X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Frio%2FTestRIO.java;h=fa704b7a3b352f82243eacab2bc11ba4df7b4d4d;hb=fbb7c0a322111e5221773fed19591da29296efb5;hp=06468af4a7df94870e82c08f790a02ae7e326320;hpb=9bad57b1ba0f75075ab8c6bda1dedb906f8c6280;p=jalview.git diff --git a/forester/java/src/org/forester/rio/TestRIO.java b/forester/java/src/org/forester/rio/TestRIO.java index 06468af..fa704b7 100644 --- a/forester/java/src/org/forester/rio/TestRIO.java +++ b/forester/java/src/org/forester/rio/TestRIO.java @@ -1,6 +1,8 @@ package org.forester.rio; +import java.io.File; + import org.forester.datastructures.IntMatrix; import org.forester.io.parsers.nhx.NHXParser; import org.forester.phylogeny.Phylogeny; @@ -8,6 +10,7 @@ import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; +import org.forester.rio.RIO.REROOTING; import org.forester.sdi.SDIutil.ALGORITHM; import org.forester.sdi.SDIutil.TaxonomyComparisonBase; import org.forester.util.ForesterUtil; @@ -15,12 +18,27 @@ 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() ) { + System.out.println( "testRIO GSDIR failed" ); + } + if ( !testRIO_GSDIR_Iterating() ) { + System.out.println( "testRIO GSDIR iterating failed" ); + } + else { + System.out.println( "OK" ); + } + } public static boolean test() { if ( !testRIO_GSDIR() ) { return false; } + if ( !testRIO_GSDIR_Iterating() ) { + return false; + } return true; } @@ -30,7 +48,182 @@ public final class TestRIO { final NHXParser nhx = new NHXParser(); nhx.setReplaceUnderscores( false ); nhx.setIgnoreQuotes( true ); - nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES ); + 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; + } 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);"; @@ -39,8 +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 = new RIO( gene_trees_1, species_tree_1, ALGORITHM.GSDIR, 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; } @@ -53,7 +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; @@ -79,7 +278,7 @@ public final class TestRIO { 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 = new RIO( gene_trees_2, species_tree_2, ALGORITHM.GSDIR, true, false ); + rio = RIO.executeAnalysis( gene_trees_2, species_tree_2 ); m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true ); // System.out.println( m.toString() ); if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) { @@ -100,6 +299,430 @@ public final class TestRIO { if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) { return false; } + // + RIO r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode.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 ) { + 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_NEMVE,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( "H2ZH97_CIOSA,200,200,201,201,201,201" ) ) { + System.out.println( m.getRowAsString( 3, ',' ) ); + return false; + } + if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE,200,200,201,201,201,43" ) ) { + System.out.println( m.getRowAsString( 4, ',' ) ); + return false; + } + if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR,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_taxid.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.ID ) { + 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_45351,201,200,201,200,200,200" ) ) { + System.out.println( m.getRowAsString( 0, ',' ) ); + return false; + } + //mouse + if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_10090,200,201,200,201,201,43" ) ) { + System.out.println( m.getRowAsString( 1, ',' ) ); + return false; + } + //human + if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_9606,201,200,201,200,200,43" ) ) { + System.out.println( m.getRowAsString( 2, ',' ) ); + return false; + } + if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_51511,200,201,200,201,201,201" ) ) { + System.out.println( m.getRowAsString( 3, ',' ) ); + return false; + } + if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_7955,200,201,200,201,201,43" ) ) { + System.out.println( m.getRowAsString( 4, ',' ) ); + return false; + } + if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_8364,200,43,43,201,43,201" ) ) { + 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.BY_ALGORITHM, + "", + -1, + -1, + true, + false, + true ); + if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { + return false; + } + if ( r0.getAnalyzedGeneTrees().length != 201 ) { + return false; + } + if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) { + 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, + // 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, + // 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, + // 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, + // 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 ); @@ -108,12 +731,97 @@ public final class TestRIO { return true; } - public static void main( final String[] args ) { - if ( !testRIO_GSDIR() ) { - System.out.println( "testRIO GSDIR failed" ); + 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 ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) { + return false; + } + 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" ) ) { + return false; + } + if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) { + return false; + } + if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) { + return false; + } + if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) { + return false; + } + if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) { + return false; + } + if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) { + 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, + 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( "CAEEL,5,5,5,5,5,5" ) ) { + return false; + } + if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) { + return false; + } + if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) { + return false; + } + if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) { + return false; + } + if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) { + return false; + } } - else { - System.out.println( "OK" ); + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; } + return true; } } \ No newline at end of file