln(int id, int n, double *points, double tn) + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + * tn tension factor [0.0, 2.0] + * 0.0 very rounded + * 2.0 not rounded at all + */ + +{ + int m; + double *sxy; /* coords of the entire spline curve */ + m = (n-1)*nb+1; + sxy = (double *) g2_malloc(m*2*sizeof(double)); + + g2_c_raspln(n, points, tn, sxy); + g2_poly_line(id, m, sxy); + + g2_free(sxy); +} + +void g2_filled_raspln(int id, int n, double *points, double tn) + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + * tn tension factor [0.0, 2.0] + * 0.0 very rounded + * 2.0 not rounded at all + */ + +{ + int m; + double *sxy; /* coords of the entire spline curve */ + m = (n-1)*nb+2; + sxy = (double *) g2_malloc(m*2*sizeof(double)); + + g2_c_raspln(n, points, tn, sxy); + sxy[(n+n-2) * nb + 2] = points[n+n-2]; + sxy[(n+n-2) * nb + 3] = points[1]; + g2_filled_polygon(id, m, sxy); + + g2_free(sxy); +} + +/* ---- And now for a rather different approach ---- */ + +/* + * FUNCTION g2_c_newton + * + * FUNCTIONAL DESCRIPTION: + * + * Use Newton's Divided Differences to calculate an interpolation + * polynomial through the specified data points. + * This function is called by + * g2_c_para_3 and + * g2_c_para_5. + * + * Dennis Mikkelson distributed in GPLOT Jan 5, 1988 F77 + * Tijs Michels t.michels@vimec.nl Jun 16, 1999 C + * + * FORMAL ARGUMENTS: + * + * n number of entries in c1 and c2, 4 <= n <= MaxPts + * for para_3 (degree 3) n = 4 + * for para_5 (degree 5) n = 6 + * for para_i (degree i) n = (i + 1) + * c1 double array holding at most MaxPts values giving the + * first coords of the points to be interpolated + * c2 double array holding at most MaxPts values giving the + * second coords of the points to be interpolated + * o number of points at which the interpolation + * polynomial is to be evaluated + * xv double array holding o points at which to + * evaluate the interpolation polynomial + * yv double array holding upon return the values of the + * interpolation polynomial at the corresponding points in xv + * + * yv is the OUTPUT + * + * IMPLICIT INPUTS: NONE + * IMPLICIT OUTPUTS: NONE + * SIDE EFFECTS: NONE + */ + +#define MaxPts 21 +#define xstr(s) __str(s) +#define __str(s) #s + +/* + * Maximum number of data points allowed + * 21 would correspond to a polynomial of degree 20 + */ + +void g2_c_newton(int n, const double *c1, const double *c2, + int o, const double *xv, double *yv) +{ + int i, j; + double p, s; + double ddt[MaxPts][MaxPts]; /* Divided Difference Table */ + + if (n < 4) { + fputs("g2_c_newton: Error! Less than 4 points passed " + "to function g2_c_newton\n", stderr); + return; + } + + if (n > MaxPts) { + fputs("g2_c_newton: Error! More than " xstr(MaxPts) " points passed " + "to function g2_c_newton\n", stderr); + return; + } + +/* First, build the divided difference table */ + + for (i = 0; i < n; i++) ddt[i][0] = c2[i]; + for (j = 1; j < n; j++) { + for (i = 0; i < n - j; i++) + ddt[i][j] = (ddt[i+1][j-1] - ddt[i][j-1]) / (c1[i+j] - c1[i]); + } + +/* Next, evaluate the polynomial at the specified points */ + + for (i = 0; i < o; i++) { + for (p = 1., s = ddt[0][0], j = 1; j < n; j++) { + p *= xv[i] - c1[j-1]; + s += p * ddt[0][j]; + } + yv[i] = s; + } +} + +/* + * FUNCTION: g2_c_para_3 + * + * FUNCTIONAL DESCRIPTION: + * + * This function draws a piecewise parametric interpolation + * polynomial of degree 3 through the specified data points. + * The effect is similar to that obtained using DISSPLA to + * draw a curve after a call to the DISSPLA routine PARA3. + * The curve is parameterized using an approximation to the + * curve's arc length. The basic interpolation is done + * using function g2_c_newton. + * + * Dennis Mikkelson distributed in GPLOT Jan 7, 1988 F77 + * Tijs Michels t.michels@vimec.nl Jun 17, 1999 C + * + * FORMAL ARGUMENTS: + * + * n number of data points through which to draw the curve + * points double array containing the x and y-coords of the data points + * + * IMPLICIT INPUTS: NONE + * IMPLICIT OUTPUTS: NONE + * SIDE EFFECTS: NONE + */ + +/* + * #undef nb + * #define nb 40 + * Number of straight connecting lines of which each polynomial consists. + * So between one data point and the next, (nb-1) points are placed. + */ + +void g2_c_para_3(int n, const double *points, double *sxy) +{ +#define dgr (3+1) +#define nb2 (nb*2) + int i, j; + double x1t, y1t; + double o, step; + double X[nb2]; /* x-coords of the current curve piece */ + double Y[nb2]; /* y-coords of the current curve piece */ + double t[dgr]; /* data point parameter values */ + double Xpts[dgr]; /* x-coords data point subsection */ + double Ypts[dgr]; /* y-coords data point subsection */ + double s[nb2]; /* parameter values at which to interpolate */ + + /* Do first TWO subintervals first */ + + g2_split(dgr, points, Xpts, Ypts); + + t[0] = 0.; + for (i = 1; i < dgr; i++) { + x1t = Xpts[i] - Xpts[i-1]; + y1t = Ypts[i] - Ypts[i-1]; + t[i] = t[i-1] + sqrt(x1t * x1t + y1t * y1t); + } + + step = t[2] / nb2; + for (i = 0; i < nb2; i++) s[i] = i * step; + + g2_c_newton(dgr, t, Xpts, nb2, s, X); + g2_c_newton(dgr, t, Ypts, nb2, s, Y); + for (i = 0; i < nb2; i++) { + sxy[i+i] = X[i]; + sxy[i+i+1] = Y[i]; + } + + /* Next, do later central subintervals */ + + for (j = 1; j < n - dgr + 1; j++) { + g2_split(dgr, points + j + j, Xpts, Ypts); + + for (i = 1; i < dgr; i++) { + x1t = Xpts[i] - Xpts[i-1]; + y1t = Ypts[i] - Ypts[i-1]; + t[i] = t[i-1] + sqrt(x1t * x1t + y1t * y1t); + } + + o = t[1]; /* look up once */ + step = (t[2] - o) / nb; + for (i = 0; i < nb; i++) s[i] = i * step + o; + + g2_c_newton(dgr, t, Xpts, nb, s, X); + g2_c_newton(dgr, t, Ypts, nb, s, Y); + + for (i = 0; i < nb; i++) { + sxy[(j + 1) * nb2 + i + i] = X[i]; + sxy[(j + 1) * nb2 + i + i + 1] = Y[i]; + } + } + + /* Now do last subinterval */ + + o = t[2]; + step = (t[3] - o) / nb; + for (i = 0; i < nb; i++) s[i] = i * step + o; + + g2_c_newton(dgr, t, Xpts, nb, s, X); + g2_c_newton(dgr, t, Ypts, nb, s, Y); + + for (i = 0; i < nb; i++) { + sxy[(n - dgr + 2) * nb2 + i + i] = X[i]; + sxy[(n - dgr + 2) * nb2 + i + i + 1] = Y[i]; + } + sxy[(n - 1) * nb2] = points[n+n-2]; + sxy[(n - 1) * nb2 + 1] = points[n+n-1]; +} + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + */ + +void g2_para_3(int id, int n, double *points) +{ + int m; + double *sxy; /* coords of the entire spline curve */ + m = (n-1)*nb+1; + sxy = (double *) g2_malloc(m*2*sizeof(double)); + + g2_c_para_3(n, points, sxy); + g2_poly_line(id, m, sxy); + + g2_free(sxy); +} + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + */ + +void g2_filled_para_3(int id, int n, double *points) +{ + int m; + double *sxy; /* coords of the entire spline curve */ + m = (n-1)*nb+2; + sxy = (double *) g2_malloc(m*2*sizeof(double)); + + g2_c_para_3(n, points, sxy); + sxy[m+m-2] = points[n+n-2]; + sxy[m+m-1] = points[1]; + g2_filled_polygon(id, m, sxy); + + g2_free(sxy); +} + +/* + * FUNCTION: g2_c_para_5 + * + * As g2_c_para_3, but now plot a polynomial of degree 5 + */ + +/* + * #undef nb + * #define nb 40 + * Number of straight connecting lines of which each polynomial consists. + * So between one data point and the next, (nb-1) points are placed. + */ + +void g2_c_para_5(int n, const double *points, double *sxy) +{ +#undef dgr +#define dgr (5+1) +#define nb3 (nb*3) + int i, j; + double x1t, y1t; + double o, step; + double X[nb3]; /* x-coords of the current curve piece */ + double Y[nb3]; /* y-coords of the current curve piece */ + double t[dgr]; /* data point parameter values */ + double Xpts[dgr]; /* x-coords data point subsection */ + double Ypts[dgr]; /* y-coords data point subsection */ + double s[nb3]; /* parameter values at which to interpolate */ + + /* Do first THREE subintervals first */ + + g2_split(dgr, points, Xpts, Ypts); + + t[0] = 0.; + for (i = 1; i < dgr; i++) { + x1t = Xpts[i] - Xpts[i-1]; + y1t = Ypts[i] - Ypts[i-1]; + t[i] = t[i-1] + sqrt(x1t * x1t + y1t * y1t); + } + + step = t[3] / nb3; + for (i = 0; i < nb3; i++) s[i] = i * step; + + g2_c_newton(dgr, t, Xpts, nb3, s, X); + g2_c_newton(dgr, t, Ypts, nb3, s, Y); + for (i = 0; i < nb3; i++) { + sxy[i+i] = X[i]; + sxy[i+i+1] = Y[i]; + } + + /* Next, do later central subintervals */ + + for (j = 1; j < n - dgr + 1; j++) { + g2_split(dgr, points + j + j, Xpts, Ypts); + + for (i = 1; i < dgr; i++) { + x1t = Xpts[i] - Xpts[i-1]; + y1t = Ypts[i] - Ypts[i-1]; + t[i] = t[i-1] + sqrt(x1t * x1t + y1t * y1t); + } + + o = t[2]; /* look up once */ + step = (t[3] - o) / nb; + for (i = 0; i < nb; i++) s[i] = i * step + o; + + g2_c_newton(dgr, t, Xpts, nb, s, X); + g2_c_newton(dgr, t, Ypts, nb, s, Y); + + for (i = 0; i < nb; i++) { + sxy[(j + 2) * nb2 + i + i] = X[i]; + sxy[(j + 2) * nb2 + i + i + 1] = Y[i]; + } + } + + /* Now do last TWO subinterval */ + + o = t[3]; + step = (t[5] - o) / nb2; + for (i = 0; i < nb2; i++) s[i] = i * step + o; + + g2_c_newton(dgr, t, Xpts, nb2, s, X); + g2_c_newton(dgr, t, Ypts, nb2, s, Y); + + for (i = 0; i < nb2; i++) { + sxy[(n - dgr + 3) * nb2 + i + i] = X[i]; + sxy[(n - dgr + 3) * nb2 + i + i + 1] = Y[i]; + } + sxy[(n - 1) * nb2] = points[n+n-2]; + sxy[(n - 1) * nb2 + 1] = points[n+n-1]; +} + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + */ + +void g2_para_5(int id, int n, double *points) +{ + int m; + double *sxy; /* coords of the entire spline curve */ + m = (n-1)*nb+1; + sxy = (double *) g2_malloc(m*2*sizeof(double)); + + g2_c_para_5(n, points, sxy); + g2_poly_line(id, m, sxy); + + g2_free(sxy); +} + +/* + * FORMAL ARGUMENTS: + * + * id device id + * n number of data points + * points data points (x[i],y[i]) + */ + +void g2_filled_para_5(int id, int n, double *points) +{ + int m; + double *sxy; /* coords of the entire spline curve */ + m = (n-1)*nb+2; + sxy = (double *) g2_malloc(m*2*sizeof(double)); + + g2_c_para_5(n, points, sxy); + sxy[m+m-2] = points[n+n-2]; + sxy[m+m-1] = points[1]; + g2_filled_polygon(id, m, sxy); + + g2_free(sxy); +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_splines.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_splines.o new file mode 100755 index 000000000..67bdd5037 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_splines.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_control.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_control.c new file mode 100755 index 000000000..d7cdf598c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_control.c @@ -0,0 +1,612 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_control_pd.h" +#include "g2_util.h" + +/** + * \ingroup interface + * \defgroup color color manipulations + * + * The color concept used in the g2 library is inspired by Sir Clive + * Sinclair solution implemented in the ZX Spectrum computer. With the + * g2_pen() function it is possible to choose a pen created by the + * g2_ink() function. Note that g2_ink function is only defined for + * physical devices. The predefined colors (see g2_test demo program) + * have pens from 0 till 26 (inclusive). + * + * Some basic colors are: + * - 0 white + * - 1 black + * - 3 blue + * - 7 green + * - 19 red + * - 25 yellow + * + */ + + +/** + * \ingroup interface + * \defgroup control output control + */ + +/** + * + * Flush output buffers. + * + * \param dev device id + * + * \ingroup control + */ +void g2_flush(int dev) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_flush: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_flush_pd(devp->d.pd); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_flush(devp->d.vd->dix[i]); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Save output + * + * \param dev device id + * + * \ingroup control + */ +void g2_save(int dev) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_save: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_save_pd(devp->d.pd); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_save(devp->d.vd->dix[i]); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Clear device + * + * \param dev device number + * + * \ingroup control + */ +void g2_clear(int dev) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_clear: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_clear_pd(devp->d.pd); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_clear(devp->d.vd->dix[i]); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + +/** + * + * Set pen color for all following operations, see also g2_ink(). + * + * \param dev device + * \param color pen (either one of default pens 0-26, or a pen returned by g2_ink() ) + * + * \ingroup color + */ +void g2_pen(int dev, int color) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_pen: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_pen_pd(devp->d.pd, color); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_pen(devp->d.vd->dix[i], color); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Set the background color + * + * \param dev device + * \param color pen (either one of default pens 0-26, or a pen returned by g2_ink() ) + * + * \ingroup color + */ +void g2_set_background(int dev, int color) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_set_background: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_set_background_pd(devp->d.pd, color); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_set_background(devp->d.vd->dix[i], color); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Create an ink. To put ink into the pen use g2_pen(). + * + * \param pd_dev physical device + * \param red red component (0-1) according to the RGB color model + * \param green green component (0-1) according to the RGB color model + * \param blue blue component (0-1) according to the RGB color model + * \return new pen, see g2_pen() + * + * \ingroup color + */ +int g2_ink(int pd_dev, double red, double green, double blue) +{ + g2_device *devp; + int rv=-1; + + if((devp=g2_get_device_pointer(pd_dev))==NULL) { + fprintf(stderr, "g2_ink: No such device: %d\n", pd_dev); + return -1; + } + + if(red < 0.0) red=0.0; + if(green < 0.0) green=0.0; + if(blue < 0.0) blue=0.0; + if(red > 1.0) red=1.0; + if(green > 1.0) green=1.0; + if(blue > 1.0) blue=1.0; + + switch(devp->t) { + case g2_PD: + rv=g2_ink_pd(devp->d.pd, red, green, blue); + break; + case g2_VD: + fprintf(stderr, "g2_ink: g2_ink is enabled only for phys. devices\n"); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=pd_dev; + return rv; +} + + + +/** + * + * Clear collor palette (remove all inks) and reallocate basic colors. + * + * \param dev device + * + * \ingroup color + */ +void g2_reset_palette(int dev) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_reset_palette: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_clear_palette(dev); + g2_allocate_basic_colors(dev); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_reset_palette(devp->d.vd->dix[i]); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Remove all inks. + * + * \param dev device + * + * \ingroup color + */ +void g2_clear_palette(int dev) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_clear_palette: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_clear_palette_pd(devp->d.pd); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_clear_palette(devp->d.vd->dix[i]); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + +/** + * + * Allocate basic colors + * + * \param dev device + * + * \ingroup color + */ +void g2_allocate_basic_colors(int dev) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_allocate_basic_colors: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_allocate_basic_colors_pd(devp->d.pd); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_allocate_basic_colors(devp->d.vd->dix[i]); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + +/** + * + * Set font size + * + * \param dev device + * \param size new font size + * + * \ingroup control + */ +void g2_set_font_size(int dev, double size) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_set_font_size: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_set_font_size_pd(devp->d.pd, size); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_set_font_size(devp->d.vd->dix[i], size); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Set line width. + * + * \param dev device + * \param w new line width + * + * \ingroup control + */ +void g2_set_line_width(int dev, double w) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_set_line_width: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_set_line_width_pd(devp->d.pd, w); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_set_line_width(devp->d.vd->dix[i], w); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Set line dash. Set \a N to 0 and \a dashes to NULL to restore solid line. + * + * \param dev device + * \param N number of dash components (0 for solid line) + * \param dashes vector of dash lengths (black, white, black, ...) + * + * \ingroup control + */ +void g2_set_dash(int dev, int N, double *dashes) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_set_dash: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_set_dash_pd(devp->d.pd, N, dashes); + break; + + case g2_VD: + for(i=0;id.vd->N;i++) + g2_set_dash(devp->d.vd->dix[i], N, dashes); + break; + + case g2_ILLEGAL: + break; + + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Set QuasiPixel size and shape. + * + * \param dev device + * \param d size + * \param shape shape (rectangle or circle, see ::QPshape ) + * + * \ingroup control + */ +void g2_set_QP(int dev, double d, enum QPshape shape) +{ + g2_device *devp; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_set_QP: No such device: %d\n", dev); + return; + } + + devp->QPd=d; + devp->QPshape=shape; + + __g2_last_device=dev; +} + + +/** + * + * Query pointer (e.g. mouse for X11) position and button state. See + * the demo program pointer.c for an example. + * + * \param dev device + * \param x returns pointer x coordinate + * \param y returns pointer y coordinate + * \param button returns button state + * + * \ingroup control + */ +void g2_query_pointer(int dev, double *x, double *y, unsigned int *button) +{ + g2_device *devp; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_query_pointer: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_query_pointer_pd(devp->d.pd, x, y, button); + break; + case g2_VD: + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Get pointers to physical device specific handles. This function + * should be used only if you are familiar with the g2 source code. + * For details see physical device source code (e.g. in src/X11/). + * Example usage can be found in demo/handles.c. + * + * \param pd physical device + * \param handles returns pointers to physical device low level handles + * + * \ingroup control + */ +void g2_get_pd_handles(int pd, void *handles[G2_PD_HANDLES_SIZE]) +{ + g2_device *devp; + int i; + + for(i=0;it) { + case g2_PD: + g2_get_pd_handles_pd(devp->d.pd, handles); + break; + case g2_VD: + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_control.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_control.o new file mode 100755 index 000000000..979b640a1 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_control.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_device.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_device.c new file mode 100755 index 000000000..418b4ed83 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_device.c @@ -0,0 +1,196 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include + +#include "g2.h" +#include "g2_funix.h" +#include "g2_device.h" +#include "g2_util.h" + +/** + * \ingroup interface + * \defgroup device devices control + */ + + +/** + * + * Close and delete a device. + * + * \param dev device + * + * \ingroup device + */ +void g2_close(int dev) +{ + g2_device *devp; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_close: Warning! No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + devp->d.pd->ff[g2_Delete].fun(devp->d.pd->pid, + devp->d.pd->pdp); + break; + case g2_VD: + while(devp->d.vd->N>0) /* close all devices */ + g2_close(devp->d.vd->dix[devp->d.vd->N-1]); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + g2_destroy_device(dev); /* destroy device */ +} + + +/** + * + * Set auto flush mode for device \a dev. Auto flush mode means that after each graphical + * operation g2 library automatically calls flush function to ensure that output is realy + * displayed. However, freqent flushing decreases performance. Alternative is to flush + * output when needed by calling g2_flush function. + * + * \param dev device + * \param on_off 1-on 0-off + * + * \ingroup device + */ +void g2_set_auto_flush(int dev, int on_off) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + g2_log(Error, "g2: Error! g2_set_auto_flush: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + break; + case g2_VD: + for(i=0;id.vd->N;i++) { + g2_set_auto_flush(devp->d.vd->dix[i], on_off); + } + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + devp->auto_flush=on_off; /* set auto flush for all (vd and pd) devices */ + __g2_last_device=dev; +} + + +/** + * + * Set the user coordinate system. + * + * \param dev device + * \param x_origin x coordinate of the new origin (expressed in the default coordinate system) + * \param y_origin x coordinate of the new origin (expressed in the default coordinate system) + * \param x_mul x scaling factor + * \param y_mul y scaling factor + * + * \ingroup device + */ +void g2_set_coordinate_system(int dev, + double x_origin, double y_origin, + double x_mul, double y_mul) +{ + g2_device *devp; + int i; + + if(x_mul==0.0 || y_mul==0.0) { + fprintf(stderr, + "g2_set_coordinate_system: Error! Multiplicator can not be 0.0"); + return; + } + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, + "g2_set_coordinate_system: Warning! No such device: %d\n", + dev); + return; + } + + switch(devp->t) { + case g2_PD: + devp->d.pd->x_origin=x_origin; + devp->d.pd->y_origin=y_origin; + devp->d.pd->x_mul=x_mul; + devp->d.pd->y_mul=y_mul; + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_set_coordinate_system(devp->d.vd->dix[i], + x_origin, y_origin, + x_mul, y_mul); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Get the last accessed device. G2LD macro is defined as the g2_ld function. + * + * \code + * g2_open_X11(100, 100); + * g2_plot(G2LD, 50, 50); + * \endcode + * + * \ingroup device + */ +int g2_ld(void) +{ + return __g2_last_device; +} + + + +/** + * + * Set the last accessed device. See also g2_ld() function. + * + * \param dev device + * + * \ingroup device + */ +void g2_set_ld(int dev) +{ + if(!g2_device_exist(dev)) { + fprintf(stderr, "g2_set_lsd: Warning! No such device: %d\n", dev); + return; + } + __g2_last_device=dev; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_device.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_device.o new file mode 100755 index 000000000..3091c62a1 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_device.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_graphic.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_graphic.c new file mode 100755 index 000000000..f8e1c015c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_graphic.c @@ -0,0 +1,1045 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include + +#include "g2_device.h" +#include "g2_graphic_pd.h" +#include "g2_util.h" + +/** + * \ingroup interface + * \defgroup graphic graphical output + */ + +/** + * + * Move graphic cursor. + * + * \param dev device + * \param x x coordinate + * \param y y coordinate + * + * \ingroup graphic + */ +void g2_move(int dev, double x, double y) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_move: No such device: %d\n", dev); + return; + } + + devp->x=x; /* set graph. cursor */ + devp->y=y; + + switch(devp->t) { + case g2_PD: + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_move(devp->d.vd->dix[i], x, y); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Move graphic cursor relative to the currner graphical cursor position. + * + * \param dev device + * \param dx x coordinate increment + * \param dy y coordinate increment + * + * \ingroup graphic + */ +void g2_move_r(int dev, double dx, double dy) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_move_r: No such device: %d\n", dev); + return; + } + + devp->x+=dx; /* set graph. cursor */ + devp->y+=dy; + + switch(devp->t) { + case g2_PD: + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_move_r(devp->d.vd->dix[i], dx, dy); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + __g2_last_device=dev; +} + + + +/** + * + * Plot a point + * + * \param dev device + * \param x x coordinate + * \param y y coordinate + * + * \ingroup graphic + */ +void g2_plot(int dev, double x, double y) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_plot: No such device: %d\n", dev); + return; + } + + devp->x=x; /* set graph. cursor */ + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_plot_pd(devp->d.pd, x, y); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_plot(devp->d.vd->dix[i], x, y); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Plot a point relative to graphical cursor. + * + * \param dev device + * \param rx relative x coordinate + * \param ry relative y coordinate + * + * \ingroup graphic + */ +void g2_plot_r(int dev, double rx, double ry) +{ + g2_device *devp; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_plot_r: No such device: %d\n", dev); + return; + } + + g2_plot(dev, devp->x+rx, devp->y+ry); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a line from \p x1, \p y1 to \p x2, \p y2. + * + * \param dev device + * \param x1 see above + * \param y1 see above + * \param x2 see above + * \param y2 see above + * + * \ingroup graphic + */ +void g2_line(int dev, double x1, double y1, double x2, double y2) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_line: No such device: %d\n", dev); + return; + } + + devp->x=x2; + devp->y=y2; + + switch(devp->t) { + case g2_PD: + g2_line_pd(devp->d.pd, x1, y1, x2, y2); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_line(devp->d.vd->dix[i], x1, y1, x2, y2); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw line relative to the graphic cursor. + * + * \param dev device + * \param dx relative x coordinate + * \param dy relative y coordinate + * + * \ingroup graphic + */ +void g2_line_r(int dev, double dx, double dy) +{ + g2_device *devp; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_line_r: No such device: %d\n", dev); + return; + } + g2_line(dev, devp->x, devp->y, devp->x+dx, devp->y+dy); + + __g2_last_device=dev; +} + + + +/** + * + * Draw line from graphic cursor to the point \a x, \a y + * + * \param dev device + * \param x x coordinate + * \param y y coordinate + * + * \ingroup graphic + */ +void g2_line_to(int dev, double x, double y) +{ + g2_device *devp; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_line_to: No such device: %d\n", dev); + return; + } + g2_line(dev, devp->x, devp->y, x, y); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a poly line. + * + * \param dev device + * \param N_pt number of points (Note: It is not size of \a points vector!) + * \param points vector of coordinates: x1, y1, x2, y2, ... + * + * \ingroup graphic + */ +void g2_poly_line(int dev, int N_pt, double *points) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_poly_line: No such device: %d\n", dev); + return; + } + + devp->x=points[2*(N_pt-1)+0]; + devp->y=points[2*(N_pt-1)+1]; + + switch(devp->t) { + case g2_PD: + g2_poly_line_pd(devp->d.pd, N_pt, points); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_poly_line(devp->d.vd->dix[i], N_pt, points); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a triangle described by 3 corner points. + * + * \param dev device + * \param x1 x coordinate of the 1st corner + * \param y1 y coordinate of the 1st corner + * \param x2 x coordinate of the 2nd corner + * \param y2 y coordinate of the 2nd corner + * \param x3 x coordinate of the 3rd corner + * \param y3 y coordinate of the 3rd corner + * + * \ingroup graphic + */ +void g2_triangle(int dev, + double x1, double y1, + double x2, double y2, + double x3, double y3) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_triangle: No such device: %d\n", dev); + return; + } + + devp->x=x3; + devp->y=y3; + + switch(devp->t) { + case g2_PD: + g2_triangle_pd(devp->d.pd, + x1, y1, + x2, y2, + x3, y3); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_triangle(devp->d.vd->dix[i], x1, y1, x2, y2, x3, y3); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a filled triangle specified by the 3 corner points. + * + * \param dev device + * \param x1 x coordinate of the 1st corner + * \param y1 y coordinate of the 1st corner + * \param x2 x coordinate of the 2nd corner + * \param y2 y coordinate of the 2nd corner + * \param x3 x coordinate of the 3rd corner + * \param y3 y coordinate of the 3rd corner + * + * \ingroup graphic + */ +void g2_filled_triangle(int dev, + double x1, double y1, + double x2, double y2, + double x3, double y3) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_filled_triangle: No such device: %d\n", dev); + return; + } + + devp->x=x3; + devp->y=y3; + + switch(devp->t) { + case g2_PD: + g2_filled_triangle_pd(devp->d.pd, + x1, y1, + x2, y2, + x3, y3); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_filled_triangle(devp->d.vd->dix[i], x1, y1, x2, y2, x3, y3); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a rectangle specified by the two opposite corner points. + * + * \param dev device + * \param x1 x coordinate of the 1st corner + * \param y1 y coordinate of the 1st corner + * \param x2 x coordinate of the 3rd corner + * \param y2 y coordinate of the 3rd corner + * + * \ingroup graphic + */ +void g2_rectangle(int dev, double x1, double y1, double x2, double y2) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_rectangle: No such device: %d\n", dev); + return; + } + + devp->x=x2; + devp->y=y2; + + switch(devp->t) { + case g2_PD: + g2_rectangle_pd(devp->d.pd, x1, y1, x2, y2); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_rectangle(devp->d.vd->dix[i], x1, y1, x2, y2); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a filled rectangle specified by the two opposite corner points. + * + * \param dev device + * \param x1 x coordinate of the 1st corner + * \param y1 y coordinate of the 1st corner + * \param x2 x coordinate of the 3rd corner + * \param y2 y coordinate of the 3rd corner + * + * \ingroup graphic + */ +void g2_filled_rectangle(int dev, double x1, double y1, double x2, double y2) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_filled_rectangle: No such device: %d\n", dev); + return; + } + + devp->x=x2; + devp->y=y2; + + switch(devp->t) { + case g2_PD: + g2_filled_rectangle_pd(devp->d.pd, x1, y1, x2, y2); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_filled_rectangle(devp->d.vd->dix[i], x1, y1, x2, y2); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a polygon. + * + * \param dev device + * \param N_pt number of points (Note: It is not size of \a points vector!) + * \param points vector of coordinates: x1, y1, x2, y2, ... + * + * \ingroup graphic + */ +void g2_polygon(int dev, int N_pt, double *points) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_polygon: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_polygon_pd(devp->d.pd, N_pt, points); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_polygon(devp->d.vd->dix[i], N_pt, points); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a filled polygon. + * + * \param dev device + * \param N_pt number of points (Note: It is not size of \a points vector!) + * \param points vector of coordinates: x1, y1, x2, y2, ... + * + * \ingroup graphic + */ +void g2_filled_polygon(int dev, int N_pt, double *points) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_filled_polygon: No such device: %d\n", dev); + return; + } + + switch(devp->t) { + case g2_PD: + g2_filled_polygon_pd(devp->d.pd, N_pt, points); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_filled_polygon(devp->d.vd->dix[i], N_pt, points); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw an ellipse. + * + * \param dev device + * \param x x coordinate of the center + * \param y y coordinate of the center + * \param r1 x radius + * \param r2 y radius + * + * \ingroup graphic + */ +void g2_ellipse(int dev, double x, double y, double r1, double r2) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_ellipse: No such device: %d\n", dev); + return; + } + + devp->x=x; + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_ellipse_pd(devp->d.pd, x, y, r1, r2); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_ellipse(devp->d.vd->dix[i], x, y, r1, r2); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a filled ellipse. + * + * \param dev device + * \param x x coordinate of the center + * \param y y coordinate of the center + * \param r1 x radius + * \param r2 y radius + * + * \ingroup graphic + */ +void g2_filled_ellipse(int dev, double x, double y, double r1, double r2) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_filled_ellipse: No such device: %d\n", dev); + return; + } + + devp->x=x; + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_filled_ellipse_pd(devp->d.pd, x, y, r1, r2); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_filled_ellipse(devp->d.vd->dix[i], x, y, r1, r2); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a circle. + * + * \param dev device + * \param x x coordinate of the center + * \param y y coordinate of the center + * \param r radius + * + * \ingroup graphic + */ +void g2_circle(int dev, double x, double y, double r) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_circle: No such device: %d\n", dev); + return; + } + + devp->x=x; + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_circle_pd(devp->d.pd, x, y, r); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_circle(devp->d.vd->dix[i], x, y, r); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a filled circle. + * + * \param dev device + * \param x x coordinate of the center + * \param y y coordinate of the center + * \param r radius + * + * \ingroup graphic + */ +void g2_filled_circle(int dev, double x, double y, double r) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_filled_circle: No such device: %d\n", dev); + return; + } + + devp->x=x; + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_filled_circle_pd(devp->d.pd, x, y, r); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_filled_circle(devp->d.vd->dix[i], x, y, r); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw an arc. + * + * \param dev device + * \param x x coordinate of the center + * \param y y coordinate of the center + * \param r1 x radius + * \param r2 y radius + * \param a1 starting angle (in deg. 0-360) + * \param a2 ending angle (in deg. 0-360) + * + * \ingroup graphic + */ +void g2_arc(int dev, + double x, double y, + double r1, double r2, + double a1, double a2) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_arc: No such device: %d\n", dev); + return; + } + + devp->x=x; + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_arc_pd(devp->d.pd, x, y, r1, r2, a1, a2); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_arc(devp->d.vd->dix[i], x, y, r1, r2, a1, a2); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a filled arc. + * + * \param dev device + * \param x x coordinate of the center + * \param y y coordinate of the center + * \param r1 x radius + * \param r2 y radius + * \param a1 starting angle (in deg. 0-360) + * \param a2 ending angle (in deg. 0-360) + * + * \ingroup graphic + */ +void g2_filled_arc(int dev, + double x, double y, + double r1, double r2, + double a1, double a2) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_filled_arc: No such device: %d\n", dev); + return; + } + + devp->x=x; + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_filled_arc_pd(devp->d.pd, x, y, r1, r2, a1, a2); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_filled_arc(devp->d.vd->dix[i], x, y, r1, r2, a1, a2); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw string, see also g2_set_font_size(). + * + * \param dev device + * \param x x coordinate + * \param y y coordinate + * \param text null terminated string + * + * \ingroup graphic + */ +void g2_string(int dev, double x, double y, const char *text) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_string: No such device: %d\n", dev); + return; + } + + devp->x=x; + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_string_pd(devp->d.pd, x, y, text); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_string(devp->d.vd->dix[i], x, y, text); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Draw a pen image + * + * \param dev device + * \param x x coordinate + * \param y y coordinate + * \param x_size x size + * \param y_size y size + * \param pens vector of x_size*y_size pens: p11, p21, ... pxy, ... + * + * \ingroup graphic + */ +void g2_image(int dev, double x, double y, int x_size, int y_size, int *pens) +{ + g2_device *devp; + int i; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_image: No such device: %d\n", dev); + return; + } + + devp->x=x; + devp->y=y; + + switch(devp->t) { + case g2_PD: + g2_image_pd(devp->d.pd, x, y, x_size, y_size, pens); + break; + case g2_VD: + for(i=0;id.vd->N;i++) + g2_image(devp->d.vd->dix[i], x, y, x_size, y_size, pens); + break; + case g2_ILLEGAL: + break; + case g2_NDEV: + break; + } + + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + +/** + * + * Quasi Pixel fake. Quasi pixel is introduced to make easier + * plotting of cellular automata and related pictures. QP is simple a big pixel as + * specified by g2_set_QP(). Coordinates are skaled accordingly, so no recalculation + * is needed on client side. + * + * \param dev device + * \param x x coordinate + * \param y y coordinate + * + * \ingroup graphic + */ +void g2_plot_QP(int dev, double x, double y) +{ + g2_device *devp; + double d; + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_plot_QP: No such device: %d\n", dev); + return; + } + + x=dtoi(x); + y=dtoi(y); + d=devp->QPd; + switch(devp->QPshape) { + case QPrect: + g2_filled_rectangle(dev, x*d-d/2, y*d-d/2, x*d+d/2, y*d+d/2); + break; + case QPcirc: + g2_filled_circle(dev, x*d, y*d, d/2.0); + break; + default: + fprintf(stderr, "g2: QP: unknown shape\n"); + break; + } + if(devp->auto_flush) + g2_flush(dev); + + __g2_last_device=dev; +} + + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_graphic.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_graphic.o new file mode 100755 index 000000000..04cabbe21 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_graphic.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_virtual_device.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_virtual_device.c new file mode 100755 index 000000000..2cdc820e1 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_virtual_device.c @@ -0,0 +1,149 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include + +#include "g2.h" +#include "g2_device.h" +#include "g2_virtual_device.h" +#include "g2_util.h" + +/** + * \ingroup interface + * \defgroup vd virtual device related functions + * + * Virtual device is a method to redirect g2 output to multiple devices. Here is an example: + * + * \code + * int d1 = g2_open_X11(100, 100); create first X11 window + * int d2 = g2_open_X11(100, 100); create 2nd X11 window + * + * int vd = g2_open_vd(); open a new virtual device + * + * g2_attach(vd, d1); attach d1 (1st window) to virtual device + * g2_attach(vd, d2); attach d2 (2nd window) to virtual device + * + * g2_plot(d1, 11, 11); output to the 1st X11 window + * g2_plot(d2, 12, 12); output to the 2nd X11 window + * g2_plot(vd, 13, 13); output to both X11 windows + * \endcode + * + */ + + + +/** + * + * Create a new virtual device. + * + * \return virtual device ID + * + * \ingroup vd + */ +int g2_open_vd(void) +{ + int dix; + dix=g2_register_virtual_device(); + __g2_last_device=dix; + return dix; +} + + +/** + * Attach a device to virtual device \a vd_dev. + * + * \param vd_dev virtual device (create virtual device by calling g2_open_vd() ) + * \param dev device + * + * \ingroup vd + */ +void g2_attach(int vd_dev, int dev) +{ + g2_device *vd_devp, *devp; + + if((vd_devp=g2_get_device_pointer(vd_dev))==NULL) { + fprintf(stderr, "g2_attach: No such device: %d\n", vd_dev); + return; + } + + if((devp=g2_get_device_pointer(dev))==NULL) { + fprintf(stderr, "g2_attach: No such device: %d\n", dev); + return; + } + + if(vd_devp->t!=g2_VD) { + fprintf(stderr, "g2_attach: Device %d is not virtual.\n", vd_dev); + return; + } + + if(devp->t==g2_VD) /* if virtual device */ + if(g2_is_attached(dev, vd_dev)) { /* check recurency */ + fprintf(stderr, + "g2_attach: Device %d is already attached to %d.\n", + dev, vd_dev); + return; + } + + vd_devp->d.vd->N++; + vd_devp->d.vd->dix=g2_realloc(vd_devp->d.vd->dix, + vd_devp->d.vd->N*sizeof(int)); + + vd_devp->d.vd->dix[vd_devp->d.vd->N-1]=dev; + + __g2_last_device=vd_dev; +} + + +/** + * + * Dettach a device from the virtual device \a vd_dev. + * + * \param vd_dev virtual device + * \param dev device + * + * \ingroup vd + */ +void g2_detach(int vd_dev, int dev) +{ + g2_device *vd_devp; + int i; + + if((vd_devp=g2_get_device_pointer(vd_dev))==NULL) { + fprintf(stderr, "g2_detach: No such device: %d\n", vd_dev); + return; + } + + if(vd_devp->t!=g2_VD) { + fprintf(stderr, "g2_detach: Device %d is not virtual.\n", vd_dev); + return; + } + + for(i=0;id.vd->N;i++) + if(vd_devp->d.vd->dix[i]==dev) { + if(vd_devp->d.vd->N>1) + vd_devp->d.vd->dix[i]=vd_devp->d.vd->dix[vd_devp->d.vd->N-1]; + vd_devp->d.vd->N--; + if(vd_devp->d.vd->N!=0) + vd_devp->d.vd->dix=g2_realloc(vd_devp->d.vd->dix, + vd_devp->d.vd->N*sizeof(int)); + return; + } + + __g2_last_device=vd_dev; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_virtual_device.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_virtual_device.o new file mode 100755 index 000000000..e498a8d38 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_ui_virtual_device.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.c new file mode 100755 index 000000000..00f04e6ce --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.c @@ -0,0 +1,224 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include +#include +#include + +#include "g2_util.h" +#include "g2_physical_device.h" +#include "g2_config.h" + + +/* + * + * Double to integer + * + */ +int dtoi(double x) +{ + return (int)(x+0.5); +} + + + +/* + * + * Transform user coord. in physical device coord (int) + * + */ +void g2_uc2pdc_int(g2_physical_device *pd, double x, double y, + int *ix, int *iy) +{ + double vx, vy; + + vx=pd->x_mul*x+pd->x_origin; + vy=pd->y_mul*y+pd->y_origin; + + *ix = dtoi(pd->a11*vx + pd->b1); + *iy = dtoi(pd->a22*vy + pd->b2); +} + + +/* + * + * Transform user coord. in physical device coord (double) + * + */ +void g2_uc2pdc_double(g2_physical_device *pd, double x, double y, + double *dx, double *dy) +{ + double vx, vy; + + vx=pd->x_mul*x+pd->x_origin; + vy=pd->y_mul*y+pd->y_origin; + + *dx = pd->a11*vx + pd->b1; + *dy = pd->a22*vy + pd->b2; +} + + +/* + * + * Transform user size in physical device size (int) + * + */ +void g2_us2pds_int(g2_physical_device *pd, double x, double y, + int *ix, int *iy) +{ + if(ix!=NULL) + *ix=dtoi(x*fabs(pd->x_mul*pd->a11)); + if(iy!=NULL) + *iy=dtoi(y*fabs(pd->y_mul*pd->a22)); +} + + +/* + * + * Transform user size in physical device size (double) + * + */ +void g2_us2pds_double(g2_physical_device *pd, double x, double y, + double *dx, double *dy) +{ + if(dx!=NULL) + *dx=x*fabs(pd->x_mul*pd->a11); + if(dy!=NULL) + *dy=y*fabs(pd->y_mul*pd->a22); +} + + +/* + * + * Transform physical device coord in user coord + * + */ +void g2_pdc2uc(g2_physical_device *pd, double ix, double iy, + double *x, double *y) +{ + double pcx, pcy; + pcx=(ix-pd->b1)/pd->a11; + pcy=(iy-pd->b2)/pd->a22; + + *x=(pcx-pd->x_origin)/pd->x_mul; + *y=(pcy-pd->y_origin)/pd->y_mul; +} + + +/* + * return a < b + */ +void g2_sort2_i(int *a, int *b) +{ + if(*a>*b) { + int t=*a; + *a=*b; *b=t; + } +} + +void g2_sort2_d(double *a, double *b) +{ + if(*a>*b) { + double t=*a; + *a=*b; *b=t; + } +} + + + +/* + * + * g2 malloc (with error message) + * + */ +void *g2_malloc(size_t size) +{ + void *rv; + + if((rv=malloc(size))==NULL) { + fprintf(stderr, "g2_malloc: Can not allocate memory\n"); + exit(-1); + } + + return rv; +} + + +/* + * + * g2 realloc (with error message) + * + */ +void *g2_realloc(void *p, size_t size) +{ + void *rv; + if((rv=realloc(p, size))==NULL) { + fprintf(stderr, "g2_realloc: Can not allocate memory\n"); + exit(-1); + } + return rv; +} + + + +/* + * + * g2 free + * + */ +void g2_free(void *p) +{ + if(p!=NULL) + free(p); +} + + +/* + * + * transform float* to double* for N elements + * + * Note: don't forget to free d + * + */ +double *g2_floatp2doublep(float *f, int N) +{ + int i; + double *d; + d=(double *)g2_malloc(N*sizeof(double)); + for(i=0;i g2_LogLevel) { + return; + } + va_start(arg, format); + vfprintf(stderr, format, arg); + va_end(arg); +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.h new file mode 100755 index 000000000..736cb565d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.h @@ -0,0 +1,48 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_UTIL_H +#define _G2_UTIL_H + +#include +#include "g2_physical_device.h" + +int dtoi(double x); + +void g2_uc2pdc_int(g2_physical_device *pd, double x, double y, + int *ix, int *iy); +void g2_uc2pdc_double(g2_physical_device *pd, double x, double y, + double *dx, double *dy); +void g2_us2pds_int(g2_physical_device *pd, double x, double y, + int *ix, int *iy); +void g2_us2pds_double(g2_physical_device *pd, double x, double y, + double *dx, double *dy); +void g2_pdc2uc(g2_physical_device *pd, double ix, double iy, + double *x, double *y); +void g2_sort2_i(int *a, int *b); +void g2_sort2_d(double *a, double *b); +void *g2_malloc(size_t size); +void *g2_realloc(void *p, size_t size); +void g2_free(void *p); + +double *g2_floatp2doublep(float *f, int N); + +enum g2_log_level {Error=1, Warning, Verbose, Debug}; +void g2_log(enum g2_log_level log_level, const char *format, ...); + +#endif /* _G2_UTIL_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.o new file mode 100755 index 000000000..39088cea0 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_util.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.c new file mode 100755 index 000000000..918c79cc9 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.c @@ -0,0 +1,82 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#include +#include "g2_virtual_device.h" +#include "g2_device.h" +#include "g2_util.h" + + +/* + * + */ +g2_virtual_device *g2_create_virtual_device() +{ + g2_virtual_device *rd; + + rd=g2_malloc(sizeof(g2_virtual_device)); + rd->N=0; + rd->dix=g2_malloc(sizeof(int)); /* later we use realloc */ + return rd; +} + + +/* + * + */ +void g2_destroy_virtual_device(g2_virtual_device *vd) +{ + g2_free(vd->dix); + g2_free(vd); +} + + + +/* + * Return 1 if dev is attached to vd + */ +int g2_is_attached(int vd, int dev) +{ + g2_device *vdp, *devp; + int i; + + if(vd==dev) + return 1; + + if((devp=g2_get_device_pointer(dev))==NULL) + return 0; + + if((vdp=g2_get_device_pointer(vd))==NULL) + return 0; + + if(devp==vdp) + return 1; + + if(vdp->t!=g2_VD) + return 0; + + for(i=0;id.vd->N;i++) { + if(vdp->d.vd->dix[i]==dev) + return 1; + if(g2_is_attached(vdp->d.vd->dix[i], dev)) + return 1; + } + + return 0; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.h new file mode 100755 index 000000000..16fb6a798 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.h @@ -0,0 +1,32 @@ +/***************************************************************************** +** Copyright (C) 1998-2001 Ljubomir Milanovic & Horst Wagner +** This file is part of the g2 library +** +** This library is free software; you can redistribute it and/or +** modify it under the terms of the GNU Lesser General Public +** License as published by the Free Software Foundation; either +** version 2.1 of the License, or (at your option) any later version. +** +** This library is distributed in the hope that it will be useful, +** but WITHOUT ANY WARRANTY; without even the implied warranty of +** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +** Lesser General Public License for more details. +** +** You should have received a copy of the GNU Lesser General Public +** License along with this library; if not, write to the Free Software +** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +******************************************************************************/ +#ifndef _G2_VIRTUAL_DEVICE_H +#define _G2_VIRTUAL_DEVICE_H + +typedef struct _g2_virtual_device { + int N; /* number of attached devices */ + int *dix; /* index of attached devices */ +} g2_virtual_device; + + +g2_virtual_device *g2_create_virtual_device(); +void g2_destroy_virtual_device(g2_virtual_device *vd); +int g2_is_attached(int vd, int dev); + +#endif /* _G2_VIRTUAL_DEVICE_H */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.o new file mode 100755 index 000000000..b46783b63 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/g2-0.70/src/g2_virtual_device.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/install-sh b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/install-sh new file mode 100755 index 000000000..11870f1b0 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/install-sh @@ -0,0 +1,251 @@ +#!/bin/sh +# +# install - install a program, script, or datafile +# This comes from X11R5 (mit/util/scripts/install.sh). +# +# Copyright 1991 by the Massachusetts Institute of Technology +# +# Permission to use, copy, modify, distribute, and sell this software and its +# documentation for any purpose is hereby granted without fee, provided that +# the above copyright notice appear in all copies and that both that +# copyright notice and this permission notice appear in supporting +# documentation, and that the name of M.I.T. not be used in advertising or +# publicity pertaining to distribution of the software without specific, +# written prior permission. M.I.T. makes no representations about the +# suitability of this software for any purpose. It is provided "as is" +# without express or implied warranty. +# +# Calling this script install-sh is preferred over install.sh, to prevent +# `make' implicit rules from creating a file called install from it +# when there is no Makefile. +# +# This script is compatible with the BSD install script, but was written +# from scratch. It can only install one file at a time, a restriction +# shared with many OS's install programs. + + +# set DOITPROG to echo to test this script + +# Don't use :- since 4.3BSD and earlier shells don't like it. +doit="${DOITPROG-}" + + +# put in absolute paths if you don't have them in your path; or use env. vars. + +mvprog="${MVPROG-mv}" +cpprog="${CPPROG-cp}" +chmodprog="${CHMODPROG-chmod}" +chownprog="${CHOWNPROG-chown}" +chgrpprog="${CHGRPPROG-chgrp}" +stripprog="${STRIPPROG-strip}" +rmprog="${RMPROG-rm}" +mkdirprog="${MKDIRPROG-mkdir}" + +transformbasename="" +transform_arg="" +instcmd="$mvprog" +chmodcmd="$chmodprog 0755" +chowncmd="" +chgrpcmd="" +stripcmd="" +rmcmd="$rmprog -f" +mvcmd="$mvprog" +src="" +dst="" +dir_arg="" + +while [ x"$1" != x ]; do + case $1 in + -c) instcmd="$cpprog" + shift + continue;; + + -d) dir_arg=true + shift + continue;; + + -m) chmodcmd="$chmodprog $2" + shift + shift + continue;; + + -o) chowncmd="$chownprog $2" + shift + shift + continue;; + + -g) chgrpcmd="$chgrpprog $2" + shift + shift + continue;; + + -s) stripcmd="$stripprog" + shift + continue;; + + -t=*) transformarg=`echo $1 | sed 's/-t=//'` + shift + continue;; + + -b=*) transformbasename=`echo $1 | sed 's/-b=//'` + shift + continue;; + + *) if [ x"$src" = x ] + then + src=$1 + else + # this colon is to work around a 386BSD /bin/sh bug + : + dst=$1 + fi + shift + continue;; + esac +done + +if [ x"$src" = x ] +then + echo "install: no input file specified" + exit 1 +else + : +fi + +if [ x"$dir_arg" != x ]; then + dst=$src + src="" + + if [ -d $dst ]; then + instcmd=: + chmodcmd="" + else + instcmd=$mkdirprog + fi +else + +# Waiting for this to be detected by the "$instcmd $src $dsttmp" command +# might cause directories to be created, which would be especially bad +# if $src (and thus $dsttmp) contains '*'. + + if [ -f "$src" ] || [ -d "$src" ] + then + : + else + echo "install: $src does not exist" + exit 1 + fi + + if [ x"$dst" = x ] + then + echo "install: no destination specified" + exit 1 + else + : + fi + +# If destination is a directory, append the input filename; if your system +# does not like double slashes in filenames, you may need to add some logic + + if [ -d $dst ] + then + dst="$dst"/`basename $src` + else + : + fi +fi + +## this sed command emulates the dirname command +dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'` + +# Make sure that the destination directory exists. +# this part is taken from Noah Friedman's mkinstalldirs script + +# Skip lots of stat calls in the usual case. +if [ ! -d "$dstdir" ]; then +defaultIFS=' + ' +IFS="${IFS-${defaultIFS}}" + +oIFS="${IFS}" +# Some sh's can't handle IFS=/ for some reason. +IFS='%' +set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'` +IFS="${oIFS}" + +pathcomp='' + +while [ $# -ne 0 ] ; do + pathcomp="${pathcomp}${1}" + shift + + if [ ! -d "${pathcomp}" ] ; + then + $mkdirprog "${pathcomp}" + else + : + fi + + pathcomp="${pathcomp}/" +done +fi + +if [ x"$dir_arg" != x ] +then + $doit $instcmd $dst && + + if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else : ; fi && + if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else : ; fi && + if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else : ; fi && + if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else : ; fi +else + +# If we're going to rename the final executable, determine the name now. + + if [ x"$transformarg" = x ] + then + dstfile=`basename $dst` + else + dstfile=`basename $dst $transformbasename | + sed $transformarg`$transformbasename + fi + +# don't allow the sed command to completely eliminate the filename + + if [ x"$dstfile" = x ] + then + dstfile=`basename $dst` + else + : + fi + +# Make a temp file name in the proper directory. + + dsttmp=$dstdir/#inst.$$# + +# Move or copy the file name to the temp name + + $doit $instcmd $src $dsttmp && + + trap "rm -f ${dsttmp}" 0 && + +# and set any options; do chmod last to preserve setuid bits + +# If any of these fail, we abort the whole thing. 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The pairwise model +is based on the following edit operations on sequence and structure: + +.br +\fIbasepair replacement/match:\fP A basepair, INCLUDING the paired bases, is substituted by another basepair. +The scoring contribution is p_m. +.br +\fIbasepair bond deletion:\fP A basepair bond WITHOUT the paired bases is removed. The scoring contribution is p_d. +.br +\fISequence edit operations:\fP Base match/mismatch and base deletion give the scoring contributions b_m and b_d, respectively. +.br + +In the multiple alignment mode (-m), parameter p_m is the score for matching a basepair bond WITHOUT the paired bases. +Thus, the score for a whole basepair replacement is p_m+2*b_m. For more information about multiple alignment refer to +the description of parameter -m. + +.SS Input +RNAforester reads RNA secondary structures from stdin by default. +It accepts sequences and structures in Fasta format, where matching brackets symbolize base +pairs and unpaired bases are represented by a dot. A line containing the primary sequence +can precede the RNA secondary structure(s). An example is given below: +.br + + > test + accaguuacccauucgggaaccggu primary structure + .((..(((...)))..((..)))). secondary structure +.br + +All characters after a "blank" are ignored and all '-' characters are removed. +The program will continue to read new +structures until a line consisting of the single character @ or an end of file +is encountered. Input lines starting with > can contain a structure name. + +Option -f=filename let RNAforester read the input from file. Results files +are then written to files prefixed by filename. + +.SS Output +Alignments in ASCII format are written to stdout. Option -2d generates postscript +drawings of structure alignments. + +.SH Options + +.TP +\fB-d\fP +Calculate distance instead of similarity. In contrast to similarity, scoring contributions are minimized. +The scoring parameters must not be negative and equal structures achieve a distance of zero. This +parameter can not be used in conjunction with multiple alignment, where relative similarity is computed. + +.TP +\fB-r\fP +Calculate relative score, defined by sr(a,b)=2*s(a,b)/(s(a,a)+s(b,b). +Relative scores are upper bounded by 1 which is the score for equal structures. + +.TP +\fB-l\fP +Calculate local similar structures. The term local refers to subwords of +the input sequences and structures. If parameter \fI-so\fP is used suboptimal +solutions are calculated. This does not mean suboptimal solutions of the +same local structures, but different substructures which do not include each other. + +.TP +\fB-so=int\fP +Calculates suboptimal local alignments within int% of the optimum. This option requires +option \fI-l\fP. + +.TP +\fB-s\fP +Calculates small-in-large similarity, i.e. the best alignment of the first structure against all +substructures of the second structure is computed. + +.TP +\fP-m, -mc=double, -mt=double, -cmin=double\fP +Multiple alignment mode. Multiple alignments of structures are calculated in a progressive +fashion. First, an all-against-all comparison of structures is performed (relative scores) and afterwards +structural alignments are joined along a guide tree (the guide tree is constructed dynamically). +If the best score which a single structure or structure alignment can achieve by aligning to all others +is below cutoff value \fI-mc\fP, it is not joined and put into the results list. Thus, a multiple +structure alignment can produce a list of alignments. The main purpose of parameter \fI-mc\fP is to +identify alternative and wrong structures produced by structure predictions. The default value for +\fI-mc\fP is zero, as this separates similar from dissimilar in a similarity scoring model. + +In each step in the multiple alignment calculation, the best scoring pair is joined and then the guide tree is +adjusted. To speed up computation, parameter \fI-mt\fP defines a threshold whereas, if this is exceeded, +multiple pairs are joined and then the guide tree is adjusted. + +Besides sequence and structure alignment, a consensus sequence and structure is computed. The minimum pair +frequency probability for a basepair in the consensus sequence is controlled by parameter \fI-cmin\fP. + +The console output could look like (just a part): +.br + + * * **** + * * **** + ** * **** + ** * **** * + ** * **** ******** **** + ** * **** ******** **** + ** * **** ******** **** + **************** ** * **************** ****** + **************** ** **************************** + **************** ** **************************** + ggggcuauagcucagcugggggagcuauagcucagcugggagcgggga + .((((....))))....((.(.(((((..((((........))))... + ************************************************ + **************** ** **************************** + **************** ** ** ************************* + **************** ** * *************** ******* + ** * **** ******** ***** + ** * **** ******** ***** + ** * **** ******* *** * + ** * **** * + * * **** + * * **** +.br + +The number of * above the primary sequence shows the frequency of the base. +Each * stands for 10% frequency. Accordingly, the number of * below the +secondary structure show the frequency of the occurrence of a paired or unpaired +base. + +The guide tree is written to a file "cluster.dot" in \fIdot\fP format. If a filename was +specified by parameter \fI-f\fP the filename is "filename_cluster.dot". Refer to +\fIhttp://www.research.att.com/sw/tools/graphviz\fP for more details about the dot format +and tools. + +.TP +\fI-p, -pmin=double\fP +Structures (in fact, a consensus of compatible structures) are predicted from the partition function +which is calculated using the Vienna RNA library [3]. Structure lines in the input are ignored. +\fI-pmin\fP is the minimum frequency of a basepair which must be exceeded to be considered for the +prediction of structures. + +.TP +\fI-pm=int,-pd=int,-bm=int,-br=int,-bd=int\fP +Scoring parameters. Refer to Section DESCRIPTION. + +.TP +\fI--RIBOSUM\fP +Uses the base and basepair substitution matrix RIBOSUM85-60 matrix as proposed in [4]. +Requires pairwise alignment model. + +.TP +\fI-2d\fP +RNAforester provides different types of visualizations for pairwise and multiple alignment. + +\fBpairwise alignment\fP +Since bases paired in a structure S1 can be aligned to bases unpaired in a structure S2, the presentation of a common secondary structure leaves some choice. For an alignment of those structures, an RNA secondary structure "$S2-at-S1" is drawn that highlights the differences as deviations of S2 from S1, or vice versa, "S1-at-S2". Both are alternative visualizations of the same alignment. +Bases printed in black show structure elements that occur in both structures with the same sequence. Sequence variations are displayed by using red letters. Bases or base pairs that can only be found in S1 are printed in blue, while bases that only occur in S2 are printed in green. + +The drawings are written to files "x_n.ps" and "y_n.ps" where n is the number of the alignment. n enumerates the suboptimal solutions if option \fI-so\fP is used. +The region of local similarity are highlighted in the original structures in the drawings "x_str.ps" and "y_str.ps". + +\fBmultiple alignment\fP +Each cluster of the result list of a multiple alignment is visualized in two alternative drawings, written to the files "filename_cons_n.ps" and "filename_n_.ps" +if option \fI-f\fP is used. In both plots, the consensus structure is shown. The lighter a basepair bond is drawn, the less frequent does it exist in the structures. Bases or basepair bonds that have a frequency of one hundred percent are drawn in red color. In "filename_cons_n.ps", the most frequent base at each residue is printed, +with the base frequency indicated by grey-scale. In "filename_n.ps", the frequencies of the bases a,c,g,u are proportional to the radius of circles +that are arranged clockwise on the corners of a square, starting at the upper left corner. Additionally, these circles are colored +red, green, blue, magenta for the bases a,c,g,u, respectively. The frequency of a gap is proportional to a black circle growing at the center of the square. + +Parameters \fI--2d_hidebasenum,--2d_basenuminterval=n,--2d_grey,--2d_scale=double\fP effect the drawings of alignments and consensus structures as implied by their names. + +.TP +\fI--score\fP +Only the optimal score of an alignment is printed. This option is useful when RNA-forester is called +by another program that only needs a similarity or distance value. + +.TP +\fI--fasta\fP +Alignments are printed in Fasta format + +.SH REFERENCES +[1] Jiang T, Wang J T L and Zhang K, (1995) +Alignment of Trees - An Alternative to Tree Edit, +Theoretical Computer Science 143(1), 137-148 + +[2] Hoechsmann M, Toeller T, Giegerich R and Kurtz S, (2003) +Local Similarity of RNA Secondary Structures, +Proc. of the IEEE Bioinformatics Conference (CSB 2003), 159-168 + +[3] Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, and Peter Schuster, (1994) +Fast Folding and Comparison of RNA Secondary Structures, +Monatsh.Chem. 125: 167-188. + +[4] Klein R.J. and Eddy S.R., (2003) +RSEARCH: finding homologs of single structured RNA sequences, +BMC Bioinformatics. 2003 Sep 22;4(1):44 + +.SH VERSION +This man page documents version 1.4 of RNAforester. + +.SH AUTHORS +Matthias Hoechsmann +.SH BUGS +I hope you wouldn't find them. +Comments should be sent to mhoechsm@techfak.uni-bielefeld.de +.br + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing new file mode 100755 index 000000000..6a37006e8 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/missing @@ -0,0 +1,336 @@ +#! /bin/sh +# Common stub for a few missing GNU programs while installing. +# Copyright (C) 1996, 1997, 1999, 2000, 2002 Free Software Foundation, Inc. +# Originally by Fran,cois Pinard , 1996. + +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2, or (at your option) +# any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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PROGRAM [ARGUMENT]... + +Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an +error status if there is no known handling for PROGRAM. + +Options: + -h, --help display this help and exit + -v, --version output version information and exit + --run try to run the given command, and emulate it if it fails + +Supported PROGRAM values: + aclocal touch file \`aclocal.m4' + autoconf touch file \`configure' + autoheader touch file \`config.h.in' + automake touch all \`Makefile.in' files + bison create \`y.tab.[ch]', if possible, from existing .[ch] + flex create \`lex.yy.c', if possible, from existing .c + help2man touch the output file + lex create \`lex.yy.c', if possible, from existing .c + makeinfo touch the output file + tar try tar, gnutar, gtar, then tar without non-portable flags + yacc create \`y.tab.[ch]', if possible, from existing .[ch]" + ;; + + -v|--v|--ve|--ver|--vers|--versi|--versio|--version) + echo "missing 0.4 - GNU automake" + ;; + + -*) + echo 1>&2 "$0: Unknown \`$1' option" + echo 1>&2 "Try \`$0 --help' for more information" + exit 1 + ;; + + aclocal*) + if test -z "$run" && ($1 --version) > /dev/null 2>&1; then + # We have it, but it failed. + exit 1 + fi + + echo 1>&2 "\ +WARNING: \`$1' is missing on your system. You should only need it if + you modified \`acinclude.m4' or \`${configure_ac}'. You might want + to install the \`Automake' and \`Perl' packages. Grab them from + any GNU archive site." + touch aclocal.m4 + ;; + + autoconf) + if test -z "$run" && ($1 --version) > /dev/null 2>&1; then + # We have it, but it failed. + exit 1 + fi + + echo 1>&2 "\ +WARNING: \`$1' is missing on your system. You should only need it if + you modified \`${configure_ac}'. You might want to install the + \`Autoconf' and \`GNU m4' packages. Grab them from any GNU + archive site." + touch configure + ;; + + autoheader) + if test -z "$run" && ($1 --version) > /dev/null 2>&1; then + # We have it, but it failed. + exit 1 + fi + + echo 1>&2 "\ +WARNING: \`$1' is missing on your system. You should only need it if + you modified \`acconfig.h' or \`${configure_ac}'. You might want + to install the \`Autoconf' and \`GNU m4' packages. Grab them + from any GNU archive site." + files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}` + test -z "$files" && files="config.h" + touch_files= + for f in $files; do + case "$f" in + *:*) touch_files="$touch_files "`echo "$f" | + sed -e 's/^[^:]*://' -e 's/:.*//'`;; + *) touch_files="$touch_files $f.in";; + esac + done + touch $touch_files + ;; + + automake*) + if test -z "$run" && ($1 --version) > /dev/null 2>&1; then + # We have it, but it failed. + exit 1 + fi + + echo 1>&2 "\ +WARNING: \`$1' is missing on your system. You should only need it if + you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'. + You might want to install the \`Automake' and \`Perl' packages. + Grab them from any GNU archive site." + find . -type f -name Makefile.am -print | + sed 's/\.am$/.in/' | + while read f; do touch "$f"; done + ;; + + autom4te) + if test -z "$run" && ($1 --version) > /dev/null 2>&1; then + # We have it, but it failed. + exit 1 + fi + + echo 1>&2 "\ +WARNING: \`$1' is needed, and you do not seem to have it handy on your + system. You might have modified some files without having the + proper tools for further handling them. + You can get \`$1Help2man' as part of \`Autoconf' from any GNU + archive site." + + file=`echo "$*" | sed -n 's/.*--output[ =]*\([^ ]*\).*/\1/p'` + test -z "$file" && file=`echo "$*" | sed -n 's/.*-o[ ]*\([^ ]*\).*/\1/p'` + if test -f "$file"; then + touch $file + else + test -z "$file" || exec >$file + echo "#! /bin/sh" + echo "# Created by GNU Automake missing as a replacement of" + echo "# $ $@" + echo "exit 0" + chmod +x $file + exit 1 + fi + ;; + + bison|yacc) + echo 1>&2 "\ +WARNING: \`$1' is missing on your system. You should only need it if + you modified a \`.y' file. You may need the \`Bison' package + in order for those modifications to take effect. You can get + \`Bison' from any GNU archive site." + rm -f y.tab.c y.tab.h + if [ $# -ne 1 ]; then + eval LASTARG="\${$#}" + case "$LASTARG" in + *.y) + SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'` + if [ -f "$SRCFILE" ]; then + cp "$SRCFILE" y.tab.c + fi + SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'` + if [ -f "$SRCFILE" ]; then + cp "$SRCFILE" y.tab.h + fi + ;; + esac + fi + if [ ! -f y.tab.h ]; then + echo >y.tab.h + fi + if [ ! -f y.tab.c ]; then + echo 'main() { return 0; }' >y.tab.c + fi + ;; + + lex|flex) + echo 1>&2 "\ +WARNING: \`$1' is missing on your system. You should only need it if + you modified a \`.l' file. You may need the \`Flex' package + in order for those modifications to take effect. You can get + \`Flex' from any GNU archive site." + rm -f lex.yy.c + if [ $# -ne 1 ]; then + eval LASTARG="\${$#}" + case "$LASTARG" in + *.l) + SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'` + if [ -f "$SRCFILE" ]; then + cp "$SRCFILE" lex.yy.c + fi + ;; + esac + fi + if [ ! -f lex.yy.c ]; then + echo 'main() { return 0; }' >lex.yy.c + fi + ;; + + help2man) + if test -z "$run" && ($1 --version) > /dev/null 2>&1; then + # We have it, but it failed. + exit 1 + fi + + echo 1>&2 "\ +WARNING: \`$1' is missing on your system. You should only need it if + you modified a dependency of a manual page. You may need the + \`Help2man' package in order for those modifications to take + effect. You can get \`Help2man' from any GNU archive site." + + file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'` + if test -z "$file"; then + file=`echo "$*" | sed -n 's/.*--output=\([^ ]*\).*/\1/p'` + fi + if [ -f "$file" ]; then + touch $file + else + test -z "$file" || exec >$file + echo ".ab help2man is required to generate this page" + exit 1 + fi + ;; + + makeinfo) + if test -z "$run" && (makeinfo --version) > /dev/null 2>&1; then + # We have makeinfo, but it failed. + exit 1 + fi + + echo 1>&2 "\ +WARNING: \`$1' is missing on your system. You should only need it if + you modified a \`.texi' or \`.texinfo' file, or any other file + indirectly affecting the aspect of the manual. The spurious + call might also be the consequence of using a buggy \`make' (AIX, + DU, IRIX). You might want to install the \`Texinfo' package or + the \`GNU make' package. Grab either from any GNU archive site." + file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'` + if test -z "$file"; then + file=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'` + file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $file` + fi + touch $file + ;; + + tar) + shift + if test -n "$run"; then + echo 1>&2 "ERROR: \`tar' requires --run" + exit 1 + fi + + # We have already tried tar in the generic part. + # Look for gnutar/gtar before invocation to avoid ugly error + # messages. + if (gnutar --version > /dev/null 2>&1); then + gnutar "$@" && exit 0 + fi + if (gtar --version > /dev/null 2>&1); then + gtar "$@" && exit 0 + fi + firstarg="$1" + if shift; then + case "$firstarg" in + *o*) + firstarg=`echo "$firstarg" | sed s/o//` + tar "$firstarg" "$@" && exit 0 + ;; + esac + case "$firstarg" in + *h*) + firstarg=`echo "$firstarg" | sed s/h//` + tar "$firstarg" "$@" && exit 0 + ;; + esac + fi + + echo 1>&2 "\ +WARNING: I can't seem to be able to run \`tar' with the given arguments. + You may want to install GNU tar or Free paxutils, or check the + command line arguments." + exit 1 + ;; + + *) + echo 1>&2 "\ +WARNING: \`$1' is needed, and you do not seem to have it handy on your + system. You might have modified some files without having the + proper tools for further handling them. Check the \`README' file, + it often tells you about the needed prerequirements for installing + this package. You may also peek at any GNU archive site, in case + some other package would contain this missing \`$1' program." + exit 1 + ;; +esac + +exit 0 diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/mkinstalldirs b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/mkinstalldirs new file mode 100755 index 000000000..8ab885ec9 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/mkinstalldirs @@ -0,0 +1,99 @@ +#! /bin/sh +# mkinstalldirs --- make directory hierarchy +# Author: Noah Friedman +# Created: 1993-05-16 +# Public domain + +errstatus=0 +dirmode="" + +usage="\ +Usage: mkinstalldirs [-h] [--help] [-m mode] dir ..." + +# process command line arguments +while test $# -gt 0 ; do + case "${1}" in + -h | --help | --h* ) # -h for help + echo "${usage}" 1>&2; exit 0 ;; + -m ) # -m PERM arg + shift + test $# -eq 0 && { echo "${usage}" 1>&2; exit 1; } + dirmode="${1}" + shift ;; + -- ) shift; break ;; # stop option processing + -* ) echo "${usage}" 1>&2; exit 1 ;; # unknown option + * ) break ;; # first non-opt arg + esac +done + +for file +do + if test -d "$file"; then + shift + else + break + fi +done + +case $# in +0) exit 0 ;; +esac + +case $dirmode in +'') + if mkdir -p -- . 2>/dev/null; then + echo "mkdir -p -- $*" + exec mkdir -p -- "$@" + fi ;; +*) + if mkdir -m "$dirmode" -p -- . 2>/dev/null; then + echo "mkdir -m $dirmode -p -- $*" + exec mkdir -m "$dirmode" -p -- "$@" + fi ;; +esac + +for file +do + set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'` + shift + + pathcomp= + for d + do + pathcomp="$pathcomp$d" + case "$pathcomp" in + -* ) pathcomp=./$pathcomp ;; + esac + + if test ! -d "$pathcomp"; then + echo "mkdir $pathcomp" + + mkdir "$pathcomp" || lasterr=$? + + if test ! -d "$pathcomp"; then + errstatus=$lasterr + else + if test ! -z "$dirmode"; then + echo "chmod $dirmode $pathcomp" + + lasterr="" + chmod "$dirmode" "$pathcomp" || lasterr=$? + + if test ! -z "$lasterr"; then + errstatus=$lasterr + fi + fi + fi + fi + + pathcomp="$pathcomp/" + done +done + +exit $errstatus + +# Local Variables: +# mode: shell-script +# sh-indentation: 3 +# End: +# mkinstalldirs ends here diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/Arguments.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/Arguments.Po new file mode 100755 index 000000000..241807a6f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/Arguments.Po @@ -0,0 +1,402 @@ +Arguments.o Arguments.o: Arguments.cpp Arguments.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/string.h /usr/include/xlocale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ + /usr/include/bits/stdio_lim.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/types.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/time.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/sched.h /usr/include/alloca.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio \ + /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ + /usr/include/libintl.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/signal.h \ + /usr/include/bits/initspin.h /usr/include/bits/sigthread.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype \ + /usr/include/ctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime \ + /usr/include/stdint.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert \ + /usr/include/assert.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_construct.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype \ + /usr/include/wctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits \ + 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+/usr/include/bits/local_lim.h: + +/usr/include/linux/limits.h: + +/usr/include/bits/posix2_lim.h: + +/usr/include/bits/xopen_lim.h: + +/usr/include/bits/stdio_lim.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/signal.h: + +/usr/include/bits/initspin.h: + +/usr/include/bits/sigthread.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype: + +/usr/include/ctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime: + +/usr/include/stdint.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert: + +/usr/include/assert.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype: + +/usr/include/wctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/glib.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/glib.Po new file mode 100755 index 000000000..f2e2333e1 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/glib.Po @@ -0,0 +1,90 @@ +glib.o glib.o: glib.c graphtypes.h /usr/include/stdlib.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/sys/types.h /usr/include/bits/types.h \ + /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h \ + /usr/include/time.h /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/sched.h /usr/include/alloca.h /usr/include/stdio.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h + +graphtypes.h: + +/usr/include/stdlib.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/stdio.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/main.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/main.Po new file mode 100755 index 000000000..cf423a122 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/main.Po @@ -0,0 +1,518 @@ +main.o main.o: main.cpp \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/deque \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h \ + 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+/usr/include/sys/times.h: + +../config.h: + +Arguments.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc: + +alignment.h: + +types.h: + +algebra.h: + +ppforest.h: + +misc.h: + +ppforestbase.h: + +ppforestali.h: + +debug.h: + +treeedit.h: + +ppforestsz.h: + +progressive_align.h: + +graphtypes.h: + +matrix.h: + +rnaforester_options.h: + +rna_profile_alignment.h: + +rna_algebra.h: + +rna_alphabet.h: + +wmatch.h: + +rna_alignment.h: + +rnaforest.h: + +rnafuncs.h: + +alignment.t.cpp: + +misc.t.cpp: + +ppforest.t.cpp: + +rnaforestsz.h: + +treeedit.t.cpp: + +ppforestsz.t.cpp: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/ppforestbase.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/ppforestbase.Po new file mode 100755 index 000000000..ab91b357e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/ppforestbase.Po @@ -0,0 +1,398 @@ +ppforestbase.o ppforestbase.o: ppforestbase.cpp misc.h types.h \ + ppforestbase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + 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+/usr/include/bits/xopen_lim.h: + +/usr/include/bits/stdio_lim.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype: + +/usr/include/wctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc: + +misc.t.cpp: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/progressive_align.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/progressive_align.Po new file mode 100755 index 000000000..0f7151687 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/progressive_align.Po @@ -0,0 +1,494 @@ +progressive_align.o progressive_align.o: progressive_align.cpp \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/string.h /usr/include/xlocale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc: + +rna_profile_alignment.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/deque: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_deque.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/deque.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/map: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tree.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/cpp_type_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_map.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_multimap.h: + +rna_algebra.h: + +debug.h: + +rna_alphabet.h: + +wmatch.h: + +alignment.t.cpp: + +misc.t.cpp: + +ppforest.t.cpp: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_algebra.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_algebra.Po new file mode 100755 index 000000000..ff7581bd0 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_algebra.Po @@ -0,0 +1,423 @@ +rna_algebra.o rna_algebra.o: rna_algebra.cpp rna_algebra.h \ + /usr/include/assert.h /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + 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\ + /usr/include/bits/stdio_lim.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/types.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/time.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/sched.h /usr/include/alloca.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h \ + 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/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc \ + misc.h types.h rna_alphabet.h rnaforester_options.h ../config.h \ + Arguments.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc + +rna_algebra.h: + +/usr/include/assert.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio: + +/usr/include/stdio.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/langinfo.h: + +/usr/include/nl_types.h: + +/usr/include/iconv.h: + +/usr/include/libintl.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/signal.h: + +/usr/include/bits/initspin.h: + +/usr/include/bits/sigthread.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype: + +/usr/include/ctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime: + +/usr/include/stdint.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h: + +algebra.h: + +debug.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype: + +/usr/include/wctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc: + +misc.h: + +types.h: + +rna_alphabet.h: + +rnaforester_options.h: + +../config.h: + +Arguments.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_alignment.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_alignment.Po new file mode 100755 index 000000000..50ba94b23 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_alignment.Po @@ -0,0 +1,473 @@ +rna_alignment.o rna_alignment.o: rna_alignment.cpp \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/string.h /usr/include/xlocale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ + /usr/include/bits/stdio_lim.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/types.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/time.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/sched.h /usr/include/alloca.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio \ + /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ + /usr/include/libintl.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/signal.h \ + /usr/include/bits/initspin.h /usr/include/bits/sigthread.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype \ + /usr/include/ctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime \ + /usr/include/stdint.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert \ + /usr/include/assert.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_construct.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc \ + ../config.h misc.h types.h rna_alignment.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype \ + /usr/include/wctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/map \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tree.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/cpp_type_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_map.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_multimap.h \ + alignment.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/list \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_list.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/list.tcc \ + algebra.h ppforest.h ppforestbase.h ppforestali.h rna_algebra.h debug.h \ + rna_alphabet.h rnaforester_options.h Arguments.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc \ + rnaforest.h rnafuncs.h alignment.t.cpp misc.t.cpp ppforest.t.cpp \ + utils.h + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/string.h: + +/usr/include/xlocale.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h: + +/usr/include/limits.h: + +/usr/include/bits/posix1_lim.h: + +/usr/include/bits/local_lim.h: + +/usr/include/linux/limits.h: + +/usr/include/bits/posix2_lim.h: + +/usr/include/bits/xopen_lim.h: + +/usr/include/bits/stdio_lim.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio: + +/usr/include/stdio.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/langinfo.h: + +/usr/include/nl_types.h: + +/usr/include/iconv.h: + +/usr/include/libintl.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/signal.h: + +/usr/include/bits/initspin.h: + +/usr/include/bits/sigthread.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype: + +/usr/include/ctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime: + +/usr/include/stdint.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert: + +/usr/include/assert.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_construct.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc: + +../config.h: + +misc.h: + +types.h: + +rna_alignment.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype: + +/usr/include/wctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/map: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tree.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/cpp_type_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_map.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_multimap.h: + +alignment.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/list: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_list.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/list.tcc: + +algebra.h: + +ppforest.h: + +ppforestbase.h: + +ppforestali.h: + +rna_algebra.h: + +debug.h: + +rna_alphabet.h: + +rnaforester_options.h: + +Arguments.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc: + +rnaforest.h: + +rnafuncs.h: + +alignment.t.cpp: + +misc.t.cpp: + +ppforest.t.cpp: + +utils.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_alphabet.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_alphabet.Po new file mode 100755 index 000000000..c33fe72a8 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_alphabet.Po @@ -0,0 +1,306 @@ +rna_alphabet.o rna_alphabet.o: rna_alphabet.cpp rna_alphabet.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/string.h /usr/include/xlocale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ + /usr/include/bits/stdio_lim.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/types.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/time.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/sched.h /usr/include/alloca.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio \ + /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ + /usr/include/libintl.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/signal.h \ + /usr/include/bits/initspin.h /usr/include/bits/sigthread.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype \ + /usr/include/ctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime \ + /usr/include/stdint.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert \ + /usr/include/assert.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_construct.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc + +rna_alphabet.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/string.h: + +/usr/include/xlocale.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h: + +/usr/include/limits.h: + +/usr/include/bits/posix1_lim.h: + +/usr/include/bits/local_lim.h: + +/usr/include/linux/limits.h: + +/usr/include/bits/posix2_lim.h: + +/usr/include/bits/xopen_lim.h: + +/usr/include/bits/stdio_lim.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio: + +/usr/include/stdio.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/langinfo.h: + +/usr/include/nl_types.h: + +/usr/include/iconv.h: + +/usr/include/libintl.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/signal.h: + +/usr/include/bits/initspin.h: + +/usr/include/bits/sigthread.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype: + +/usr/include/ctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime: + +/usr/include/stdint.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert: + +/usr/include/assert.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_construct.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_profile_alignment.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_profile_alignment.Po new file mode 100755 index 000000000..bb199f028 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rna_profile_alignment.Po @@ -0,0 +1,524 @@ +rna_profile_alignment.o rna_profile_alignment.o: \ + rna_profile_alignment.cpp ../config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cmath \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/cpp_type_traits.h \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/cmath.tcc \ + ../g2-0.70/include/g2.h ../g2-0.70/include/g2_PS.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/fstream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/string.h /usr/include/xlocale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio \ + /usr/include/stdio.h /usr/include/bits/types.h \ + /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ + /usr/include/libintl.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/signal.h /usr/include/bits/sigset.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/initspin.h \ + /usr/include/bits/sigthread.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype \ + /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime \ + /usr/include/stdint.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/sys/sysmacros.h /usr/include/alloca.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert \ + /usr/include/assert.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_construct.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype \ + /usr/include/wctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/basic_file.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/fstream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iomanip \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/functional \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc \ + matrix.h rna_profile_alignment.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/deque \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_deque.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/deque.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/map \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tree.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_map.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_multimap.h \ + alignment.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/list \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_list.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/list.tcc \ + types.h algebra.h ppforest.h misc.h ppforestbase.h ppforestali.h \ + rna_algebra.h debug.h rna_alphabet.h rnaforester_options.h Arguments.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc \ + rnafuncs.h utils.h part_func.h fold_vars.h fold.h ppforest.t.cpp + +../config.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cmath: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/functional: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc: + +matrix.h: + +rna_profile_alignment.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/deque: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_deque.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/deque.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/map: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tree.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_map.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_multimap.h: + +alignment.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/list: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_list.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/list.tcc: + +types.h: + +algebra.h: + +ppforest.h: + +misc.h: + +ppforestbase.h: + +ppforestali.h: + +rna_algebra.h: + +debug.h: + +rna_alphabet.h: + +rnaforester_options.h: + +Arguments.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc: + +rnafuncs.h: + +utils.h: + +part_func.h: + +fold_vars.h: + +fold.h: + +ppforest.t.cpp: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforest.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforest.Po new file mode 100755 index 000000000..0abc2b50d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforest.Po @@ -0,0 +1,416 @@ +rnaforest.o rnaforest.o: rnaforest.cpp ../config.h rnaforest.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios \ + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype: + +/usr/include/wctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc: + +algebra.h: + +ppforest.h: + +misc.h: + +types.h: + +ppforestbase.h: + +rna_alphabet.h: + +rnafuncs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/list: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_list.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/list.tcc: + +ppforest.t.cpp: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforester_options.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforester_options.Po new file mode 100755 index 000000000..0353cc8bc --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforester_options.Po @@ -0,0 +1,412 @@ +rnaforester_options.o rnaforester_options.o: rnaforester_options.cpp \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/string.h /usr/include/xlocale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio \ + /usr/include/stdio.h /usr/include/bits/types.h \ + /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ + /usr/include/libintl.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/signal.h /usr/include/bits/sigset.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/initspin.h \ + /usr/include/bits/sigthread.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype \ + /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime \ + /usr/include/stdint.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/sys/sysmacros.h /usr/include/alloca.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert \ + /usr/include/assert.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_construct.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype \ + /usr/include/wctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc \ + ../config.h rnaforester_options.h Arguments.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc \ + types.h + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/langinfo.h: + +/usr/include/nl_types.h: + +/usr/include/iconv.h: + +/usr/include/libintl.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/time.h: + +/usr/include/bits/sched.h: + +/usr/include/bits/time.h: + +/usr/include/signal.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/initspin.h: + +/usr/include/bits/sigthread.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/sstream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/sstream.tcc: + +../config.h: + +rnaforester_options.h: + +Arguments.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/vector: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_vector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_bvector.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/vector.tcc: + +types.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforestsz.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforestsz.Po new file mode 100755 index 000000000..a57ef48d4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnaforestsz.Po @@ -0,0 +1,424 @@ +rnaforestsz.o rnaforestsz.o: rnaforestsz.cpp rnaforestsz.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/string.h /usr/include/xlocale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio \ + /usr/include/stdio.h /usr/include/bits/types.h \ + /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ + /usr/include/libintl.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h \ + 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+/usr/include/iconv.h: + +/usr/include/libintl.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/time.h: + +/usr/include/bits/sched.h: + +/usr/include/bits/time.h: + +/usr/include/signal.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/initspin.h: + +/usr/include/bits/sigthread.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype: + +/usr/include/ctype.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + 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+/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype: + +/usr/include/wctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc: + +ppforestsz.h: + +misc.h: + +types.h: + +rna_alphabet.h: + +rnafuncs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/list: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_list.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/list.tcc: + +ppforestsz.t.cpp: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/map: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tree.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/cpp_type_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_map.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_multimap.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnafuncs.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnafuncs.Po new file mode 100755 index 000000000..5e1fb1b89 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/rnafuncs.Po @@ -0,0 +1,421 @@ +rnafuncs.o rnafuncs.o: rnafuncs.cpp \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/string.h /usr/include/xlocale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ + /usr/include/bits/stdio_lim.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/sys/types.h \ + /usr/include/bits/types.h /usr/include/bits/wordsize.h \ + /usr/include/bits/typesizes.h /usr/include/time.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/sched.h /usr/include/alloca.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio \ + /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ + /usr/include/libintl.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/signal.h \ + /usr/include/bits/initspin.h /usr/include/bits/sigthread.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype \ + /usr/include/ctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime \ + /usr/include/stdint.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_pair.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/type_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_types.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator_base_funcs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/concept_check.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/debug/debug.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cassert \ + /usr/include/assert.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_construct.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_uninitialized.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iomanip \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype \ + /usr/include/wctype.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/functional \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream \ + debug.h misc.h types.h rnafuncs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/list \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_list.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/list.tcc \ + utils.h ../config.h ../g2-0.70/include/g2.h ../g2-0.70/include/g2_PS.h \ + ../g2-0.70/include/g2_FIG.h + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/algorithm: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algobase.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++config.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstring: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstddef: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/string.h: + +/usr/include/xlocale.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/climits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/limits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/syslimits.h: + +/usr/include/limits.h: + +/usr/include/bits/posix1_lim.h: + +/usr/include/bits/local_lim.h: + +/usr/include/linux/limits.h: + +/usr/include/bits/posix2_lim.h: + +/usr/include/bits/xopen_lim.h: + +/usr/include/bits/stdio_lim.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/new: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iosfwd: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++locale.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cstdio: + +/usr/include/stdio.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/langinfo.h: + +/usr/include/nl_types.h: + +/usr/include/iconv.h: + +/usr/include/libintl.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++io.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/signal.h: + +/usr/include/bits/initspin.h: + +/usr/include/bits/sigthread.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cctype: + +/usr/include/ctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stringfwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/postypes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwchar: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ctime: + +/usr/include/stdint.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/functexcept.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/exception_defines.h: + 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+ +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_algo.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_heap.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_tempbuf.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/memory: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/c++allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ext/new_allocator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_raw_storage_iter.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iomanip: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/istream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ios: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/char_traits.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/localefwd.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ios_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/atomicity.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/atomic_word.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_classes.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/string: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_function.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_string.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/streambuf: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/streambuf_iterator.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/cwctype: + +/usr/include/wctype.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_base.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/ctype_inline.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/codecvt.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/codecvt_specializations.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/time_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/i686-pc-linux-gnu/bits/messages_members.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/basic_ios.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/limits: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/istream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/locale: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/locale_facets.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/typeinfo: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/ostream: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/ostream.tcc: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/functional: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/iostream: + +debug.h: + +misc.h: + +types.h: + +rnafuncs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/list: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/stl_list.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/../../../../include/c++/3.4.1/bits/list.tcc: + +utils.h: + +../config.h: + +../g2-0.70/include/g2.h: + +../g2-0.70/include/g2_PS.h: + +../g2-0.70/include/g2_FIG.h: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/wmatch.Po b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/wmatch.Po new file mode 100755 index 000000000..6537804d1 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/.deps/wmatch.Po @@ -0,0 +1,92 @@ +wmatch.o wmatch.o: wmatch.c match.defs graphtypes.h wmatch.h pairs.c \ + pointer.c readgraph.c /usr/include/stdlib.h /usr/include/features.h \ + /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h \ + /usr/include/sys/types.h /usr/include/bits/types.h \ + /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h \ + /usr/include/time.h /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/sched.h /usr/include/alloca.h /usr/include/stdio.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/include/bits/wchar.h /usr/include/gconv.h \ + /usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h term.c unpairs.c + +match.defs: + +graphtypes.h: + +wmatch.h: + +pairs.c: + +pointer.c: + +readgraph.c: + +/usr/include/stdlib.h: + +/usr/include/features.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stddef.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/wordsize.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/sched.h: + +/usr/include/alloca.h: + +/usr/include/stdio.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/include/bits/wchar.h: + +/usr/include/gconv.h: + +/usr/local/lib/gcc/i686-pc-linux-gnu/3.4.1/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +term.c: + +unpairs.c: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.cpp new file mode 100755 index 000000000..eae31f21e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.cpp @@ -0,0 +1,221 @@ +/* + * Arguments 2.0 Beta - A Command Line Processing Library + * Copyright (C) 2000, 2001 Jared Davis + * + * This program is free software; you can redistribute it and/or modify it + * under the terms of the GNU General Public License as published by the + * Free Software Foundation; either version 2 of the License, or (at your + * option) any later version. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + * for more details. + * + * You should have received a copy of the GNU General Public License along + * with this program; if not, write to the Free Software Foundation, Inc., + * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + */ + +#include "Arguments.h" +#include + +std::vector Arguments::s_spaceArgs; + +// +// ExplodeString function +// ---------------------- +// Explodes a string into tokens, which it adds to a vector. +// (This function is taken from the AFA library, also by Jared Davis) +// +void Arguments::ExplodeString(const std::string& str, std::vector& tokens, char delimiter) +throw(std::bad_alloc) +{ + string::size_type next, prev = 0; + + do + { + next = str.find(delimiter, prev); + + tokens.push_back( str.substr(prev, next - prev) ); + + prev = next + 1; + + } while(next != string::npos); +} + +// +// findArgument +// ------------ +// Performs a binary search on the argument vector and returns the integer +// corresponding to the argument, if it exists. Otherwise returns -1. +// arg is a pipe-delimited list of acceptable arguments. +// +int Arguments::findArgument(const string& arg) const throw() +{ + if (d_arguments.size() == 0) + { + return -1; + } + + vector tokens; + ExplodeString(arg, tokens, '|'); + + for(unsigned int i = 0;i < tokens.size();++i) + { + int low = 0; + int high = d_arguments.size() - 1; + + while(low <= high) + { + unsigned int mid = (low + high) / 2; + + if (tokens[i] < d_arguments[mid].first) + { + high = mid - 1; + } + + else if (tokens[i] > d_arguments[mid].first) + { + low = mid + 1; + } + + else + { + return mid; + } + } + } + + return -1; +} + + +// +// Arguments::setArgumentsWithSpaces +// --------------------------------- +// Adds all tokens of the pipe-delimited string, args, to the +// spaces vector. keeps the vector sorted. +// +void Arguments::setArgumentsWithSpaces(const string& args) +throw(std::bad_alloc) +{ + ExplodeString(args, s_spaceArgs, '|'); + std::sort(s_spaceArgs.begin(), s_spaceArgs.end()); +} + + +Arguments::Arguments(int argc, const char** argv) throw(std::bad_alloc) +{ + // start at 1 to skip program's name. + for(int i = 1;i < argc;++i) + { + // Extract this token. + string this_arg = argv[i]; + + // Try to find a colon or an equals sign. + string::size_type colon = this_arg.find(':'); + if (colon == string::npos) + { + colon = this_arg.find('='); + } + + // Add arg/val pair if we have a colon or equals sign. + if (colon != string::npos) + { + d_arguments.push_back(make_pair( + this_arg.substr(0, colon), + make_pair(this_arg.substr(colon + 1), true) + )); + + continue; + } + + // If we get here, we didn't find a colon or an equals, we need to + // consult the spaces list. + if (i < (argc - 1)) + { + if (std::binary_search(s_spaceArgs.begin(), s_spaceArgs.end(), this_arg)) + { + // if parameter value starts with "-" consider it as an option + if(argv[i+1][0]=='-') + { + d_arguments.push_back(make_pair( + this_arg, + make_pair(string(""), false))); + continue; // i is not incrented !! + } + else + { + d_arguments.push_back(make_pair( + this_arg, + make_pair(argv[++i], true) + )); + continue; + } + } + } + + // If we get here, we either don't have a space, or we are at the last + // argument that we were passed, so we can't possibly have a value for + // this argument. Throw it into the map with an empty value. + d_arguments.push_back(make_pair( + this_arg, + make_pair(string(""), false) + )); + } + + // Now let's sort the argument list so it's fast to find them. + std::sort(d_arguments.begin(), d_arguments.end()); +} + + +// +// Arguments::size +// --------------- +// Returns the number of command-line arguments that your program was passed. +// This is not the same as argc: it does not include your program's name, nor +// does it include the values passed to your command-line arguments. +// +unsigned int Arguments::size() const throw() +{ + return d_arguments.size(); +} + + +// +// Arguments::has +// -------------- +// Cycle through the tokens of argument and return true if any of them +// are found. +// +bool Arguments::has(const std::string& argument) const throw(std::bad_alloc) +{ + return findArgument(argument) != -1; +} + + + + +/* +#ifndef NDEBUG + + #include + + void Arguments::debug() const + { + cout << "Arguments Debug Information-----\n" << endl; + cout << "Number of space-taking arguments: " << s_spaceArgs.size() << "\n\t"; + copy(s_spaceArgs.begin(), s_spaceArgs.end(), ostream_iterator(cout, "\n\t")); + + cout << "Arguments Map: " << size() << " Elements. " << endl; + for(unsigned int i = 0;i < size();++i) + { + cout << "\t" << d_arguments[i].first << " = " << d_arguments[i].second.first << " (" + << d_arguments[i].second.second << ")\n"; + } + cout << "\n-----End of Arguments Debug Information" << endl; + } + +#endif +*/ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.h new file mode 100755 index 000000000..b5f025ae2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.h @@ -0,0 +1,110 @@ +/* + * Arguments 2.0 Beta - A Command Line Processing Library + * Copyright (C) 2000, 2001 Jared Davis + * + * This program is free software; you can redistribute it and/or modify it + * under the terms of the GNU General Public License as published by the + * Free Software Foundation; either version 2 of the License, or (at your + * option) any later version. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + * for more details. + * + * You should have received a copy of the GNU General Public License along + * with this program; if not, write to the Free Software Foundation, Inc., + * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + */ + +#ifndef INCLUDED_OPENDELI_ARGUMENTS_H +#define INCLUDED_OPENDELI_ARGUMENTS_H + +#if (defined(_WIN32) && defined(_DEBUG)) +// In visual studio, compiling this library gives you a billion and a half +// error messages that "debug information has been truncated to 255 chars" +// because the visual studio debugger can't handle symbols longer than 255 +// characters. This disables this warning so we comile cleanly. + #pragma warning( disable: 4786 ) +#endif + +#include +#include +#include + +using namespace std; + +class Arguments +{ + private: + + // Vector of the arguments that take spaces. + static std::vector s_spaceArgs; + + // Vector of argument-value pairs. + std::vector< std::pair > > d_arguments; + + + // explodes a delimited string into its tokens. + static void ExplodeString(const std::string& str, std::vector& tokens, char delimiter) + throw(std::bad_alloc); + + // finds the index of the argument arg. + int findArgument(const std::string& arg) const throw(); + + // + // convert(source, target) + // Converts a variable of type A into a variable of type B by passing + // it through a strstream. + // + template + static bool convert(const A& source, B& target) throw() + { + std::stringstream ss; + ss.clear(); + ss << source; + ss >> target; + return (!ss.bad() && !ss.fail()); + } + + + public: + + static void setArgumentsWithSpaces(const std::string& args) + throw(std::bad_alloc); + + Arguments(int argc, const char** argv) + throw(std::bad_alloc); + + unsigned int size() const throw(); + + bool has(const std::string& arg) const throw(std::bad_alloc); + + template bool get + (const std::string& arg, A& value, const B& default_value) const + throw(std::bad_alloc) + { + int index = findArgument(arg); + + if (index == -1) { + value = default_value; + return false; + } + + else + { + bool ret = convert(d_arguments[index].second.first, value); + if (!ret) + value = default_value; + return ret; + } + } + + + #ifndef NDEBUG + void debug() const; + #endif + +}; + +#endif // INCLUDED_OPENDELI_ARGUMENTS_H diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.o new file mode 100755 index 000000000..15221440f Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Arguments.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Makefile b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Makefile new file mode 100755 index 000000000..3cc6bf8e6 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/Makefile @@ -0,0 +1,493 @@ +# Makefile.in generated by automake 1.9.5 from Makefile.am. +# src/Makefile. Generated from Makefile.in by configure. + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005 Free Software Foundation, Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + + + +SOURCES = $(RNAforester_SOURCES) + +srcdir = . +top_srcdir = .. + +pkgdatadir = $(datadir)/RNAforester +pkglibdir = $(libdir)/RNAforester +pkgincludedir = $(includedir)/RNAforester +top_builddir = .. +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +INSTALL = /usr/bin/install -c +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = 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GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/RNAforester b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/RNAforester new file mode 100755 index 000000000..02e74685a Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/RNAforester differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/algebra.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/algebra.h new file mode 100755 index 000000000..0c382706b --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/algebra.h @@ -0,0 +1,66 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _ALGEBRA_H_ +#define _ALGEBRA_H_ + +/** Algebra is a virtual class (interface) for algebra used by the Alignment template classes. + * This is in the spirit of the Algebraic Dynamic Programming (ADP) approach where a Dynamic Programming + * algorithm is seperated into a grammar and an algebra. + */ +template +class Algebra +{ +public: + virtual R empty() const =0; /**< Result for the empty tree alignment */ + virtual R replace(L a,R down, L b, R over) const =0; /**< Result for the tree edit function 'replace' */ + virtual R del(L a,R down, R over) const =0; /**< Result for the tree edit function 'delete' */ + virtual R insert(R down,L b,R over) const =0; /**< Result for the tree edit function 'insert' */ + virtual R choice(R a,R b) const =0; /**< The choice function. Commonly used functions are 'min' and 'max' */ + virtual R worst_score() const =0; /**< The worst_score with respect to choice is specified by this function */ + + virtual ~Algebra() {}; +}; + +/** Extended Algebra for aligning RNA secondary structure trees where basepair replacements + * are considered as a single edit operation. + */ +template +class RNA_Algebra : public Algebra +{ +public: + /** Result for the replacement of a basepair */ + virtual R replacepair(L la, L lb, R down, L ra, L rb, R over) const =0; +}; + +/** Algebra for the tree edit model */ +template +class SZAlgebra +{ +public: + virtual R empty() const =0; /**< Result for the empty tree alignment */ + virtual R replace(L a,R down, L b) const =0; /**< Result for the tree edit function 'replace' */ + virtual R del(L a,R down) const =0; /**< Result for the tree edit function 'delete' */ + virtual R insert(R down,L b) const =0; /**< Result for the tree edit function 'insert' */ + virtual R choice(R a,R b) const =0; /**< The choice function. Commonly used functions are 'min' and 'max' */ + virtual R worst_score() const =0; /**< The worst_score with respect to choice is specified by this function */ + + virtual ~SZAlgebra() {}; +}; + +#endif + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/alignment.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/alignment.h new file mode 100755 index 000000000..8a44919da --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/alignment.h @@ -0,0 +1,93 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _ALIGNMENT_H_ +#define _ALIGNMENT_H_ + +#include +#include + +#include "types.h" +#include "algebra.h" +#include "ppforest.h" +#include "ppforestali.h" + +template +class Alignment +{ +private: + struct CSFPair + { + Uint i; + Uint j; + Uint k; + Uint l; + + CSFPair(Uint i, Uint j, Uint k, Uint l) : i(i),j(j),k(k),l(l) {}; + }; + + R *m_mtrx; + Ulong *m_rowStart; + Ulong m_mtrxSize; + + PPForest *m_ppfx; + PPForest *m_ppfy; + + const Algebra *m_alg; + const RNA_Algebra *m_rnaAlg; + + R m_localOptimum; + R m_localSubOptimum; + std::list m_localAlis; // holds which alignments are already produced by getOptLocalAlignment + double m_suboptimalsPercent; // percentage is stores as a value between 0 and 1 + + inline R getMtrxVal(Ulong i,Ulong j) const + { + assert(m_rowStart[i]+jchoice(m_localOptimum,val); // here we calculate local similarity on the fly + }; + + void calculateLocal(const PPForest *ppfx, const PPForest *ppfy,const Algebra &alg, bool noSpeedup=false); + void calculateGlobal(const PPForest *ppfx, const PPForest *ppfy,const Algebra &alg, bool noSpeedup=false); + Uint backtrack(PPForestAli &ppf,Uint i, Uint j, Uint k, Uint l, Uint &node); +public: + Alignment(const PPForest *ppfx, const PPForest *ppfy,const Algebra &alg, bool local, bool noSpeedup=false); + Alignment(const PPForest *ppfx, const PPForest *ppfy,const RNA_Algebra &rnaAlg); + ~Alignment(); + + R getGlobalOptimum(); + + /** This function should only be used in conjunction with + * similarity based algebras + */ + double getGlobalOptimumRelative(); + + inline R getLocalOptimum(){return m_localSubOptimum;}; + R getSILOptimum(); + void getOptGlobalAlignment(PPForestAli &ppfali); + + void resetOptLocalAlignment(int suboptimalsPercent=100); + bool nextLocalSuboptimum(); + void getOptLocalAlignment(PPForestAli &ppfali,Uint &xbasepos, Uint &ybasepos); + void getOptSILAlignment(PPForestAli &ppfali,Uint &ybasepos); +}; + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/alignment.t.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/alignment.t.cpp new file mode 100755 index 000000000..178f3aa28 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/alignment.t.cpp @@ -0,0 +1,1004 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _ALIGNMENT_T_CPP_ +#define _ALIGNMENT_T_CPP_ + +#include +#include + +#include "alignment.h" +#include "debug.h" + +#include "misc.t.cpp" +#include "ppforest.t.cpp" + +/* ****************************************** */ +/* Constructor and Destruktor functions */ +/* ****************************************** */ + +template +Alignment::Alignment(const PPForest *ppfx, const PPForest *ppfy, const Algebra &alg, bool local, bool noSpeedup) +: m_suboptimalsPercent(100) +{ + if(local) + calculateLocal(ppfx,ppfy,alg,noSpeedup); + else + calculateGlobal(ppfx,ppfy,alg,noSpeedup); +} + +template +Alignment::Alignment(const PPForest *ppfx, const PPForest *ppfy, const RNA_Algebra &rnaAlg) +: m_suboptimalsPercent(100) +{ + assert(ppfx != NULL); + assert(ppfy != NULL); + + Ulong m,n,h,cols; + long i,k; + Uint j,l,r; + + R score,h_score; + + // alloc space for the score matrix, backtrack structure and , if wanted, for the calculation-order-matrix + m_mtrxSize=ppfx->getNumCSFs()*ppfy->getNumCSFs(); + + m_mtrx=new R[m_mtrxSize]; + m_rowStart=new Ulong[ppfx->getNumCSFs()]; + m_ppfx = new PPForest(*ppfx); // copy the ppforests + m_ppfy = new PPForest(*ppfy); + m_rnaAlg=&rnaAlg; + m_alg=(const Algebra*)&rnaAlg; + m_localOptimum=rnaAlg.worst_score(); + + // initialize variables + m=ppfx->size(); + n=ppfy->size(); + cols=ppfy->getNumCSFs(); + + m_rowStart[0]=0; + for(h=1;hgetNumCSFs();h++) + m_rowStart[h]=m_rowStart[h-1]+cols; + + // align forests fx and fy + + // the easiest case .. + setMtrxVal(0,0,rnaAlg.empty()); + + // align fx to the empty forest (fill first row of array) + for(i=m-1;i>=0;i--) // for all nodes in fx + { + for(j=1;j<=ppfx->getMaxLength(i);j++) // for all non empty csfs induced by i + { + score = rnaAlg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),0), + getMtrxVal(ppfx->over(i,j),0)); + + setMtrxVal(ppfx->indexpos(i,j),0,score); + } + } + + // align fy to the empty forest (fill first column of array) + for(k=n-1;k>=0;k--) // for all nodes in fx + { + for(l=1;l<=ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + score = rnaAlg.insert(getMtrxVal(0,ppfy->down(k)), + ppfy->label(k), + getMtrxVal(0,ppfy->over(k,l))); + + setMtrxVal(0,ppfy->indexpos(k,l),score); + } + } + + // align the rest + for(i=m-1;i>=0;i--) // for all nodes in fx + for(k=n-1;k>=0;k--) // for all nodes in fx + for(j=1;j<=ppfx->getMaxLength(i);j++) // for all non empty csfs induced by i + for(l=1;l<=ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + // basepair replacement + if(ppfx->down(i) && ppfy->down(k)) + { + // must be two P nodes !! + h_score = rnaAlg.replacepair(ppfx->label(i+1), + ppfy->label(k+1), + getMtrxVal(ppfx->mdown(i),ppfy->mdown(k)), + ppfx->label(ppfx->getRightmostBrotherIndex(i+1)), + ppfy->label(ppfy->getRightmostBrotherIndex(k+1)), + getMtrxVal(ppfx->over(i,j),ppfy->over(k,l))); + } + else + { + h_score = rnaAlg.replace(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->over(i,j),ppfy->over(k,l))); + } + + score=h_score; + + // delete + h=k; // h is the node where the suffix of the split begins + for(r=0;r<=l;r++) // for all splits of fy + { + h_score = rnaAlg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->indexpos(k,r)), + getMtrxVal(ppfx->over(i,j),ppfy->indexpos(h,l-r))); + + score=rnaAlg.choice(score,h_score); + h=ppfy->rb(h); + } + + // insert + h=i; + for(r=0;r<=j;r++) // for all splits of fx + { + h_score = rnaAlg.insert(getMtrxVal(ppfx->indexpos(i,r),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->indexpos(h,j-r),ppfy->over(k,l))); + + score=rnaAlg.choice(score,h_score); + h=ppfx->rb(h); + } + + // set value + setMtrxVal(ppfx->indexpos(i,j),ppfy->indexpos(k,l),score); + } + + // showArray(m_mtrx,ppfx->getNumCSFs(),ppfy->getNumCSFs()); + resetOptLocalAlignment(100); +} + + + +template +Alignment::~Alignment() +{ + delete[] m_mtrx; + delete[] m_rowStart; + delete m_ppfx; + delete m_ppfy; +} + + + +/* ****************************************** */ +/* Private functions */ +/* ****************************************** */ + +template +void Alignment::calculateLocal(const PPForest *ppfx, const PPForest *ppfy, const Algebra &alg, bool noSpeedup) +{ + assert(ppfx != NULL); + assert(ppfy != NULL); + + Ulong m,n,h,cols; + long i,k; + Uint j,l,r; + + R score,h_score; + + // alloc space for the score matrix, backtrack structure and , if wanted, for the calculation-order-matrix + m_mtrxSize=ppfx->getNumCSFs()*ppfy->getNumCSFs(); + + m_mtrx=new R[m_mtrxSize]; + m_rowStart=new Ulong[ppfx->getNumCSFs()]; + m_ppfx = new PPForest(*ppfx); // copy the ppforests + m_ppfy = new PPForest(*ppfy); + m_alg=&alg; + m_rnaAlg=NULL; + m_localOptimum=alg.worst_score(); + + + // initialize variables + m=ppfx->size(); + n=ppfy->size(); + cols=ppfy->getNumCSFs(); + + m_rowStart[0]=0; + for(h=1;hgetNumCSFs();h++) + m_rowStart[h]=m_rowStart[h-1]+cols; + + // align forests fx and fy + + // the easiest case .. + setMtrxVal(0,0,alg.empty()); + + // align fx to the empty forest (fill first row of array) + for(i=m-1;i>=0;i--) // for all nodes in fx + { + for(j=1;j<=ppfx->getMaxLength(i);j++) // for all non empty csfs induced by i + { + score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),0), + getMtrxVal(ppfx->over(i,j),0)); + + setMtrxVal(ppfx->indexpos(i,j),0,score); + } + } + + // align fy to the empty forest (fill first column of array) + for(k=n-1;k>=0;k--) // for all nodes in fx + { + for(l=1;l<=ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + score = alg.insert(getMtrxVal(0,ppfy->down(k)), + ppfy->label(k), + getMtrxVal(0,ppfy->over(k,l))); + + setMtrxVal(0,ppfy->indexpos(k,l),score); + } + } + + // align the rest + for(i=m-1;i>=0;i--) // for all nodes in fx + for(k=n-1;k>=0;k--) // for all nodes in fx + for(j=1;j<=ppfx->getMaxLength(i);j++) // for all non empty csfs induced by i + for(l=1;l<=ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + // replace + score = alg.replace(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->over(i,j),ppfy->over(k,l))); + + // delete + if(ppfx->noc(i)==0 && !noSpeedup) // no child + { + h_score = alg.del(ppfx->label(i),0, + getMtrxVal(ppfx->over(i,j),ppfy->indexpos(k,l))); + + score=alg.choice(score,h_score); + } + else + { + if(ppfx->rb(i)==0 && !noSpeedup) // no right brother + { + h_score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->indexpos(k,l)), + 0); + + score=alg.choice(score,h_score); + } + else + { + h=k; // h is the node where the suffix of the split begins + for(r=0;r<=l;r++) // for all splits of fy + { + h_score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->indexpos(k,r)), + getMtrxVal(ppfx->over(i,j),ppfy->indexpos(h,l-r))); + + score=alg.choice(score,h_score); + h=ppfy->rb(h); + } + } + } + + // insert + if(ppfy->noc(k)==0 && !noSpeedup) // no child + { + h_score = alg.insert(0, + ppfy->label(k), + getMtrxVal(ppfx->indexpos(i,j),ppfy->over(k,l))); + + score=alg.choice(score,h_score); + } + else + { + if(ppfy->rb(k)==0 && !noSpeedup) // no right brother + { + h_score = alg.insert(getMtrxVal(ppfx->indexpos(i,j),ppfy->down(k)), + ppfy->label(k), + 0); + + score=alg.choice(score,h_score); + } + else + { + h=i; + for(r=0;r<=j;r++) // for all splits of fx + { + h_score = alg.insert(getMtrxVal(ppfx->indexpos(i,r),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->indexpos(h,j-r),ppfy->over(k,l))); + + score=alg.choice(score,h_score); + h=ppfx->rb(h); + } + } + } + + // set value + setMtrxVal(ppfx->indexpos(i,j),ppfy->indexpos(k,l),score); + } + + /* + // delete + h=k; // h is the node where the suffix of the split begins + for(r=0;r<=l;r++) // for all splits of fy + { + h_score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->indexpos(k,r)), + getMtrxVal(ppfx->over(i,j),ppfy->indexpos(h,l-r))); + + score=alg.choice(score,h_score); + h=ppfy->rb(h); + } + + // insert + h=i; + for(r=0;r<=j;r++) // for all splits of fx + { + h_score = alg.insert(getMtrxVal(ppfx->indexpos(i,r),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->indexpos(h,j-r),ppfy->over(k,l))); + + score=alg.choice(score,h_score); + h=ppfx->rb(h); + } + + // set value + setMtrxVal(ppfx->indexpos(i,j),ppfy->indexpos(k,l),score); + */ + + + // showArray(m_mtrx,ppfx->getNumCSFs(),ppfy->getNumCSFs()); + resetOptLocalAlignment(100); +} + +template +void Alignment::calculateGlobal(const PPForest *ppfx, const PPForest *ppfy, const Algebra &alg, bool noSpeedup) +{ + assert(ppfx != NULL); + assert(ppfy != NULL); + + Ulong m,n,h,cols; + long i,k; + Uint j,l,r; + + R score,h_score; + + // alloc space for the score matrix, backtrack structure and , if wanted, for the calculation-order-matrix + m_mtrxSize=ppfx->getNumCSFs()*ppfy->getNumCSFs(); + + m_mtrx=new R[m_mtrxSize]; + m_rowStart=new Ulong[ppfx->getNumCSFs()]; + m_ppfx = new PPForest(*ppfx); // copy the ppforests + m_ppfy = new PPForest(*ppfy); + m_alg=&alg; + m_rnaAlg=NULL; + m_localOptimum=alg.worst_score(); + + + // initialize variables + m=ppfx->size(); + n=ppfy->size(); + cols=ppfy->getNumCSFs(); + + m_rowStart[0]=0; + for(h=1;hgetNumCSFs();h++) + m_rowStart[h]=m_rowStart[h-1]+cols; + + // align forests fx and fy + + // the easiest case .. + setMtrxVal(0,0,alg.empty()); + + // align fx to the empty forest (fill first row of array) + for(i=m-1;i>=0;i--) // for all nodes in fx + { + for(j=1;j<=ppfx->getMaxLength(i);j++) // for all non empty csfs induced by i + { + score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),0), + getMtrxVal(ppfx->over(i,j),0)); + + setMtrxVal(ppfx->indexpos(i,j),0,score); + } + } + + // align fy to the empty forest (fill first column of array) + for(k=n-1;k>=0;k--) // for all nodes in fx + { + for(l=1;l<=ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + score = alg.insert(getMtrxVal(0,ppfy->down(k)), + ppfy->label(k), + getMtrxVal(0,ppfy->over(k,l))); + + setMtrxVal(0,ppfy->indexpos(k,l),score); + } + } + + // align the rest + for(i=m-1;i>=0;i--) // for all nodes in fx + for(k=n-1;k>=0;k--) // for all nodes in fx + { + j=ppfx->getMaxLength(i); + for(l=1;l<=ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + // replace + + score = alg.replace(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->over(i,j),ppfy->over(k,l))); + + // delete + if(ppfx->noc(i)==0 && !noSpeedup) // no child + { + h_score = alg.del(ppfx->label(i),0, + getMtrxVal(ppfx->over(i,j),ppfy->indexpos(k,l))); + + score=alg.choice(score,h_score); + } + else + { + if(ppfx->rb(i)==0 && !noSpeedup) // no right brother + { + h_score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->indexpos(k,l)), + 0); + + score=alg.choice(score,h_score); + } + else + { + h=k; // h is the node where the suffix of the split begins + for(r=0;r<=l;r++) // for all splits of fy + { + h_score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->indexpos(k,r)), + getMtrxVal(ppfx->over(i,j),ppfy->indexpos(h,l-r))); + + score=alg.choice(score,h_score); + h=ppfy->rb(h); + } + } + } + + // insert + if(ppfy->noc(k)==0 && !noSpeedup) // no child + { + h_score = alg.insert(0, + ppfy->label(k), + getMtrxVal(ppfx->indexpos(i,j),ppfy->over(k,l))); + + score=alg.choice(score,h_score); + } + else + { + if(ppfy->rb(k)==0 && !noSpeedup) // no right brother + { + h_score = alg.insert(getMtrxVal(ppfx->indexpos(i,j),ppfy->down(k)), + ppfy->label(k), + 0); + + score=alg.choice(score,h_score); + } + else + { + h=i; + for(r=0;r<=j;r++) // for all splits of fx + { + h_score = alg.insert(getMtrxVal(ppfx->indexpos(i,r),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->indexpos(h,j-r),ppfy->over(k,l))); + + score=alg.choice(score,h_score); + h=ppfx->rb(h); + } + } + } + + // set value + setMtrxVal(ppfx->indexpos(i,j),ppfy->indexpos(k,l),score); + } + + l=ppfy->getMaxLength(k); + for(j=1;j<=ppfx->getMaxLength(i);j++) // for all non empty csfs induced by i + { + // replace + score = alg.replace(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->over(i,j),ppfy->over(k,l))); + + // delete + if(ppfx->noc(i)==0 && !noSpeedup) // no child + { + h_score = alg.del(ppfx->label(i),0, + getMtrxVal(ppfx->over(i,j),ppfy->indexpos(k,l))); + + score=alg.choice(score,h_score); + } + else + { + if(ppfx->rb(i)==0 && !noSpeedup) // no right brother + { + h_score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->indexpos(k,l)), + 0); + + score=alg.choice(score,h_score); + } + else + { + h=k; // h is the node where the suffix of the split begins + for(r=0;r<=l;r++) // for all splits of fy + { + h_score = alg.del(ppfx->label(i), + getMtrxVal(ppfx->down(i),ppfy->indexpos(k,r)), + getMtrxVal(ppfx->over(i,j),ppfy->indexpos(h,l-r))); + + score=alg.choice(score,h_score); + h=ppfy->rb(h); + } + } + } + + // insert + if(ppfy->noc(k)==0 && !noSpeedup) // no child + { + h_score = alg.insert(0, + ppfy->label(k), + getMtrxVal(ppfx->indexpos(i,j),ppfy->over(k,l))); + + score=alg.choice(score,h_score); + } + else + { + if(ppfy->rb(k)==0 && !noSpeedup) // no right brother + { + h_score = alg.insert(getMtrxVal(ppfx->indexpos(i,j),ppfy->down(k)), + ppfy->label(k), + 0); + + score=alg.choice(score,h_score); + } + else + { + h=i; + for(r=0;r<=j;r++) // for all splits of fx + { + h_score = alg.insert(getMtrxVal(ppfx->indexpos(i,r),ppfy->down(k)), + ppfy->label(k), + getMtrxVal(ppfx->indexpos(h,j-r),ppfy->over(k,l))); + + score=alg.choice(score,h_score); + h=ppfx->rb(h); + } + } + } + + // set value + setMtrxVal(ppfx->indexpos(i,j),ppfy->indexpos(k,l),score); + } + } + + // showArray(m_mtrx,ppfx->getNumCSFs(),ppfy->getNumCSFs()); + resetOptLocalAlignment(100); +} + +template +Uint Alignment::backtrack(PPForestAli &ppf,Uint i, Uint j, Uint k, Uint l, Uint &node) +{ + R score, h_score; + Uint p_node,rb_node,noc,rbs,r,h; + + // empty alignment + if(j==0 && l==0) + { + return 0; + } + + score = getMtrxVal(m_ppfx->indexpos(i,j),m_ppfy->indexpos(k,l)); + p_node=node; + node++; + + // could it be a replacement + if(j>0 && l>0) + { + // check for basepair replacement only if Algebra is of type RNA_Algebra + if(m_rnaAlg && m_ppfx->down(i) && m_ppfy->down(k)) + { + h_score = m_rnaAlg->replacepair(m_ppfx->label(i+1), + m_ppfy->label(k+1), + getMtrxVal(m_ppfx->mdown(i),m_ppfy->mdown(k)), + m_ppfx->label(m_ppfx->getRightmostBrotherIndex2(i+1)), + m_ppfy->label(m_ppfy->getRightmostBrotherIndex2(k+1)), + getMtrxVal(m_ppfx->over(i,j),m_ppfy->over(k,l))); + + if(score == h_score) + { + // it is a basepair replacement + ppf.makeRepLabel(p_node,m_ppfx->label(i),m_ppfy->label(k)); // P + + // set labels of leftmost child + ppf.makeRepLabel(p_node+1,m_ppfx->label(i+1),m_ppfy->label(k+1)); + ppf.setRightBrotherIndex(p_node+1,p_node+1+1); + ppf.setNumChildren(p_node+1,0); // base node has no children + node++; + + // down alignment + assert(m_ppfx->noc(i)>=2); + assert(m_ppfy->noc(k)>=2); + noc=backtrack(ppf,i+1+1,m_ppfx->noc(i)-2,k+1+1,m_ppfy->noc(k)-2,node); // !! mdown !! + ppf.setNumChildren(p_node,noc+2); + + if(noc==0) + { + ppf.setRightBrotherIndex(p_node+1,p_node+1+1); + ppf.setRightBrotherIndex(p_node+1+1,0); + } + else + { + ppf.setRightBrotherIndex(ppf.getRightmostBrotherIndex2(p_node+1+1),node); + } + + + // set labels of leftmost child + ppf.makeRepLabel(node,m_ppfx->label(m_ppfx->getRightmostBrotherIndex2(i+1+1)),m_ppfy->label(m_ppfy->getRightmostBrotherIndex2(k+1+1))); + ppf.setRightBrotherIndex(node,0); + ppf.setNumChildren(node,0); // base node has no children + node++; + rb_node=node; // !! + + // right alignment + rbs=backtrack(ppf,m_ppfx->rb(i),j-1,m_ppfy->rb(k),l-1,node); + if(rbs) + ppf.setRightBrotherIndex(p_node,rb_node); + else + ppf.setRightBrotherIndex(p_node,0); + + return rbs+1; + } + } + else + { + h_score = m_alg->replace(m_ppfx->label(i), + getMtrxVal(m_ppfx->down(i),m_ppfy->down(k)), + m_ppfy->label(k), + getMtrxVal(m_ppfx->over(i,j),m_ppfy->over(k,l))); + + if(score == h_score) + { + // it is a replacement + ppf.makeRepLabel(p_node,m_ppfx->label(i),m_ppfy->label(k)); + + // down alignment + noc=backtrack(ppf,i+1,m_ppfx->noc(i),k+1,m_ppfy->noc(k),node); + ppf.setNumChildren(p_node,noc); + rb_node=node; + + // right alignment + rbs=backtrack(ppf,m_ppfx->rb(i),j-1,m_ppfy->rb(k),l-1,node); + if(rbs) + ppf.setRightBrotherIndex(p_node,rb_node); + else + ppf.setRightBrotherIndex(p_node,0); + + return rbs+1; + } + } + } + + // could it be a deletion + if(j>0) + { + h=k; // h is the node where the suffix of the split begins + for(r=0;r<=l;r++) // for all splits of fy + { + h_score = m_alg->del(m_ppfx->label(i), + getMtrxVal(m_ppfx->down(i),m_ppfy->indexpos(k,r)), + getMtrxVal(m_ppfx->over(i,j),m_ppfy->indexpos(h,l-r))); + + if(score == h_score) + { + // it is a deletion + ppf.makeDelLabel(p_node,m_ppfx->label(i)); + + // down alignment + noc=backtrack(ppf,i+1,m_ppfx->noc(i),k,r,node); + ppf.setNumChildren(p_node,noc); + rb_node=node; + + // right alignment + rbs=backtrack(ppf,m_ppfx->rb(i),j-1,h,l-r,node); + if(rbs) + ppf.setRightBrotherIndex(p_node,rb_node); + else + ppf.setRightBrotherIndex(p_node,0); + + return rbs+1; + } + + // if(rrb(h); + } + } + + // could it be an insertion + if(l>0) + { + h=i; + for(r=0;r<=j;r++) // for all splits of fx + { + h_score = m_alg->insert(getMtrxVal(m_ppfx->indexpos(i,r),m_ppfy->down(k)), + m_ppfy->label(k), + getMtrxVal(m_ppfx->indexpos(h,j-r),m_ppfy->over(k,l))); + + if(score == h_score) + { + // it is an insertion + ppf.makeInsLabel(p_node,m_ppfy->label(k)); + + // down alignment + noc=backtrack(ppf,i,r,k+1,m_ppfy->noc(k),node); + ppf.setNumChildren(p_node,noc); + rb_node=node; + + // right alignment + rbs=backtrack(ppf,h,j-r,m_ppfy->rb(k),l-1,node); + if(rbs) + ppf.setRightBrotherIndex(p_node,rb_node); + else + ppf.setRightBrotherIndex(p_node,0); + + return rbs+1; + } + + // if(rrb(h); + } + } + + // you should never be here + cerr << "Strange things happening in backtrack" << endl; + exit(EXIT_FAILURE); +} + + + +/* ****************************************** */ +/* Public functions */ +/* ****************************************** */ + +template +R Alignment::getGlobalOptimum() +{ + return getMtrxVal(m_ppfx->indexpos(0,m_ppfx->getMaxLength(0)),m_ppfy->indexpos(0,m_ppfy->getMaxLength(0))); +}; + +template +double Alignment::getGlobalOptimumRelative() +{ + double opt; + double max_x,max_y; + + opt=(double)getGlobalOptimum(); + + if(m_rnaAlg) + { + max_x=(double)m_ppfx->maxScore(*m_rnaAlg); + max_y=(double)m_ppfy->maxScore(*m_rnaAlg); + } + else + { + max_x=(double)m_ppfx->maxScore(*m_alg); + max_y=(double)m_ppfy->maxScore(*m_alg); + } + + assert(max_x+max_y>0); + opt=2*opt/(max_x+max_y); + + return opt; +}; + +template +R Alignment::getSILOptimum() +{ + R silOptimum; + int k=0; + Uint j,l=0; + Ulong n; + + n=m_ppfy->size(); + + if(m_rnaAlg) + silOptimum=m_rnaAlg->worst_score(); + else + silOptimum=m_alg->worst_score(); + + j=m_ppfx->getMaxLength(0); + + // find the best match + for(k=n-1;k>=0;k--) // for all nodes in fx + for(l=1;l<=m_ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + silOptimum=m_alg->choice(silOptimum,getMtrxVal(m_ppfx->indexpos(0,j),m_ppfy->indexpos(k,l))); + } + + return silOptimum; +} + +template +void Alignment::getOptGlobalAlignment(PPForestAli &ppfali) +{ + Uint node=0; + + // allocate a forest of the maximal size that a forest alignment can have + ppfali.initialize(m_ppfx->size()+m_ppfy->size()); + backtrack(ppfali,0,m_ppfx->getMaxLength(0),0,m_ppfy->getMaxLength(0),node); + ppfali.setSize(node); + ppfali.calcSumUpCSF(); + ppfali.calcRMB(); +} + +template +void Alignment::resetOptLocalAlignment(int suboptimalsPercent) +{ + m_localAlis.clear(); + m_suboptimalsPercent=suboptimalsPercent/100.0; + m_localSubOptimum=m_localOptimum; +}; + +// calculate the score of the next best local alignment that is not "included" +// in a local alignment returned by getOptLocalAlignment before +template +bool Alignment::nextLocalSuboptimum() +{ + Ulong m,n; + int i=0,k=0; + Uint j=0,l=0; + + m_localSubOptimum=m_alg->worst_score(); + m=m_ppfx->size(); + n=m_ppfy->size(); + + // find a matrix element that is optimal + for(i=m-1;i>=0;i--) // for all nodes in fx + for(k=n-1;k>=0;k--) // for all nodes in fx + for(j=1;j<=m_ppfx->getMaxLength(i);j++) // for all non empty csfs induced by i + for(l=1;l<=m_ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + bool disjoint=true; + + // check if i,j,k,l is included + typename list::const_iterator it; + for(it=m_localAlis.begin();it!=m_localAlis.end();it++) + { + if(!m_ppfx->isDisjoint(it->i,it->j,i,j) || !m_ppfy->isDisjoint(k,l,it->k,it->l)) + { + disjoint=false; + break; + } + + } + + if(disjoint) + { + if(getMtrxVal(m_ppfx->indexpos(i,j),m_ppfy->indexpos(k,l))>=m_suboptimalsPercent*m_localOptimum) + m_localSubOptimum=m_alg->choice(m_localSubOptimum,getMtrxVal(m_ppfx->indexpos(i,j),m_ppfy->indexpos(k,l))); + } + } + + return m_localSubOptimum!=m_alg->worst_score(); +} + +template +void Alignment::getOptLocalAlignment(PPForestAli &ppfali,Uint &xbasepos, Uint &ybasepos) +{ + Ulong m,n; + int i=0,k=0; + Uint j=0,l=0,node=0; + + m=m_ppfx->size(); + n=m_ppfy->size(); + // allocate a forest of the maximal size that a forest alignment can have + ppfali.initialize(m_ppfx->size()+m_ppfy->size()); + + // find a matrix element that is optimal + for(i=m-1;i>=0;i--) // for all nodes in fx + for(k=n-1;k>=0;k--) // for all nodes in fx + for(j=1;j<=m_ppfx->getMaxLength(i);j++) // for all non empty csfs induced by i + for(l=1;l<=m_ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + bool disjoint=true; + + // check if i,j,k,l is included + typename list::const_iterator it; + for(it=m_localAlis.begin();it!=m_localAlis.end();it++) + { + if(!m_ppfx->isDisjoint(it->i,it->j,i,j) || !m_ppfy->isDisjoint(k,l,it->k,it->l)) + { + disjoint=false; + break; + } + + } + + if(disjoint && getMtrxVal(m_ppfx->indexpos(i,j),m_ppfy->indexpos(k,l)) == m_localSubOptimum) + goto found; + } + + found: + backtrack(ppfali,i,j,k,l,node); + ppfali.setSize(node); + ppfali.calcSumUpCSF(); + ppfali.calcRMB(); + + m_localAlis.push_back(CSFPair(i,j,k,l)); + xbasepos=m_ppfx->countLeaves(i); + ybasepos=m_ppfy->countLeaves(k); +} + +template +void Alignment::getOptSILAlignment(PPForestAli &ppfali,Uint &ybasepos) +{ + R silOptimum; + Ulong m,n; + int k=0; + Uint j=0,l=0,node=0; + + m=m_ppfx->size(); + n=m_ppfy->size(); + // allocate a forest of the maximal size that a forest alignment can have + ppfali.initialize(m_ppfx->size()+m_ppfy->size()); + + silOptimum=getSILOptimum(); + j=m_ppfx->getMaxLength(0); + + // find a matrix element that is optimal + for(k=n-1;k>=0;k--) // for all nodes in fx + for(l=1;l<=m_ppfy->getMaxLength(k);l++) // for all non empty csfs induced by k + { + if(silOptimum == getMtrxVal(m_ppfx->indexpos(0,j),m_ppfy->indexpos(k,l))) + goto found; + } + + found: + backtrack(ppfali,0,j,k,l,node); + ppfali.setSize(node); + ppfali.calcSumUpCSF(); + ppfali.calcRMB(); + + ybasepos=m_ppfy->countLeaves(k); +} + + +#endif + + + + + + + + + + + + + + + + + + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/debug.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/debug.h new file mode 100755 index 000000000..88dc28739 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/debug.h @@ -0,0 +1,30 @@ +#ifndef _DEBUG_H_ +#define _DEBUG_H_ + +#include + +#ifndef RNAF_DEBUGLEVEL + #define RNAF_DEBUGLEVEL 5 +#endif + +#define DBG_OFF 6 +#define DBG_QWATCH 1 + +// program intern debug levels +#define DBG_BACKTRACK DBG_OFF +#define DBG_GET_PROFILE_STRUCTURE DBG_OFF +#define DBG_ALGEBRA DBG_OFF +#define DBG_ALIGNMENT DBG_OFF +#define DBG_MULTIPLE DBG_OFF + +#ifdef NDEBUG + #define TRACE(L,C,M) + #define WATCH(L,C,M) + #define QWATCH(L,C,M) +#else + #define TRACE(L,C,M) if(L <= RNAF_DEBUGLEVEL) cout << C << " - " << M << endl; + #define WATCH(L,C,M) if(L <= RNAF_DEBUGLEVEL) cout << C << " - " << #M << ": " << M << endl; + #define QWATCH(M) if(DBG_QWATCH <= RNAF_DEBUGLEVEL) cout << #M << ": " << M << endl; +#endif + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/fold.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/fold.h new file mode 100755 index 000000000..703aa2d0f --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/fold.h @@ -0,0 +1,8 @@ +/* function from fold.c */ +extern float fold(const char *sequence, char *structure); +/* calculate mfe-structure of sequence */ +extern float energy_of_struct(const char *string, const char *structure); +/* calculate energy of string on structure */ +extern void free_arrays(void); /* free arrays for mfe folding */ +extern void initialize_fold(int length); /* allocate arrays for folding */ +extern void update_fold_params(void); /* recalculate parameters */ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/fold_vars.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/fold_vars.h new file mode 100755 index 000000000..243f50465 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/fold_vars.h @@ -0,0 +1,37 @@ +/* to use floats instead of doubles in pf_fold() comment next line */ +#define LARGE_PF +#ifdef LARGE_PF +#define FLT_OR_DBL double +#else +#define FLT_OR_DBL float +#endif + +extern int noGU; /* GU not allowed at all */ +extern int no_closingGU; /* GU allowed only inside stacks */ +extern int tetra_loop; /* Fold with specially stable 4-loops */ +extern int energy_set; /* 0 = BP; 1=any mit GC; 2=any mit AU-parameter */ +extern int dangles; /* use dangling end energies (not in part_func!) */ +/*@null@*/ +extern char *nonstandards; /* contains allowed non standard bases */ +extern double temperature; /* rescale parameters to this temperature */ +extern int james_rule; /* interior loops of size 2 get energy 0.8Kcal and + no mismatches, default 1 */ +extern int logML; /* use logarithmic multiloop energy function */ +extern int cut_point; /* first position of 2nd strand for co-folding */ + +struct bond { /* base pair */ + int i; + int j; +}; +typedef struct bond bondT; +extern bondT *base_pair; /* list of base pairs */ + +extern FLT_OR_DBL *pr; /* base pairing prob. matrix */ +extern int *iindx; /* pr[i,j] -> pr[iindx[i]-j] */ +extern double pf_scale; /* scaling factor to avoid float overflows*/ +extern int fold_constrained; /* fold with constraints */ +extern int do_backtrack; /* calculate pair prob matrix in part_func() */ +extern int noLonelyPairs; /* avoid helices of length 1 */ +extern char backtrack_type; /* usually 'F'; 'C' require (1,N) to be bonded; + 'M' seq is part of a multi loop */ +char * option_string(void); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/glib.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/glib.c new file mode 100755 index 000000000..ea99e5214 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/glib.c @@ -0,0 +1,355 @@ +#include "graphtypes.h" +#include +#include +#include + +void AddEdge (Graph g,int n,int m,int label) +{ Edge edge1,edge2; + + edge1 = (Edge) malloc(2*sizeof(struct edge_ent)); + edge2 = edge1 + 1; + + edge1->label = label; + edge1->endpoint = m; + edge1->otheredge = edge2; + edge1->prevedge = NULL; + edge1->nextedge = g[n].adj_list; + if (edge1->nextedge != NULL) + edge1->nextedge->prevedge = edge1; + g[n].adj_list = edge1; + g[n].degree++; + + edge2->label = label; + edge2->endpoint = n; + edge2->otheredge = edge1; + edge2->prevedge = NULL; + edge2->nextedge = g[m].adj_list; + if (edge2->nextedge != NULL) + edge2->nextedge->prevedge = edge2; + g[m].adj_list = edge2; + g[m].degree++; +} + +Edge FindEdge(Graph graph,int i,int j) +{ Edge edge; + + edge = graph[i].adj_list; + while (edge!=NULL && edge->endpoint!=j) + edge = edge->nextedge; + if (edge==NULL) return(NULL); + else return(edge); +} + +int RemoveEdge(Graph graph,Edge edge) +{ Edge other; + int i,j; + + if (edge==NULL) return(0); + other = edge->otheredge; + i = other->endpoint; + j = edge->endpoint; + graph[i].degree--; graph[j].degree--; + if (edge->prevedge == NULL) { + graph[i].adj_list = edge->nextedge; + if (edge->nextedge != NULL) + edge->nextedge->prevedge = NULL; + } + else if (edge->nextedge == NULL) + (edge->prevedge)->nextedge = NULL; + else { + (edge->nextedge)->prevedge = edge->prevedge; + (edge->prevedge)->nextedge = edge->nextedge; + } + if (other->prevedge == NULL) { + graph[j].adj_list = other->nextedge; + if (other->nextedge != NULL) + other->nextedge->prevedge = NULL; + } + else if (other->nextedge == NULL) + (other->prevedge)->nextedge = NULL; + else { + (other->nextedge)->prevedge = other->prevedge; + (other->prevedge)->nextedge = other->nextedge; + } + free((edge < other) ? edge : other); + return(1); +} + +int NumEdges(Graph g) +{ int i,size,edges; + + edges = 0; + size = Degree(g,0); + for (i=1; i<=size; i++) + edges += Degree(g,i); + edges /= 2; + return(edges); +} + +Graph NewGraph(int size) +{ Graph tmp; + int i; + + tmp = (Graph) malloc((size+1)*sizeof(struct node_entry)); + for (i=1; i<=size; i++) { + Degree(tmp,i) = 0; + FirstEdge(tmp,i) = NULL; + NLabel(tmp,i) = i; + } + Degree(tmp,0) = size; + return(tmp); +} + +EuclidGraph NewEuclid(int size) +{ + EuclidGraph xy; + + xy = (EuclidGraph) malloc((size+1)*2*sizeof(int)); + xy[0][0] = size; + return(xy); +} + +MatrixGraph NewMatrix(int size) +{ + MatrixGraph graph; + int i; + + graph = (MatrixGraph) malloc((size*(size+1)+1)*sizeof(int)); + graph[0] = size; + + for (i=1; i<=size; i++) /* zero the diagonal */ + graph[i*(size+1)] = 0; + + return(graph); +} + +Graph CopyGraph(Graph g) +{ int i,j,size; + Edge edge; + Graph cp; + + size = Degree(g,0); + cp = NewGraph(size); + for (i=1; i<=size; i++) { + Xcoord(cp,i) = Xcoord(g,i); + Ycoord(cp,i) = Ycoord(g,i); + edge = FirstEdge(g,i); + for (j=1; j<=Degree(g,i); j++) { + if (i < EndPoint(edge)) + AddEdge(cp,i,EndPoint(edge),ELabel(edge)); + edge = NextEdge(edge); + } + } + return (cp); +} + +/* Graph I/O routines */ + +Graph ReadGraph (int *size,char *file) +{ Graph graph; + FILE *fp; + char c; + int edges, degree, vlabel, elabel, adj_node, i, j; + int xcoord, ycoord; + + if (file[0] == '\0') fp = stdin; + else fp = fopen(file,"r"); + if (fp==NULL) { + printf("ReadGraph: file %s can't be opened\n",file); + exit(0); + } + fscanf(fp,"%d%d %c",size,&edges,&c); + if (c !='U' && c!='u') { + printf("ReadGraph: file %s does not contain an undirected graph\n",file); + exit(0); + } + while (getc(fp)!='\n') ; + + graph = NewGraph(*size); + for (i = 1; i <= *size; ++i) { + fscanf(fp,"%d%d%d%d",°ree,&vlabel,&xcoord,&ycoord); + NLabel(graph,i) = vlabel; + Xcoord(graph,i) = xcoord; + Ycoord(graph,i) = ycoord; + while (getc(fp)!='\n') ; + for (j = 1; j <= degree; ++j) { + fscanf(fp,"%d%d", &adj_node, &elabel); + while (getc(fp)!='\n') ; + if (i>1; + l = (l + k/l)>>1; + l = (l + k/l)>>1; + l = (l + k/l)>>1; + return ((l*l .000000001) ? l+1 : l); +} + + +int eucdistsq(EuclidGraph graph,int i,int j) /* Find the square of the dist between two points */ +{ + register int dv,dh; + + dv = graph[i][0]-graph[j][0]; + dh = graph[i][1]-graph[j][1]; + return(dv*dv+dh*dh); +} + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/glib.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/glib.o new file mode 100755 index 000000000..656641e8d Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/glib.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/graphtypes.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/graphtypes.h new file mode 100755 index 000000000..4bf4b8327 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/graphtypes.h @@ -0,0 +1,89 @@ +#ifndef _GRAPHTYPES_H_ +#define _GRAPHTYPES_H_ + +#define INF 100000000 + +#ifndef NULL +#define NULL 0 +#endif + +struct node_entry { + int degree; + int label; + int x; + int y; + struct edge_ent *adj_list; + }; +typedef struct node_entry *Graph; + +struct edge_ent { + int endpoint; + int label; + int label2; + struct edge_ent *nextedge; + struct edge_ent *prevedge; + struct edge_ent *otheredge; + }; +typedef struct edge_ent *Edge; + +#define Degree(graph,n) (graph[n].degree) +#define NLabel(graph,n) (graph[n].label) +#define Xcoord(graph,n) (graph[n].x) +#define Ycoord(graph,n) (graph[n].y) +#define FirstEdge(graph,n) (graph[n].adj_list) + +#define EndPoint(e) (e->endpoint) +#define ELabel(e) (e->label) +#define ELabel2(e) (e->label2) +#define Other(e) (e->otheredge) +#define NextEdge(e) (e->nextedge) + + +extern Graph Prim(); +//extern int *EulerTraverse(),*Match(),*Weighted_Match(),*Dijkstra(),*Concomp(); + +/* Euclidean graph type */ +typedef int (*EuclidGraph)[2]; + +extern Graph EuclidPrim(); +extern EuclidGraph ReadEuclid(),NewEuclid(); +extern int eucdist(),eucdistsq(); + +extern int *CvxHull(); + +/* Distance matrix graph type */ +typedef int *MatrixGraph; + +extern int *MatrixDijkstra(); +extern Graph MatrixPrim(); +extern Graph MatrixMaxFlow(); +extern MatrixGraph ReadMatrix(), NewMatrix(); + +#ifdef __cplusplus +extern "C" +{ +#endif + +void AddEdge (Graph g,int n,int m,int label); +Edge FindEdge(Graph graph,int i,int j); +int RemoveEdge(Graph graph,Edge edge); +int NumEdges(Graph g); +Graph NewGraph(int size); +EuclidGraph NewEuclid(int size); +MatrixGraph NewMatrix(int size); +Graph CopyGraph(Graph g); +Graph ReadGraph (int *size,char *file); +void WriteGraph (Graph graph,char *file); +EuclidGraph ReadEuclid(int *size,char *file); +void WriteEuclid(EuclidGraph graph,char *file); +MatrixGraph ReadMatrix(int *size,char *file); +void WriteMatrix(MatrixGraph graph,char *file); +int eucdist (EuclidGraph graph,int i,int j); +int eucdist2 (EuclidGraph graph,int i,int j); +int eucdistsq(EuclidGraph graph,int i,int j); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/main.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/main.cpp new file mode 100755 index 000000000..0bd487718 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/main.cpp @@ -0,0 +1,908 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +//#include +#include +#include + +#ifndef WIN32 +#include "config.h" +#endif + +#include "Arguments.h" +#include "alignment.h" +#include "debug.h" + +//#include "global_alignment.h" +#include "treeedit.h" + +#include "misc.h" +#include "progressive_align.h" +#include "rna_alignment.h" +#include "rnaforest.h" +#include "rnaforestsz.h" +#include "rnafuncs.h" +#include "rna_profile_alignment.h" +#include "rna_algebra.h" +#include "rnaforester_options.h" + + +#include "alignment.t.cpp" +//#include "global_alignment.t.cpp" +#include "treeedit.t.cpp" +//#include "ppforest.t.cpp" + +using namespace std; + +/* ****************************************** */ +/* Definitions and typedefs */ +/* ****************************************** */ + +struct ToLower : public unary_function { + char operator()(char a) + { + return tolower(a); + }; +}; + +template +void makeDotFileAli(const PPForest &ppf, const RNAforesterOptions &options) +{ + if(options.has(RNAforesterOptions::OutputAlignmentDotFormat)) + { + string filename; + options.get(RNAforesterOptions::OutputAlignmentDotFormat,filename,string("ali.dot")); + ofstream s(filename.c_str()); + ppf.printDot(s); + } +} + +template +void makeDotFileInp(const PPForest &ppf, const RNAforesterOptions &options, Uint count) +{ + if(options.has(RNAforesterOptions::MakeDotForInputTrees)) + { + ostringstream ss; + ofstream os; + ss << "input" << count << ".dot"; + os.open(ss.str().c_str()); + ppf.printDot(os); + os.close(); + } +} + +static const string RNAFORESTER_VERSION = "1.5"; +static const string PROMPT = "Input string (upper or lower case); & to end for multiple alignments, @ to quit\n"; +static const string SCALE = "....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8\n"; + +void alignMultiple(deque &alignList, Score &score,const RNAforesterOptions &options); +void alignPairwise(deque &inputListPW,Score &score,const RNAforesterOptions &options); +void cutAfterChar(string &s,char c); + +void editPairwise(list &inputListSZ,Score &score,RNAforesterOptions &options); +void alignPairwiseSimple(deque &inputListPW,Score &score,RNAforesterOptions &options); + +static void showversion(const char *prog) +{ + cout << prog << ", version " << RNAFORESTER_VERSION << endl; + cout << "Copyright Matthias Hoechsmann 2001-2004," << endl << "mhoechsm@techfak.uni-bielefeld.de" << endl; +} + +int main(int argc, const char **argv) +{ + string buffer; + string baseStr,viennaStr,nameStr; + Ulong basePairCount,maxDepth; + deque inputListPW; + deque alignList; + bool showScale=true,multipleAlign=false; + istream *inputStream=NULL; + ifstream *inputFile=NULL; + Uint structure_count=1; + int suboptPercent=100; + double minPairProb=0.25; + + list inputListSZ; + + try + { + RNAforesterOptions options(argc,argv); + + // check options + if(options.has(RNAforesterOptions::Help)) + { + options.help(); + exit(EXIT_SUCCESS); + } + + if(options.has(RNAforesterOptions::SecretHelp)) + { + options.secretHelp(); + exit(EXIT_SUCCESS); + } + + if(options.has(RNAforesterOptions::Version)) + { + showversion(argv[0]); + exit(EXIT_SUCCESS); + } + + // read score values + Score score(options); + if(!options.has(RNAforesterOptions::ShowOnlyScore)) + score.print(); + + // check option suboptimals + if(options.has(RNAforesterOptions::LocalSubopts)) + { + options.get(RNAforesterOptions::LocalSubopts,suboptPercent,100); + if(suboptPercent<0 || suboptPercent>100) + { + cerr << "error: value for parameter --subopts must be in range from 0 to 100" << endl; + exit(EXIT_FAILURE); + } + } + +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library + options.get(RNAforesterOptions::PredictMinPairProb,minPairProb,0.25); + if(options.has(RNAforesterOptions::PredictProfile)) + cout << "Minumim required basepair probability (-pmin): " << minPairProb << endl; +#endif + + // show if suboptimals + if(!options.has(RNAforesterOptions::ShowOnlyScore)) + if(options.has(RNAforesterOptions::LocalSimilarity) && options.has(RNAforesterOptions::LocalSubopts)) + cout << "calculate suboptimals within " << suboptPercent << "% of global optimum" << endl << endl; + + // profile search + if(options.has(RNAforesterOptions::ProfileSearch)) + { + string filename; + + options.get(RNAforesterOptions::ProfileSearch,filename,string("")); + if(filename=="") + { + cerr << "no profile filename" << endl; + exit(EXIT_FAILURE); + } + + RNAProfileAlignment *rnaProfileAli=new RNAProfileAlignment(filename); + alignList.push_back(rnaProfileAli); + } + + if(options.has(RNAforesterOptions::ReadFromFile)) + { + string filename; + options.get(RNAforesterOptions::ReadFromFile,filename,string("")); + inputFile=new ifstream(filename.c_str()); + if(inputFile->fail()) + { + cerr << "cannot open file: \"" << filename << "\"" << endl; + exit(EXIT_FAILURE); + } + inputStream=inputFile; + } + else + { + inputStream=&cin; + } + + + if(showScale) + { + if(!options.has(RNAforesterOptions::NoScale) && !options.has(RNAforesterOptions::ReadFromFile)) + cout << endl << PROMPT << SCALE; + showScale=false; + } + + for(;;) + { + getline(*inputStream,buffer); + + if(inputStream->eof()) + { + if(options.has(RNAforesterOptions::Multiple) && !options.has(RNAforesterOptions::ProfileSearch)) + buffer="&"; + else + exit(EXIT_SUCCESS); + } + + if(buffer.empty()) + continue; + + // quit if character is @ + if(buffer[0]=='@') + break; + + // delete '\r' at line end from non unix files + if(buffer[buffer.size()-1]=='\r') + buffer.erase(buffer.size()-1); + + // check for name of structure + if(buffer[0]=='>') + { + nameStr=&buffer[1]; + continue; + } + + // cut after blank + cutAfterChar(buffer,' '); + + // check for aligning multiple structures + // if input is read from file the eof has the same meaning as & + if( buffer[0]=='&') + multipleAlign=true; + else + { + // check for base string + + if(RNAFuncs::isRNAString(buffer)) + { + baseStr=buffer; + // convert to small letters + transform(baseStr.begin(),baseStr.end(),baseStr.begin(),ToLower()); + // t -> u + replace(baseStr.begin(),baseStr.end(),'t','u'); + // delete '.' and '-' from alignment files + remove(baseStr.begin(),baseStr.end(),'.'); + remove(baseStr.begin(),baseStr.end(),'-'); + +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library + if(options.has(RNAforesterOptions::PredictProfile)) + { + ostringstream ss; + string constraint; + + // if there is no name given (> ...) use a counter + if(nameStr=="") + ss << "> " << structure_count; + else + ss << nameStr; + + cout << "Predicting structure profile for sequence: " << ss.str() << endl; + RNAProfileAlignment *rnaProfileAli=new RNAProfileAlignment(baseStr,ss.str(),constraint,minPairProb); + alignList.push_back(rnaProfileAli); + makeDotFileInp(*rnaProfileAli,options,structure_count); + structure_count++; + } +#endif + + // continue; + } + else + { + + // check for vienna string + if(RNAFuncs::isViennaString(buffer,basePairCount,maxDepth)) + { + +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library + // skip structure lines if structures are predicted + if(options.has(RNAforesterOptions::PredictProfile)) + { + cout << "ignoring structure: " << buffer << endl; + continue; + } +#endif + + viennaStr=buffer; + } + else + { + cerr << "The input sequence is neither an RNA/DNA string nor in vienna format." << endl; + cerr << "line: " << buffer << endl; + showScale=true; + exit(EXIT_FAILURE); + } + + // add structure to input list + if(options.has(RNAforesterOptions::Multiple)) + { + ostringstream ss; + + // if there is no name given (> ...) use a counter + if(nameStr=="") + ss << "> " << structure_count; + else + ss << nameStr; + + + RNAProfileAlignment *rnaProfileAli=new RNAProfileAlignment(baseStr,viennaStr,ss.str()); + makeDotFileInp(*rnaProfileAli,options,structure_count); + alignList.push_back(rnaProfileAli); + } + else + { + if(options.has(RNAforesterOptions::TreeEdit)) + { + RNAForestSZ *rnaForestSZ=new RNAForestSZ(baseStr,viennaStr,nameStr); + inputListSZ.push_back(rnaForestSZ); + } + else + { + RNAForest *rnaForest=new RNAForest(baseStr,viennaStr,nameStr); + nameStr=""; + makeDotFileInp(*rnaForest,options,structure_count); + inputListPW.push_back(rnaForest); + } + } + + structure_count++; + showScale=true; + } + } + + // ***** multiple alignment + if((options.has(RNAforesterOptions::Multiple) && multipleAlign) || (options.has(RNAforesterOptions::ProfileSearch) && alignList.size()==2)) + { + alignMultiple(alignList,score,options); + multipleAlign=false; + structure_count=1; + + if(options.has(RNAforesterOptions::ProfileSearch)) + { + string filename; + + options.get(RNAforesterOptions::ProfileSearch,filename,string("")); + RNAProfileAlignment *rnaProfileAli=new RNAProfileAlignment(filename); + alignList.push_back(rnaProfileAli); + } + else + break; + + // break; + } + + // ***** pairwise alignment + if(inputListPW.size()==2) + { + if(options.has(RNAforesterOptions::GlobalAlignment)) + alignPairwiseSimple(inputListPW,score,options); + else + alignPairwise(inputListPW,score,options); + break; + } + + if(inputListSZ.size()==2) + { + editPairwise(inputListSZ,score,options); + break; + } + + } + + // free dynamic allocated memory + deque::const_iterator it; + for(it = inputListPW.begin(); it!=inputListPW.end(); it++) + delete *it; + + DELETE(inputFile); + + // getchar(); // only for testing + return (0); + } + catch(RNAforesterOptions::IncompatibleException e) + { + e.showError(); + return(EXIT_FAILURE); + } + catch(RNAforesterOptions::RequiresException e) + { + e.showError(); + return(EXIT_FAILURE); + } +} + + + +void cutAfterChar(string &s,char c){ + string::size_type pos=s.find(c); + if(pos!=string::npos) + s.erase(pos); +} + +void alignMultiple(deque &alignList, Score &score,const RNAforesterOptions &options) +{ + DoubleScoreProfileAlgebraType *alg; + deque > resultList; +// double optScore; + Uint clusterNr=1; + double minPairProb; + + options.get(RNAforesterOptions::ConsensusMinPairProb,minPairProb,0.5); + + // distance or similarity + if(options.has(RNAforesterOptions::CalculateDistance)) + alg=new DoubleDistProfileAlgebra(score); + else + alg=new DoubleSimiProfileAlgebra(score); + + cout << endl; + + progressiveAlign(alignList,resultList,alg,options); + + cout << endl; + cout << "*** Results ***" << endl << endl; + cout << "Minimum basepair probability for consensus structure (-cmin): " << minPairProb << endl << endl; + + deque >::const_iterator it; + for(it=resultList.begin();it!=resultList.end();it++) + { + cout << "RNA Structure Cluster Nr: " << clusterNr << endl; + cout << "Score: " << it->first << endl; + cout << "Members: " << it->second->getNumStructures() << endl << endl; + + if(options.has(RNAforesterOptions::FastaOutput)) + { + it->second->printFastaAli(false); + cout << endl; + } + else + { + + it->second->printSeqAli(); + +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library + // print alignment + it->second->printStrAli(); + cout << endl; +#endif + } + + // save profile + if(options.has(RNAforesterOptions::SaveProfile)) + { + string filename; + filename=options.generateFilename(RNAforesterOptions::SaveProfile,".pro", "rna.pro",clusterNr); + it->second->save(filename); + } + + + // print consensus structure + cout << "Consensus sequence/structure:" << endl; + it->second->printConsensus(minPairProb); + cout << endl; + +#ifdef HAVE_LIBG2 // This features require the g2 library + // generate squiggle plots + if(options.has(RNAforesterOptions::MakeSquigglePlot)) + { + RNAProfileAlignment::SquigglePlotOptions sqOptions; + string filename; + + // plot showing full base information + filename=options.generateFilename(RNAforesterOptions::MakeSquigglePlot,".ps", "rnaprofile.ps",clusterNr); + sqOptions.greyColors=options.has(RNAforesterOptions::SquiggleGreyColors); + sqOptions.minPairProb=minPairProb; + sqOptions.mostLikelySequence=false; + it->second->squigglePlot(filename,sqOptions); + + // plot showing consensus sequence + filename=options.generateFilename(RNAforesterOptions::MakeSquigglePlot,"_cons.ps", "rnaprofile_cs.ps",clusterNr); + sqOptions.mostLikelySequence=true; + it->second->squigglePlot(filename,sqOptions); + } +#endif + + clusterNr++; + } + + + /* + if(!options.has(RNAforesterOptions::ShowOnlyScore)) + { + cout << "global optimal score: "; + } + cout << optScore << endl; + + list::iterator it=inputMapProfile.begin(); + RNAProfileAlignment *ppf=it; + if(!options.has(RNAforesterOptions::ShowOnlyScore)) + { + // generate dot file + makeDotFileAli(*ppf,options); + + ppf->print(); + cout << endl; + ppf->printConsensus(); + } + */ + + // save profile alignment to binary file + /* if(options.has(RNAforesterOptions::SaveMultipleAliFile)) + { + string filename; + + filename=generateFilename(options,RNAforesterOptions::SaveMultipleAliFile,".mta", "unknown.dot"); + ofstream s(filename.c_str()); + f1->save(s); + } + */ + + /* + // generate squiggle plots + if(options.has(RNAforesterOptions::MakeSquigglePlot)) + { + RNAProfileAlignment::SquigglePlotOptions sqOptions; + string filename; + + // plot showing full base information + filename=options.generateFilename(RNAforesterOptions::MakeSquigglePlot,".ps", "rnaprofile.ps"); + sqOptions.greyColors=options.has(RNAforesterOptions::SquiggleGreyColors); + sqOptions.mostLikelySequence=false; + ppf->squigglePlot(filename,sqOptions); + + // plot showing consensus sequence + filename=options.generateFilename(RNAforesterOptions::MakeSquigglePlot,"_cons.ps", "rnaprofile_cons.ps"); + sqOptions.greyColors=options.has(RNAforesterOptions::SquiggleGreyColors); + sqOptions.mostLikelySequence=true; + ppf->squigglePlot(filename,sqOptions); + } + */ + + + delete alg; +} + + +void alignPairwise(deque &inputListPW,Score &score,const RNAforesterOptions &options) +{ + IntScoreRNA_AlgebraType *alg; + Uint xbasepos,ybasepos,xlen,ylen; + list > xsubopts; + list > ysubopts; + string seq1,seq2,str1,str2; + char s[8]; + int suboptPercent; + Uint count=1; + RNAFuncs::SquigglePlotOptions sqOptions; + tms tmsStart, tmsEnd; + + // read options + options.get(RNAforesterOptions::LocalSubopts,suboptPercent,100); + +#ifdef HAVE_LIBG2 // This features require the g2 library + // generate squiggle plot + if(options.has(RNAforesterOptions::MakeSquigglePlot)) + { + // get sq options + sqOptions.hideBaseNumbers=options.has(RNAforesterOptions::SquiggleHideBaseNumbers); + options.get(RNAforesterOptions::SquiggleBaseNumberInterval,sqOptions.baseNumInterval,(Uint)20); + sqOptions.greyColors=options.has(RNAforesterOptions::SquiggleGreyColors); + options.get(RNAforesterOptions::SquiggleScaleFactor,sqOptions.scale,1.0); + sqOptions.generateFIG=options.has(RNAforesterOptions::SquiggleGenerateFIG); +#ifdef HAVE_LIBGD + sqOptions.generatePNG=options.has(RNAforesterOptions::SquiggleGeneratePNG); + sqOptions.generateJPG=options.has(RNAforesterOptions::SquiggleGenerateJPG); +#endif + + } +#endif + + // distance or similarity + if(options.has(RNAforesterOptions::CalculateDistance)) + alg=new IntDistRNA_Algebra(score); + else + { + if(options.has(RNAforesterOptions::RIBOSUMScore)) + alg=new RIBOSUM8560(score); + else + alg=new IntSimiRNA_Algebra(score); + } + + RNAForest *f1=inputListPW.front(); + RNAForest *f2=inputListPW.back(); + + if(options.has(RNAforesterOptions::SpaceTimeInfo)) + { + IntScore_AlgebraType *algGlobClassic; + + algGlobClassic=new IntDist_Algebra(score); + + if(!options.has(RNAforesterOptions::ShowOnlyScore)) + { + cout << "F1_NUMNODES" << ";"; + cout << "F2_NUMNODES" << ";"; + cout << "F1_DEGREE" << ";"; + cout << "F2_DEGREE" << ";"; + cout << "F1_LEAVES" << ";"; + cout << "F2_LEAVES" << ";"; + cout << "F1_DEPTH" << ";"; + cout << "F2_DEPTH" << ";"; + cout << "F1_NUMCSFS" << ";"; + cout << "F2_NUMCSFS" << ";"; + cout << "TABLE_SIZE_4D" << ";"; + cout << "TABLE_SIZE_2D" << ";"; + cout << "GLOBALI_TIME" << ";"; + cout << "GLOBALI_TIME_SPEEDUP" << ";"; + cout << "LOCALALI_TIME" << ";"; + cout << "LOCALALI_TIME_SPEEDUP" << ";"; + + cout << endl; + } + + cout << f1->size() << "\t"; + cout << f2->size() << "\t"; + cout << f1->maxDegree() << "\t"; + cout << f2->maxDegree() << "\t"; + cout << f1->numLeaves() << "\t"; + cout << f2->numLeaves() << "\t"; + cout << f1->maxDepth() << "\t"; + cout << f2->maxDepth() << "\t"; + cout << f1->getNumCSFs() << "\t"; + cout << f2->getNumCSFs() << "\t"; + cout << f1->size()*f2->size()*f1->maxDegree()*f1->maxDegree() << "\t"; + cout << f1->getNumCSFs()*f2->getNumCSFs() << "\t"; + + // global alignment + { + times(&tmsStart); + Alignment ali(f1,f2,*algGlobClassic,false,true); + times(&tmsEnd); + cout <<((double) (tmsEnd.tms_utime - tmsStart.tms_utime))/sysconf(_SC_CLK_TCK) << "\t"; + // cerr << "#" << ali.getGlobalOptimum() << "#"; + } + + // global alignment speedup + { + times(&tmsStart); + Alignment ali(f1,f2,*algGlobClassic,false,false); + times(&tmsEnd); + cout <<((double) (tmsEnd.tms_utime - tmsStart.tms_utime))/sysconf(_SC_CLK_TCK) << "\t"; + // cerr << "#" << ali.getGlobalOptimum() << "#"; + } + + // local alignment + { + times(&tmsStart); + Alignment ali(f1,f2,*algGlobClassic,true,true); + times(&tmsEnd); + cout <<((double) (tmsEnd.tms_utime - tmsStart.tms_utime))/sysconf(_SC_CLK_TCK) << "\t"; + // cerr << "#" << ali.getLocalOptimum() << "#"; + } + + // local alignment speedup + { + times(&tmsStart); + Alignment ali(f1,f2,*algGlobClassic,true,false); + times(&tmsEnd); + cout <<((double) (tmsEnd.tms_utime - tmsStart.tms_utime))/sysconf(_SC_CLK_TCK) << "\t"; + // cerr << "#" << ali.getLocalOptimum() << "#"; + } + + + cout << endl; + + exit(EXIT_SUCCESS); + } + + Alignment ali(f1,f2,*alg); + RNA_Alignment ppfali; + ppfali.setStructureNames(f1->getName(),f2->getName()); + + + if(!options.has(RNAforesterOptions::ShowOnlyScore)) + { + if(options.has(RNAforesterOptions::SmallInLarge)) + { + cout << "small-in-large optimal score: "; + } + else + { + if(options.has(RNAforesterOptions::LocalSimilarity)) + cout << "local optimal score: "; + else + cout << "global optimal score: "; + } + } + + if(options.has(RNAforesterOptions::SmallInLarge)) + { + cout << ali.getSILOptimum() << endl; + } + else + { + if(options.has(RNAforesterOptions::LocalSimilarity)) + { + cout << ali.getLocalOptimum() << endl; + } + else + { + cout << ali.getGlobalOptimum() << endl; + if(options.has(RNAforesterOptions::RelativeScore)) + cout << ali.getGlobalOptimumRelative() << endl; + } + } + + + if(!options.has(RNAforesterOptions::ShowOnlyScore)) + { + if(options.has(RNAforesterOptions::SmallInLarge)) + { + ali.getOptSILAlignment(ppfali,ybasepos); + cout << "starting at position: " << ybasepos << endl << endl; + } + else + { + if(options.has(RNAforesterOptions::LocalSimilarity)) + { + ali.resetOptLocalAlignment(suboptPercent); + ali.getOptLocalAlignment(ppfali,xbasepos,ybasepos); + cout << "starting at positions: " << xbasepos << "," << ybasepos << endl << endl; + } + else + ali.getOptGlobalAlignment(ppfali); + } + + // generate dot file + makeDotFileAli(ppfali,options); + + // print alignment + ppfali.getSequenceAlignments(seq1,seq2); + ppfali.getStructureAlignment(str1,true); + ppfali.getStructureAlignment(str2,false); + + if(options.has(RNAforesterOptions::FastaOutput)) + { + cout << ppfali.getStructureNameX() << endl; + cout << seq1 << endl; + cout << str1 << endl; + cout << ppfali.getStructureNameY() << endl; + cout << seq2 << endl; + cout << str2 << endl; + cout << endl; + } + else + RNAFuncs::printAli(ppfali.getStructureNameX(),ppfali.getStructureNameY(),seq1,seq2,str1,str2); + + + xlen=seq1.size(); + ylen=seq2.size(); + if(options.has(RNAforesterOptions::LocalSimilarity)) + { + xsubopts.push_back(pair(xbasepos,xlen)); + ysubopts.push_back(pair(ybasepos,ylen)); + } + +#ifdef HAVE_LIBG2 // This features require the g2 library + if(options.has(RNAforesterOptions::MakeSquigglePlot)) + { + sprintf(s,"%d",count); + ppfali.squigglePlot(s,sqOptions); + } +#endif + + // suboptimal alignments + if(options.has(RNAforesterOptions::LocalSubopts)) + { + while(ali.nextLocalSuboptimum()) + { + count++; + cout << "local optimal score: "; + cout << ali.getLocalOptimum() << endl; + ali.getOptLocalAlignment(ppfali,xbasepos,ybasepos); + cout << "starting at positions: " << xbasepos << "," << ybasepos << endl << endl; + + // print alignment + ppfali.getSequenceAlignments(seq1,seq2); + ppfali.getStructureAlignment(str1,true); + ppfali.getStructureAlignment(str2,false); + RNAFuncs::printAli(ppfali.getStructureNameX(),ppfali.getStructureNameY(),seq1,seq2,str1,str2); + xlen=seq1.size(); + ylen=seq2.size(); + xsubopts.push_back(pair(xbasepos,xlen)); + ysubopts.push_back(pair(ybasepos,ylen)); + +#ifdef HAVE_LIBG2 // This features require the g2 library + if(options.has(RNAforesterOptions::MakeSquigglePlot)) + { + sprintf(s,"%d",count); + ppfali.squigglePlot(s,sqOptions); + } +#endif + } + } + + } + +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library + // generate xml + if(options.has(RNAforesterOptions::GenerateXML)) + { + string filename; + + filename=options.generateFilename(RNAforesterOptions::GenerateXML,".xml", "ali.xml"); + ofstream s(filename.c_str()); + ppfali.generateXML(s); + } +#endif + +#ifdef HAVE_LIBG2 // This features require the g2 library + // generate squiggle plot + if(options.has(RNAforesterOptions::MakeSquigglePlot)) + { + f1->plot2d("x_str", xsubopts, sqOptions); + f2->plot2d("y_str", ysubopts, sqOptions); + } +#endif + + // clear input list + deque::const_iterator it; + for(it = inputListPW.begin(); it!=inputListPW.end(); it++) + delete *it; + inputListPW.clear(); + delete alg; +} + + +void editPairwise(list &inputListSZ,Score &score,RNAforesterOptions &options) +{ + // timeb t1,t2; + IntScoreSZAlgebraType *alg; + +// if(options.has(RNAforesterOptions::CalculateDistance)) + alg=new IntDistSZAlgebra(score); +// else +// alg=new IntSimiSZAlgebra(score); + + RNAForestSZ *f1=inputListSZ.front(); + RNAForestSZ *f2=inputListSZ.back(); + + // ftime(&t1); + Mapping mapping(f1,f2,*alg); + // ftime(&t2); + +// f1->printParameters("F1"); +// f2->printParameters("F2"); + + cout << "Global optimum: " << mapping.getGlobalOptimum() << endl; + // cout << "Calculation Time ms: " << (t2.time*1000+t2.millitm) - (t1.time*1000+t1.millitm) << endl; +} + + + +void alignPairwiseSimple(deque &inputListPW,Score &score,RNAforesterOptions &options) +{ + // timeb t1,t2; + IntScore_AlgebraType *alg; + +// if(options.has(RNAforesterOptions::CalculateDistance)) + alg=new IntDist_Algebra(score); +// else +// alg=new ScoreAlgebraSimple(score); + + RNAForest *f1=inputListPW.front(); + RNAForest *f2=inputListPW.back(); + + // ftime(&t1); + Alignment ali(f1,f2,*alg,false); + // ftime(&t2); + +// f1->printParameters("F1"); + //f2->printParameters("F2"); + + cout << "Global optimum: " << ali.getGlobalOptimum() << endl; + // cout << "Calculation Time ms: " << (t2.time*1000+t2.millitm) - (t1.time*1000+t1.millitm) << endl; +} + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/main.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/main.o new file mode 100755 index 000000000..49733abbe Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/main.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/match.defs b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/match.defs new file mode 100755 index 000000000..0e194e4f1 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/match.defs @@ -0,0 +1,40 @@ +#define MAXWT 1000000 + +#define NULL 0 + + +/* the number of the blossom entered by edge e */ +#define BEND(e) (BASE[END[e]]) + +/* the blossom matched with v's blossom */ +#define BMATE(v) (BASE[END[MATE[v]]]) + +/* the blossom entered by the edge that links v's blossom */ +#define BLINK(v) (BASE[END[LINK[v]]]) + +/* the edge e with it's direction reversed */ +#define OPPEDGE(e) (((e - U) % 2 == 0) ? (e - 1) : (e + 1)) + +/* the slack of edge e */ +#define SLACK(e) (Y[END[e]] + Y[END[OPPEDGE(e)]] - WEIGHT[e]) + + +/* Global variables */ +static int *A,*END,*WEIGHT,*NEXTPAIR; +static int *MATE,*LINK,*BASE,*NEXTVTX,*LASTVTX,*Y,*NEXT_D,*NEXTEDGE; + +static int LAST_D, DELTA; + +static int LASTEDGE[3]; + +static int DUMMYVERTEX, DUMMYEDGE; +static int U, V; + +static int newbase, /* oldbase, */ nextbase, stopscan, pairpoint; +static int neighbor, nextpoint, newlast; +static int /* newmate, oldmate,*/ oldfirst, /* firstmate, */ secondmate; +static int f, nextedge, nexte, nextu; + +static int v,i,e; + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/matrix.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/matrix.h new file mode 100755 index 000000000..6b39d9055 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/matrix.h @@ -0,0 +1,61 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2003 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _MATRIX_H_ +#define _MATRIX_H_ + +#include + +template +class Matrix +{ + private: + long m_m; + long m_n; + T *m_mtrx; + + public: + Matrix(long m, long n) : m_m(m), m_n(n) + { + m_mtrx=new T[m*n]; + } + + ~Matrix() + { + delete m_mtrx; + } + + inline const long xDim() const + { + return m_m; + } + + inline const long yDim() const + { + return m_n; + } + + inline const T& getAt(long x,long y) const + { + assert(x +void showArray(T *array, Uint m,Uint n); + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/misc.t.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/misc.t.cpp new file mode 100755 index 000000000..f560d3b8d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/misc.t.cpp @@ -0,0 +1,37 @@ +#ifndef _MISC_T_CPP_ +#define _MISC_T_CPP_ + +// #include + +#include "misc.h" + +template +void showArray(T *array, Uint m,Uint n) +{ +// char buf[20]; + Uint i,maxElemLen; + T maxValue; + + // check for the largest value + maxValue=0; + for(i=0;i= SLACK (nextpoint)/2) + return; + nextpoint = NEXTPAIR[nextpoint]; + } + NEXTPAIR[pairpoint] = e; + pairpoint = e; + NEXTPAIR[e] = nextpoint; + if (NEXT_D[newbase] > del_e) + NEXT_D[newbase] = del_e; +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/part_func.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/part_func.h new file mode 100755 index 000000000..7973dc2b4 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/part_func.h @@ -0,0 +1,13 @@ +extern "C" +{ + +/* functions from part_func.c */ +float pf_fold(char *sequence, char *structure); +/* calculate partition function and base pair probabilities */ +void init_pf_fold(int length); /* allocate space for pf_fold() */ +void free_pf_arrays(void); /* free arrays from pf_fold() */ +void update_pf_params(int length); /*recalculate energy parameters */ +char bppm_symbol(float *x); /* string representation of structure */ +double mean_bp_dist(int length); /* mean pair distance of ensemble */ + +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/pointer.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/pointer.c new file mode 100755 index 000000000..9e38c35ae --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/pointer.c @@ -0,0 +1,80 @@ +/* Assign a pointer link to a vertex. Edge e joins a vertex in blossom */ +/* u to a linked vertex. */ + +#include "wmatch.h" + +void POINTER (int u, int v, int e) +{ int i, del; + +#ifdef DEBUG + printf("Pointer u,v,e=%d %d %d-%d\n",u,v,END[OPPEDGE(e)],END[e]); +#endif + + LINK[u] = -DUMMYEDGE; + NEXTVTX[LASTVTX[u]] = DUMMYVERTEX; + NEXTVTX[LASTVTX[v]] = DUMMYVERTEX; + + if (LASTVTX[u] != u) { + i = MATE[NEXTVTX[u]]; + del = -SLACK(i) / 2; + } + else del = LAST_D; + + i = u; + while (i != DUMMYVERTEX) { + Y[i] += del; + NEXT_D[i] += del; + i = NEXTVTX[i]; + } + if (LINK[v] < 0) { + LINK[v] = e; + NEXTPAIR[DUMMYEDGE] = DUMMYEDGE; + SCAN (v, DELTA); + return; + } + else { + LINK[v] = e; + return; + } +} + + +/* Scan each vertex in the blossom whose base is x */ + +void SCAN (int x, int del) +{ int u, del_e; + +#ifdef DEBUG + printf("Scan del=%d x=%d\n",del,x); +#endif + + newbase = BASE[x]; + stopscan = NEXTVTX[LASTVTX[x]]; + while (x != stopscan) { + Y[x] += del; + NEXT_D[x] = LAST_D; + pairpoint = DUMMYEDGE; + e = A[x]; + while (e != 0) { + neighbor = END[e]; + u = BASE[neighbor]; + if (LINK[u] < 0) { + if (LINK[BMATE (u)] < 0 || LASTVTX[u] != u) { + del_e = SLACK (e); + if (NEXT_D[neighbor] > del_e) { + NEXT_D[neighbor] = del_e; + NEXTEDGE[neighbor] = e; + } + } + } + else if (u != newbase) { + INSERT_PAIR(); + } + e = A[e]; + } + x = NEXTVTX[x]; + } + NEXTEDGE[newbase] = NEXTPAIR[DUMMYEDGE]; +} + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforest.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforest.h new file mode 100755 index 000000000..0b6bee383 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforest.h @@ -0,0 +1,124 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _PPFOREST_H_ +#define _PPFOREST_H_ + +#include +#include + +#include "algebra.h" +//#include "alignment.h" +#include "misc.h" +#include "ppforestbase.h" + +using namespace std; + +//template +//class Alignment; + +/** The template class PPForest is the basic class that is handled by the alignmnent + * algorithms of the RNAforester template library. The template parameter L is the + * datatype of the forest labels. + */ +template +class PPForest : public PPForestBase +{ + template + friend class Alignment; + + public: + typedef typename PPForestBase::size_type size_type; + +private: + /** internal function used by '<<' operator to print bracket notation of the forest*/ + void print(ostream &s,size_type node,bool brackets) const; + + /** Calculate maximal score of csf (i,j) for a certain Algebra. + * It is assumed that a perfect match of the forest obtains the best + * possible score. + */ + template + R maxScore(const Algebra &alg, size_type i, size_type j) const; + /** Calculate maximal score of csf (i,j) for a certain RNAAlgebra. + * It is assumed that a perfect match of the forest obtains the best + * possible score. + */ + template + R maxScore(const RNA_Algebra &alg, size_type i, size_type j) const; + + /** Function showLabel is used by print routines of PPForest */ +// virtual void showLabel(ostream &s,char c) const {s << c;}; + virtual void showLabel(ostream &s,L l) const {s << 'X';}; + + /** Function makeLabel is used by function buildForest */ +// virtual void makeLabel(char &a,char c) {a=c;}; + + void makeLabel(L &a,char c) {}; + + +protected: + L *m_lb; + + void initialize(size_type size); + +public: + typedef L label_type; + + /** Default Constructor */ + PPForest() : PPForestBase(), m_lb(NULL) {}; + /** Construct a PPForest with 'size' nodes */ + PPForest(size_type size); + /** Copy constructor */ + PPForest(const PPForest &ppf); + /** Read PPForest from binary file */ + PPForest(istream &s); + + virtual ~PPForest(); + + /** returns label of node i */ + inline L label(size_type i) const {return m_lb[i];}; + + /** Calculate maximal score of a forest alignment against itself for a certain Algebra. + * It is assumed that a perfect match of the forest obtains the best + * possible score. + */ + template + inline R maxScore(const Algebra &alg) const + { + return maxScore(alg,0,getMaxLength(0)); + } + + /** Calculate maximal score of a forest alignment against itself for a certain RNA_Algebra. + * It is assumed that a perfect match of the forest obtains the best + * possible score. + */ + template + inline R maxScore(const RNA_Algebra &alg) const + { + return maxScore(alg,0,getMaxLength(0)); + } + + /** Print forest in GraphViz format */ + void printDot(ostream &s) const; + + /** Save forest to binary file */ + void save(ostream &s) const; +}; + +/** Stream output operator for PPForest */ +template +ostream& operator<< (ostream &s, PPForest &ppf); + +#endif + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforest.t.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforest.t.cpp new file mode 100755 index 000000000..dfde8be23 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforest.t.cpp @@ -0,0 +1,226 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _PPFOREST_T_CPP_ +#define _PPFOREST_T_CPP_ + +#include "misc.h" +#include "ppforest.h" + +/* ****************************************** */ +/* Constructor and Destruktor functions */ +/* ****************************************** */ + +template +PPForest::PPForest(size_type size): PPForestBase(size) +{ + m_lb=new L[size]; +} + +template +PPForest::PPForest(const PPForest &ppf) : PPForestBase(ppf) +{ + m_lb=new L[ppf.size()]; + + // copy labels + for(size_type i=0;i +PPForest::PPForest(istream &s) +{ + /* + // read ppforest from file + + // first of all save the size + s.read(static_cast(m_size),sizeof(PPForestBase::size_type)); + + // initialize structures + ::PPForestBase(m_size); + m_lb=new L[ppf.size()]; + + // save the arrays + s.read(static_cast(m_lb),sizeof(label_type)*m_size); + s.read(static_cast(m_rb),sizeof(PPForestBase::size_type)*m_size); + s.read(static_cast(m_noc),sizeof(PPForestBase::size_type)*m_size); + s.read(static_cast(m_sumUpCSF),sizeof(PPForestBase::size_type)*m_size); + s.read(static_cast(m_rmb),sizeof(PPForestBase::size_type)*m_size); + */ +} + +template +PPForest::~PPForest() +{ + DELETE_ARRAY(m_lb); +} + +/* ****************************************** */ +/* Private functions */ +/* ****************************************** */ + +template +void PPForest::print(ostream &s,size_type node,bool brackets) const +{ + if(brackets) + s << "("; + + s << "{" << node << "}"; + showLabel(s,m_lb[node]); + if(m_noc[node]) + print(s,node+1,true); + if(m_rb[node]) + print(s,m_rb[node],false); + + if(brackets) + s << ")"; +} + +/** Calculate maximal score of csf (i,j) for a certain Algebra. + * It is assumed that a perfect match of the forest obtains the best + * possible score. + */ +template +template +R PPForest::maxScore(const Algebra &alg, size_type i, size_type j) const +{ + R down, over; + + if(j==0) + return 0; + + if(isLeave(i)) + { + over=maxScore(alg,rb(i),j-1); + return alg.replace(label(i),0,label(i),over); + } + else + { + down=maxScore(alg,i+1,noc(i)); + over=maxScore(alg,rb(i),j-1); + return alg.replace(label(i),down,label(i),over); + } +} + +/** Calculate maximal score of csf (i,j) for a certain RNA_Algebra. + * It is assumed that a perfect match of the forest obtains the best + * possible score. + */ +template +template +R PPForest::maxScore(const RNA_Algebra &alg, Uint i, Uint j) const +{ + R down, over; + + if(j==0) + return 0; + + if(isLeave(i)) + { + over=maxScore(alg,rb(i),j-1); + return alg.replace(label(i),0,label(i),over); + } + else + { + down=maxScore(alg,i+1+1,noc(i)-2); + over=maxScore(alg,rb(i),j-1); + return alg.replacepair(label(i+1),label(i+1),down,label(getRightmostBrotherIndex(i+1)),label(getRightmostBrotherIndex(i+1)),over); + } +} + +/* ****************************************** */ +/* Protected function */ +/* ****************************************** */ + +template +void PPForest::initialize(size_type size) +{ + PPForestBase::initialize(size); + m_lb=new L[size]; +} + +/* ****************************************** */ +/* Public functions */ +/* ****************************************** */ + + +template +void PPForest::printDot(ostream &s) const +{ + size_type i,h; + + s << "digraph forest" << endl << "{" << endl; + + // edges + for(i=0;i {"; + h=i+1; + for(Uint r=0;r +void PPForest::save(ostream &s) const +{ + /* + // save the pforest to stream in binary format + + // first of all save the size + s.write(reinterpret_cast(&m_size),sizeof(PPForestBase::size_type)); + // save the arrays + s.write(reinterpret_cast(m_lb),sizeof(label_type)*m_size); + s.write(reinterpret_cast(m_rb),sizeof(PPForestBase::size_type)*m_size); + s.write(reinterpret_cast(m_noc),sizeof(PPForestBase::size_type)*m_size); + s.write(reinterpret_cast(m_sumUpCSF),sizeof(PPForestBase::size_type)*m_size); + s.write(reinterpret_cast(m_rmb),sizeof(PPForestBase::size_type)*m_size); + */ +} + +template +ostream& operator<< (ostream &s, PPForest &ppf) +{ + ppf.print(s,0,true); + return s; +} + +#endif + + + + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestali.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestali.h new file mode 100755 index 000000000..db0825399 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestali.h @@ -0,0 +1,52 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _PPFORESTALI_H_ +#define _PPFORESTALI_H_ + +//#include "alignment.h" +#include "ppforest.h" + +//template +//class Alignment; + +/** PPForestAli is the Base class of forest Alignemnts. + * The pure virtual functions must be implemented when + * inherited to allow the construction of alignments. + */ + +template +class PPForestAli : public PPForest +{ +public: + typedef typename PPForest::size_type size_type; + + //private: +public: + /** @name Interface functions for alignment construction */ + //@{ + + virtual void makeRepLabel(size_type node,L a, L b) = 0; + virtual void makeDelLabel(size_type node,L a) = 0; + virtual void makeInsLabel(size_type node,L b) = 0; + + //@} + +public: + PPForestAli() : PPForest(){}; + PPForestAli(size_type size) : PPForest(size) {}; + + // virtual ~PPForestAli(){}; +}; + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestbase.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestbase.cpp new file mode 100755 index 000000000..7a7e9a4c2 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestbase.cpp @@ -0,0 +1,202 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#include "misc.h" +#include "ppforestbase.h" +#include "debug.h" + +#include +#include +#include + +#include "misc.t.cpp" + +/* ****************************************** */ +/* Constructor and Destructor functions */ +/* ****************************************** */ + +PPForestBase::PPForestBase(size_type size) +{ + initialize(size); +}; + +PPForestBase::PPForestBase(const PPForestBase &ppfBase) +{ + initialize(ppfBase.size()); + + memcpy(m_rb,ppfBase.m_rb,sizeof(size_type)*m_size); + memcpy(m_noc,ppfBase.m_noc,sizeof(size_type)*m_size); + memcpy(m_sumUpCSF,ppfBase.m_sumUpCSF,sizeof(size_type)*(m_size+1)); + memcpy(m_rmb,ppfBase.m_rmb,sizeof(size_type)*m_size); + + m_isSumUpCSFValid=ppfBase.m_isSumUpCSFValid; + m_isRMBValid=ppfBase.m_isRMBValid; +} + +PPForestBase::~PPForestBase() +{ + DELETE_ARRAY(m_rb); + DELETE_ARRAY(m_noc); + DELETE_ARRAY(m_sumUpCSF); + DELETE_ARRAY(m_rmb); +}; + +/* ****************************************** */ +/* Private functions */ +/* ****************************************** */ + +PPForestBase::size_type PPForestBase::countLeaves(size_type i) const +{ + size_type numLeaves=0; + + for(size_type k=0;k=0;i--) + { + if(m_rb[i]) + m_rmb[i]=m_rmb[m_rb[i]]; + else + m_rmb[i]=i; + } + + m_isRMBValid=true; +} + +void PPForestBase::initialize(size_type size) +{ + m_size=size; + m_rb=new size_type[size]; + m_noc=new size_type[size]; + m_sumUpCSF=new size_type[size+1]; + m_rmb=new size_type[size]; + + m_isSumUpCSFValid=false; + m_isRMBValid=false; +} + +/* ****************************************** */ +/* Public functions */ +/* ****************************************** */ + +PPForestBase::size_type PPForestBase::rb(size_type i, size_type k) const +{ + if(k==0) + return i; + else + return rb(rb(i),k-1); +} + +PPForestBase::size_type PPForestBase::maxDegree() const +{ + size_type degree=0; + + for(size_type i=0;i +*/ + +#ifndef _PPFOREST_BASE_H +#define _PPFOREST_BASE_H + +#include +#include + +#include "misc.h" +#include "types.h" + +using namespace std; + +/** PPForestBase is the base class of the template class PPForest. + * To reduce the size of compiled programs functions and variables that are + * independent of the labelling are implemented in this class. + */ +class PPForestBase +{ + //template + //friend class Alignment; + + public: + typedef Uint size_type; + + private: + bool m_isSumUpCSFValid; + bool m_isRMBValid; + + size_type getNumRightBrothers(size_type i) const; + size_type countLeaves(size_type i,size_type k) const; + +protected: + size_type m_size; /**< size is the number of nodes of a tree */ + size_type *m_rb; /**< m_rb[i] stores the preorder index of the rightbrother node of the ith node, or 0 if there is none. */ + size_type *m_noc; /**< m_noc[i] stores the number of children of the ith node */ + size_type *m_sumUpCSF; /**< m_sumUpCSF[i] stores the sum of non empty closed subforests of nodes k=i && i2<=max_node) + return false; + + if(rb(i2,j2-1)>=i && rb(i2,j2-1)<=max_node) + return false; + + // (i,j) included in (i2,j2) + max_node=getRightmostBrotherIndex(i2); + if(noc(max_node)) + max_node=getRightmostBrotherIndex(max_node+1); + + + if(i>=i2 && i<=max_node) + return false; + + if(rb(i,j-1)>=i2 && rb(i,j-1)<=max_node) + return false; + + return true; + } +}; + +#endif + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestbase.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestbase.o new file mode 100755 index 000000000..f19de9d2b Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestbase.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestsz.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestsz.h new file mode 100755 index 000000000..8f7b8245d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/ppforestsz.h @@ -0,0 +1,69 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _PPFORESTSZ_H +#define _PPFORESTSZ_H + +#include +#include + +#include "misc.h" +#include "types.h" + +using namespace std; + +template +class PPForestSZ +{ + protected: + Uint m_size; + Uint *m_lml; // postorder index of leftmost leaf descandant of the subtree rootet at T[i] + L *m_lb; // labels of nodes in postorder + bool *m_keyroot; // is node a keyroot + + void calcKeyroots(); + + public: + typedef Uint size_type; + typedef L label_type; + + PPForestSZ() : m_size(0), m_lml(NULL), m_lb(NULL),m_keyroot(NULL) {}; + PPForestSZ(Uint nrOfNodes); + PPForestSZ(const PPForestSZ &ppf); + ~PPForestSZ(); + + inline size_type size() const {return m_size;}; + inline Uint lml(Ulong i) const {return m_lml[i];}; + inline L label(Ulong i) const {return m_lb[i];}; + inline bool keyroot(Ulong i) const {return m_keyroot[i];}; + + Uint numKeyroots() const + { + Uint count=0; + for(Uint i=0;i +*/ + +#ifndef _PPFORESTSZ_T_CPP_ +#define _PPFORESTSZ_T_CPP_ + +#include + +#include "misc.h" +#include "ppforestsz.h" + + +// PPForest + +template +PPForestSZ::PPForestSZ(Uint nrOfNodes) +: m_size(nrOfNodes) +{ + m_lml=new Uint[nrOfNodes]; + m_lb=new L[nrOfNodes]; + m_keyroot=new bool[nrOfNodes]; +} + +template +PPForestSZ::PPForestSZ(const PPForestSZ &ppf) +{ + m_size=ppf.size(); + + m_lml=new Uint[ppf.size()]; + m_lb=new L[ppf.size()]; + m_keyroot=new bool[ppf.size()]; + + memcpy(m_lml,ppf.m_lml,sizeof(Uint)*m_size); + memcpy(m_keyroot,ppf.m_keyroot,sizeof(bool)*m_size); + + for(Uint i=0;i +PPForestSZ::~PPForestSZ() +{ + DELETE_ARRAY(m_lml); + DELETE_ARRAY(m_lb); + DELETE_ARRAY(m_keyroot); +} + +template +void PPForestSZ::calcKeyroots() +{ + std::map keyrootMap; + + for(Uint i=0;i::const_iterator it; + for(it=keyrootMap.begin();it!=keyrootMap.end();it++) + { + m_keyroot[it->second]=true; + } + +} + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.cpp new file mode 100755 index 000000000..ddeb9e9e0 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.cpp @@ -0,0 +1,343 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#include +#include + +#include "alignment.h" +#include "progressive_align.h" + +#include "alignment.t.cpp" + +using namespace std; + +// !!! this operator is defined as > !!! +bool operator < (pair &l, pair &r) +{ + if(l.second->getNumStructures() < r.second->getNumStructures()) + return false; + else + return true; +} + +void progressiveAlign(deque &inputList, deque > &resultList, const DoubleScoreProfileAlgebraType *alg,const RNAforesterOptions &options) +{ + RNAProfileAliMapType inputMapProfile; + deque alignList; + RNAProfileAliMapType::iterator it,it2; + long x,y,bestx,besty; // keys of stuctures in inputMapProfile + RNAProfileAlignment *ppfx=NULL,*ppfy=NULL,*ppf=NULL; + int level=1; + double bestScore,threshold,cutoff; + string clusterfilename; + ofstream s; + Matrix *score_mtrx; + bool local; + + local=options.has(RNAforesterOptions::LocalSimilarity); + + cout << "*** Calculation ***" << endl << endl; + + // create inputMapProfile to access a profile by an index value + deque::const_iterator inpIt; + long i=1; + for(inpIt=inputList.begin();inpIt!=inputList.end();inpIt++) + { + inputMapProfile[i]=*inpIt; + i++; + } + inputList.clear(); + + // create matrix for all against all comparison + bestScore=alg->worst_score(); + score_mtrx=new Matrix(inputMapProfile.size(),inputMapProfile.size()); + + // set threshold for the clustering algorithm + if(options.has(RNAforesterOptions::CalculateDistance)) + options.get(RNAforesterOptions::ClusterThreshold,threshold,20.0); + else + options.get(RNAforesterOptions::ClusterThreshold,threshold,0.7); + cout << "clustering threshold is: " << threshold << endl; + + // set cutoff value for clustering + if(options.has(RNAforesterOptions::CalculateDistance)) + options.get(RNAforesterOptions::ClusterJoinCutoff,cutoff,100.0); + else + options.get(RNAforesterOptions::ClusterJoinCutoff,cutoff,0.0); + cout << "join clusters cutoff is: " << cutoff << endl << endl; + + // generate dot file + clusterfilename=options.generateFilename(RNAforesterOptions::Help,"_cluster.dot", "cluster.dot"); // use Help as dummy + s.open(clusterfilename.c_str()); + s << "digraph forest" << endl << "{" << endl; + + // generate nodes for the input forests + for(it=inputMapProfile.begin();it!=inputMapProfile.end();it++) + { + ppf=it->second; + + s << "\"" << ppf->getName() << "\"" << "[label=\"" << ppf->getName() << "\"]" << endl; + s << "\"" << ppf->getName() << "\"" << "[label=\"" << ppf->getName() << "\"]" << endl; + } + + + // compute all pairwise distances + // !! NOTE !! iterating through the map is ordered by key number + // as i only calculate a triangle matrix this is a prerequisite + cout << "Computing all pairwise similarities" << endl; + for(it=inputMapProfile.begin();it!=inputMapProfile.end();it++) + { + x=it->first; + ppfx=it->second; + for(it2=inputMapProfile.begin();it2->firstfirst;it2++) + { + y=it2->first; + ppfy=it2->second; + + Alignment ali(ppfx,ppfy,*alg,local); + if(local) + score_mtrx->setAt(x-1,y-1,ali.getLocalOptimum()); + else + score_mtrx->setAt(x-1,y-1,ali.getGlobalOptimumRelative()); + + cout << x << "," << y << ": " << score_mtrx->getAt(x-1,y-1) << endl; + + WATCH(DBG_MULTIPLE,"progressiveAlign",x); + WATCH(DBG_MULTIPLE,"progressiveAlign",y); + WATCH(DBG_MULTIPLE,"progressiveAlign",ali.getGlobalOptimumRelative()); + } + } + cout << endl; + + while(inputMapProfile.size()>1) + { + // find the best score of all pairwise alignments + bestScore=alg->worst_score(); + for(it=inputMapProfile.begin();it!=inputMapProfile.end();it++) + { + x=it->first; + for(it2=inputMapProfile.begin();it2->first < it->first;it2++) + { + double old_bestScore=bestScore; + + y=it2->first; + WATCH(DBG_MULTIPLE,"progressiveAlign",x); + WATCH(DBG_MULTIPLE,"progressiveAlign",y); + WATCH(DBG_MULTIPLE,"progressiveAlign",score_mtrx->getAt(x-1,y-1)); + + WATCH(DBG_MULTIPLE,"progressiveAlign",bestScore); + bestScore=alg->choice(bestScore,score_mtrx->getAt(x-1,y-1)); + + if(bestScore!=old_bestScore) + { + bestx=it->first; + besty=it2->first; + old_bestScore=bestScore; + } + } + } + + WATCH(DBG_MULTIPLE,"progressiveAlign",bestScore); + cout << "joining alignments:" << endl; + + // if threshold is set generate a list of best pairs within threshold + if(alg->choice(bestScore,threshold)!= threshold) + { + Graph graph; + int *mate; + int maximize; + + graph=makePairsGraph(inputMapProfile,alg,score_mtrx,threshold); + if(options.has(RNAforesterOptions::CalculateDistance)) + maximize=0; + else + maximize=1; + + mate = Weighted_Match(graph,1,maximize); + for(x=1;x<=score_mtrx->xDim();x++) // !! begins at 1 !! + { + if(x1) + { + string aliName; + + x=alignList.front().first; + ppfx=alignList.front().second; + alignList.erase(alignList.begin()); + y=alignList.front().first; + ppfy=alignList.front().second; + alignList.erase(alignList.begin()); + + // compute alignment again + Alignment bestali(ppfx,ppfy,*alg,local); + if(local) + bestScore=bestali.getLocalOptimum(); + else + bestScore=bestali.getGlobalOptimumRelative(); + + // test, if score is worse than the cutoff value + if(alg->choice(bestScore,cutoff)== cutoff) + { + // copy involved forests to the result list + cout << x << "," << y << ": alignment is below cutoff." << endl; + if(ppfx->getNumStructures()>1) + resultList.push_back(make_pair(ppfx->maxScore(*alg),ppfx)); + if(ppfy->getNumStructures()>1) + resultList.push_back(make_pair(ppfy->maxScore(*alg),ppfy)); + } + else + { + // calculate optimal alignment and add it to inputMapProfile + + ppf=new RNAProfileAlignment(ppfx->getNumStructures(),ppfy->getNumStructures()); + + if(local) + { + Uint xbasepos,ybasepos; + bestali.getOptLocalAlignment(*ppf,xbasepos,ybasepos); + } + else + { + bestali.getOptGlobalAlignment(*ppf); + } + + ppf->addStrNames(ppfx->getStrNames()); + ppf->addStrNames(ppfy->getStrNames()); + aliName=ppfx->getName() + "." +ppfy->getName(); + ppf->setName(aliName); + + // for debug purposes + //string dotfilename; + //dotfilename=ppf->getName() + string(".dot"); + // ofstream s("test.dot"); + // ppf->printDot(s); + + // generate nodes in cluster file (dot format) + s << "\"" << ppf->getName() << "\"" << "[shape=\"diamond\" label=\"" << bestScore << "\"]" << endl; + s << "\"" << ppf->getName() << "\"" << "-> {\"" << ppfx->getName() << "\" \"" << ppfy->getName() << "\"}"; + + cout << x << "," << y << ": " << bestScore << " -> " << min(x,y) << endl; + + delete ppfx; + delete ppfy; + + // calculate distance to all forests in the list + cout << "Calculate similarities to other clusters" << endl; + ppfx=ppf; + // x remains x !! + for(it=inputMapProfile.begin();it!=inputMapProfile.end();it++) + { + y=it->first; + ppfy=it->second; + Alignment ali(ppfx,ppfy,*alg,local); + if(local) + { + score_mtrx->setAt(min(x-1,y-1),max(x-1,y-1),ali.getLocalOptimum()); // min - max = fill the upper triangle + cout << min(x,y) << "," << max(x,y) << ": " << ali.getLocalOptimum() << endl; + } + else + { + score_mtrx->setAt(min(x-1,y-1),max(x-1,y-1),ali.getGlobalOptimumRelative()); // min - max = fill the upper triangle + cout << min(x,y) << "," << max(x,y) << ": " << ali.getGlobalOptimumRelative() << endl; + } + } + cout << endl; + + // ... and append it to the list + inputMapProfile.insert(make_pair(x,ppf)); + } + } + + level++; + } + + assert(inputMapProfile.size()<2); + + // copy last profile to resultList + if(inputMapProfile.size()==1) + { + ppf=inputMapProfile.begin()->second; + resultList.push_back(make_pair(ppf->maxScore(*alg),ppf)); + inputMapProfile.clear(); + } + + // end of dot file + s << "}" << endl; + + // sort result list + // std::sort(resultList.begin(),resultList.end()); + + + delete score_mtrx; +} + +Graph makePairsGraph(const RNAProfileAliMapType &inputMapProfile, const DoubleScoreProfileAlgebraType *alg, const Matrix *score_mtrx, double threshold) +{ + Graph graph; + RNAProfileAliMapType::const_iterator it,it2; + RNAProfileAlignment *ppfx=NULL,*ppfy=NULL; + + graph = NewGraph(score_mtrx->xDim()); + + for(int i=0;ixDim();i++) + { + Xcoord(graph,i+1) = 0; + Ycoord(graph,i+1) = 0; + } + + for(it=inputMapProfile.begin();it!=inputMapProfile.end();it++) + { + ppfx=it->second; + for(it2=inputMapProfile.begin();it2->firstfirst;it2++) + { + double score; + ppfy=it2->second; + + score=score_mtrx->getAt(it->first-1,it2->first-1); + if(alg->choice(score,threshold) != threshold) // is it better than the threshold ? + { + AddEdge (graph,it->first,it2->first,(int)(score*100.0)); + } + } + } + + + WriteGraph (graph,"test.out"); + return graph; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.h new file mode 100755 index 000000000..16485194c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.h @@ -0,0 +1,32 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#include "graphtypes.h" +#include "matrix.h" +#include "rnaforester_options.h" +#include "rna_profile_alignment.h" +#include "wmatch.h" + +/* ****************************************** */ +/* Definitions and typedefs */ +/* ****************************************** */ + +typedef map RNAProfileAliMapType; +typedef pair RNAProfileAliKeyPairType; + +/* ****************************************** */ +/* Function prototypes */ +/* ****************************************** */ + +void progressiveAlign(deque &inputList, deque > &resultList, const DoubleScoreProfileAlgebraType *alg,const RNAforesterOptions &options); +Graph makePairsGraph(const RNAProfileAliMapType &inputListProfile, const DoubleScoreProfileAlgebraType *alg, const Matrix *score_mtrx, double threshold); diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.o new file mode 100755 index 000000000..1bd867a9e Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/progressive_align.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/readgraph.c b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/readgraph.c new file mode 100755 index 000000000..772a73094 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/readgraph.c @@ -0,0 +1,129 @@ +/* set up data structures for weighted match */ + +/* to add a new type, add new case in SetUp() and a Set_X() routine */ + +#include +#include + +#include "wmatch.h" + +void SetUp (void* gptr, int type) +{ int i,allocsize; + Graph g=NULL; + EuclidGraph xy=NULL; + MatrixGraph matg=NULL; + + if (type==1) { + g = (Graph) gptr; + U = Degree(g,0); + V = NumEdges(g); + } + else if (type==2) { + xy = (EuclidGraph) gptr; + U = xy[0][0]; + V = U*(U-1)/2; + } + else if (type==3) { + matg = (MatrixGraph) gptr; + U = matg[0]; + V = U*(U-1)/2; + } + + allocsize = (U+2*V+2)*sizeof(int); + A = (int *) malloc(allocsize); + END = (int *) malloc(allocsize); + WEIGHT = (int *) malloc(allocsize); + for (i=0; i adj_node) + break; + u = v; + v = A[v]; + } + A[u] = currentedge; + A[currentedge] = v; + } + u = adj_node; + v = A[u]; + while (v != 0) { + u = v; + v = A[v]; + } + A[u] = currentedge - 1; + currentedge += 2; + } + edge = NextEdge(edge); + } + } +} + +/* set up from Euclidean graph */ + +void SetEuclid(EuclidGraph graph) +{ int i,j,currentedge; + + currentedge = U+2; + + for (i=U; i>=1; --i) + for (j = i-1; j >= 1; --j) { + WEIGHT[currentedge-1] = WEIGHT[currentedge] + = 2*eucdist2(graph,i,j); + END[currentedge-1] = i; + END[currentedge] = j; + A[currentedge] = A[i]; + A[i] = currentedge; + A[currentedge-1] = A[j]; + A[j] = currentedge-1; + currentedge += 2; + } +} + +void SetMatrix(MatrixGraph graph) +{ int i,j,currentedge; + + currentedge = U+2; + + for (i=U; i>=1; --i) + for (j = i-1; j >= 1; --j) { + WEIGHT[currentedge-1] = WEIGHT[currentedge] + = 2*graph[j*U+i]; + END[currentedge-1] = i; + END[currentedge] = j; + A[currentedge] = A[i]; + A[i] = currentedge; + A[currentedge-1] = A[j]; + A[j] = currentedge-1; + currentedge += 2; + } +} + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.cpp new file mode 100755 index 000000000..108d82e52 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.cpp @@ -0,0 +1,89 @@ +#include "rna_algebra.h" + +Score::Score(RNAforesterOptions &options) +{ + m_isLocal=options.has(RNAforesterOptions::LocalSimilarity); + m_isRIBOSUM=options.has(RNAforesterOptions::RIBOSUMScore); + + // distance or similarity ? + if(options.has(RNAforesterOptions::CalculateDistance)) + { + m_isDistance=true; + m_bp_rep_score = 0; + m_bp_del_score = 3; + m_b_match_score = 0; + m_b_rep_score =1; + m_b_del_score =2; + } + else + { + m_isDistance=false; + + if(options.has(RNAforesterOptions::RIBOSUMScore)) + { + m_bp_del_score=-100; + m_b_del_score=-200; + } + else + { + m_bp_rep_score = 10; + m_bp_del_score =-5; + m_b_match_score = 1; + m_b_rep_score = 0; + m_b_del_score =-10; + } + } + + // read scores + options.get(RNAforesterOptions::BpRepScore,m_bp_rep_score,m_bp_rep_score); + options.get(RNAforesterOptions::BpDelScore,m_bp_del_score,m_bp_del_score); + options.get(RNAforesterOptions::BMatchScore,m_b_match_score,m_b_match_score); + options.get(RNAforesterOptions::BRepScore,m_b_rep_score,m_b_rep_score); + options.get(RNAforesterOptions::BDelScore,m_b_del_score,m_b_del_score); +} + +Score::Score(const Score &s) +{ + // copy scores + m_isDistance = s.m_isDistance; + m_isLocal = s.m_isLocal; + m_bp_rep_score = s.m_bp_rep_score; + m_bp_del_score = s.m_bp_del_score; + m_b_match_score = s.m_b_match_score; + m_b_rep_score = s.m_b_rep_score; + m_b_del_score = s.m_b_del_score; +} + +void Score::print() +{ + // show score parameters + cout << "*** Scoring parameters ***" << endl << endl; + + cout << "Scoring type: "; + if(m_isDistance) + cout << "distance" << endl; + else + { + if(m_isLocal) + cout << "local "; + + cout << "similarity" << endl; + } + + cout << "Scoring parameters:" << endl; + + if(m_isRIBOSUM) + { + cout << "RIBOSUM85-60 Scoring matrix" << endl; + cout << "pd: " << m_bp_del_score << endl; + cout << "bd: " << m_b_del_score << endl << endl; + } + else + { + cout << "pm: " << m_bp_rep_score << endl; + cout << "pd: " << m_bp_del_score << endl; + cout << "bm: " << m_b_match_score << endl; + cout << "br: " << m_b_rep_score << endl; + cout << "bd: " << m_b_del_score << endl << endl; + } +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.h new file mode 100755 index 000000000..ae5bc07c7 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.h @@ -0,0 +1,636 @@ +#ifndef _RNA_ALGEBRA_H_ +#define _RNA_ALGEBRA_H_ + +#include +#include + +#include "algebra.h" +#include "debug.h" +#include "misc.h" +#include "rna_alphabet.h" +#include "rnaforester_options.h" + +/* ****************************************** */ +/* Definitions and typedefs */ +/* ****************************************** */ + +const double DBL_NEG = -100000000.0; // the values from limits.h caused problems.. +const double DBL_POS = 100000000.0; + +typedef Algebra DoubleScoreProfileAlgebraType; +typedef Algebra IntScore_AlgebraType; +typedef RNA_Algebra IntScoreRNA_AlgebraType; +typedef SZAlgebra IntScoreSZAlgebraType; + +/* ****************************************** */ +/* Class Score */ +/* ****************************************** */ + +/** Class Score reads scoring parameters from RNAforester command line. */ +class Score +{ + private: + bool m_isDistance; + bool m_isLocal; + bool m_isRIBOSUM; + + public: + int m_bp_rep_score; + int m_bp_del_score; + int m_b_match_score; + int m_b_rep_score; + int m_b_del_score; + + Score(RNAforesterOptions &options); + Score(const Score &s); + void print(); +}; + +/* ****************************************** */ +/* RNA Algebra Classes */ +/* ****************************************** */ + +/** Similarity algebra for RNA forests */ +class IntSimiRNA_Algebra : public IntScoreRNA_AlgebraType +{ + private: + Score m_s; + + public: + int empty() const {return 0;}; + int replacepair(RNA_Alphabet la, RNA_Alphabet lb, int down, RNA_Alphabet ra, RNA_Alphabet rb, int over) const + { + return m_s.m_bp_rep_score+down+over; + }; + + int replace(RNA_Alphabet a,int down, RNA_Alphabet b, int over) const + { + if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR) + return m_s.m_bp_rep_score+down+over; + else + { + if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) + return INT_MIN/4; + else + { + if(a==b) + return m_s.m_b_match_score+down+over; + else + return m_s.m_b_rep_score+down+over; + } + } + }; + + int del(RNA_Alphabet a,int down, int over) const + { + if(a==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down+over; + else + return m_s.m_b_del_score+down+over; + }; + + int insert(int down,RNA_Alphabet b,int over) const + { + if(b==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down+over; + else + return m_s.m_b_del_score+down+over; + }; + + int choice(int a, int b) const + { + return max(a,b); + }; + + int worst_score() const + { + return INT_MIN; + }; + + IntSimiRNA_Algebra(const Score &s) + : m_s(s) {}; +}; + +/** Distance algebra for RNA forests */ +class IntDistRNA_Algebra : public IntScoreRNA_AlgebraType +{ + private: + Score m_s; + + public: + int empty() const {return 0;}; + int replacepair(RNA_Alphabet la, RNA_Alphabet lb, int down, RNA_Alphabet ra, RNA_Alphabet rb, int over) const + { + return m_s.m_bp_rep_score+down+over; + }; + + int replace(RNA_Alphabet a,int down, RNA_Alphabet b, int over) const + { + if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR) + return m_s.m_bp_rep_score+down+over; + else + { + if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) + return INT_MAX/4; + else + { + if(a==b) + return m_s.m_b_match_score+down+over; + else + return m_s.m_b_rep_score+down+over; + } + } + }; + + int del(RNA_Alphabet a,int down,int over) const + { + if(a==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down+over; + else + return m_s.m_b_del_score+down+over; + }; + + int insert(int down,RNA_Alphabet b,int over) const + { + if(b==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down+over; + else + return m_s.m_b_del_score+down+over; + }; + + int choice(int a, int b) const + { + return min(a,b); + }; + + int worst_score() const + { + return INT_MAX; + }; + + IntDistRNA_Algebra(const Score &s) + : m_s(s) {}; +}; + +/** RIBOSUM85-60 matrix published in RSEARCH: Finding homologs of single structured RNA sequences + * R. Klein and S. Eddy, BMC Bioinformatics 2003 Vol.4 + */ +class RIBOSUM8560 : public IntScoreRNA_AlgebraType +{ + private: + Score m_s; + int m_baseSubstMtrx[4][4]; + int m_basepairSubstMtrx[4][4][4][4]; + + public: + int empty() const {return 0;}; + int replacepair(RNA_Alphabet la, RNA_Alphabet lb, int down, RNA_Alphabet ra, RNA_Alphabet rb, int over) const + { + int i,j,k,l; + i=alpha2RNA_Alpha(la); + j=alpha2RNA_Alpha(ra); + k=alpha2RNA_Alpha(lb); + l=alpha2RNA_Alpha(rb); + + return m_basepairSubstMtrx[i][j][k][l]+down+over; + }; + + int replace(RNA_Alphabet a,int down, RNA_Alphabet b, int over) const + { + assert(!(a==ALPHA_BASEPAIR && b==ALPHA_BASEPAIR)); + + if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) + return INT_MIN/4; + else + { + int i,j; + i=alpha2RNA_Alpha(a); + j=alpha2RNA_Alpha(b); + + return m_baseSubstMtrx[i][j]+down+over; + } + }; + + int del(RNA_Alphabet a,int down, int over) const + { + if(a==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down+over; + else + return m_s.m_b_del_score+down+over; + }; + + int insert(int down,RNA_Alphabet b,int over) const + { + if(b==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down+over; + else + return m_s.m_b_del_score+down+over; + }; + + int choice(int a, int b) const + { + return max(a,b); + }; + + int worst_score() const + { + return INT_MIN; + }; + + RIBOSUM8560(const Score &s) + : m_s(s) + { + int i,j,k,l; + + // set substitution matrices + + // base replacement + m_baseSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_A]=222; + m_baseSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_C]=-186; + m_baseSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_G]=-146; + m_baseSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U]=-139; + + m_baseSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_C]=116; + m_baseSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G]=-248; + m_baseSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_U]=-105; + + m_baseSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_G]=103; + m_baseSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U]=-174; + + m_baseSubstMtrx[ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_U]=165; + + // copy triangle + for(i=0;i<=ALPHA_PRO_BASE_U;i++) + for(j=0;j0 && b.p[ALPHA_PRO_BASEPAIR]>0) + { + // pair replacement + return a.p[ALPHA_PRO_BASEPAIR]*b.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_rep_score + + down+over; + } + else + { + if(a.p[ALPHA_PRO_BASE]>0 && b.p[ALPHA_PRO_BASE]>0) + { + double s=0; + + // base replacement + for(int i=ALPHA_PRO_BASE_A;i<=ALPHA_PRO_BASE_U;i++) + for(int j=ALPHA_PRO_BASE_A;j<=ALPHA_PRO_BASE_U;j++) + s+= i==j ? a.p[i]*b.p[j]*m_s.m_b_match_score : a.p[i]*b.p[j]*m_s.m_b_rep_score; + + if(s==0) // no sequence information + s=a.p[ALPHA_PRO_BASE]*b.p[ALPHA_PRO_BASE]*m_s.m_b_rep_score; + + return s+down+over; + } + else + { + // undefined operation (replace base by basepair ??) + return DBL_NEG/4; + } + } + }; + + double del(RNA_Alphabet_Profile a,double down, double over) const + { + if(a.p[ALPHA_PRO_BASEPAIR]>0) + return a.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_del_score+down+over; + else + return a.p[ALPHA_PRO_BASE]*m_s.m_b_del_score+down+over; + }; + + double insert(double down,RNA_Alphabet_Profile b,double over) const + { + if(b.p[ALPHA_PRO_BASEPAIR]>0) + return b.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_del_score+down+over; + else + return b.p[ALPHA_PRO_BASE]*m_s.m_b_del_score+down+over; + }; + + double choice(double a, double b) const + { + return max(a,b); + }; + + double worst_score() const + { + return DBL_NEG; + }; + + DoubleSimiProfileAlgebra(const Score &s) + : m_s(s) {}; +}; + +/** Distance algebra for RNA profile forests */ +class DoubleDistProfileAlgebra : public DoubleScoreProfileAlgebraType +{ + private: + Score m_s; + + public: + double empty() const {return 0.0;}; + double replace(RNA_Alphabet_Profile a,double down, RNA_Alphabet_Profile b, double over) const + { + TRACE(DBG_ALGEBRA,"rep","inside!!!"); + + if(a.p[ALPHA_PRO_BASEPAIR]>0 && b.p[ALPHA_PRO_BASEPAIR]>0) + { + // pair replacement + return a.p[ALPHA_PRO_BASEPAIR]*b.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_rep_score + + down+over; + } + else + { + if(a.p[ALPHA_PRO_BASE]>0 && b.p[ALPHA_PRO_BASE]>0) + { + double s=0; + + // base replacement + for(int i=ALPHA_PRO_BASE_A;i<=ALPHA_PRO_BASE_U;i++) + for(int j=ALPHA_PRO_BASE_A;j<=ALPHA_PRO_BASE_U;j++) + s+= i==j ? a.p[i]*b.p[j]*m_s.m_b_match_score : a.p[i]*b.p[j]*m_s.m_b_rep_score; + + if(s==0) // no sequence information + s=a.p[ALPHA_PRO_BASE]*b.p[ALPHA_PRO_BASE]*m_s.m_b_rep_score; + + return s+down+over; + } + else + { + // undefined operation (replace base by basepair ??) + return DBL_POS/4; + } + } + }; + + double del(RNA_Alphabet_Profile a,double down, double over) const + { + if(a.p[ALPHA_PRO_BASEPAIR]>0) + return a.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_del_score+down+over; + else + return a.p[ALPHA_PRO_BASE]*m_s.m_b_del_score+down+over; + }; + + double insert(double down,RNA_Alphabet_Profile b,double over) const + { + if(b.p[ALPHA_PRO_BASEPAIR]>0) + return b.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_del_score+down+over; + else + return b.p[ALPHA_PRO_BASE]*m_s.m_b_del_score+down+over; + }; + + double choice(double a, double b) const + { + return min(a,b); + }; + + double worst_score() const + { + return DBL_POS; + }; + + DoubleDistProfileAlgebra(const Score &s) + : m_s(s) {}; +}; + +/* ****************************************** */ +/* SZAlgebra Classes */ +/* ****************************************** */ + +class IntSimiSZAlgebra : public IntScoreSZAlgebraType +{ + private: + Score m_s; + + public: + int empty() const {return 0;}; + int replace(RNA_Alphabet a,int down, RNA_Alphabet b) const + { + if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR) + return m_s.m_bp_rep_score+down; + else + { + if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) + return INT_MIN/4; + else + { + if(a==b) + return m_s.m_b_match_score+down; + else + return m_s.m_b_rep_score+down; + } + } + }; + + int del(RNA_Alphabet a,int down) const + { + if(a==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down; + else + return m_s.m_b_del_score+down; + }; + + int insert(int down,RNA_Alphabet b) const + { + if(b==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down; + else + return m_s.m_b_del_score+down; + }; + + int choice(int a, int b) const + { + return max(a,b); + }; + + int worst_score() const + { + return INT_MIN; + }; + + IntSimiSZAlgebra(const Score &s) + : m_s(s) {}; +}; + + +class IntDistSZAlgebra : public IntScoreSZAlgebraType +{ + private: + Score m_s; + + public: + int empty() const {return 0;}; + int replace(RNA_Alphabet a,int down, RNA_Alphabet b) const + { + if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR) + return m_s.m_bp_rep_score+down; + else + { + if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) + return INT_MAX/4; + else + { + if(a==b) + return m_s.m_b_match_score+down; + else + return m_s.m_b_rep_score+down; + } + } + }; + + int del(RNA_Alphabet a,int down) const + { + if(a==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down; + else + return m_s.m_b_del_score+down; + }; + + int insert(int down,RNA_Alphabet b) const + { + if(b==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down; + else + return m_s.m_b_del_score+down; + }; + + int choice(int a, int b) const + { + return min(a,b); + }; + + int worst_score() const + { + return INT_MAX; + }; + + IntDistSZAlgebra(const Score &s) + : m_s(s) {}; +}; + +/* ****************************************** */ +/* General Algebra Classe */ +/* ****************************************** */ + +/** Distance algebra for forests */ +class IntDist_Algebra : public IntScore_AlgebraType +{ + private: + Score m_s; + + public: + int empty() const {return 0;}; + + int replace(RNA_Alphabet a,int down, RNA_Alphabet b, int over) const + { + if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR) + return m_s.m_bp_rep_score+down+over; + else + { + if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) + return INT_MAX/4; + else + { + if(a==b) + return m_s.m_b_match_score+down+over; + else + return m_s.m_b_rep_score+down+over; + } + } + }; + + int del(RNA_Alphabet a,int down,int over) const + { + if(a==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down+over; + else + return m_s.m_b_del_score+down+over; + }; + + int insert(int down,RNA_Alphabet b,int over) const + { + if(b==ALPHA_BASEPAIR) + return m_s.m_bp_del_score+down+over; + else + return m_s.m_b_del_score+down+over; + }; + + int choice(int a, int b) const + { + return min(a,b); + }; + + int worst_score() const + { + return INT_MAX; + }; + + IntDist_Algebra(const Score &s) + : m_s(s) {}; +}; + + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.o new file mode 100755 index 000000000..7e1d067b4 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_algebra.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alignment.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alignment.cpp new file mode 100755 index 000000000..f99d7c29c --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alignment.cpp @@ -0,0 +1,191 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#include +#include + +#ifndef WIN32 +#include "config.h" +#endif + +#include "misc.h" +#include "rna_alignment.h" +#include "rnafuncs.h" +#include "utils.h" + +/* ****************************************** */ +/* Private functions */ +/* ****************************************** */ + +void RNA_Alignment::makePairTable(map &pairs, bool first) const +{ + pair *baseIndex; // stores for each node in the alignment the index position of the left and right base (or -1) + RNA_Alphabet c; + + baseIndex=new pair[m_size]; + + // initialize pairs, all gaps + for(int i=size()-1;i>=0;i--) + { + baseIndex[i].first=-1; + baseIndex[i].second=-1; + } + + for(int i=size()-1;i>=0;i--) + { + // first or second component + if(first) + c=m_lb[i].a; + else + c=m_lb[i].b; + + if(isLeave(i)) + { + if(c!=ALPHA_GAP) + { + baseIndex[i].first=i; + baseIndex[i].second=i; + } + } + else + { + // internal node + // leftmost and rightmost base + bool lmBaseFound=false; + for(size_type r=0,h=i+1;r pairs; + makePairTable(pairs, first); + + // iterate through leaves nodes and use information of pairs + for(size_type i=0;i +*/ + +#ifndef _RNA_ALIGNMENT_H +#define _RNA_ALIGNMENT_H + +#include +#include +#include + +#include "alignment.h" +#include "ppforestali.h" +#include "rna_algebra.h" +#include "rnaforest.h" +#include "rnafuncs.h" +#include "types.h" + +#include "alignment.t.cpp" + +using namespace std; + +/** Alignment of RNAForests */ +class RNA_Alignment : public PPForestAli +{ +private: + string m_strname1; + string m_strname2; + + /** @name Implementations of virtual functions */ + //@{ + + void makeRepLabel(size_type node, RNA_Alphabet a, RNA_Alphabet b) + { + m_lb[node].a=a; + m_lb[node].b=b; + }; + + void makeDelLabel(size_type node, RNA_Alphabet a) + { + m_lb[node].a=a; + m_lb[node].b=ALPHA_GAP; + }; + + void makeInsLabel(size_type node, RNA_Alphabet b) + { + m_lb[node].a=ALPHA_GAP; + m_lb[node].b=b; + }; + + void showLabel(ostream &s,RNA_AlphaPair p) const + { + s << "[" << p.a << p.b << "]"; + }; + + //@} + + void makePairTable(map &pairs, bool first) const; + +public: + void setStructureNames(const string &s1,const string &s2); + const string& getStructureNameX() const {return m_strname1;}; + const string& getStructureNameY() const {return m_strname2;}; + void getSequenceAlignments(string &s1, string &s2) const; + void getStructureAlignment(string &s, bool first) const; + void generateXML(ostream &s) const; + void squigglePlot(const string &filename_suffix, const RNAFuncs::SquigglePlotOptions &options) const; +}; + +/* +class PW_RNA_Alignment: public Alignment +{ + public: + PW_RNA_Alignment(const RNAForest *ppfx, const RNAForest *ppfy, const IntScoreRNA_AlgebraType &alg) + : Alignment((const PPForest*)ppfx,(const PPForest*)ppfy,alg) {}; +};*/ + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alignment.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alignment.o new file mode 100755 index 000000000..76e83d0ae Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alignment.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.cpp new file mode 100755 index 000000000..183334e74 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.cpp @@ -0,0 +1,33 @@ +#include "rna_alphabet.h" + +#include + +int alpha2RNA_Alpha(char c) +{ + switch(c) + { + case ALPHA_BASE_A: + return ALPHA_PRO_BASE_A; + case ALPHA_BASE_C: + return ALPHA_PRO_BASE_C; + case ALPHA_BASE_G: + return ALPHA_PRO_BASE_G; + case ALPHA_BASE_U: + return ALPHA_PRO_BASE_U; + case ALPHA_GAP: + return ALPHA_PRO_GAP; + case ALPHA_BASEPAIR: + return ALPHA_PRO_BASEPAIR; + case ALPHA_BASE: + return ALPHA_PRO_BASE; + default: + assert(true); + } + + return 0; // never reached !! +} + + + + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.h new file mode 100755 index 000000000..c48f8a668 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.h @@ -0,0 +1,99 @@ +#ifndef _RNA_ALPHABET_ +#define _RNA_ALPHABET_ + +#include + +using namespace std; + +/* +not every c++ compiler allows that enum types are used as +template arguments + +typedef enum + { + ALPHA_UNDEFINED=-1, + ALPHA_BASE_A=0, + ALPHA_BASE_C, + ALPHA_BASE_G, + ALPHA_BASE_U, + ALPHA_BASEPAIR, + ALPHA_GAP, + ALPHA_BASE, + RNA_ALPHABET_SIZE, + } RNA_Alphabet; +*/ + +typedef char RNA_Alphabet; + +/** pair alphabet of RNA_Alphabet */ +typedef struct {RNA_Alphabet a; RNA_Alphabet b;} RNA_AlphaPair; + + +//const int ALPHA_UNDEFINED=-1; +/* +const int ALPHA_BASE_A=0; +const int ALPHA_BASE_C=1; +const int ALPHA_BASE_G=2; +const int ALPHA_BASE_U=3; +const int ALPHA_BASEPAIR=4; +const int ALPHA_GAP=5; +const int ALPHA_BASE=6;*/ + + +const int ALPHA_BASE_A='a'; +const int ALPHA_BASE_C='c'; +const int ALPHA_BASE_G='g'; +const int ALPHA_BASE_U='u'; +const int ALPHA_BASEPAIR='P'; +const int ALPHA_GAP='-'; +const int ALPHA_BASE='B'; + +const int RNA_ALPHABET_SIZE=7; + +/*const int ALPHABET_SIZE = 256;*/ + +/* +class RNA_AlphabetTransformation +{ +private: + const static int m_alphabetsize; + const static int m_rna_alphabetsize; + + RNA_Alphabet m_alpha2RNA_Alpha[ALPHABET_SIZE]; + char m_RNA_Alpha2alpha[RNA_ALPHABET_SIZE]; + + void setMapEntry(RNA_Alphabet a, char c); +public: + RNA_AlphabetTransformation(); + + inline RNA_Alphabet RNA_AlphabetTransformation::alpha2RNA_Alpha(char c) + { + return m_alpha2RNA_Alpha[(unsigned int)c]; + }; + + inline char RNA_AlphabetTransformation::RNA_Alpha2alpha(RNA_Alphabet a) + { + return m_RNA_Alpha2alpha[(unsigned int)a]; + }; + +};*/ + +const int ALPHA_PRO_BASE_A=0; +const int ALPHA_PRO_BASE_C=1; +const int ALPHA_PRO_BASE_G=2; +const int ALPHA_PRO_BASE_U=3; +const int ALPHA_PRO_BASEPAIR=4; +const int ALPHA_PRO_GAP=5; +const int ALPHA_PRO_BASE=6; + +struct RNA_Alphabet_Profile +{ + RNA_Alphabet_Profile() {}; + + double p[RNA_ALPHABET_SIZE]; + string columnStr; +}; + +int alpha2RNA_Alpha(char c); + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.o new file mode 100755 index 000000000..a926598f0 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_alphabet.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.cpp new file mode 100755 index 000000000..8eea4840e --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.cpp @@ -0,0 +1,1179 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef WIN32 +#include "config.h" +#endif + +#include + +#ifdef HAVE_LIBG2 +#include +#include +#endif + +#include +#include +#include +#include + +#include "matrix.h" +#include "rna_profile_alignment.h" +#include "rnafuncs.h" +#include "utils.h" + +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library +#include "part_func.h" +#include "fold_vars.h" + +extern "C"{ +#include "fold.h" +} + +#endif + +#include "ppforest.t.cpp" + +ostream& operator <<(ostream &s,RNA_Alphabet_Profile p) +{ + + s.precision(2); + s << p.p[ALPHA_PRO_BASE_A] << "\\n"; + s.precision(2); + s << p.p[ALPHA_PRO_BASE_C] << "\\n"; + s.precision(2); + s << p.p[ALPHA_PRO_BASE_G] << "\\n"; + s.precision(2); + s << p.p[ALPHA_PRO_BASE_U] << "\\n"; + s.precision(2); + s << p.p[ALPHA_PRO_BASEPAIR] << "\\n"; + s.precision(2); + s << p.p[ALPHA_PRO_GAP]; + s.precision(2); + s << p.p[ALPHA_PRO_BASE]; + + // for(Uint i=0;i(RNAFuncs::treeSize(viennaStr)), + m_name(name), + m_numStructures(1) +{ + buildForest(baseStr,viennaStr); + addStrName(name); +}; + +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library +RNAProfileAlignment::RNAProfileAlignment(const string &baseStr, const string &name, const string &constraint, double t) + : PPForestAli(2*baseStr.length()), + m_name(name), + m_numStructures(1) +{ + char *viennaStr=NULL; + + // calculate partition function for the sequence + do_backtrack=1; + init_pf_fold(baseStr.length()); + + //if(constraint.length()>0) + //pf_fold((char*)baseStr.c_str(),(char*)constraint.c_str()); // expicit conversion to non-const value, but pf_fold does not alter baseStr + //else + pf_fold((char*)baseStr.c_str(),NULL); // expicit conversion to non-const value, but pf_fold does not alter baseStr + + viennaStr=new char[baseStr.length()+1]; + dangles=2; + fold((char*)baseStr.c_str(),viennaStr); + + setSize(RNAFuncs::treeSize(viennaStr)); + buildForest(baseStr,viennaStr,true); + + free_pf_arrays(); + delete[] viennaStr; + + // hasSequence=true; + addStrName(name); +} +#endif + +RNAProfileAlignment::RNAProfileAlignment(const string &filename) +{ + // read ppforest from file + size_type size; + ifstream s; + char *colStr; + + s.open(filename.c_str()); + + // first of all save the size + s.read((char*)&size,sizeof(size_type)); + s.read((char*)&m_numStructures,sizeof(Uint)); + + colStr=new char[m_numStructures+1]; + colStr[m_numStructures]=0; // terminate string + + // initialize structures + // ::PPForestBase(m_size); + // m_lb=new L[ppf.size()]; + initialize(size); + + // save the arrays + for(Uint i=0;i(&d),sizeof(double)); + l.p[r]=d; + } + + s.read(colStr,sizeof(char)*m_numStructures); + + l.columnStr=colStr; + m_lb[i]=l; + } + + s.read(reinterpret_cast(m_rb),sizeof(size_type)*size); + s.read(reinterpret_cast(m_noc),sizeof(size_type)*size); + // s.read((char*)m_sumUpCSF,sizeof(size_type)*size); + // s.read((char*)m_rmb,sizeof(size_type)*size); + + for(Uint r=0;r(ppf) +{ + m_numStructures=ppf.m_numStructuresX+ppf.m_numStructuresY; +}*/ + +/* ****************************************** */ +/* Private functions */ +/* ****************************************** */ + +void RNAProfileAlignment::makeRepLabel(size_type node, RNA_Alphabet_Profile a, RNA_Alphabet_Profile b) + { + double p,q; + double m; + + p=m_numStructuresX; // weight number of structures in profile + q=m_numStructuresY; + m=p+q; + p/=m; + q/=m; + + // profile + for(int i=0;i 0) + // if(baseStr.length() != viennaStrLen) + // throw RNAForestExceptionInput(RNAForestExceptionInput::Error_BaseStringAndViennaStringIncompatible); + + nodeStack=new Uint[maxDepth+1]; + numChildrenStack=new Uint[maxDepth+1]; + baseposStack=new Uint[maxDepth+1]; + memset(nodeStack,0,sizeof(Uint)*maxDepth+1); + memset(numChildrenStack,0,sizeof(Uint)*maxDepth+1); + memset(baseposStack,0,sizeof(Uint)*maxDepth+1); + + // fill PPForest structure + stackPtr=0; + node=0; + for(Uint i=0;i &pairprob, double t,size_type i, size_type j) const +{ + size_type h; + double bestPairScore; + // list leftPairList; + //list rightPairList; + //Uint bestLeftIndex,bestRightIndex; + //Uint lastLeftIndex,lastRightIndex; + + // QWATCH(i); + // QWATCH(j); + + if(j==0) + return; + + if(isPair(i)) + { + // TRACE(DBG_GET_PROFILE_STRUCTURE,"Profile_RNA_Alignment_Forest::getStructureAlignmentFromCSF","basepair"); + // WATCH(DBG_GET_PROFILE_STRUCTURE,"Profile_RNA_Alignment_Forest::getStructureAlignmentFromCSF",m_lb[i].p[ALPHA_BASEPAIR]); + + bestPairScore=bestPairs(i); + + // backtrack best pairs + if(bestPairScore == bestPairs(i+1) + bestPairs(getRightmostBrotherIndex(i+1)) || m_lb[i].p[ALPHA_PRO_BASEPAIR] < t) + { + // i pairs not + // cout << "unpaired" << endl; + getStructureAlignmentFromCSF(s,pairprob,t,i+1,noc(i)); + // cout << "back to:" << endl; + // QWATCH(i); + // QWATCH(j); + } + else + { + // cout << "paired" << endl; + // i pairs + s += '('; + pairprob.push_back(m_lb[i].p[ALPHA_PRO_BASEPAIR]); + + // left path - righthand best pairs + h=i+1; + while(h < size() && isPair(h)) + { + // cout << "left" << endl; + // QWATCH(h); + + assert((int)noc(h)-1>=0); + getStructureAlignmentFromCSF(s,pairprob,t,rb(h+1),noc(h)-1); + h=h+1; + } + + + assert((int)noc(i)-2>=0); + getStructureAlignmentFromCSF(s,pairprob,t,rb(i+1),noc(i)-2); + // cout << "back to:" << endl; + // QWATCH(i); + // QWATCH(j); + + // right path - lefthand best pairs + h=getRightmostBrotherIndex(i+1); + while(h < size() && isPair(h)) + { + // cout << "right" << endl; + // QWATCH(h); + + assert((int)noc(h)-1>=0); + getStructureAlignmentFromCSF(s,pairprob,t,h+1,noc(h)-1); + //h=h+1; + h=getRightmostBrotherIndex(h+1); + } + + + s += ')'; + pairprob.push_back(m_lb[i].p[ALPHA_PRO_BASEPAIR]); + } + } + else + { + s+= '.'; + pairprob.push_back(m_lb[i].p[ALPHA_PRO_BASE]); + } + + // right forest + getStructureAlignmentFromCSF(s,pairprob,t,rb(i),j-1); +} + +double RNAProfileAlignment::bestPairs(size_type node) const +{ + size_type i=node; + double d1,d2; + + WATCH(DBG_GET_PROFILE_STRUCTURE,"RNAProfileForest::getStructureAlignment",node); + + if(isBase(node)) + return 0; + else + { + // node pairs not + d1=bestPairs(node+1) + bestPairs(getRightmostBrotherIndex(node+1)); + + // node pairs + d2=label(node).p[ALPHA_PRO_BASEPAIR]; + + // left path - righthand best pairs + i=node+1; + while(i < size() && isPair(i)) + { + d2+=bestPairs(getRightmostBrotherIndex(i+1)); + i=i+1; + } + + // right path - lefthand best pairs + i=getRightmostBrotherIndex(node+1); + while(isPair(i) && i < size()) + { + d2+=bestPairs(i+1); + i=getRightmostBrotherIndex(i+1); + } + + return max(d1,d2); + } +} + +#ifdef HAVE_LIBG2 // This features require the g2 library +void RNAProfileAlignment::drawBaseCircles(int device_id,const BaseProbs &bp,double center_x,double center_y) const +{ + const double box_size=6.0; + const double max_radius=3.0; + + double xpos,ypos; + int color; + // double dashes=0.5; + + // draw the base probabilities as circles on the edges of the square and the gap probability + // as the center square + + // upper left corner = a + xpos=center_x-box_size/2.0; + ypos=center_y+box_size/2.0; + + color=g2_ink(device_id,1,0,0); + g2_pen(device_id,color); + g2_filled_circle(device_id,xpos,ypos,max_radius*bp.a); + + // upper right corner = c + xpos=center_x+box_size/2.0; + ypos=center_y+box_size/2.0; + + color=g2_ink(device_id,0,1,0); + g2_pen(device_id,color); + g2_filled_circle(device_id,xpos,ypos,max_radius*bp.c); + + // lower right corner = g + xpos=center_x+box_size/2.0; + ypos=center_y-box_size/2.0; + + color=g2_ink(device_id,0,0,1); + g2_pen(device_id,color); + g2_filled_circle(device_id,xpos,ypos,max_radius*bp.g); + + // lower right corner = u + xpos=center_x-box_size/2.0; + ypos=center_y-box_size/2.0; + + color=g2_ink(device_id,1,0,1); + g2_pen(device_id,color); + g2_filled_circle(device_id,xpos,ypos,max_radius*bp.u); + + // gap in the center + color=g2_ink(device_id,0,0,0); + g2_pen(device_id,color); + g2_filled_circle(device_id,center_x,center_y,max_radius*bp.gap); + + // draw rectangle for orientation + //g2_set_dash(device_id,1,&dashes); + color=g2_ink(device_id,0.75,0.75,0.75); + g2_pen(device_id,color); + g2_rectangle(device_id,center_x-box_size/2,center_y-box_size/2,center_x+box_size/2,center_y+box_size/2); +} +#endif + +inline double RNAProfileAlignment::getMlBaseFreq(const BaseProbs &bp) const +{ + return max(max(max(bp.a,bp.c),bp.g),bp.u); +} + +char RNAProfileAlignment::getMlBase(const BaseProbs &bp) const +{ + double p = getMlBaseFreq(bp); + if(bp.a==p) + return ALPHA_BASE_A; + if(bp.c==p) + return ALPHA_BASE_C; + if(bp.g==p) + return ALPHA_BASE_G; + if(bp.u==p) + return ALPHA_BASE_U; + + assert(false); // you should never get so far ... + return 'x'; +} + +void RNAProfileAlignment::getSeqAli(string &seq,Uint row, Uint i, Uint j) const +{ + if(i==0 && j==getMaxLength(0)) + seq=""; + + if(j==0) + return; + + // basepair=internal node + if(isPair(i)) + { + getSeqAli(seq,row,i+1,noc(i)); + getSeqAli(seq,row,rb(i),j-1); + } + else + { + // base=leaf + seq+=m_lb[i].columnStr[row]; + getSeqAli(seq,row,rb(i),j-1); + } +} + +void RNAProfileAlignment::getStructAli(string &s,Uint row) const +{ + s=""; + + map pairs; + makePairTable(pairs, row); + + // iterate through leaves nodes and use information of pairs + for(Uint i=0;i &pairs, Uint row) const +{ + pair *baseIndex; // left and right base + RNA_Alphabet c; + + assert(row[m_size]; + + // initialize pairs, all gaps + for(int i=size()-1;i>=0;i--) + { + baseIndex[i].first=-1; + baseIndex[i].second=-1; + } + + for(int i=size()-1;i>=0;i--) + { + c=m_lb[i].columnStr[row]; + + if(isLeave(i)) + { + if(c!=ALPHA_GAP) + { + baseIndex[i].first=i; + baseIndex[i].second=i; + } + } + else + { + // internal node + // leftmost and rightmost base + bool lmBaseFound=false; + for(size_type r=0,h=i+1;r &pairprob, deque &baseprobs, double minFreq) const +{ + deque::iterator itPP; + // deque::iterator itBP; + string::iterator it; + + for(itPP=pairprob.begin(),it=structure.begin();itPP!=pairprob.end();itPP++,it++) + { + if(*itPPbase &baseprob) const +{ + BaseProbs bp; + + // generate base strings + for(size_type i=0;i &pairprob) const +{ + WATCH(DBG_GET_PROFILE_STRUCTURE,"Profile_RNA_Alignment_Forest::getStructureAlignment",size()); + + s=""; + getStructureAlignmentFromCSF(s,pairprob,t,0,getMaxLength(0)); +} + +#ifdef HAVE_LIBG2 // This features require the g2 library +void RNAProfileAlignment::squigglePlot(const string &filename, SquigglePlotOptions &options) const +{ + const double base_fontsize=8; + const Uint num_grey_colors=100; + const double min_grey_color=1.0; + + string seq,structure; + string base,structname; + float *X,*Y,min_X=0,max_X=0,min_Y=0,max_Y=0; + Uint i; + short *pair_table; + int id_PS,id; + int ps_grey_colors[num_grey_colors]; + int ps_color_red; + int ps_color_black; + double xpos,ypos; + + deque pairprob; + deque baseprobs; + + getStructureAlignment(options.minPairProb,structure,pairprob); + getSequenceAlignment(baseprobs); + + // filterConsensus(structure,pairprob,baseprobs,0.5); + + //assert(baseprobs.size() == structure.size()); + if(baseprobs.size() != structure.size()) + cerr << "Error in resolving consensus structure!" << endl; + + X = new float[structure.size()]; + Y = new float[structure.size()]; + + pair_table = make_pair_table(structure.c_str()); + i = naview_xy_coordinates(pair_table, X, Y); + if(i!=structure.size()) + cerr << "strange things happening in squigglePlot ..." << endl; + + // calculate image dimesions + for(i=0;ii+1) + { + // pairs in both structures + if(pairprob[i]==1) + g2_pen(id,ps_color_red); + else + g2_pen(id,ps_grey_colors[(int)floor(pairprob[i]*num_grey_colors-1)]); + + g2_line(id,X[i],Y[i],X[pair_table[i+1]-1],Y[pair_table[i+1]-1]); + } + } + + g2_flush(id); + g2_close(id); + + free(pair_table); + DELETE(X); + DELETE(Y); +} +#endif + +void RNAProfileAlignment::printSeqAli() const +{ + Uint i,l; + deque seqs; + string seq,info; + + // get alignment rows + for(i=0;i strs; + string str,info; + + // get alignment rows + for(i=0;i" << m_strNames[i] << endl; + cout << seq << endl; + if(!noStructure) + cout << str << endl; + } +} + +void RNAProfileAlignment::printConsensus(double minPairProb) const +{ + const int mountain_high=10; + int j; + + string seq,structure; + + deque baseprobs; + deque pairprob; + + getSequenceAlignment(baseprobs); + getStructureAlignment(minPairProb,structure,pairprob); + + // build sequence + deque::const_iterator it; + for(it=baseprobs.begin();it!=baseprobs.end();it++) + { + seq += getMlBase(*it); + } + +// assert(seq.size() == structure.size()); + if(seq.size() != structure.size()) + cerr << "Error in resolving consensus structure!" << endl; + + for(Uint i=0;i=1-(1/(double)mountain_high)*(double)j) + cout << "*"; + else + cout << " "; + } + } + cout << endl; + } + + cout << setw(25) << " " << seq.substr(i,55) << endl; + cout << setw(25) << " " << structure.substr(i,55) << endl; + + // show structure frequency mountain + for(j=0;j=(1/(double)mountain_high)*(double)j) + cout << "*"; + else + cout << " "; + } + } + cout << endl; + } + + cout << endl; + } +} + +void RNAProfileAlignment::addStrNames(const deque& strNames) +{ + deque::const_iterator it; + for(it=strNames.begin();it!=strNames.end();it++) + m_strNames.push_back(*it); +} + +void RNAProfileAlignment::save(const string &filename) +{ + ofstream s(filename.c_str()); + + // save the pforest to stream in binary format + + // first of all save the size + s.write(reinterpret_cast(&m_size),sizeof(size_type)); + s.write(reinterpret_cast(&m_numStructures),sizeof(Uint)); + + // save the arrays + for(Uint i=0;i(&m_lb[i].p[r]),sizeof(double)); + + s.write(reinterpret_cast(m_lb[i].columnStr.c_str()),sizeof(char)*m_numStructures); + } + + + // for(Uint i=0;i(&m_lb[i]),sizeof(label_type)*m_size); + // } + + // s.write(reinterpret_cast(m_lb),sizeof(label_type)*m_size); + s.write(reinterpret_cast(m_rb),sizeof(size_type)*m_size); + s.write(reinterpret_cast(m_noc),sizeof(size_type)*m_size); + + for(Uint r=0;r(ss.str().c_str()),sizeof(char)*20); + } + + + // s.write(reinterpret_cast(m_sumUpCSF),sizeof(size_type)*m_size); + // s.write(reinterpret_cast(m_rmb),sizeof(size_type)*m_size); + + // s.write(m_name; + //Uint m_numStructures; + //Uint m_numStructuresX; + //Uint m_numStructuresY; + //deque m_strNames; + //bool hasSequence; +} diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.h new file mode 100755 index 000000000..57b2e18de --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.h @@ -0,0 +1,141 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _RNA_PROFILE_ALIGNMENT_H +#define _RNA_PROFILE_ALIGNMENT_H + +#include +#include +#include + +#include "alignment.h" +#include "matrix.h" +#include "ppforestali.h" +#include "rna_algebra.h" +#include "types.h" + +//#include "alignment.t.cpp" + +using namespace std; + +class RNAProfileAlignment + : public PPForestAli +{ + public: + // typedef typename PPForestAli::size_type size_type; + + struct SquigglePlotOptions + { + bool hideBaseNumbers; + Uint baseNumInterval; + bool greyColors; + bool mostLikelySequence; + double minPairProb; + }; + + struct BaseProbs + { + double a; + double c; + double g; + double u; + double gap; + double base; + }; + + private: + string m_name; + Uint m_numStructures; + Uint m_numStructuresX; + Uint m_numStructuresY; + deque m_strNames; + bool hasSequence; + + void makeRepLabel(size_type node, RNA_Alphabet_Profile a, RNA_Alphabet_Profile b); + void makeDelLabel(size_type node, RNA_Alphabet_Profile a); + void makeInsLabel(size_type node, RNA_Alphabet_Profile b); + + void showLabel(ostream &s,RNA_Alphabet_Profile p) const; + void makeLabel(RNA_Alphabet_Profile &a,char c); + + /** Build forest from structure, sequence pair. */ + void buildForest(const string &baseStr, const string &viennaStr, bool use_bp_prob=false); + + void getStructureAlignmentFromCSF(string &s, deque &pairprop, double t,size_type i, size_type j) const; + double bestPairs(size_type node) const; + void drawBaseCircles(int device_id,const BaseProbs &bp,double center_x,double center_y) const; + double getMlBaseFreq(const BaseProbs &baseprobs) const; + char getMlBase(const BaseProbs &bp) const; + void getSeqAli(string &seq,Uint row,Uint i,Uint j) const; + void getStructAli(string &str,Uint row) const; + void makePairTable(map &pairs, Uint row) const; + void filterConsensus(string &structure, deque &pairprob, deque &baseprobs, double minFreq) const; + void addStrName(const string &strName) {m_strNames.push_back(strName);}; + + inline bool isBase(size_type node) const + { + if(label(node).p[ALPHA_PRO_BASE] > 0) + return true; + else + return false; + }; + + inline bool isPair(size_type node) const {return !isBase(node);}; + +public: + RNAProfileAlignment(const string &baseStr, const string &viennaStr, const string &name); + RNAProfileAlignment(const string &baseStr, const string &constraint, const string &name, double t); + RNAProfileAlignment(const string &filename); + + void printSeqAli() const; + void printStrAli() const; + void printConsensus(double minPairProb) const; + void printFastaAli(bool noStructure=false) const; + + void squigglePlot(const string &filename, SquigglePlotOptions &options) const; + void getSequenceAlignment(deque &baseprob) const; + void getStructureAlignment(double t, string &s, deque &pairprob) const; + string getName() const {return m_name;}; + void setName(const string &name) {m_name=name;}; + Uint getNumStructures() const {return m_numStructures;}; + const deque& getStrNames() const {return m_strNames;}; + void addStrNames(const deque& strNames); + void save(const string &filename); + + RNAProfileAlignment(Uint numStructuresX,Uint numStructuresY) : + PPForestAli(), + m_numStructures(numStructuresX + numStructuresY), + m_numStructuresX(numStructuresX), + m_numStructuresY(numStructuresY){}; +}; + +/* +class Profile_RNA_Alignment: public Alignment +{ + private: + string m_name; + + public: + Profile_RNA_Alignment(const RNAProfileForest *ppfx, const RNAProfileForest *ppfy, const DoubleScoreProfileAlgebraType &alg) + : Alignment((const PPForest*)ppfx,(const PPForest*)ppfy,alg) + { + m_name=ppfx->getName(); + m_name+="."; + m_name+=ppfy->getName(); + }; + + string getName() const {return m_name;}; +}; +*/ + +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.o new file mode 100755 index 000000000..35c332b81 Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rna_profile_alignment.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.cpp new file mode 100755 index 000000000..5bab01a21 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.cpp @@ -0,0 +1,181 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef WIN32 +#include "config.h" +#endif + +#ifndef HAVE_LIBRNA +#undef HAVE_LIBG2 +#endif + +#include "rnaforest.h" +#include "rnafuncs.h" + +#include "ppforest.t.cpp" + +/* ****************************************** */ +/* Constructor and Destruktor functions */ +/* ****************************************** */ + +RNAForest::RNAForest(const string &baseStr, const string &viennaStr, const string &name) +: PPForest(RNAFuncs::treeSize(viennaStr)), + m_baseStr(baseStr), + m_viennaStr(viennaStr) +{ + if(name.empty()) + m_name="unknown"; + else + m_name=name; + + buildForest(baseStr,viennaStr); +}; + +/* ****************************************** */ +/* Private functions */ +/* ****************************************** */ + +inline void RNAForest::makeLabel(RNA_Alphabet &a,char c) +{ + a=c; +} + +inline void RNAForest::showLabel(ostream &s,RNA_Alphabet a) const +{ + s << a; +} + +void RNAForest::buildForest(const string &baseStr, const string &viennaStr) +{ + Ulong basePairCount=0,maxDepth=0,stackPtr; + Uint baseStrLen,viennaStrLen,node,*nodeStack, *numChildrenStack; + + assert(RNAFuncs::isRNAString(baseStr)); + + RNAFuncs::isViennaString(viennaStr,basePairCount,maxDepth); + + baseStrLen=baseStr.length(); + viennaStrLen=viennaStr.length(); + + // check if base string and vienna string have the same length + // if(baseStr.length() > 0) + // if(baseStr.length() != viennaStrLen) + // throw RNAForestExceptionInput(RNAForestExceptionInput::Error_BaseStringAndViennaStringIncompatible); + + nodeStack=new Uint[maxDepth+1]; + numChildrenStack=new Uint[maxDepth+1]; + memset(nodeStack,0,sizeof(Uint)*maxDepth+1); + memset(numChildrenStack,0,sizeof(Uint)*maxDepth+1); + + // fill PPForest structure + stackPtr=0; + node=0; + for(Uint i=0;i > ®ions, const RNAFuncs::SquigglePlotOptions &sqOptions) const +{ + RNAFuncs::drawRNAStructure(m_baseStr,m_viennaStr,filename_prefix,m_name,regions,sqOptions); +} +#endif diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.h b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.h new file mode 100755 index 000000000..1fdb5e79d --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.h @@ -0,0 +1,61 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#ifndef _RNA_FOREST_H_ +#define _RNA_FOREST_H_ + +#include + +#include "algebra.h" +#include "ppforest.h" +#include "rna_alphabet.h" +#include "rnafuncs.h" + + +using namespace std; + + +/** RNAForest encapsulates the forest representation of an RNA */ +class RNAForest + : public PPForest +{ +private: + typedef PPForest PPForestRNAType; + + string m_name; + string m_baseStr; + string m_viennaStr; + + void showLabel(ostream &s,RNA_Alphabet a) const; // virtual function of PPForest + void makeLabel(RNA_Alphabet &a,char c); + + /** Build forest from structure, sequence pair. */ + void buildForest(const string &baseStr, const string &viennaStr); + +public: + /** Build forest from structure sequence pair. + * This allows for direct use of Vienna RNA strings. + * e.g.: str="(..(...))", seq="accguuucu" + */ + RNAForest(const string &baseStr, const string &viennaStr, const string &name); + + const string& getName() const {return m_name;}; + const string& getBaseStr() const {return m_baseStr;}; + const string& getViennaStr() const {return m_viennaStr;}; + + void plot2d(const string &filename_prefix, const list > ®ions, const RNAFuncs::SquigglePlotOptions &sqOptions) const; +}; + +#endif + + diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.o b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.o new file mode 100755 index 000000000..832eba7ad Binary files /dev/null and b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforest.o differ diff --git a/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforester_options.cpp b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforester_options.cpp new file mode 100755 index 000000000..410b770f8 --- /dev/null +++ b/modules/local/pita/templates/Bin/ViennaRNA/ViennaRNA-1.6/RNAforester/src/rnaforester_options.cpp @@ -0,0 +1,228 @@ +/* + Copyright by Matthias Hoechsmann (C) 2002-2004 + ===================================== + You may use, copy and distribute this file freely as long as you + - do not change the file, + - leave this copyright notice in the file, + - do not make any profit with the distribution of this file + - give credit where credit is due + You are not allowed to copy or distribute this file otherwise + The commercial usage and distribution of this file is prohibited + Please report bugs and suggestions to +*/ + +#include +#include + +#ifndef WIN32 +#include "config.h" +#endif + +#ifndef HAVE_LIBRNA +#undef HAVE_LIBG2 +#endif + +#include "rnaforester_options.h" + +RNAforesterOptions::RNAforesterOptions(int argc, const char **argv) +: m_argv(argv) +{ + m_options=new OptionsInfo[NumberOfOptions]; + + setOption(Help, "--help",""," ","shows this help info",false); + setOption(Version, "--version",""," ","shows version information",false); + setOption(OutputAlignmentDotFormat, "-dot","=file"," ","show alignment forest in dot format",true); + setOption(CalculateDistance, "-d",""," ","calculate distance instead of similarity",false); + setOption(RelativeScore, "-r",""," ","calculate relative score",false); + setOption(LocalSimilarity, "-l",""," ","local similarity",false); + setOption(LocalSubopts, "-so","=int"," ","local suboptimal alignments within int%",false); + setOption(SmallInLarge, "-s",""," ","small-in-large similarity",false); + setOption(Multiple, "-m",""," ","multiple alignment mode",false); + setOption(ClusterThreshold, "-mt","=double"," ","clustering threshold",false); + setOption(ClusterJoinCutoff, "-mc","=double"," ","clustering cutoff",false); +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library + setOption(PredictProfile, "-p",""," ","predict structures from sequences",false); + setOption(PredictMinPairProb, "-pmin","=double"," ","minimum basepair frequency for prediction",false); +#endif + setOption(SaveProfile, "-sp","=file"," ","save profile",false); + setOption(ProfileSearch, "-ps","=file"," ","profile search",false); + + setOption(TreeEdit, "-e",""," ","use tree edit model to calculate distance and similarity",true); + setOption(GlobalAlignment, "-g",""," ","calculate global alignment in its original version",true); + setOption(BpRepScore, "-pm","=int"," ","basepair(bond) match score",false); + setOption(BpDelScore, "-pd","=int"," ","basepair bond indel score",false); + setOption(BMatchScore, "-bm","=int"," ","base match score",false); + setOption(BRepScore, "-br","=int"," ","base mismatch score",false); + setOption(BDelScore, "-bd","=int"," ","base indel score",false); + setOption(RIBOSUMScore, "--RIBOSUM",""," ","RIBOSUM85-60 scoring matrix (base-pair substitutions)",false); + setOption(ConsensusMinPairProb, "-cmin","=double"," ","minimum basepair frequency for consensus structure",false); +#ifdef HAVE_LIBG2 // This features require the g2 library + setOption(MakeSquigglePlot, "-2d",""," ","generate alignment 2D plots in postscript format",false); + setOption(SquiggleHideBaseNumbers, "--2d_hidebasenum",""," ","hide base numbers in 2D plot",false); + setOption(SquiggleBaseNumberInterval,"--2d_basenuminterval","=n"," ","show every n-th base number",false); + setOption(SquiggleGreyColors, "--2d_grey",""," ","use only grey colors in 2D plots",false); + setOption(SquiggleScaleFactor, "--2d_scale","=double"," ","scale factor for the 2d plots",false); + setOption(SquiggleGenerateFIG, "--2d_fig",""," ","generate additional fig file of 2d plot",false); +#ifdef HAVE_LIBGD // This features require the gd library + setOption(SquiggleGeneratePNG, "--2d_png",""," ","generate additional png file of 2d plot",false); + setOption(SquiggleGenerateJPG, "--2d_jpg",""," ","generate additional jpg file of 2d plot",false); +#endif +#endif + setOption(ReadFromFile, "-f","=file"," ","read input from file",false); + // setOption(SaveMultipleAliFile, "-sm","=file"," ","save multiple alignment as binary file",true); + setOption(NoScale, "--noscale",""," ","suppress output of scale",false); + setOption(MakeDotForInputTrees, "-idot",""," ","make dot files for the input trees",true); +#ifdef HAVE_LIBRNA // This features require the ViennaRNA library + setOption(GenerateXML, "--xml",""," ","generate xml output for Jforester",true); +#endif + setOption(SecretHelp, "--shelp",""," ","shows this help info",true); + setOption(ShowOnlyScore, "--score",""," ","compute only scores, no alignment",false); + setOption(FastaOutput, "--fasta",""," ","generate fasta output of alignments",false); + + setOption(SpaceTimeInfo, "--spacetime",""," ","space and time measurements",true); + + // set the arguments that can be seperated by spaces + stringstream ss; + for(int i=0;ihas(m_options[option].tag); +} + +void RNAforesterOptions::help() +{ + cout << "Usage: " << m_argv[0] << " [options]" << endl; + + for(int i=0;i