+ nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ //
+ final String gene_trees_00_str = "(MOUSE,RAT);(MOUSE,RAT);(MOUSE,RAT);(RAT,MOUSE);";
+ final Phylogeny[] gene_trees_00 = factory.create( gene_trees_00_str, nhx );
+ final String species_trees_00_str = "(MOUSE,RAT);";
+ final Phylogeny species_tree_00 = factory.create( species_trees_00_str, new NHXParser() )[ 0 ];
+ species_tree_00.setRooted( true );
+ PhylogenyMethods.transferNodeNameToField( species_tree_00, PhylogenyNodeField.TAXONOMY_CODE, true );
+ RIO rio = RIO.executeAnalysis( gene_trees_00,
+ species_tree_00,
+ ALGORITHM.GSDIR,
+ REROOTING.BY_ALGORITHM,
+ "",
+ true,
+ false,
+ true );
+ if ( rio.getAnalyzedGeneTrees().length != 4 ) {
+ return false;
+ }
+ if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+ return false;
+ }
+ if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
+ return false;
+ }
+ if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+ return false;
+ }
+ IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+ if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE,4,4" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ if ( !m.getRowAsString( 1, ',' ).equals( "RAT,4,4" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ final String gene_trees_000_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
+ final Phylogeny[] gene_trees_000 = factory.create( gene_trees_000_str, nhx );
+ final String species_trees_000_str = "[&&NHX:S=MOUSE];";
+ final Phylogeny species_tree_000 = factory.create( species_trees_000_str, new NHXParser() )[ 0 ];
+ species_tree_000.setRooted( true );
+ rio = RIO.executeAnalysis( gene_trees_000,
+ species_tree_000,
+ ALGORITHM.GSDIR,
+ REROOTING.BY_ALGORITHM,
+ "",
+ true,
+ false,
+ true );
+ if ( rio.getAnalyzedGeneTrees().length != 2 ) {
+ return false;
+ }
+ if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+ return false;
+ }
+ if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+ return false;
+ }
+ m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+ if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,2,0" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,2" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ //
+ //
+ final String gene_trees_0000_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
+ final Phylogeny[] gene_trees_0000 = factory.create( gene_trees_0000_str, nhx );
+ final String species_trees_0000_str = "([&&NHX:S=MOUSE]);";
+ final Phylogeny species_tree_0000 = factory.create( species_trees_0000_str, new NHXParser() )[ 0 ];
+ species_tree_0000.setRooted( true );
+ rio = RIO.executeAnalysis( gene_trees_0000,
+ species_tree_0000,
+ ALGORITHM.GSDIR,
+ REROOTING.BY_ALGORITHM,
+ "",
+ true,
+ false,
+ true );
+ if ( rio.getAnalyzedGeneTrees().length != 3 ) {
+ return false;
+ }
+ if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+ return false;
+ }
+ if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+ return false;
+ }
+ m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+ if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,3,0" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,3" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ //
+ final String gene_trees_x_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
+ final Phylogeny[] gene_trees_x = factory.create( gene_trees_x_str, nhx );
+ final String species_trees_x_str = "[&&NHX:S=MOUSE];";
+ final Phylogeny species_tree_x = factory.create( species_trees_x_str, new NHXParser() )[ 0 ];
+ species_tree_x.setRooted( true );
+ rio = RIO.executeAnalysis( gene_trees_x,
+ species_tree_x,
+ ALGORITHM.GSDIR,
+ REROOTING.BY_ALGORITHM,
+ "",
+ true,
+ false,
+ true );
+ if ( rio.getAnalyzedGeneTrees().length != 1 ) {
+ return false;
+ }
+ if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+ return false;
+ }
+ if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+ return false;
+ }
+ m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+ if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,1,0" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,1" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ final String gene_trees_xx_str = "(MOUSE1[&&NHX:S=MOUSE],RAT1[&&NHX:S=RAT])";
+ final Phylogeny[] gene_trees_xx = factory.create( gene_trees_xx_str, nhx );
+ final String species_trees_xx_str = "([&&NHX:S=MOUSE],[&&NHX:S=RAT]);";
+ final Phylogeny species_tree_xx = factory.create( species_trees_xx_str, new NHXParser() )[ 0 ];
+ species_tree_xx.setRooted( true );
+ rio = RIO.executeAnalysis( gene_trees_xx,
+ species_tree_xx,
+ ALGORITHM.GSDIR,
+ REROOTING.BY_ALGORITHM,
+ "",
+ true,
+ false,
+ true );
+ if ( rio.getAnalyzedGeneTrees().length != 1 ) {
+ return false;
+ }
+ if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+ return false;
+ }
+ if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+ return false;
+ }
+ m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+ if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,1,1" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }
+ if ( !m.getRowAsString( 1, ',' ).equals( "RAT1,1,1" ) ) {
+ System.out.println( m.toString() );
+ return false;
+ }