final Phylogeny gene_0 = factory0.create( gene_0_str, new NHXParser() )[ 0 ];
s_0.setRooted( true );
gene_0.setRooted( true );
- final GSDIR sdi0 = new GSDIR( gene_0, s_0, true, true );
+ final GSDIR sdi0 = new GSDIR( gene_0, s_0, true, true, true );
if ( sdi0.getSpeciationsSum() != 0 ) {
return false;
}
final Phylogeny gene_00 = factory00.create( gene_00_str, new NHXParser() )[ 0 ];
s_00.setRooted( true );
gene_00.setRooted( true );
- final GSDIR sdi00 = new GSDIR( gene_00, s_00, true, true );
+ final GSDIR sdi00 = new GSDIR( gene_00, s_00, true, true, true );
if ( sdi00.getSpeciationsSum() != 0 ) {
return false;
}
s1.setRooted( true );
final Phylogeny g1 = TestGSDI
.createPhylogeny( "(HUMAN[&&NHX:S=HUMAN],(RAT[&&NHX:S=RAT],(CAEEL[&&NHX:T=:S=CAEEL],YEAST[&&NHX:S=YEAST])))" );
- final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false );
+ final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false, true );
if ( sdi1.getMinDuplicationsSum() != 0 ) {
return false;
}
final Phylogeny g2 = TestGSDI
.createPhylogeny( "(((HUMAN[&&NHX:S=HUMAN],RAT[&&NHX:S=RAT]),CAEEL[&&NHX:T=:S=CAEEL]),YEAST[&&NHX:S=YEAST])" );
- final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false );
+ final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false, true );
if ( sdi2.getMinDuplicationsSum() != 0 ) {
return false;
}
final Phylogeny g3 = TestGSDI
.createPhylogeny( "(RAT[&&NHX:S=RAT],HUMAN[&&NHX:S=HUMAN],(YEAST[&&NHX:S=YEAST],CAEEL[&&NHX:T=:S=CAEEL]))" );
- final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false );
+ final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false, true );
if ( sdi3.getMinDuplicationsSum() != 0 ) {
return false;
}
final Phylogeny g4 = TestGSDI
.createPhylogeny( "(((((MOUSE[&&NHX:S=MOUSE],[&&NHX:S=RAT]),[&&NHX:S=HUMAN]),([&&NHX:S=ARATH],[&&NHX:S=YEAST])),[&&NHX:S=CAEEL]),[&&NHX:S=CAEBR])" );
- final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false );
+ final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false, true );
if ( sdi4.getMinDuplicationsSum() != 0 ) {
return false;
}
final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2str, new NHXParser() )[ 0 ];
s2.setRooted( true );
final Phylogeny g5 = TestGSDI.createPhylogeny( s2str );
- final GSDIR sdi5 = new GSDIR( g5, s2, false, false );
+ final GSDIR sdi5 = new GSDIR( g5, s2, false, false, true );
if ( sdi5.getMinDuplicationsSum() != 0 ) {
System.out.println( sdi5.getMinDuplicationsSum() );
return false;