- void executeFunctionAnalysis() {
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
- return;
- }
- final GoAnnotation a = new GoAnnotation( this,
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getCurrentPhylogeny() );
- new Thread( a ).start();
- }
-
- void executeGSDI() {
- if ( !isOKforSDI( false, true ) ) {
- return;
- }
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not rooted.",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- GSDI gsdi = null;
- final Phylogeny species_tree = _species_tree.copy();
- try {
- gsdi = new GSDI( gene_tree, species_tree, false, true, true );
- }
- catch ( final SDIException e ) {
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Error during GSDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- AptxUtil.unexpectedException( e );
- return;
- }
- gene_tree.setRerootable( false );
- gene_tree.clearHashIdToNodeMap();
- gene_tree.recalculateNumberOfExternalDescendants( true );
- _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
- getControlPanel().setShowEvents( true );
- showWhole();
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
- showWhole();
- _mainpanel.getTabbedPane().setSelectedIndex( selected );
- showWhole();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
- if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
- JOptionPane.showMessageDialog( this,
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"
- + "Potential duplications: "
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDI successfully completed",
- JOptionPane.WARNING_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"
- + "Potential duplications: "
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDI successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
- }
-
- void executeGSDIR() {
- if ( !isOKforSDI( false, false ) ) {
- return;
- }
- final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
- if ( ( p > 0 )
- && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not completely binary",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- GSDIR gsdir = null;
- final Phylogeny species_tree = _species_tree.copy();
- try {
- gsdir = new GSDIR( gene_tree, species_tree, true, true );
- }
- catch ( final SDIException e ) {
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Error during GSDIR",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- AptxUtil.unexpectedException( e );
- return;
- }
- final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
- result_gene_tree.setRerootable( false );
- result_gene_tree.clearHashIdToNodeMap();
- result_gene_tree.recalculateNumberOfExternalDescendants( true );
- _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
- getControlPanel().setShowEvents( true );
- showWhole();
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
- showWhole();
- _mainpanel.getTabbedPane().setSelectedIndex( selected );
- showWhole();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
- if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
- JOptionPane.showMessageDialog( this,
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDIR successfully completed",
- JOptionPane.WARNING_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDIR successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
- }
-