import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
import org.forester.sdi.SDIR;
import org.forester.sequence.Sequence;
import org.forester.util.BasicDescriptiveStatistics;
private JMenu _analysis_menu;
private JMenuItem _load_species_tree_item;
private JMenuItem _gsdi_item;
+ private JMenuItem _gsdir_item;
private JMenuItem _root_min_dups_item;
private JMenuItem _root_min_cost_l_item;
private JMenuItem _lineage_inference;
}
executeGSDI();
}
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
else if ( o == _root_min_dups_item ) {
if ( isSubtreeDisplayed() ) {
return;
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
_analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (re-rooting)" ) );
_analysis_menu.addSeparator();
_analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
_analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
_analysis_menu.addSeparator();
_analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
customizeJMenuItem( _gsdi_item );
+ customizeJMenuItem( _gsdir_item );
customizeJMenuItem( _root_min_dups_item );
customizeJMenuItem( _root_min_cost_l_item );
customizeJMenuItem( _load_species_tree_item );
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.copy(), false, true, true );
+ 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 ) {
- JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
+ AptxUtil.unexpectedException( e );
+ return;
}
gene_tree.setRerootable( false );
_mainpanel.getCurrentTreePanel().setTree( gene_tree );
getControlPanel().setShowEvents( true );
showWhole();
final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
- _mainpanel.addPhylogenyInNewTab( gsdi.getSpeciesTree(), getConfiguration(), "species tree", null );
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
showWhole();
_mainpanel.getTabbedPane().setSelectedIndex( selected );
showWhole();
+ gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
}
+ void executeGSDIR() {
+ if ( !isOKforSDI( false, true ) ) {
+ 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 List<Phylogeny> assigned_trees = gsdir.getMinDuplicationsSumGeneTrees();
+ final List<Integer> shortests = GSDIR.getIndexesOfShortestTree( assigned_trees );
+ final Phylogeny result_gene_tree = assigned_trees.get( shortests.get( 0 ) );
+ 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 );
+ JOptionPane.showMessageDialog( this,
+ "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
+ + gsdir.getSpeciationsSum() + "\n"
+ + "Number of root positions minimizing duplications sum: "
+ + gsdir.getMinDuplicationsSumGeneTrees().size() + "\n"
+ + "Number of shortest trees: " + shortests.size(),
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+
void executeFunctionAnalysis() {
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
return;