2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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.
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.
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
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.sdi;
28 import java.io.IOException;
30 import org.forester.development.DevelopmentTools;
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;
38 public final class TestGSDI {
40 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
41 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
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();
50 public static boolean test() {
51 if ( !TestGSDI.testGSDI_general() ) {
54 if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
60 private static boolean testGSDI_against_binary_gene_tree() {
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 ) {
81 if ( sdi.getDuplicationsSum() != 0 ) {
85 catch ( final Exception e ) {
86 e.printStackTrace( System.out );
92 private static boolean testGSDI_general() {
94 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
95 final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
96 final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
98 final Phylogeny g1 = TestGSDI
99 .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
100 final GSDI sdi1 = new GSDI( g1, s1, false );
101 if ( sdi1.getDuplicationsSum() != 1 ) {
104 if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
107 if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
108 .isSpeciationOrDuplication() ) {
111 if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) {
114 if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
117 final Phylogeny g2 = TestGSDI
118 .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
119 final GSDI sdi2 = new GSDI( g2, s1, false );
120 if ( sdi2.getDuplicationsSum() != 0 ) {
123 if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
126 if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
129 if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
130 .isSpeciationOrDuplication() ) {
133 if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
136 final Phylogeny g3 = TestGSDI
137 .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
138 final GSDI sdi3 = new GSDI( g3, s1, false );
139 if ( sdi3.getDuplicationsSum() != 0 ) {
142 if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
145 if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
148 if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
149 .isSpeciationOrDuplication() ) {
152 if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
155 final Phylogeny g4 = TestGSDI
156 .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
157 final GSDI sdi4 = new GSDI( g4, s1, false );
158 if ( sdi4.getDuplicationsSum() != 1 ) {
161 if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
164 if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
167 if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
170 final Phylogeny g5 = TestGSDI
171 .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]))" );
172 final GSDI sdi5 = new GSDI( g5, s1, false );
173 if ( sdi5.getDuplicationsSum() != 3 ) {
176 if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
179 if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
182 if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
185 if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
188 if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
191 final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
192 + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
193 + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
194 + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
195 + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
196 final Phylogeny gene7_2 = TestGSDI
197 .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])" );
198 gene7_2.setRooted( true );
199 final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
200 if ( sdi7_2.getDuplicationsSum() != 1 ) {
203 if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
206 if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
209 if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
212 if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
215 if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
218 if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
221 if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
224 if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
227 if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
230 final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
231 + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
232 + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
233 + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
234 + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
235 + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
236 + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
237 + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
238 + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
239 + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
240 + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
241 + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
242 + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
243 + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
244 + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
245 + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
246 + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
247 final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
248 s2.setRooted( true );
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 ) {
254 if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
257 if ( sdi2_0.getSpeciationsSum() != 1 ) {
260 if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
268 if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
271 if ( sdi2_1.getSpeciationsSum() != 1 ) {
274 if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
282 if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
285 if ( sdi2_2.getSpeciationsSum() != 1 ) {
288 if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
296 if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
299 if ( sdi2_3.getSpeciationsSum() != 0 ) {
302 if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
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 ) {
310 if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
313 if ( sdi2_4.getSpeciationsSum() != 2 ) {
316 if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
319 if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
327 if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
330 if ( sdi2_5.getSpeciationsSum() != 2 ) {
333 if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
336 if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
344 if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
347 if ( sdi2_6.getSpeciationsSum() != 2 ) {
350 if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
353 if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
361 if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
364 if ( sdi2_7.getSpeciationsSum() != 1 ) {
367 if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
370 if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
371 .isSpeciationOrDuplication() ) {
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 ) {
379 if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
382 if ( sdi2_8.getSpeciationsSum() != 1 ) {
385 if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
386 .isSpeciationOrDuplication() ) {
389 if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
397 if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
400 if ( sdi2_9.getSpeciationsSum() != 2 ) {
403 if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
406 if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
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 ) {
414 if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
417 if ( sdi2_10.getSpeciationsSum() != 1 ) {
420 if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
423 if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
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 ) {
431 if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
434 if ( sdi2_11.getSpeciationsSum() != 1 ) {
437 if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
440 if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
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 ) {
448 if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
451 if ( sdi2_12.getSpeciationsSum() != 1 ) {
454 if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
457 if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
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 ) {
465 if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
468 if ( sdi2_13.getSpeciationsSum() != 1 ) {
471 if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
474 if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
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 ) {
482 if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
485 if ( sdi2_14.getSpeciationsSum() != 1 ) {
488 if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
491 if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
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 ) {
499 if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
502 if ( sdi2_15.getSpeciationsSum() != 1 ) {
505 if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
508 if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
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 ) {
516 if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
519 if ( sdi2_16.getSpeciationsSum() != 1 ) {
522 if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
525 if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
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 ) {
533 if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
536 if ( sdi2_17.getSpeciationsSum() != 1 ) {
539 if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
542 if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
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 ) {
551 if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
554 if ( sdi2_18.getSpeciationsSum() != 0 ) {
557 if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
560 if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
563 if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
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 ) {
572 if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
575 if ( sdi2_19.getSpeciationsSum() != 2 ) {
578 if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
581 if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
584 if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
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 ) {
593 if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
596 if ( sdi2_20.getSpeciationsSum() != 2 ) {
599 if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
602 if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
605 if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
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 ) {
614 if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
617 if ( sdi2_21.getSpeciationsSum() != 2 ) {
620 if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
623 if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
626 if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
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 if ( sdi2_22.getDuplicationsSum() != 0 ) {
635 if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
638 if ( sdi2_22.getSpeciationsSum() != 2 ) {
641 if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
644 if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
647 if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
650 final Phylogeny g2_23 = TestGSDI
651 .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
652 final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
653 if ( sdi2_23.getDuplicationsSum() != 0 ) {
656 if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
659 if ( sdi2_23.getSpeciationsSum() != 2 ) {
662 if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
665 if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
668 if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
671 final Phylogeny g2_24 = TestGSDI
672 .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
673 final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
674 if ( sdi2_24.getDuplicationsSum() != 0 ) {
677 if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
680 if ( sdi2_24.getSpeciationsSum() != 2 ) {
683 if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
686 if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
689 if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
692 final Phylogeny g2_25 = TestGSDI
693 .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
694 final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
695 if ( sdi2_25.getDuplicationsSum() != 0 ) {
698 if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
701 if ( sdi2_25.getSpeciationsSum() != 2 ) {
704 if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
707 if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
710 if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
713 final Phylogeny g2_26 = TestGSDI
714 .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
715 final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
716 if ( sdi2_26.getDuplicationsSum() != 0 ) {
719 if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
722 if ( sdi2_26.getSpeciationsSum() != 3 ) {
725 if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
728 if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
731 if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
734 final Phylogeny g2_27 = TestGSDI
735 .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
736 final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
737 if ( sdi2_27.getDuplicationsSum() != 0 ) {
740 if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
743 if ( sdi2_27.getSpeciationsSum() != 2 ) {
746 if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
749 if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
752 if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
755 final Phylogeny g2_28 = TestGSDI
756 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
757 final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
758 if ( sdi2_28.getDuplicationsSum() != 0 ) {
761 if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
764 if ( sdi2_28.getSpeciationsSum() != 2 ) {
767 if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
770 if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
773 if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
776 final Phylogeny g2_29 = TestGSDI
777 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
778 final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
779 if ( sdi2_29.getDuplicationsSum() != 0 ) {
782 if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
785 if ( sdi2_29.getSpeciationsSum() != 1 ) {
788 if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
791 if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
794 if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
797 final Phylogeny g2_30 = TestGSDI
798 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
799 final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
800 if ( sdi2_30.getDuplicationsSum() != 1 ) {
803 if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
806 if ( sdi2_30.getSpeciationsSum() != 1 ) {
809 if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
812 if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
815 if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
818 final Phylogeny g2_31 = TestGSDI
819 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
820 final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
821 if ( sdi2_31.getDuplicationsSum() != 1 ) {
824 if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
827 if ( sdi2_31.getSpeciationsSum() != 1 ) {
830 if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
833 if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
836 if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
839 final Phylogeny g2_32 = TestGSDI
840 .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])" );
841 final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
842 if ( sdi2_32.getDuplicationsSum() != 0 ) {
845 if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
848 if ( sdi2_32.getSpeciationsSum() != 3 ) {
851 if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
854 if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
857 if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
860 if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
863 if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
866 if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
869 if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
872 if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
875 if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
878 if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
881 final Phylogeny g2_33 = TestGSDI
882 .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])" );
883 final GSDI sdi2_33 = new GSDI( g2_33, s2, false );
884 if ( sdi2_33.getDuplicationsSum() != 1 ) {
887 if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
890 if ( sdi2_33.getSpeciationsSum() != 3 ) {
893 if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
896 if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
899 if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
902 if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
905 if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
908 if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
911 if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
914 if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
917 if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
920 if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
923 if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
926 final Phylogeny g2_34 = TestGSDI
927 .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])" );
928 final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
929 if ( sdi2_34.getDuplicationsSum() != 1 ) {
932 if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
935 if ( sdi2_34.getSpeciationsSum() != 2 ) {
938 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
941 if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
944 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
947 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
950 final Phylogeny g2_35 = TestGSDI
951 .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])" );
952 final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
953 if ( sdi2_35.getDuplicationsSum() != 1 ) {
956 if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
959 if ( sdi2_35.getSpeciationsSum() != 3 ) {
962 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
965 if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
968 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
971 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
974 if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
977 final Phylogeny g2_36 = TestGSDI
978 .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])" );
979 final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
980 if ( sdi2_36.getDuplicationsSum() != 1 ) {
983 if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
986 if ( sdi2_36.getSpeciationsSum() != 2 ) {
989 if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
992 if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
995 if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
998 if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1001 final Phylogeny g2_37 = TestGSDI
1002 .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])" );
1003 final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
1004 if ( sdi2_37.getDuplicationsSum() != 1 ) {
1007 if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
1010 if ( sdi2_37.getSpeciationsSum() != 2 ) {
1013 if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
1016 if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
1019 if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
1022 if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1025 final Phylogeny g2_38 = TestGSDI
1026 .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
1027 final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
1028 if ( sdi2_38.getDuplicationsSum() != 5 ) {
1031 if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
1034 if ( sdi2_38.getSpeciationsSum() != 0 ) {
1037 final Phylogeny g2_100 = TestGSDI
1038 .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])))" );
1039 final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
1040 if ( sdi2_100.getDuplicationsSum() != 4 ) {
1043 if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
1046 if ( sdi2_100.getSpeciationsSum() != 4 ) {
1049 if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
1052 if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
1055 if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
1058 if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
1061 if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
1064 if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
1067 if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
1070 if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
1073 final Phylogeny g2_101 = TestGSDI
1074 .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])))" );
1075 final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
1076 if ( sdi2_101.getDuplicationsSum() != 2 ) {
1079 if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
1082 if ( sdi2_101.getSpeciationsSum() != 5 ) {
1085 if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
1088 if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
1091 if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
1094 if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
1097 if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
1100 if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
1103 if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
1106 if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
1109 final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
1110 DevelopmentTools.numberSpeciesInOrder( s_7_4 );
1111 final Phylogeny g_7_4_1 = TestGSDI
1112 .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1113 + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1114 + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1115 + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1116 + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1117 + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1118 + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1119 + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1120 + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1121 + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1122 + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1123 + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
1124 final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
1125 if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
1128 if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1131 if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
1134 if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
1137 if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
1140 if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
1143 if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
1146 if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
1149 if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
1152 if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
1155 if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
1158 if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
1161 if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
1164 if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
1167 final Phylogeny g_7_4_2 = TestGSDI
1168 .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1169 + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1170 + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1171 + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1172 + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1173 + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1174 + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1175 + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1176 + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1177 + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1178 + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1179 + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
1180 + "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])" );
1181 final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
1182 if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
1185 if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
1188 if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
1191 // final String g2_0_ =
1192 // "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
1193 // final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[
1195 // g2_0.setRooted( true );
1196 // final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
1197 // if ( sdi2_0.getDuplicationsSum() != 0 ) {
1200 // final String g2_1_= "";
1201 // final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
1203 // g2_1.setRooted( true );
1204 // final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
1205 // if ( sdi2_1.getDuplicationsSum() != 0 ) {
1209 catch ( final Exception e ) {
1210 e.printStackTrace( System.out );