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.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;
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 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 ) {
123 if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
126 if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
127 .isSpeciationOrDuplication() ) {
130 if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) {
133 if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
142 if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
145 if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
148 if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
149 .isSpeciationOrDuplication() ) {
152 if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
161 if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
164 if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
167 if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
168 .isSpeciationOrDuplication() ) {
171 if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
180 if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
183 if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
186 if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
195 if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
198 if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
201 if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
204 if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
207 if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
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 ) {
222 if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
225 if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
228 if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
231 if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
234 if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
237 if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
240 if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
243 if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
246 if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
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 Archaeopteryx.createApplication( g2_22 );
633 Archaeopteryx.createApplication( s2 );
634 if ( sdi2_22.getDuplicationsSum() != 0 ) {
637 if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
640 if ( sdi2_22.getSpeciationsSum() != 2 ) {
643 if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
646 if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
649 if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
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 ) {
658 // if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
661 // if ( sdi2_23.getSpeciationsSum() != 2 ) {
664 // if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
667 // if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
670 // if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
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 ) {
679 // if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
682 // if ( sdi2_24.getSpeciationsSum() != 2 ) {
685 // if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
688 // if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
691 // if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
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 ) {
700 // if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
703 // if ( sdi2_25.getSpeciationsSum() != 2 ) {
706 // if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
709 // if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
712 // if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
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 ) {
721 // if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
724 // if ( sdi2_26.getSpeciationsSum() != 3 ) {
727 // if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
730 // if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
733 // if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
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 ) {
742 // if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
745 // if ( sdi2_27.getSpeciationsSum() != 2 ) {
748 // if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
751 // if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
754 // if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
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 ) {
763 // if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
766 // if ( sdi2_28.getSpeciationsSum() != 2 ) {
769 // if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
772 // if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
775 // if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
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 ) {
784 // if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
787 // if ( sdi2_29.getSpeciationsSum() != 1 ) {
790 // if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
793 // if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
796 // if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
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 ) {
805 // if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
808 // if ( sdi2_30.getSpeciationsSum() != 1 ) {
811 // if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
814 // if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
817 // if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
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 ) {
826 // if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
829 // if ( sdi2_31.getSpeciationsSum() != 1 ) {
832 // if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
835 // if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
838 // if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
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 ) {
847 // if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
850 // if ( sdi2_32.getSpeciationsSum() != 3 ) {
853 // if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
856 // if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
859 // if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
862 // if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
865 // if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
868 // if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
871 // if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
874 // if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
877 // if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
880 // if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
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 );
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 ) {
898 // if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
901 // if ( sdi2_33.getSpeciationsSum() != 3 ) {
904 // if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
907 // if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
910 // if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
913 // if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
916 // if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
919 // if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
922 // if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
925 // if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
928 // if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
931 // if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
934 // if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
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 ) {
943 // if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
946 // if ( sdi2_34.getSpeciationsSum() != 2 ) {
949 // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
952 // if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
955 // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
958 // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
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 ) {
967 // if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
970 // if ( sdi2_35.getSpeciationsSum() != 3 ) {
973 // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
976 // if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
979 // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
982 // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
985 // if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
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 ) {
994 // if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
997 // if ( sdi2_36.getSpeciationsSum() != 2 ) {
1000 // if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
1003 // if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
1006 // if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
1009 // if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
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 ) {
1018 // if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
1021 // if ( sdi2_37.getSpeciationsSum() != 2 ) {
1024 // if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
1027 // if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
1030 // if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
1033 // if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
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 ) {
1042 // if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
1045 // if ( sdi2_38.getSpeciationsSum() != 0 ) {
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 ) {
1054 // if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
1057 // if ( sdi2_100.getSpeciationsSum() != 4 ) {
1060 // if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
1063 // if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
1066 // if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
1069 // if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
1072 // if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
1075 // if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
1078 // if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
1081 // if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
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 ) {
1090 // if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
1093 // if ( sdi2_101.getSpeciationsSum() != 5 ) {
1096 // if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
1099 // if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
1102 // if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
1105 // if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
1108 // if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
1111 // if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
1114 // if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
1117 // if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
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 ) {
1139 // if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1142 // if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
1145 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
1148 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
1151 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
1154 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
1157 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
1160 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
1163 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
1166 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
1169 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
1172 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
1175 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
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 ) {
1196 // if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
1199 // if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
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() )[
1207 // g2_0.setRooted( true );
1208 // final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
1209 // if ( sdi2_0.getDuplicationsSum() != 0 ) {
1212 // final String g2_1_= "";
1213 // final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
1215 // g2_1.setRooted( true );
1216 // final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
1217 // if ( sdi2_1.getDuplicationsSum() != 0 ) {
1221 catch ( final Exception e ) {
1222 e.printStackTrace( System.out );
1228 public static void main( final String[] args ) {
1229 if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
1230 System.out.println( "binary failed" );
1232 if ( !TestGSDI.testGSDI_general() ) {
1233 System.out.println( "general failed" );
1235 // boolean success = test();
1237 // System.out.println( "OK" );
1240 // System.out.println( "failed" );