rio

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrameApplication.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 0ff8a49..14b480f 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -100,6 +100,7 @@ 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;
@@ -663,7 +664,6 @@ public final class MainFrameApplication extends MainFrame {
         _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)" ) );
@@ -1237,12 +1237,20 @@ public final class MainFrameApplication extends MainFrame {
         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 );
-            return; 
+            AptxUtil.unexpectedException( e );
+            return;
         }
         gene_tree.setRerootable( false );
         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
@@ -1253,7 +1261,7 @@ public final class MainFrameApplication extends MainFrame {
         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();
@@ -1267,42 +1275,50 @@ public final class MainFrameApplication extends MainFrame {
         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.copy(),  true, 1 );
+            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 ) {
-            JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDIR", JOptionPane.ERROR_MESSAGE );
+            AptxUtil.unexpectedException( e );
             return;
         }
-        final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTrees().get( 0 );
+        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 );
-        
-        //_mainpanel.getCurrentTreePanel().setTree( gene_tree );
-        
-       // _mainpanel.getCurrentTreePanel().setEdited( true );
+        _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
         getControlPanel().setShowEvents( true );
         showWhole();
         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
-        _mainpanel.addPhylogenyInNewTab( gsdir.getSpeciesTree(), getConfiguration(), "species tree", null );
+        _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
         showWhole();
         _mainpanel.getTabbedPane().setSelectedIndex( selected );
         showWhole();
         _mainpanel.getCurrentTreePanel().setEdited( true );
-        JOptionPane.showMessageDialog( this, "Duplications: " + gsdir.getDuplicationsSum() + "\n"
-                + "Potential duplications: " + gsdir.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
-                + gsdir.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
+        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;