diff --git a/build.gradle b/build.gradle
index 7ffee9fb6d..7aa7d191df 100644
--- a/build.gradle
+++ b/build.gradle
@@ -38,6 +38,7 @@ buildscript {
repositories {
mavenCentral()
+ mavenLocal()
}
java {
@@ -112,7 +113,7 @@ dependencies {
[group: 'org.apache.commons', name: 'commons-lang3', version: '3.9'],
[group: 'com.github.samtools', name: 'htsjdk', version: '4.0.2'],
[group: 'org.swinglabs', name: 'swing-layout', version: '1.0.3'],
- //[group: 'org.bidib.com.jidesoft', name: 'jide-common', version: '3.7.3'], // no longer in Maven Central
+ [group: 'com.formdev', name: 'jide-oss', version: '3.7.12'],
[group: 'com.google.guava', name: 'guava', version: '27.0.1-jre'],
[group: 'org.apache.xmlgraphics', name: 'batik-dom', version: '1.11'],
[group: 'org.apache.xmlgraphics', name: 'batik-svggen', version: '1.11'],
diff --git a/lib/jide-common-3.7.3.jar b/lib/jide-common-3.7.3.jar
deleted file mode 100644
index caca761ba4..0000000000
Binary files a/lib/jide-common-3.7.3.jar and /dev/null differ
diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
index 15bb2a73f2..6754cec47a 100644
--- a/src/main/java/module-info.java
+++ b/src/main/java/module-info.java
@@ -20,7 +20,6 @@
requires java.xml;
requires jdk.xml.dom;
requires swing.layout;
- requires jide.common;
requires org.apache.commons.io;
requires org.apache.commons.lang3;
requires batik.codec;
diff --git a/src/main/java/org/broad/igv/feature/genome/ColorSpaceSequence.java b/src/main/java/org/broad/igv/feature/genome/ColorSpaceSequence.java
deleted file mode 100644
index 3e1754ba76..0000000000
--- a/src/main/java/org/broad/igv/feature/genome/ColorSpaceSequence.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2007-2015 Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-
-package org.broad.igv.feature.genome;
-
-/**
- * Created with IntelliJ IDEA.
- * User: jrobinso
- * Date: 6/25/12
- * Time: 11:00 AM
- * To change this template use File | Settings | File Templates.
- */
-public class ColorSpaceSequence {
-
- Sequence sequence;
-
- public ColorSpaceSequence(Sequence sequence) {
- this.sequence = sequence;
- }
-
- /**
- * Return the sequence in Color Space (SOLID alignment encoding)
- *
- * @param chr
- * @param start
- * @param end
- * @return
- */
- public byte[] getSequence(String chr, int start, int end) {
- // We need to know the base just to the left of the start
- int csStart = (start == 0 ? 0 : start - 1);
- byte[] baseSequence = sequence.getSequence(chr, csStart, end);
- if (baseSequence == null || baseSequence.length == 0) {
- return baseSequence;
- }
-
- byte[] csSequence = new byte[end - start];
- int i = 0;
- int c1 = start == 0 ? 0 : baseToCS(baseSequence[i++]);
- for (; i < baseSequence.length; i++) {
- int c2 = baseToCS(baseSequence[i]);
- csSequence[i] = (byte) (c1 ^ c2);
- }
- return csSequence;
-
- }
-
- private static int baseToCS(byte base) {
- switch (base) {
- case 'A':
- case 'a':
- return 0;
- case 'C':
- case 'c':
- return 1;
- case 'T':
- case 't':
- return 2;
- case 'G':
- case 'g':
- return 3;
- }
- return -1;
- }
-
-
- public byte getBase(String chr, int position) {
- return 0; //To change body of implemented methods use File | Settings | File Templates.
- }
-}
diff --git a/src/main/java/org/broad/igv/feature/genome/GenomeBuilderDialog.java b/src/main/java/org/broad/igv/feature/genome/GenomeBuilderDialog.java
deleted file mode 100644
index fbc4b4b12e..0000000000
--- a/src/main/java/org/broad/igv/feature/genome/GenomeBuilderDialog.java
+++ /dev/null
@@ -1,215 +0,0 @@
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2007-2015 Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-
-/*
- * Created by JFormDesigner on Wed Apr 11 16:44:25 EDT 2012
- */
-
-package org.broad.igv.feature.genome;
-
-import org.broad.igv.prefs.PreferencesManager;
-import org.broad.igv.ui.IGV;
-import org.broad.igv.ui.util.FileDialogUtils;
-import org.broad.igv.ui.util.MessageUtils;
-
-import javax.swing.*;
-import javax.swing.border.EmptyBorder;
-import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.File;
-
-/**
- * @author Stan Diamond
- */
-public class GenomeBuilderDialog extends org.broad.igv.ui.IGVDialog {
-
- boolean canceled;
- File archiveFile;
-
- public GenomeBuilderDialog(Frame owner, IGV igv) {
- super(owner, "Create .genome file");
- setModal(true);
- initComponents();
- this.panel1.setIgv(igv);
- }
-
- public boolean isCanceled() {
- return canceled;
- }
-
- public File getArchiveFile() {
- return archiveFile;
- }
-
- private void okButtonActionPerformed(ActionEvent e) {
- boolean valid = validateFields();
- if (valid) {
- archiveFile = chooseArchiveFile();
- canceled = (archiveFile == null);
- setVisible(false);
- dispose();
- }
- }
-
- private void cancelButtonActionPerformed(ActionEvent e) {
- canceled = true;
- setVisible(false);
- dispose();
- }
-
- private File chooseArchiveFile() {
- File dir = PreferencesManager.getPreferences().getLastGenomeImportDirectory();
- File initFile = new File(getGenomeId() + ".genome");
- return FileDialogUtils.chooseFile("Save .genome file", dir, initFile, FileDialog.SAVE);
- }
-
- private boolean validateFields() {
- StringBuffer errors = new StringBuffer();
- String id = getGenomeId();
- String name = getGenomeDisplayName();
- String fastaFile = getFastaFileName();
- if (id == null || id.length() == 0) {
- errors.append(errors.length() == 0 ? "" : "
");
- errors.append("Unique ID is required");
- }
- if (name == null || name.length() == 0) {
- errors.append(errors.length() == 0 ? "" : "
");
- errors.append("Descriptive name is required");
- }
- if (fastaFile == null || fastaFile.length() == 0) {
- errors.append(errors.length() == 0 ? "" : "
");
- errors.append("FASTA file is required");
- }
- if (errors.length() == 0) {
- return true;
- } else {
- MessageUtils.showMessage(errors.toString());
- return false;
- }
- }
-
- private void initComponents() {
- // JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
- // Generated using JFormDesigner non-commercial license
- dialogPane = new JPanel();
- contentPanel = new JPanel();
- panel1 = new GenomeBuilderPane();
- buttonBar = new JPanel();
- okButton = new JButton();
- cancelButton = new JButton();
-
- //======== this ========
- Container contentPane = getContentPane();
- contentPane.setLayout(new BorderLayout());
-
- //======== dialogPane ========
- {
- dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
- dialogPane.setLayout(new BorderLayout());
-
- //======== contentPanel ========
- {
- contentPanel.setLayout(new BorderLayout());
- contentPanel.add(panel1, BorderLayout.CENTER);
- }
- dialogPane.add(contentPanel, BorderLayout.CENTER);
-
- //======== buttonBar ========
- {
- buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0));
- buttonBar.setLayout(new GridBagLayout());
- ((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 85, 80};
- ((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{1.0, 0.0, 0.0};
-
- //---- okButton ----
- okButton.setText("OK");
- okButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- okButtonActionPerformed(e);
- }
- });
- buttonBar.add(okButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(0, 0, 0, 5), 0, 0));
-
- //---- cancelButton ----
- cancelButton.setText("Cancel");
- cancelButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- cancelButtonActionPerformed(e);
- }
- });
- buttonBar.add(cancelButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(0, 0, 0, 0), 0, 0));
- }
- dialogPane.add(buttonBar, BorderLayout.SOUTH);
- }
- contentPane.add(dialogPane, BorderLayout.CENTER);
- setSize(870, 430);
- setLocationRelativeTo(getOwner());
- // JFormDesigner - End of component initialization //GEN-END:initComponents
- }
-
- // JFormDesigner - Variables declaration - DO NOT MODIFY //GEN-BEGIN:variables
- // Generated using JFormDesigner non-commercial license
- private JPanel dialogPane;
- private JPanel contentPanel;
- private GenomeBuilderPane panel1;
- private JPanel buttonBar;
- private JButton okButton;
- private JButton cancelButton;
- // JFormDesigner - End of variables declaration //GEN-END:variables
-
- public String getCytobandFileName() {
- return panel1.getCytobandFileName();
- }
-
- public String getGeneAnnotFileName() {
- return panel1.getGeneAnnotFileName();
- }
-
- public String getFastaFileName() {
- return panel1.getFastaFileName();
- }
-
- public String getChrAliasFileName() {
- return panel1.getChrAliasFileName();
- }
-
-
- public String getGenomeDisplayName() {
- return panel1.getGenomeDisplayName();
- }
-
- public String getGenomeId() {
- return panel1.getGenomeId();
- }
-
- public String getArchiveFileName() {
- return panel1.getArchiveFileName();
- }
-}
diff --git a/src/main/java/org/broad/igv/feature/genome/GenomeBuilderPane.java b/src/main/java/org/broad/igv/feature/genome/GenomeBuilderPane.java
deleted file mode 100644
index 6ef33da281..0000000000
--- a/src/main/java/org/broad/igv/feature/genome/GenomeBuilderPane.java
+++ /dev/null
@@ -1,475 +0,0 @@
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2007-2015 Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-
-package org.broad.igv.feature.genome;
-
-import org.broad.igv.logging.*;
-import org.broad.igv.Globals;
-import org.broad.igv.prefs.PreferencesManager;
-import org.broad.igv.ui.IGV;
-import org.broad.igv.ui.commandbar.GenomeListManager;
-import org.broad.igv.ui.util.FileDialogUtils;
-
-import javax.swing.*;
-import javax.swing.border.EmptyBorder;
-import javax.swing.border.TitledBorder;
-import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.File;
-import java.io.Serializable;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Set;
-
-/**
- * @author eflakes
- */
-public class GenomeBuilderPane extends javax.swing.JPanel implements Serializable {
-
- private static Logger logger = LogManager.getLogger(GenomeBuilderPane.class);
- private String genomeArchiveLocation;
- private String genomeFilename;
- GenomeImporter importer;
- IGV igv;
-
-
- public GenomeBuilderPane() {
- initComponents();
- importer = new GenomeImporter();
- }
-
- public void setIgv(IGV igv) {
- this.igv = igv;
- }
-
- public String getCytobandFileName() {
- String cytobandFile = cytobandFileTextField.getText();
- if (cytobandFile != null && cytobandFile.trim().equals("")) {
- cytobandFile = null;
- }
- return cytobandFile;
- }
-
- public String getGeneAnnotFileName() {
- String refFlatFile = geneAnnotFileTextField.getText();
- if (refFlatFile != null && refFlatFile.trim().equals("")) {
- refFlatFile = null;
- }
- return refFlatFile;
- }
-
- public String getFastaFileName() {
- String fastaFile = fastaFileTextField.getText();
- if (fastaFile != null && fastaFile.trim().equals("")) {
- fastaFile = null;
- }
- return fastaFile;
- }
-
- public String getChrAliasFileName() {
- String chrAliasFile = chrAliasField.getText();
- if (chrAliasFile != null && chrAliasFile.trim().equals("")) {
- chrAliasFile = null;
- }
- return chrAliasFile;
- }
-
-
- public String getGenomeId() {
- return idField.getText();
- }
-
-// public String getSequenceURL() {
-// return sequenceURLField.getText();
-// }
-
-
- public String getGenomeDisplayName() {
- String name = genomeDisplayNameTextField.getText();
- if (name != null && name.trim().equals("")) {
- name = null;
- } else {
- name = name.trim();
- }
- return name;
- }
-
- public String getGenomeArchiveLocation() {
- if (genomeArchiveLocation != null && genomeArchiveLocation.trim().equals("")) {
- genomeArchiveLocation = null;
- }
- return genomeArchiveLocation;
- }
-
- public String getArchiveFileName() {
-
- if (genomeFilename == null) {
- genomeFilename = getGenomeId() + Globals.GENOME_FILE_EXTENSION;
- }
- return genomeFilename;
- }
-
-
- protected File showGenomeArchiveDirectoryChooser() {
-
- File directory = PreferencesManager.getPreferences().getLastGenomeImportDirectory();
- File archiveName = new File(getGenomeId() + Globals.GENOME_FILE_EXTENSION);
- File file = FileDialogUtils.chooseFile("Save Genome File", directory, archiveName, FileDialogUtils.SAVE);
-
- if (file != null) {
-
- genomeFilename = file.getName();
- if (genomeFilename != null) {
- if (!genomeFilename.endsWith(Globals.GENOME_FILE_EXTENSION)) {
- genomeFilename += Globals.GENOME_FILE_EXTENSION;
- file = new File(file.getParentFile(), genomeFilename);
- }
- genomeArchiveLocation = file.getParentFile().getAbsolutePath();
- }
- }
- return file;
- }
-
- public boolean validateSelection() {
-
- try {
-
- if (!isIdValid()) {
- return false;
- }
-
- if (!isGenomeDisplayNameValid()) {
- genomeDisplayNameTextField.setText(null);
- return false;
- }
-
- if (!isFASTAFileValid()) {
- JOptionPane.showMessageDialog(this, "A fasta file is required!");
- return false;
- }
-
- } catch (Exception e) {
- logger.error("Error during Genome Builder validation!", e);
- return false;
- }
- return true;
- }
-
- private boolean isFASTAFileValid() {
-
- String file = fastaFileTextField.getText();
- return file != null && file.trim().length() > 0;
- }
-
- private Boolean isIdValid() {
-
- String id = getGenomeId();
- if (id == null || id.trim().length() == 0) {
- JOptionPane.showMessageDialog(this, "Genome ID is required");
- return false;
- }
-
- Collection inUseIds = GenomeListManager.getInstance().getSelectableGenomeIDs();
- if (inUseIds.contains(id)) {
- JOptionPane.showMessageDialog(this,
- "The genome ID '" + id + "' is already in use - please select another!");
- return false;
- }
- return true;
- }
-
- private boolean isGenomeDisplayNameValid() {
-
- String displayName = getGenomeDisplayName();
- if (displayName == null || displayName.trim().length() == 0) {
- JOptionPane.showMessageDialog(this, "Genome name is required");
- return false;
- }
-
- Collection inUseDisplayNames = getGenomeDisplayNames();
-
- if (inUseDisplayNames.contains(displayName)) {
- JOptionPane.showMessageDialog(this,
- "The genome name '" + displayName + "' is already in use - please enter another!");
- return false;
- }
- return true;
- }
-
-
- public Collection getGenomeDisplayNames() {
-
- Set displayNames = new HashSet();
- Collection listItems = GenomeListManager.getInstance().getGenomeListItems();
- for (GenomeListItem genomeListItem : listItems) {
- displayNames.add(genomeListItem.getDisplayableName());
- }
- return displayNames;
- }
-
-
- /**
- * This method is called from within the constructor to
- * initialize the form.
- * WARNING: Do NOT modify this code. The content of this method is
- * always regenerated by the Form Editor.
- */
- @SuppressWarnings("unchecked")
- // //GEN-BEGIN:initComponents
- // Generated using JFormDesigner non-commercial license
- private void initComponents() {
- panel3 = new JPanel();
- panel2 = new JPanel();
- genomeDisplayNameLabel2 = new JLabel();
- idField = new JTextField();
- genomeDisplayNameLabel = new JLabel();
- genomeDisplayNameTextField = new JTextField();
- fastaFileLabel = new JLabel();
- fastaFileTextField = new JTextField();
- fastaFileButton = new JButton();
- panel1 = new JPanel();
- cytobandFileLabel = new JLabel();
- cytobandFileTextField = new JTextField();
- cytobandFileButton = new JButton();
- geneAnnotFileLabel = new JLabel();
- geneAnnotFileTextField = new JTextField();
- geneAnnotFileButton = new JButton();
- aliasFileLabel = new JLabel();
- chrAliasField = new JTextField();
- chrAliasButton = new JButton();
- vSpacer2 = new JPanel(null);
-
- //======== this ========
- setFont(new Font("Tahoma", Font.ITALIC, 12));
- setMaximumSize(new Dimension(900, 500));
- setMinimumSize(new Dimension(400, 200));
- setPreferredSize(new Dimension(700, 200));
- setLayout(new BorderLayout());
-
- //======== panel3 ========
- {
- panel3.setBorder(new EmptyBorder(20, 20, 20, 20));
- panel3.setLayout(new BoxLayout(panel3, BoxLayout.Y_AXIS));
-
- //======== panel2 ========
- {
- panel2.setBorder(new EmptyBorder(0, 0, 30, 0));
- panel2.setLayout(null);
-
- //---- genomeDisplayNameLabel2 ----
- genomeDisplayNameLabel2.setText("Unique identifier");
- genomeDisplayNameLabel2.setToolTipText("Unique identifier (e.g. hg18)");
- genomeDisplayNameLabel2.setMaximumSize(new Dimension(84, 16));
- genomeDisplayNameLabel2.setMinimumSize(new Dimension(84, 16));
- genomeDisplayNameLabel2.setPreferredSize(new Dimension(14, 16));
- panel2.add(genomeDisplayNameLabel2);
- genomeDisplayNameLabel2.setBounds(15, 22, 125, 28);
-
- //---- idField ----
- idField.setToolTipText("A uniqe identifier for the genome");
- panel2.add(idField);
- idField.setBounds(145, 22, 548, 29);
-
- //---- genomeDisplayNameLabel ----
- genomeDisplayNameLabel.setText("Descriptive name");
- panel2.add(genomeDisplayNameLabel);
- genomeDisplayNameLabel.setBounds(15, 56, 175, 28);
-
- //---- genomeDisplayNameTextField ----
- genomeDisplayNameTextField.setToolTipText("The user-readable name of the genome");
- genomeDisplayNameTextField.setPreferredSize(new Dimension(400, 28));
- genomeDisplayNameTextField.setMinimumSize(new Dimension(25, 28));
- panel2.add(genomeDisplayNameTextField);
- genomeDisplayNameTextField.setBounds(145, 56, 548, 29);
-
- //---- fastaFileLabel ----
- fastaFileLabel.setText("FASTA file");
- panel2.add(fastaFileLabel);
- fastaFileLabel.setBounds(15, 88, 175, 29);
-
- //---- fastaFileTextField ----
- fastaFileTextField.setToolTipText("A FASTA data file");
- fastaFileTextField.setPreferredSize(new Dimension(400, 28));
- fastaFileTextField.setMinimumSize(new Dimension(25, 28));
- panel2.add(fastaFileTextField);
- fastaFileTextField.setBounds(145, 88, 548, 29);
-
- //---- fastaFileButton ----
- fastaFileButton.setText("Browse");
- fastaFileButton.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- fastaFileButtonActionPerformed(e);
- }
- });
- panel2.add(fastaFileButton);
- fastaFileButton.setBounds(698, 88, 83, fastaFileButton.getPreferredSize().height);
- }
- panel3.add(panel2);
-
- //======== panel1 ========
- {
- panel1.setBorder(new TitledBorder(null, "Optional", TitledBorder.LEADING, TitledBorder.DEFAULT_POSITION,
- new Font("Lucida Grande", Font.BOLD, 13)));
- panel1.setLayout(null);
-
- //---- cytobandFileLabel ----
- cytobandFileLabel.setText("Cytoband file");
- panel1.add(cytobandFileLabel);
- cytobandFileLabel.setBounds(15, 25, 105, 29);
-
- //---- cytobandFileTextField ----
- cytobandFileTextField.setToolTipText("A cytoband data file");
- cytobandFileTextField.setPreferredSize(new Dimension(400, 28));
- cytobandFileTextField.setMinimumSize(new Dimension(25, 28));
- panel1.add(cytobandFileTextField);
- cytobandFileTextField.setBounds(145, 22, 548, 29);
-
- //---- cytobandFileButton ----
- cytobandFileButton.setText("Browse");
- cytobandFileButton.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- cytobandFileButtonActionPerformed(e);
- }
- });
- panel1.add(cytobandFileButton);
- cytobandFileButton.setBounds(698, 22, 83, cytobandFileButton.getPreferredSize().height);
-
- //---- geneAnnotFileLabel ----
- geneAnnotFileLabel.setText("Gene file");
- panel1.add(geneAnnotFileLabel);
- geneAnnotFileLabel.setBounds(15, 56, 84, 29);
-
- //---- geneAnnotFileTextField ----
- geneAnnotFileTextField.setToolTipText("An annotation file");
- geneAnnotFileTextField.setPreferredSize(new Dimension(400, 28));
- geneAnnotFileTextField.setMinimumSize(new Dimension(25, 28));
- panel1.add(geneAnnotFileTextField);
- geneAnnotFileTextField.setBounds(145, 56, 548, 29);
-
- //---- geneAnnotFileButton ----
- geneAnnotFileButton.setText("Browse");
- geneAnnotFileButton.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- refFlatFileButtonActionPerformed(e);
- }
- });
- panel1.add(geneAnnotFileButton);
- geneAnnotFileButton.setBounds(698, 56, 83, geneAnnotFileButton.getPreferredSize().height);
-
- //---- aliasFileLabel ----
- aliasFileLabel.setText("Alias file");
- panel1.add(aliasFileLabel);
- aliasFileLabel.setBounds(15, 90, 84, 29);
-
- //---- chrAliasField ----
- chrAliasField.setPreferredSize(new Dimension(400, 28));
- chrAliasField.setMinimumSize(new Dimension(25, 28));
- panel1.add(chrAliasField);
- chrAliasField.setBounds(145, 90, 548, 29);
-
- //---- chrAliasButton ----
- chrAliasButton.setText("Browse");
- chrAliasButton.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- chrAliasButtonActionPerformed(e);
- }
- });
- panel1.add(chrAliasButton);
- chrAliasButton.setBounds(698, 90, 83, chrAliasButton.getPreferredSize().height);
- panel1.add(vSpacer2);
- vSpacer2.setBounds(6, 124, 84, 20);
- }
- panel3.add(panel1);
- }
- add(panel3, BorderLayout.CENTER);
- }// //GEN-END:initComponents
-
- private void chrAliasButtonActionPerformed(ActionEvent e) {
- File directory = PreferencesManager.getPreferences().getDefineGenomeInputDirectory();
- File file = FileDialogUtils.chooseFile("Select Chromosome Alias File", directory, FileDialogUtils.LOAD);
- if (file != null) {
- chrAliasField.setText(file.getAbsolutePath());
- PreferencesManager.getPreferences().setDefineGenomeInputDirectory(file.getParentFile());
- }
- }
-
-
- private void cytobandFileButtonActionPerformed(java.awt.event.ActionEvent evt) {
- File directory = PreferencesManager.getPreferences().getDefineGenomeInputDirectory();
- File file = FileDialogUtils.chooseFile("Select Cytoband File", directory, FileDialogUtils.LOAD);
- if (file != null) {
- cytobandFileTextField.setText(file.getAbsolutePath());
- PreferencesManager.getPreferences().setDefineGenomeInputDirectory(file.getParentFile());
- }
- }
-
- private void refFlatFileButtonActionPerformed(java.awt.event.ActionEvent evt) {
- File directory = PreferencesManager.getPreferences().getDefineGenomeInputDirectory();
- File file = FileDialogUtils.chooseFile("Select Annotation File", directory, FileDialogUtils.LOAD);
- if (file != null) {
- geneAnnotFileTextField.setText(file.getAbsolutePath());
- PreferencesManager.getPreferences().setDefineGenomeInputDirectory(file.getParentFile());
- }
- }
-
- private void fastaFileButtonActionPerformed(java.awt.event.ActionEvent evt) {
- File directory = PreferencesManager.getPreferences().getDefineGenomeInputDirectory();
- File file = FileDialogUtils.chooseFile("Select Fasta File", directory, null, FileDialogUtils.LOAD);
- if (file != null) {
- fastaFileTextField.setText(file.getAbsolutePath());
- PreferencesManager.getPreferences().setDefineGenomeInputDirectory(file.getParentFile());
- }
- }
-
- // Variables declaration - do not modify//GEN-BEGIN:variables
- // Generated using JFormDesigner non-commercial license
- private JPanel panel3;
- private JPanel panel2;
- private JLabel genomeDisplayNameLabel2;
- private JTextField idField;
- private JLabel genomeDisplayNameLabel;
- private JTextField genomeDisplayNameTextField;
- private JLabel fastaFileLabel;
- private JTextField fastaFileTextField;
- private JButton fastaFileButton;
- private JPanel panel1;
- private JLabel cytobandFileLabel;
- private JTextField cytobandFileTextField;
- private JButton cytobandFileButton;
- private JLabel geneAnnotFileLabel;
- private JTextField geneAnnotFileTextField;
- private JButton geneAnnotFileButton;
- private JLabel aliasFileLabel;
- private JTextField chrAliasField;
- private JButton chrAliasButton;
- private JPanel vSpacer2;
- // End of variables declaration//GEN-END:variables
-
-}
diff --git a/src/main/java/org/broad/igv/track/TribbleFeatureSource.java b/src/main/java/org/broad/igv/track/TribbleFeatureSource.java
index 904aaff93e..50639e32d1 100644
--- a/src/main/java/org/broad/igv/track/TribbleFeatureSource.java
+++ b/src/main/java/org/broad/igv/track/TribbleFeatureSource.java
@@ -344,6 +344,7 @@ private NonIndexedFeatureSource(AbstractFeatureReader basicReader, FeatureCodec
List featureList = featureMap.computeIfAbsent(igvChr, k -> new ArrayList<>());
featureList.add(f);
+
if (f instanceof IGVNamedFeature named) FeatureDB.addFeature(named, genome);
if (this.isVCF && f instanceof Variant v) {
diff --git a/src/main/java/org/broad/igv/ui/IGV.java b/src/main/java/org/broad/igv/ui/IGV.java
index f9a9ac31f6..193bdcfe52 100644
--- a/src/main/java/org/broad/igv/ui/IGV.java
+++ b/src/main/java/org/broad/igv/ui/IGV.java
@@ -333,71 +333,6 @@ public void selectGenomeFromList(String genomeId) {
contentPane.getCommandBar().selectGenome(genomeId);
}
-
- public void defineGenome(javax.swing.ProgressMonitor monitor) {
-
- ProgressBar.ProgressDialog progressDialog = null;
- File archiveFile = null;
-
- try {
- GenomeBuilderDialog genomeBuilderDialog = new GenomeBuilderDialog(mainFrame, this);
- genomeBuilderDialog.setVisible(true);
-
- File genomeZipFile = genomeBuilderDialog.getArchiveFile();
- if (genomeBuilderDialog.isCanceled() || genomeZipFile == null) {
- return;
- }
-
-
- String cytobandFileName = genomeBuilderDialog.getCytobandFileName();
- String geneAnnotFileName = genomeBuilderDialog.getGeneAnnotFileName();
- String fastaFileName = genomeBuilderDialog.getFastaFileName();
- String chrAliasFile = genomeBuilderDialog.getChrAliasFileName();
- String genomeDisplayName = genomeBuilderDialog.getGenomeDisplayName();
- String genomeId = genomeBuilderDialog.getGenomeId();
-
- GenomeListItem genomeListItem = GenomeManager.getInstance().defineGenome(
- genomeZipFile, cytobandFileName, geneAnnotFileName,
- fastaFileName, chrAliasFile, genomeDisplayName,
- genomeId, monitor);
-
- if (genomeListItem != null) {
- contentPane.getCommandBar().refreshGenomeListComboBox();
- contentPane.getCommandBar().selectGenome(genomeListItem.getId());
- }
- if (monitor != null) {
- monitor.setProgress(100);
- }
-
- } catch (MaximumContigGenomeException e) {
-
- String genomePath = "";
- if (archiveFile != null) {
- genomePath = archiveFile.getAbsolutePath();
- }
-
- log.error("Failed to define genome: " + genomePath, e);
-
- JOptionPane.showMessageDialog(mainFrame, "Failed to define genome " +
- genomePath + "\n" + e.getMessage());
- } catch (GenomeException e) {
- log.error("Failed to define genome.", e);
- MessageUtils.showMessage(e.getMessage());
- } catch (Exception e) {
- String genomePath = "";
- if (archiveFile != null) {
- genomePath = archiveFile.getAbsolutePath();
- }
-
- log.error("Failed to define genome: " + genomePath, e);
- MessageUtils.showMessage("Unexpected error while importing a genome: " + e.getMessage());
- } finally {
- if (progressDialog != null) {
- progressDialog.setVisible(false);
- }
- }
- }
-
public void enableExtrasMenu() {
menuBar.enableExtrasMenu();
diff --git a/src/main/java/org/broad/igv/ui/Main.java b/src/main/java/org/broad/igv/ui/Main.java
index 6343275589..0f5db3c7d9 100644
--- a/src/main/java/org/broad/igv/ui/Main.java
+++ b/src/main/java/org/broad/igv/ui/Main.java
@@ -210,6 +210,7 @@ private static void initApplication(Main.IGVArgs igvArgs) {
log.info("IGV Directory: " + DirectoryManager.getIgvDirectory().getAbsolutePath());
System.setProperty("http.agent", Globals.applicationString());
+ System.setProperty("samjdk.optimistic_vcf_4_4", "true");
Runtime.getRuntime().addShutdownHook(new ShutdownThread());
diff --git a/src/main/resources/org/broad/igv/feature/genome/GenomeBuilderDialog.jfd b/src/main/resources/org/broad/igv/feature/genome/GenomeBuilderDialog.jfd
deleted file mode 100644
index 88f08b9be3..0000000000
--- a/src/main/resources/org/broad/igv/feature/genome/GenomeBuilderDialog.jfd
+++ /dev/null
@@ -1,209 +0,0 @@
-
-
-
-
diff --git a/src/main/resources/org/broad/igv/feature/genome/GenomeBuilderPane.jfd b/src/main/resources/org/broad/igv/feature/genome/GenomeBuilderPane.jfd
deleted file mode 100644
index c16b0c7eef..0000000000
--- a/src/main/resources/org/broad/igv/feature/genome/GenomeBuilderPane.jfd
+++ /dev/null
@@ -1,784 +0,0 @@
-
-
-
-
diff --git a/src/main/resources/org/broad/igv/feature/genome/RemoveGenomesDialog.jfd b/src/main/resources/org/broad/igv/feature/genome/RemoveGenomesDialog.jfd
deleted file mode 100644
index 92cdfa27fa..0000000000
--- a/src/main/resources/org/broad/igv/feature/genome/RemoveGenomesDialog.jfd
+++ /dev/null
@@ -1,115 +0,0 @@
-JFDML JFormDesigner: "5.2.4.0.321" Java: "1.8.0_76-release" encoding: "UTF-8"
-
-new FormModel {
- contentType: "form/swing"
- root: new FormRoot {
- add( new FormWindow( "javax.swing.JDialog", new FormLayoutManager( class java.awt.BorderLayout ) ) {
- name: "this"
- "$sizePolicy": 0
- "defaultCloseOperation": 2
- "modalityType": enum java.awt.Dialog$ModalityType DOCUMENT_MODAL
- "title": "Remove Genomes"
- add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class java.awt.BorderLayout ) ) {
- name: "dialogPane"
- "border": new javax.swing.border.EmptyBorder( 12, 12, 12, 12 )
- "preferredSize": new java.awt.Dimension( 270, 400 )
- add( new FormComponent( "javax.swing.JTextArea" ) {
- name: "label1"
- "rows": 2
- "editable": false
- "background": new com.jformdesigner.model.SwingColor( "Button.background" )
- "wrapStyleWord": true
- "lineWrap": true
- }, new FormLayoutConstraints( class java.lang.String ) {
- "value": "North"
- } )
- add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class javax.swing.BoxLayout ) {
- "axis": 1
- } ) {
- name: "contentPanel"
- add( new FormContainer( "javax.swing.JScrollPane", new FormLayoutManager( class javax.swing.JScrollPane ) ) {
- name: "scrollPane1"
- add( new FormComponent( "javax.swing.JList" ) {
- name: "genomeList"
- "maximumSize": new java.awt.Dimension( 39, 5000 )
- "dropMode": enum javax.swing.DropMode INSERT
- "dragEnabled": true
- auxiliary() {
- "JavaCodeGenerator.typeParameters": "GenomeListItem"
- }
- addEvent( new FormEvent( "java.awt.event.KeyListener", "keyReleased", "genomeListKeyReleased", true ) )
- } )
- } )
- add( new FormComponent( "javax.swing.JLabel" ) {
- name: "label2"
- "text": "Sequence on local machine"
- "labelFor": new FormReference( "genomeList" )
- "alignmentX": 1.0f
- "componentOrientation": sfield java.awt.ComponentOrientation LEFT_TO_RIGHT
- "preferredSize": new java.awt.Dimension( 400, 16 )
- "maximumSize": new java.awt.Dimension( 400, 16 )
- "minimumSize": new java.awt.Dimension( 100, 16 )
- auxiliary() {
- "JavaCodeGenerator.postInitCode": "${field}.setText(LOCAL_SEQUENCE_CHAR + ${field}.getText());"
- }
- } )
- }, new FormLayoutConstraints( class java.lang.String ) {
- "value": "Center"
- } )
- add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class javax.swing.BoxLayout ) {
- "axis": 1
- } ) {
- name: "panel1"
- add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class java.awt.FlowLayout ) {
- "alignment": 4
- "hgap": 1
- } ) {
- name: "addRemBar"
- "border": &EmptyBorder0 new javax.swing.border.EmptyBorder( 12, 0, 0, 0 )
- "preferredSize": new java.awt.Dimension( 196, 51 )
- "minimumSize": new java.awt.Dimension( 201, 51 )
- add( new FormComponent( "javax.swing.JButton" ) {
- name: "removeButton"
- "text": "Remove"
- "toolTipText": "Remove selected genomes from list"
- addEvent( new FormEvent( "java.awt.event.ActionListener", "actionPerformed", "removeButtonActionPerformed", true ) )
- } )
- } )
- add( new FormComponent( "javax.swing.JSeparator" ) {
- name: "separator1"
- } )
- add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class java.awt.FlowLayout ) {
- "alignment": 4
- } ) {
- name: "buttonBar"
- "border": #EmptyBorder0
- "preferredSize": new java.awt.Dimension( 196, 51 )
- add( new FormComponent( "javax.swing.JButton" ) {
- name: "okButton"
- "text": "Save"
- "maximumSize": new java.awt.Dimension( 93, 29 )
- "minimumSize": new java.awt.Dimension( 93, 29 )
- "preferredSize": new java.awt.Dimension( 93, 29 )
- addEvent( new FormEvent( "java.awt.event.ActionListener", "actionPerformed", "saveButtonActionPerformed", true ) )
- } )
- add( new FormComponent( "javax.swing.JButton" ) {
- name: "cancelButton"
- "text": "Cancel"
- "minimumSize": new java.awt.Dimension( 93, 29 )
- "preferredSize": new java.awt.Dimension( 93, 29 )
- "maximumSize": new java.awt.Dimension( 93, 29 )
- addEvent( new FormEvent( "java.awt.event.ActionListener", "actionPerformed", "cancelButtonActionPerformed", true ) )
- } )
- } )
- }, new FormLayoutConstraints( class java.lang.String ) {
- "value": "South"
- } )
- }, new FormLayoutConstraints( class java.lang.String ) {
- "value": "Center"
- } )
- }, new FormLayoutConstraints( null ) {
- "location": new java.awt.Point( 0, 0 )
- "size": new java.awt.Dimension( 400, 300 )
- } )
- }
-}