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 babcf6d..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;
@@ -1236,12 +1237,19 @@ public final class MainFrameApplication extends MainFrame {
         gene_tree.setAllNodesToNotCollapse();
         gene_tree.recalculateNumberOfExternalDescendants( false );
         GSDI gsdi = null;
-        Phylogeny species_tree = _species_tree.copy();
+        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 ) {
-            JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
+            AptxUtil.unexpectedException( e );
             return;
         }
         gene_tree.setRerootable( false );
@@ -1271,21 +1279,28 @@ public final class MainFrameApplication extends MainFrame {
         gene_tree.setAllNodesToNotCollapse();
         gene_tree.recalculateNumberOfExternalDescendants( false );
         GSDIR gsdir = null;
-        Phylogeny species_tree = _species_tree.copy();
+        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 ) {
-            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 );
         getControlPanel().setShowEvents( true );
         showWhole();
         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
@@ -1295,10 +1310,11 @@ public final class MainFrameApplication extends MainFrame {
         showWhole();
         _mainpanel.getCurrentTreePanel().setEdited( true );
         JOptionPane.showMessageDialog( this,
-                                       "Duplications: " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
+                                       "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
                                                + gsdir.getSpeciationsSum() + "\n"
                                                + "Number of root positions minimizing duplications sum: "
-                                               + gsdir.getMinDuplicationsSumGeneTrees().size(),
+                                               + gsdir.getMinDuplicationsSumGeneTrees().size() + "\n"
+                                               + "Number of shortest trees: " + shortests.size(),
                                        "GSDIR successfully completed",
                                        JOptionPane.INFORMATION_MESSAGE );
     }