2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.sdi;
28 import java.io.IOException;
30 import org.forester.archaeopteryx.Archaeopteryx;
31 import org.forester.io.parsers.nhx.NHXParser;
32 import org.forester.phylogeny.Phylogeny;
33 import org.forester.phylogeny.PhylogenyMethods;
34 import org.forester.phylogeny.data.Event;
35 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
36 import org.forester.phylogeny.factories.PhylogenyFactory;
38 public final class TestGSDI {
40 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
41 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
46 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
47 return PhylogenyMethods.getInstance().obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
50 public static boolean test() {
51 if ( !TestGSDI.testGSDI_general() ) {
54 if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
60 private static boolean testGSDI_against_binary_gene_tree() {
62 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
63 final String multi_species_2_str = "(((((([&&NHX:S=1],[&&NHX:S=2]),"
64 + "([&&NHX:S=3],[&&NHX:S=4],[&&NHX:S=5])),"
65 + "([&&NHX:S=6],[&&NHX:S=7],[&&NHX:S=8],[&&NHX:S=9])),"
66 + "([&&NHX:S=10],[&&NHX:S=11])),"
67 + "([&&NHX:S=12],[&&NHX:S=13],[&&NHX:S=14])),"
68 + "([&&NHX:S=15],([&&NHX:S=16],[&&NHX:S=17]),([&&NHX:S=18],[&&NHX:S=19],[&&NHX:S=20]),([&&NHX:S=21],[&&NHX:S=22],[&&NHX:S=23],[&&NHX:S=24])));";
69 final String gene_2_1_str = "(((((([&&NHX:S=1],[&&NHX:S=2])1_2,([&&NHX:S=3],[&&NHX:S=4])),"
70 + "([&&NHX:S=6],[&&NHX:S=7])6_7_8_9)1_9,([&&NHX:S=10],[&&NHX:S=11])),"
71 + "([&&NHX:S=12],[&&NHX:S=13])12_13_14)1_14,"
72 + "([&&NHX:S=15],([&&NHX:S=21],[&&NHX:S=24])21_22_23_24)15_24);";
73 final Phylogeny multi_species_2 = factory.create( multi_species_2_str, new NHXParser() )[ 0 ];
74 final Phylogeny gene_2_1 = factory.create( gene_2_1_str, new NHXParser() )[ 0 ];
75 multi_species_2.setRooted( true );
76 gene_2_1.setRooted( true );
77 final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false );
78 if ( sdi.getSpeciationOrDuplicationEventsSum() != 0 ) {
81 if ( sdi.getDuplicationsSum() != 0 ) {
85 catch ( final Exception e ) {
86 e.printStackTrace( System.out );
92 private static boolean testGSDI_general() {
94 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
95 final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
96 + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
97 + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
98 + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
99 + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
100 + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
101 + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
102 + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
103 + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
104 + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
105 + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
106 + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
107 + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
108 + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
109 + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
110 + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
111 + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
112 final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
113 s2.setRooted( true );
114 final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
115 final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
116 s1.setRooted( true );
117 final Phylogeny g1 = TestGSDI
118 .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
119 final GSDI sdi1 = new GSDI( g1, s1, false );
120 Archaeopteryx.createApplication( g1 );
121 Archaeopteryx.createApplication( s1 );
122 if ( sdi1.getDuplicationsSum() != 1 ) {
125 if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
128 if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
129 .isSpeciationOrDuplication() ) {
132 if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) {
135 if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
138 // final Phylogeny g2 = TestGSDI
139 // .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
140 // final GSDI sdi2 = new GSDI( g2, s1, false );
141 // if ( sdi2.getDuplicationsSum() != 0 ) {
144 // if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
147 // if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
150 // if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
151 // .isSpeciationOrDuplication() ) {
154 // if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
157 // final Phylogeny g3 = TestGSDI
158 // .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
159 // final GSDI sdi3 = new GSDI( g3, s1, false );
160 // if ( sdi3.getDuplicationsSum() != 0 ) {
163 // if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
166 // if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
169 // if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
170 // .isSpeciationOrDuplication() ) {
173 // if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
176 // final Phylogeny g4 = TestGSDI
177 // .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
178 // final GSDI sdi4 = new GSDI( g4, s1, false );
179 // if ( sdi4.getDuplicationsSum() != 1 ) {
182 // if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
185 // if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
188 // if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
191 // final Phylogeny g5 = TestGSDI
192 // .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]))" );
193 // final GSDI sdi5 = new GSDI( g5, s1, false );
194 // if ( sdi5.getDuplicationsSum() != 3 ) {
197 // if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
200 // if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
203 // if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
206 // if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
209 // if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
212 // final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
213 // + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
214 // + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
215 // + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
216 // + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
217 // final Phylogeny gene7_2 = TestGSDI
218 // .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])" );
219 // gene7_2.setRooted( true );
220 // final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
221 // if ( sdi7_2.getDuplicationsSum() != 1 ) {
224 // if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
227 // if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
230 // if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
233 // if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
236 // if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
239 // if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
242 // if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
245 // if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
248 // if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
251 // final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
252 // final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
253 // if ( sdi2_0.getDuplicationsSum() != 0 ) {
256 // if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
259 // if ( sdi2_0.getSpeciationsSum() != 1 ) {
262 // if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
265 // final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
266 // final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
267 // if ( sdi2_1.getDuplicationsSum() != 0 ) {
270 // if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
273 // if ( sdi2_1.getSpeciationsSum() != 1 ) {
276 // if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
279 // final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
280 // final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
281 // if ( sdi2_2.getDuplicationsSum() != 0 ) {
284 // if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
287 // if ( sdi2_2.getSpeciationsSum() != 1 ) {
290 // if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
293 // final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
294 // final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
295 // if ( sdi2_3.getDuplicationsSum() != 1 ) {
298 // if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
301 // if ( sdi2_3.getSpeciationsSum() != 0 ) {
304 // if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
307 // final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
308 // final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
309 // if ( sdi2_4.getDuplicationsSum() != 0 ) {
312 // if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
315 // if ( sdi2_4.getSpeciationsSum() != 2 ) {
318 // if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
321 // if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
324 // final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
325 // final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
326 // if ( sdi2_5.getDuplicationsSum() != 0 ) {
329 // if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
332 // if ( sdi2_5.getSpeciationsSum() != 2 ) {
335 // if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
338 // if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
341 // final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
342 // final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
343 // if ( sdi2_6.getDuplicationsSum() != 0 ) {
346 // if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
349 // if ( sdi2_6.getSpeciationsSum() != 2 ) {
352 // if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
355 // if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
358 // final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
359 // final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
360 // if ( sdi2_7.getDuplicationsSum() != 0 ) {
363 // if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
366 // if ( sdi2_7.getSpeciationsSum() != 1 ) {
369 // if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
372 // if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
373 // .isSpeciationOrDuplication() ) {
376 // final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
377 // final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
378 // if ( sdi2_8.getDuplicationsSum() != 0 ) {
381 // if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
384 // if ( sdi2_8.getSpeciationsSum() != 1 ) {
387 // if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
388 // .isSpeciationOrDuplication() ) {
391 // if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
394 // final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
395 // final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
396 // if ( sdi2_9.getDuplicationsSum() != 0 ) {
399 // if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
402 // if ( sdi2_9.getSpeciationsSum() != 2 ) {
405 // if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
408 // if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
411 // final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
412 // final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
413 // if ( sdi2_10.getDuplicationsSum() != 0 ) {
416 // if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
419 // if ( sdi2_10.getSpeciationsSum() != 1 ) {
422 // if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
425 // if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
428 // final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
429 // final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
430 // if ( sdi2_11.getDuplicationsSum() != 0 ) {
433 // if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
436 // if ( sdi2_11.getSpeciationsSum() != 1 ) {
439 // if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
442 // if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
445 // final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
446 // final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
447 // if ( sdi2_12.getDuplicationsSum() != 0 ) {
450 // if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
453 // if ( sdi2_12.getSpeciationsSum() != 1 ) {
456 // if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
459 // if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
462 // final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
463 // final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
464 // if ( sdi2_13.getDuplicationsSum() != 0 ) {
467 // if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
470 // if ( sdi2_13.getSpeciationsSum() != 1 ) {
473 // if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
476 // if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
479 // final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
480 // final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
481 // if ( sdi2_14.getDuplicationsSum() != 1 ) {
484 // if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
487 // if ( sdi2_14.getSpeciationsSum() != 1 ) {
490 // if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
493 // if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
496 // final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
497 // final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
498 // if ( sdi2_15.getDuplicationsSum() != 1 ) {
501 // if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
504 // if ( sdi2_15.getSpeciationsSum() != 1 ) {
507 // if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
510 // if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
513 // final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
514 // final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
515 // if ( sdi2_16.getDuplicationsSum() != 1 ) {
518 // if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
521 // if ( sdi2_16.getSpeciationsSum() != 1 ) {
524 // if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
527 // if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
530 // final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
531 // final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
532 // if ( sdi2_17.getDuplicationsSum() != 1 ) {
535 // if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
538 // if ( sdi2_17.getSpeciationsSum() != 1 ) {
541 // if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
544 // if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
547 // final Phylogeny g2_18 = TestGSDI
548 // .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
549 // final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
550 // if ( sdi2_18.getDuplicationsSum() != 3 ) {
553 // if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
556 // if ( sdi2_18.getSpeciationsSum() != 0 ) {
559 // if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
562 // if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
565 // if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
568 // final Phylogeny g2_19 = TestGSDI
569 // .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
570 // final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
571 // if ( sdi2_19.getDuplicationsSum() != 1 ) {
574 // if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
577 // if ( sdi2_19.getSpeciationsSum() != 2 ) {
580 // if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
583 // if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
586 // if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
589 // final Phylogeny g2_20 = TestGSDI
590 // .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
591 // final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
592 // if ( sdi2_20.getDuplicationsSum() != 1 ) {
595 // if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
598 // if ( sdi2_20.getSpeciationsSum() != 2 ) {
601 // if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
604 // if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
607 // if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
610 // final Phylogeny g2_21 = TestGSDI
611 // .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
612 // final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
613 // if ( sdi2_21.getDuplicationsSum() != 1 ) {
616 // if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
619 // if ( sdi2_21.getSpeciationsSum() != 2 ) {
622 // if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
625 // if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
628 // if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
631 // final Phylogeny g2_22 = TestGSDI
632 // .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
633 // final GSDI sdi2_22 = new GSDI( g2_22, s2, false );
634 // //Archaeopteryx.createApplication( g2_22 );
635 // //Archaeopteryx.createApplication( s2 );
636 // if ( sdi2_22.getDuplicationsSum() != 0 ) {
639 // if ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
642 // if ( sdi2_22.getSpeciationsSum() != 2 ) {
645 // if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
648 // if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
651 // if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
654 // final Phylogeny g2_23 = TestGSDI
655 // .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
656 // final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
657 // if ( sdi2_23.getDuplicationsSum() != 0 ) {
660 // if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
663 // if ( sdi2_23.getSpeciationsSum() != 2 ) {
666 // if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
669 // if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
672 // if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
675 // final Phylogeny g2_24 = TestGSDI
676 // .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
677 // final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
678 // if ( sdi2_24.getDuplicationsSum() != 0 ) {
681 // if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
684 // if ( sdi2_24.getSpeciationsSum() != 2 ) {
687 // if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
690 // if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
693 // if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
696 // final Phylogeny g2_25 = TestGSDI
697 // .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
698 // final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
699 // if ( sdi2_25.getDuplicationsSum() != 0 ) {
702 // if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
705 // if ( sdi2_25.getSpeciationsSum() != 2 ) {
708 // if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
711 // if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
714 // if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
717 // final Phylogeny g2_26 = TestGSDI
718 // .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
719 // final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
720 // if ( sdi2_26.getDuplicationsSum() != 0 ) {
723 // if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
726 // if ( sdi2_26.getSpeciationsSum() != 3 ) {
729 // if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
732 // if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
735 // if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
738 // final Phylogeny g2_27 = TestGSDI
739 // .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
740 // final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
741 // if ( sdi2_27.getDuplicationsSum() != 0 ) {
744 // if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
747 // if ( sdi2_27.getSpeciationsSum() != 2 ) {
750 // if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
753 // if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
756 // if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
759 // final Phylogeny g2_28 = TestGSDI
760 // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
761 // final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
762 // if ( sdi2_28.getDuplicationsSum() != 0 ) {
765 // if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
768 // if ( sdi2_28.getSpeciationsSum() != 2 ) {
771 // if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
774 // if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
777 // if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
780 // final Phylogeny g2_29 = TestGSDI
781 // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
782 // final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
783 // if ( sdi2_29.getDuplicationsSum() != 0 ) {
786 // if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
789 // if ( sdi2_29.getSpeciationsSum() != 1 ) {
792 // if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
795 // if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
798 // if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
801 // final Phylogeny g2_30 = TestGSDI
802 // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
803 // final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
804 // if ( sdi2_30.getDuplicationsSum() != 1 ) {
807 // if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
810 // if ( sdi2_30.getSpeciationsSum() != 1 ) {
813 // if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
816 // if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
819 // if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
822 // final Phylogeny g2_31 = TestGSDI
823 // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
824 // final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
825 // if ( sdi2_31.getDuplicationsSum() != 1 ) {
828 // if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
831 // if ( sdi2_31.getSpeciationsSum() != 1 ) {
834 // if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
837 // if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
840 // if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
843 // final Phylogeny g2_32 = TestGSDI
844 // .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])" );
845 // final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
846 // if ( sdi2_32.getDuplicationsSum() != 0 ) {
849 // if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
852 // if ( sdi2_32.getSpeciationsSum() != 3 ) {
855 // if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
858 // if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
861 // if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
864 // if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
867 // if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
870 // if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
873 // if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
876 // if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
879 // if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
882 // if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
886 // final Phylogeny g2_33_d = TestGSDI
887 // .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=?])" );
888 // final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false );
889 // Archaeopteryx.createApplication( g2_33_d );
890 // // Archaeopteryx.createApplication( s2 );
892 // final Phylogeny g2_33 = TestGSDI
893 // .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])" );
894 // final GSDI sdi2_33 = new GSDI( g2_33, s2, false );
895 // Archaeopteryx.createApplication( g2_33 );
896 // Archaeopteryx.createApplication( s2 );
897 // if ( sdi2_33.getDuplicationsSum() != 1 ) {
900 // if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
903 // if ( sdi2_33.getSpeciationsSum() != 3 ) {
906 // if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
909 // if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
912 // if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
915 // if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
918 // if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
921 // if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
924 // if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
927 // if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
930 // if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
933 // if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
936 // if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
939 // final Phylogeny g2_34 = TestGSDI
940 // .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])" );
941 // final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
942 // if ( sdi2_34.getDuplicationsSum() != 1 ) {
945 // if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
948 // if ( sdi2_34.getSpeciationsSum() != 2 ) {
951 // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
954 // if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
957 // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
960 // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
963 // final Phylogeny g2_35 = TestGSDI
964 // .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])" );
965 // final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
966 // if ( sdi2_35.getDuplicationsSum() != 1 ) {
969 // if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
972 // if ( sdi2_35.getSpeciationsSum() != 3 ) {
975 // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
978 // if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
981 // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
984 // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
987 // if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
990 // final Phylogeny g2_36 = TestGSDI
991 // .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])" );
992 // final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
993 // if ( sdi2_36.getDuplicationsSum() != 1 ) {
996 // if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
999 // if ( sdi2_36.getSpeciationsSum() != 2 ) {
1002 // if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
1005 // if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
1008 // if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
1011 // if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1014 // final Phylogeny g2_37 = TestGSDI
1015 // .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])" );
1016 // final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
1017 // if ( sdi2_37.getDuplicationsSum() != 1 ) {
1020 // if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
1023 // if ( sdi2_37.getSpeciationsSum() != 2 ) {
1026 // if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
1029 // if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
1032 // if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
1035 // if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
1038 // final Phylogeny g2_38 = TestGSDI
1039 // .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
1040 // final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
1041 // if ( sdi2_38.getDuplicationsSum() != 5 ) {
1044 // if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
1047 // if ( sdi2_38.getSpeciationsSum() != 0 ) {
1050 // final Phylogeny g2_100 = TestGSDI
1051 // .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])))" );
1052 // final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
1053 // if ( sdi2_100.getDuplicationsSum() != 4 ) {
1056 // if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
1059 // if ( sdi2_100.getSpeciationsSum() != 4 ) {
1062 // if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
1065 // if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
1068 // if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
1071 // if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
1074 // if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
1077 // if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
1080 // if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
1083 // if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
1086 // final Phylogeny g2_101 = TestGSDI
1087 // .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])))" );
1088 // final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
1089 // if ( sdi2_101.getDuplicationsSum() != 2 ) {
1092 // if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
1095 // if ( sdi2_101.getSpeciationsSum() != 5 ) {
1098 // if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
1101 // if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
1104 // if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
1107 // if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
1110 // if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
1113 // if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
1116 // if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
1119 // if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
1122 // final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
1123 // DevelopmentTools.numberSpeciesInOrder( s_7_4 );
1124 // final Phylogeny g_7_4_1 = TestGSDI
1125 // .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1126 // + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1127 // + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1128 // + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1129 // + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1130 // + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1131 // + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1132 // + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1133 // + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1134 // + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1135 // + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1136 // + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
1137 // final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
1138 // if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
1141 // if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
1144 // if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
1147 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
1150 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
1153 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
1156 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
1159 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
1162 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
1165 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
1168 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
1171 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
1174 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
1177 // if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
1180 // final Phylogeny g_7_4_2 = TestGSDI
1181 // .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
1182 // + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
1183 // + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
1184 // + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
1185 // + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
1186 // + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
1187 // + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
1188 // + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
1189 // + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
1190 // + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
1191 // + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
1192 // + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
1193 // + "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])" );
1194 // final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
1195 // if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
1198 // if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
1201 // if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
1204 //---------------------
1205 // final String g2_0_ =
1206 // "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
1207 // final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[
1209 // g2_0.setRooted( true );
1210 // final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
1211 // if ( sdi2_0.getDuplicationsSum() != 0 ) {
1214 // final String g2_1_= "";
1215 // final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
1217 // g2_1.setRooted( true );
1218 // final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
1219 // if ( sdi2_1.getDuplicationsSum() != 0 ) {
1223 catch ( final Exception e ) {
1224 e.printStackTrace( System.out );
1230 public static void main( final String[] args ) {
1231 if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
1232 System.out.println( "binary failed" );
1234 if ( !TestGSDI.testGSDI_general() ) {
1235 System.out.println( "general failed" );
1238 System.out.println( "general OK" );
1240 // boolean success = test();
1242 // System.out.println( "OK" );
1245 // System.out.println( "failed" );