forester/java/src/org/forester/sdi/TestGSDI.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.sdi;
  27
  28 import java.io.IOException;
  29
  30 import org.forester.archaeopteryx.Archaeopteryx;
  31 import org.forester.io.parsers.nhx.NHXParser;
  32 import org.forester.phylogeny.Phylogeny;
  33 import org.forester.phylogeny.PhylogenyMethods;
  34 import org.forester.phylogeny.data.Event;
  35 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  36 import org.forester.phylogeny.factories.PhylogenyFactory;
  37
  38 public final class TestGSDI {
  39
  40     private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
  41         final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
  42         p.setRooted( true );
  43         return p;
  44     }
  45
  46     private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
  47         return PhylogenyMethods.getInstance().obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
  48     }
  49
  50     public static boolean test() {
  51         if ( !TestGSDI.testGSDI_general() ) {
  52             return false;
  53         }
  54         if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
  55             return false;
  56         }
  57         return true;
  58     }
  59
  60     private static boolean testGSDI_against_binary_gene_tree() {
  61         try {
  62             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  63             final String multi_species_2_str = "(((((([&&NHX:S=1],[&&NHX:S=2]),"
  64                     + "([&&NHX:S=3],[&&NHX:S=4],[&&NHX:S=5])),"
  65                     + "([&&NHX:S=6],[&&NHX:S=7],[&&NHX:S=8],[&&NHX:S=9])),"
  66                     + "([&&NHX:S=10],[&&NHX:S=11])),"
  67                     + "([&&NHX:S=12],[&&NHX:S=13],[&&NHX:S=14])),"
  68                     + "([&&NHX:S=15],([&&NHX:S=16],[&&NHX:S=17]),([&&NHX:S=18],[&&NHX:S=19],[&&NHX:S=20]),([&&NHX:S=21],[&&NHX:S=22],[&&NHX:S=23],[&&NHX:S=24])));";
  69             final String gene_2_1_str = "(((((([&&NHX:S=1],[&&NHX:S=2])1_2,([&&NHX:S=3],[&&NHX:S=4])),"
  70                     + "([&&NHX:S=6],[&&NHX:S=7])6_7_8_9)1_9,([&&NHX:S=10],[&&NHX:S=11])),"
  71                     + "([&&NHX:S=12],[&&NHX:S=13])12_13_14)1_14,"
  72                     + "([&&NHX:S=15],([&&NHX:S=21],[&&NHX:S=24])21_22_23_24)15_24);";
  73             final Phylogeny multi_species_2 = factory.create( multi_species_2_str, new NHXParser() )[ 0 ];
  74             final Phylogeny gene_2_1 = factory.create( gene_2_1_str, new NHXParser() )[ 0 ];
  75             multi_species_2.setRooted( true );
  76             gene_2_1.setRooted( true );
  77             final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false );
  78             if ( sdi.getSpeciationOrDuplicationEventsSum() != 0 ) {
  79                 return false;
  80             }
  81             if ( sdi.getDuplicationsSum() != 0 ) {
  82                 return false;
  83             }
  84         }
  85         catch ( final Exception e ) {
  86             e.printStackTrace( System.out );
  87             return false;
  88         }
  89         return true;
  90     }
  91
  92     private static boolean testGSDI_general() {
  93         try {
  94             final PhylogenyMethods pm = PhylogenyMethods.getInstance();
  95             final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
  96                     + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
  97                     + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
  98                     + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
  99                     + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
 100                     + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
 101                     + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
 102                     + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
 103                     + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
 104                     + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
 105                     + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
 106                     + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
 107                     + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
 108                     + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
 109                     + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
 110                     + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
 111                     + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
 112             final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
 113             s2.setRooted( true );
 114             final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
 115             final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
 116             s1.setRooted( true );
 117             final Phylogeny g1 = TestGSDI
 118                     .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
 119             final GSDI sdi1 = new GSDI( g1, s1, false );
 120             Archaeopteryx.createApplication( g1 );
 121             Archaeopteryx.createApplication( s1 );
 122             if ( sdi1.getDuplicationsSum() != 1 ) {
 123                 return false;
 124             }
 125             if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
 126                 return false;
 127             }
 128             if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
 129                     .isSpeciationOrDuplication() ) {
 130                 return false;
 131             }
 132             if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) {
 133                 return false;
 134             }
 135             if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
 136                 return false;
 137             }
 138             //            final Phylogeny g2 = TestGSDI
 139             //                    .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
 140             //            final GSDI sdi2 = new GSDI( g2, s1, false );
 141             //            if ( sdi2.getDuplicationsSum() != 0 ) {
 142             //                return false;
 143             //            }
 144             //            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
 145             //                return false;
 146             //            }
 147             //            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
 148             //                return false;
 149             //            }
 150             //            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
 151             //                    .isSpeciationOrDuplication() ) {
 152             //                return false;
 153             //            }
 154             //            if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
 155             //                return false;
 156             //            }
 157             //            final Phylogeny g3 = TestGSDI
 158             //                    .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
 159             //            final GSDI sdi3 = new GSDI( g3, s1, false );
 160             //            if ( sdi3.getDuplicationsSum() != 0 ) {
 161             //                return false;
 162             //            }
 163             //            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
 164             //                return false;
 165             //            }
 166             //            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
 167             //                return false;
 168             //            }
 169             //            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
 170             //                    .isSpeciationOrDuplication() ) {
 171             //                return false;
 172             //            }
 173             //            if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
 174             //                return false;
 175             //            }
 176             //            final Phylogeny g4 = TestGSDI
 177             //                    .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
 178             //            final GSDI sdi4 = new GSDI( g4, s1, false );
 179             //            if ( sdi4.getDuplicationsSum() != 1 ) {
 180             //                return false;
 181             //            }
 182             //            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
 183             //                return false;
 184             //            }
 185             //            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
 186             //                return false;
 187             //            }
 188             //            if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
 189             //                return false;
 190             //            }
 191             //            final Phylogeny g5 = TestGSDI
 192             //                    .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]))" );
 193             //            final GSDI sdi5 = new GSDI( g5, s1, false );
 194             //            if ( sdi5.getDuplicationsSum() != 3 ) {
 195             //                return false;
 196             //            }
 197             //            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
 198             //                return false;
 199             //            }
 200             //            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
 201             //                return false;
 202             //            }
 203             //            if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
 204             //                return false;
 205             //            }
 206             //            if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
 207             //                return false;
 208             //            }
 209             //            if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
 210             //                return false;
 211             //            }
 212             //            final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
 213             //                    + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
 214             //                    + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
 215             //                    + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
 216             //                    + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
 217             //            final Phylogeny gene7_2 = TestGSDI
 218             //                    .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])" );
 219             //            gene7_2.setRooted( true );
 220             //            final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
 221             //            if ( sdi7_2.getDuplicationsSum() != 1 ) {
 222             //                return false;
 223             //            }
 224             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
 225             //                return false;
 226             //            }
 227             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
 228             //                return false;
 229             //            }
 230             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
 231             //                return false;
 232             //            }
 233             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
 234             //                return false;
 235             //            }
 236             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
 237             //                return false;
 238             //            }
 239             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
 240             //                return false;
 241             //            }
 242             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
 243             //                return false;
 244             //            }
 245             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
 246             //                return false;
 247             //            }
 248             //            if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
 249             //                return false;
 250             //            }
 251             //            final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
 252             //            final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
 253             //            if ( sdi2_0.getDuplicationsSum() != 0 ) {
 254             //                return false;
 255             //            }
 256             //            if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
 257             //                return false;
 258             //            }
 259             //            if ( sdi2_0.getSpeciationsSum() != 1 ) {
 260             //                return false;
 261             //            }
 262             //            if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
 263             //                return false;
 264             //            }
 265             //            final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
 266             //            final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
 267             //            if ( sdi2_1.getDuplicationsSum() != 0 ) {
 268             //                return false;
 269             //            }
 270             //            if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
 271             //                return false;
 272             //            }
 273             //            if ( sdi2_1.getSpeciationsSum() != 1 ) {
 274             //                return false;
 275             //            }
 276             //            if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
 277             //                return false;
 278             //            }
 279             //            final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
 280             //            final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
 281             //            if ( sdi2_2.getDuplicationsSum() != 0 ) {
 282             //                return false;
 283             //            }
 284             //            if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
 285             //                return false;
 286             //            }
 287             //            if ( sdi2_2.getSpeciationsSum() != 1 ) {
 288             //                return false;
 289             //            }
 290             //            if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
 291             //                return false;
 292             //            }
 293             //            final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
 294             //            final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
 295             //            if ( sdi2_3.getDuplicationsSum() != 1 ) {
 296             //                return false;
 297             //            }
 298             //            if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
 299             //                return false;
 300             //            }
 301             //            if ( sdi2_3.getSpeciationsSum() != 0 ) {
 302             //                return false;
 303             //            }
 304             //            if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
 305             //                return false;
 306             //            }
 307             //            final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
 308             //            final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
 309             //            if ( sdi2_4.getDuplicationsSum() != 0 ) {
 310             //                return false;
 311             //            }
 312             //            if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
 313             //                return false;
 314             //            }
 315             //            if ( sdi2_4.getSpeciationsSum() != 2 ) {
 316             //                return false;
 317             //            }
 318             //            if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
 319             //                return false;
 320             //            }
 321             //            if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
 322             //                return false;
 323             //            }
 324             //            final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
 325             //            final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
 326             //            if ( sdi2_5.getDuplicationsSum() != 0 ) {
 327             //                return false;
 328             //            }
 329             //            if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
 330             //                return false;
 331             //            }
 332             //            if ( sdi2_5.getSpeciationsSum() != 2 ) {
 333             //                return false;
 334             //            }
 335             //            if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
 336             //                return false;
 337             //            }
 338             //            if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
 339             //                return false;
 340             //            }
 341             //            final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
 342             //            final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
 343             //            if ( sdi2_6.getDuplicationsSum() != 0 ) {
 344             //                return false;
 345             //            }
 346             //            if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
 347             //                return false;
 348             //            }
 349             //            if ( sdi2_6.getSpeciationsSum() != 2 ) {
 350             //                return false;
 351             //            }
 352             //            if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
 353             //                return false;
 354             //            }
 355             //            if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
 356             //                return false;
 357             //            }
 358             //            final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
 359             //            final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
 360             //            if ( sdi2_7.getDuplicationsSum() != 0 ) {
 361             //                return false;
 362             //            }
 363             //            if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
 364             //                return false;
 365             //            }
 366             //            if ( sdi2_7.getSpeciationsSum() != 1 ) {
 367             //                return false;
 368             //            }
 369             //            if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
 370             //                return false;
 371             //            }
 372             //            if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
 373             //                    .isSpeciationOrDuplication() ) {
 374             //                return false;
 375             //            }
 376             //            final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
 377             //            final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
 378             //            if ( sdi2_8.getDuplicationsSum() != 0 ) {
 379             //                return false;
 380             //            }
 381             //            if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
 382             //                return false;
 383             //            }
 384             //            if ( sdi2_8.getSpeciationsSum() != 1 ) {
 385             //                return false;
 386             //            }
 387             //            if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
 388             //                    .isSpeciationOrDuplication() ) {
 389             //                return false;
 390             //            }
 391             //            if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
 392             //                return false;
 393             //            }
 394             //            final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
 395             //            final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
 396             //            if ( sdi2_9.getDuplicationsSum() != 0 ) {
 397             //                return false;
 398             //            }
 399             //            if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
 400             //                return false;
 401             //            }
 402             //            if ( sdi2_9.getSpeciationsSum() != 2 ) {
 403             //                return false;
 404             //            }
 405             //            if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
 406             //                return false;
 407             //            }
 408             //            if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
 409             //                return false;
 410             //            }
 411             //            final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
 412             //            final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
 413             //            if ( sdi2_10.getDuplicationsSum() != 0 ) {
 414             //                return false;
 415             //            }
 416             //            if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
 417             //                return false;
 418             //            }
 419             //            if ( sdi2_10.getSpeciationsSum() != 1 ) {
 420             //                return false;
 421             //            }
 422             //            if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
 423             //                return false;
 424             //            }
 425             //            if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
 426             //                return false;
 427             //            }
 428             //            final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
 429             //            final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
 430             //            if ( sdi2_11.getDuplicationsSum() != 0 ) {
 431             //                return false;
 432             //            }
 433             //            if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
 434             //                return false;
 435             //            }
 436             //            if ( sdi2_11.getSpeciationsSum() != 1 ) {
 437             //                return false;
 438             //            }
 439             //            if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
 440             //                return false;
 441             //            }
 442             //            if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
 443             //                return false;
 444             //            }
 445             //            final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
 446             //            final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
 447             //            if ( sdi2_12.getDuplicationsSum() != 0 ) {
 448             //                return false;
 449             //            }
 450             //            if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
 451             //                return false;
 452             //            }
 453             //            if ( sdi2_12.getSpeciationsSum() != 1 ) {
 454             //                return false;
 455             //            }
 456             //            if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
 457             //                return false;
 458             //            }
 459             //            if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
 460             //                return false;
 461             //            }
 462             //            final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
 463             //            final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
 464             //            if ( sdi2_13.getDuplicationsSum() != 0 ) {
 465             //                return false;
 466             //            }
 467             //            if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
 468             //                return false;
 469             //            }
 470             //            if ( sdi2_13.getSpeciationsSum() != 1 ) {
 471             //                return false;
 472             //            }
 473             //            if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
 474             //                return false;
 475             //            }
 476             //            if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
 477             //                return false;
 478             //            }
 479             //            final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
 480             //            final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
 481             //            if ( sdi2_14.getDuplicationsSum() != 1 ) {
 482             //                return false;
 483             //            }
 484             //            if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
 485             //                return false;
 486             //            }
 487             //            if ( sdi2_14.getSpeciationsSum() != 1 ) {
 488             //                return false;
 489             //            }
 490             //            if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
 491             //                return false;
 492             //            }
 493             //            if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
 494             //                return false;
 495             //            }
 496             //            final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
 497             //            final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
 498             //            if ( sdi2_15.getDuplicationsSum() != 1 ) {
 499             //                return false;
 500             //            }
 501             //            if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
 502             //                return false;
 503             //            }
 504             //            if ( sdi2_15.getSpeciationsSum() != 1 ) {
 505             //                return false;
 506             //            }
 507             //            if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
 508             //                return false;
 509             //            }
 510             //            if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
 511             //                return false;
 512             //            }
 513             //            final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
 514             //            final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
 515             //            if ( sdi2_16.getDuplicationsSum() != 1 ) {
 516             //                return false;
 517             //            }
 518             //            if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
 519             //                return false;
 520             //            }
 521             //            if ( sdi2_16.getSpeciationsSum() != 1 ) {
 522             //                return false;
 523             //            }
 524             //            if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
 525             //                return false;
 526             //            }
 527             //            if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
 528             //                return false;
 529             //            }
 530             //            final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
 531             //            final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
 532             //            if ( sdi2_17.getDuplicationsSum() != 1 ) {
 533             //                return false;
 534             //            }
 535             //            if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
 536             //                return false;
 537             //            }
 538             //            if ( sdi2_17.getSpeciationsSum() != 1 ) {
 539             //                return false;
 540             //            }
 541             //            if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
 542             //                return false;
 543             //            }
 544             //            if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
 545             //                return false;
 546             //            }
 547             //            final Phylogeny g2_18 = TestGSDI
 548             //                    .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
 549             //            final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
 550             //            if ( sdi2_18.getDuplicationsSum() != 3 ) {
 551             //                return false;
 552             //            }
 553             //            if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
 554             //                return false;
 555             //            }
 556             //            if ( sdi2_18.getSpeciationsSum() != 0 ) {
 557             //                return false;
 558             //            }
 559             //            if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
 560             //                return false;
 561             //            }
 562             //            if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
 563             //                return false;
 564             //            }
 565             //            if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
 566             //                return false;
 567             //            }
 568             //            final Phylogeny g2_19 = TestGSDI
 569             //                    .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
 570             //            final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
 571             //            if ( sdi2_19.getDuplicationsSum() != 1 ) {
 572             //                return false;
 573             //            }
 574             //            if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
 575             //                return false;
 576             //            }
 577             //            if ( sdi2_19.getSpeciationsSum() != 2 ) {
 578             //                return false;
 579             //            }
 580             //            if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
 581             //                return false;
 582             //            }
 583             //            if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
 584             //                return false;
 585             //            }
 586             //            if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
 587             //                return false;
 588             //            }
 589             //            final Phylogeny g2_20 = TestGSDI
 590             //                    .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
 591             //            final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
 592             //            if ( sdi2_20.getDuplicationsSum() != 1 ) {
 593             //                return false;
 594             //            }
 595             //            if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
 596             //                return false;
 597             //            }
 598             //            if ( sdi2_20.getSpeciationsSum() != 2 ) {
 599             //                return false;
 600             //            }
 601             //            if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
 602             //                return false;
 603             //            }
 604             //            if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
 605             //                return false;
 606             //            }
 607             //            if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
 608             //                return false;
 609             //            }
 610             //            final Phylogeny g2_21 = TestGSDI
 611             //                    .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
 612             //            final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
 613             //            if ( sdi2_21.getDuplicationsSum() != 1 ) {
 614             //                return false;
 615             //            }
 616             //            if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
 617             //                return false;
 618             //            }
 619             //            if ( sdi2_21.getSpeciationsSum() != 2 ) {
 620             //                return false;
 621             //            }
 622             //            if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
 623             //                return false;
 624             //            }
 625             //            if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
 626             //                return false;
 627             //            }
 628             //            if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
 629             //                return false;
 630             //            }
 631             //            final Phylogeny g2_22 = TestGSDI
 632             //                    .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
 633             //            final GSDI sdi2_22 = new GSDI( g2_22, s2, false );
 634             //            //Archaeopteryx.createApplication( g2_22 );
 635             //            //Archaeopteryx.createApplication( s2 );
 636             //            if ( sdi2_22.getDuplicationsSum() != 0 ) {
 637             //                return false;
 638             //            }
 639             //            if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
 640             //                return false;
 641             //            }
 642             //            if ( sdi2_22.getSpeciationsSum() != 2 ) {
 643             //                return false;
 644             //            }
 645             //            if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
 646             //                return false;
 647             //            }
 648             //            if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
 649             //                return false;
 650             //            }
 651             //            if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
 652             //                return false;
 653             //            }
 654             //            final Phylogeny g2_23 = TestGSDI
 655             //                    .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
 656             //            final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
 657             //            if ( sdi2_23.getDuplicationsSum() != 0 ) {
 658             //                return false;
 659             //            }
 660             //            if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
 661             //                return false;
 662             //            }
 663             //            if ( sdi2_23.getSpeciationsSum() != 2 ) {
 664             //                return false;
 665             //            }
 666             //            if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
 667             //                return false;
 668             //            }
 669             //            if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
 670             //                return false;
 671             //            }
 672             //            if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
 673             //                return false;
 674             //            }
 675             //            final Phylogeny g2_24 = TestGSDI
 676             //                    .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
 677             //            final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
 678             //            if ( sdi2_24.getDuplicationsSum() != 0 ) {
 679             //                return false;
 680             //            }
 681             //            if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
 682             //                return false;
 683             //            }
 684             //            if ( sdi2_24.getSpeciationsSum() != 2 ) {
 685             //                return false;
 686             //            }
 687             //            if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
 688             //                return false;
 689             //            }
 690             //            if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
 691             //                return false;
 692             //            }
 693             //            if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
 694             //                return false;
 695             //            }
 696             //            final Phylogeny g2_25 = TestGSDI
 697             //                    .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
 698             //            final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
 699             //            if ( sdi2_25.getDuplicationsSum() != 0 ) {
 700             //                return false;
 701             //            }
 702             //            if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
 703             //                return false;
 704             //            }
 705             //            if ( sdi2_25.getSpeciationsSum() != 2 ) {
 706             //                return false;
 707             //            }
 708             //            if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
 709             //                return false;
 710             //            }
 711             //            if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
 712             //                return false;
 713             //            }
 714             //            if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
 715             //                return false;
 716             //            }
 717             //            final Phylogeny g2_26 = TestGSDI
 718             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
 719             //            final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
 720             //            if ( sdi2_26.getDuplicationsSum() != 0 ) {
 721             //                return false;
 722             //            }
 723             //            if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
 724             //                return false;
 725             //            }
 726             //            if ( sdi2_26.getSpeciationsSum() != 3 ) {
 727             //                return false;
 728             //            }
 729             //            if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
 730             //                return false;
 731             //            }
 732             //            if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
 733             //                return false;
 734             //            }
 735             //            if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
 736             //                return false;
 737             //            }
 738             //            final Phylogeny g2_27 = TestGSDI
 739             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
 740             //            final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
 741             //            if ( sdi2_27.getDuplicationsSum() != 0 ) {
 742             //                return false;
 743             //            }
 744             //            if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
 745             //                return false;
 746             //            }
 747             //            if ( sdi2_27.getSpeciationsSum() != 2 ) {
 748             //                return false;
 749             //            }
 750             //            if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
 751             //                return false;
 752             //            }
 753             //            if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
 754             //                return false;
 755             //            }
 756             //            if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
 757             //                return false;
 758             //            }
 759             //            final Phylogeny g2_28 = TestGSDI
 760             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
 761             //            final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
 762             //            if ( sdi2_28.getDuplicationsSum() != 0 ) {
 763             //                return false;
 764             //            }
 765             //            if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
 766             //                return false;
 767             //            }
 768             //            if ( sdi2_28.getSpeciationsSum() != 2 ) {
 769             //                return false;
 770             //            }
 771             //            if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
 772             //                return false;
 773             //            }
 774             //            if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
 775             //                return false;
 776             //            }
 777             //            if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
 778             //                return false;
 779             //            }
 780             //            final Phylogeny g2_29 = TestGSDI
 781             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
 782             //            final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
 783             //            if ( sdi2_29.getDuplicationsSum() != 0 ) {
 784             //                return false;
 785             //            }
 786             //            if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
 787             //                return false;
 788             //            }
 789             //            if ( sdi2_29.getSpeciationsSum() != 1 ) {
 790             //                return false;
 791             //            }
 792             //            if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
 793             //                return false;
 794             //            }
 795             //            if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
 796             //                return false;
 797             //            }
 798             //            if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
 799             //                return false;
 800             //            }
 801             //            final Phylogeny g2_30 = TestGSDI
 802             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
 803             //            final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
 804             //            if ( sdi2_30.getDuplicationsSum() != 1 ) {
 805             //                return false;
 806             //            }
 807             //            if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
 808             //                return false;
 809             //            }
 810             //            if ( sdi2_30.getSpeciationsSum() != 1 ) {
 811             //                return false;
 812             //            }
 813             //            if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
 814             //                return false;
 815             //            }
 816             //            if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
 817             //                return false;
 818             //            }
 819             //            if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
 820             //                return false;
 821             //            }
 822             //            final Phylogeny g2_31 = TestGSDI
 823             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
 824             //            final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
 825             //            if ( sdi2_31.getDuplicationsSum() != 1 ) {
 826             //                return false;
 827             //            }
 828             //            if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
 829             //                return false;
 830             //            }
 831             //            if ( sdi2_31.getSpeciationsSum() != 1 ) {
 832             //                return false;
 833             //            }
 834             //            if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
 835             //                return false;
 836             //            }
 837             //            if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
 838             //                return false;
 839             //            }
 840             //            if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
 841             //                return false;
 842             //            }
 843             //            final Phylogeny g2_32 = TestGSDI
 844             //                    .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])" );
 845             //            final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
 846             //            if ( sdi2_32.getDuplicationsSum() != 0 ) {
 847             //                return false;
 848             //            }
 849             //            if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
 850             //                return false;
 851             //            }
 852             //            if ( sdi2_32.getSpeciationsSum() != 3 ) {
 853             //                return false;
 854             //            }
 855             //            if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
 856             //                return false;
 857             //            }
 858             //            if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
 859             //                return false;
 860             //            }
 861             //            if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
 862             //                return false;
 863             //            }
 864             //            if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
 865             //                return false;
 866             //            }
 867             //            if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
 868             //                return false;
 869             //            }
 870             //            if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
 871             //                return false;
 872             //            }
 873             //            if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
 874             //                return false;
 875             //            }
 876             //            if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
 877             //                return false;
 878             //            }
 879             //            if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
 880             //                return false;
 881             //            }
 882             //            if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
 883             //                return false;
 884             //            }
 885             //            //            //-
 886             //            final Phylogeny g2_33_d = TestGSDI
 887             //                    .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=?])" );
 888             //            final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false );
 889             //            Archaeopteryx.createApplication( g2_33_d );
 890             //            //  Archaeopteryx.createApplication( s2 );
 891             //            //-
 892             //            final Phylogeny g2_33 = TestGSDI
 893             //                    .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])" );
 894             //            final GSDI sdi2_33 = new GSDI( g2_33, s2, false );
 895             //            Archaeopteryx.createApplication( g2_33 );
 896             //            Archaeopteryx.createApplication( s2 );
 897             //            if ( sdi2_33.getDuplicationsSum() != 1 ) {
 898             //                return false;
 899             //            }
 900             //            if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
 901             //                return false;
 902             //            }
 903             //            if ( sdi2_33.getSpeciationsSum() != 3 ) {
 904             //                return false;
 905             //            }
 906             //            if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
 907             //                return false;
 908             //            }
 909             //            if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
 910             //                return false;
 911             //            }
 912             //            if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
 913             //                return false;
 914             //            }
 915             //            if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
 916             //                return false;
 917             //            }
 918             //            if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
 919             //                return false;
 920             //            }
 921             //            if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
 922             //                return false;
 923             //            }
 924             //            if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
 925             //                return false;
 926             //            }
 927             //            if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
 928             //                return false;
 929             //            }
 930             //            if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
 931             //                return false;
 932             //            }
 933             //            if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
 934             //                return false;
 935             //            }
 936             //            if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
 937             //                return false;
 938             //            }
 939             //            final Phylogeny g2_34 = TestGSDI
 940             //                    .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])" );
 941             //            final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
 942             //            if ( sdi2_34.getDuplicationsSum() != 1 ) {
 943             //                return false;
 944             //            }
 945             //            if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
 946             //                return false;
 947             //            }
 948             //            if ( sdi2_34.getSpeciationsSum() != 2 ) {
 949             //                return false;
 950             //            }
 951             //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
 952             //                return false;
 953             //            }
 954             //            if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
 955             //                return false;
 956             //            }
 957             //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
 958             //                return false;
 959             //            }
 960             //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
 961             //                return false;
 962             //            }
 963             //            final Phylogeny g2_35 = TestGSDI
 964             //                    .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])" );
 965             //            final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
 966             //            if ( sdi2_35.getDuplicationsSum() != 1 ) {
 967             //                return false;
 968             //            }
 969             //            if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
 970             //                return false;
 971             //            }
 972             //            if ( sdi2_35.getSpeciationsSum() != 3 ) {
 973             //                return false;
 974             //            }
 975             //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
 976             //                return false;
 977             //            }
 978             //            if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
 979             //                return false;
 980             //            }
 981             //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
 982             //                return false;
 983             //            }
 984             //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
 985             //                return false;
 986             //            }
 987             //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
 988             //                return false;
 989             //            }
 990             //            final Phylogeny g2_36 = TestGSDI
 991             //                    .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])" );
 992             //            final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
 993             //            if ( sdi2_36.getDuplicationsSum() != 1 ) {
 994             //                return false;
 995             //            }
 996             //            if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
 997             //                return false;
 998             //            }
 999             //            if ( sdi2_36.getSpeciationsSum() != 2 ) {
1000             //                return false;
1001             //            }
1002             //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
1003             //                return false;
1004             //            }
1005             //            if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
1006             //                return false;
1007             //            }
1008             //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
1009             //                return false;
1010             //            }
1011             //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1012             //                return false;
1013             //            }
1014             //            final Phylogeny g2_37 = TestGSDI
1015             //                    .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])" );
1016             //            final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
1017             //            if ( sdi2_37.getDuplicationsSum() != 1 ) {
1018             //                return false;
1019             //            }
1020             //            if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
1021             //                return false;
1022             //            }
1023             //            if ( sdi2_37.getSpeciationsSum() != 2 ) {
1024             //                return false;
1025             //            }
1026             //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
1027             //                return false;
1028             //            }
1029             //            if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
1030             //                return false;
1031             //            }
1032             //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
1033             //                return false;
1034             //            }
1035             //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1036             //                return false;
1037             //            }
1038             //            final Phylogeny g2_38 = TestGSDI
1039             //                    .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
1040             //            final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
1041             //            if ( sdi2_38.getDuplicationsSum() != 5 ) {
1042             //                return false;
1043             //            }
1044             //            if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
1045             //                return false;
1046             //            }
1047             //            if ( sdi2_38.getSpeciationsSum() != 0 ) {
1048             //                return false;
1049             //            }
1050             //            final Phylogeny g2_100 = TestGSDI
1051             //                    .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])))" );
1052             //            final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
1053             //            if ( sdi2_100.getDuplicationsSum() != 4 ) {
1054             //                return false;
1055             //            }
1056             //            if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
1057             //                return false;
1058             //            }
1059             //            if ( sdi2_100.getSpeciationsSum() != 4 ) {
1060             //                return false;
1061             //            }
1062             //            if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
1063             //                return false;
1064             //            }
1065             //            if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
1066             //                return false;
1067             //            }
1068             //            if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
1069             //                return false;
1070             //            }
1071             //            if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
1072             //                return false;
1073             //            }
1074             //            if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
1075             //                return false;
1076             //            }
1077             //            if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
1078             //                return false;
1079             //            }
1080             //            if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
1081             //                return false;
1082             //            }
1083             //            if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
1084             //                return false;
1085             //            }
1086             //            final Phylogeny g2_101 = TestGSDI
1087             //                    .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])))" );
1088             //            final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
1089             //            if ( sdi2_101.getDuplicationsSum() != 2 ) {
1090             //                return false;
1091             //            }
1092             //            if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
1093             //                return false;
1094             //            }
1095             //            if ( sdi2_101.getSpeciationsSum() != 5 ) {
1096             //                return false;
1097             //            }
1098             //            if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
1099             //                return false;
1100             //            }
1101             //            if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
1102             //                return false;
1103             //            }
1104             //            if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
1105             //                return false;
1106             //            }
1107             //            if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
1108             //                return false;
1109             //            }
1110             //            if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
1111             //                return false;
1112             //            }
1113             //            if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
1114             //                return false;
1115             //            }
1116             //            if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
1117             //                return false;
1118             //            }
1119             //            if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
1120             //                return false;
1121             //            }
1122             //            final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
1123             //            DevelopmentTools.numberSpeciesInOrder( s_7_4 );
1124             //            final Phylogeny g_7_4_1 = TestGSDI
1125             //                    .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1126             //                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1127             //                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1128             //                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1129             //                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1130             //                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1131             //                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1132             //                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1133             //                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1134             //                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1135             //                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1136             //                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
1137             //            final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
1138             //            if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
1139             //                return false;
1140             //            }
1141             //            if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1142             //                return false;
1143             //            }
1144             //            if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
1145             //                return false;
1146             //            }
1147             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
1148             //                return false;
1149             //            }
1150             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
1151             //                return false;
1152             //            }
1153             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
1154             //                return false;
1155             //            }
1156             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
1157             //                return false;
1158             //            }
1159             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
1160             //                return false;
1161             //            }
1162             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
1163             //                return false;
1164             //            }
1165             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
1166             //                return false;
1167             //            }
1168             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
1169             //                return false;
1170             //            }
1171             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
1172             //                return false;
1173             //            }
1174             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
1175             //                return false;
1176             //            }
1177             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
1178             //                return false;
1179             //            }
1180             //            final Phylogeny g_7_4_2 = TestGSDI
1181             //                    .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1182             //                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1183             //                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1184             //                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1185             //                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1186             //                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1187             //                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1188             //                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1189             //                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1190             //                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1191             //                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1192             //                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
1193             //                            + "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])" );
1194             //            final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
1195             //            if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
1196             //                return false;
1197             //            }
1198             //            if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
1199             //                return false;
1200             //            }
1201             //            if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
1202             //                return false;
1203             //            }
1204             //---------------------
1205             //             final String g2_0_ =
1206             //             "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
1207             //             final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[
1208             //             0 ];
1209             //             g2_0.setRooted( true );
1210             //             final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
1211             //             if ( sdi2_0.getDuplicationsSum() != 0 ) {
1212             //             return false;
1213             //             }
1214             //             final String g2_1_= "";
1215             //             final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
1216             //             0 ];
1217             //             g2_1.setRooted( true );
1218             //             final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
1219             //             if ( sdi2_1.getDuplicationsSum() != 0 ) {
1220             //             return false;
1221             //             }
1222         }
1223         catch ( final Exception e ) {
1224             e.printStackTrace( System.out );
1225             return false;
1226         }
1227         return true;
1228     }
1229
1230     public static void main( final String[] args ) {
1231         if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
1232             System.out.println( "binary failed" );
1233         }
1234         if ( !TestGSDI.testGSDI_general() ) {
1235             System.out.println( "general failed" );
1236         }
1237         else {
1238             System.out.println( "general OK" );
1239         }
1240         //        boolean success = test();
1241         //        if ( success ) {
1242         //            System.out.println( "OK" );
1243         //        }
1244         //        else {
1245         //            System.out.println( "failed" );
1246         //        }
1247     }
1248 }