X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=b80a5841bbf68ac7947cd951d44beaefe0ecbb90;hb=bf7ff064d7b1e3a513653f5161c9b56cfb81a74b;hp=683955eb9df2f26a91f54d5e571d3dbd42d68a2b;hpb=1fb74b4b31f626b7d1c96405b4edb43db61ce56f;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 683955e..b80a584 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -52,7 +52,6 @@ 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.nhx.NHXParser2; import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.io.parsers.tol.TolParser; import org.forester.io.parsers.util.ParserUtils; @@ -226,6 +225,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "NHX parsing iterating: " ); + if ( Test.testNHParsingIter() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "NH parsing: " ); if ( Test.testNHParsing() ) { System.out.println( "OK." ); @@ -271,8 +279,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "NHX parsing iterating: " ); - if ( Test.testNHParsingIter() ) { + System.out.print( "Nexus characters parsing: " ); + if ( Test.testNexusCharactersParsing() ) { System.out.println( "OK." ); succeeded++; } @@ -280,9 +288,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.exit( 0 ); - System.out.print( "Nexus characters parsing: " ); - if ( Test.testNexusCharactersParsing() ) { + System.out.print( "Nexus tree parsing iterating: " ); + if ( Test.testNexusTreeParsingIterating() ) { System.out.println( "OK." ); succeeded++; } @@ -380,6 +387,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Tree methods: " ); + if ( Test.testTreeMethods() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Postorder Iterator: " ); if ( Test.testPostOrderIterator() ) { System.out.println( "OK." ); @@ -810,63 +826,74 @@ public final class Test { private static boolean testExtractTaxonomyCodeFromNodeName() { try { - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "RAT" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES ) - .equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES ) - .equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES ) - .equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "RAT" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) .equals( "PIG" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES ) + if ( !ParserUtils + .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) .equals( "MOUSE" ) ) { return false; } @@ -885,11 +912,11 @@ public final class Test { } final PhylogenyNode n1 = new PhylogenyNode(); final PhylogenyNode n2 = PhylogenyNode - .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); final PhylogenyNode n4 = PhylogenyNode - .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( n1.isHasAssignedEvent() ) { return false; } @@ -1912,7 +1939,7 @@ public final class Test { if ( t8.getHeight() != 15 ) { return false; } - final char[] a9 = new char[] {}; + final char[] a9 = new char[] { 'a' }; final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ]; if ( t9.getHeight() != 0 ) { return false; @@ -1930,6 +1957,34 @@ public final class Test { return true; } + private static boolean testTreeMethods() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) ); + if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) { + System.out.println( t0.toNewHampshireX() ); + return false; + } + final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testConfidenceAssessor() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); @@ -4410,383 +4465,1000 @@ public final class Test { return true; } - private static boolean testNexusTreeParsingTranslating() { + private static boolean testNexusTreeParsingIterating() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); - Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser ); - if ( phylogenies.length != 1 ) { + final NexusPhylogeniesParser p = new NexusPhylogeniesParser(); + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" ); + if ( !p.hasNext() ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + Phylogeny phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( phy.getNumberOfExternalNodes() != 25 ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( p.hasNext() ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser ); - if ( phylogenies.length != 3 ) { + // + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( phy.getNumberOfExternalNodes() != 25 ) { return false; } - if ( phylogenies[ 0 ].isRooted() ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( p.hasNext() ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" ); + if ( !p.hasNext() ) { return false; } - if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( phylogenies[ 1 ].isRooted() ) { + if ( !phy.getName().equals( "name" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( p.hasNext() ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + // + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( !phylogenies[ 2 ].isRooted() ) { + if ( !phy.getName().equals( "name" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( p.hasNext() ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" ); + if ( !p.hasNext() ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser ); - if ( phylogenies.length != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( phylogenies[ 0 ].isRooted() ) { + if ( phy.isRooted() ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( p.hasNext() ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + // + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( phylogenies[ 1 ].isRooted() ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( p.hasNext() ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" ); + // if ( phylogenies.length != 18 ) { + // return false; + // } + //0 + if ( !p.hasNext() ) { return false; } - if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( !phylogenies[ 2 ].isRooted() ) { + if ( !phy.getName().equals( "tree 0" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + //1 + if ( !p.hasNext() ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNHParsing() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ]; - if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) { + if ( !phy.getName().equals( "tree 1" ) ) { return false; } - final NHXParser nhxp = new NHXParser(); - 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 " ) ) { + //2 + if ( !p.hasNext() ) { return false; } - if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - final Phylogeny p1b = factory - .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ", - new NHXParser() )[ 0 ]; - if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ]; - final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ]; - final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ]; - final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ]; - final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() ); - final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() ); - final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() ); - final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() ); - final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() ); - final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() ); - final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;" - + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " - + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", - new NHXParser() ); - if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) { + if ( phy.isRooted() ) { return false; } - if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) { + //3 + if ( !p.hasNext() ) { return false; } - if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) { + if ( phy.getNumberOfExternalNodes() != 4 ) { return false; } - final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() ); - final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() ); - final String p16_S = "((A,B),C)"; - final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() ); - if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - final String p17_S = "(C,(A,B))"; - final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() ); - if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) { + if ( !phy.isRooted() ) { return false; } - final String p18_S = "((A,B),(C,D))"; - final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() ); - if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) { + //4 + if ( !p.hasNext() ) { return false; } - final String p19_S = "(((A,B),C),D)"; - final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() ); - if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - final String p20_S = "(A,(B,(C,D)))"; - final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() ); - if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) { + if ( phy.getNumberOfExternalNodes() != 5 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - final String p21_S = "(A,(B,(C,(D,E))))"; - final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() ); - if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - final String p22_S = "((((A,B),C),D),E)"; - final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() ); - if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) { + if ( !phy.isRooted() ) { return false; } - final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() ); - if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) { + //5 + if ( !p.hasNext() ) { return false; } - final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() ); - if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() ); - if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)" - + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D," - + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)" - + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde," - + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd," - + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)" - + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde" - + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde"; - final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() ); - if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) { + if ( phy.isRooted() ) { return false; } - final String p26_S = "(A,B)ab"; - final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() ); - if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) { + //6 + if ( !p.hasNext() ) { return false; } - final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ), - new NHXParser() ); - if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final String p28_S3 = "(A,B)ab"; - final String p28_S4 = "((((A,B),C),D),;E;)"; - final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ), - new NHXParser() ); - if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) { + if ( phy.getNumberOfExternalNodes() != 2 ) { return false; } - if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) { + if ( !phy.isRooted() ) { return false; } - if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) { + //7 + if ( !p.hasNext() ) { return false; } - final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345"; - final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() ); - if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72"; - final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() ); - if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) { + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { return false; } - final String p32_S = " ; ; \n \t \b \f \r ;;;;;; "; - final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() ); - if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) { + if ( !phy.isRooted() ) { return false; } - final String p33_S = "A"; - final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() ); - if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) { + //8 + if ( !p.hasNext() ) { return false; } - final String p34_S = "B;"; - final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() ); - if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - final String p35_S = "B:0.2"; - final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() ); - if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) { + if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) { return false; } - final String p36_S = "(A)"; - final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() ); - if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) { + if ( !phy.getName().equals( "tree 8" ) ) { return false; } - final String p37_S = "((A))"; - final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() ); - if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) { + //9 + if ( !p.hasNext() ) { return false; } - final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; - final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() ); - if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; - final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() ); - if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) { + if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) { return false; } - final String p40_S = "(A,B,C)"; - final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() ); - if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) { + if ( !phy.getName().equals( "tree 9" ) ) { return false; } - final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)"; - final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() ); - if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) { + //10 + if ( !p.hasNext() ) { return false; } - final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)"; - final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() ); - if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; - final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() ); - if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) { + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { return false; } - final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; - final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() ); + if ( !phy.getName().equals( "tree 10" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //11 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 11" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + //12 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 12" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //13 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 13" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //14 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); + return false; + } + if ( !phy.getName().equals( "tree 14" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //15 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); + return false; + } + if ( !phy.getName().equals( "tree 15" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + //16 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); + return false; + } + if ( !phy.getName().equals( "tree 16" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //17 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); + return false; + } + if ( !phy.getName().equals( "tree 17" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + // + if ( p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy != null ) { + return false; + } + p.reset(); + //0 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phy.getName().equals( "tree 0" ) ) { + return false; + } + //1 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phy.getName().equals( "tree 1" ) ) { + return false; + } + //2 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + //3 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 4 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //4 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 5 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //5 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNexusTreeParsingTranslating() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); + Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser ); + if ( phylogenies.length != 1 ) { + return false; + } + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { + return false; + } + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser ); + if ( phylogenies.length != 3 ) { + return false; + } + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + return false; + } + if ( phylogenies[ 0 ].isRooted() ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { + return false; + } + if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { + return false; + } + if ( phylogenies[ 1 ].isRooted() ) { + return false; + } + if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { + return false; + } + if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { + return false; + } + if ( !phylogenies[ 2 ].isRooted() ) { + return false; + } + if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { + return false; + } + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser ); + if ( phylogenies.length != 3 ) { + return false; + } + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + return false; + } + if ( phylogenies[ 0 ].isRooted() ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { + return false; + } + if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { + return false; + } + if ( phylogenies[ 1 ].isRooted() ) { + return false; + } + if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { + return false; + } + if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { + return false; + } + if ( !phylogenies[ 2 ].isRooted() ) { + return false; + } + if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNHParsing() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ]; + if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) { + return false; + } + final NHXParser nhxp = new NHXParser(); + 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 " ) ) { + return false; + } + if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) { + return false; + } + final Phylogeny p1b = factory + .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ", + new NHXParser() )[ 0 ]; + if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) { + return false; + } + if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) { + return false; + } + final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ]; + final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ]; + final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ]; + final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ]; + final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() ); + final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() ); + final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() ); + final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() ); + final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() ); + final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() ); + final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;" + + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " + + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", + new NHXParser() ); + if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) { + return false; + } + if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) { + return false; + } + if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) { + return false; + } + if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) { + return false; + } + final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() ); + final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() ); + final String p16_S = "((A,B),C)"; + final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() ); + if ( p16.length != 1 ) { + return false; + } + if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) { + return false; + } + final String p17_S = "(C,(A,B))"; + final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() ); + if ( p17.length != 1 ) { + return false; + } + if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) { + return false; + } + final String p18_S = "((A,B),(C,D))"; + final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() ); + if ( p18.length != 1 ) { + return false; + } + if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) { + return false; + } + final String p19_S = "(((A,B),C),D)"; + final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() ); + if ( p19.length != 1 ) { + return false; + } + if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) { + return false; + } + final String p20_S = "(A,(B,(C,D)))"; + final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() ); + if ( p20.length != 1 ) { + return false; + } + if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) { + return false; + } + final String p21_S = "(A,(B,(C,(D,E))))"; + final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() ); + if ( p21.length != 1 ) { + return false; + } + if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) { + return false; + } + final String p22_S = "((((A,B),C),D),E)"; + final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() ); + if ( p22.length != 1 ) { + return false; + } + if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) { + return false; + } + final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() ); + if ( p23.length != 1 ) { + System.out.println( "xl=" + p23.length ); + System.exit( -1 ); + return false; + } + if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) { + return false; + } + final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() ); + if ( p24.length != 1 ) { + return false; + } + if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) { + return false; + } + final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() ); + if ( p241.length != 2 ) { + return false; + } + if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) { + return false; + } + if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) { + return false; + } + final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)" + + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D," + + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)" + + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde," + + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd," + + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)" + + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde" + + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde"; + final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() ); + if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) { + return false; + } + final String p26_S = "(A,B)ab"; + final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() ); + if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) { + return false; + } + final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() ); + if ( p27s.length != 1 ) { + System.out.println( "xxl=" + p27s.length ); + System.exit( -1 ); + return false; + } + if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) { + System.out.println( p27s[ 0 ].toNewHampshireX() ); + System.exit( -1 ); + return false; + } + final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ), + new NHXParser() ); + if ( p27.length != 1 ) { + System.out.println( "yl=" + p27.length ); + System.exit( -1 ); + return false; + } + if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) { + System.out.println( p27[ 0 ].toNewHampshireX() ); + System.exit( -1 ); + return false; + } + final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + final String p28_S3 = "(A,B)ab"; + final String p28_S4 = "((((A,B),C),D),;E;)"; + final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ), + new NHXParser() ); + if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) { + return false; + } + if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) { + return false; + } + if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) { + return false; + } + if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) { + return false; + } + if ( p28.length != 4 ) { + return false; + } + final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345"; + final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() ); + if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) { + return false; + } + final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72"; + final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() ); + if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) { + return false; + } + final String p32_S = " ; ; \n \t \b \f \r ;;;;;; "; + final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() ); + if ( ( p32.length != 0 ) ) { + return false; + } + final String p33_S = "A"; + final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() ); + if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) { + return false; + } + final String p34_S = "B;"; + final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() ); + if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) { + return false; + } + final String p35_S = "B:0.2"; + final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() ); + if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) { + return false; + } + final String p36_S = "(A)"; + final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() ); + if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) { + return false; + } + final String p37_S = "((A))"; + final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() ); + if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) { + return false; + } + final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; + final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() ); + if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) { + return false; + } + final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; + final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() ); + if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) { + return false; + } + final String p40_S = "(A,B,C)"; + final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() ); + if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) { + return false; + } + final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)"; + final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() ); + if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) { + return false; + } + final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)"; + final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() ); + if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) { + return false; + } + final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; + final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() ); + if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) { + return false; + } + final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; + final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() ); if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) { return false; } @@ -4797,7 +5469,7 @@ public final class Test { } final String p46_S = ""; final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() ); - if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) { + if ( p46.length != 0 ) { return false; } final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ]; @@ -4862,107 +5534,386 @@ public final class Test { private static boolean testNHParsingIter() { try { - String p0_str = "(A,B);"; - NHXParser2 p = new NHXParser2(); + final String p0_str = "(A,B);"; + final NHXParser p = new NHXParser(); p.setSource( p0_str ); - Phylogeny p0 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + final Phylogeny p0 = p.next(); if ( !p0.toNewHampshire().equals( p0_str ) ) { System.out.println( p0.toNewHampshire() ); return false; } - //if ( p.getNext() != null ) { - // return false; - //} + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } // - String p00_str = "(A,B)root;"; - //p = new NHXParser2(); + final String p00_str = "(A,B)root;"; p.setSource( p00_str ); - Phylogeny p00 = p.getNext(); + final Phylogeny p00 = p.next(); if ( !p00.toNewHampshire().equals( p00_str ) ) { System.out.println( p00.toNewHampshire() ); return false; } // - String p000_str = "A;"; + final String p000_str = "A;"; p.setSource( p000_str ); - Phylogeny p000 = p.getNext(); + final Phylogeny p000 = p.next(); if ( !p000.toNewHampshire().equals( p000_str ) ) { System.out.println( p000.toNewHampshire() ); return false; } // - String p0000_str = "A"; + final String p0000_str = "A"; p.setSource( p0000_str ); - Phylogeny p0000 = p.getNext(); + final Phylogeny p0000 = p.next(); if ( !p0000.toNewHampshire().equals( "A;" ) ) { System.out.println( p0000.toNewHampshire() ); return false; } // p.setSource( "(A)" ); - Phylogeny p00000 = p.getNext(); + final Phylogeny p00000 = p.next(); if ( !p00000.toNewHampshire().equals( "(A);" ) ) { System.out.println( p00000.toNewHampshire() ); return false; } // - // p.setSource( " " ); - // Phylogeny p000000 = p.getNext(); - // if ( !p000000.toNewHampshire().equals( "(A);" ) ) { - // System.out.println( p000000.toNewHampshire() ); - // return false; - // } - // - String p1_str = "(A,B)(C,D)(E,F)(G,H)"; + final String p1_str = "(A,B)(C,D)(E,F)(G,H)"; p.setSource( p1_str ); - Phylogeny p1_0 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + final Phylogeny p1_0 = p.next(); if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) { System.out.println( p1_0.toNewHampshire() ); return false; } - Phylogeny p1_1 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + final Phylogeny p1_1 = p.next(); if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) { System.out.println( "(C,D) != " + p1_1.toNewHampshire() ); return false; } - Phylogeny p1_2 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + final Phylogeny p1_2 = p.next(); if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) { System.out.println( "(E,F) != " + p1_2.toNewHampshire() ); return false; } - Phylogeny p1_3 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + final Phylogeny p1_3 = p.next(); if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) { System.out.println( "(G,H) != " + p1_3.toNewHampshire() ); return false; } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } // - String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)"; + final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)"; p.setSource( p2_str ); - Phylogeny p2_0 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p2_0 = p.next(); + if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) { + System.out.println( p2_0.toNewHampshire() ); + return false; + } + if ( !p.hasNext() ) { + return false; + } + Phylogeny p2_1 = p.next(); + if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( "(C,D) != " + p2_1.toNewHampshire() ); + return false; + } + if ( !p.hasNext() ) { + return false; + } + Phylogeny p2_2 = p.next(); + if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) { + System.out.println( "(E,F)root != " + p2_2.toNewHampshire() ); + return false; + } + if ( !p.hasNext() ) { + return false; + } + Phylogeny p2_3 = p.next(); + if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) { + System.out.println( "(G,H) != " + p2_3.toNewHampshire() ); + return false; + } + if ( !p.hasNext() ) { + return false; + } + Phylogeny p2_4 = p.next(); + if ( !p2_4.toNewHampshire().equals( "(X);" ) ) { + System.out.println( "(X) != " + p2_4.toNewHampshire() ); + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + //// + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p2_0 = p.next(); if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) { System.out.println( p2_0.toNewHampshire() ); return false; } - Phylogeny p2_1 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + p2_1 = p.next(); if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) { System.out.println( "(C,D) != " + p2_1.toNewHampshire() ); return false; } - Phylogeny p2_2 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + p2_2 = p.next(); if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) { System.out.println( "(E,F)root != " + p2_2.toNewHampshire() ); return false; } - Phylogeny p2_3 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + p2_3 = p.next(); if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) { System.out.println( "(G,H) != " + p2_3.toNewHampshire() ); return false; } - Phylogeny p2_4 = p.getNext(); + if ( !p.hasNext() ) { + return false; + } + p2_4 = p.next(); if ( !p2_4.toNewHampshire().equals( "(X);" ) ) { System.out.println( "(X) != " + p2_4.toNewHampshire() ); return false; } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + final String p3_str = "((A,B),C)abc"; + p.setSource( p3_str ); + if ( !p.hasNext() ) { + return false; + } + final Phylogeny p3_0 = p.next(); + if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + final String p4_str = "((A,B)ab,C)abc"; + p.setSource( p4_str ); + if ( !p.hasNext() ) { + return false; + } + final Phylogeny p4_0 = p.next(); + if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + final String p5_str = "(((A,B)ab,C)abc,D)abcd"; + p.setSource( p5_str ); + if ( !p.hasNext() ) { + return false; + } + final Phylogeny p5_0 = p.next(); + if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + p.setSource( p6_str ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p6_0 = p.next(); + if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p6_0 = p.next(); + if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + p.setSource( p7_str ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p7_0 = p.next(); + if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p7_0 = p.next(); + if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde"; + p.setSource( p8_str ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p8_0 = p.next(); + if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + return false; + } + if ( !p.hasNext() ) { + return false; + } + if ( !p.hasNext() ) { + return false; + } + Phylogeny p8_1 = p.next(); + if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p8_0 = p.next(); + if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + return false; + } + if ( !p.hasNext() ) { + return false; + } + p8_1 = p.next(); + if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + // + p.setSource( "" ); + if ( p.hasNext() ) { + return false; + } + // + p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p_27 = p.next(); + if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { + System.out.println( p_27.toNewHampshireX() ); + System.exit( -1 ); + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p_27 = p.next(); + if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { + System.out.println( p_27.toNewHampshireX() ); + System.exit( -1 ); + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -4978,9 +5929,9 @@ public final class Test { final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" ); final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" ); final PhylogenyNode n5 = PhylogenyNode - .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" ); + .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" ); final PhylogenyNode n6 = PhylogenyNode - .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" ); + .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" ); if ( !n1.toNewHampshireX().equals( "" ) ) { return false; } @@ -4993,11 +5944,11 @@ public final class Test { if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) { return false; } - if ( !n5.toNewHampshireX() - .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) { + if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) { return false; } - if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) { + if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) { + System.out.println( n6.toNewHampshireX() ); return false; } } @@ -5010,109 +5961,132 @@ public final class Test { private static boolean testTaxonomyExtraction() { try { - final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n0 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n0.getNodeData().isHasTaxonomy() ) { return false; } - final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n1 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n1.getNodeData().isHasTaxonomy() ) { System.out.println( n1.toString() ); return false; } - final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n2 = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE ); if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n2.toString() ); return false; } - final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n2x = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n2x.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n3 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n3.toString() ); return false; } - final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n4 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n4.getNodeData().isHasTaxonomy() ) { System.out.println( n4.toString() ); return false; } - final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n5 = PhylogenyNode + .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n5.getNodeData().isHasTaxonomy() ) { System.out.println( n5.toString() ); return false; } - final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n6 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n6.getNodeData().isHasTaxonomy() ) { System.out.println( n6.toString() ); return false; } - final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n7 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n7.getNodeData().isHasTaxonomy() ) { System.out.println( n7.toString() ); return false; } - final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n8 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n8.toString() ); return false; } - final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n9 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n9.toString() ); return false; } - final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) { + final PhylogenyNode n10x = PhylogenyNode + .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n10x.getNodeData().isHasTaxonomy() ) { + System.out.println( n10x.toString() ); + return false; + } + final PhylogenyNode n10xx = PhylogenyNode + .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n10xx.getNodeData().isHasTaxonomy() ) { + System.out.println( n10xx.toString() ); + return false; + } + final PhylogenyNode n10 = PhylogenyNode + .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { System.out.println( n10.toString() ); return false; } - final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n11 = PhylogenyNode + .createInstanceFromNhxString( "blag_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { System.out.println( n11.toString() ); return false; } - final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n12 = PhylogenyNode + .createInstanceFromNhxString( "blag_Mus_musculus_musculus", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { System.out.println( n12.toString() ); return false; } - final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n13 = PhylogenyNode + .createInstanceFromNhxString( "blag_Mus_musculus1", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n13.getNodeData().isHasTaxonomy() ) { System.out.println( n13.toString() ); return false; } - final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n14 = PhylogenyNode + .createInstanceFromNhxString( "blag_Mus_musculus_11", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n14.getNodeData().isHasTaxonomy() ) { System.out.println( n14.toString() ); return false; } - final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n15 = PhylogenyNode + .createInstanceFromNhxString( "blag_Mus_musculus_v11", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) { System.out.println( n15.toString() ); return false; } - final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n16 = PhylogenyNode + .createInstanceFromNhxString( "blag_Mus_musculus_/11", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n16.getNodeData().isHasTaxonomy() ) { System.out.println( n16.toString() ); return false; } - final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n17 = PhylogenyNode + .createInstanceFromNhxString( "blag_Mus_musculus_v", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n17.getNodeData().isHasTaxonomy() ) { System.out.println( n17.toString() ); return false; @@ -5172,11 +6146,8 @@ public final class Test { if ( !n5.isHasAssignedEvent() ) { return false; } - if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) { - return false; - } final PhylogenyNode n8 = PhylogenyNode - .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n8.getName().equals( "n8_ECOLI/12" ) ) { return false; } @@ -5184,7 +6155,8 @@ public final class Test { return false; } final PhylogenyNode n9 = PhylogenyNode - .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) { return false; } @@ -5192,20 +6164,20 @@ public final class Test { return false; } final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n10.getName().equals( "n10.ECOLI" ) ) { return false; } final PhylogenyNode n20 = PhylogenyNode - .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); 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", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n20x = PhylogenyNode + .createInstanceFromNhxString( "n20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) { return false; } @@ -5213,7 +6185,7 @@ public final class Test { return false; } final PhylogenyNode n20xx = PhylogenyNode - .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) { return false; } @@ -5221,7 +6193,7 @@ public final class Test { return false; } final PhylogenyNode n20xxx = PhylogenyNode - .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) { return false; } @@ -5229,15 +6201,15 @@ public final class Test { return false; } final PhylogenyNode n20xxxx = PhylogenyNode - .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); 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", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n21 = PhylogenyNode + .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n21.getName().equals( "n21_PIG" ) ) { return false; } @@ -5245,7 +6217,7 @@ public final class Test { return false; } final PhylogenyNode n21x = PhylogenyNode - .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n21x.getName().equals( "n21_PIG" ) ) { return false; } @@ -5253,7 +6225,7 @@ public final class Test { return false; } final PhylogenyNode n22 = PhylogenyNode - .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n22.getName().equals( "n22/PIG" ) ) { return false; } @@ -5261,7 +6233,7 @@ public final class Test { return false; } final PhylogenyNode n23 = PhylogenyNode - .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n23.getName().equals( "n23/PIG_1" ) ) { return false; } @@ -5269,7 +6241,7 @@ public final class Test { return false; } final PhylogenyNode a = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) { return false; } @@ -5277,7 +6249,7 @@ public final class Test { return false; } final PhylogenyNode b = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) { return false; } @@ -5286,7 +6258,7 @@ public final class Test { } final PhylogenyNode c = PhylogenyNode .createInstanceFromNhxString( "n10_RATAF12/1000-2000", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) { return false; } @@ -5295,7 +6267,7 @@ public final class Test { } final PhylogenyNode c1 = PhylogenyNode .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) { return false; } @@ -5304,7 +6276,7 @@ public final class Test { } final PhylogenyNode c2 = PhylogenyNode .createInstanceFromNhxString( "n10_Bovin_1/1000-2000", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) { return false; } @@ -5312,7 +6284,7 @@ public final class Test { return false; } final PhylogenyNode d = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !d.getName().equals( "n10_RAT1/1-2" ) ) { return false; } @@ -5320,23 +6292,23 @@ public final class Test { return false; } final PhylogenyNode e = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !e.getName().equals( "n10_RAT1" ) ) { return false; } if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) { return false; } - final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode e2 = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !e2.getName().equals( "n10_RAT1" ) ) { return false; } if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) { return false; } - final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode e3 = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !e3.getName().equals( "n10_RAT~" ) ) { return false; } @@ -5345,7 +6317,7 @@ public final class Test { } final PhylogenyNode n11 = PhylogenyNode .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) { return false; } @@ -5357,7 +6329,7 @@ public final class Test { } final PhylogenyNode n12 = PhylogenyNode .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) { return false; } @@ -5367,16 +6339,16 @@ public final class Test { if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) { return false; } - final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode m = PhylogenyNode + .createInstanceFromNhxString( "n10_MOUSEa", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !m.getName().equals( "n10_MOUSEa" ) ) { return false; } if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) { return false; } - final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode o = PhylogenyNode + .createInstanceFromNhxString( "n10_MOUSE_", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !o.getName().equals( "n10_MOUSE_" ) ) { return false; } @@ -5402,7 +6374,7 @@ public final class Test { return false; } final PhylogenyNode n00 = PhylogenyNode - .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" ); + .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" ); if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) { return false; } @@ -5414,7 +6386,7 @@ public final class Test { return false; } final PhylogenyNode n13 = PhylogenyNode - .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE ); if ( !n13.getName().equals( "blah_12345/1-2" ) ) { return false; } @@ -5428,16 +6400,16 @@ public final class Test { return false; } final PhylogenyNode n14 = PhylogenyNode - .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n14.getName().equals( "blah_12X45/1-2" ) ) { + .createInstanceFromNhxString( "blah_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n14.getName().equals( "blah_9QX45/1-2" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) { + if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) { return false; } final PhylogenyNode n15 = PhylogenyNode .createInstanceFromNhxString( "something_wicked[123]", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n15.getName().equals( "something_wicked" ) ) { return false; } @@ -5448,7 +6420,8 @@ public final class Test { return false; } final PhylogenyNode n16 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "something_wicked2[9]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n16.getName().equals( "something_wicked2" ) ) { return false; } @@ -5459,7 +6432,8 @@ public final class Test { return false; } final PhylogenyNode n17 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "something_wicked3[a]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n17.getName().equals( "something_wicked3" ) ) { return false; } @@ -5467,7 +6441,7 @@ public final class Test { return false; } final PhylogenyNode n18 = PhylogenyNode - .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) { return false; } @@ -5477,29 +6451,31 @@ public final class Test { if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) { return false; } - final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n19 = PhylogenyNode + .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { return false; } if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { return false; } - final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n30 = PhylogenyNode + .createInstanceFromNhxString( "blah_1234567-roejojoej", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) { return false; } if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { return false; } - final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n31 = PhylogenyNode + .createInstanceFromNhxString( "blah_12345678-roejojoej", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n31.getNodeData().isHasTaxonomy() ) { return false; } - final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n32 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n32.getNodeData().isHasTaxonomy() ) { return false; } @@ -6302,7 +7278,7 @@ public final class Test { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ]; - final int count = PhylogenyNode.getNodeCount(); + final long count = PhylogenyNode.getNodeCount(); p.levelOrderReID(); if ( p.getNode( "r" ).getId() != count ) { return false;