Merge pull request #613 from stevenweaver/2.3.1-alpha

Merge 2.3.1 into master

.travis.yml

@@ -20,7 +20,10 @@ cache:
       - $HOME/cmake-3.3.2-Linux-x86_64/ 
 
 env:
-  - MPI=openmpi
+  - METHOD_TEST=tests/hbltests/libv3/SLAC.wbf
+  - METHOD_TEST=tests/hbltests/libv3/SLAC-partitioned.wbf
+  - METHOD_TEST=tests/hbltests/libv3/FEL.wbf
+  - METHOD_TEST=tests/hbltests/libv3/MEME.wbf
 
 language: c++
 compiler: 
@@ -52,5 +55,4 @@ script:
   - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/math.bf
   - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/iofunctions.bf
   - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/utilityfunctions.bf
-  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/SLAC.wbf
-  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/SLAC-partitioned.wbf
+  - ./HYPHYMP LIBPATH=`pwd`/res/ $METHOD_TEST

res/TemplateBatchFiles/BUSTED-SRV.bf

@@ -1,5 +1,9 @@
 RequireVersion ("2.1320141020");
 
+console.log("ERROR: THIS BATCHFILE WILL NOT RUN PROPERLY WITH UPDATED TERMS BASE. QUITTING.");
+exit();
+
+
 _BUSTED_timers  = {3,1};
 busted.taskTimerStart (2);
 

res/TemplateBatchFiles/BranchSiteREL.bf

@@ -85,8 +85,6 @@ codon3x4					= BuildCodonFrequencies (nucCF);
 
 tree_info = trees.LoadAnnotatedTopology (1);
 
-//fprintf (stdout, tree_info, "\n");
-
 Model	  MGL				= (MGMatrixLocal, codon3x4, 0);
 
 tree_info_models = tree_info["model_map"];

res/TemplateBatchFiles/LHT.bf

@@ -22,7 +22,8 @@ SelectTemplateModel(filteredData);
 
 /*check if there are any partitions.*/
 
-partitionsFound = partitionsFound;
+
+partitionsFound = Rows (DATA_FILE_PARTITION_MATRIX);
 
 fprintf (stdout,"\n\n",partitionsFound," character sets found\n");
 if (partitionsFound==0)
@@ -56,7 +57,7 @@ bestTree	=	{partitionsFound,1};
 bestLk2		=	{partitionsFound,1};
 globalLk	=	{ntree,1};
 
-/*GET LIKELIHOOD FOR TREES FOR ALL PARTITIONS AND CHOOSE THE BEST TREE*/    
+/*GET LIKELIHOOD FOR TREES FOR ALL PARTITIONS AND CHOOSE THE BEST TREE*/
 for (part=0; part<partitionsFound; part=part+1)
 {
   DataSetFilter dsf=CreateFilter (ds,1,DATA_FILE_PARTITION_MATRIX[1][part]);
@@ -66,14 +67,14 @@ for (part=0; part<partitionsFound; part=part+1)
       MBF = PopulateModelMatrix ("filterModelMatrix", baseFreqs);
       Model filterModel = (filterModelMatrix, baseFreqs, MBF);
   }
-  
+
   fprintf(stdout,"Analysis for partition ",DATA_FILE_PARTITION_MATRIX[0][part]," given trees:\n");
   for (i=0; i<ntree; i=i+1)
   {
 		Tree uniqueTree=NEXUS_FILE_TREE_MATRIX[i][1];
 		LikelihoodFunction lf = (dsf,uniqueTree);
 		Optimize (mles,lf);
-		if (part==0) 
+		if (part==0)
 			{fprintf(stdout,lf);}
 		listOfLk[part][i]=mles[1][0];
 		if (i==0)
@@ -100,7 +101,7 @@ lk1=0;  /*H0: constrained same tree for different partition*/
 for (i=0; i<ntree; i=i+1)
 {
 	globalLk[i]=0;
-	for (part=0; part<partitionsFound; part=part+1) 
+	for (part=0; part<partitionsFound; part=part+1)
 	{
 		globalLk[i]=globalLk[i]+listOfLk[part][i];
 	}
@@ -120,7 +121,7 @@ for (i=0; i<ntree; i=i+1)
 }
 
 fprintf (stdout,"\n| Tree n.  |");
-for (i=0;i<partitionsFound;i=i+1) 
+for (i=0;i<partitionsFound;i=i+1)
 {
 	fprintf(stdout," ",DATA_FILE_PARTITION_MATRIX[0][i],"\t|");
 }
@@ -143,7 +144,7 @@ fprintf(stdout,"L1= ",Format(lk2,10,10),"\n");
 lnlikDelta= 2*(lk2-lk1);
 fprintf(stdout,"LRT= ",Format(lnlikDelta,10,10),"\n\n");
 
-/*PARAMETRIC BOOTSTRAP*/    
+/*PARAMETRIC BOOTSTRAP*/
 count=0;
 
 for (replicate=0;replicate<nreplicates;replicate=replicate+1)
@@ -165,25 +166,26 @@ for (replicate=0;replicate<nreplicates;replicate=replicate+1)
 
 		/*simulate constrained different partition*/
 		DataSet simData = SimulateDataSet(lf);
-		DataSetFilter simDataf=CreateFilter (simData,1);     
+		DataSetFilter simDataf=CreateFilter (simData,1);
 		if (FREQUENCY_SENSITIVE)
 		{
 			HarvestFrequencies (baseFreqs, simDataf, 1,1,1);
 			MBF = PopulateModelMatrix ("filterModelMatrix", baseFreqs);
 			Model filterModel = (filterModelMatrix, baseFreqs, MBF);
 		}
 
-		/*H0: constrained same tree for different partition*/ 
+		/*H0: constrained same tree for different partition*/
 		Tree globalTree=NEXUS_FILE_TREE_MATRIX[theBestTree][1];
 		LikelihoodFunction lfsim = (simDataf,globalTree);
 		Optimize (mles,lfsim);
-		lk1=lk1+mles[1][0];  
+		lk1=lk1+mles[1][0];
 
 		/*H1: unconstrained difffeent tree for different partition*/
 		for (i=0; i<ntree; i=i+1)
 		{
 			Tree uniqueTree=NEXUS_FILE_TREE_MATRIX[i][1];
-			LikelihoodFunction lfsim2 = (simDataf,uniqueTree);
+		    DataSetFilter simDataf2=CreateFilter (simData,1);
+			LikelihoodFunction lfsim2 = (simDataf2,uniqueTree);
 			Optimize (mles,lfsim2);
 			if (i==0) {bestLk=mles[1][0];} else {bestLk=Max(bestLk,mles[1][0]);}
 		}
@@ -198,7 +200,7 @@ for (replicate=0;replicate<nreplicates;replicate=replicate+1)
 	{
 		fprintf(stdout,"replicate ",replicate,"- 0.00000 *",simLRT,"\n");
 	}
-	if (lnlikDelta>simLRT) 
+	if (lnlikDelta>simLRT)
 	{
 		count = count+1;
 	}

res/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf

@@ -15,15 +15,21 @@ utility.SetEnvVariable ("OPTIMIZATION_PRECISION", 0.1); // for testing purposes.
 utility.ToggleEnvVariable ("PRODUCE_OPTIMIZATION_LOG", 1); // for testing purposes
 
 io.DisplayAnalysisBanner({
-    "info": "Fit a general time reversible model to a collection
+    terms.io.info: "Fit a general time reversible model to a collection
     of training protein sequence alignments. Generate substitution
     and scoring matrices following the procedures described in Nickle et al 2007",
-    "version": "0.01",
-    "reference": "Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, Kosakovsky Pond SL (2007) HIV-Specific Probabilistic Models of Protein Evolution. PLoS ONE 2(6): e503. doi:10.1371/journal.pone.0000503",
-    "authors": "Sergei L Kosakovsky Pond and Stephanie J Spielman",
-    "contact": "{spond,stephanie.spielman}@temple.edu"
+    terms.io.version: "0.01",
+    terms.io.reference: "Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, Kosakovsky Pond SL (2007) HIV-Specific Probabilistic Models of Protein Evolution. PLoS ONE 2(6): e503. doi:10.1371/journal.pone.0000503",
+    terms.io.authors: "Sergei L Kosakovsky Pond and Stephanie J Spielman",
+    terms.io.contact: "{spond,stephanie.spielman}@temple.edu"
 });
 
+
+protein_gtr.filename_to_index = terms.data.filename_to_index;
+protein_gtr.logl = terms.fit.log_likelihood;
+protein_gtr.phase = terms.model.phase;
+
+
 /********************************************** MENU PROMPTS ********************************************************/
 /********************************************************************************************************************/
 
@@ -139,7 +145,7 @@ mpi.QueueComplete (protein_gtr.queue);
 
 
 // Sum of the logL from fitted baseline model across each data set
-protein_gtr.baseline_fit_logL = math.Sum (utility.Map (utility.Filter (protein_gtr.analysis_results, "_value_", "_value_/protein_gtr.phase_key"), "_value_", "(_value_[protein_gtr.phase_key])['LogL']"));
+protein_gtr.baseline_fit_logL = math.Sum (utility.Map (utility.Filter (protein_gtr.analysis_results, "_value_", "_value_/protein_gtr.phase_key"), "_value_", "(_value_[protein_gtr.phase_key])[terms.fit.log_likelihood]"));
 
 io.ReportProgressMessageMD ("Protein GTR Fitter", " * Initial branch length fit",
                             "Overall Log(L) = " + protein_gtr.baseline_fit_logL);
@@ -155,14 +161,14 @@ result_key = "REV-Phase-" + protein_gtr.fit_phase;
 
 if (utility.Has (protein_gtr.analysis_results, result_key, None)) {
     io.ReportProgressMessageMD ("Protein GTR Fitter", result_key,
-                                "Loaded cached results for '" + result_key + "'. Log(L) = " + (protein_gtr.analysis_results[result_key])["LogL"] );
+                                "Loaded cached results for '" + result_key + "'. Log(L) = " + (protein_gtr.analysis_results[result_key])[terms.fit.log_likelihood] );
     protein_gtr.current_gtr_fit = protein_gtr.analysis_results [result_key];
 } else {
     protein_gtr.current_gtr_fit = protein_gtr.fitGTRtoFileList (utility.Map (utility.Filter (protein_gtr.analysis_results, "_value_", "_value_/'" + protein_gtr.phase_key + "'"), "_value_", "_value_['" + protein_gtr.phase_key + "']"), protein_gtr.current_gtr_fit, result_key, FALSE);
 }
 
 // Record logL
-protein_gtr.scores + (protein_gtr.analysis_results[result_key])["LogL"];
+protein_gtr.scores + (protein_gtr.analysis_results[result_key])[terms.fit.log_likelihood];
 
 /* Now that the initial GTR fit has been performed, we toggle between a GTR fit and a branch length fit under the estimated GTR parameters */
 protein_gtr.shared_EFV = (utility.Values (protein_gtr.current_gtr_fit [terms.efv_estimate]))[0];
@@ -215,8 +221,8 @@ for (;;) {
         for (l1 = 0; l1 < 20; l1 += 1) {
             for (l2 = l1 + 1; l2 < 20; l2 += 1) {
 
-                previous = (previous_Q[ terms.aminoacidRate (models.protein.alphabet[l1],models.protein.alphabet[l2]) ])[terms.MLE];
-                current = (current_Q[ terms.aminoacidRate (models.protein.alphabet[l1],models.protein.alphabet[l2]) ])[terms.MLE];
+                previous = (previous_Q[ terms.aminoacidRate (models.protein.alphabet[l1],models.protein.alphabet[l2]) ])[terms.fit.MLE];
+                current = (current_Q[ terms.aminoacidRate (models.protein.alphabet[l1],models.protein.alphabet[l2]) ])[terms.fit.MLE];
 
                 rmse += (previous - current)^2;
                 N += 1;