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: https://sites.google.com/site/cmzmasek/home/software/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.io.parsers.util.ParserUtils;
33 import org.forester.phylogeny.Phylogeny;
34 import org.forester.phylogeny.PhylogenyMethods;
35 import org.forester.phylogeny.data.Event;
36 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
37 import org.forester.phylogeny.factories.PhylogenyFactory;
38 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
39 import org.forester.util.ForesterUtil;
41 public final class TestGSDI {
43 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
44 + "test_data" + ForesterUtil.getFileSeparator();
46 public static void main( final String[] args ) {
47 if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
48 System.out.println( "binary failed" );
50 if ( !TestGSDI.testGSDI_general() ) {
51 System.out.println( "general failed" );
53 if ( !TestGSDI.testGSDIR_general() ) {
54 System.out.println( "general re-rooting failed" );
57 System.out.println( "OK" );
59 // boolean success = test();
61 // System.out.println( "OK" );
64 // System.out.println( "failed" );
68 public static boolean test() {
69 if ( !TestGSDI.testGSDI_general() ) {
72 if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
75 if ( !TestGSDI.testGSDIR_general() ) {
81 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
82 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
87 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
88 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
91 private static boolean testGSDI_against_binary_gene_tree() {
93 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
94 final String multi_species_2_str = "(((((([&&NHX:S=1],[&&NHX:S=2]),"
95 + "([&&NHX:S=3],[&&NHX:S=4],[&&NHX:S=5])),"
96 + "([&&NHX:S=6],[&&NHX:S=7],[&&NHX:S=8],[&&NHX:S=9])),"
97 + "([&&NHX:S=10],[&&NHX:S=11])),"
98 + "([&&NHX:S=12],[&&NHX:S=13],[&&NHX:S=14])),"
99 + "([&&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])));";
100 final String gene_2_1_str = "(((((([&&NHX:S=1],[&&NHX:S=2])1_2,([&&NHX:S=3],[&&NHX:S=4])),"
101 + "([&&NHX:S=6],[&&NHX:S=7])6_7_8_9)1_9,([&&NHX:S=10],[&&NHX:S=11])),"
102 + "([&&NHX:S=12],[&&NHX:S=13])12_13_14)1_14,"
103 + "([&&NHX:S=15],([&&NHX:S=21],[&&NHX:S=24])21_22_23_24)15_24);";
104 final Phylogeny multi_species_2 = factory.create( multi_species_2_str, new NHXParser() )[ 0 ];
105 final Phylogeny gene_2_1 = factory.create( gene_2_1_str, new NHXParser() )[ 0 ];
106 multi_species_2.setRooted( true );
107 gene_2_1.setRooted( true );
108 final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false, false, false );
109 if ( sdi.getSpeciationOrDuplicationEventsSum() != 0 ) {
112 if ( sdi.getDuplicationsSum() != 0 ) {
116 catch ( final Exception e ) {
117 e.printStackTrace( System.out );
123 private static boolean testGSDI_general() {
125 final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
126 + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
127 + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
128 + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
129 + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
130 + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
131 + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
132 + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
133 + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
134 + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
135 + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
136 + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
137 + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
138 + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
139 + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
140 + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
141 + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
142 final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
143 s2.setRooted( true );
144 final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
145 final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
146 s1.setRooted( true );
147 final Phylogeny g1 = TestGSDI
148 .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
149 final GSDI sdi1 = new GSDI( g1, s1, false, false, false );
150 // Archaeopteryx.createApplication( g1 );
151 // Archaeopteryx.createApplication( s1 );
152 if ( sdi1.getDuplicationsSum() != 1 ) {
155 if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
159 if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
160 .isSpeciationOrDuplication() ) {
163 if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
164 .isDuplication() ) ) {
167 if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
171 final Phylogeny g2 = TestGSDI
172 .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
173 final GSDI sdi2 = new GSDI( g2, s1, false, false, false );
174 if ( sdi2.getDuplicationsSum() != 0 ) {
177 if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent()
181 if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent()
185 if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
186 .isSpeciationOrDuplication() ) {
189 if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent()
193 final Phylogeny g3 = TestGSDI
194 .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
195 final GSDI sdi3 = new GSDI( g3, s1, false, false, false );
196 if ( sdi3.getDuplicationsSum() != 0 ) {
199 if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent()
203 if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent()
207 if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
208 .isSpeciationOrDuplication() ) {
211 if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent()
215 final Phylogeny g4 = TestGSDI
216 .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
217 final GSDI sdi4 = new GSDI( g4, s1, false, false, false );
218 if ( sdi4.getDuplicationsSum() != 1 ) {
221 if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent()
225 if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent()
229 if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent()
233 final Phylogeny g5 = TestGSDI
234 .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]))" );
235 final GSDI sdi5 = new GSDI( g5, s1, false, false, false );
236 if ( sdi5.getDuplicationsSum() != 3 ) {
239 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent()
243 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent()
247 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent()
251 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent()
255 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent()
259 final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
260 + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
261 + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
262 + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
263 + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
264 final Phylogeny gene7_2 = TestGSDI
265 .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])" );
266 gene7_2.setRooted( true );
267 final GSDI sdi7_2 = new GSDI( gene7_2, species7, false, false, false );
268 if ( sdi7_2.getDuplicationsSum() != 1 ) {
271 if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
274 if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
277 if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
280 if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
283 if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
286 if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
289 if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
292 if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
295 if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
298 final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
299 final GSDI sdi2_0 = new GSDI( g2_0, s2, false, false, false );
300 if ( sdi2_0.getDuplicationsSum() != 0 ) {
303 if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
306 if ( sdi2_0.getSpeciationsSum() != 1 ) {
309 if ( !PhylogenyMethods.calculateLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent()
313 final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
314 final GSDI sdi2_1 = new GSDI( g2_1, s2, false, false, false );
315 if ( sdi2_1.getDuplicationsSum() != 0 ) {
318 if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
321 if ( sdi2_1.getSpeciationsSum() != 1 ) {
324 if ( !PhylogenyMethods.calculateLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent()
328 final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
329 final GSDI sdi2_2 = new GSDI( g2_2, s2, false, false, false );
330 if ( sdi2_2.getDuplicationsSum() != 0 ) {
333 if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
336 if ( sdi2_2.getSpeciationsSum() != 1 ) {
339 if ( !PhylogenyMethods.calculateLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent()
343 final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
344 final GSDI sdi2_3 = new GSDI( g2_3, s2, false, false, false );
345 if ( sdi2_3.getDuplicationsSum() != 1 ) {
348 if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
351 if ( sdi2_3.getSpeciationsSum() != 0 ) {
354 if ( !PhylogenyMethods.calculateLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData()
355 .getEvent().isDuplication() ) {
358 final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
359 final GSDI sdi2_4 = new GSDI( g2_4, s2, false, false, false );
360 if ( sdi2_4.getDuplicationsSum() != 0 ) {
363 if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
366 if ( sdi2_4.getSpeciationsSum() != 2 ) {
369 if ( !PhylogenyMethods.calculateLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent()
373 if ( !PhylogenyMethods.calculateLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent()
377 final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
378 final GSDI sdi2_5 = new GSDI( g2_5, s2, false, false, false );
379 if ( sdi2_5.getDuplicationsSum() != 0 ) {
382 if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
385 if ( sdi2_5.getSpeciationsSum() != 2 ) {
388 if ( !PhylogenyMethods.calculateLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent()
392 if ( !PhylogenyMethods.calculateLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent()
396 final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
397 final GSDI sdi2_6 = new GSDI( g2_6, s2, false, false, false );
398 if ( sdi2_6.getDuplicationsSum() != 0 ) {
401 if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
404 if ( sdi2_6.getSpeciationsSum() != 2 ) {
407 if ( !PhylogenyMethods.calculateLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent()
411 if ( !PhylogenyMethods.calculateLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent()
415 final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
416 final GSDI sdi2_7 = new GSDI( g2_7, s2, false, false, false );
417 if ( sdi2_7.getDuplicationsSum() != 0 ) {
420 if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
423 if ( sdi2_7.getSpeciationsSum() != 1 ) {
426 if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent()
430 if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
431 .isSpeciationOrDuplication() ) {
434 final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
435 final GSDI sdi2_8 = new GSDI( g2_8, s2, false, false, false );
436 if ( sdi2_8.getDuplicationsSum() != 0 ) {
439 if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
442 if ( sdi2_8.getSpeciationsSum() != 1 ) {
445 if ( !PhylogenyMethods.calculateLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
446 .isSpeciationOrDuplication() ) {
449 if ( !PhylogenyMethods.calculateLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent()
453 final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
454 final GSDI sdi2_9 = new GSDI( g2_9, s2, false, false, false );
455 if ( sdi2_9.getDuplicationsSum() != 0 ) {
458 if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
461 if ( sdi2_9.getSpeciationsSum() != 2 ) {
464 if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
467 if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
470 final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
471 final GSDI sdi2_10 = new GSDI( g2_10, s2, false, false, false );
472 if ( sdi2_10.getDuplicationsSum() != 0 ) {
475 if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
478 if ( sdi2_10.getSpeciationsSum() != 1 ) {
481 if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
484 if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
487 final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
488 final GSDI sdi2_11 = new GSDI( g2_11, s2, false, false, false );
489 if ( sdi2_11.getDuplicationsSum() != 0 ) {
492 if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
495 if ( sdi2_11.getSpeciationsSum() != 1 ) {
498 if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
501 if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
504 final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
505 final GSDI sdi2_12 = new GSDI( g2_12, s2, false, false, false );
506 if ( sdi2_12.getDuplicationsSum() != 0 ) {
509 if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
512 if ( sdi2_12.getSpeciationsSum() != 1 ) {
515 if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
518 if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
521 final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
522 final GSDI sdi2_13 = new GSDI( g2_13, s2, false, false, false );
523 if ( sdi2_13.getDuplicationsSum() != 0 ) {
526 if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
529 if ( sdi2_13.getSpeciationsSum() != 1 ) {
532 if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
535 if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
538 final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
539 final GSDI sdi2_14 = new GSDI( g2_14, s2, false, false, false );
540 if ( sdi2_14.getDuplicationsSum() != 1 ) {
543 if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
546 if ( sdi2_14.getSpeciationsSum() != 1 ) {
549 if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
552 if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
555 final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
556 final GSDI sdi2_15 = new GSDI( g2_15, s2, false, false, false );
557 if ( sdi2_15.getDuplicationsSum() != 1 ) {
560 if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
563 if ( sdi2_15.getSpeciationsSum() != 1 ) {
566 if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
569 if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
572 final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
573 final GSDI sdi2_16 = new GSDI( g2_16, s2, false, false, false );
574 if ( sdi2_16.getDuplicationsSum() != 1 ) {
577 if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
580 if ( sdi2_16.getSpeciationsSum() != 1 ) {
583 if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
586 if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
589 final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
590 final GSDI sdi2_17 = new GSDI( g2_17, s2, false, false, false );
591 if ( sdi2_17.getDuplicationsSum() != 1 ) {
594 if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
597 if ( sdi2_17.getSpeciationsSum() != 1 ) {
600 if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
603 if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
606 final Phylogeny g2_18 = TestGSDI
607 .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
608 final GSDI sdi2_18 = new GSDI( g2_18, s2, false, false, false );
609 if ( sdi2_18.getDuplicationsSum() != 3 ) {
612 if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
615 if ( sdi2_18.getSpeciationsSum() != 0 ) {
618 if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
621 if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
624 if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
627 final Phylogeny g2_19 = TestGSDI
628 .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
629 final GSDI sdi2_19 = new GSDI( g2_19, s2, false, false, false );
630 if ( sdi2_19.getDuplicationsSum() != 1 ) {
633 if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
636 if ( sdi2_19.getSpeciationsSum() != 2 ) {
639 if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
642 if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
645 if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
648 final Phylogeny g2_20 = TestGSDI
649 .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
650 final GSDI sdi2_20 = new GSDI( g2_20, s2, false, false, false );
651 if ( sdi2_20.getDuplicationsSum() != 1 ) {
654 if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
657 if ( sdi2_20.getSpeciationsSum() != 2 ) {
660 if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
663 if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
666 if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
669 final Phylogeny g2_21 = TestGSDI
670 .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
671 final GSDI sdi2_21 = new GSDI( g2_21, s2, false, false, false );
672 if ( sdi2_21.getDuplicationsSum() != 1 ) {
675 if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
678 if ( sdi2_21.getSpeciationsSum() != 2 ) {
681 if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
684 if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
687 if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
690 final Phylogeny g2_22 = TestGSDI
691 .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
692 final GSDI sdi2_22 = new GSDI( g2_22, s2, false, false, false );
693 //Archaeopteryx.createApplication( g2_22 );
694 //Archaeopteryx.createApplication( s2 );
695 if ( sdi2_22.getDuplicationsSum() != 0 ) {
698 if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
701 if ( sdi2_22.getSpeciationsSum() != 2 ) {
704 if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
707 if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
710 if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
713 final Phylogeny g2_23 = TestGSDI
714 .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
715 final GSDI sdi2_23 = new GSDI( g2_23, s2, false, false, false );
716 if ( sdi2_23.getDuplicationsSum() != 0 ) {
719 if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
722 if ( sdi2_23.getSpeciationsSum() != 2 ) {
725 if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
728 if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
731 if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
734 final Phylogeny g2_24 = TestGSDI
735 .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
736 final GSDI sdi2_24 = new GSDI( g2_24, s2, false, false, false );
737 if ( sdi2_24.getDuplicationsSum() != 0 ) {
740 if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
743 if ( sdi2_24.getSpeciationsSum() != 2 ) {
746 if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
749 if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
752 if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
755 final Phylogeny g2_25 = TestGSDI
756 .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
757 final GSDI sdi2_25 = new GSDI( g2_25, s2, false, false, false );
758 if ( sdi2_25.getDuplicationsSum() != 0 ) {
761 if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
764 if ( sdi2_25.getSpeciationsSum() != 2 ) {
767 if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
770 if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
773 if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
776 final Phylogeny g2_26 = TestGSDI
777 .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
778 final GSDI sdi2_26 = new GSDI( g2_26, s2, false, false, false );
779 if ( sdi2_26.getDuplicationsSum() != 0 ) {
782 if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
785 if ( sdi2_26.getSpeciationsSum() != 3 ) {
788 if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
791 if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
794 if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
797 final Phylogeny g2_27 = TestGSDI
798 .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
799 final GSDI sdi2_27 = new GSDI( g2_27, s2, false, false, false );
800 if ( sdi2_27.getDuplicationsSum() != 0 ) {
803 if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
806 if ( sdi2_27.getSpeciationsSum() != 2 ) {
809 if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
812 if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
815 if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
818 final Phylogeny g2_28 = TestGSDI
819 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
820 final GSDI sdi2_28 = new GSDI( g2_28, s2, false, false, false );
821 if ( sdi2_28.getDuplicationsSum() != 0 ) {
824 if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
827 if ( sdi2_28.getSpeciationsSum() != 2 ) {
830 if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
833 if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
836 if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
839 final Phylogeny g2_29 = TestGSDI
840 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
841 final GSDI sdi2_29 = new GSDI( g2_29, s2, false, false, false );
842 if ( sdi2_29.getDuplicationsSum() != 0 ) {
845 if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
848 if ( sdi2_29.getSpeciationsSum() != 1 ) {
851 if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
854 if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
857 if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
860 final Phylogeny g2_30 = TestGSDI
861 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
862 final GSDI sdi2_30 = new GSDI( g2_30, s2, false, false, false );
863 if ( sdi2_30.getDuplicationsSum() != 1 ) {
866 if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
869 if ( sdi2_30.getSpeciationsSum() != 1 ) {
872 if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
875 if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
878 if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
881 final Phylogeny g2_31 = TestGSDI
882 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
883 final GSDI sdi2_31 = new GSDI( g2_31, s2, false, false, false );
884 if ( sdi2_31.getDuplicationsSum() != 1 ) {
887 if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
890 if ( sdi2_31.getSpeciationsSum() != 1 ) {
893 if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
896 if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
899 if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
902 final Phylogeny g2_32 = TestGSDI
903 .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])" );
904 final GSDI sdi2_32 = new GSDI( g2_32, s2, false, false, false );
905 if ( sdi2_32.getDuplicationsSum() != 0 ) {
908 if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
911 if ( sdi2_32.getSpeciationsSum() != 3 ) {
914 if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
917 if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
920 if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
923 if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
926 if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
929 if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
932 if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
935 if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
938 if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
941 if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
944 final Phylogeny g2_33 = TestGSDI
945 .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])" );
946 final GSDI sdi2_33 = new GSDI( g2_33, s2, false, false, false );
947 if ( sdi2_33.getDuplicationsSum() != 1 ) {
950 if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
953 if ( sdi2_33.getSpeciationsSum() != 3 ) {
956 if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
959 if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
962 if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
965 if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
968 if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
971 if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
974 if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
977 if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
980 if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
983 if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
986 if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
989 final Phylogeny g2_33_d = TestGSDI
990 .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=?])" );
991 final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false, false, false );
992 if ( sdi2_33_d.getDuplicationsSum() != 3 ) {
995 if ( sdi2_33_d.getSpeciationOrDuplicationEventsSum() != 14 ) {
998 if ( sdi2_33_d.getSpeciationsSum() != 6 ) {
1001 final Phylogeny g2_34 = TestGSDI
1002 .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])" );
1003 final GSDI sdi2_34 = new GSDI( g2_34, s2, false, false, false );
1004 if ( sdi2_34.getDuplicationsSum() != 1 ) {
1007 if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
1010 if ( sdi2_34.getSpeciationsSum() != 2 ) {
1013 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
1016 if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
1019 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
1022 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
1025 final Phylogeny g2_35 = TestGSDI
1026 .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])" );
1027 final GSDI sdi2_35 = new GSDI( g2_35, s2, false, false, false );
1028 if ( sdi2_35.getDuplicationsSum() != 1 ) {
1031 if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
1034 if ( sdi2_35.getSpeciationsSum() != 3 ) {
1037 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
1040 if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
1043 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
1046 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
1049 if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
1052 final Phylogeny g2_36 = TestGSDI
1053 .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])" );
1054 final GSDI sdi2_36 = new GSDI( g2_36, s2, false, false, false );
1055 if ( sdi2_36.getDuplicationsSum() != 1 ) {
1058 if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
1061 if ( sdi2_36.getSpeciationsSum() != 2 ) {
1064 if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
1067 if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
1070 if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
1073 if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1076 final Phylogeny g2_37 = TestGSDI
1077 .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])" );
1078 final GSDI sdi2_37 = new GSDI( g2_37, s2, false, false, false );
1079 if ( sdi2_37.getDuplicationsSum() != 1 ) {
1082 if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
1085 if ( sdi2_37.getSpeciationsSum() != 2 ) {
1088 if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
1091 if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
1094 if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
1097 if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1100 final Phylogeny g2_38 = TestGSDI
1101 .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
1102 final GSDI sdi2_38 = new GSDI( g2_38, s2, false, false, false );
1103 if ( sdi2_38.getDuplicationsSum() != 5 ) {
1106 if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
1109 if ( sdi2_38.getSpeciationsSum() != 0 ) {
1112 final Phylogeny g2_100 = TestGSDI
1113 .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])))" );
1114 final GSDI sdi2_100 = new GSDI( g2_100, s2, false, false, false );
1115 if ( sdi2_100.getDuplicationsSum() != 4 ) {
1118 if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
1121 if ( sdi2_100.getSpeciationsSum() != 4 ) {
1124 if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
1127 if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
1130 if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
1133 if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
1136 if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
1139 if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
1142 if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
1145 if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
1148 final Phylogeny g2_101 = TestGSDI
1149 .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])))" );
1150 final GSDI sdi2_101 = new GSDI( g2_101, s2, false, false, false );
1151 if ( sdi2_101.getDuplicationsSum() != 2 ) {
1154 if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
1157 if ( sdi2_101.getSpeciationsSum() != 5 ) {
1160 if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
1163 if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
1166 if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
1169 if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
1172 if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
1175 if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
1178 if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
1181 if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
1184 final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
1185 DevelopmentTools.numberSpeciesInOrder( s_7_4 );
1186 final Phylogeny g_7_4_1 = TestGSDI
1187 .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1188 + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1189 + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1190 + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1191 + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1192 + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1193 + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1194 + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1195 + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1196 + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1197 + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1198 + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
1199 final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false, false, false );
1200 if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
1203 if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1206 if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
1209 if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
1212 if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
1215 if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
1218 if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
1221 if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
1224 if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
1227 if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
1230 if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
1233 if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
1236 if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
1239 if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
1242 final Phylogeny g_7_4_2 = TestGSDI
1243 .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1244 + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1245 + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1246 + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1247 + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1248 + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1249 + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1250 + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1251 + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1252 + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1253 + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1254 + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
1255 + "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])" );
1256 final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false, false, false );
1257 if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
1260 if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
1263 if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
1266 final String g2_0_ = "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
1267 final Phylogeny g2_0p = TestGSDI.createPhylogeny( g2_0_ );
1268 g2_0.setRooted( true );
1269 final GSDI sdi2_0p = new GSDI( g2_0p, s2, false, false, false );
1270 if ( sdi2_0p.getDuplicationsSum() != 0 ) {
1274 final Phylogeny tol_143_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + "tol_143.xml" )[ 0 ];
1275 final Phylogeny gene_tree_tax_code_4_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1276 + "gene_tree_tax_code_4.xml" )[ 0 ];
1277 final GSDI gsdi_143_4_1 = new GSDI( gene_tree_tax_code_4_.copy(), tol_143_.copy(), false, true, true );
1278 if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) {
1281 if ( gsdi_143_4_1.getSpeciationsSum() != 28 ) {
1284 if ( gsdi_143_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1288 final Phylogeny gsdi_test_gene_tree_sn_wnt = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1289 + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ];
1290 gsdi_test_gene_tree_sn_wnt.setRooted( true );
1291 final GSDI a = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), tol_143_.copy(), false, true, true );
1292 if ( a.getDuplicationsSum() != 33 ) {
1295 if ( a.getSpeciationsSum() != 31 ) {
1298 if ( a.getSpeciationOrDuplicationEventsSum() != 0 ) {
1301 if ( a.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
1304 if ( a.getMappedExternalSpeciesTreeNodes().size() != 26 ) {
1307 if ( a.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
1311 final Phylogeny gsdi_test_species_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1312 + "gsdi_test_species_tree_sn.xml" )[ 0 ];
1313 final GSDI b = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
1314 gsdi_test_species_tree_sn_xml.copy(),
1318 if ( b.getDuplicationsSum() != 8 ) {
1321 if ( b.getSpeciationsSum() != 2 ) {
1324 if ( b.getSpeciationOrDuplicationEventsSum() != 0 ) {
1327 if ( b.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
1330 if ( b.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
1333 if ( b.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
1336 if ( b.getStrippedExternalGeneTreeNodes().size() != 87 ) {
1339 if ( b.getStrippedSpeciesTreeNodes().size() != 17 ) {
1343 final Phylogeny gsdi_test_species_tree_sn_nh = TestGSDI
1344 .createPhylogeny( "((((((('Homo sapiens','Mus musculus')Euarchontoglires,'Petromyzon marinus')Vertebrata,'Nematostella vectensis')'Bilateria Cnidaria',(('Mycosphaerella graminicola','Mycosphaerella pini')Mycosphaerella,'Saccharomyces cerevisiae')'Pezizomycotina Saccharomycetales')Opisthokonta,('Plasmodium chabaudi','Plasmodium falciparum','Plasmodium yoelii yoelii')Plasmodium)Eukaryota,'Pyrococcus horikoshii')Neomura,(('Kineococcus radiotolerans','Kocuria rhizophila','Streptomyces coelicolor','Thermobifida fusca','Microlunatus phosphovorus'),'Bacteroides thetaiotaomicron'))'cellular organisms';" );
1345 PhylogenyMethods.transferNodeNameToField( gsdi_test_species_tree_sn_nh,
1346 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1348 final GSDI c = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
1349 gsdi_test_species_tree_sn_nh.copy(),
1353 if ( c.getDuplicationsSum() != 8 ) {
1356 if ( c.getSpeciationsSum() != 2 ) {
1359 if ( c.getSpeciationOrDuplicationEventsSum() != 0 ) {
1362 if ( c.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
1365 if ( c.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
1368 if ( c.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
1371 if ( c.getStrippedExternalGeneTreeNodes().size() != 87 ) {
1374 if ( c.getStrippedSpeciesTreeNodes().size() != 15 ) {
1378 final Phylogeny gsdi_test_gene_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1379 + "gsdi_test_gene_tree_codes.xml" )[ 0 ];
1380 final Phylogeny gsdi_test_species_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1381 + "gsdi_test_species_tree_codes.xml" )[ 0 ];
1382 final GSDI d = new GSDI( gsdi_test_gene_tree_codes_xml.copy(),
1383 gsdi_test_species_tree_codes_xml.copy(),
1387 if ( d.getDuplicationsSum() != 21 ) {
1390 if ( d.getSpeciationsSum() != 28 ) {
1393 if ( d.getSpeciationOrDuplicationEventsSum() != 6 ) {
1396 if ( d.getTaxCompBase() != TaxonomyComparisonBase.CODE ) {
1399 if ( d.getMappedExternalSpeciesTreeNodes().size() != 17 ) {
1402 if ( d.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
1405 if ( d.getStrippedExternalGeneTreeNodes().size() != 12 ) {
1408 if ( d.getStrippedSpeciesTreeNodes().size() != 3 ) {
1412 final Phylogeny gsdi_test_gene_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1413 + "gsdi_test_gene_tree_sn.xml" )[ 0 ];
1414 final GSDI e = new GSDI( gsdi_test_gene_tree_sn_xml.copy(),
1415 gsdi_test_species_tree_sn_xml.copy(),
1419 if ( e.getDuplicationsSum() != 7 ) {
1422 if ( e.getSpeciationsSum() != 9 ) {
1425 if ( e.getSpeciationOrDuplicationEventsSum() != 1 ) {
1428 if ( e.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
1431 if ( e.getMappedExternalSpeciesTreeNodes().size() != 12 ) {
1434 if ( e.getReMappedScientificNamesFromGeneTree().size() != 8 ) {
1437 if ( e.getStrippedExternalGeneTreeNodes().size() != 3 ) {
1440 if ( e.getStrippedSpeciesTreeNodes().size() != 7 ) {
1444 catch ( final Exception e ) {
1445 e.printStackTrace( System.out );
1451 private static boolean testGSDIR_general() {
1453 final String s1str = "(((([&&NHX:S=HUMAN],([&&NHX:S=MOUSE],[&&NHX:S=RAT])),([&&NHX:S=CAEEL],[&&NHX:S=CAEBR])),[&&NHX:S=YEAST]),[&&NHX:S=ARATH])";
1454 final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1str, new NHXParser() )[ 0 ];
1455 s1.setRooted( true );
1456 final Phylogeny g1 = TestGSDI
1457 .createPhylogeny( "(HUMAN[&&NHX:S=HUMAN],(RAT[&&NHX:S=RAT],(CAEEL[&&NHX:T=:S=CAEEL],YEAST[&&NHX:S=YEAST])))" );
1458 final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false );
1459 if ( sdi1.getMinDuplicationsSum() != 0 ) {
1462 final Phylogeny g2 = TestGSDI
1463 .createPhylogeny( "(((HUMAN[&&NHX:S=HUMAN],RAT[&&NHX:S=RAT]),CAEEL[&&NHX:T=:S=CAEEL]),YEAST[&&NHX:S=YEAST])" );
1464 final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false );
1465 if ( sdi2.getMinDuplicationsSum() != 0 ) {
1468 final Phylogeny g3 = TestGSDI
1469 .createPhylogeny( "(RAT[&&NHX:S=RAT],HUMAN[&&NHX:S=HUMAN],(YEAST[&&NHX:S=YEAST],CAEEL[&&NHX:T=:S=CAEEL]))" );
1470 final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false );
1471 if ( sdi3.getMinDuplicationsSum() != 0 ) {
1474 final Phylogeny g4 = TestGSDI
1475 .createPhylogeny( "(((((MOUSE[&&NHX:S=MOUSE],[&&NHX:S=RAT]),[&&NHX:S=HUMAN]),([&&NHX:S=ARATH],[&&NHX:S=YEAST])),[&&NHX:S=CAEEL]),[&&NHX:S=CAEBR])" );
1476 final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false );
1477 if ( sdi4.getMinDuplicationsSum() != 0 ) {
1481 catch ( final Exception e ) {
1482 e.printStackTrace( System.out );