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