+ final String s = ( String ) JOptionPane.showInputDialog( getThisFrame(),
+ "Please enter the minimum branch length value\n",
+ "Minimal Branch Length Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getMinNotCollapseBlValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ setMinNotCollapseBlValue( m );
+ collapseBl( phy );
+ }
+ }
+ }
+ }
+ }
+
+ private void collapseBelowThreshold() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final String s = ( String ) JOptionPane.showInputDialog( getThisFrame(),
+ "Please enter the minimum confidence value\n",
+ "Minimal Confidence Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getMinNotCollapseConfidenceValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ setMinNotCollapseConfidenceValue( m );
+ collapseBelowThreshold( phy );
+ }
+ }
+ }
+ }
+ }
+
+ private void collapseBl( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
+ double min_bl = Double.MAX_VALUE;
+ boolean bl_present = false;
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && !n.isRoot() ) {
+ final double bl = n.getDistanceToParent();
+ if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
+ bl_present = true;
+ if ( bl < getMinNotCollapseBlValue() ) {
+ to_be_removed.add( n );
+ }
+ if ( bl < min_bl ) {
+ min_bl = bl;
+ }
+ }
+ }
+ }
+ if ( bl_present ) {
+ for( final PhylogenyNode node : to_be_removed ) {
+ PhylogenyMethods.removeNode( node, phy );
+ }
+ if ( to_be_removed.size() > 0 ) {
+ phy.externalNodesHaveChanged();
+ phy.clearHashIdToNodeMap();
+ phy.recalculateNumberOfExternalDescendants( true );
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+ getCurrentTreePanel().calculateLongestExtNodeInfo();
+ getCurrentTreePanel().setNodeInPreorderToNull();
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();
+ getCurrentTreePanel().resetPreferredSize();
+ getCurrentTreePanel().setEdited( true );
+ getCurrentTreePanel().repaint();
+ repaint();
+ }
+ if ( to_be_removed.size() > 0 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Collapsed " + to_be_removed.size()
+ + " branches with\nbranch length values below "
+ + getMinNotCollapseBlValue(),
+ "Collapsed " + to_be_removed.size() + " branches",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No branch collapsed,\nminimum branch length is " + min_bl,
+ "No branch collapsed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No branch collapsed because no branch length values present",
+ "No branch length values present",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ private PhyloXmlParser createPhyloXmlParser() {
+ PhyloXmlParser xml_parser = null;
+ if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
+ try {
+ xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
+ }
+ catch ( final Exception e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "failed to create validating XML parser",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ if ( xml_parser == null ) {
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();
+ }
+ return xml_parser;
+ }
+
+ private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
+ final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
+ getPhylogeneticInferenceOptions(),
+ from_unaligned_seqs );
+ dialog.activate();
+ if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
+ if ( !from_unaligned_seqs ) {
+ if ( getMsa() != null ) {
+ final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
+ getPhylogeneticInferenceOptions()
+ .copy(),
+ this );
+ new Thread( inferrer ).start();
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No multiple sequence alignment selected",
+ "Phylogenetic Inference Not Launched",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ else {
+ if ( getSeqs() != null ) {
+ final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
+ getPhylogeneticInferenceOptions()
+ .copy(),
+ this );
+ new Thread( inferrer ).start();
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No input sequences selected",
+ "Phylogenetic Inference Not Launched",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+ }
+
+ private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
+ final StringBuilder sb = new StringBuilder();
+ final StringBuilder sb_failed = new StringBuilder();
+ int counter = 0;
+ int counter_failed = 0;
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ final String name = n.getName().trim();
+ if ( !ForesterUtil.isEmpty( name ) ) {
+ final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
+ TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !ForesterUtil.isEmpty( nt ) ) {
+ if ( counter < 15 ) {
+ sb.append( name + ": " + nt + "\n" );
+ }
+ else if ( counter == 15 ) {
+ sb.append( "...\n" );
+ }
+ counter++;
+ }
+ else {
+ if ( counter_failed < 15 ) {
+ sb_failed.append( name + "\n" );
+ }
+ else if ( counter_failed == 15 ) {
+ sb_failed.append( "...\n" );
+ }
+ counter_failed++;
+ }
+ }
+ }
+ if ( counter > 0 ) {
+ String failed = "";
+ String all = "all ";
+ if ( counter_failed > 0 ) {
+ all = "";
+ failed = "\nCould not extract taxonomic data for " + counter_failed + " named external nodes:\n"
+ + sb_failed;
+ }
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Extracted taxonomic data from " + all + counter
+ + " named external nodes:\n" + sb.toString() + failed,
+ "Taxonomic Data Extraction Completed",
+ counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
+ : JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
+ + "or nodes already have taxonomic data?\n",
+ "No Taxonomic Data Extracted",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ }
+ }
+ }
+
+ private double getMinNotCollapseBlValue() {
+ return _min_not_collapse_bl;
+ }
+
+ private double getMinNotCollapseConfidenceValue() {
+ return _min_not_collapse;
+ }
+
+ private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
+ if ( _phylogenetic_inference_options == null ) {
+ _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
+ }
+ return _phylogenetic_inference_options;
+ }
+
+ private boolean isUnsavedDataPresent() {
+ final List<TreePanel> tps = getMainPanel().getTreePanels();
+ for( final TreePanel tp : tps ) {
+ if ( tp.isEdited() ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ PhylogenyMethods.transferNodeNameToField( phy,
+ PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME,
+ false );
+ }
+ }
+ }
+
+ private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ PhylogenyMethods.transferNodeNameToField( phy,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ false );
+ }
+ }
+ }