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" );
}
if ( !testRIO_GSDIR() ) {
return false;
}
+ if ( !testRIO_GSDIR_Iterating() ) {
+ return false;
+ }
return true;
}
- private static boolean testRIO_GSDIR() {
+ 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.YES );
+ nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
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);";
- final Phylogeny[] gene_trees_1 = factory.create( gene_trees_1_str, nhx );
+ 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( gene_trees_1,
+ RIO rio = RIO.executeAnalysis( nhx,
species_tree_1,
ALGORITHM.GSDIR,
REROOTING.BY_ALGORITHM,
"",
true,
false );
+ 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 );
+ 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;
+ }
+ }
+ 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.AGRESSIVE );
+ //
+ 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 != 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 );
+ 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 );
+ 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 );
+ 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 );
+ 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);";
+ final Phylogeny[] gene_trees_1 = factory.create( gene_trees_1_str, nhx );
+ 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 );
+ rio = RIO.executeAnalysis( gene_trees_1,
+ species_tree_1,
+ ALGORITHM.GSDIR,
+ REROOTING.BY_ALGORITHM,
+ "",
+ true,
+ false );
if ( rio.getAnalyzedGeneTrees().length != 5 ) {
return false;
}
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;
git://source.jalview.org / jalview.git / blobdiff