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.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 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
47 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
52 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
53 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
56 public static boolean test() {
57 if ( !TestGSDI.testGSDI_general() ) {
60 if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
63 if ( !TestGSDI.testGSDIR_general() ) {
69 private static boolean testGSDI_against_binary_gene_tree() {
71 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
72 final String multi_species_2_str = "(((((([&&NHX:S=1],[&&NHX:S=2]),"
73 + "([&&NHX:S=3],[&&NHX:S=4],[&&NHX:S=5])),"
74 + "([&&NHX:S=6],[&&NHX:S=7],[&&NHX:S=8],[&&NHX:S=9])),"
75 + "([&&NHX:S=10],[&&NHX:S=11])),"
76 + "([&&NHX:S=12],[&&NHX:S=13],[&&NHX:S=14])),"
77 + "([&&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])));";
78 final String gene_2_1_str = "(((((([&&NHX:S=1],[&&NHX:S=2])1_2,([&&NHX:S=3],[&&NHX:S=4])),"
79 + "([&&NHX:S=6],[&&NHX:S=7])6_7_8_9)1_9,([&&NHX:S=10],[&&NHX:S=11])),"
80 + "([&&NHX:S=12],[&&NHX:S=13])12_13_14)1_14,"
81 + "([&&NHX:S=15],([&&NHX:S=21],[&&NHX:S=24])21_22_23_24)15_24);";
82 final Phylogeny multi_species_2 = factory.create( multi_species_2_str, new NHXParser() )[ 0 ];
83 final Phylogeny gene_2_1 = factory.create( gene_2_1_str, new NHXParser() )[ 0 ];
84 multi_species_2.setRooted( true );
85 gene_2_1.setRooted( true );
86 final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false, false, false );
87 if ( sdi.getSpeciationOrDuplicationEventsSum() != 0 ) {
90 if ( sdi.getDuplicationsSum() != 0 ) {
94 catch ( final Exception e ) {
95 e.printStackTrace( System.out );
101 private static boolean testGSDI_general() {
103 final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
104 + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
105 + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
106 + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
107 + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
108 + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
109 + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
110 + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
111 + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
112 + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
113 + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
114 + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
115 + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
116 + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
117 + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
118 + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
119 + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
120 final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
121 s2.setRooted( true );
122 final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
123 final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
124 s1.setRooted( true );
125 final Phylogeny g1 = TestGSDI
126 .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
127 final GSDI sdi1 = new GSDI( g1, s1, false, false, false );
128 // Archaeopteryx.createApplication( g1 );
129 // Archaeopteryx.createApplication( s1 );
130 if ( sdi1.getDuplicationsSum() != 1 ) {
133 if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
137 if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
138 .isSpeciationOrDuplication() ) {
141 if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
142 .isDuplication() ) ) {
145 if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
149 final Phylogeny g2 = TestGSDI
150 .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
151 final GSDI sdi2 = new GSDI( g2, s1, false, false, false );
152 if ( sdi2.getDuplicationsSum() != 0 ) {
155 if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent()
159 if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent()
163 if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
164 .isSpeciationOrDuplication() ) {
167 if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent()
171 final Phylogeny g3 = TestGSDI
172 .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
173 final GSDI sdi3 = new GSDI( g3, s1, false, false, false );
174 if ( sdi3.getDuplicationsSum() != 0 ) {
177 if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent()
181 if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent()
185 if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
186 .isSpeciationOrDuplication() ) {
189 if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent()
193 final Phylogeny g4 = TestGSDI
194 .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
195 final GSDI sdi4 = new GSDI( g4, s1, false, false, false );
196 if ( sdi4.getDuplicationsSum() != 1 ) {
199 if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent()
203 if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent()
207 if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent()
211 final Phylogeny g5 = TestGSDI
212 .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]))" );
213 final GSDI sdi5 = new GSDI( g5, s1, false, false, false );
214 if ( sdi5.getDuplicationsSum() != 3 ) {
217 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent()
221 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent()
225 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent()
229 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent()
233 if ( !PhylogenyMethods.calculateLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent()
237 final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
238 + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
239 + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
240 + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
241 + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
242 final Phylogeny gene7_2 = TestGSDI
243 .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])" );
244 gene7_2.setRooted( true );
245 final GSDI sdi7_2 = new GSDI( gene7_2, species7, false, false, false );
246 if ( sdi7_2.getDuplicationsSum() != 1 ) {
249 if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
252 if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
255 if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
258 if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
261 if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
264 if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
267 if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
270 if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
273 if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
276 final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
277 final GSDI sdi2_0 = new GSDI( g2_0, s2, false, false, false );
278 if ( sdi2_0.getDuplicationsSum() != 0 ) {
281 if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
284 if ( sdi2_0.getSpeciationsSum() != 1 ) {
287 if ( !PhylogenyMethods.calculateLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent()
291 final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
292 final GSDI sdi2_1 = new GSDI( g2_1, s2, false, false, false );
293 if ( sdi2_1.getDuplicationsSum() != 0 ) {
296 if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
299 if ( sdi2_1.getSpeciationsSum() != 1 ) {
302 if ( !PhylogenyMethods.calculateLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent()
306 final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
307 final GSDI sdi2_2 = new GSDI( g2_2, s2, false, false, false );
308 if ( sdi2_2.getDuplicationsSum() != 0 ) {
311 if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
314 if ( sdi2_2.getSpeciationsSum() != 1 ) {
317 if ( !PhylogenyMethods.calculateLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent()
321 final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
322 final GSDI sdi2_3 = new GSDI( g2_3, s2, false, false, false );
323 if ( sdi2_3.getDuplicationsSum() != 1 ) {
326 if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
329 if ( sdi2_3.getSpeciationsSum() != 0 ) {
332 if ( !PhylogenyMethods.calculateLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData()
333 .getEvent().isDuplication() ) {
336 final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
337 final GSDI sdi2_4 = new GSDI( g2_4, s2, false, false, false );
338 if ( sdi2_4.getDuplicationsSum() != 0 ) {
341 if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
344 if ( sdi2_4.getSpeciationsSum() != 2 ) {
347 if ( !PhylogenyMethods.calculateLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent()
351 if ( !PhylogenyMethods.calculateLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent()
355 final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
356 final GSDI sdi2_5 = new GSDI( g2_5, s2, false, false, false );
357 if ( sdi2_5.getDuplicationsSum() != 0 ) {
360 if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
363 if ( sdi2_5.getSpeciationsSum() != 2 ) {
366 if ( !PhylogenyMethods.calculateLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent()
370 if ( !PhylogenyMethods.calculateLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent()
374 final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
375 final GSDI sdi2_6 = new GSDI( g2_6, s2, false, false, false );
376 if ( sdi2_6.getDuplicationsSum() != 0 ) {
379 if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
382 if ( sdi2_6.getSpeciationsSum() != 2 ) {
385 if ( !PhylogenyMethods.calculateLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent()
389 if ( !PhylogenyMethods.calculateLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent()
393 final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
394 final GSDI sdi2_7 = new GSDI( g2_7, s2, false, false, false );
395 if ( sdi2_7.getDuplicationsSum() != 0 ) {
398 if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
401 if ( sdi2_7.getSpeciationsSum() != 1 ) {
404 if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent()
408 if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
409 .isSpeciationOrDuplication() ) {
412 final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
413 final GSDI sdi2_8 = new GSDI( g2_8, s2, false, false, false );
414 if ( sdi2_8.getDuplicationsSum() != 0 ) {
417 if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
420 if ( sdi2_8.getSpeciationsSum() != 1 ) {
423 if ( !PhylogenyMethods.calculateLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
424 .isSpeciationOrDuplication() ) {
427 if ( !PhylogenyMethods.calculateLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent()
431 final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
432 final GSDI sdi2_9 = new GSDI( g2_9, s2, false, false, false );
433 if ( sdi2_9.getDuplicationsSum() != 0 ) {
436 if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
439 if ( sdi2_9.getSpeciationsSum() != 2 ) {
442 if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
445 if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
448 final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
449 final GSDI sdi2_10 = new GSDI( g2_10, s2, false, false, false );
450 if ( sdi2_10.getDuplicationsSum() != 0 ) {
453 if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
456 if ( sdi2_10.getSpeciationsSum() != 1 ) {
459 if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
462 if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
465 final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
466 final GSDI sdi2_11 = new GSDI( g2_11, s2, false, false, false );
467 if ( sdi2_11.getDuplicationsSum() != 0 ) {
470 if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
473 if ( sdi2_11.getSpeciationsSum() != 1 ) {
476 if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
479 if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
482 final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
483 final GSDI sdi2_12 = new GSDI( g2_12, s2, false, false, false );
484 if ( sdi2_12.getDuplicationsSum() != 0 ) {
487 if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
490 if ( sdi2_12.getSpeciationsSum() != 1 ) {
493 if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
496 if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
499 final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
500 final GSDI sdi2_13 = new GSDI( g2_13, s2, false, false, false );
501 if ( sdi2_13.getDuplicationsSum() != 0 ) {
504 if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
507 if ( sdi2_13.getSpeciationsSum() != 1 ) {
510 if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
513 if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
516 final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
517 final GSDI sdi2_14 = new GSDI( g2_14, s2, false, false, false );
518 if ( sdi2_14.getDuplicationsSum() != 1 ) {
521 if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
524 if ( sdi2_14.getSpeciationsSum() != 1 ) {
527 if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
530 if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
533 final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
534 final GSDI sdi2_15 = new GSDI( g2_15, s2, false, false, false );
535 if ( sdi2_15.getDuplicationsSum() != 1 ) {
538 if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
541 if ( sdi2_15.getSpeciationsSum() != 1 ) {
544 if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
547 if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
550 final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
551 final GSDI sdi2_16 = new GSDI( g2_16, s2, false, false, false );
552 if ( sdi2_16.getDuplicationsSum() != 1 ) {
555 if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
558 if ( sdi2_16.getSpeciationsSum() != 1 ) {
561 if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
564 if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
567 final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
568 final GSDI sdi2_17 = new GSDI( g2_17, s2, false, false, false );
569 if ( sdi2_17.getDuplicationsSum() != 1 ) {
572 if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
575 if ( sdi2_17.getSpeciationsSum() != 1 ) {
578 if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
581 if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
584 final Phylogeny g2_18 = TestGSDI
585 .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
586 final GSDI sdi2_18 = new GSDI( g2_18, s2, false, false, false );
587 if ( sdi2_18.getDuplicationsSum() != 3 ) {
590 if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
593 if ( sdi2_18.getSpeciationsSum() != 0 ) {
596 if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
599 if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
602 if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
605 final Phylogeny g2_19 = TestGSDI
606 .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
607 final GSDI sdi2_19 = new GSDI( g2_19, s2, false, false, false );
608 if ( sdi2_19.getDuplicationsSum() != 1 ) {
611 if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
614 if ( sdi2_19.getSpeciationsSum() != 2 ) {
617 if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
620 if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
623 if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
626 final Phylogeny g2_20 = TestGSDI
627 .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
628 final GSDI sdi2_20 = new GSDI( g2_20, s2, false, false, false );
629 if ( sdi2_20.getDuplicationsSum() != 1 ) {
632 if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
635 if ( sdi2_20.getSpeciationsSum() != 2 ) {
638 if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
641 if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
644 if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
647 final Phylogeny g2_21 = TestGSDI
648 .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
649 final GSDI sdi2_21 = new GSDI( g2_21, s2, false, false, false );
650 if ( sdi2_21.getDuplicationsSum() != 1 ) {
653 if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
656 if ( sdi2_21.getSpeciationsSum() != 2 ) {
659 if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
662 if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
665 if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
668 final Phylogeny g2_22 = TestGSDI
669 .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
670 final GSDI sdi2_22 = new GSDI( g2_22, s2, false, false, false );
671 //Archaeopteryx.createApplication( g2_22 );
672 //Archaeopteryx.createApplication( s2 );
673 if ( sdi2_22.getDuplicationsSum() != 0 ) {
676 if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
679 if ( sdi2_22.getSpeciationsSum() != 2 ) {
682 if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
685 if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
688 if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
691 final Phylogeny g2_23 = TestGSDI
692 .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
693 final GSDI sdi2_23 = new GSDI( g2_23, s2, false, false, false );
694 if ( sdi2_23.getDuplicationsSum() != 0 ) {
697 if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
700 if ( sdi2_23.getSpeciationsSum() != 2 ) {
703 if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
706 if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
709 if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
712 final Phylogeny g2_24 = TestGSDI
713 .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
714 final GSDI sdi2_24 = new GSDI( g2_24, s2, false, false, false );
715 if ( sdi2_24.getDuplicationsSum() != 0 ) {
718 if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
721 if ( sdi2_24.getSpeciationsSum() != 2 ) {
724 if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
727 if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
730 if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
733 final Phylogeny g2_25 = TestGSDI
734 .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
735 final GSDI sdi2_25 = new GSDI( g2_25, s2, false, false, false );
736 if ( sdi2_25.getDuplicationsSum() != 0 ) {
739 if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
742 if ( sdi2_25.getSpeciationsSum() != 2 ) {
745 if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
748 if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
751 if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
754 final Phylogeny g2_26 = TestGSDI
755 .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
756 final GSDI sdi2_26 = new GSDI( g2_26, s2, false, false, false );
757 if ( sdi2_26.getDuplicationsSum() != 0 ) {
760 if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
763 if ( sdi2_26.getSpeciationsSum() != 3 ) {
766 if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
769 if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
772 if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
775 final Phylogeny g2_27 = TestGSDI
776 .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
777 final GSDI sdi2_27 = new GSDI( g2_27, s2, false, false, false );
778 if ( sdi2_27.getDuplicationsSum() != 0 ) {
781 if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
784 if ( sdi2_27.getSpeciationsSum() != 2 ) {
787 if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
790 if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
793 if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
796 final Phylogeny g2_28 = TestGSDI
797 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
798 final GSDI sdi2_28 = new GSDI( g2_28, s2, false, false, false );
799 if ( sdi2_28.getDuplicationsSum() != 0 ) {
802 if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
805 if ( sdi2_28.getSpeciationsSum() != 2 ) {
808 if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
811 if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
814 if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
817 final Phylogeny g2_29 = TestGSDI
818 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
819 final GSDI sdi2_29 = new GSDI( g2_29, s2, false, false, false );
820 if ( sdi2_29.getDuplicationsSum() != 0 ) {
823 if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
826 if ( sdi2_29.getSpeciationsSum() != 1 ) {
829 if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
832 if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
835 if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
838 final Phylogeny g2_30 = TestGSDI
839 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
840 final GSDI sdi2_30 = new GSDI( g2_30, s2, false, false, false );
841 if ( sdi2_30.getDuplicationsSum() != 1 ) {
844 if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
847 if ( sdi2_30.getSpeciationsSum() != 1 ) {
850 if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
853 if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
856 if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
859 final Phylogeny g2_31 = TestGSDI
860 .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
861 final GSDI sdi2_31 = new GSDI( g2_31, s2, false, false, false );
862 if ( sdi2_31.getDuplicationsSum() != 1 ) {
865 if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
868 if ( sdi2_31.getSpeciationsSum() != 1 ) {
871 if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
874 if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
877 if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
880 final Phylogeny g2_32 = TestGSDI
881 .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])" );
882 final GSDI sdi2_32 = new GSDI( g2_32, s2, false, false, false );
883 if ( sdi2_32.getDuplicationsSum() != 0 ) {
886 if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
889 if ( sdi2_32.getSpeciationsSum() != 3 ) {
892 if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
895 if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
898 if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
901 if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
904 if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
907 if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
910 if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
913 if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
916 if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
919 if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
922 final Phylogeny g2_33 = TestGSDI
923 .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])" );
924 final GSDI sdi2_33 = new GSDI( g2_33, s2, false, false, false );
925 if ( sdi2_33.getDuplicationsSum() != 1 ) {
928 if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
931 if ( sdi2_33.getSpeciationsSum() != 3 ) {
934 if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
937 if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
940 if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
943 if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
946 if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
949 if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
952 if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
955 if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
958 if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
961 if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
964 if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
967 final Phylogeny g2_33_d = TestGSDI
968 .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=?])" );
969 final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false, false, false );
970 if ( sdi2_33_d.getDuplicationsSum() != 3 ) {
973 if ( sdi2_33_d.getSpeciationOrDuplicationEventsSum() != 14 ) {
976 if ( sdi2_33_d.getSpeciationsSum() != 6 ) {
979 final Phylogeny g2_34 = TestGSDI
980 .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])" );
981 final GSDI sdi2_34 = new GSDI( g2_34, s2, false, false, false );
982 if ( sdi2_34.getDuplicationsSum() != 1 ) {
985 if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
988 if ( sdi2_34.getSpeciationsSum() != 2 ) {
991 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
994 if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
997 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
1000 if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
1003 final Phylogeny g2_35 = TestGSDI
1004 .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])" );
1005 final GSDI sdi2_35 = new GSDI( g2_35, s2, false, false, false );
1006 if ( sdi2_35.getDuplicationsSum() != 1 ) {
1009 if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
1012 if ( sdi2_35.getSpeciationsSum() != 3 ) {
1015 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
1018 if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
1021 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
1024 if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
1027 if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
1030 final Phylogeny g2_36 = TestGSDI
1031 .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])" );
1032 final GSDI sdi2_36 = new GSDI( g2_36, s2, false, false, false );
1033 if ( sdi2_36.getDuplicationsSum() != 1 ) {
1036 if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
1039 if ( sdi2_36.getSpeciationsSum() != 2 ) {
1042 if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
1045 if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
1048 if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
1051 if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1054 final Phylogeny g2_37 = TestGSDI
1055 .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])" );
1056 final GSDI sdi2_37 = new GSDI( g2_37, s2, false, false, false );
1057 if ( sdi2_37.getDuplicationsSum() != 1 ) {
1060 if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
1063 if ( sdi2_37.getSpeciationsSum() != 2 ) {
1066 if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
1069 if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
1072 if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
1075 if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1078 final Phylogeny g2_38 = TestGSDI
1079 .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
1080 final GSDI sdi2_38 = new GSDI( g2_38, s2, false, false, false );
1081 if ( sdi2_38.getDuplicationsSum() != 5 ) {
1084 if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
1087 if ( sdi2_38.getSpeciationsSum() != 0 ) {
1090 final Phylogeny g2_100 = TestGSDI
1091 .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])))" );
1092 final GSDI sdi2_100 = new GSDI( g2_100, s2, false, false, false );
1093 if ( sdi2_100.getDuplicationsSum() != 4 ) {
1096 if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
1099 if ( sdi2_100.getSpeciationsSum() != 4 ) {
1102 if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
1105 if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
1108 if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
1111 if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
1114 if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
1117 if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
1120 if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
1123 if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
1126 final Phylogeny g2_101 = TestGSDI
1127 .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])))" );
1128 final GSDI sdi2_101 = new GSDI( g2_101, s2, false, false, false );
1129 if ( sdi2_101.getDuplicationsSum() != 2 ) {
1132 if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
1135 if ( sdi2_101.getSpeciationsSum() != 5 ) {
1138 if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
1141 if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
1144 if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
1147 if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
1150 if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
1153 if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
1156 if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
1159 if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
1162 final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
1163 DevelopmentTools.numberSpeciesInOrder( s_7_4 );
1164 final Phylogeny g_7_4_1 = TestGSDI
1165 .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1166 + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1167 + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1168 + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1169 + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1170 + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1171 + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1172 + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1173 + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1174 + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1175 + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1176 + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
1177 final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false, false, false );
1178 if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
1181 if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1184 if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
1187 if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
1190 if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
1193 if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
1196 if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
1199 if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
1202 if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
1205 if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
1208 if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
1211 if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
1214 if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
1217 if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
1220 final Phylogeny g_7_4_2 = TestGSDI
1221 .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1222 + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1223 + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1224 + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1225 + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1226 + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1227 + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1228 + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1229 + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1230 + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1231 + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1232 + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
1233 + "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])" );
1234 final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false, false, false );
1235 if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
1238 if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
1241 if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
1244 final String g2_0_ = "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
1245 final Phylogeny g2_0p = TestGSDI.createPhylogeny( g2_0_ );
1246 g2_0.setRooted( true );
1247 final GSDI sdi2_0p = new GSDI( g2_0p, s2, false, false, false );
1248 if ( sdi2_0p.getDuplicationsSum() != 0 ) {
1252 final Phylogeny tol_143_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + "tol_143.xml" )[ 0 ];
1253 final Phylogeny gene_tree_tax_code_4_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1254 + "gene_tree_tax_code_4.xml" )[ 0 ];
1255 final GSDI gsdi_143_4_1 = new GSDI( gene_tree_tax_code_4_.copy(), tol_143_.copy(), false, true, true );
1256 if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) {
1259 if ( gsdi_143_4_1.getSpeciationsSum() != 28 ) {
1262 if ( gsdi_143_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1266 final Phylogeny gsdi_test_gene_tree_sn_wnt = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1267 + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ];
1268 gsdi_test_gene_tree_sn_wnt.setRooted( true );
1269 final GSDI a = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), tol_143_.copy(), false, true, true );
1270 if ( a.getDuplicationsSum() != 33 ) {
1273 if ( a.getSpeciationsSum() != 31 ) {
1276 if ( a.getSpeciationOrDuplicationEventsSum() != 0 ) {
1279 if ( a.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
1282 if ( a.getMappedExternalSpeciesTreeNodes().size() != 26 ) {
1285 if ( a.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
1289 final Phylogeny gsdi_test_species_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1290 + "gsdi_test_species_tree_sn.xml" )[ 0 ];
1291 final GSDI b = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
1292 gsdi_test_species_tree_sn_xml.copy(),
1296 if ( b.getDuplicationsSum() != 8 ) {
1299 if ( b.getSpeciationsSum() != 2 ) {
1302 if ( b.getSpeciationOrDuplicationEventsSum() != 0 ) {
1305 if ( b.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
1308 if ( b.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
1311 if ( b.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
1314 if ( b.getStrippedExternalGeneTreeNodes().size() != 87 ) {
1317 if ( b.getStrippedSpeciesTreeNodes().size() != 17 ) {
1321 final Phylogeny gsdi_test_species_tree_sn_nh = TestGSDI
1322 .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';" );
1323 PhylogenyMethods.transferNodeNameToField( gsdi_test_species_tree_sn_nh,
1324 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1326 final GSDI c = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
1327 gsdi_test_species_tree_sn_nh.copy(),
1331 if ( c.getDuplicationsSum() != 8 ) {
1334 if ( c.getSpeciationsSum() != 2 ) {
1337 if ( c.getSpeciationOrDuplicationEventsSum() != 0 ) {
1340 if ( c.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
1343 if ( c.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
1346 if ( c.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
1349 if ( c.getStrippedExternalGeneTreeNodes().size() != 87 ) {
1352 if ( c.getStrippedSpeciesTreeNodes().size() != 15 ) {
1356 final Phylogeny gsdi_test_gene_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1357 + "gsdi_test_gene_tree_codes.xml" )[ 0 ];
1358 final Phylogeny gsdi_test_species_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1359 + "gsdi_test_species_tree_codes.xml" )[ 0 ];
1360 final GSDI d = new GSDI( gsdi_test_gene_tree_codes_xml.copy(),
1361 gsdi_test_species_tree_codes_xml.copy(),
1365 if ( d.getDuplicationsSum() != 21 ) {
1368 if ( d.getSpeciationsSum() != 28 ) {
1371 if ( d.getSpeciationOrDuplicationEventsSum() != 6 ) {
1374 if ( d.getTaxCompBase() != TaxonomyComparisonBase.CODE ) {
1377 if ( d.getMappedExternalSpeciesTreeNodes().size() != 17 ) {
1380 if ( d.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
1383 if ( d.getStrippedExternalGeneTreeNodes().size() != 12 ) {
1386 if ( d.getStrippedSpeciesTreeNodes().size() != 3 ) {
1390 final Phylogeny gsdi_test_gene_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
1391 + "gsdi_test_gene_tree_sn.xml" )[ 0 ];
1392 final GSDI e = new GSDI( gsdi_test_gene_tree_sn_xml.copy(),
1393 gsdi_test_species_tree_sn_xml.copy(),
1397 if ( e.getDuplicationsSum() != 7 ) {
1400 if ( e.getSpeciationsSum() != 9 ) {
1403 if ( e.getSpeciationOrDuplicationEventsSum() != 1 ) {
1406 if ( e.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
1409 if ( e.getMappedExternalSpeciesTreeNodes().size() != 12 ) {
1412 if ( e.getReMappedScientificNamesFromGeneTree().size() != 8 ) {
1415 if ( e.getStrippedExternalGeneTreeNodes().size() != 3 ) {
1418 if ( e.getStrippedSpeciesTreeNodes().size() != 7 ) {
1422 catch ( final Exception e ) {
1423 e.printStackTrace( System.out );
1429 private static boolean testGSDIR_general() {
1431 final String s1str = "(((([&&NHX:S=HUMAN],([&&NHX:S=MOUSE],[&&NHX:S=RAT])),([&&NHX:S=CAEEL],[&&NHX:S=CAEBR])),[&&NHX:S=YEAST]),[&&NHX:S=ARATH])";
1432 final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1str, new NHXParser() )[ 0 ];
1433 s1.setRooted( true );
1434 final Phylogeny g1 = TestGSDI
1435 .createPhylogeny( "(HUMAN[&&NHX:S=HUMAN],(RAT[&&NHX:S=RAT],(CAEEL[&&NHX:T=:S=CAEEL],YEAST[&&NHX:S=YEAST])))" );
1436 final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false );
1437 if ( sdi1.getMinDuplicationsSum() != 0 ) {
1440 final Phylogeny g2 = TestGSDI
1441 .createPhylogeny( "(((HUMAN[&&NHX:S=HUMAN],RAT[&&NHX:S=RAT]),CAEEL[&&NHX:T=:S=CAEEL]),YEAST[&&NHX:S=YEAST])" );
1442 final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false );
1443 if ( sdi2.getMinDuplicationsSum() != 0 ) {
1446 final Phylogeny g3 = TestGSDI
1447 .createPhylogeny( "(RAT[&&NHX:S=RAT],HUMAN[&&NHX:S=HUMAN],(YEAST[&&NHX:S=YEAST],CAEEL[&&NHX:T=:S=CAEEL]))" );
1448 final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false );
1449 if ( sdi3.getMinDuplicationsSum() != 0 ) {
1452 final Phylogeny g4 = TestGSDI
1453 .createPhylogeny( "(((((MOUSE[&&NHX:S=MOUSE],[&&NHX:S=RAT]),[&&NHX:S=HUMAN]),([&&NHX:S=ARATH],[&&NHX:S=YEAST])),[&&NHX:S=CAEEL]),[&&NHX:S=CAEBR])" );
1454 final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false );
1455 if ( sdi4.getMinDuplicationsSum() != 0 ) {
1459 catch ( final Exception e ) {
1460 e.printStackTrace( System.out );
1466 public static void main( final String[] args ) {
1467 if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
1468 System.out.println( "binary failed" );
1470 if ( !TestGSDI.testGSDI_general() ) {
1471 System.out.println( "general failed" );
1473 if ( !TestGSDI.testGSDIR_general() ) {
1474 System.out.println( "general re-rooting failed" );
1477 System.out.println( "OK" );
1479 // boolean success = test();
1481 // System.out.println( "OK" );
1484 // System.out.println( "failed" );