X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Frio%2FTestRIO.java;h=fa704b7a3b352f82243eacab2bc11ba4df7b4d4d;hb=886c0c0a7a7cef72503df9f21762db1dab594362;hp=58b2050580944b0c308dd47d4a4ad6a20159087e;hpb=3e6923f2f1a9802f78f7989b42590e5adfccac34;p=jalview.git diff --git a/forester/java/src/org/forester/rio/TestRIO.java b/forester/java/src/org/forester/rio/TestRIO.java index 58b2050..fa704b7 100644 --- a/forester/java/src/org/forester/rio/TestRIO.java +++ b/forester/java/src/org/forester/rio/TestRIO.java @@ -18,7 +18,7 @@ import org.forester.util.ForesterUtil; public final class TestRIO { private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() - + "test_data" + ForesterUtil.getFileSeparator(); + + "test_data" + ForesterUtil.getFileSeparator(); public static void main( final String[] args ) { if ( !testRIO_GSDIR() ) { @@ -42,33 +42,32 @@ public final class TestRIO { return true; } - private static boolean testRIO_GSDIR_Iterating() { + private static boolean testRIO_GSDIR() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final NHXParser nhx = new NHXParser(); nhx.setReplaceUnderscores( false ); nhx.setIgnoreQuotes( true ); - nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES ); - final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);" - + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));" - + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);"; - nhx.setSource( gene_trees_1_str ); - final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"; - final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ]; - species_tree_1.setRooted( true ); - PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true ); - //Archaeopteryx.createApplication( species_trees_1 ); - RIO rio = RIO.executeAnalysis( nhx, - species_tree_1, + 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 ); - //if ( rio.getAnalyzedGeneTrees().length != 5 ) { - // return false; - //} - if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) { + false, + true ); + if ( rio.getAnalyzedGeneTrees().length != 4 ) { + return false; + } + if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) { return false; } if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) { @@ -77,67 +76,154 @@ public final class TestRIO { if ( rio.getRemovedGeneTreeNodes().size() != 0 ) { return false; } - IntMatrix m = rio.getOrthologTable(); - //System.out.println( m.toString() ); - if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) { + 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( "CAEEL,5,5,5,5,5,5" ) ) { + if ( !m.getRowAsString( 1, ',' ).equals( "RAT,4,4" ) ) { + System.out.println( m.toString() ); return false; } - if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) { + 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 ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) { + if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) { return false; } - if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) { + if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { return false; } - if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) { + 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 species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);"; - final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ]; - species_tree_2.setRooted( true ); - PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true ); - rio = RIO.executeAnalysis( nhx, species_tree_2, ALGORITHM.GSDIR, REROOTING.BY_ALGORITHM, "", true, false ); - m = rio.getOrthologTable(); - // System.out.println( m.toString() ); - if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) { + // + 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 ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) { + if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) { return false; } - if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) { + if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { return false; } - if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) { + if ( rio.getRemovedGeneTreeNodes().size() != 0 ) { return false; } - if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) { + m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true ); + if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,3,0" ) ) { + System.out.println( m.toString() ); return false; } - if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) { + 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; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testRIO_GSDIR() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final NHXParser nhx = new NHXParser(); - nhx.setReplaceUnderscores( false ); - nhx.setIgnoreQuotes( true ); - nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES ); final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);" + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));" + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);"; @@ -146,14 +232,14 @@ public final class TestRIO { final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ]; species_tree_1.setRooted( true ); PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true ); - //Archaeopteryx.createApplication( species_trees_1 ); - RIO rio = RIO.executeAnalysis( gene_trees_1, - species_tree_1, - ALGORITHM.GSDIR, - REROOTING.BY_ALGORITHM, - "", - true, - false ); + rio = RIO.executeAnalysis( gene_trees_1, + species_tree_1, + ALGORITHM.GSDIR, + REROOTING.BY_ALGORITHM, + "", + true, + false, + true ); if ( rio.getAnalyzedGeneTrees().length != 5 ) { return false; } @@ -166,7 +252,7 @@ public final class TestRIO { if ( rio.getRemovedGeneTreeNodes().size() != 0 ) { return false; } - IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true ); + m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true ); // System.out.println( m.toString() ); if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) { return false; @@ -222,7 +308,8 @@ public final class TestRIO { -1, -1, true, - false ); + false, + true ); if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) { return false; } @@ -230,6 +317,7 @@ public final class TestRIO { return false; } if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { + System.out.println( r0.getExtNodesOfAnalyzedGeneTrees() ); return false; } if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { @@ -266,7 +354,6 @@ public final class TestRIO { System.out.println( m.getRowAsString( 5, ',' ) ); return false; } - // r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxid.run1.t" ), new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), ALGORITHM.GSDIR, @@ -275,7 +362,8 @@ public final class TestRIO { -1, -1, true, - false ); + false, + true ); if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.ID ) { return false; } @@ -329,7 +417,8 @@ public final class TestRIO { -1, -1, true, - false ); + false, + true ); if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { return false; } @@ -337,298 +426,397 @@ public final class TestRIO { return false; } if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { - return false; - } - if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { - return false; - } - if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { - return false; - } - if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) { - return false; - } - m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); - if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,200,200,200" ) ) { - System.out.println( m.getRowAsString( 0, ',' ) ); - return false; - } - if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,200,200,43" ) ) { - System.out.println( m.getRowAsString( 1, ',' ) ); - return false; - } - if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,201,201,43" ) ) { - System.out.println( m.getRowAsString( 2, ',' ) ); - return false; - } - if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,200,200,201,201,201,201" ) ) { - System.out.println( m.getRowAsString( 3, ',' ) ); - return false; - } - if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,201,201,43" ) ) { - System.out.println( m.getRowAsString( 4, ',' ) ); - return false; - } - if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,201,43,201" ) ) { - System.out.println( m.getRowAsString( 5, ',' ) ); - return false; - } + System.out.println( r0.getExtNodesOfAnalyzedGeneTrees() ); + return false; + } + // if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { + // return false; + // } + // if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { + // return false; + // } + // if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) { + // return false; + // } + // m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); + // if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,200,200,200" ) ) { + // System.out.println( m.getRowAsString( 0, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,200,200,43" ) ) { + // System.out.println( m.getRowAsString( 1, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,201,201,43" ) ) { + // System.out.println( m.getRowAsString( 2, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,200,200,201,201,201,201" ) ) { + // System.out.println( m.getRowAsString( 3, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,201,201,43" ) ) { + // System.out.println( m.getRowAsString( 4, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,201,43,201" ) ) { + // System.out.println( m.getRowAsString( 5, ',' ) ); + // return false; + // } // - r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ), - new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), - ALGORITHM.GSDIR, - REROOTING.MIDPOINT, - "", - -1, - -1, - true, - false ); - if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { - return false; - } - if ( r0.getAnalyzedGeneTrees().length != 201 ) { - return false; - } - if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { - return false; - } - if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { - return false; - } - if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { - return false; - } - if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) { - return false; - } - m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); - if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,94,93,160,93,93" ) ) { - System.out.println( m.getRowAsString( 0, ',' ) ); - return false; - } - if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,94,201,200,53,200,43" ) ) { - System.out.println( m.getRowAsString( 1, ',' ) ); - return false; - } - if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,93,200,201,53,201,43" ) ) { - System.out.println( m.getRowAsString( 2, ',' ) ); - return false; - } - if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,160,53,53,201,53,53" ) ) { - System.out.println( m.getRowAsString( 3, ',' ) ); - return false; - } - if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,93,200,201,53,201,43" ) ) { - System.out.println( m.getRowAsString( 4, ',' ) ); - return false; - } - if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,93,43,43,53,43,201" ) ) { - System.out.println( m.getRowAsString( 5, ',' ) ); - return false; - } + // r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ), + // new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), + // ALGORITHM.GSDIR, + // REROOTING.MIDPOINT, + // "", + // -1, + // -1, + // true, + // false, + // true ); + // if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { + // return false; + // } + // if ( r0.getAnalyzedGeneTrees().length != 201 ) { + // return false; + // } + // if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { + // return false; + // } + // if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { + // return false; + // } + // if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { + // return false; + // } + // if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) { + // return false; + // } + // m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); + // if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,94,93,160,93,93" ) ) { + // System.out.println( m.getRowAsString( 0, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,94,201,200,53,200,43" ) ) { + // System.out.println( m.getRowAsString( 1, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,93,200,201,53,201,43" ) ) { + // System.out.println( m.getRowAsString( 2, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,160,53,53,201,53,53" ) ) { + // System.out.println( m.getRowAsString( 3, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,93,200,201,53,201,43" ) ) { + // System.out.println( m.getRowAsString( 4, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,93,43,43,53,43,201" ) ) { + // System.out.println( m.getRowAsString( 5, ',' ) ); + // return false; + // } // - r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ), - new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), - ALGORITHM.GSDIR, - REROOTING.OUTGROUP, - "H2ZH97_Ciona_savignyi", - -1, - -1, - true, - false ); - if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { - return false; - } - if ( r0.getAnalyzedGeneTrees().length != 201 ) { - return false; - } - if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { - return false; - } - if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { - return false; - } - if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { - return false; - } - if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) { - return false; - } - m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); - if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,0,200,200" ) ) { - System.out.println( m.getRowAsString( 0, ',' ) ); - return false; - } - if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,0,200,43" ) ) { - System.out.println( m.getRowAsString( 1, ',' ) ); - return false; - } - if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,0,201,43" ) ) { - System.out.println( m.getRowAsString( 2, ',' ) ); - return false; - } - if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,0,0,0,201,0,0" ) ) { - System.out.println( m.getRowAsString( 3, ',' ) ); - return false; - } - if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,0,201,43" ) ) { - System.out.println( m.getRowAsString( 4, ',' ) ); - return false; - } - if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,0,43,201" ) ) { - System.out.println( m.getRowAsString( 5, ',' ) ); - return false; - } + // r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ), + // new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), + // ALGORITHM.GSDIR, + // REROOTING.OUTGROUP, + // "H2ZH97_Ciona_savignyi", + // -1, + // -1, + // true, + // false, + // true ); + // if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { + // return false; + // } + // if ( r0.getAnalyzedGeneTrees().length != 201 ) { + // return false; + // } + // if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { + // return false; + // } + // if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { + // return false; + // } + // if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { + // return false; + // } + // if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) { + // return false; + // } + // m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); + // if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,0,200,200" ) ) { + // System.out.println( m.getRowAsString( 0, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,0,200,43" ) ) { + // System.out.println( m.getRowAsString( 1, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,0,201,43" ) ) { + // System.out.println( m.getRowAsString( 2, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,0,0,0,201,0,0" ) ) { + // System.out.println( m.getRowAsString( 3, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,0,201,43" ) ) { + // System.out.println( m.getRowAsString( 4, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,0,43,201" ) ) { + // System.out.println( m.getRowAsString( 5, ',' ) ); + // return false; + // } // // - r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ), - new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), - ALGORITHM.GSDIR, - REROOTING.NONE, - null, - 10, - 19, - true, - false ); - if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { - return false; - } - if ( r0.getAnalyzedGeneTrees().length != 10 ) { - return false; - } - if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { - return false; - } - if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { - return false; - } - if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { - return false; - } - if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 4 ) { - return false; - } - m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); - if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,10,0,0,10,0,0" ) ) { - System.out.println( m.getRowAsString( 0, ',' ) ); - return false; - } - if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,0,10,0,0,0,0" ) ) { - System.out.println( m.getRowAsString( 1, ',' ) ); - return false; - } - if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,0,0,10,0,0,0" ) ) { - System.out.println( m.getRowAsString( 2, ',' ) ); - return false; - } - if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,10,0,0,10,0,0" ) ) { - System.out.println( m.getRowAsString( 3, ',' ) ); - return false; - } - if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,0,0,0,0,10,0" ) ) { - System.out.println( m.getRowAsString( 4, ',' ) ); - return false; - } - if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,0,0,0,0,0,10" ) ) { - System.out.println( m.getRowAsString( 5, ',' ) ); - return false; - } + // r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ), + // new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), + // ALGORITHM.GSDIR, + // REROOTING.NONE, + // null, + // 10, + // 19, + // true, + // false, + // true ); + // if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { + // return false; + // } + // if ( r0.getAnalyzedGeneTrees().length != 10 ) { + // return false; + // } + // if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { + // return false; + // } + // if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { + // return false; + // } + // if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { + // return false; + // } + // if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 4 ) { + // return false; + // } + // m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); + // if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,10,0,0,10,0,0" ) ) { + // System.out.println( m.getRowAsString( 0, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,0,10,0,0,0,0" ) ) { + // System.out.println( m.getRowAsString( 1, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,0,0,10,0,0,0" ) ) { + // System.out.println( m.getRowAsString( 2, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,10,0,0,10,0,0" ) ) { + // System.out.println( m.getRowAsString( 3, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,0,0,0,0,10,0" ) ) { + // System.out.println( m.getRowAsString( 4, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,0,0,0,0,0,10" ) ) { + // System.out.println( m.getRowAsString( 5, ',' ) ); + // return false; + // } // - r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_1.run1.t" ), - new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), - ALGORITHM.GSDIR, - REROOTING.BY_ALGORITHM, - "", - -1, - -1, - true, - false ); - if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) { + // r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_1.run1.t" ), + // new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), + // ALGORITHM.GSDIR, + // REROOTING.BY_ALGORITHM, + // "", + // -1, + // -1, + // true, + // false, + // true ); + // if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) { + // return false; + // } + // if ( r0.getAnalyzedGeneTrees().length != 201 ) { + // return false; + // } + // if ( r0.getExtNodesOfAnalyzedGeneTrees() != 3 ) { + // return false; + // } + // if ( r0.getIntNodesOfAnalyzedGeneTrees() != 2 ) { + // return false; + // } + // if ( r0.getRemovedGeneTreeNodes().size() != 3 ) { + // return false; + // } + // if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 0 ) { + // return false; + // } + // m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); + // if ( !m.getRowAsString( 0, ',' ).equals( "BCDO2_HUMAN,201,201,201" ) ) { + // System.out.println( m.getRowAsString( 0, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 1, ',' ).equals( "Q1RLW1_DANRE,201,201,201" ) ) { + // System.out.println( m.getRowAsString( 1, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 2, ',' ).equals( "Q6DIN7_XENTR,201,201,201" ) ) { + // System.out.println( m.getRowAsString( 2, ',' ) ); + // return false; + // } + // + // + // r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_2.run1.t" ), + // new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), + // ALGORITHM.GSDIR, + // REROOTING.BY_ALGORITHM, + // "", + // -1, + // -1, + // true, + // false, + // true ); + // if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) { + // return false; + // } + // if ( r0.getAnalyzedGeneTrees().length != 201 ) { + // return false; + // } + // if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { + // return false; + // } + // if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { + // return false; + // } + // if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { + // return false; + // } + // if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) { + // return false; + // } + // m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); + // if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE&1,201,201,200,200,200,200" ) ) { + // System.out.println( m.getRowAsString( 0, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN+,201,201,200,200,200,43" ) ) { + // System.out.println( m.getRowAsString( 1, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) { + // System.out.println( m.getRowAsString( 2, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 3, ',' ).equals( "CIOSA,200,200,201,201,201,201" ) ) { + // System.out.println( m.getRowAsString( 3, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE/12-45,200,200,201,201,201,43" ) ) { + // System.out.println( m.getRowAsString( 4, ',' ) ); + // return false; + // } + // if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR-LOUSE,200,43,43,201,43,201" ) ) { + // System.out.println( m.getRowAsString( 5, ',' ) ); + // return false; + // } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testRIO_GSDIR_Iterating() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final NHXParser nhx = new NHXParser(); + nhx.setReplaceUnderscores( false ); + nhx.setIgnoreQuotes( true ); + nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);" + + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));" + + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);"; + nhx.setSource( gene_trees_1_str ); + final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"; + final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ]; + species_tree_1.setRooted( true ); + PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true ); + //Archaeopteryx.createApplication( species_trees_1 ); + RIO rio = RIO.executeAnalysis( nhx, + species_tree_1, + ALGORITHM.GSDIR, + REROOTING.BY_ALGORITHM, + "", + true, + false, + true ); + if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) { return false; } - if ( r0.getAnalyzedGeneTrees().length != 201 ) { + if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) { return false; } - if ( r0.getExtNodesOfAnalyzedGeneTrees() != 3 ) { + if ( rio.getRemovedGeneTreeNodes().size() != 0 ) { return false; } - if ( r0.getIntNodesOfAnalyzedGeneTrees() != 2 ) { + IntMatrix m = rio.getOrthologTable(); + //System.out.println( m.toString() ); + if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) { return false; } - if ( r0.getRemovedGeneTreeNodes().size() != 3 ) { + if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) { return false; } - if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 0 ) { + if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) { return false; } - m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); - if ( !m.getRowAsString( 0, ',' ).equals( "BCDO2_HUMAN,201,201,201" ) ) { - System.out.println( m.getRowAsString( 0, ',' ) ); + if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) { return false; } - if ( !m.getRowAsString( 1, ',' ).equals( "Q1RLW1_DANRE,201,201,201" ) ) { - System.out.println( m.getRowAsString( 1, ',' ) ); + if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) { return false; } - if ( !m.getRowAsString( 2, ',' ).equals( "Q6DIN7_XENTR,201,201,201" ) ) { - System.out.println( m.getRowAsString( 2, ',' ) ); + if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) { return false; } // - // - r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_2.run1.t" ), - new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ), - ALGORITHM.GSDIR, - REROOTING.BY_ALGORITHM, - "", - -1, - -1, - true, - false ); - if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) { - return false; - } - if ( r0.getAnalyzedGeneTrees().length != 201 ) { - return false; - } - if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { - return false; - } - if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) { - return false; - } - if ( r0.getRemovedGeneTreeNodes().size() != 0 ) { - return false; - } - if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) { - return false; - } - m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true ); - if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE&1,201,201,200,200,200,200" ) ) { - System.out.println( m.getRowAsString( 0, ',' ) ); + final String species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);"; + final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ]; + species_tree_2.setRooted( true ); + PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true ); + rio = RIO.executeAnalysis( nhx, + species_tree_2, + ALGORITHM.GSDIR, + REROOTING.BY_ALGORITHM, + "", + true, + false, + true ); + m = rio.getOrthologTable(); + // System.out.println( m.toString() ); + if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) { return false; } - if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN+,201,201,200,200,200,43" ) ) { - System.out.println( m.getRowAsString( 1, ',' ) ); + if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) { return false; } - if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) { - System.out.println( m.getRowAsString( 2, ',' ) ); + if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) { return false; } - if ( !m.getRowAsString( 3, ',' ).equals( "CIOSA,200,200,201,201,201,201" ) ) { - System.out.println( m.getRowAsString( 3, ',' ) ); + if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) { return false; } - if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE/12-45,200,200,201,201,201,43" ) ) { - System.out.println( m.getRowAsString( 4, ',' ) ); + if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) { return false; } - if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR-LOUSE,200,43,43,201,43,201" ) ) { - System.out.println( m.getRowAsString( 5, ',' ) ); + if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) { return false; } - // } catch ( final Exception e ) { e.printStackTrace( System.out );