X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=19d01c13675f8618fe8168e77f02e0908404bac0;hb=877d1e4a2f3e2a937197dc57253ba2cead14a4d6;hp=1ca9fe058682ed96ebf758e81c1fdbac231929ad;hpb=149c4d125eaba81f80bf76548f47f3ba75b384c6;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 1ca9fe0..19d01c1 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -52,8 +52,10 @@ import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser; import org.forester.io.parsers.nexus.NexusCharactersParser; import org.forester.io.parsers.nexus.NexusPhylogeniesParser; import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.io.parsers.tol.TolParser; +import org.forester.io.parsers.util.ParserUtils; import org.forester.io.writers.PhylogenyWriter; import org.forester.msa.BasicMsa; import org.forester.msa.Mafft; @@ -64,9 +66,8 @@ import org.forester.pccx.TestPccx; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyBranch; import org.forester.phylogeny.PhylogenyMethods; -import org.forester.phylogeny.PhylogenyMethods.TAXONOMY_EXTRACTION; import org.forester.phylogeny.PhylogenyNode; -import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; import org.forester.phylogeny.data.BinaryCharacters; import org.forester.phylogeny.data.BranchWidth; import org.forester.phylogeny.data.Confidence; @@ -86,8 +87,8 @@ import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.protein.Protein; +import org.forester.rio.RIO; import org.forester.sdi.GSDI; -import org.forester.sdi.RIO; import org.forester.sdi.SDI; import org.forester.sdi.SDIR; import org.forester.sdi.SDIse; @@ -181,7 +182,6 @@ public final class Test { } else { System.out.println( "failed." ); - System.exit( -1 ); //TODO FIXME remove me!! ~ failed++; } System.out.print( "Hmmscan output parser: " ); @@ -202,6 +202,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Taxonomy extraction: " ); + if ( Test.testExtractTaxonomyCodeFromNodeName() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Basic node construction and parsing of NHX (node level): " ); if ( Test.testNHXNodeParsing() ) { System.out.println( "OK." ); @@ -756,15 +765,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // System.out.print( "WABI TxSearch: " ); - // if ( Test.testWabiTxSearch() ) { - // System.out.println( "OK." ); - // succeeded++; - // } - // else { - // System.out - // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" ); - // } System.out.println(); final Runtime rt = java.lang.Runtime.getRuntime(); final long free_memory = rt.freeMemory() / 1000000; @@ -781,73 +781,76 @@ public final class Test { else { System.out.println( "Not OK." ); } - // System.out.println(); - // Development.setTime( true ); - //try { - // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() - // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx"; - // final String multi = Test.PATH_TO_EXAMPLE_FILES + - // "multifurcations_ex_1.nhx"; - // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx"; - // final Phylogeny t1 = factory.create( new File( domains ), new - // NHXParser() )[ 0 ]; - // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ]; - // } - // catch ( final Exception e ) { - // e.printStackTrace(); - // } - // t1.getRoot().preorderPrint(); - // final PhylogenyFactory factory = ParserBasedPhylogenyFactory - // .getInstance(); - // try { - // - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\AtNBSpos.nhx" ) ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ), - // new NHXParser() ); - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\AtNBSpos.nhx" ) ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ), - // new NHXParser() ); - // - // - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\big_tree.nhx" ) ); - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\big_tree.nhx" ) ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ), - // new NHXParser() ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ), - // new NHXParser() ); - // - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\big_tree.nhx" ) ); - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\big_tree.nhx" ) ); - // - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ), - // new NHXParser() ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ), - // new NHXParser() ); - // - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\AtNBSpos.nhx" ) ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ), - // new NHXParser() ); - // - // } - // catch ( IOException e ) { - // // TODO Auto-generated catch block - // e.printStackTrace(); - // } + } + + private static boolean testExtractTaxonomyCodeFromNodeName() { + try { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) { + return false; + } + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES ) + .equals( "MOUSE" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES ) + .equals( "MOUSE" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES ) + .equals( "MOUSE" ) ) { + return false; + } + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + return false; + } + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES ) + .equals( "RAT" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES ) + .equals( "RAT" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES ) + .equals( "RAT" ) ) { + return false; + } + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + return false; + } + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) + .equals( "PIG" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES ) + .equals( "MOUSE" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) + .equals( "MOUSE" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; } private static boolean testBasicNodeMethods() { @@ -857,11 +860,11 @@ public final class Test { } final PhylogenyNode n1 = new PhylogenyNode(); final PhylogenyNode n2 = PhylogenyNode - .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); final PhylogenyNode n4 = PhylogenyNode - .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( n1.isHasAssignedEvent() ) { return false; } @@ -3331,6 +3334,49 @@ public final class Test { private static boolean testGetLCA2() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p_a ); + final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ), + p_a.getNode( "a" ) ); + if ( !p_a_1.getName().equals( "a" ) ) { + return false; + } + final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p_b ); + final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ), + p_b.getNode( "a" ) ); + if ( !p_b_1.getName().equals( "b" ) ) { + return false; + } + final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ), + p_b.getNode( "b" ) ); + if ( !p_b_2.getName().equals( "b" ) ) { + return false; + } + final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p_c ); + final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ), + p_c.getNode( "a" ) ); + if ( !p_c_1.getName().equals( "b" ) ) { + return false; + } + final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ), + p_c.getNode( "c" ) ); + if ( !p_c_2.getName().equals( "c" ) ) { + System.out.println( p_c_2.getName() ); + System.exit( -1 ); + return false; + } + final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ), + p_c.getNode( "b" ) ); + if ( !p_c_3.getName().equals( "b" ) ) { + return false; + } + final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ), + p_c.getNode( "a" ) ); + if ( !p_c_4.getName().equals( "c" ) ) { + return false; + } final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh", new NHXParser() )[ 0 ]; PhylogenyMethods.preOrderReId( p1 ); @@ -4442,7 +4488,7 @@ public final class Test { return false; } final NHXParser nhxp = new NHXParser(); - nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO ); + nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO ); nhxp.setReplaceUnderscores( true ); final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ]; if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) { @@ -4819,38 +4865,36 @@ public final class Test { return false; } final PhylogenyNode n8 = PhylogenyNode - .createInstanceFromNhxString( "n8_ECOLI/12:0.01", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n8.getName().equals( "n8_ECOLI/12" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) { + if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) { return false; } final PhylogenyNode n9 = PhylogenyNode - .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) { + if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) { return false; } final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n10.getName().equals( "n10.ECOLI" ) ) { return false; } final PhylogenyNode n20 = PhylogenyNode - .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) { return false; } if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) { return false; } - final PhylogenyNode n20x = PhylogenyNode - .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2", + NHXParser.TAXONOMY_EXTRACTION.YES ); if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) { return false; } @@ -4858,7 +4902,7 @@ public final class Test { return false; } final PhylogenyNode n20xx = PhylogenyNode - .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) { return false; } @@ -4866,7 +4910,7 @@ public final class Test { return false; } final PhylogenyNode n20xxx = PhylogenyNode - .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) { return false; } @@ -4874,15 +4918,15 @@ public final class Test { return false; } final PhylogenyNode n20xxxx = PhylogenyNode - .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) { return false; } if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) { return false; } - final PhylogenyNode n21 = PhylogenyNode - .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG", + NHXParser.TAXONOMY_EXTRACTION.YES ); if ( !n21.getName().equals( "n21_PIG" ) ) { return false; } @@ -4890,7 +4934,7 @@ public final class Test { return false; } final PhylogenyNode n21x = PhylogenyNode - .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n21x.getName().equals( "n21_PIG" ) ) { return false; } @@ -4898,7 +4942,7 @@ public final class Test { return false; } final PhylogenyNode n22 = PhylogenyNode - .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n22.getName().equals( "n22/PIG" ) ) { return false; } @@ -4906,7 +4950,7 @@ public final class Test { return false; } final PhylogenyNode n23 = PhylogenyNode - .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n23.getName().equals( "n23/PIG_1" ) ) { return false; } @@ -4914,7 +4958,7 @@ public final class Test { return false; } final PhylogenyNode a = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) { return false; } @@ -4922,35 +4966,34 @@ public final class Test { return false; } final PhylogenyNode b = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI1/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) { + if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) { return false; } final PhylogenyNode c = PhylogenyNode .createInstanceFromNhxString( "n10_RATAF12/1000-2000", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) { + if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) { return false; } final PhylogenyNode c1 = PhylogenyNode .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { + if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { return false; } final PhylogenyNode c2 = PhylogenyNode .createInstanceFromNhxString( "n10_Bovin_1/1000-2000", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) { return false; } @@ -4958,31 +5001,31 @@ public final class Test { return false; } final PhylogenyNode d = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !d.getName().equals( "n10_RAT1/1-2" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) { + if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) { return false; } final PhylogenyNode e = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !e.getName().equals( "n10_RAT1" ) ) { return false; } if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) { return false; } - final PhylogenyNode e2 = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1", + NHXParser.TAXONOMY_EXTRACTION.YES ); if ( !e2.getName().equals( "n10_RAT1" ) ) { return false; } if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) { return false; } - final PhylogenyNode e3 = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT~", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~", + NHXParser.TAXONOMY_EXTRACTION.YES ); if ( !e3.getName().equals( "n10_RAT~" ) ) { return false; } @@ -4991,19 +5034,19 @@ public final class Test { } final PhylogenyNode n11 = PhylogenyNode .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) { return false; } if ( n11.getDistanceToParent() != 0.4 ) { return false; } - if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) { + if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) { return false; } final PhylogenyNode n12 = PhylogenyNode .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) { return false; } @@ -5013,16 +5056,16 @@ public final class Test { if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) { return false; } - final PhylogenyNode m = PhylogenyNode - .createInstanceFromNhxString( "n10_MOUSEa", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa", + NHXParser.TAXONOMY_EXTRACTION.YES ); if ( !m.getName().equals( "n10_MOUSEa" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) { + if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) { return false; } - final PhylogenyNode o = PhylogenyNode - .createInstanceFromNhxString( "n10_MOUSE_", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_", + NHXParser.TAXONOMY_EXTRACTION.YES ); if ( !o.getName().equals( "n10_MOUSE_" ) ) { return false; } @@ -5108,8 +5151,7 @@ public final class Test { return false; } final PhylogenyNode n13 = PhylogenyNode - .createInstanceFromNhxString( "blah_12345/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n13.getName().equals( "blah_12345/1-2" ) ) { return false; } @@ -5117,8 +5159,7 @@ public final class Test { return false; } final PhylogenyNode n14 = PhylogenyNode - .createInstanceFromNhxString( "blah_12X45/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n14.getName().equals( "blah_12X45/1-2" ) ) { return false; } @@ -5127,7 +5168,7 @@ public final class Test { } final PhylogenyNode n15 = PhylogenyNode .createInstanceFromNhxString( "something_wicked[123]", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n15.getName().equals( "something_wicked" ) ) { return false; } @@ -5138,8 +5179,7 @@ public final class Test { return false; } final PhylogenyNode n16 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked2[9]", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n16.getName().equals( "something_wicked2" ) ) { return false; } @@ -5150,8 +5190,7 @@ public final class Test { return false; } final PhylogenyNode n17 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked3[a]", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n17.getName().equals( "something_wicked3" ) ) { return false; } @@ -5159,7 +5198,7 @@ public final class Test { return false; } final PhylogenyNode n18 = PhylogenyNode - .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) { return false; } @@ -6842,7 +6881,7 @@ public final class Test { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny s1 = factory.create( Test.PATH_TO_TEST_DATA + "rio_species.xml", new PhyloXmlParser() )[ 0 ]; final NHXParser p = new NHXParser(); - p.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES ); + p.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES ); final Phylogeny g1[] = factory.create( new File( Test.PATH_TO_TEST_DATA + "rio_Bcl-2_e1_20_mafft_05_40_fme.mlt" ), p ); for( final Phylogeny gt : g1 ) {