rio - gsdir work...

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index a238164..0ff8a49 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -99,6 +99,7 @@ import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 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.SDIR;
 import org.forester.sequence.Sequence;
 import org.forester.util.BasicDescriptiveStatistics;
@@ -204,6 +205,7 @@ public final class MainFrameApplication extends MainFrame {
     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;
@@ -581,6 +583,12 @@ public final class MainFrameApplication extends MainFrame {
                 }
                 executeGSDI();
             }
+            else if ( o == _gsdir_item ) {
+                if ( isSubtreeDisplayed() ) {
+                    return;
+                }
+                executeGSDIR();
+            }
             else if ( o == _root_min_dups_item ) {
                 if ( isSubtreeDisplayed() ) {
                     return;
@@ -654,12 +662,15 @@ public final class MainFrameApplication extends MainFrame {
     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 );
@@ -1231,6 +1242,7 @@ public final class MainFrameApplication extends MainFrame {
         }
         catch ( final Exception e ) {
             JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
+            return; 
         }
         gene_tree.setRerootable( false );
         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
@@ -1251,6 +1263,46 @@ public final class MainFrameApplication extends MainFrame {
                 + 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;
+        try {
+            gsdir = new GSDIR( gene_tree, _species_tree.copy(),  true, 1 );
+        }
+        catch ( final Exception e ) {
+            JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDIR", JOptionPane.ERROR_MESSAGE );
+            return;
+        }
+        final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTrees().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();
+        _mainpanel.addPhylogenyInNewTab( gsdir.getSpeciesTree(), 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 );
+    }
+    
     void executeFunctionAnalysis() {
         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
             return;

diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index 19e2b7d..71f4e45 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -69,8 +69,8 @@ public class GSDI extends SDI {
     private final boolean             _most_parsimonious_duplication_model;
     private final boolean             _strip_gene_tree;
     private final boolean             _strip_species_tree;
-    private int                       _speciation_or_duplication_events_sum;
-    private int                       _speciations_sum;
+    protected int                       _speciation_or_duplication_events_sum;
+    protected int                       _speciations_sum;
     private final List<PhylogenyNode> _stripped_gene_tree_nodes;
     private final List<PhylogenyNode> _stripped_species_tree_nodes;
     private final Set<PhylogenyNode>  _mapped_species_tree_nodes;

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 8eeca62..34efda2 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -35,44 +35,53 @@ import org.forester.util.BasicDescriptiveStatistics;
 \r
 public class GSDIR extends GSDI {\r
 \r
-    private int                   _min_duplications_sum;\r
-    private final BasicDescriptiveStatistics                  _duplications_sum_stats;\r
-    private final List<Phylogeny> _min_duplications_sum_gene_trees;\r
+    private int                              _min_duplications_sum;\r
+    private final BasicDescriptiveStatistics _duplications_sum_stats;\r
+    private final List<Phylogeny>            _min_duplications_sum_gene_trees;\r
 \r
     public GSDIR( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean strip_gene_tree, final int x )\r
             throws SDIException {\r
         super( gene_tree, species_tree, true, strip_gene_tree, true, 1 );\r
         _min_duplications_sum = Integer.MAX_VALUE;\r
         _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();\r
-        _duplications_sum_stats = new  BasicDescriptiveStatistics();\r
+        _duplications_sum_stats = new BasicDescriptiveStatistics();\r
         linkNodesOfG();\r
         final List<PhylogenyNode> gene_tree_nodes_post_order = new ArrayList<PhylogenyNode>();\r
         for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
             gene_tree_nodes_post_order.add( it.next() );\r
         }\r
         for( final PhylogenyNode root : gene_tree_nodes_post_order ) {\r
-            _gene_tree.reRoot( root );\r
+            _duplications_sum = 0;\r
+            _speciation_or_duplication_events_sum = 0;\r
+            _speciations_sum = 0;\r
+          \r
+            _gene_tree.reRoot( root.getId() ); //TODO reRoot( root )\r
             PhylogenyMethods.preOrderReId( getSpeciesTree() );\r
             //TEST, remove later\r
-            for( final PhylogenyNodeIterator it = getGeneTree().iteratorPostorder(); it.hasNext(); ) {\r
+            for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
                 final PhylogenyNode g = it.next();\r
                 if ( g.isInternal() ) {\r
                     g.setLink( null );\r
                 }\r
             }\r
             geneTreePostOrderTraversal();\r
-            _duplications_sum_stats.addValue( getMinDuplicationsSum() );\r
-            if ( getDuplicationsSum() < getMinDuplicationsSum() ) {\r
-                _min_duplications_sum = getDuplicationsSum();\r
+           \r
+            if (  _duplications_sum < _min_duplications_sum ) {\r
+                _min_duplications_sum = _duplications_sum;\r
                 _min_duplications_sum_gene_trees.clear();\r
                 _min_duplications_sum_gene_trees.add( getGeneTree().copy() );\r
             }\r
-            else if ( getDuplicationsSum() == getMinDuplicationsSum() ) {\r
+            else if (  _duplications_sum == _min_duplications_sum ) {\r
                 _min_duplications_sum_gene_trees.add( getGeneTree().copy() );\r
             }\r
+            System.out.println( getDuplicationsSum() );\r
+            _duplications_sum_stats.addValue(  _duplications_sum );\r
         }\r
     }\r
 \r
+   \r
+   \r
+\r
     public int getMinDuplicationsSum() {\r
         return _min_duplications_sum;\r
     }\r

diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java
index 8ad459e..54d5255 100644 (file)
--- a/forester/java/src/org/forester/sdi/TestGSDI.java
+++ b/forester/java/src/org/forester/sdi/TestGSDI.java
@@ -27,6 +27,7 @@ package org.forester.sdi;
 
 import java.io.IOException;
 
+import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.development.DevelopmentTools;
 import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.io.parsers.util.ParserUtils;
@@ -97,7 +98,6 @@ public final class TestGSDI {
 
     private static boolean testGSDI_general() {
         try {
-           
             final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
                     + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
                     + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
@@ -1423,57 +1423,66 @@ public final class TestGSDI {
         }
         return true;
     }
-    
+
     private static boolean testGSDIR_general() {
         try {
-           
-            final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
-                    + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
-                    + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
-                    + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
-                    + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
-                    + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
-                    + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
-                    + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
-                    + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
-                    + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
-                    + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
-                    + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
-                    + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
-                    + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
-                    + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
-                    + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
-                    + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
-            final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
-            s2.setRooted( true );
-            final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
-            final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
+            final String s1str = "(((([&&NHX:S=HUMAN],([&&NHX:S=MOUSE],[&&NHX:S=RAT])),([&&NHX:S=CAEEL],[&&NHX:S=CAEBR])),[&&NHX:S=YEAST]),[&&NHX:S=ARATH])";
+            final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1str, new NHXParser() )[ 0 ];
             s1.setRooted( true );
+            //  Archaeopteryx.createApplication( s1.copy() );
             final Phylogeny g1 = TestGSDI
-                    .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
-            final GSDIR sdi1 = new GSDIR( g1, s1, false, 1 );
-            // Archaeopteryx.createApplication( g1 );
-            // Archaeopteryx.createApplication( s1 );
-            if ( sdi1.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
-                    .isSpeciation() ) {
-                return false;
-            }
-            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
-                    .isSpeciationOrDuplication() ) {
+                    .createPhylogeny( "(HUMAN[&&NHX:S=HUMAN],(RAT[&&NHX:S=RAT],(CAEEL[&&NHX:T=:S=CAEEL],YEAST[&&NHX:S=YEAST])))" );
+            final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, 1 );
+            if ( sdi1.getMinDuplicationsSum() != 0 ) {
                 return false;
             }
-            if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
-                    .isDuplication() ) ) {
+            System.out.println( sdi1.getDuplicationsSumStats().getSummaryAsString() );
+            // Archaeopteryx.createApplication( sdi1.getMinDuplicationsSumGeneTrees().get( 0 ) );
+            //
+            final Phylogeny g2 = TestGSDI
+                    .createPhylogeny( "(((HUMAN[&&NHX:S=HUMAN],RAT[&&NHX:S=RAT]),CAEEL[&&NHX:T=:S=CAEEL]),YEAST[&&NHX:S=YEAST])" );
+            final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, 1 );
+            if ( sdi2.getMinDuplicationsSum() != 0 ) {
                 return false;
             }
-            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
-                    .isSpeciation() ) {
+            System.out.println( sdi2.getDuplicationsSumStats().getSummaryAsString() );
+            // Archaeopteryx.createApplication( sdi2.getMinDuplicationsSumGeneTrees().get( 0 ) );
+            //
+            final Phylogeny g3 = TestGSDI
+                    .createPhylogeny( "(RAT[&&NHX:S=RAT],HUMAN[&&NHX:S=HUMAN],(YEAST[&&NHX:S=YEAST],CAEEL[&&NHX:T=:S=CAEEL]))" );
+            //   Archaeopteryx.createApplication( g3 );
+            final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, 1 );
+            if ( sdi3.getMinDuplicationsSum() != 0 ) {
                 return false;
             }
-            
+            System.out.println( sdi3.getDuplicationsSumStats().getSummaryAsString() );
+            //   Archaeopteryx.createApplication( sdi3.getMinDuplicationsSumGeneTrees().get( 0 ) );
+            //
+            final Phylogeny g4 = TestGSDI
+                    .createPhylogeny( "(((((MOUSE[&&NHX:S=MOUSE],[&&NHX:S=RAT]),[&&NHX:S=HUMAN]),([&&NHX:S=ARATH],[&&NHX:S=YEAST])),[&&NHX:S=CAEEL]),[&&NHX:S=CAEBR])" );
+            Archaeopteryx.createApplication( g4 );
+            final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, 1 );
+            if ( sdi4.getMinDuplicationsSum() != 0 ) {
+                return false;
+            }
+            System.out.println( sdi4.getDuplicationsSumStats().getSummaryAsString() );
+            Archaeopteryx.createApplication( sdi4.getMinDuplicationsSumGeneTrees().get( 0 ) );
+            //            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+            //                    .isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+            //                    .isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+            //                    .isDuplication() ) ) {
+            //                return false;
+            //            }
+            //            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+            //                    .isSpeciation() ) {
+            //                return false;
+            //            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );