+ final String g2_0_ = "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
+ final Phylogeny g2_0p = TestGSDI.createPhylogeny( g2_0_ );
+ g2_0.setRooted( true );
+ final GSDI sdi2_0p = new GSDI( g2_0p, s2, false );
+ if ( sdi2_0p.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ //--
+ final Phylogeny tol_143_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + "tol_143.xml" )[ 0 ];
+ final Phylogeny gene_tree_tax_code_4_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gene_tree_tax_code_4.xml" )[ 0 ];
+ final GSDI gsdi_143_4_1 = new GSDI( gene_tree_tax_code_4_.copy(), tol_143_.copy(), false, true, true );
+ if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) {
+ return false;
+ }
+ if ( gsdi_143_4_1.getSpeciationsSum() != 28 ) {
+ return false;
+ }
+ if ( gsdi_143_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_gene_tree_sn_wnt = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ];
+ gsdi_test_gene_tree_sn_wnt.setRooted( true );
+ final GSDI a = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), tol_143_.copy(), false, true, true );
+ if ( a.getDuplicationsSum() != 33 ) {
+ return false;
+ }
+ if ( a.getSpeciationsSum() != 31 ) {
+ return false;
+ }
+ if ( a.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( a.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( a.getMappedExternalSpeciesTreeNodes().size() != 26 ) {
+ return false;
+ }
+ if ( a.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_species_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_species_tree_sn.xml" )[ 0 ];
+ final GSDI b = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
+ gsdi_test_species_tree_sn_xml.copy(),
+ false,
+ true,
+ true );
+ if ( b.getDuplicationsSum() != 8 ) {
+ return false;
+ }
+ if ( b.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( b.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( b.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( b.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
+ return false;
+ }
+ if ( b.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+ return false;
+ }
+ if ( b.getStrippedExternalGeneTreeNodes().size() != 87 ) {
+ return false;
+ }
+ if ( b.getStrippedSpeciesTreeNodes().size() != 17 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_species_tree_sn_nh = TestGSDI
+ .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';" );
+ PhylogenyMethods.transferNodeNameToField( gsdi_test_species_tree_sn_nh,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ true );
+ final GSDI c = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
+ gsdi_test_species_tree_sn_nh.copy(),
+ false,
+ true,
+ true );
+ if ( c.getDuplicationsSum() != 8 ) {
+ return false;
+ }
+ if ( c.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( c.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( c.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( c.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
+ return false;
+ }
+ if ( c.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+ return false;
+ }
+ if ( c.getStrippedExternalGeneTreeNodes().size() != 87 ) {
+ return false;
+ }
+ if ( c.getStrippedSpeciesTreeNodes().size() != 15 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_gene_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_gene_tree_codes.xml" )[ 0 ];
+ final Phylogeny gsdi_test_species_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_species_tree_codes.xml" )[ 0 ];
+ final GSDI d = new GSDI( gsdi_test_gene_tree_codes_xml.copy(),
+ gsdi_test_species_tree_codes_xml.copy(),
+ false,
+ true,
+ true );
+ if ( d.getDuplicationsSum() != 21 ) {
+ return false;
+ }
+ if ( d.getSpeciationsSum() != 28 ) {
+ return false;
+ }
+ if ( d.getSpeciationOrDuplicationEventsSum() != 6 ) {
+ return false;
+ }
+ if ( d.getTaxCompBase() != TaxonomyComparisonBase.CODE ) {
+ return false;
+ }
+ if ( d.getMappedExternalSpeciesTreeNodes().size() != 17 ) {
+ return false;
+ }
+ if ( d.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+ return false;
+ }
+ if ( d.getStrippedExternalGeneTreeNodes().size() != 12 ) {
+ return false;
+ }
+ if ( d.getStrippedSpeciesTreeNodes().size() != 3 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_gene_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_gene_tree_sn.xml" )[ 0 ];
+ final GSDI e = new GSDI( gsdi_test_gene_tree_sn_xml.copy(),
+ gsdi_test_species_tree_sn_xml.copy(),
+ false,
+ true,
+ true );
+ if ( e.getDuplicationsSum() != 7 ) {
+ return false;
+ }
+ if ( e.getSpeciationsSum() != 9 ) {
+ return false;
+ }
+ if ( e.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( e.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( e.getMappedExternalSpeciesTreeNodes().size() != 12 ) {
+ return false;
+ }
+ if ( e.getReMappedScientificNamesFromGeneTree().size() != 8 ) {
+ return false;
+ }
+ if ( e.getStrippedExternalGeneTreeNodes().size() != 3 ) {
+ return false;
+ }
+ if ( e.getStrippedSpeciesTreeNodes().size() != 7 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testGSDIR_general() {
+ try {
+
+ 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 ];
+ s1.setRooted( true );
+ final Phylogeny g1 = TestGSDI
+ .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
+ final GSDIR sdi1 = new GSDIR( g1, s1, false, 1 );
+ // Archaeopteryx.createApplication( g1 );
+ // Archaeopteryx.createApplication( s1 );
+ if ( sdi1.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isDuplication() ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
+ return false;
+ }
+