rio - gsdir work...
[jalview.git] / forester / java / src / org / forester / sdi / TestGSDI.java
index 18ce53f..8ad459e 100644 (file)
@@ -27,17 +27,22 @@ package org.forester.sdi;
 
 import java.io.IOException;
 
-import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.development.DevelopmentTools;
 import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sdi.SDI.TaxonomyComparisonBase;
+import org.forester.util.ForesterUtil;
 
 public final class TestGSDI {
 
+    private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
+                                                          + "test_data" + ForesterUtil.getFileSeparator();
+
     private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
         final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
         p.setRooted( true );
@@ -45,7 +50,7 @@ public final class TestGSDI {
     }
 
     private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
-        return PhylogenyMethods.getInstance().obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
+        return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
     }
 
     public static boolean test() {
@@ -92,7 +97,7 @@ public final class TestGSDI {
 
     private static boolean testGSDI_general() {
         try {
-            final PhylogenyMethods pm = PhylogenyMethods.getInstance();
+           
             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]),"
@@ -118,20 +123,25 @@ public final class TestGSDI {
             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 );
+            // Archaeopteryx.createApplication( g1 );
+            // Archaeopteryx.createApplication( s1 );
             if ( sdi1.getDuplicationsSum() != 1 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
                     .isSpeciationOrDuplication() ) {
                 return false;
             }
-            if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) {
+            if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+                    .isDuplication() ) ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
             final Phylogeny g2 = TestGSDI
@@ -140,17 +150,20 @@ public final class TestGSDI {
             if ( sdi2.getDuplicationsSum() != 0 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
+            if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
                     .isSpeciationOrDuplication() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
             final Phylogeny g3 = TestGSDI
@@ -159,17 +172,20 @@ public final class TestGSDI {
             if ( sdi3.getDuplicationsSum() != 0 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
+            if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
                     .isSpeciationOrDuplication() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
             final Phylogeny g4 = TestGSDI
@@ -178,13 +194,16 @@ public final class TestGSDI {
             if ( sdi4.getDuplicationsSum() != 1 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
+            if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent()
+                    .isDuplication() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
             final Phylogeny g5 = TestGSDI
@@ -193,19 +212,24 @@ public final class TestGSDI {
             if ( sdi5.getDuplicationsSum() != 3 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
+            if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent()
+                    .isDuplication() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
+            if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent()
+                    .isDuplication() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
+            if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent()
+                    .isDuplication() ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
                 return false;
             }
             final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
@@ -258,7 +282,8 @@ public final class TestGSDI {
             if ( sdi2_0.getSpeciationsSum() != 1 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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])" );
@@ -272,7 +297,8 @@ public final class TestGSDI {
             if ( sdi2_1.getSpeciationsSum() != 1 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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])" );
@@ -286,7 +312,8 @@ public final class TestGSDI {
             if ( sdi2_2.getSpeciationsSum() != 1 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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])" );
@@ -300,7 +327,8 @@ public final class TestGSDI {
             if ( sdi2_3.getSpeciationsSum() != 0 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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])" );
@@ -314,10 +342,12 @@ public final class TestGSDI {
             if ( sdi2_4.getSpeciationsSum() != 2 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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])" );
@@ -331,10 +361,12 @@ public final class TestGSDI {
             if ( sdi2_5.getSpeciationsSum() != 2 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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])" );
@@ -348,10 +380,12 @@ public final class TestGSDI {
             if ( sdi2_6.getSpeciationsSum() != 2 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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])" );
@@ -365,10 +399,11 @@ public final class TestGSDI {
             if ( sdi2_7.getSpeciationsSum() != 1 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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()
+            if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
                     .isSpeciationOrDuplication() ) {
                 return false;
             }
@@ -383,11 +418,12 @@ public final class TestGSDI {
             if ( sdi2_8.getSpeciationsSum() != 1 ) {
                 return false;
             }
-            if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
+            if ( !PhylogenyMethods.calculateLCA( 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() ) {
+            if ( !PhylogenyMethods.calculateLCA( 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])" );
@@ -630,8 +666,8 @@ public final class TestGSDI {
             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 );
-            Archaeopteryx.createApplication( g2_22 );
-            Archaeopteryx.createApplication( s2 );
+            //Archaeopteryx.createApplication( g2_22 );
+            //Archaeopteryx.createApplication( s2 );
             if ( sdi2_22.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -650,574 +686,794 @@ public final class TestGSDI {
             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;
-                        }
-                        if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
-                            return false;
-                        }
-                        if ( sdi2_33.getSpeciationsSum() != 3 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        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 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() )[
-//             0 ];
-//             g2_0.setRooted( true );
-//             final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
-//             if ( sdi2_0.getDuplicationsSum() != 0 ) {
-//             return false;
-//             }
-//             final String g2_1_= "";
-//             final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
-//             0 ];
-//             g2_1.setRooted( true );
-//             final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
-//             if ( sdi2_1.getDuplicationsSum() != 0 ) {
-//             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 = 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 );
+            if ( sdi2_33.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
+                return false;
+            }
+            if ( sdi2_33.getSpeciationsSum() != 3 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "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 );
+            if ( sdi2_33_d.getDuplicationsSum() != 3 ) {
+                return false;
+            }
+            if ( sdi2_33_d.getSpeciationOrDuplicationEventsSum() != 14 ) {
+                return false;
+            }
+            if ( sdi2_33_d.getSpeciationsSum() != 6 ) {
+                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_0p = TestGSDI.createPhylogeny( g2_0_ );
+            g2_0.setRooted( true );
+            final GSDI sdi2_0p = new GSDI( g2_0p, s2, false );
+            if ( sdi2_0p.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            //--
+            final Phylogeny tol_143_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + "tol_143.xml" )[ 0 ];
+            final Phylogeny gene_tree_tax_code_4_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+                    + "gene_tree_tax_code_4.xml" )[ 0 ];
+            final GSDI gsdi_143_4_1 = new GSDI( gene_tree_tax_code_4_.copy(), tol_143_.copy(), false, true, true );
+            if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) {
+                return false;
+            }
+            if ( gsdi_143_4_1.getSpeciationsSum() != 28 ) {
+                return false;
+            }
+            if ( gsdi_143_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
+                return false;
+            }
+            //--
+            final Phylogeny gsdi_test_gene_tree_sn_wnt = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+                    + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ];
+            gsdi_test_gene_tree_sn_wnt.setRooted( true );
+            final GSDI a = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), tol_143_.copy(), false, true, true );
+            if ( a.getDuplicationsSum() != 33 ) {
+                return false;
+            }
+            if ( a.getSpeciationsSum() != 31 ) {
+                return false;
+            }
+            if ( a.getSpeciationOrDuplicationEventsSum() != 0 ) {
+                return false;
+            }
+            if ( a.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( a.getMappedExternalSpeciesTreeNodes().size() != 26 ) {
+                return false;
+            }
+            if ( a.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+                return false;
+            }
+            //--
+            final Phylogeny gsdi_test_species_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+                    + "gsdi_test_species_tree_sn.xml" )[ 0 ];
+            final GSDI b = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
+                                     gsdi_test_species_tree_sn_xml.copy(),
+                                     false,
+                                     true,
+                                     true );
+            if ( b.getDuplicationsSum() != 8 ) {
+                return false;
+            }
+            if ( b.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( b.getSpeciationOrDuplicationEventsSum() != 0 ) {
+                return false;
+            }
+            if ( b.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( b.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
+                return false;
+            }
+            if ( b.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+                return false;
+            }
+            if ( b.getStrippedExternalGeneTreeNodes().size() != 87 ) {
+                return false;
+            }
+            if ( b.getStrippedSpeciesTreeNodes().size() != 17 ) {
+                return false;
+            }
+            //--
+            final Phylogeny gsdi_test_species_tree_sn_nh = TestGSDI
+                    .createPhylogeny( "((((((('Homo sapiens','Mus musculus')Euarchontoglires,'Petromyzon marinus')Vertebrata,'Nematostella vectensis')'Bilateria Cnidaria',(('Mycosphaerella graminicola','Mycosphaerella pini')Mycosphaerella,'Saccharomyces cerevisiae')'Pezizomycotina Saccharomycetales')Opisthokonta,('Plasmodium chabaudi','Plasmodium falciparum','Plasmodium yoelii yoelii')Plasmodium)Eukaryota,'Pyrococcus horikoshii')Neomura,(('Kineococcus radiotolerans','Kocuria rhizophila','Streptomyces coelicolor','Thermobifida fusca','Microlunatus phosphovorus'),'Bacteroides thetaiotaomicron'))'cellular organisms';" );
+            PhylogenyMethods.transferNodeNameToField( gsdi_test_species_tree_sn_nh,
+                                                      PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+                                                      true );
+            final GSDI c = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
+                                     gsdi_test_species_tree_sn_nh.copy(),
+                                     false,
+                                     true,
+                                     true );
+            if ( c.getDuplicationsSum() != 8 ) {
+                return false;
+            }
+            if ( c.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( c.getSpeciationOrDuplicationEventsSum() != 0 ) {
+                return false;
+            }
+            if ( c.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( c.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
+                return false;
+            }
+            if ( c.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+                return false;
+            }
+            if ( c.getStrippedExternalGeneTreeNodes().size() != 87 ) {
+                return false;
+            }
+            if ( c.getStrippedSpeciesTreeNodes().size() != 15 ) {
+                return false;
+            }
+            //--
+            final Phylogeny gsdi_test_gene_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+                    + "gsdi_test_gene_tree_codes.xml" )[ 0 ];
+            final Phylogeny gsdi_test_species_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+                    + "gsdi_test_species_tree_codes.xml" )[ 0 ];
+            final GSDI d = new GSDI( gsdi_test_gene_tree_codes_xml.copy(),
+                                     gsdi_test_species_tree_codes_xml.copy(),
+                                     false,
+                                     true,
+                                     true );
+            if ( d.getDuplicationsSum() != 21 ) {
+                return false;
+            }
+            if ( d.getSpeciationsSum() != 28 ) {
+                return false;
+            }
+            if ( d.getSpeciationOrDuplicationEventsSum() != 6 ) {
+                return false;
+            }
+            if ( d.getTaxCompBase() != TaxonomyComparisonBase.CODE ) {
+                return false;
+            }
+            if ( d.getMappedExternalSpeciesTreeNodes().size() != 17 ) {
+                return false;
+            }
+            if ( d.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+                return false;
+            }
+            if ( d.getStrippedExternalGeneTreeNodes().size() != 12 ) {
+                return false;
+            }
+            if ( d.getStrippedSpeciesTreeNodes().size() != 3 ) {
+                return false;
+            }
+            //--
+            final Phylogeny gsdi_test_gene_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+                    + "gsdi_test_gene_tree_sn.xml" )[ 0 ];
+            final GSDI e = new GSDI( gsdi_test_gene_tree_sn_xml.copy(),
+                                     gsdi_test_species_tree_sn_xml.copy(),
+                                     false,
+                                     true,
+                                     true );
+            if ( e.getDuplicationsSum() != 7 ) {
+                return false;
+            }
+            if ( e.getSpeciationsSum() != 9 ) {
+                return false;
+            }
+            if ( e.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( e.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( e.getMappedExternalSpeciesTreeNodes().size() != 12 ) {
+                return false;
+            }
+            if ( e.getReMappedScientificNamesFromGeneTree().size() != 8 ) {
+                return false;
+            }
+            if ( e.getStrippedExternalGeneTreeNodes().size() != 3 ) {
+                return false;
+            }
+            if ( e.getStrippedSpeciesTreeNodes().size() != 7 ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    private static boolean testGSDIR_general() {
+        try {
+           
+            final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
+                    + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
+                    + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
+                    + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
+                    + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
+                    + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
+                    + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
+                    + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
+                    + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
+                    + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
+                    + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
+                    + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
+                    + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
+                    + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
+                    + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
+                    + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
+                    + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
+            final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
+            s2.setRooted( true );
+            final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
+            final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
+            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 GSDIR sdi1 = new GSDIR( g1, s1, false, 1 );
+            // Archaeopteryx.createApplication( g1 );
+            // Archaeopteryx.createApplication( s1 );
+            if ( sdi1.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+                    .isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+                    .isDuplication() ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+                    .isSpeciation() ) {
+                return false;
+            }
+            
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );
@@ -1233,6 +1489,12 @@ public final class TestGSDI {
         if ( !TestGSDI.testGSDI_general() ) {
             System.out.println( "general failed" );
         }
+        if ( !TestGSDI.testGSDIR_general() ) {
+            System.out.println( "general re-rooting failed" );
+        }
+        else {
+            System.out.println( "OK" );
+        }
         //        boolean success = test();
         //        if ( success ) {
         //            System.out.println( "OK" );