X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FTestGSDI.java;h=027e09b0dd3bccca1801fc9c54c8fcdfc4ca4c2b;hb=06b38f91bc061d8ab1dfea3b6238c94c95a30d26;hp=0539759a5605483ff7595589f97847398a798434;hpb=0ee466206ea1e3ac3025df1110538e3815c160b4;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java
index 0539759..027e09b 100644
--- a/forester/java/src/org/forester/sdi/TestGSDI.java
+++ b/forester/java/src/org/forester/sdi/TestGSDI.java
@@ -21,13 +21,12 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 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;
@@ -36,6 +35,7 @@ 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.SDIutil.TaxonomyComparisonBase;
 import org.forester.util.ForesterUtil;
 
 public final class TestGSDI {
@@ -43,14 +43,19 @@ 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 );
-        return p;
-    }
-
-    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();
+    public static void main( final String[] args ) {
+        if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
+            System.out.println( "binary failed" );
+        }
+        if ( !TestGSDI.testGSDI_general() ) {
+            System.out.println( "general failed" );
+        }
+        if ( !TestGSDI.testGSDIR_general() ) {
+            System.out.println( "general re-rooting failed" );
+        }
+        else {
+            System.out.println( "OK" );
+        }
     }
 
     public static boolean test() {
@@ -60,11 +65,41 @@ public final class TestGSDI {
         if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
             return false;
         }
+        if ( !TestGSDI.testGSDIR_general() ) {
+            return false;
+        }
         return true;
     }
 
+    private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
+        final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
+        p.setRooted( true );
+        return p;
+    }
+
+    private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
+        return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
+    }
+
     private static boolean testGSDI_against_binary_gene_tree() {
         try {
+            final PhylogenyFactory factory0 = ParserBasedPhylogenyFactory.getInstance();
+            final String s0 = "([&&NHX:S=1]);";
+            final String gene_0_str = "([&&NHX:S=1],[&&NHX:S=1]);";
+            final Phylogeny s_0 = factory0.create( s0, new NHXParser() )[ 0 ];
+            final Phylogeny gene_0 = factory0.create( gene_0_str, new NHXParser() )[ 0 ];
+            s_0.setRooted( true );
+            gene_0.setRooted( true );
+            final GSDI sdi0 = new GSDI( gene_0, s_0, false, false, false );
+            if ( sdi0.getSpeciationOrDuplicationEventsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi0.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi0.getSpeciationsSum() != 0 ) {
+                return false;
+            }
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final String multi_species_2_str = "(((((([&&NHX:S=1],[&&NHX:S=2]),"
                     + "([&&NHX:S=3],[&&NHX:S=4],[&&NHX:S=5])),"
@@ -80,7 +115,7 @@ public final class TestGSDI {
             final Phylogeny gene_2_1 = factory.create( gene_2_1_str, new NHXParser() )[ 0 ];
             multi_species_2.setRooted( true );
             gene_2_1.setRooted( true );
-            final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false );
+            final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false, false, false );
             if ( sdi.getSpeciationOrDuplicationEventsSum() != 0 ) {
                 return false;
             }
@@ -97,7 +132,6 @@ 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]),"
@@ -122,97 +156,114 @@ public final class TestGSDI {
             s1.setRooted( true );
             final Phylogeny g1 = TestGSDI
                     .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
-            final GSDI sdi1 = new GSDI( g1, s1, false );
+            final GSDI sdi1 = new GSDI( g1, s1, false, false, 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
                     .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
-            final GSDI sdi2 = new GSDI( g2, s1, false );
+            final GSDI sdi2 = new GSDI( g2, s1, false, false, false );
             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
                     .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
-            final GSDI sdi3 = new GSDI( g3, s1, false );
+            final GSDI sdi3 = new GSDI( g3, s1, false, false, false );
             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
                     .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
-            final GSDI sdi4 = new GSDI( g4, s1, false );
+            final GSDI sdi4 = new GSDI( g4, s1, false, false, false );
             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
                     .createPhylogeny( "(((D1[&&NHX:S=D],A1[&&NHX:S=A1]),B[&&NHX:S=B]),((D2[&&NHX:S=D],D3[&&NHX:S=D]),C[&&NHX:S=C]))" );
-            final GSDI sdi5 = new GSDI( g5, s1, false );
+            final GSDI sdi5 = new GSDI( g5, s1, false, false, false );
             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]),"
@@ -223,7 +274,7 @@ public final class TestGSDI {
             final Phylogeny gene7_2 = TestGSDI
                     .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
             gene7_2.setRooted( true );
-            final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
+            final GSDI sdi7_2 = new GSDI( gene7_2, species7, false, false, false );
             if ( sdi7_2.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -255,7 +306,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
-            final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
+            final GSDI sdi2_0 = new GSDI( g2_0, s2, false, false, false );
             if ( sdi2_0.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -265,11 +316,12 @@ 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])" );
-            final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
+            final GSDI sdi2_1 = new GSDI( g2_1, s2, false, false, false );
             if ( sdi2_1.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -279,11 +331,12 @@ 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])" );
-            final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
+            final GSDI sdi2_2 = new GSDI( g2_2, s2, false, false, false );
             if ( sdi2_2.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -293,11 +346,12 @@ 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])" );
-            final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
+            final GSDI sdi2_3 = new GSDI( g2_3, s2, false, false, false );
             if ( sdi2_3.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -307,11 +361,12 @@ 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])" );
-            final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
+            final GSDI sdi2_4 = new GSDI( g2_4, s2, false, false, false );
             if ( sdi2_4.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -321,14 +376,16 @@ 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])" );
-            final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
+            final GSDI sdi2_5 = new GSDI( g2_5, s2, false, false, false );
             if ( sdi2_5.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -338,14 +395,16 @@ 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])" );
-            final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
+            final GSDI sdi2_6 = new GSDI( g2_6, s2, false, false, false );
             if ( sdi2_6.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -355,14 +414,16 @@ 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])" );
-            final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
+            final GSDI sdi2_7 = new GSDI( g2_7, s2, false, false, false );
             if ( sdi2_7.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -372,15 +433,16 @@ 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;
             }
             final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
-            final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
+            final GSDI sdi2_8 = new GSDI( g2_8, s2, false, false, false );
             if ( sdi2_8.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -390,15 +452,16 @@ 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])" );
-            final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
+            final GSDI sdi2_9 = new GSDI( g2_9, s2, false, false, false );
             if ( sdi2_9.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -415,7 +478,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
-            final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
+            final GSDI sdi2_10 = new GSDI( g2_10, s2, false, false, false );
             if ( sdi2_10.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -432,7 +495,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
-            final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
+            final GSDI sdi2_11 = new GSDI( g2_11, s2, false, false, false );
             if ( sdi2_11.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -449,7 +512,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
-            final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
+            final GSDI sdi2_12 = new GSDI( g2_12, s2, false, false, false );
             if ( sdi2_12.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -466,7 +529,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
-            final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
+            final GSDI sdi2_13 = new GSDI( g2_13, s2, false, false, false );
             if ( sdi2_13.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -483,7 +546,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
-            final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
+            final GSDI sdi2_14 = new GSDI( g2_14, s2, false, false, false );
             if ( sdi2_14.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -500,7 +563,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
-            final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
+            final GSDI sdi2_15 = new GSDI( g2_15, s2, false, false, false );
             if ( sdi2_15.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -517,7 +580,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
-            final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
+            final GSDI sdi2_16 = new GSDI( g2_16, s2, false, false, false );
             if ( sdi2_16.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -534,7 +597,7 @@ public final class TestGSDI {
                 return false;
             }
             final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
-            final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
+            final GSDI sdi2_17 = new GSDI( g2_17, s2, false, false, false );
             if ( sdi2_17.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -552,7 +615,7 @@ public final class TestGSDI {
             }
             final Phylogeny g2_18 = TestGSDI
                     .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
-            final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
+            final GSDI sdi2_18 = new GSDI( g2_18, s2, false, false, false );
             if ( sdi2_18.getDuplicationsSum() != 3 ) {
                 return false;
             }
@@ -573,7 +636,7 @@ public final class TestGSDI {
             }
             final Phylogeny g2_19 = TestGSDI
                     .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
-            final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
+            final GSDI sdi2_19 = new GSDI( g2_19, s2, false, false, false );
             if ( sdi2_19.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -594,7 +657,7 @@ public final class TestGSDI {
             }
             final Phylogeny g2_20 = TestGSDI
                     .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
-            final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
+            final GSDI sdi2_20 = new GSDI( g2_20, s2, false, false, false );
             if ( sdi2_20.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -615,7 +678,7 @@ public final class TestGSDI {
             }
             final Phylogeny g2_21 = TestGSDI
                     .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
-            final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
+            final GSDI sdi2_21 = new GSDI( g2_21, s2, false, false, false );
             if ( sdi2_21.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -636,7 +699,7 @@ 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 );
+            final GSDI sdi2_22 = new GSDI( g2_22, s2, false, false, false );
             //Archaeopteryx.createApplication( g2_22 );
             //Archaeopteryx.createApplication( s2 );
             if ( sdi2_22.getDuplicationsSum() != 0 ) {
@@ -659,7 +722,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_23 = new GSDI( g2_23, s2, false, false, false );
             if ( sdi2_23.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -680,7 +743,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_24 = new GSDI( g2_24, s2, false, false, false );
             if ( sdi2_24.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -701,7 +764,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_25 = new GSDI( g2_25, s2, false, false, false );
             if ( sdi2_25.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -722,7 +785,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_26 = new GSDI( g2_26, s2, false, false, false );
             if ( sdi2_26.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -743,7 +806,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_27 = new GSDI( g2_27, s2, false, false, false );
             if ( sdi2_27.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -764,7 +827,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_28 = new GSDI( g2_28, s2, false, false, false );
             if ( sdi2_28.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -785,7 +848,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_29 = new GSDI( g2_29, s2, false, false, false );
             if ( sdi2_29.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -806,7 +869,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_30 = new GSDI( g2_30, s2, false, false, false );
             if ( sdi2_30.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -827,7 +890,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_31 = new GSDI( g2_31, s2, false, false, false );
             if ( sdi2_31.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -848,7 +911,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_32 = new GSDI( g2_32, s2, false, false, false );
             if ( sdi2_32.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -890,7 +953,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_33 = new GSDI( g2_33, s2, false, false, false );
             if ( sdi2_33.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -935,7 +998,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false, false, false );
             if ( sdi2_33_d.getDuplicationsSum() != 3 ) {
                 return false;
             }
@@ -947,7 +1010,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_34 = new GSDI( g2_34, s2, false, false, false );
             if ( sdi2_34.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -971,7 +1034,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_35 = new GSDI( g2_35, s2, false, false, false );
             if ( sdi2_35.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -998,7 +1061,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_36 = new GSDI( g2_36, s2, false, false, false );
             if ( sdi2_36.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -1022,7 +1085,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_37 = new GSDI( g2_37, s2, false, false, false );
             if ( sdi2_37.getDuplicationsSum() != 1 ) {
                 return false;
             }
@@ -1046,7 +1109,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_38 = new GSDI( g2_38, s2, false, false, false );
             if ( sdi2_38.getDuplicationsSum() != 5 ) {
                 return false;
             }
@@ -1058,7 +1121,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_100 = new GSDI( g2_100, s2, false, false, false );
             if ( sdi2_100.getDuplicationsSum() != 4 ) {
                 return false;
             }
@@ -1094,7 +1157,7 @@ public final class TestGSDI {
             }
             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 );
+            final GSDI sdi2_101 = new GSDI( g2_101, s2, false, false, false );
             if ( sdi2_101.getDuplicationsSum() != 2 ) {
                 return false;
             }
@@ -1143,7 +1206,7 @@ public final class TestGSDI {
                             + "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 );
+            final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false, false, false );
             if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
                 return false;
             }
@@ -1200,7 +1263,7 @@ public final class TestGSDI {
                             + "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 );
+            final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false, false, false );
             if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
                 return false;
             }
@@ -1213,7 +1276,7 @@ public final class TestGSDI {
             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 );
+            final GSDI sdi2_0p = new GSDI( g2_0p, s2, false, false, false );
             if ( sdi2_0p.getDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -1222,7 +1285,6 @@ public final class TestGSDI {
             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 );
-            Archaeopteryx.createApplication( gsdi_143_4_1.getGeneTree() );
             if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) {
                 return false;
             }
@@ -1232,6 +1294,162 @@ public final class TestGSDI {
             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 );
@@ -1240,22 +1458,80 @@ public final class TestGSDI {
         return true;
     }
 
-    public static void main( final String[] args ) {
-        if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
-            System.out.println( "binary failed" );
-        }
-        if ( !TestGSDI.testGSDI_general() ) {
-            System.out.println( "general failed" );
+    private static boolean testGSDIR_general() {
+        try {
+            final PhylogenyFactory factory0 = ParserBasedPhylogenyFactory.getInstance();
+            final String s0 = "([&&NHX:S=1]);";
+            final String gene_0_str = "([&&NHX:S=1],[&&NHX:S=1]);";
+            final Phylogeny s_0 = factory0.create( s0, new NHXParser() )[ 0 ];
+            final Phylogeny gene_0 = factory0.create( gene_0_str, new NHXParser() )[ 0 ];
+            s_0.setRooted( true );
+            gene_0.setRooted( true );
+            final GSDIR sdi0 = new GSDIR( gene_0, s_0, true, true, true );
+            if ( sdi0.getSpeciationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi0.getMinDuplicationsSum() != 1 ) {
+                return false;
+            }
+            //
+            final PhylogenyFactory factory00 = ParserBasedPhylogenyFactory.getInstance();
+            final String s00 = "[&&NHX:S=1];";
+            final String gene_00_str = "([&&NHX:S=1],[&&NHX:S=1]);";
+            final Phylogeny s_00 = factory00.create( s00, new NHXParser() )[ 0 ];
+            final Phylogeny gene_00 = factory00.create( gene_00_str, new NHXParser() )[ 0 ];
+            s_00.setRooted( true );
+            gene_00.setRooted( true );
+            final GSDIR sdi00 = new GSDIR( gene_00, s_00, true, true, true );
+            if ( sdi00.getSpeciationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi00.getMinDuplicationsSum() != 1 ) {
+                return false;
+            }
+            //
+            final String s1str = "(((([&&NHX:S=HUMAN],([&&NHX:S=MOUSE],[&&NHX:S=RAT])),([&&NHX:S=CAEEL],[&&NHX:S=CAEBR])),[&&NHX:S=YEAST]),[&&NHX:S=ARATH])";
+            final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1str, new NHXParser() )[ 0 ];
+            s1.setRooted( true );
+            final Phylogeny g1 = TestGSDI
+                    .createPhylogeny( "(HUMAN[&&NHX:S=HUMAN],(RAT[&&NHX:S=RAT],(CAEEL[&&NHX:T=:S=CAEEL],YEAST[&&NHX:S=YEAST])))" );
+            final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false, true );
+            if ( sdi1.getMinDuplicationsSum() != 0 ) {
+                return false;
+            }
+            final Phylogeny g2 = TestGSDI
+                    .createPhylogeny( "(((HUMAN[&&NHX:S=HUMAN],RAT[&&NHX:S=RAT]),CAEEL[&&NHX:T=:S=CAEEL]),YEAST[&&NHX:S=YEAST])" );
+            final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false, true );
+            if ( sdi2.getMinDuplicationsSum() != 0 ) {
+                return false;
+            }
+            final Phylogeny g3 = TestGSDI
+                    .createPhylogeny( "(RAT[&&NHX:S=RAT],HUMAN[&&NHX:S=HUMAN],(YEAST[&&NHX:S=YEAST],CAEEL[&&NHX:T=:S=CAEEL]))" );
+            final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false, true );
+            if ( sdi3.getMinDuplicationsSum() != 0 ) {
+                return false;
+            }
+            final Phylogeny g4 = TestGSDI
+                    .createPhylogeny( "(((((MOUSE[&&NHX:S=MOUSE],[&&NHX:S=RAT]),[&&NHX:S=HUMAN]),([&&NHX:S=ARATH],[&&NHX:S=YEAST])),[&&NHX:S=CAEEL]),[&&NHX:S=CAEBR])" );
+            final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false, true );
+            if ( sdi4.getMinDuplicationsSum() != 0 ) {
+                return false;
+            }
+            //
+            final String s2str = "(((([&&NHX:S=HUMAN],([&&NHX:S=MOUSE],[&&NHX:S=RAT])),([&&NHX:S=CAEEL],[&&NHX:S=CAEBR])),[&&NHX:S=YEAST]),([&&NHX:S=ARATH],[&&NHX:S=SOYBN]))";
+            final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2str, new NHXParser() )[ 0 ];
+            s2.setRooted( true );
+            final Phylogeny g5 = TestGSDI.createPhylogeny( s2str );
+            final GSDIR sdi5 = new GSDIR( g5, s2, false, false, true );
+            if ( sdi5.getMinDuplicationsSum() != 0 ) {
+                System.out.println( sdi5.getMinDuplicationsSum() );
+                return false;
+            }
         }
-        else {
-            System.out.println( "general OK" );
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
         }
-        //        boolean success = test();
-        //        if ( success ) {
-        //            System.out.println( "OK" );
-        //        }
-        //        else {
-        //            System.out.println( "failed" );
-        //        }
+        return true;
     }
 }