in progress

diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java
index 4b625cd..676d5da 100644 (file)
--- a/forester/java/src/org/forester/application/gsdi.java
+++ b/forester/java/src/org/forester/application/gsdi.java
@@ -205,7 +205,7 @@ public final class gsdi {
                     case SCIENTIFIC_NAME:
                         PhylogenyMethods
                                 .transferNodeNameToField( species_tree,
-                                                          PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID_UNIPROT_1,
+                                                          PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
                                                           true );
                         break;
                     case CODE:

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index a4658f0..94db898 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -192,6 +192,20 @@ public class PhylogenyMethods {
         return trees;
     }
 
+    public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
+            throws IOException {
+        final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
+        for( final File file : files ) {
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final Phylogeny[] trees = factory.create( file, parser );
+            if ( ( trees == null ) || ( trees.length == 0 ) ) {
+                throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+            }
+            tree_list.addAll( Arrays.asList( trees ) );
+        }
+        return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
+    }
+
     final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy ) {
         final PhylogenyNodeIterator it = phy.iteratorPostorder();
         while ( it.hasNext() ) {
@@ -406,16 +420,6 @@ public class PhylogenyMethods {
             if ( !ForesterUtil.isEmpty( name ) ) {
                 switch ( field ) {
                     case TAXONOMY_CODE:
-                        //temp hack
-                        //                        if ( name.length() > 5 ) {
-                        //                            n.setName( "" );
-                        //                            if ( !n.getNodeData().isHasTaxonomy() ) {
-                        //                                n.getNodeData().setTaxonomy( new Taxonomy() );
-                        //                            }
-                        //                            n.getNodeData().getTaxonomy().setScientificName( name );
-                        //                            break;
-                        //                        }
-                        //
                         n.setName( "" );
                         setTaxonomyCode( n, name );
                         break;
@@ -1246,8 +1250,9 @@ public class PhylogenyMethods {
             double blue = 0.0;
             int n = 0;
             if ( node.isInternal() ) {
-                for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
-                    final PhylogenyNode child_node = iterator.next();
+                //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
+                for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
+                    final PhylogenyNode child_node = node.getChildNode( i );
                     final Color child_color = getBranchColorValue( child_node );
                     if ( child_color != null ) {
                         ++n;

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 58dd0a3..c1d15db 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -38,8 +38,6 @@ import org.forester.phylogeny.data.BranchData;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
-import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.ForesterUtil;
 
@@ -750,13 +748,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     // ---------------------------------------------------------
-    // Iterator
-    // ---------------------------------------------------------
-    final public PhylogenyNodeIterator iterateChildNodesForward() {
-        return new ChildNodeIteratorForward( this );
-    }
-
-    // ---------------------------------------------------------
     // Basic printing
     // ---------------------------------------------------------
     /**

diff --git a/forester/java/src/org/forester/phylogeny/iterators/ChildNodeIteratorForward.java b/forester/java/src/org/forester/phylogeny/iterators/ChildNodeIteratorForward.java
deleted file mode 100644 (file)
index 264f515..0000000
--- a/forester/java/src/org/forester/phylogeny/iterators/ChildNodeIteratorForward.java
+++ /dev/null
@@ -1,145 +0,0 @@
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.phylogeny.iterators;
-
-import java.util.NoSuchElementException;
-
-import org.forester.phylogeny.PhylogenyNode;
-
-/*
- * An iterator to forward iterate over child nodes of a PhylogenyNode. Created:
- * 10/23/2005 by Christian M. Zmasek. Last modified: 12/28/2006 by Christian M.
- * Zmasek.
- * 
- * @author Christian M. Zmasek
- * 
- * @version 1.000
- */
-public class ChildNodeIteratorForward implements PhylogenyNodeIterator {
-
-    // Instance variables
-    // ------------------
-    private int                 _i;
-    final private PhylogenyNode _node;
-
-    // Constructor
-    // -----------
-    /**
-     * Creates a new ChildNodeIteratorForward.
-     * 
-     * @param node
-     *            the parent of the PhylogenyNodes to iterate over.
-     * @throws IllegalArgumentException
-     *             if node has no child nodes
-     */
-    public ChildNodeIteratorForward( final PhylogenyNode node ) throws IllegalArgumentException {
-        if ( node.getNumberOfDescendants() < 1 ) {
-            throw new IllegalArgumentException( "Attempt to use ChildNodeIteratorForward on node with no child nodes." );
-        }
-        _node = node;
-        reset();
-    }
-
-    // Private methods
-    // ---------------
-    /**
-     * Returns the counter.
-     */
-    private int getI() {
-        return _i;
-    }
-
-    /**
-     * Returns the parent of the nodes to iterate over.
-     * 
-     * @return the parent of the nodes to iterate over.
-     */
-    private PhylogenyNode getNode() {
-        return _node;
-    }
-
-    // Public methods
-    // --------------
-    /**
-     * Returns true is this iterator has at least one more element, false
-     * otherwise.
-     * 
-     * @return true is this iterator has at least one more element, false
-     *         otherwise
-     */
-    @Override
-    public boolean hasNext() {
-        return ( getI() < getNode().getNumberOfDescendants() );
-    }
-
-    /**
-     * Increases the counter by one.
-     */
-    private void increaseI() {
-        ++_i;
-    }
-
-    /**
-     * Returns the next PhylogenyNode.
-     * 
-     * @return the next PhylogenyNode
-     * @throws NoSuchElementException
-     *             if iteration is complete
-     */
-    @Override
-    public PhylogenyNode next() throws NoSuchElementException {
-        if ( !hasNext() ) {
-            throw new NoSuchElementException( "Attempt to call \"next()\" on iterator which has no more next elements." );
-        }
-        final PhylogenyNode n = getNode().getChildNode( getI() );
-        increaseI();
-        return n;
-    }
-
-    /**
-     * Not supported.
-     * 
-     */
-    @Override
-    public void remove() {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * Resets the iterator.
-     */
-    @Override
-    public void reset() {
-        setI( 0 );
-    }
-
-    /**
-     * Sets the counter.
-     */
-    private void setI( final int i ) {
-        _i = i;
-    }
-} // end of class ChildNodeIteratorForward.

diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index d0ee90e..b8e452c 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -149,8 +149,9 @@ public final class GSDI extends SDI {
         Event event = null;
         // Determine how many children map to same node as parent.
         int sum_g_childs_mapping_to_s = 0;
-        for( final PhylogenyNodeIterator iter = g.iterateChildNodesForward(); iter.hasNext(); ) {
-            if ( iter.next().getLink() == s ) {
+        for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
+            final PhylogenyNode c = g.getChildNode( i );
+            if ( c.getLink() == s ) {
                 ++sum_g_childs_mapping_to_s;
             }
         }
@@ -159,8 +160,8 @@ public final class GSDI extends SDI {
         int max_traversals = 0;
         PhylogenyNode max_traversals_node = null;
         if ( !s.isExternal() ) {
-            for( final PhylogenyNodeIterator iter = s.iterateChildNodesForward(); iter.hasNext(); ) {
-                final PhylogenyNode current_node = iter.next();
+            for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
+                final PhylogenyNode current_node = s.getChildNode( i );
                 final int traversals = getTraversalCount( current_node );
                 traversals_sum += traversals;
                 if ( traversals > max_traversals ) {
@@ -175,6 +176,7 @@ public final class GSDI extends SDI {
         if ( sum_g_childs_mapping_to_s > 0 ) {
             if ( traversals_sum == 2 ) {
                 event = createDuplicationEvent();
+                //  _transversal_counts.clear();
             }
             else if ( traversals_sum > 2 ) {
                 if ( max_traversals <= 1 ) {
@@ -187,11 +189,14 @@ public final class GSDI extends SDI {
                 }
                 else {
                     event = createDuplicationEvent();
+                    System.out.println( g.toString() );
                     _transversal_counts.put( max_traversals_node, 1 );
+                    //  _transversal_counts.clear();
                 }
             }
             else {
                 event = createDuplicationEvent();
+                //   _transversal_counts.clear();
             }
         }
         else {
@@ -214,8 +219,18 @@ public final class GSDI extends SDI {
      */
     final void geneTreePostOrderTraversal( final PhylogenyNode g ) {
         if ( !g.isExternal() ) {
-            for( final PhylogenyNodeIterator iter = g.iterateChildNodesForward(); iter.hasNext(); ) {
-                geneTreePostOrderTraversal( iter.next() );
+            boolean all_ext = true;
+            for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
+                if ( g.getChildNode( i ).isInternal() ) {
+                    all_ext = false;
+                    break;
+                }
+            }
+            if ( all_ext ) {
+                _transversal_counts.clear();
+            }
+            for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
+                geneTreePostOrderTraversal( g.getChildNode( i ) );
             }
             final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
             for( int i = 0; i < linked_nodes.length; ++i ) {
@@ -240,7 +255,6 @@ public final class GSDI extends SDI {
             g.setLink( s );
             // Determines whether dup. or spec.
             determineEvent( s, g );
-            // _transversal_counts.clear();
         }
     }
 
@@ -304,7 +318,7 @@ public final class GSDI extends SDI {
         final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
         final List<PhylogenyNode> species_tree_ext_nodes = new ArrayList<PhylogenyNode>();
         final TaxonomyComparisonBase tax_comp_base = determineTaxonomyComparisonBase( _gene_tree );
-        System.out.println( "comp base is: " + tax_comp_base );
+        // System.out.println( "comp base is: " + tax_comp_base );
         // Stringyfied taxonomy is the key, node is the value.
         for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
             final PhylogenyNode s = iter.next();
@@ -352,7 +366,7 @@ public final class GSDI extends SDI {
                     else {
                         g.setLink( s );
                         _mapped_species_tree_nodes.add( s );
-                        System.out.println( "setting link of " + g + " to " + s );
+                        //  System.out.println( "setting link of " + g + " to " + s );
                     }
                 }
             }
@@ -363,21 +377,10 @@ public final class GSDI extends SDI {
             }
         }
         if ( _strip_species_tree ) {
-            for( final PhylogenyNode x : _mapped_species_tree_nodes ) {
-                System.out.println( ">>" + x );
-            }
             for( final PhylogenyNode s : species_tree_ext_nodes ) {
-                System.out.print( ">>>>>>>>>" + s );
                 if ( !_mapped_species_tree_nodes.contains( s ) ) {
                     _species_tree.deleteSubtree( s, true );
-                    System.out.println( " DELETING" );
                 }
-                else {
-                    System.out.println();
-                }
-            }
-            for( final PhylogenyNode x : _mapped_species_tree_nodes ) {
-                System.out.println( ">>" + x );
             }
         }
     }

diff --git a/forester/java/src/org/forester/sdi/TaxonomyAssigner.java b/forester/java/src/org/forester/sdi/TaxonomyAssigner.java
index c24d97e..a71e70e 100644 (file)
--- a/forester/java/src/org/forester/sdi/TaxonomyAssigner.java
+++ b/forester/java/src/org/forester/sdi/TaxonomyAssigner.java
@@ -28,7 +28,6 @@ package org.forester.sdi;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 
 public class TaxonomyAssigner extends SDI {
 
@@ -41,8 +40,8 @@ public class TaxonomyAssigner extends SDI {
 
     void geneTreePostOrderTraversal( final PhylogenyNode g ) {
         if ( !g.isExternal() ) {
-            for( final PhylogenyNodeIterator iter = g.iterateChildNodesForward(); iter.hasNext(); ) {
-                geneTreePostOrderTraversal( iter.next() );
+            for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
+                geneTreePostOrderTraversal( g.getChildNode( i ) );
             }
             final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
             for( int i = 0; i < linked_nodes.length; ++i ) {

diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java
index 0c67a61..14278a9 100644 (file)
--- a/forester/java/src/org/forester/sdi/TestGSDI.java
+++ b/forester/java/src/org/forester/sdi/TestGSDI.java
@@ -27,7 +27,7 @@ package org.forester.sdi;
 
 import java.io.IOException;
 
-import org.forester.development.DevelopmentTools;
+import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
@@ -92,795 +92,805 @@ public final class TestGSDI {
     private static boolean testGSDI_general() {
         try {
             final PhylogenyMethods pm = PhylogenyMethods.getInstance();
-            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 ];
-            s1.setRooted( true );
-            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 GSDI sdi1 = new GSDI( g1, s1, false );
-            if ( sdi1.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
-                    .isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2 = TestGSDI
-                    .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
-            final GSDI sdi2 = new GSDI( g2, s1, false );
-            if ( sdi2.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
-                    .isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g3 = TestGSDI
-                    .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
-            final GSDI sdi3 = new GSDI( g3, s1, false );
-            if ( sdi3.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
-                    .isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g4 = TestGSDI
-                    .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
-            final GSDI sdi4 = new GSDI( g4, s1, false );
-            if ( sdi4.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g5 = TestGSDI
-                    .createPhylogeny( "(((D1[&&NHX:S=D],A1[&&NHX:S=A1]),B[&&NHX:S=B]),((D2[&&NHX:S=D],D3[&&NHX:S=D]),C[&&NHX:S=C]))" );
-            final GSDI sdi5 = new GSDI( g5, s1, false );
-            if ( sdi5.getDuplicationsSum() != 3 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
-                    + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
-                    + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
-                    + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
-                    + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
-            final Phylogeny gene7_2 = TestGSDI
-                    .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
-            gene7_2.setRooted( true );
-            final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
-            if ( sdi7_2.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
-                return false;
-            }
-            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 Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
-            final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
-            if ( sdi2_0.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_0.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
-            final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
-            if ( sdi2_1.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_1.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
-            final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
-            if ( sdi2_2.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_2.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
-            final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
-            if ( sdi2_3.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_3.getSpeciationsSum() != 0 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
-            final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
-            if ( sdi2_4.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_4.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
-            final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
-            if ( sdi2_5.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_5.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
-            final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
-            if ( sdi2_6.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_6.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
-            final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
-            if ( sdi2_7.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_7.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
-                    .isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
-            final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
-            if ( sdi2_8.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_8.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
-                    .isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
-            final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
-            if ( sdi2_9.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_9.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
-            final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
-            if ( sdi2_10.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_10.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
-            final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
-            if ( sdi2_11.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_11.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
-            final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
-            if ( sdi2_12.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_12.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
-            final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
-            if ( sdi2_13.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_13.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
-            final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
-            if ( sdi2_14.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_14.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
-            final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
-            if ( sdi2_15.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_15.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
-            final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
-            if ( sdi2_16.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_16.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
-            final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
-            if ( sdi2_17.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_17.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_18 = TestGSDI
-                    .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
-            final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
-            if ( sdi2_18.getDuplicationsSum() != 3 ) {
-                return false;
-            }
-            if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_18.getSpeciationsSum() != 0 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_19 = TestGSDI
-                    .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
-            final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
-            if ( sdi2_19.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_19.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_20 = TestGSDI
-                    .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
-            final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
-            if ( sdi2_20.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_20.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_21 = TestGSDI
-                    .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
-            final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
-            if ( sdi2_21.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_21.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_22 = TestGSDI
-                    .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
-            final GSDI sdi2_22 = new GSDI( g2_22, s2, false );
-            if ( sdi2_22.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_22.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_23 = TestGSDI
-                    .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
-            final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
-            if ( sdi2_23.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_23.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_24 = TestGSDI
-                    .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
-            final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
-            if ( sdi2_24.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_24.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_25 = TestGSDI
-                    .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
-            final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
-            if ( sdi2_25.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_25.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_26 = TestGSDI
-                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
-            final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
-            if ( sdi2_26.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_26.getSpeciationsSum() != 3 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_27 = TestGSDI
-                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
-            final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
-            if ( sdi2_27.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_27.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_28 = TestGSDI
-                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
-            final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
-            if ( sdi2_28.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_28.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_29 = TestGSDI
-                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
-            final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
-            if ( sdi2_29.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
-                return false;
-            }
-            if ( sdi2_29.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_30 = TestGSDI
-                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
-            final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
-            if ( sdi2_30.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_30.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_31 = TestGSDI
-                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
-            final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
-            if ( sdi2_31.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_31.getSpeciationsSum() != 1 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_32 = TestGSDI
-                    .createPhylogeny( "((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
-            final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
-            if ( sdi2_32.getDuplicationsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
-                return false;
-            }
-            if ( sdi2_32.getSpeciationsSum() != 3 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
+            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 ];
+            //            s1.setRooted( true );
+            //            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 GSDI sdi1 = new GSDI( g1, s1, false );
+            //            if ( sdi1.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+            //                    .isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2 = TestGSDI
+            //                    .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
+            //            final GSDI sdi2 = new GSDI( g2, s1, false );
+            //            if ( sdi2.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
+            //                    .isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g3 = TestGSDI
+            //                    .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
+            //            final GSDI sdi3 = new GSDI( g3, s1, false );
+            //            if ( sdi3.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
+            //                    .isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g4 = TestGSDI
+            //                    .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
+            //            final GSDI sdi4 = new GSDI( g4, s1, false );
+            //            if ( sdi4.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g5 = TestGSDI
+            //                    .createPhylogeny( "(((D1[&&NHX:S=D],A1[&&NHX:S=A1]),B[&&NHX:S=B]),((D2[&&NHX:S=D],D3[&&NHX:S=D]),C[&&NHX:S=C]))" );
+            //            final GSDI sdi5 = new GSDI( g5, s1, false );
+            //            if ( sdi5.getDuplicationsSum() != 3 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
+            //                    + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
+            //                    + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
+            //                    + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
+            //                    + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
+            //            final Phylogeny gene7_2 = TestGSDI
+            //                    .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
+            //            gene7_2.setRooted( true );
+            //            final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
+            //            if ( sdi7_2.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //           
+            //            final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
+            //            final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
+            //            if ( sdi2_0.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_0.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
+            //            final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
+            //            if ( sdi2_1.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_1.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
+            //            final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
+            //            if ( sdi2_2.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_2.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
+            //            final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
+            //            if ( sdi2_3.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_3.getSpeciationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
+            //            final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
+            //            if ( sdi2_4.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_4.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
+            //            final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
+            //            if ( sdi2_5.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_5.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
+            //            final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
+            //            if ( sdi2_6.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_6.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
+            //            final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
+            //            if ( sdi2_7.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_7.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
+            //                    .isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
+            //            final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
+            //            if ( sdi2_8.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_8.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
+            //                    .isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
+            //            final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
+            //            if ( sdi2_9.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_9.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
+            //            final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
+            //            if ( sdi2_10.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_10.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
+            //            final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
+            //            if ( sdi2_11.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_11.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
+            //            final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
+            //            if ( sdi2_12.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_12.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
+            //            final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
+            //            if ( sdi2_13.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_13.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
+            //            final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
+            //            if ( sdi2_14.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_14.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
+            //            final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
+            //            if ( sdi2_15.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_15.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
+            //            final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
+            //            if ( sdi2_16.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_16.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
+            //            final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
+            //            if ( sdi2_17.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_17.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_18 = TestGSDI
+            //                    .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
+            //            final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
+            //            if ( sdi2_18.getDuplicationsSum() != 3 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_18.getSpeciationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_19 = TestGSDI
+            //                    .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
+            //            final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
+            //            if ( sdi2_19.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_19.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_20 = TestGSDI
+            //                    .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
+            //            final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
+            //            if ( sdi2_20.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_20.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_21 = TestGSDI
+            //                    .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
+            //            final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
+            //            if ( sdi2_21.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_21.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_22 = TestGSDI
+            //                    .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
+            //            final GSDI sdi2_22 = new GSDI( g2_22, s2, false );
+            //            if ( sdi2_22.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_22.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_23 = TestGSDI
+            //                    .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
+            //            final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
+            //            if ( sdi2_23.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_23.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_24 = TestGSDI
+            //                    .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
+            //            final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
+            //            if ( sdi2_24.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_24.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_25 = TestGSDI
+            //                    .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
+            //            final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
+            //            if ( sdi2_25.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_25.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_26 = TestGSDI
+            //                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
+            //            final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
+            //            if ( sdi2_26.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_26.getSpeciationsSum() != 3 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_27 = TestGSDI
+            //                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
+            //            final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
+            //            if ( sdi2_27.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_27.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_28 = TestGSDI
+            //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
+            //            final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
+            //            if ( sdi2_28.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_28.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_29 = TestGSDI
+            //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
+            //            final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
+            //            if ( sdi2_29.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_29.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_30 = TestGSDI
+            //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
+            //            final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
+            //            if ( sdi2_30.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_30.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_31 = TestGSDI
+            //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
+            //            final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
+            //            if ( sdi2_31.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_31.getSpeciationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_32 = TestGSDI
+            //                    .createPhylogeny( "((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
+            //            final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
+            //            if ( sdi2_32.getDuplicationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_32.getSpeciationsSum() != 3 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //-
+            final Phylogeny g2_33_d = TestGSDI
+                    .createPhylogeny( "((((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?],(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?])" );
+            final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false );
+            Archaeopteryx.createApplication( g2_33_d );
+            //  Archaeopteryx.createApplication( s2 );
+            //-
             final Phylogeny g2_33 = TestGSDI
                     .createPhylogeny( "(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),k2[&&NHX:S=k2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
             final GSDI sdi2_33 = new GSDI( g2_33, s2, false );
+            Archaeopteryx.createApplication( g2_33 );
+            // Archaeopteryx.createApplication( s2 );
             if ( sdi2_33.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -923,271 +933,272 @@ public final class TestGSDI {
             if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
                 return false;
             }
-            final Phylogeny g2_34 = TestGSDI
-                    .createPhylogeny( "(((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4])" );
-            final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
-            if ( sdi2_34.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_34.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_35 = TestGSDI
-                    .createPhylogeny( "((((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4]),a1_0[&&NHX:S=a1])" );
-            final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
-            if ( sdi2_35.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_35.getSpeciationsSum() != 3 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g2_36 = TestGSDI
-                    .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
-            final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
-            if ( sdi2_36.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_36.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_37 = TestGSDI
-                    .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
-            final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
-            if ( sdi2_37.getDuplicationsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_37.getSpeciationsSum() != 2 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_38 = TestGSDI
-                    .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
-            final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
-            if ( sdi2_38.getDuplicationsSum() != 5 ) {
-                return false;
-            }
-            if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_38.getSpeciationsSum() != 0 ) {
-                return false;
-            }
-            final Phylogeny g2_100 = TestGSDI
-                    .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" );
-            final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
-            if ( sdi2_100.getDuplicationsSum() != 4 ) {
-                return false;
-            }
-            if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                return false;
-            }
-            if ( sdi2_100.getSpeciationsSum() != 4 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny g2_101 = TestGSDI
-                    .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" );
-            final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
-            if ( sdi2_101.getDuplicationsSum() != 2 ) {
-                return false;
-            }
-            if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                return false;
-            }
-            if ( sdi2_101.getSpeciationsSum() != 5 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
-                return false;
-            }
-            final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
-            DevelopmentTools.numberSpeciesInOrder( s_7_4 );
-            final Phylogeny g_7_4_1 = TestGSDI
-                    .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
-                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
-                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
-                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
-                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
-                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
-                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
-                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
-                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
-                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
-                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
-                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
-            final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
-            if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
-                return false;
-            }
-            if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
-                return false;
-            }
-            if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
-                return false;
-            }
-            if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
-                return false;
-            }
-            final Phylogeny g_7_4_2 = TestGSDI
-                    .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
-                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
-                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
-                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
-                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
-                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
-                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
-                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
-                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
-                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
-                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
-                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
-                            + "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" );
-            final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
-            if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
-                return false;
-            }
-            if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
-                return false;
-            }
-            if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
-                return false;
-            }
+            //            final Phylogeny g2_34 = TestGSDI
+            //                    .createPhylogeny( "(((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4])" );
+            //            final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
+            //            if ( sdi2_34.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_34.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_35 = TestGSDI
+            //                    .createPhylogeny( "((((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4]),a1_0[&&NHX:S=a1])" );
+            //            final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
+            //            if ( sdi2_35.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_35.getSpeciationsSum() != 3 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_36 = TestGSDI
+            //                    .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
+            //            final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
+            //            if ( sdi2_36.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_36.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_37 = TestGSDI
+            //                    .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
+            //            final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
+            //            if ( sdi2_37.getDuplicationsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_37.getSpeciationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_38 = TestGSDI
+            //                    .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
+            //            final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
+            //            if ( sdi2_38.getDuplicationsSum() != 5 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_38.getSpeciationsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_100 = TestGSDI
+            //                    .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" );
+            //            final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
+            //            if ( sdi2_100.getDuplicationsSum() != 4 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_100.getSpeciationsSum() != 4 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g2_101 = TestGSDI
+            //                    .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" );
+            //            final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
+            //            if ( sdi2_101.getDuplicationsSum() != 2 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
+            //                return false;
+            //            }
+            //            if ( sdi2_101.getSpeciationsSum() != 5 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
+            //            DevelopmentTools.numberSpeciesInOrder( s_7_4 );
+            //            final Phylogeny g_7_4_1 = TestGSDI
+            //                    .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
+            //                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
+            //                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
+            //                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
+            //                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
+            //                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
+            //                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
+            //                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
+            //                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
+            //                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
+            //                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
+            //                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
+            //            final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
+            //            if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
+            //                return false;
+            //            }
+            //            if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
+            //                return false;
+            //            }
+            //            if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
+            //                return false;
+            //            }
+            //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
+            //                return false;
+            //            }
+            //            final Phylogeny g_7_4_2 = TestGSDI
+            //                    .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
+            //                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
+            //                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
+            //                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
+            //                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
+            //                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
+            //                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
+            //                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
+            //                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
+            //                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
+            //                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
+            //                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
+            //                            + "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" );
+            //            final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
+            //            if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
+            //                return false;
+            //            }
+            //            if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
+            //                return false;
+            //            }
+            //            if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
+            //                return false;
+            //            }
+            //---------------------
             // final String g2_0_ =
             // "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
             // final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[
@@ -1212,4 +1223,20 @@ public final class TestGSDI {
         }
         return true;
     }
+
+    public static void main( final String[] args ) {
+        if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
+            System.out.println( "binary failed" );
+        }
+        if ( !TestGSDI.testGSDI_general() ) {
+            System.out.println( "general failed" );
+        }
+        //        boolean success = test();
+        //        if ( success ) {
+        //            System.out.println( "OK" );
+        //        }
+        //        else {
+        //            System.out.println( "failed" );
+        //        }
+    }
 }

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 4a8b8d8..d1ab3bb 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -1924,26 +1924,6 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n = t3.getNode( "ABC" );
-            PhylogenyNodeIterator it;
-            for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
-                it.next();
-            }
-            for( it.reset(); it.hasNext(); ) {
-                it.next();
-            }
-            final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
-            if ( !it2.next().getName().equals( "A" ) ) {
-                return false;
-            }
-            if ( !it2.next().getName().equals( "B" ) ) {
-                return false;
-            }
-            if ( !it2.next().getName().equals( "C" ) ) {
-                return false;
-            }
-            if ( it2.hasNext() ) {
-                return false;
-            }
             final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ];
             if ( t4.getNumberOfExternalNodes() != 9 ) {
                 return false;