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             final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
 250             final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
 251             if ( sdi2_0.getDuplicationsSum() != 0 ) {
 252                 return false;
 253             }
 254             if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
 255                 return false;
 256             }
 257             if ( sdi2_0.getSpeciationsSum() != 1 ) {
 258                 return false;
 259             }
 260             if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
 261                 return false;
 262             }
 263             final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
 264             final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
 265             if ( sdi2_1.getDuplicationsSum() != 0 ) {
 266                 return false;
 267             }
 268             if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
 269                 return false;
 270             }
 271             if ( sdi2_1.getSpeciationsSum() != 1 ) {
 272                 return false;
 273             }
 274             if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
 275                 return false;
 276             }
 277             final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
 278             final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
 279             if ( sdi2_2.getDuplicationsSum() != 0 ) {
 280                 return false;
 281             }
 282             if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
 283                 return false;
 284             }
 285             if ( sdi2_2.getSpeciationsSum() != 1 ) {
 286                 return false;
 287             }
 288             if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
 289                 return false;
 290             }
 291             final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
 292             final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
 293             if ( sdi2_3.getDuplicationsSum() != 1 ) {
 294                 return false;
 295             }
 296             if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
 297                 return false;
 298             }
 299             if ( sdi2_3.getSpeciationsSum() != 0 ) {
 300                 return false;
 301             }
 302             if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
 303                 return false;
 304             }
 305             final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
 306             final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
 307             if ( sdi2_4.getDuplicationsSum() != 0 ) {
 308                 return false;
 309             }
 310             if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
 311                 return false;
 312             }
 313             if ( sdi2_4.getSpeciationsSum() != 2 ) {
 314                 return false;
 315             }
 316             if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
 317                 return false;
 318             }
 319             if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
 320                 return false;
 321             }
 322             final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
 323             final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
 324             if ( sdi2_5.getDuplicationsSum() != 0 ) {
 325                 return false;
 326             }
 327             if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
 328                 return false;
 329             }
 330             if ( sdi2_5.getSpeciationsSum() != 2 ) {
 331                 return false;
 332             }
 333             if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
 334                 return false;
 335             }
 336             if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
 337                 return false;
 338             }
 339             final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
 340             final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
 341             if ( sdi2_6.getDuplicationsSum() != 0 ) {
 342                 return false;
 343             }
 344             if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
 345                 return false;
 346             }
 347             if ( sdi2_6.getSpeciationsSum() != 2 ) {
 348                 return false;
 349             }
 350             if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
 351                 return false;
 352             }
 353             if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
 354                 return false;
 355             }
 356             final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
 357             final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
 358             if ( sdi2_7.getDuplicationsSum() != 0 ) {
 359                 return false;
 360             }
 361             if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
 362                 return false;
 363             }
 364             if ( sdi2_7.getSpeciationsSum() != 1 ) {
 365                 return false;
 366             }
 367             if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
 368                 return false;
 369             }
 370             if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
 371                     .isSpeciationOrDuplication() ) {
 372                 return false;
 373             }
 374             final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
 375             final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
 376             if ( sdi2_8.getDuplicationsSum() != 0 ) {
 377                 return false;
 378             }
 379             if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
 380                 return false;
 381             }
 382             if ( sdi2_8.getSpeciationsSum() != 1 ) {
 383                 return false;
 384             }
 385             if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
 386                     .isSpeciationOrDuplication() ) {
 387                 return false;
 388             }
 389             if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
 390                 return false;
 391             }
 392             final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
 393             final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
 394             if ( sdi2_9.getDuplicationsSum() != 0 ) {
 395                 return false;
 396             }
 397             if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
 398                 return false;
 399             }
 400             if ( sdi2_9.getSpeciationsSum() != 2 ) {
 401                 return false;
 402             }
 403             if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
 404                 return false;
 405             }
 406             if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
 407                 return false;
 408             }
 409             final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
 410             final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
 411             if ( sdi2_10.getDuplicationsSum() != 0 ) {
 412                 return false;
 413             }
 414             if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
 415                 return false;
 416             }
 417             if ( sdi2_10.getSpeciationsSum() != 1 ) {
 418                 return false;
 419             }
 420             if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
 421                 return false;
 422             }
 423             if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
 424                 return false;
 425             }
 426             final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
 427             final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
 428             if ( sdi2_11.getDuplicationsSum() != 0 ) {
 429                 return false;
 430             }
 431             if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
 432                 return false;
 433             }
 434             if ( sdi2_11.getSpeciationsSum() != 1 ) {
 435                 return false;
 436             }
 437             if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
 438                 return false;
 439             }
 440             if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
 441                 return false;
 442             }
 443             final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
 444             final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
 445             if ( sdi2_12.getDuplicationsSum() != 0 ) {
 446                 return false;
 447             }
 448             if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
 449                 return false;
 450             }
 451             if ( sdi2_12.getSpeciationsSum() != 1 ) {
 452                 return false;
 453             }
 454             if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
 455                 return false;
 456             }
 457             if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
 458                 return false;
 459             }
 460             final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
 461             final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
 462             if ( sdi2_13.getDuplicationsSum() != 0 ) {
 463                 return false;
 464             }
 465             if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
 466                 return false;
 467             }
 468             if ( sdi2_13.getSpeciationsSum() != 1 ) {
 469                 return false;
 470             }
 471             if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
 472                 return false;
 473             }
 474             if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
 475                 return false;
 476             }
 477             final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
 478             final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
 479             if ( sdi2_14.getDuplicationsSum() != 1 ) {
 480                 return false;
 481             }
 482             if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
 483                 return false;
 484             }
 485             if ( sdi2_14.getSpeciationsSum() != 1 ) {
 486                 return false;
 487             }
 488             if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
 489                 return false;
 490             }
 491             if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
 492                 return false;
 493             }
 494             final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
 495             final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
 496             if ( sdi2_15.getDuplicationsSum() != 1 ) {
 497                 return false;
 498             }
 499             if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
 500                 return false;
 501             }
 502             if ( sdi2_15.getSpeciationsSum() != 1 ) {
 503                 return false;
 504             }
 505             if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
 506                 return false;
 507             }
 508             if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
 509                 return false;
 510             }
 511             final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
 512             final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
 513             if ( sdi2_16.getDuplicationsSum() != 1 ) {
 514                 return false;
 515             }
 516             if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
 517                 return false;
 518             }
 519             if ( sdi2_16.getSpeciationsSum() != 1 ) {
 520                 return false;
 521             }
 522             if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
 523                 return false;
 524             }
 525             if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
 526                 return false;
 527             }
 528             final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
 529             final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
 530             if ( sdi2_17.getDuplicationsSum() != 1 ) {
 531                 return false;
 532             }
 533             if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
 534                 return false;
 535             }
 536             if ( sdi2_17.getSpeciationsSum() != 1 ) {
 537                 return false;
 538             }
 539             if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
 540                 return false;
 541             }
 542             if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
 543                 return false;
 544             }
 545             final Phylogeny g2_18 = TestGSDI
 546                     .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
 547             final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
 548             if ( sdi2_18.getDuplicationsSum() != 3 ) {
 549                 return false;
 550             }
 551             if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
 552                 return false;
 553             }
 554             if ( sdi2_18.getSpeciationsSum() != 0 ) {
 555                 return false;
 556             }
 557             if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
 558                 return false;
 559             }
 560             if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
 561                 return false;
 562             }
 563             if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
 564                 return false;
 565             }
 566             final Phylogeny g2_19 = TestGSDI
 567                     .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
 568             final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
 569             if ( sdi2_19.getDuplicationsSum() != 1 ) {
 570                 return false;
 571             }
 572             if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
 573                 return false;
 574             }
 575             if ( sdi2_19.getSpeciationsSum() != 2 ) {
 576                 return false;
 577             }
 578             if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
 579                 return false;
 580             }
 581             if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
 582                 return false;
 583             }
 584             if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
 585                 return false;
 586             }
 587             final Phylogeny g2_20 = TestGSDI
 588                     .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
 589             final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
 590             if ( sdi2_20.getDuplicationsSum() != 1 ) {
 591                 return false;
 592             }
 593             if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
 594                 return false;
 595             }
 596             if ( sdi2_20.getSpeciationsSum() != 2 ) {
 597                 return false;
 598             }
 599             if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
 600                 return false;
 601             }
 602             if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
 603                 return false;
 604             }
 605             if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
 606                 return false;
 607             }
 608             final Phylogeny g2_21 = TestGSDI
 609                     .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
 610             final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
 611             if ( sdi2_21.getDuplicationsSum() != 1 ) {
 612                 return false;
 613             }
 614             if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
 615                 return false;
 616             }
 617             if ( sdi2_21.getSpeciationsSum() != 2 ) {
 618                 return false;
 619             }
 620             if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
 621                 return false;
 622             }
 623             if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
 624                 return false;
 625             }
 626             if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
 627                 return false;
 628             }
 629             final Phylogeny g2_22 = TestGSDI
 630                     .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
 631             final GSDI sdi2_22 = new GSDI( g2_22, s2, false );
 632             Archaeopteryx.createApplication( g2_22 );
 633             Archaeopteryx.createApplication( s2 );
 634             if ( sdi2_22.getDuplicationsSum() != 0 ) {
 635                 return false;
 636             }
 637             if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
 638                 return false;
 639             }
 640             if ( sdi2_22.getSpeciationsSum() != 2 ) {
 641                 return false;
 642             }
 643             if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
 644                 return false;
 645             }
 646             if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
 647                 return false;
 648             }
 649             if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
 650                 return false;
 651             }
 652             //            final Phylogeny g2_23 = TestGSDI
 653             //                    .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
 654             //            final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
 655             //            if ( sdi2_23.getDuplicationsSum() != 0 ) {
 656             //                return false;
 657             //            }
 658             //            if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
 659             //                return false;
 660             //            }
 661             //            if ( sdi2_23.getSpeciationsSum() != 2 ) {
 662             //                return false;
 663             //            }
 664             //            if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
 665             //                return false;
 666             //            }
 667             //            if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
 668             //                return false;
 669             //            }
 670             //            if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
 671             //                return false;
 672             //            }
 673             //            final Phylogeny g2_24 = TestGSDI
 674             //                    .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
 675             //            final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
 676             //            if ( sdi2_24.getDuplicationsSum() != 0 ) {
 677             //                return false;
 678             //            }
 679             //            if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
 680             //                return false;
 681             //            }
 682             //            if ( sdi2_24.getSpeciationsSum() != 2 ) {
 683             //                return false;
 684             //            }
 685             //            if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
 686             //                return false;
 687             //            }
 688             //            if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
 689             //                return false;
 690             //            }
 691             //            if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
 692             //                return false;
 693             //            }
 694             //            final Phylogeny g2_25 = TestGSDI
 695             //                    .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
 696             //            final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
 697             //            if ( sdi2_25.getDuplicationsSum() != 0 ) {
 698             //                return false;
 699             //            }
 700             //            if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
 701             //                return false;
 702             //            }
 703             //            if ( sdi2_25.getSpeciationsSum() != 2 ) {
 704             //                return false;
 705             //            }
 706             //            if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
 707             //                return false;
 708             //            }
 709             //            if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
 710             //                return false;
 711             //            }
 712             //            if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
 713             //                return false;
 714             //            }
 715             //            final Phylogeny g2_26 = TestGSDI
 716             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
 717             //            final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
 718             //            if ( sdi2_26.getDuplicationsSum() != 0 ) {
 719             //                return false;
 720             //            }
 721             //            if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
 722             //                return false;
 723             //            }
 724             //            if ( sdi2_26.getSpeciationsSum() != 3 ) {
 725             //                return false;
 726             //            }
 727             //            if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
 728             //                return false;
 729             //            }
 730             //            if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
 731             //                return false;
 732             //            }
 733             //            if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
 734             //                return false;
 735             //            }
 736             //            final Phylogeny g2_27 = TestGSDI
 737             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
 738             //            final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
 739             //            if ( sdi2_27.getDuplicationsSum() != 0 ) {
 740             //                return false;
 741             //            }
 742             //            if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
 743             //                return false;
 744             //            }
 745             //            if ( sdi2_27.getSpeciationsSum() != 2 ) {
 746             //                return false;
 747             //            }
 748             //            if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
 749             //                return false;
 750             //            }
 751             //            if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
 752             //                return false;
 753             //            }
 754             //            if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
 755             //                return false;
 756             //            }
 757             //            final Phylogeny g2_28 = TestGSDI
 758             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
 759             //            final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
 760             //            if ( sdi2_28.getDuplicationsSum() != 0 ) {
 761             //                return false;
 762             //            }
 763             //            if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
 764             //                return false;
 765             //            }
 766             //            if ( sdi2_28.getSpeciationsSum() != 2 ) {
 767             //                return false;
 768             //            }
 769             //            if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
 770             //                return false;
 771             //            }
 772             //            if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
 773             //                return false;
 774             //            }
 775             //            if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
 776             //                return false;
 777             //            }
 778             //            final Phylogeny g2_29 = TestGSDI
 779             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
 780             //            final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
 781             //            if ( sdi2_29.getDuplicationsSum() != 0 ) {
 782             //                return false;
 783             //            }
 784             //            if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
 785             //                return false;
 786             //            }
 787             //            if ( sdi2_29.getSpeciationsSum() != 1 ) {
 788             //                return false;
 789             //            }
 790             //            if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
 791             //                return false;
 792             //            }
 793             //            if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
 794             //                return false;
 795             //            }
 796             //            if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
 797             //                return false;
 798             //            }
 799             //            final Phylogeny g2_30 = TestGSDI
 800             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
 801             //            final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
 802             //            if ( sdi2_30.getDuplicationsSum() != 1 ) {
 803             //                return false;
 804             //            }
 805             //            if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
 806             //                return false;
 807             //            }
 808             //            if ( sdi2_30.getSpeciationsSum() != 1 ) {
 809             //                return false;
 810             //            }
 811             //            if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
 812             //                return false;
 813             //            }
 814             //            if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
 815             //                return false;
 816             //            }
 817             //            if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
 818             //                return false;
 819             //            }
 820             //            final Phylogeny g2_31 = TestGSDI
 821             //                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
 822             //            final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
 823             //            if ( sdi2_31.getDuplicationsSum() != 1 ) {
 824             //                return false;
 825             //            }
 826             //            if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
 827             //                return false;
 828             //            }
 829             //            if ( sdi2_31.getSpeciationsSum() != 1 ) {
 830             //                return false;
 831             //            }
 832             //            if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
 833             //                return false;
 834             //            }
 835             //            if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
 836             //                return false;
 837             //            }
 838             //            if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
 839             //                return false;
 840             //            }
 841             //            final Phylogeny g2_32 = TestGSDI
 842             //                    .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])" );
 843             //            final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
 844             //            if ( sdi2_32.getDuplicationsSum() != 0 ) {
 845             //                return false;
 846             //            }
 847             //            if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
 848             //                return false;
 849             //            }
 850             //            if ( sdi2_32.getSpeciationsSum() != 3 ) {
 851             //                return false;
 852             //            }
 853             //            if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
 854             //                return false;
 855             //            }
 856             //            if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
 857             //                return false;
 858             //            }
 859             //            if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
 860             //                return false;
 861             //            }
 862             //            if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
 863             //                return false;
 864             //            }
 865             //            if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
 866             //                return false;
 867             //            }
 868             //            if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
 869             //                return false;
 870             //            }
 871             //            if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
 872             //                return false;
 873             //            }
 874             //            if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
 875             //                return false;
 876             //            }
 877             //            if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
 878             //                return false;
 879             //            }
 880             //            if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
 881             //                return false;
 882             //            }
 883             //            //-
 884             //            final Phylogeny g2_33_d = TestGSDI
 885             //                    .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=?])" );
 886             //            final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false );
 887             //            Archaeopteryx.createApplication( g2_33_d );
 888             //            //  Archaeopteryx.createApplication( s2 );
 889             //            //-
 890             //            final Phylogeny g2_33 = TestGSDI
 891             //                    .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])" );
 892             //            final GSDI sdi2_33 = new GSDI( g2_33, s2, false );
 893             //            Archaeopteryx.createApplication( g2_33 );
 894             //            // Archaeopteryx.createApplication( s2 );
 895             //            if ( sdi2_33.getDuplicationsSum() != 1 ) {
 896             //                return false;
 897             //            }
 898             //            if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
 899             //                return false;
 900             //            }
 901             //            if ( sdi2_33.getSpeciationsSum() != 3 ) {
 902             //                return false;
 903             //            }
 904             //            if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
 905             //                return false;
 906             //            }
 907             //            if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
 908             //                return false;
 909             //            }
 910             //            if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
 911             //                return false;
 912             //            }
 913             //            if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
 914             //                return false;
 915             //            }
 916             //            if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
 917             //                return false;
 918             //            }
 919             //            if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
 920             //                return false;
 921             //            }
 922             //            if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
 923             //                return false;
 924             //            }
 925             //            if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
 926             //                return false;
 927             //            }
 928             //            if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
 929             //                return false;
 930             //            }
 931             //            if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
 932             //                return false;
 933             //            }
 934             //            if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
 935             //                return false;
 936             //            }
 937             //            final Phylogeny g2_34 = TestGSDI
 938             //                    .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])" );
 939             //            final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
 940             //            if ( sdi2_34.getDuplicationsSum() != 1 ) {
 941             //                return false;
 942             //            }
 943             //            if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
 944             //                return false;
 945             //            }
 946             //            if ( sdi2_34.getSpeciationsSum() != 2 ) {
 947             //                return false;
 948             //            }
 949             //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
 950             //                return false;
 951             //            }
 952             //            if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
 953             //                return false;
 954             //            }
 955             //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
 956             //                return false;
 957             //            }
 958             //            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
 959             //                return false;
 960             //            }
 961             //            final Phylogeny g2_35 = TestGSDI
 962             //                    .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])" );
 963             //            final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
 964             //            if ( sdi2_35.getDuplicationsSum() != 1 ) {
 965             //                return false;
 966             //            }
 967             //            if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
 968             //                return false;
 969             //            }
 970             //            if ( sdi2_35.getSpeciationsSum() != 3 ) {
 971             //                return false;
 972             //            }
 973             //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
 974             //                return false;
 975             //            }
 976             //            if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
 977             //                return false;
 978             //            }
 979             //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
 980             //                return false;
 981             //            }
 982             //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
 983             //                return false;
 984             //            }
 985             //            if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
 986             //                return false;
 987             //            }
 988             //            final Phylogeny g2_36 = TestGSDI
 989             //                    .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])" );
 990             //            final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
 991             //            if ( sdi2_36.getDuplicationsSum() != 1 ) {
 992             //                return false;
 993             //            }
 994             //            if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
 995             //                return false;
 996             //            }
 997             //            if ( sdi2_36.getSpeciationsSum() != 2 ) {
 998             //                return false;
 999             //            }
1000             //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
1001             //                return false;
1002             //            }
1003             //            if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
1004             //                return false;
1005             //            }
1006             //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
1007             //                return false;
1008             //            }
1009             //            if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1010             //                return false;
1011             //            }
1012             //            final Phylogeny g2_37 = TestGSDI
1013             //                    .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])" );
1014             //            final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
1015             //            if ( sdi2_37.getDuplicationsSum() != 1 ) {
1016             //                return false;
1017             //            }
1018             //            if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
1019             //                return false;
1020             //            }
1021             //            if ( sdi2_37.getSpeciationsSum() != 2 ) {
1022             //                return false;
1023             //            }
1024             //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
1025             //                return false;
1026             //            }
1027             //            if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
1028             //                return false;
1029             //            }
1030             //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
1031             //                return false;
1032             //            }
1033             //            if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1034             //                return false;
1035             //            }
1036             //            final Phylogeny g2_38 = TestGSDI
1037             //                    .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
1038             //            final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
1039             //            if ( sdi2_38.getDuplicationsSum() != 5 ) {
1040             //                return false;
1041             //            }
1042             //            if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
1043             //                return false;
1044             //            }
1045             //            if ( sdi2_38.getSpeciationsSum() != 0 ) {
1046             //                return false;
1047             //            }
1048             //            final Phylogeny g2_100 = TestGSDI
1049             //                    .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])))" );
1050             //            final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
1051             //            if ( sdi2_100.getDuplicationsSum() != 4 ) {
1052             //                return false;
1053             //            }
1054             //            if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
1055             //                return false;
1056             //            }
1057             //            if ( sdi2_100.getSpeciationsSum() != 4 ) {
1058             //                return false;
1059             //            }
1060             //            if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
1061             //                return false;
1062             //            }
1063             //            if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
1064             //                return false;
1065             //            }
1066             //            if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
1067             //                return false;
1068             //            }
1069             //            if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
1070             //                return false;
1071             //            }
1072             //            if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
1073             //                return false;
1074             //            }
1075             //            if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
1076             //                return false;
1077             //            }
1078             //            if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
1079             //                return false;
1080             //            }
1081             //            if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
1082             //                return false;
1083             //            }
1084             //            final Phylogeny g2_101 = TestGSDI
1085             //                    .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])))" );
1086             //            final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
1087             //            if ( sdi2_101.getDuplicationsSum() != 2 ) {
1088             //                return false;
1089             //            }
1090             //            if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
1091             //                return false;
1092             //            }
1093             //            if ( sdi2_101.getSpeciationsSum() != 5 ) {
1094             //                return false;
1095             //            }
1096             //            if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
1097             //                return false;
1098             //            }
1099             //            if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
1100             //                return false;
1101             //            }
1102             //            if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
1103             //                return false;
1104             //            }
1105             //            if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
1106             //                return false;
1107             //            }
1108             //            if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
1109             //                return false;
1110             //            }
1111             //            if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
1112             //                return false;
1113             //            }
1114             //            if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
1115             //                return false;
1116             //            }
1117             //            if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
1118             //                return false;
1119             //            }
1120             //            final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
1121             //            DevelopmentTools.numberSpeciesInOrder( s_7_4 );
1122             //            final Phylogeny g_7_4_1 = TestGSDI
1123             //                    .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1124             //                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1125             //                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1126             //                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1127             //                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1128             //                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1129             //                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1130             //                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1131             //                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1132             //                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1133             //                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1134             //                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
1135             //            final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
1136             //            if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
1137             //                return false;
1138             //            }
1139             //            if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1140             //                return false;
1141             //            }
1142             //            if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
1143             //                return false;
1144             //            }
1145             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
1146             //                return false;
1147             //            }
1148             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
1149             //                return false;
1150             //            }
1151             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
1152             //                return false;
1153             //            }
1154             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
1155             //                return false;
1156             //            }
1157             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
1158             //                return false;
1159             //            }
1160             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
1161             //                return false;
1162             //            }
1163             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
1164             //                return false;
1165             //            }
1166             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
1167             //                return false;
1168             //            }
1169             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
1170             //                return false;
1171             //            }
1172             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
1173             //                return false;
1174             //            }
1175             //            if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
1176             //                return false;
1177             //            }
1178             //            final Phylogeny g_7_4_2 = TestGSDI
1179             //                    .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1180             //                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1181             //                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1182             //                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1183             //                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1184             //                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1185             //                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1186             //                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1187             //                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1188             //                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1189             //                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1190             //                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
1191             //                            + "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])" );
1192             //            final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
1193             //            if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
1194             //                return false;
1195             //            }
1196             //            if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
1197             //                return false;
1198             //            }
1199             //            if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
1200             //                return false;
1201             //            }
1202             //---------------------
1203             // final String g2_0_ =
1204             // "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
1205             // final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[
1206             // 0 ];
1207             // g2_0.setRooted( true );
1208             // final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
1209             // if ( sdi2_0.getDuplicationsSum() != 0 ) {
1210             // return false;
1211             // }
1212             // final String g2_1_= "";
1213             // final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
1214             // 0 ];
1215             // g2_1.setRooted( true );
1216             // final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
1217             // if ( sdi2_1.getDuplicationsSum() != 0 ) {
1218             // return false;
1219             // }
1220         }
1221         catch ( final Exception e ) {
1222             e.printStackTrace( System.out );
1223             return false;
1224         }
1225         return true;
1226     }
1227
1228     public static void main( final String[] args ) {
1229         if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
1230             System.out.println( "binary failed" );
1231         }
1232         if ( !TestGSDI.testGSDI_general() ) {
1233             System.out.println( "general failed" );
1234         }
1235         //        boolean success = test();
1236         //        if ( success ) {
1237         //            System.out.println( "OK" );
1238         //        }
1239         //        else {
1240         //            System.out.println( "failed" );
1241         //        }
1242     }
1243 }