-
- final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
- + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
- + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
- + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
- + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
- + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
- + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
- + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
- + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
- + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
- + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
- + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
- + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
- + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
- + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
- + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
- + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
- final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
- s2.setRooted( true );
- final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
- final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
+ final PhylogenyFactory factory0 = ParserBasedPhylogenyFactory.getInstance();
+ final String s0 = "([&&NHX:S=1]);";
+ final String gene_0_str = "([&&NHX:S=1],[&&NHX:S=1]);";
+ final Phylogeny s_0 = factory0.create( s0, new NHXParser() )[ 0 ];
+ 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, true );
+ if ( sdi0.getSpeciationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi0.getMinDuplicationsSum() != 1 ) {
+ return false;
+ }
+ //
+ final PhylogenyFactory factory00 = ParserBasedPhylogenyFactory.getInstance();
+ final String s00 = "[&&NHX:S=1];";
+ final String gene_00_str = "([&&NHX:S=1],[&&NHX:S=1]);";
+ final Phylogeny s_00 = factory00.create( s00, new NHXParser() )[ 0 ];
+ 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, true );
+ if ( sdi00.getSpeciationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi00.getMinDuplicationsSum() != 1 ) {
+ return false;
+ }
+ //
+ final String s1str = "(((([&&NHX:S=HUMAN],([&&NHX:S=MOUSE],[&&NHX:S=RAT])),([&&NHX:S=CAEEL],[&&NHX:S=CAEBR])),[&&NHX:S=YEAST]),[&&NHX:S=ARATH])";
+ final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1str, new NHXParser() )[ 0 ];