X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=e3666a8d93bd9d5d7563f5fbe02ac56ca1e39d22;hb=0d0b9cde030d50b153eb6d1ff7ce13bc273edc17;hp=af74f007d928503a7d05c6c0854b5a1ef6426d20;hpb=3b40e07c1b3964dee89b5d24209946ac54a5e21f;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index af74f00..e3666a8 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -44,6 +44,7 @@ import org.forester.application.support_transfer; import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.TreePanelUtil; import org.forester.archaeopteryx.webservices.WebserviceUtil; +import org.forester.clade_analysis.CladeAnalysisTest; import org.forester.development.DevelopmentTools; import org.forester.evoinference.TestPhylogenyReconstruction; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -88,7 +89,7 @@ import org.forester.phylogeny.data.Identifier; import org.forester.phylogeny.data.PhylogenyData; import org.forester.phylogeny.data.PhylogenyDataUtil; import org.forester.phylogeny.data.Polygon; -import org.forester.phylogeny.data.PropertiesMap; +import org.forester.phylogeny.data.PropertiesList; import org.forester.phylogeny.data.Property; import org.forester.phylogeny.data.Property.AppliesTo; import org.forester.phylogeny.data.ProteinDomain; @@ -125,39 +126,31 @@ import org.forester.util.SequenceAccessionTools; import org.forester.ws.seqdb.SequenceDatabaseEntry; import org.forester.ws.seqdb.SequenceDbWsTools; import org.forester.ws.seqdb.UniProtTaxonomy; -import org.forester.ws.wabi.TxSearch; -import org.forester.ws.wabi.TxSearch.RANKS; -import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS; -import org.forester.ws.wabi.TxSearch.TAX_RANK; @SuppressWarnings( "unused") public final class Test { private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "resources" - + ForesterUtil.getFileSeparator(); + + ForesterUtil.getFileSeparator() + "resources" + ForesterUtil.getFileSeparator(); private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "test_data" - + ForesterUtil.getFileSeparator(); - private final static boolean PERFORM_DB_TESTS = true; - private static final boolean PERFORM_WEB_TREE_ACCESS = true; + + ForesterUtil.getFileSeparator() + "test_data" + ForesterUtil.getFileSeparator(); + private final static boolean PERFORM_DB_TESTS = false; + private static final boolean PERFORM_WEB_TREE_ACCESS = false; private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/" - + ForesterConstants.PHYLO_XML_VERSION + "/" - + ForesterConstants.PHYLO_XML_XSD; + + ForesterConstants.PHYLO_XML_VERSION + "/" + ForesterConstants.PHYLO_XML_XSD; private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/" - + ForesterConstants.PHYLO_XML_VERSION + "/" - + ForesterConstants.PHYLO_XML_XSD; + + ForesterConstants.PHYLO_XML_VERSION + "/" + ForesterConstants.PHYLO_XML_XSD; private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true; private final static double ZERO_DIFF = 1.0E-9; - public static boolean isEqual( final double a, final double b ) { + private static boolean isEqual( final double a, final double b ) { return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF ); } public static void main( final String[] args ) { System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION - + "]" ); + + "]" ); Locale.setDefault( Locale.US ); System.out.println( "[Locale: " + Locale.getDefault() + "]" ); int failed = 0; @@ -226,6 +219,33 @@ public final class Test { succeeded++; } System.out.println( "OK." ); + System.out.print( "Common prefix: " ); + if ( !testCommonPrefix() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); + System.out.print( "Common prefix sep: " ); + if ( !testCommonPrefixSep() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); + System.out.print( "Contains prefix: " ); + if ( !testContainsPrefix() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); System.out.print( "Sequence writer: " ); if ( testSequenceWriter() ) { System.out.println( "OK." ); @@ -343,6 +363,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Node construction and parsing of NHX (node level): " ); + if ( Test.testNHXNodeParsing2() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "NHX parsing iterating: " ); if ( Test.testNHParsingIter() ) { System.out.println( "OK." ); @@ -361,6 +390,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "NH parsing - special chars: " ); + if ( Test.testNHParsingSpecialChars() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Conversion to NHX (node level): " ); if ( Test.testNHXconversion() ) { System.out.println( "OK." ); @@ -460,6 +498,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "phyloXML parsing (validating against schema): " ); + if ( testPhyloXMLparsingValidating() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Roundtrip phyloXML parsing (validating against schema): " ); if ( Test.testBasicPhyloXMLparsingRoundtrip() ) { System.out.println( "OK." ); @@ -487,6 +534,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "UTF-8 parsing from file: " ); + if ( Test.testUTF8ParsingFromFile() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Copying of node data: " ); if ( Test.testCopyOfNodeData() ) { System.out.println( "OK." ); @@ -523,6 +579,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Phylogeny methods:" ); + if ( Test.testPhylogenyMethods() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Postorder Iterator: " ); if ( Test.testPostOrderIterator() ) { System.out.println( "OK." ); @@ -739,6 +804,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Clade analyis: " ); + if ( CladeAnalysisTest.test() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Phylogeny reconstruction:" ); System.out.println(); if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) { @@ -971,8 +1045,8 @@ public final class Test { } } if ( PERFORM_WEB_TREE_ACCESS ) { - System.out.print( "NHX parsing from URL: " ); - if ( Test.testNHXparsingFromURL() ) { + System.out.print( "TreeBase acccess: " ); + if ( Test.testTreeBaseReading() ) { System.out.println( "OK." ); succeeded++; } @@ -980,8 +1054,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "NHX parsing from URL 2: " ); - if ( Test.testNHXparsingFromURL2() ) { + System.out.print( "ToL access: " ); + if ( Test.testToLReading() ) { System.out.println( "OK." ); succeeded++; } @@ -989,8 +1063,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "phyloXML parsing from URL: " ); - if ( Test.testPhyloXMLparsingFromURL() ) { + System.out.print( "NHX parsing from URL: " ); + if ( Test.testNHXparsingFromURL() ) { System.out.println( "OK." ); succeeded++; } @@ -998,8 +1072,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "TreeBase acccess: " ); - if ( Test.testTreeBaseReading() ) { + System.out.print( "NHX parsing from URL 2: " ); + if ( Test.testNHXparsingFromURL2() ) { System.out.println( "OK." ); succeeded++; } @@ -1007,9 +1081,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - // - System.out.print( "ToL access: " ); - if ( Test.testToLReading() ) { + System.out.print( "phyloXML parsing from URL: " ); + if ( Test.testPhyloXMLparsingFromURL() ) { System.out.println( "OK." ); succeeded++; } @@ -1017,7 +1090,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // System.out.print( "TreeFam access: " ); if ( Test.testTreeFamReading() ) { System.out.println( "OK." ); @@ -1027,8 +1099,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // - // System.out.print( "Pfam tree access: " ); if ( Test.testPfamTreeReading() ) { System.out.println( "OK." ); @@ -1057,7 +1127,7 @@ public final class Test { } } - public static boolean testEngulfingOverlapRemoval() { + private static boolean testEngulfingOverlapRemoval() { try { final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 ); @@ -1066,7 +1136,7 @@ public final class Test { final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 ); - final List covered = new ArrayList(); + final List covered = new ArrayList<>(); covered.add( true ); // 0 covered.add( false ); // 1 covered.add( true ); // 2 @@ -1156,15 +1226,11 @@ public final class Test { return true; } - public static final boolean testNHXparsingFromURL2() { + private static final boolean testNHXparsingFromURL2() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; - final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ), - false, - false, - false, - TAXONOMY_EXTRACTION.NO, - false ); + final Phylogeny phys[] = AptxUtil + .readPhylogeniesFromUrl( new URL( s ), false, false, false, TAXONOMY_EXTRACTION.NO, false ); if ( ( phys == null ) || ( phys.length != 5 ) ) { return false; } @@ -1176,12 +1242,8 @@ public final class Test { System.out.println( phys[ 1 ].toNewHampshire() ); return false; } - final Phylogeny phys2[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ), - false, - false, - false, - TAXONOMY_EXTRACTION.NO, - false ); + final Phylogeny phys2[] = AptxUtil + .readPhylogeniesFromUrl( new URL( s ), false, false, false, TAXONOMY_EXTRACTION.NO, false ); if ( ( phys2 == null ) || ( phys2.length != 5 ) ) { return false; } @@ -1194,23 +1256,31 @@ public final class Test { return false; } final Phylogeny phys3[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/" - + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false ); + + "SwissTree/ST001/consensus_tree.nhx" ), + false, + false, + false, + TAXONOMY_EXTRACTION.NO, + false ); if ( ( phys3 == null ) || ( phys3.length != 1 ) ) { return false; } - if ( !phys3[ 0 ] - .toNewHampshire() + if ( !phys3[ 0 ].toNewHampshire() .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) { System.out.println( phys3[ 0 ].toNewHampshire() ); return false; } final Phylogeny phys4[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/" - + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false ); + + "SwissTree/ST001/consensus_tree.nhx" ), + false, + false, + false, + TAXONOMY_EXTRACTION.NO, + false ); if ( ( phys4 == null ) || ( phys4.length != 1 ) ) { return false; } - if ( !phys4[ 0 ] - .toNewHampshire() + if ( !phys4[ 0 ].toNewHampshire() .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) { System.out.println( phys4[ 0 ].toNewHampshire() ); return false; @@ -1223,7 +1293,7 @@ public final class Test { return true; } - public static final boolean testNHXparsingFromURL() { + private static final boolean testNHXparsingFromURL() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; final URL u = new URL( s ); @@ -1291,14 +1361,14 @@ public final class Test { return true; } - public static boolean testOverlapRemoval() { + private static boolean testOverlapRemoval() { try { final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 ); - final List covered = new ArrayList(); + final List covered = new ArrayList<>(); covered.add( true ); // 0 covered.add( false ); // 1 covered.add( true ); // 2 @@ -1353,7 +1423,13 @@ public final class Test { ( short ) 1, 0.0000001, 1 ); - final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 ); + final Domain e = new BasicDomain( "e", + ( short ) 5000, + ( short ) 5500, + ( short ) 1, + ( short ) 1, + 0.0001, + 1 ); final Protein cde = new BasicProtein( "cde", "varanus", 0 ); cde.addProteinDomain( c ); cde.addProteinDomain( d ); @@ -1445,15 +1521,14 @@ public final class Test { return true; } - public static final boolean testPfamTreeReading() { + private static final boolean testPfamTreeReading() { try { final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" ); final NHXParser parser = new NHXParser(); parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); parser.setReplaceUnderscores( false ); parser.setGuessRootedness( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } @@ -1463,84 +1538,200 @@ public final class Test { } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testPhyloXMLparsingFromURL() { + private static final boolean testPhyloXMLparsingFromURL() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml"; final URL u = new URL( s ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() ); if ( ( phys == null ) || ( phys.length != 2 ) ) { return false; } + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() ); + if ( ( phys2 == null ) || ( phys2.length != 2 ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testToLReading() { + private static final boolean testToLReading() { try { final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, new TolParser() ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) { return false; } - if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) { + if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName() + .equals( "Protacanthopterygii" ) ) { return false; } if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) { return false; } + // + final URL u2 = new URL( WebserviceUtil.TOL_URL_BASE + "17706" ); + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, new TolParser() ); + if ( ( phys2 == null ) || ( phys2.length != 1 ) ) { + return false; + } + if ( !phys2[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "17706" ) ) { + return false; + } + if ( phys2[ 0 ].getNumberOfExternalNodes() < 5 ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testTreeBaseReading() { + private static final boolean testTreeBaseReading() { try { - final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" ); + final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "72557?format=nexus" ); final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); parser.setReplaceUnderscores( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } + final URL u_1 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2406?format=nexus" ); + final NexusPhylogeniesParser parser_1 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_1 = ForesterUtil.readPhylogeniesFromUrl( u_1, parser_1 ); + if ( ( phys_1 == null ) || ( phys_1.length != 1 ) ) { + return false; + } + final URL u_2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "422?format=nexus" ); + final NexusPhylogeniesParser parser_2 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_2 = ForesterUtil.readPhylogeniesFromUrl( u_2, parser_2 ); + if ( ( phys_2 == null ) || ( phys_2.length != 1 ) ) { + return false; + } + final URL u_3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2654?format=nexus" ); + final NexusPhylogeniesParser parser_3 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_3 = ForesterUtil.readPhylogeniesFromUrl( u_3, parser_3 ); + if ( ( phys_3 == null ) || ( phys_3.length != 1 ) ) { + return false; + } + final URL u_4 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" ); + final NexusPhylogeniesParser parser_4 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_4 = ForesterUtil.readPhylogeniesFromUrl( u_4, parser_4 ); + if ( ( phys_4 == null ) || ( phys_4.length != 1 ) ) { + return false; + } final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" ); final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser(); parser2.setReplaceUnderscores( true ); - final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 ); + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, parser2 ); if ( ( phys2 == null ) || ( phys2.length != 9 ) ) { return false; } + final URL u3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14909?format=nexus" ); + final NexusPhylogeniesParser parser3 = new NexusPhylogeniesParser(); + final Phylogeny[] phys3 = ForesterUtil.readPhylogeniesFromUrl( u3, parser3 ); + if ( ( phys3 == null ) || ( phys3.length != 2 ) ) { + return false; + } + final Phylogeny[] phys4 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "14525?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys4 == null ) || ( phys4.length != 1 ) ) { + return false; + } + final Phylogeny[] phys5 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "15632?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys5 == null ) || ( phys5.length != 1 ) ) { + return false; + } + final Phylogeny[] phys6 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "10190?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys6 == null ) || ( phys6.length != 1 ) ) { + return false; + } + final Phylogeny[] phys7 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "13246?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys7 == null ) || ( phys7.length != 2 ) ) { + return false; + } + final Phylogeny[] phys8 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "11662?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys8 == null ) || ( phys8.length != 2 ) ) { + return false; + } + final Phylogeny[] phys9 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "562?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys9 == null ) || ( phys9.length != 4 ) ) { + return false; + } + final Phylogeny[] phys16424 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "16424?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys16424 == null ) || ( phys16424.length != 1 ) ) { + return false; + } + final Phylogeny[] phys17878 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "17878?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys17878 == null ) || ( phys17878.length != 17 ) ) { + return false; + } + final Phylogeny[] phys18804 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "18804?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys18804 == null ) || ( phys18804.length != 2 ) ) { + return false; + } + final Phylogeny[] phys346 = ForesterUtil.readPhylogeniesFromUrl( + new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + + "346?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys346 == null ) || ( phys346.length != 1 ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testTreeFamReading() { + private static final boolean testTreeFamReading() { try { final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" ); final NHXParser parser = new NHXParser(); parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO ); parser.setReplaceUnderscores( false ); parser.setGuessRootedness( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } @@ -1550,6 +1741,7 @@ public final class Test { } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } @@ -1697,12 +1889,431 @@ public final class Test { return true; } + private static boolean testCommonPrefix() { + final List l0 = new ArrayList<>(); + l0.add( "abc" ); + if ( !ForesterUtil.greatestCommonPrefix( l0 ).equals( "abc" ) ) { + return false; + } + final List l1 = new ArrayList<>(); + l1.add( "abc" ); + l1.add( "abX" ); + if ( !ForesterUtil.greatestCommonPrefix( l1 ).equals( "ab" ) ) { + return false; + } + final List l2 = new ArrayList<>(); + l2.add( "abc" ); + l2.add( "abX" ); + l2.add( "axy" ); + if ( !ForesterUtil.greatestCommonPrefix( l2 ).equals( "a" ) ) { + return false; + } + final List l3 = new ArrayList<>(); + l3.add( "abXsdfsdfsdfsdfsdfsd" ); + l3.add( "abXsdfsdfsdfsdfsdfsd" ); + l3.add( "abc" ); + l3.add( "abXsdfsdfsdfsdfsdfsd" ); + l3.add( "ab" ); + l3.add( "abc" ); + l3.add( "ab" ); + if ( !ForesterUtil.greatestCommonPrefix( l3 ).equals( "ab" ) ) { + return false; + } + final List l4 = new ArrayList<>(); + l4.add( "abXsdfsdfsdfsdfsdfsd" ); + l4.add( "abXsdfsdfsdfsdfsdfsd" ); + l4.add( "abc" ); + l4.add( "Xsdfsdfsdfsdfsdfsd" ); + l4.add( "ab" ); + l4.add( "abc" ); + if ( !ForesterUtil.greatestCommonPrefix( l4 ).equals( "" ) ) { + return false; + } + final List l5 = new ArrayList<>(); + l5.add( "" ); + if ( !ForesterUtil.greatestCommonPrefix( l5 ).equals( "" ) ) { + return false; + } + final List l6 = new ArrayList<>(); + l6.add( "abc" ); + l6.add( "abX" ); + l6.add( "" ); + if ( !ForesterUtil.greatestCommonPrefix( l6 ).equals( "" ) ) { + return false; + } + return true; + } + + private static boolean testCommonPrefixSep() { + final List l0 = new ArrayList<>(); + l0.add( "a.b.c" ); + if ( !ForesterUtil.greatestCommonPrefix( l0, "." ).equals( "a.b.c" ) ) { + return false; + } + final List l1 = new ArrayList<>(); + l1.add( "a.b.c" ); + l1.add( "a.b.X" ); + if ( !ForesterUtil.greatestCommonPrefix( l1, "." ).equals( "a.b" ) ) { + return false; + } + final List l2 = new ArrayList<>(); + l2.add( "a.b.c." ); + l2.add( "a.b.X." ); + l2.add( "a.x.y." ); + if ( !ForesterUtil.greatestCommonPrefix( l2, "." ).equals( "a" ) ) { + return false; + } + final List l3 = new ArrayList<>(); + l3.add( "a/b/X/s/d/f/s/d/f/s/d/f/s/d/f/s/d/f/s/d/" ); + l3.add( "a/b/X/s/d/f/s/d/f/s/d/f/s/d/f/s/d/f/s/d" ); + l3.add( "a/b/c" ); + l3.add( "a/b/X/s/d/f/s/d/f/s/d/f/s/d/f/s/d/f/s/d/" ); + l3.add( "a/b/" ); + l3.add( "a/b/c/" ); + l3.add( "a/b////////" ); + if ( !ForesterUtil.greatestCommonPrefix( l3, "/" ).equals( "a/b" ) ) { + return false; + } + final List l4 = new ArrayList<>(); + l4.add( "a.b.X.s.d.f.s.d.f.s.d.f.s.d.f.s.d.f.s.d" ); + l4.add( "a.b.X.s.d.f.s.d.f.s.d.f.s.d.f.s.d.f.s.d" ); + l4.add( "a.b.c" ); + l4.add( "X.s.d.f.s.d.f.s.d.f.s.d.f.s.d.f.s.d..." ); + l4.add( "a.b" ); + l4.add( "a.b.c" ); + if ( !ForesterUtil.greatestCommonPrefix( l4, "." ).equals( "" ) ) { + return false; + } + final List l5 = new ArrayList<>(); + l5.add( "" ); + if ( !ForesterUtil.greatestCommonPrefix( l5, "_" ).equals( "" ) ) { + return false; + } + final List l6 = new ArrayList<>(); + l6.add( "_" ); + l6.add( "__" ); + if ( !ForesterUtil.greatestCommonPrefix( l6, "_" ).equals( "" ) ) { + return false; + } + final List l7 = new ArrayList<>(); + l7.add( "a,b,c" ); + l7.add( "a,b,X" ); + l7.add( "" ); + l7.add( ",,,,,,,,,," ); + if ( !ForesterUtil.greatestCommonPrefix( l7, "," ).equals( "" ) ) { + return false; + } + final List l8 = new ArrayList<>(); + l8.add( "123.304.403.04" ); + l8.add( "123.304.403.04.02" ); + l8.add( "123.304.403.03.03" ); + if ( !ForesterUtil.greatestCommonPrefix( l8, "." ).equals( "123.304.403" ) ) { + return false; + } + final List l9 = new ArrayList<>(); + l9.add( "123.304.403.04" ); + l9.add( "123.304.403.04.02" ); + l9.add( "123.304.402.03.03" ); + if ( !ForesterUtil.greatestCommonPrefix( l9, "." ).equals( "123.304" ) ) { + return false; + } + final List l10 = new ArrayList<>(); + l10.add( "abcde" ); + l10.add( "adc" ); + if ( !ForesterUtil.greatestCommonPrefix( l10, "." ).equals( "" ) ) { + return false; + } + return true; + } + + private static boolean testContainsPrefix() { + if ( !ForesterUtil.isContainsPrefix( "a.b", "a", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( "a.b.c", "a", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( "a.b.c", "a.b", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( "a.b", "a.b", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( "a", "a", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( ".a.b", ".a", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( ".a.b.", ".a", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( ".a.b.", ".a.", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( "a..b.", "a", "." ) ) { + return false; + } + if ( !ForesterUtil.isContainsPrefix( "a..b.", "a..", "." ) ) { + return false; + } + if ( ForesterUtil.isContainsPrefix( "a", "a.b", "." ) ) { + return false; + } + if ( ForesterUtil.isContainsPrefix( "a_b", "a", "." ) ) { + return false; + } + if ( ForesterUtil.isContainsPrefix( ".a.", ".a.b.", "." ) ) { + return false; + } + if ( ForesterUtil.isContainsPrefix( "a.b.c", "a.x", "." ) ) { + return false; + } + return true; + } + + private static boolean testUTF8ParsingFromFile() { + try { + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); + final Phylogeny[] phylogenies_xml = ParserBasedPhylogenyFactory.getInstance() + .create( new File( Test.PATH_TO_TEST_DATA + "chars.xml" ), xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); + return false; + } + if ( phylogenies_xml.length != 1 ) { + return false; + } + final Phylogeny[] phylogenies_xml2 = ParserBasedPhylogenyFactory.getInstance() + .create( new StringBuffer( phylogenies_xml[ 0 ].toPhyloXML( 0 ) ), xml_parser ); + final Phylogeny[] phylogenies_nh = ParserBasedPhylogenyFactory.getInstance() + .create( new File( Test.PATH_TO_TEST_DATA + "chars.nh" ), new NHXParser() ); + if ( phylogenies_nh.length != 1 ) { + return false; + } + final Phylogeny[] phylogenies_nex = ParserBasedPhylogenyFactory.getInstance() + .create( new File( Test.PATH_TO_TEST_DATA + "chars.nex" ), new NexusPhylogeniesParser() ); + if ( phylogenies_nex.length != 1 ) { + return false; + } + final String[] xml_n = phylogenies_xml[ 0 ].getAllExternalNodeNames(); + final String[] xml_n2 = phylogenies_xml2[ 0 ].getAllExternalNodeNames(); + final String[] nh_n = phylogenies_nh[ 0 ].getAllExternalNodeNames(); + final String[] nex_n = phylogenies_nex[ 0 ].getAllExternalNodeNames(); + final String n0 = "AQ~!@#$%^&*()_+-=\\{}|;:\"<>?,./"; + final String n1 = "€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ"; + final String n2 = "漢字ひらがなカタカナ"; + final String n3 = "อักษรไทย"; + final String n4 = "繁體字"; + final String n5 = "한글"; + final String n6 = "देवनागरी"; + final String n7 = "chữ Quốc ngữ"; + final String n8 = "ру́сский язы́к"; + final String n9 = "អក្សរខ្មែរ"; + if ( !xml_n[ 0 ].equals( n0 ) ) { + System.out.println( xml_n[ 0 ] ); + System.out.println( n0 ); + return false; + } + if ( !xml_n2[ 0 ].equals( n0 ) ) { + System.out.println( xml_n2[ 0 ] ); + System.out.println( n0 ); + return false; + } + if ( !nh_n[ 0 ].equals( n0 ) ) { + System.out.println( nh_n[ 0 ] ); + System.out.println( n0 ); + return false; + } + if ( !nex_n[ 0 ].equals( n0 ) ) { + System.out.println( nex_n[ 0 ] ); + System.out.println( n0 ); + return false; + } + if ( !xml_n[ 1 ].equals( n1 ) ) { + System.out.println( xml_n[ 1 ] ); + System.out.println( n1 ); + return false; + } + if ( !xml_n2[ 1 ].equals( n1 ) ) { + System.out.println( xml_n2[ 1 ] ); + System.out.println( n1 ); + return false; + } + if ( !nh_n[ 1 ].equals( n1 ) ) { + System.out.println( nh_n[ 1 ] ); + System.out.println( n1 ); + return false; + } + if ( !nex_n[ 1 ].equals( n1 ) ) { + System.out.println( nex_n[ 1 ] ); + System.out.println( n1 ); + return false; + } + if ( !xml_n[ 2 ].equals( n2 ) ) { + System.out.println( xml_n[ 2 ] ); + System.out.println( n2 ); + return false; + } + if ( !xml_n2[ 2 ].equals( n2 ) ) { + System.out.println( xml_n2[ 2 ] ); + System.out.println( n2 ); + return false; + } + if ( !nh_n[ 2 ].equals( n2 ) ) { + System.out.println( nh_n[ 2 ] ); + System.out.println( n2 ); + return false; + } + if ( !nex_n[ 2 ].equals( n2 ) ) { + System.out.println( nex_n[ 2 ] ); + System.out.println( n2 ); + return false; + } + // + if ( !xml_n[ 3 ].equals( n3 ) ) { + System.out.println( xml_n[ 3 ] ); + System.out.println( n3 ); + return false; + } + if ( !xml_n2[ 3 ].equals( n3 ) ) { + System.out.println( xml_n2[ 3 ] ); + System.out.println( n3 ); + return false; + } + if ( !nh_n[ 3 ].equals( n3 ) ) { + System.out.println( nh_n[ 3 ] ); + System.out.println( n3 ); + return false; + } + if ( !nex_n[ 3 ].equals( n3 ) ) { + System.out.println( nex_n[ 3 ] ); + System.out.println( n3 ); + return false; + } + // + if ( !xml_n[ 4 ].equals( n4 ) ) { + System.out.println( xml_n[ 4 ] ); + System.out.println( n4 ); + return false; + } + if ( !nh_n[ 4 ].equals( n4 ) ) { + System.out.println( nh_n[ 4 ] ); + System.out.println( n4 ); + return false; + } + if ( !nex_n[ 4 ].equals( n4 ) ) { + System.out.println( nex_n[ 4 ] ); + System.out.println( n4 ); + return false; + } + // + if ( !xml_n[ 5 ].equals( n5 ) ) { + System.out.println( xml_n[ 5 ] ); + System.out.println( n5 ); + return false; + } + if ( !nh_n[ 5 ].equals( n5 ) ) { + System.out.println( nh_n[ 5 ] ); + System.out.println( n5 ); + return false; + } + if ( !nex_n[ 5 ].equals( n5 ) ) { + System.out.println( nex_n[ 5 ] ); + System.out.println( n5 ); + return false; + } + // + if ( !xml_n[ 6 ].equals( n6 ) ) { + System.out.println( xml_n[ 6 ] ); + System.out.println( n6 ); + return false; + } + if ( !nh_n[ 6 ].equals( n6 ) ) { + System.out.println( nh_n[ 6 ] ); + System.out.println( n6 ); + return false; + } + if ( !nex_n[ 6 ].equals( n6 ) ) { + System.out.println( nex_n[ 6 ] ); + System.out.println( n6 ); + return false; + } + // + if ( !xml_n[ 7 ].equals( n7 ) ) { + System.out.println( xml_n[ 7 ] ); + System.out.println( n7 ); + return false; + } + if ( !nh_n[ 7 ].equals( n7 ) ) { + System.out.println( nh_n[ 7 ] ); + System.out.println( n7 ); + return false; + } + if ( !nex_n[ 7 ].equals( n7 ) ) { + System.out.println( nex_n[ 7 ] ); + System.out.println( n7 ); + return false; + } + if ( !xml_n[ 8 ].equals( n8 ) ) { + System.out.println( xml_n[ 8 ] ); + System.out.println( n8 ); + return false; + } + if ( !nh_n[ 8 ].equals( n8 ) ) { + System.out.println( nh_n[ 8 ] ); + System.out.println( n8 ); + return false; + } + if ( !nex_n[ 8 ].equals( n8 ) ) { + System.out.println( nex_n[ 8 ] ); + System.out.println( n8 ); + return false; + } + if ( !xml_n[ 9 ].equals( n9 ) ) { + System.out.println( xml_n[ 9 ] ); + System.out.println( n9 ); + return false; + } + if ( !xml_n2[ 9 ].equals( n9 ) ) { + System.out.println( xml_n2[ 9 ] ); + System.out.println( n9 ); + return false; + } + if ( !nh_n[ 9 ].equals( n9 ) ) { + System.out.println( nh_n[ 9 ] ); + System.out.println( n9 ); + return false; + } + if ( !nex_n[ 9 ].equals( n9 ) ) { + System.out.println( nex_n[ 9 ] ); + System.out.println( n9 ); + return false; + } + if ( !phylogenies_xml[ 0 ].toNewHampshire().equals( phylogenies_nh[ 0 ].toNewHampshire() ) ) { + System.out.println( phylogenies_xml[ 0 ].toNewHampshire() ); + System.out.println( phylogenies_nh[ 0 ].toNewHampshire() ); + return false; + } + if ( !phylogenies_xml[ 0 ].toNewHampshire().equals( phylogenies_nex[ 0 ].toNewHampshire() ) ) { + System.out.println( phylogenies_xml[ 0 ].toNewHampshire() ); + System.out.println( phylogenies_nex[ 0 ].toNewHampshire() ); + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testBasicPhyloXMLparsing() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", - xml_parser ); + final Phylogeny[] phylogenies_0 = factory + .create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( xml_parser.getErrorMessages().toString() ); return false; @@ -1804,7 +2415,8 @@ public final class Test { if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) { return false; } - if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) { + if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource() + .equals( "UniProtKB" ) ) { return false; } if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() @@ -1831,8 +2443,8 @@ public final class Test { .getValue() != 1 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() - .getType().equals( "ml" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence().getType() + .equals( "ml" ) ) { return false; } if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() @@ -1840,27 +2452,27 @@ public final class Test { return false; } if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { + .getProperties( "AFFY:expression" ).get( 0 ).getAppliesTo() != AppliesTo.ANNOTATION ) { return false; } if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { + .getProperties( "AFFY:expression" ).get( 0 ).getDataType().equals( "xsd:double" ) ) { return false; } if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { + .getProperties( "AFFY:expression" ).get( 0 ).getRef().equals( "AFFY:expression" ) ) { return false; } if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { + .getProperties( "AFFY:expression" ).get( 0 ).getUnit().equals( "AFFY:x" ) ) { return false; } if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { + .getProperties( "AFFY:expression" ).get( 0 ).getValue().equals( "0.2" ) ) { return false; } if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { + .getProperties( "MED:disease" ).get( 0 ).getValue().equals( "lymphoma" ) ) { return false; } if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() @@ -1915,8 +2527,8 @@ public final class Test { else { xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); } - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", - xml_parser ); + final Phylogeny[] phylogenies_0 = factory + .create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( xml_parser.getErrorMessages().toString() ); return false; @@ -1995,7 +2607,8 @@ public final class Test { if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue() + .equals( "Q9BZR8" ) ) { return false; } if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource() @@ -2035,27 +2648,27 @@ public final class Test { return false; } if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { + .getProperties( "AFFY:expression" ).get( 0 ).getAppliesTo() != AppliesTo.ANNOTATION ) { return false; } if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { + .getProperties( "AFFY:expression" ).get( 0 ).getDataType().equals( "xsd:double" ) ) { return false; } if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { + .getProperties( "AFFY:expression" ).get( 0 ).getRef().equals( "AFFY:expression" ) ) { return false; } if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { + .getProperties( "AFFY:expression" ).get( 0 ).getUnit().equals( "AFFY:x" ) ) { return false; } if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { + .getProperties( "AFFY:expression" ).get( 0 ).getValue().equals( "0.2" ) ) { return false; } if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { + .getProperties( "MED:disease" ).get( 0 ).getValue().equals( "lymphoma" ) ) { return false; } if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() @@ -2066,7 +2679,8 @@ public final class Test { .equals( "intracellular organelle" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType() + .equals( "source" ) ) ) { return false; } if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription() @@ -2076,11 +2690,13 @@ public final class Test { if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi() + .equals( "10.1038/387489a0" ) ) ) { return false; } if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) { + System.out.println( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() ); return false; } if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) { @@ -2089,7 +2705,8 @@ public final class Test { if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName() + .equals( "molting animals" ) ) { return false; } if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { @@ -2099,7 +2716,8 @@ public final class Test { .equals( "ncbi" ) ) { return false; } - if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) { + if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture() + .getTotalLength() != 124 ) { return false; } if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) @@ -2110,7 +2728,8 @@ public final class Test { .getFrom() != 21 ) { return false; } - if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) { + if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) + .getTo() != 44 ) { return false; } if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) @@ -2206,7 +2825,8 @@ public final class Test { .equalsIgnoreCase( "435" ) ) { return false; } - if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) { + if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString() + .equalsIgnoreCase( "416" ) ) { return false; } if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString() @@ -2267,8 +2887,8 @@ public final class Test { xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); } } - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", - xml_parser ); + final Phylogeny[] phylogenies_0 = factory + .create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( xml_parser.getErrorMessages().toString() ); return false; @@ -2302,7 +2922,7 @@ public final class Test { return false; } final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml"; - final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser ); + final Phylogeny[] phylogenies_1 = factory.create( new File( x2 ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( "errors:" ); System.out.println( xml_parser.getErrorMessages().toString() ); @@ -2311,8 +2931,8 @@ public final class Test { if ( phylogenies_1.length != 4 ) { return false; } - final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml", - xml_parser ); + final Phylogeny[] phylogenies_2 = factory + .create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml" ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( "errors:" ); System.out.println( xml_parser.getErrorMessages().toString() ); @@ -2324,8 +2944,8 @@ public final class Test { if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) { return false; } - final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml", - xml_parser ); + final Phylogeny[] phylogenies_3 = factory + .create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml" ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( xml_parser.getErrorMessages().toString() ); return false; @@ -2346,8 +2966,8 @@ public final class Test { if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) { return false; } - final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml", - xml_parser ); + final Phylogeny[] phylogenies_4 = factory + .create( new File( Test.PATH_TO_TEST_DATA + "special_characters.xml" ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( xml_parser.getErrorMessages().toString() ); return false; @@ -2373,6 +2993,42 @@ public final class Test { return true; } + private static boolean testPhyloXMLparsingValidating() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + PhyloXmlParser xml_parser = null; + try { + xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating(); + } + catch ( final Exception e ) { + // Do nothing -- means were not running from jar. + } + if ( xml_parser == null ) { + xml_parser = PhyloXmlParser.createPhyloXmlParser(); + if ( USE_LOCAL_PHYLOXML_SCHEMA ) { + xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); + } + else { + xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); + } + } + final Phylogeny[] phylogenies_0 = factory + .create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_1.xml" ), xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); + return false; + } + if ( phylogenies_0.length != 3 ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testBasicProtein() { try { final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 ); @@ -2550,7 +3206,7 @@ public final class Test { p.addProteinDomain( A20 ); p.addProteinDomain( B25 ); p.addProteinDomain( D80 ); - List domains_ids = new ArrayList(); + List domains_ids = new ArrayList<>(); domains_ids.add( "A" ); domains_ids.add( "B" ); domains_ids.add( "C" ); @@ -2567,7 +3223,7 @@ public final class Test { if ( p.contains( domains_ids, true ) ) { return false; } - domains_ids = new ArrayList(); + domains_ids = new ArrayList<>(); domains_ids.add( "A" ); domains_ids.add( "C" ); domains_ids.add( "D" ); @@ -2577,7 +3233,7 @@ public final class Test { if ( !p.contains( domains_ids, true ) ) { return false; } - domains_ids = new ArrayList(); + domains_ids = new ArrayList<>(); domains_ids.add( "A" ); domains_ids.add( "D" ); domains_ids.add( "C" ); @@ -2587,7 +3243,7 @@ public final class Test { if ( p.contains( domains_ids, true ) ) { return false; } - domains_ids = new ArrayList(); + domains_ids = new ArrayList<>(); domains_ids.add( "A" ); domains_ids.add( "A" ); domains_ids.add( "B" ); @@ -2597,7 +3253,7 @@ public final class Test { if ( !p.contains( domains_ids, true ) ) { return false; } - domains_ids = new ArrayList(); + domains_ids = new ArrayList<>(); domains_ids.add( "A" ); domains_ids.add( "A" ); domains_ids.add( "A" ); @@ -2609,7 +3265,7 @@ public final class Test { if ( !p.contains( domains_ids, true ) ) { return false; } - domains_ids = new ArrayList(); + domains_ids = new ArrayList<>(); domains_ids.add( "A" ); domains_ids.add( "A" ); domains_ids.add( "B" ); @@ -2638,7 +3294,7 @@ public final class Test { private static boolean testBasicTable() { try { - final BasicTable t0 = new BasicTable(); + final BasicTable t0 = new BasicTable<>(); if ( t0.getNumberOfColumns() != 0 ) { return false; } @@ -2821,7 +3477,8 @@ public final class Test { if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) { return false; } - if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) { + if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName() + .equals( "Rhombozoa" ) ) { return false; } if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) { @@ -2854,7 +3511,8 @@ public final class Test { if ( t2.getRoot().getNumberOfDescendants() != 24 ) { return false; } - if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) { + if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName() + .equals( "Aquificae" ) ) { return false; } if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName() @@ -2939,7 +3597,7 @@ public final class Test { if ( t2.getNumberOfExternalNodes() != 4 ) { return false; } - if ( t2.getHeight() != 8.5 ) { + if ( t2.calculateHeight( false ) != 8.5 ) { return false; } if ( !t2.isCompletelyBinary() ) { @@ -2952,57 +3610,58 @@ public final class Test { if ( t3.getNumberOfExternalNodes() != 5 ) { return false; } - if ( t3.getHeight() != 11 ) { + if ( t3.calculateHeight( true ) != 11 ) { return false; } if ( t3.isCompletelyBinary() ) { return false; } final PhylogenyNode n = t3.getNode( "ABC" ); - final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ]; + final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", + new NHXParser() )[ 0 ]; if ( t4.getNumberOfExternalNodes() != 9 ) { return false; } - if ( t4.getHeight() != 11 ) { + if ( t4.calculateHeight( false ) != 11 ) { return false; } if ( t4.isCompletelyBinary() ) { return false; } final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" ); - final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; + final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ]; if ( t5.getNumberOfExternalNodes() != 8 ) { return false; } - if ( t5.getHeight() != 15 ) { + if ( t5.calculateHeight( false ) != 15 ) { return false; } final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" ); - final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ]; - if ( t6.getHeight() != 15 ) { + final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ]; + if ( t6.calculateHeight( true ) != 15 ) { return false; } final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" ); - final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ]; - if ( t7.getHeight() != 15 ) { + final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ]; + if ( t7.calculateHeight( true ) != 15 ) { return false; } final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" ); - final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ]; + final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ]; if ( t8.getNumberOfExternalNodes() != 10 ) { return false; } - if ( t8.getHeight() != 15 ) { + if ( t8.calculateHeight( true ) != 15 ) { return false; } final char[] a9 = new char[] { 'a' }; final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ]; - if ( t9.getHeight() != 0 ) { + if ( t9.calculateHeight( true ) != 0 ) { return false; } final char[] a10 = new char[] { 'a', ':', '6' }; final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ]; - if ( t10.getHeight() != 6 ) { + if ( t10.calculateHeight( true ) != 6 ) { return false; } } @@ -3017,9 +3676,9 @@ public final class Test { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev0 = factory - .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);", - new NHXParser() ); + final Phylogeny[] ev0 = factory.create( + "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);", + new NHXParser() ); ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 ); if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) { return false; @@ -3028,9 +3687,9 @@ public final class Test { return false; } final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev1 = factory - .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));", - new NHXParser() ); + final Phylogeny[] ev1 = factory.create( + "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));", + new NHXParser() ); ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 ); if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) { return false; @@ -3039,9 +3698,9 @@ public final class Test { return false; } final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev_b = factory - .create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd", - new NHXParser() ); + final Phylogeny[] ev_b = factory.create( + "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd", + new NHXParser() ); ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 ); if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) { return false; @@ -3051,9 +3710,9 @@ public final class Test { } // final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev1x = factory - .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));", - new NHXParser() ); + final Phylogeny[] ev1x = factory.create( + "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));", + new NHXParser() ); ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 ); if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) { return false; @@ -3062,9 +3721,9 @@ public final class Test { return false; } final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev_bx = factory - .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd", - new NHXParser() ); + final Phylogeny[] ev_bx = factory.create( + "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd", + new NHXParser() ); ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 ); if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; @@ -3072,12 +3731,12 @@ public final class Test { if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; } - final Phylogeny[] t2 = factory - .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);", - new NHXParser() ); - final Phylogeny[] ev2 = factory - .create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);", - new NHXParser() ); + final Phylogeny[] t2 = factory.create( + "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);", + new NHXParser() ); + final Phylogeny[] ev2 = factory.create( + "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);", + new NHXParser() ); for( final Phylogeny target : t2 ) { ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 ); } @@ -3150,19 +3809,23 @@ public final class Test { return false; } n.setName( "B0LM41_HUMAN" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) { + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ) + .equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) { return false; } n.setName( "NP_001025424" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) { + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ) + .equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) { return false; } n.setName( "_NM_001030253-" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) { + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ) + .equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) { return false; } n.setName( "XM_002122186" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) { + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ) + .equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) { return false; } n.setName( "dgh_AAA34956_gdg" ); @@ -3330,7 +3993,7 @@ public final class Test { final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 ); final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 ); final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 ); - final ArrayList domains0 = new ArrayList(); + final ArrayList domains0 = new ArrayList<>(); domains0.add( d2 ); domains0.add( d0 ); domains0.add( d3 ); @@ -3349,7 +4012,7 @@ public final class Test { if ( ds1.getNumberOfDomains() != 4 ) { return false; } - final ArrayList domains1 = new ArrayList(); + final ArrayList domains1 = new ArrayList<>(); domains1.add( d1 ); domains1.add( d2 ); domains1.add( d4 ); @@ -4031,7 +4694,7 @@ public final class Test { System.out.println( entry.getAnnotations().first().getRefSource() ); return false; } - if ( entry.getCrossReferences().size() != 5 ) { + if ( entry.getCrossReferences().size() < 1 ) { return false; } final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); @@ -4054,7 +4717,7 @@ public final class Test { System.out.println( entry1.getGeneName() ); return false; } - if ( entry1.getCrossReferences().size() != 6 ) { + if ( entry1.getCrossReferences().size() < 1 ) { return false; } final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); @@ -4078,10 +4741,15 @@ public final class Test { System.out.println( entry2.getGeneName() ); return false; } - if ( entry2.getCrossReferences().size() != 3 ) { + if ( entry2.getCrossReferences().size() < 1 ) { + return false; + } + if ( !entry2.getChromosome().equals( "20" ) ) { + return false; + } + if ( !entry2.getMap().equals( "20q11.22" ) ) { return false; } - // final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" ); if ( !entry3.getAccession().equals( "HM043801" ) ) { return false; @@ -4105,7 +4773,7 @@ public final class Test { if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { return false; } - if ( entry3.getCrossReferences().size() < 7 ) { + if ( entry3.getCrossReferences().size() < 1 ) { return false; } final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); @@ -4128,21 +4796,6 @@ public final class Test { System.out.println( entry4.getGeneName() ); return false; } - // if ( !entry4.getChromosome().equals( "ras" ) ) { - // System.out.println( entry4.getChromosome() ); - // return false; - // } - // if ( !entry4.getMap().equals( "ras" ) ) { - // System.out.println( entry4.getMap() ); - // return false; - // } - //TODO FIXME gi... - // - //TODO fails: - // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" ); - // if ( !entry5.getAccession().equals( "HM043801" ) ) { - // return false; - // } final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" ); if ( !entry5.getAccession().equals( "AAZ45343" ) ) { return false; @@ -4159,6 +4812,25 @@ public final class Test { System.out.println( entry5.getTaxonomyIdentifier() ); return false; } + final SequenceDatabaseEntry entry6 = SequenceDbWsTools.obtainEntry( "M30539" ); + if ( !entry6.getAccession().equals( "M30539" ) ) { + return false; + } + if ( !entry6.getGeneName().equals( "ras" ) ) { + return false; + } + if ( !entry6.getSequenceName().equals( "Human SK2 c-Ha-ras-1 oncogene-encoded protein gene, exon 1" ) ) { + return false; + } + if ( !entry6.getTaxonomyIdentifier().equals( "9606" ) ) { + return false; + } + if ( !entry6.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + return false; + } + if ( entry6.getCrossReferences().size() < 1 ) { + return false; + } } catch ( final IOException e ) { System.out.println(); @@ -4254,7 +4926,8 @@ public final class Test { for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) { final PhylogenyNode node = iter.next(); } - final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ]; + final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", + new NHXParser() )[ 0 ]; final PhylogenyNodeIterator iter = t6.iteratorExternalForward(); if ( !iter.next().getName().equals( "A" ) ) { return false; @@ -4323,7 +4996,8 @@ public final class Test { .equals( "Mus musculus musculus" ) ) { return false; } - if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) { + if ( ParserUtils + .extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) { return false; } if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) { @@ -4567,7 +5241,8 @@ public final class Test { private static boolean testExtractTaxonomyCodeFromNodeName() { try { - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) @@ -4582,13 +5257,16 @@ public final class Test { .equals( "ARATH" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "RAT" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "RAT" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) @@ -4623,34 +5301,36 @@ public final class Test { .equals( "SOYBN" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", + TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE ) .equals( "SOYBN" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01", - TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) { + if ( !ParserUtils + .extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) + .equals( "ECOLI" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blagg_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE ) .equals( "9YX45" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", @@ -4662,15 +5342,18 @@ public final class Test { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "RAT" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "RAT" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "RAT" ) ) { return false; } if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", @@ -4698,7 +5381,8 @@ public final class Test { .equals( "MOUSE" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } } @@ -4885,12 +5569,22 @@ public final class Test { private static boolean testFastaParser() { try { - if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) { + final FileInputStream fis1 = new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ); + if ( !FastaParser.isLikelyFasta( fis1 ) ) { + fis1.close(); return false; } - if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) { + else { + fis1.close(); + } + final FileInputStream fis2 = new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ); + if ( FastaParser.isLikelyFasta( fis2 ) ) { + fis2.close(); return false; } + else { + fis2.close(); + } final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ); if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) { return false; @@ -4929,7 +5623,8 @@ public final class Test { if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) { return false; } - if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) { + if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ) + .equals( "AY423861.24" ) ) { return false; } if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) { @@ -4971,13 +5666,13 @@ public final class Test { private static boolean testGeneralMsaParser() { try { final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n"; - final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) ); + final Msa msa_0 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_0.getBytes() ) ); final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n"; - final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) ); + final Msa msa_1 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_1.getBytes() ) ); final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n"; - final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) ); + final Msa msa_2 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_2.getBytes() ) ); final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n"; - final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) ); + final Msa msa_3 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_3.getBytes() ) ); if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { return false; } @@ -5014,7 +5709,7 @@ public final class Test { if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) { return false; } - final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) ); + final Msa msa_4 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) ); if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) { return false; } @@ -5024,7 +5719,7 @@ public final class Test { if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { return false; } - final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) ); + final Msa msa_5 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) ); if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) { return false; } @@ -5034,7 +5729,7 @@ public final class Test { if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) { return false; } - final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ); + final Msa msa_6 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ); if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) { return false; } @@ -5054,7 +5749,7 @@ public final class Test { private static boolean testGeneralTable() { try { - final GeneralTable t0 = new GeneralTable(); + final GeneralTable t0 = new GeneralTable<>(); t0.setValue( 3, 2, "23" ); t0.setValue( 10, 1, "error" ); t0.setValue( 10, 1, "110" ); @@ -5090,7 +5785,7 @@ public final class Test { if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) { return false; } - final GeneralTable t1 = new GeneralTable(); + final GeneralTable t1 = new GeneralTable<>(); t1.setValue( "3", "2", "23" ); t1.setValue( "10", "1", "error" ); t1.setValue( "10", "1", "110" ); @@ -5409,9 +6104,9 @@ public final class Test { if ( !rt.getName().equals( "r" ) ) { return false; } - final Phylogeny p3 = factory - .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", - new NHXParser() )[ 0 ]; + final Phylogeny p3 = factory.create( + "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", + new NHXParser() )[ 0 ]; final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) ); if ( !bc_3.getName().equals( "bc" ) ) { return false; @@ -5695,9 +6390,9 @@ public final class Test { if ( !rt.getName().equals( "r" ) ) { return false; } - final Phylogeny p3 = factory - .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", - new NHXParser() )[ 0 ]; + final Phylogeny p3 = factory.create( + "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", + new NHXParser() )[ 0 ]; PhylogenyMethods.preOrderReId( p3 ); final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ), p3.getNode( "c" ) ); @@ -5821,10 +6516,14 @@ public final class Test { final String test_dir = Test.PATH_TO_TEST_DATA; try { final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); + + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), + "MONBR", + INDIVIDUAL_SCORE_CUTOFF.NONE ); parser1.parse(); final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); + + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), + "MONBR", + INDIVIDUAL_SCORE_CUTOFF.NONE ); final List proteins = parser2.parse(); if ( parser2.getProteinsEncountered() != 4 ) { return false; @@ -6097,7 +6796,7 @@ public final class Test { private static boolean testMafft( final String path ) { try { - final List opts = new ArrayList(); + final List opts = new ArrayList<>(); opts.add( "--maxiterate" ); opts.add( "1000" ); opts.add( "--localpair" ); @@ -6193,7 +6892,7 @@ public final class Test { final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" ); final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" ); final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" ); - final List l = new ArrayList(); + final List l = new ArrayList<>(); l.add( s0 ); l.add( s1 ); l.add( s2 ); @@ -6234,7 +6933,7 @@ public final class Test { final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" ); final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" ); final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" ); - final List l = new ArrayList(); + final List l = new ArrayList<>(); l.add( s0 ); l.add( s1 ); l.add( s2 ); @@ -6257,7 +6956,7 @@ public final class Test { // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) ); // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) ); // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) ); - final List l2 = new ArrayList(); + final List l2 = new ArrayList<>(); l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) ); l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) ); l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) ); @@ -6301,7 +7000,7 @@ public final class Test { final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" ); final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" ); final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" ); - final List l0 = new ArrayList(); + final List l0 = new ArrayList<>(); l0.add( s0 ); l0.add( s1 ); l0.add( s2 ); @@ -6349,7 +7048,7 @@ public final class Test { final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" ); final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" ); final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" ); - final List l1 = new ArrayList(); + final List l1 = new ArrayList<>(); l1.add( s_0 ); l1.add( s_1 ); l1.add( s_2 ); @@ -6389,7 +7088,7 @@ public final class Test { final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" ); final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" ); final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" ); - final List l2 = new ArrayList(); + final List l2 = new ArrayList<>(); l2.add( s__0 ); l2.add( s__1 ); l2.add( s__2 ); @@ -6455,9 +7154,9 @@ public final class Test { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); PhylogenyNode n; - List ext = new ArrayList(); + List ext = new ArrayList<>(); final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ]; + final Phylogeny t0 = factory.create( sb0.toString(), new NHXParser() )[ 0 ]; t0.getNode( "cd" ).setCollapse( true ); t0.getNode( "cde" ).setCollapse( true ); n = t0.getFirstExternalNode(); @@ -6485,12 +7184,12 @@ public final class Test { } ext.clear(); final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ]; + final Phylogeny t1 = factory.create( sb1.toString(), new NHXParser() )[ 0 ]; t1.getNode( "ab" ).setCollapse( true ); t1.getNode( "cd" ).setCollapse( true ); t1.getNode( "cde" ).setCollapse( true ); n = t1.getNode( "ab" ); - ext = new ArrayList(); + ext = new ArrayList<>(); while ( n != null ) { ext.add( n ); n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); @@ -6512,7 +7211,7 @@ public final class Test { } ext.clear(); final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ]; + final Phylogeny t2 = factory.create( sb2.toString(), new NHXParser() )[ 0 ]; t2.getNode( "ab" ).setCollapse( true ); t2.getNode( "cd" ).setCollapse( true ); t2.getNode( "cde" ).setCollapse( true ); @@ -6521,7 +7220,7 @@ public final class Test { t2.getNode( "e" ).setCollapse( true ); t2.getNode( "gh" ).setCollapse( true ); n = t2.getNode( "ab" ); - ext = new ArrayList(); + ext = new ArrayList<>(); while ( n != null ) { ext.add( n ); n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); @@ -6540,7 +7239,7 @@ public final class Test { } ext.clear(); final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ]; + final Phylogeny t3 = factory.create( sb3.toString(), new NHXParser() )[ 0 ]; t3.getNode( "ab" ).setCollapse( true ); t3.getNode( "cd" ).setCollapse( true ); t3.getNode( "cde" ).setCollapse( true ); @@ -6550,7 +7249,7 @@ public final class Test { t3.getNode( "gh" ).setCollapse( true ); t3.getNode( "fgh" ).setCollapse( true ); n = t3.getNode( "ab" ); - ext = new ArrayList(); + ext = new ArrayList<>(); while ( n != null ) { ext.add( n ); n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); @@ -6566,7 +7265,7 @@ public final class Test { } ext.clear(); final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ]; + final Phylogeny t4 = factory.create( sb4.toString(), new NHXParser() )[ 0 ]; t4.getNode( "ab" ).setCollapse( true ); t4.getNode( "cd" ).setCollapse( true ); t4.getNode( "cde" ).setCollapse( true ); @@ -6581,7 +7280,7 @@ public final class Test { return false; } final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; + final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ]; ext.clear(); n = t5.getFirstExternalNode(); while ( n != null ) { @@ -6616,7 +7315,7 @@ public final class Test { return false; } final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ]; + final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ]; ext.clear(); t6.getNode( "ab" ).setCollapse( true ); n = t6.getNode( "ab" ); @@ -6649,7 +7348,7 @@ public final class Test { return false; } final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ]; + final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ]; ext.clear(); t7.getNode( "cd" ).setCollapse( true ); n = t7.getNode( "a" ); @@ -6682,7 +7381,7 @@ public final class Test { return false; } final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ]; + final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ]; ext.clear(); t8.getNode( "cd" ).setCollapse( true ); t8.getNode( "c" ).setCollapse( true ); @@ -6718,7 +7417,7 @@ public final class Test { return false; } final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ]; + final Phylogeny t9 = factory.create( sb9.toString(), new NHXParser() )[ 0 ]; ext.clear(); t9.getNode( "gh" ).setCollapse( true ); n = t9.getNode( "a" ); @@ -6751,7 +7450,7 @@ public final class Test { return false; } final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ]; + final Phylogeny t10 = factory.create( sb10.toString(), new NHXParser() )[ 0 ]; ext.clear(); t10.getNode( "gh" ).setCollapse( true ); t10.getNode( "g" ).setCollapse( true ); @@ -6786,7 +7485,7 @@ public final class Test { return false; } final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ]; + final Phylogeny t11 = factory.create( sb11.toString(), new NHXParser() )[ 0 ]; ext.clear(); t11.getNode( "gh" ).setCollapse( true ); t11.getNode( "fgh" ).setCollapse( true ); @@ -6817,7 +7516,7 @@ public final class Test { return false; } final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ]; + final Phylogeny t12 = factory.create( sb12.toString(), new NHXParser() )[ 0 ]; ext.clear(); t12.getNode( "gh" ).setCollapse( true ); t12.getNode( "fgh" ).setCollapse( true ); @@ -6851,7 +7550,7 @@ public final class Test { return false; } final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ]; + final Phylogeny t13 = factory.create( sb13.toString(), new NHXParser() )[ 0 ]; ext.clear(); t13.getNode( "ab" ).setCollapse( true ); t13.getNode( "b" ).setCollapse( true ); @@ -6881,7 +7580,7 @@ public final class Test { return false; } final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ]; + final Phylogeny t14 = factory.create( sb14.toString(), new NHXParser() )[ 0 ]; ext.clear(); t14.getNode( "ab" ).setCollapse( true ); t14.getNode( "a" ).setCollapse( true ); @@ -6911,7 +7610,7 @@ public final class Test { return false; } final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ]; + final Phylogeny t15 = factory.create( sb15.toString(), new NHXParser() )[ 0 ]; ext.clear(); t15.getNode( "ab" ).setCollapse( true ); t15.getNode( "a" ).setCollapse( true ); @@ -6946,7 +7645,7 @@ public final class Test { // // final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ]; + final Phylogeny t16 = factory.create( sb16.toString(), new NHXParser() )[ 0 ]; ext.clear(); t16.getNode( "ab" ).setCollapse( true ); t16.getNode( "a" ).setCollapse( true ); @@ -7311,12 +8010,12 @@ public final class Test { if ( phylogenies.length != 9 ) { return false; } - if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" ) - .getDistanceToParent() ) ) { + if ( !isEqual( 0.48039661496919533, + phylogenies[ 0 ].getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) { return false; } - if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" ) - .getDistanceToParent() ) ) { + if ( !isEqual( 0.3959796191512233, + phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) { return false; } if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) { @@ -7711,8 +8410,7 @@ public final class Test { System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !phy - .toNewHampshire() + 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; @@ -7732,8 +8430,7 @@ public final class Test { System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !phy - .toNewHampshire() + 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; @@ -7753,8 +8450,7 @@ public final class Test { System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !phy - .toNewHampshire() + 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; @@ -7774,8 +8470,7 @@ public final class Test { System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !phy - .toNewHampshire() + 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; @@ -8157,19 +8852,19 @@ public final class Test { 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 ]; + 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 p2 = factory.create( new StringBuffer( "(A,B2)" ).toString(), 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 p5 = factory.create( new StringBuffer( "(A,B5);" ).toString(), 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() ); @@ -8177,9 +8872,8 @@ public final class Test { 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() ); + + " 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; } @@ -8427,21 +9121,24 @@ public final class Test { if ( p46.length != 0 ) { return false; } - final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ).toString(), + new NHXParser() )[ 0 ]; if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ).toString(), + new NHXParser() )[ 0 ]; if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } final Phylogeny p49 = factory - .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ), + .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ).toString(), new NHXParser() )[ 0 ]; if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ).toString(), + new NHXParser() )[ 0 ]; if ( p50.getNode( "A" ) == null ) { return false; } @@ -8456,79 +9153,200 @@ public final class Test { .equals( "((A,B)88:2.0,C);" ) ) { return false; } - final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ).toString(), + new NHXParser() )[ 0 ]; if ( p51.getNode( "A(A" ) == null ) { return false; } - final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ).toString(), + new NHXParser() )[ 0 ]; if ( p52.getNode( "A(A" ) == null ) { return false; } final Phylogeny p53 = factory - .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ), + .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) { return false; } - final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ).toString(), + new NHXParser() )[ 0 ]; if ( p54.getNode( "A" ) == null ) { return false; } - if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) { + if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) + .equals( "((A,B)[88],C);" ) ) { return false; } final Phylogeny p55 = factory - .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ), - new NHXParser() )[ 0 ]; - if ( !p55 - .toNewHampshire() + .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ) + .toString(), new NHXParser() )[ 0 ]; + if ( !p55.toNewHampshire() .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,lcl|HPV66_L1.1x:0.0798012);" ) ) { System.out.println( p55.toNewHampshire() ); return false; } final Phylogeny p56 = factory - .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ), - new NHXParser() )[ 0 ]; - if ( !p56 - .toNewHampshire() + .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ) + .toString(), new NHXParser() )[ 0 ]; + if ( !p56.toNewHampshire() .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) { System.out.println( p56.toNewHampshire() ); return false; } final Phylogeny p57 = factory - .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ), - new NHXParser() )[ 0 ]; - if ( !p57 - .toNewHampshire() + .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ) + .toString(), new NHXParser() )[ 0 ]; + if ( !p57.toNewHampshire() .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) { System.out.println( p56.toNewHampshire() ); return false; } final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';"; - final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ]; + final Phylogeny p58 = factory.create( s58, new NHXParser() )[ 0 ]; if ( !p58.toNewHampshire().equals( s58 ) ) { System.out.println( p58.toNewHampshire() ); return false; } final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";"; - final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ]; + final Phylogeny p59 = factory.create( s59, new NHXParser() )[ 0 ]; if ( !p59.toNewHampshire().equals( s59 ) ) { System.out.println( p59.toNewHampshire() ); return false; } final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');"; - final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ]; + final Phylogeny p60 = factory.create( s60, new NHXParser() )[ 0 ]; if ( !p60.toNewHampshire().equals( s60 ) ) { System.out.println( p60.toNewHampshire() ); return false; } final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';"; - final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ]; + final Phylogeny p61 = factory.create( s61, new NHXParser() )[ 0 ]; if ( !p61.toNewHampshire() .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) { System.out.println( p61.toNewHampshire() ); return false; } + final String s62 = "(1[&type=\"X\",size=123,subtree=(1,2);]:0.003,2[&type=\"(X,Y:3)\"]:0.004)[&type=\"(X,Y)\"]:0.0;"; + final Phylogeny p62 = factory.create( s62, new NHXParser() )[ 0 ]; + if ( !p62.toNewHampshire().equals( "(1:0.003,2:0.004):0.0;" ) ) { + System.out.println( p62.toNewHampshire() ); + return false; + } + final String s63 = "(1:0.003[&type=\"X\",size=123,subtree=(1,2);],2:0.004[&type=\"(X,Y:3)\"]):0.0[&type=\"(X,Y)\"];"; + final Phylogeny p63 = factory.create( s63, new NHXParser() )[ 0 ]; + if ( !p63.toNewHampshire().equals( "(1:0.003,2:0.004):0.0;" ) ) { + System.out.println( p63.toNewHampshire() ); + return false; + } + final String s64 = "((1,2):[95.5],3);"; + final Phylogeny p64 = factory.create( s64, new NHXParser() )[ 0 ]; + if ( !p64.toNewHampshireX().equals( "((1,2)[&&NHX:B=95.5],3)" ) ) { + System.out.println( p64.toNewHampshireX() ); + return false; + } + final String s65 = "((1:0.1,2:0.2):0.3[10.2],3);"; + final Phylogeny p65 = factory.create( s65, new NHXParser() )[ 0 ]; + if ( !p65.toNewHampshireX().equals( "((1:0.1,2:0.2):0.3[&&NHX:B=10.2],3)" ) ) { + System.out.println( p65.toNewHampshireX() ); + return false; + } + final Phylogeny p66 = factory.create( "((A,B)ab:2[0.44],C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 0.44, p66.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p67 = factory.create( "((A,B):2[0.67],C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 0.67, p67.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p68 = factory.create( "((A,B):[0.68],C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 0.68, p68.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p69 = factory.create( "((A,B)[0.69],C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 0.69, p69.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p70 = factory.create( "((A,B)[+0.7],C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 0.7, p70.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p71 = factory.create( "((A,B)[-0.71],C)", new NHXParser() )[ 0 ]; + if ( !isEqual( -0.71, p71.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p72 = factory.create( "((A,B)[],C)", new NHXParser() )[ 0 ]; + if ( !p72.toNewHampshireX().equals( "((A,B),C)" ) ) { + return false; + } + final Phylogeny p73 = factory.create( "((A,B)[12x],C)", new NHXParser() )[ 0 ]; + if ( !p73.toNewHampshireX().equals( "((A,B),C)" ) ) { + return false; + } + final Phylogeny p74 = factory.create( "((A,B)[12+],C)", new NHXParser() )[ 0 ]; + if ( !p74.toNewHampshireX().equals( "((A,B),C)" ) ) { + return false; + } + final Phylogeny p75 = factory.create( "((A,B)ab[222]:3,C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 222, p75.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p76 = factory.create( "((A,B)[100]:12,C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 100, p76.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p77 = factory.create( "((A,B)abcde:13[77],C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 77, p77.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p78 = factory.create( "((A,B):14[0],C)", new NHXParser() )[ 0 ]; + if ( !isEqual( 0, p78.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final String the_one = "((((((a,b)ab:3.0[2],c):12.0[100],(d,e)de)abcde:13.0[2],f):14.0[0]):0.0[0]):0.0[0];"; + final Phylogeny p79 = factory.create( + "((((((a,b)ab[2]:3,c)[100]:12,(d,e)de)abcde:13[2],f):14[0]):0[0])[0]:0;", + new NHXParser() )[ 0 ]; + final String str79 = p79.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); + if ( !str79.equals( the_one ) ) { + System.out.println( str79 ); + return false; + } + final Phylogeny p80 = factory.create( + "((((((a[a)],b[12])ab[2]:3,c)[+100]:12,(d,e)de[12d,)])ab[]c[]de:13[2],f):14[0]):0[0])[0]:0;", + new NHXParser() )[ 0 ]; + final String str80 = p80.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); + if ( !str80.equals( the_one ) ) { + System.out.println( str80 ); + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNHParsingSpecialChars() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final String i0 = "(A!+=~QWERTY!@#$%^&*-,€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ)"; + final Phylogeny p0 = factory.create( i0, new NHXParser() )[ 0 ]; + if ( !p0.toNewHampshireX().equals( i0 ) ) { + System.out.println(); + System.out.println( p0.toNewHampshireX() ); + System.out.println( i0 ); + return false; + } + final String i1 = "(हिंदी,한글,ไทย,'Tiếng Việt',ひらがなカタカナ漢字,繁體字,русский)"; + final Phylogeny p1 = factory.create( i1, new NHXParser() )[ 0 ]; + if ( !p1.toNewHampshireX().equals( i1 ) ) { + System.out.println(); + System.out.println( p1.toNewHampshireX() ); + System.out.println( i1 ); + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -9022,7 +9840,7 @@ public final class Test { if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) { System.out.println( n7 - .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) ); + .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) ); return false; } } @@ -9338,7 +10156,8 @@ public final class Test { return false; } final PhylogenyNode n19 = PhylogenyNode - .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAH_1-roejojoej", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { return false; } @@ -9398,10 +10217,184 @@ public final class Test { return true; } + private static boolean testNHXNodeParsing2() { + try { + final PhylogenyNode n0_0 = PhylogenyNode.createInstanceFromNhxString( "n0:[ignore me 123]:1E-3", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n0_0.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_0.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_1 = PhylogenyNode.createInstanceFromNhxString( "n0[ignore me 123]:1E-3", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n0_1.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_1.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_2 = PhylogenyNode.createInstanceFromNhxString( "n0:1E-3[ignore me 123]", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n0_2.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_2.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_3 = PhylogenyNode.createInstanceFromNhxString( "n0:1E-3:[ignore me 123]", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n0_3.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_3.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_4 = PhylogenyNode.createInstanceFromNhxString( "n0:0.001:[ignore me 123]", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n0_4.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_4.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_0 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n1_0.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_0.getBranchData().getBranchColor().getValue().getGreen() != 255 ) { + return false; + } + final PhylogenyNode n1_1 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]:0.001", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n1_1.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_1.getBranchData().getBranchColor().getValue().getGreen() != 255 ) { + return false; + } + if ( !isEqual( n1_1.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_2 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:0.001[&!color=#FFFFFF]", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n1_2.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_2.getBranchData().getBranchColor().getValue().getGreen() != 255 ) { + return false; + } + if ( !isEqual( n1_2.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_3 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[&boostrap=69,&!color=#FFFFFF]", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n1_3.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_3.getBranchData().getBranchColor().getValue().getGreen() != 255 ) { + return false; + } + if ( !isEqual( n1_3.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_3.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + if ( !n1_3.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) { + return false; + } + final PhylogenyNode n1_4 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&bootstrap=69,&!colour=#FFFFFF]:1e-3", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n1_4.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_4.getBranchData().getBranchColor().getValue().getGreen() != 255 ) { + return false; + } + if ( !isEqual( n1_4.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_4.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + if ( !n1_4.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) { + return false; + } + final PhylogenyNode n1_5 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[69.0]", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n1_5.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( !isEqual( n1_5.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_5.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + final PhylogenyNode n1_6 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00]:1e-3", + NHXParser.TAXONOMY_EXTRACTION.NO, + true, + true ); + if ( !n1_6.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( !isEqual( n1_6.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.11 ) ) { + return false; + } + if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getValue(), 0.95 ) ) { + return false; + } + if ( !n1_6.getBranchData().getConfidence( 0 ).getType().equals( "posterior probability" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testNHXParsing() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ]; + final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", + new NHXParser() )[ 0 ]; if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) { return false; } @@ -9415,21 +10408,21 @@ public final class Test { if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) { return false; } - final Phylogeny[] p3 = factory - .create( "[ comment&&NHX,())))](((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]", - new NHXParser() ); + final Phylogeny[] p3 = factory.create( + "[ comment&&NHX,())))](((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]", + new NHXParser() ); if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) { return false; } - final Phylogeny[] p4 = factory - .create( "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(]", - new NHXParser() ); + final Phylogeny[] p4 = factory.create( + "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(]", + new NHXParser() ); if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) { return false; } - final Phylogeny[] p5 = factory - .create( "[] ( [][ ][ ] ([((( &&NHXcomment only![[[[[[]([]((((A:0.2[&&NHX:S=q[comment )))]werty][,,,,))]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=a[comment,,))]sdf])[comment(((]:0.4[&&NHX:S=zxc][comment(((][comment(((]):0.5[&&NHX:S=a]):0.6[&&NHX:S=a[comment(((]sd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(((]", - new NHXParser() ); + final Phylogeny[] p5 = factory.create( + "[] ( [][ ][ ] ([((( &&NHXcomment only![[[[[[]([]((((A:0.2[&&NHX:S=q[comment )))]werty][,,,,))]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=a[comment,,))]sdf])[comment(((]:0.4[&&NHX:S=zxc][comment(((][comment(((]):0.5[&&NHX:S=a]):0.6[&&NHX:S=a[comment(((]sd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(((]", + new NHXParser() ); if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) { return false; } @@ -9455,15 +10448,15 @@ public final class Test { if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } - final Phylogeny p10 = factory - .create( " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]", - new NHXParser() )[ 0 ]; + final Phylogeny p10 = factory.create( + " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]", + new NHXParser() )[ 0 ]; if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } - final Phylogeny p11 = factory - .create( " [79] ( ('A: \" ' [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]", - new NHXParser() )[ 0 ]; + final Phylogeny p11 = factory.create( + " [79] ( ('A: \" ' [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]", + new NHXParser() )[ 0 ]; if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } @@ -9517,8 +10510,7 @@ public final class Test { + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," - + "7.369400000000000e-02}])", - new NHXParser() )[ 0 ]; + + "7.369400000000000e-02}])", new NHXParser() )[ 0 ]; if ( p2.getNode( "1" ) == null ) { return false; } @@ -9595,9 +10587,9 @@ public final class Test { if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) { return false; } - final Phylogeny p10 = factory - .create( " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]", - new NHXParser() )[ 0 ]; + final Phylogeny p10 = factory.create( + " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]", + new NHXParser() )[ 0 ]; final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]"; if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) { return false; @@ -9606,9 +10598,9 @@ public final class Test { if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) { return false; } - final Phylogeny p12 = factory - .create( " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]", - new NHXParser() )[ 0 ]; + final Phylogeny p12 = factory.create( + " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]", + new NHXParser() )[ 0 ]; final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]"; if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) { return false; @@ -9720,8 +10712,8 @@ public final class Test { xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); } } - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml", - xml_parser ); + final Phylogeny[] phylogenies_0 = factory + .create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml" ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( xml_parser.getErrorMessages().toString() ); return false; @@ -10020,7 +11012,8 @@ public final class Test { for( it0.reset(); it0.hasNext(); ) { it0.next(); } - final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ]; + final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", + new NHXParser() )[ 0 ]; final PhylogenyNodeIterator it = t1.iteratorPostorder(); if ( !it.next().getName().equals( "A" ) ) { return false; @@ -10114,7 +11107,8 @@ public final class Test { if ( it.hasNext() ) { return false; } - final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ]; + final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", + new NHXParser() )[ 0 ]; it = t1.iteratorPreorder(); if ( !it.next().getName().equals( "r" ) ) { return false; @@ -10174,7 +11168,7 @@ public final class Test { private static boolean testPropertiesMap() { try { - final PropertiesMap pm = new PropertiesMap(); + final PropertiesList pm = new PropertiesList(); final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE ); final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE ); final Property p2 = new Property( "something:else", @@ -10185,10 +11179,10 @@ public final class Test { pm.addProperty( p0 ); pm.addProperty( p1 ); pm.addProperty( p2 ); - if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) { + if ( !pm.getProperties( "dimensions:diameter" ).get( 0 ).getValue().equals( "1" ) ) { return false; } - if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) { + if ( !pm.getProperties( "dimensions:length" ).get( 0 ).getValue().equals( "2" ) ) { return false; } if ( pm.getProperties().size() != 3 ) { @@ -10203,16 +11197,6 @@ public final class Test { if ( pm.getProperties().size() != 3 ) { return false; } - pm.removeProperty( "dimensions:diameter" ); - if ( pm.getProperties().size() != 2 ) { - return false; - } - if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) { - return false; - } - if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) { - return false; - } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -10542,12 +11526,12 @@ public final class Test { if ( !gene1.getRoot().isDuplication() ) { return false; } - final Phylogeny species2 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene2 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", - new NHXParser() )[ 0 ]; + final Phylogeny species2 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene2 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + new NHXParser() )[ 0 ]; species2.setRooted( true ); gene2.setRooted( true ); final SDI sdi2 = new SDI( gene2, species2 ); @@ -10572,12 +11556,12 @@ public final class Test { if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) { return false; } - final Phylogeny species3 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene3 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", - new NHXParser() )[ 0 ]; + final Phylogeny species3 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene3 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + new NHXParser() )[ 0 ]; species3.setRooted( true ); gene3.setRooted( true ); final SDI sdi3 = new SDI( gene3, species3 ); @@ -10590,12 +11574,12 @@ public final class Test { if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) { return false; } - final Phylogeny species4 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene4 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", - new NHXParser() )[ 0 ]; + final Phylogeny species4 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene4 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + new NHXParser() )[ 0 ]; species4.setRooted( true ); gene4.setRooted( true ); final SDI sdi4 = new SDI( gene4, species4 ); @@ -10617,12 +11601,12 @@ public final class Test { if ( gene4.getNumberOfExternalNodes() != 6 ) { return false; } - final Phylogeny species5 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene5 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", - new NHXParser() )[ 0 ]; + final Phylogeny species5 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene5 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + new NHXParser() )[ 0 ]; species5.setRooted( true ); gene5.setRooted( true ); final SDI sdi5 = new SDI( gene5, species5 ); @@ -10647,15 +11631,15 @@ public final class Test { // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith // Conjecture for Comparing Molecular Phylogenies" // J. of Comput Bio. Vol. 4, No 2, pp.177-187 - final Phylogeny species6 = factory - .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; - final Phylogeny gene6 = factory - .create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1," - + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;", - new NHXParser() )[ 0 ]; + final Phylogeny species6 = factory.create( + "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; + final Phylogeny gene6 = factory.create( + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1," + + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;", + new NHXParser() )[ 0 ]; species6.setRooted( true ); gene6.setRooted( true ); final SDI sdi6 = new SDI( gene6, species6 ); @@ -10777,7 +11761,8 @@ public final class Test { private static boolean testSDIunrooted() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ]; + final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", + new NHXParser() )[ 0 ]; final List l = SDIR.getBranchesInPreorder( p0 ); final Iterator iter = l.iterator(); PhylogenyBranch br = iter.next(); @@ -10942,12 +11927,12 @@ public final class Test { if ( iter2.hasNext() ) { return false; } - final Phylogeny species0 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene1 = factory - .create( "(((((A:0.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])", - new NHXParser() )[ 0 ]; + final Phylogeny species0 = factory.create( + "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene1 = factory.create( + "(((((A:0.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])", + new NHXParser() )[ 0 ]; species0.setRooted( true ); gene1.setRooted( true ); final SDIR sdi_unrooted = new SDIR(); @@ -10967,9 +11952,9 @@ public final class Test { if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { return false; } - final Phylogeny gene2 = factory - .create( "(((((A:2.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])", - new NHXParser() )[ 0 ]; + final Phylogeny gene2 = factory.create( + "(((((A:2.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])", + new NHXParser() )[ 0 ]; gene2.setRooted( true ); sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 ); if ( sdi_unrooted.getCount() != 1 ) { @@ -10987,17 +11972,17 @@ public final class Test { if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { return false; } - final Phylogeny species6 = factory - .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; - final Phylogeny gene6 = factory - .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; + final Phylogeny species6 = factory.create( + "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; + final Phylogeny gene6 = factory.create( + "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; species6.setRooted( true ); gene6.setRooted( true ); Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 ); @@ -11041,17 +12026,17 @@ public final class Test { return false; } p6 = null; - final Phylogeny species7 = factory - .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; - final Phylogeny gene7 = factory - .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; + final Phylogeny species7 = factory.create( + "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; + final Phylogeny gene7 = factory.create( + "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; species7.setRooted( true ); gene7.setRooted( true ); Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 ); @@ -11095,17 +12080,17 @@ public final class Test { return false; } p7 = null; - final Phylogeny species8 = factory - .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; - final Phylogeny gene8 = factory - .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; + final Phylogeny species8 = factory.create( + "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; + final Phylogeny gene8 = factory.create( + "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; species8.setRooted( true ); gene8.setRooted( true ); Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 ); @@ -11300,7 +12285,8 @@ public final class Test { } final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" ); SequenceDbWsTools.obtainSeqInformation( n2 ); - if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) { + if ( !n2.getNodeData().getSequence().getName() + .equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) { return false; } if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { @@ -11579,7 +12565,7 @@ public final class Test { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ]; //Archaeopteryx.createApplication( p0 ); - final Set ex = new HashSet(); + final Set ex = new HashSet<>(); ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -11592,13 +12578,13 @@ public final class Test { final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex ); // System.out.println( s0.toString() ); // - Set query_nodes = new HashSet(); + Set query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -11610,7 +12596,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -11618,7 +12604,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); @@ -11627,7 +12613,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -11636,20 +12622,20 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( !s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( !s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -11658,14 +12644,14 @@ public final class Test { if ( !s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); if ( !s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -11673,13 +12659,13 @@ public final class Test { if ( !s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -11687,7 +12673,7 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -11696,71 +12682,71 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11833,7 +12819,7 @@ public final class Test { // return false; // } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -11842,7 +12828,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11852,7 +12838,7 @@ public final class Test { } /////////////////////////// // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11861,7 +12847,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11870,7 +12856,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11879,7 +12865,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11888,7 +12874,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11897,7 +12883,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -11905,7 +12891,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11915,7 +12901,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -11925,7 +12911,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -11935,7 +12921,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -11957,7 +12943,7 @@ public final class Test { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ]; - final Set ex = new HashSet(); + final Set ex = new HashSet<>(); ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -11966,13 +12952,13 @@ public final class Test { ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex ); - Set query_nodes = new HashSet(); + Set query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); if ( s0.match( query_nodes ) ) { return false; } - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -11984,7 +12970,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -11992,7 +12978,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); @@ -12001,7 +12987,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -12010,7 +12996,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -12018,14 +13004,14 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( !s0.match( query_nodes ) ) { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); @@ -12035,7 +13021,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -12043,7 +13029,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -12052,14 +13038,14 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); if ( s0.match( query_nodes ) ) { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -12068,7 +13054,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -12078,7 +13064,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -12086,49 +13072,49 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); if ( s0.match( query_nodes ) ) { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); if ( s0.match( query_nodes ) ) { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); if ( s0.match( query_nodes ) ) { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); if ( s0.match( query_nodes ) ) { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); if ( s0.match( query_nodes ) ) { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( s0.match( query_nodes ) ) { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -12136,7 +13122,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -12144,7 +13130,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -12152,7 +13138,7 @@ public final class Test { return false; } // - query_nodes = new HashSet(); + query_nodes = new HashSet<>(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -12248,24 +13234,16 @@ public final class Test { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ]; final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))" - + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))" - + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))" - + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))" - + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))", - new NHXParser() ); + + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))" + + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))" + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))", + new NHXParser() ); SupportCount.count( t0_1, phylogenies_1, true, false ); final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ]; final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),((F,G),X))" - + "(((((A,Y),B),C),D),((F,G),E))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G),Z)" - + "(((((A,B),C),D),E),(F,G))" - + "((((((A,B),C),D),E),F),G)" - + "(((((X,Y),F,G),E),((A,B),C)),D)", - new NHXParser() ); + + "(((((A,B),C),D),E),((F,G),X))" + "(((((A,Y),B),C),D),((F,G),E))" + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G))" + "(((((A,B),C),D),E),(F,G))" + "(((((A,B),C),D),E),(F,G),Z)" + + "(((((A,B),C),D),E),(F,G))" + "((((((A,B),C),D),E),F),G)" + "(((((X,Y),F,G),E),((A,B),C)),D)", + new NHXParser() ); SupportCount.count( t0_2, phylogenies_2, true, false ); final PhylogenyNodeIterator it = t0_2.iteratorPostorder(); while ( it.hasNext() ) { @@ -12310,8 +13288,8 @@ public final class Test { return false; } final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) " - + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() ); + final Phylogeny[] phylogenies_4 = factory + .create( "((((((A,X),C),B),D),E),F) " + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() ); SupportCount.count( t0_4, phylogenies_4, true, false ); t0_4.reRoot( t0_4.getNode( "F" ).getId() ); if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) { @@ -12381,8 +13359,9 @@ public final class Test { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny p1 = factory.create( "(((A,B)ab:97,C)abc:57,((D,E)de:10,(F,G)fg:50,(H,I)hi:64)defghi)", new NHXParser() )[ 0 ]; - final Phylogeny p2 = factory - .create( "(((A:0.1,B:0.3)ab:0.4,C)abc:0.5,((D,E)de,(F,G)fg,(H,I)hi:0.59)defghi)", new NHXParser() )[ 0 ]; + final Phylogeny p2 = factory.create( + "(((A:0.1,B:0.3)ab:0.4,C)abc:0.5,((D,E)de,(F,G)fg,(H,I)hi:0.59)defghi)", + new NHXParser() )[ 0 ]; if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) { return false; } @@ -12442,7 +13421,7 @@ public final class Test { return false; } final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAGG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n3.toString() ); return false; @@ -12460,62 +13439,80 @@ public final class Test { return false; } final PhylogenyNode n6 = PhylogenyNode - .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAGG-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.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BL-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.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAGG_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.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAGG_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 n10x = PhylogenyNode - .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .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 ); + .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 ); + .createInstanceFromNhxString( "BLAGG_9YX45-blag", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { System.out.println( n10.toString() ); return false; } + final PhylogenyNode n10v = PhylogenyNode + .createInstanceFromNhxString( "BLAGG_BPM1-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n10v.getNodeData().getTaxonomy().getTaxonomyCode().equals( "BPM1" ) ) { + System.out.println( n10v.toString() ); + return false; + } + final PhylogenyNode n10v2 = PhylogenyNode + .createInstanceFromNhxString( "BLAGG_ABV-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n10v2.getNodeData().getTaxonomy().getTaxonomyCode().equals( "ABV" ) ) { + System.out.println( n10v2.toString() ); + return false; + } final PhylogenyNode n11 = PhylogenyNode - .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + .createInstanceFromNhxString( "BLAG@_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { System.out.println( n11.toString() ); return false; } final PhylogenyNode n12 = PhylogenyNode - .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus", + .createInstanceFromNhxString( "BLA_G_Mus_musculus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); 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.AGGRESSIVE ); + .createInstanceFromNhxString( "BLAaG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( n13.getNodeData().isHasTaxonomy() ) { System.out.println( n13.toString() ); return false; @@ -12545,7 +13542,8 @@ public final class Test { return false; } final PhylogenyNode n18 = PhylogenyNode - .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + .createInstanceFromNhxString( "Mus_musculus_musculus_392", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { System.out.println( n18.toString() ); return false; @@ -12558,7 +13556,8 @@ public final class Test { return false; } final PhylogenyNode n20 = PhylogenyNode - .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + .createInstanceFromNhxString( "Mus musculus musculus 392", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { System.out.println( n20.toString() ); return false; @@ -12675,6 +13674,74 @@ public final class Test { return true; } + private static boolean testPhylogenyMethods() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)r", new NHXParser() )[ 0 ]; + if ( PhylogenyMethods.calculateLevel( t0.getNode( "A" ) ) != 0 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t0.getNode( "B" ) ) != 0 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t0.getNode( "ab" ) ) != 1 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t0.getNode( "C" ) ) != 0 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t0.getNode( "abc" ) ) != 2 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t0.getNode( "D" ) ) != 0 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t0.getNode( "abcd" ) ) != 3 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t0.getNode( "E" ) ) != 0 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t0.getNode( "r" ) ) != 4 ) { + return false; + } + final Phylogeny t1 = factory.create( "((((A,B)ab,C)abc,D)abcd,E,((((((X)1)2)3)4)5)6)r", + new NHXParser() )[ 0 ]; + if ( PhylogenyMethods.calculateLevel( t1.getNode( "r" ) ) != 7 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t1.getNode( "X" ) ) != 0 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t1.getNode( "6" ) ) != 6 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t1.getNode( "5" ) ) != 5 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t1.getNode( "4" ) ) != 4 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t1.getNode( "3" ) ) != 3 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t1.getNode( "2" ) ) != 2 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t1.getNode( "1" ) ) != 1 ) { + return false; + } + if ( PhylogenyMethods.calculateLevel( t1.getNode( "abcd" ) ) != 3 ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testUniprotEntryRetrieval() { try { final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 ); @@ -12699,9 +13766,7 @@ public final class Test { if ( entry.getMolecularSequence() == null ) { return false; } - if ( !entry - .getMolecularSequence() - .getMolecularSequenceAsString() + if ( !entry.getMolecularSequence().getMolecularSequenceAsString() .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" ) || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) { System.out.println( "got: " + entry.getMolecularSequence().getMolecularSequenceAsString() ); @@ -12908,60 +13973,4 @@ public final class Test { } return true; } - - private static boolean testWabiTxSearch() { - try { - String result = ""; - result = TxSearch.searchSimple( "nematostella" ); - result = TxSearch.getTxId( "nematostella" ); - if ( !result.equals( "45350" ) ) { - return false; - } - result = TxSearch.getTxName( "45350" ); - if ( !result.equals( "Nematostella" ) ) { - return false; - } - result = TxSearch.getTxId( "nematostella vectensis" ); - if ( !result.equals( "45351" ) ) { - return false; - } - result = TxSearch.getTxName( "45351" ); - if ( !result.equals( "Nematostella vectensis" ) ) { - return false; - } - result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" ); - if ( !result.equals( "536089" ) ) { - return false; - } - result = TxSearch.getTxName( "536089" ); - if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) { - return false; - } - final List queries = new ArrayList(); - queries.add( "Campylobacter coli" ); - queries.add( "Escherichia coli" ); - queries.add( "Arabidopsis" ); - queries.add( "Trichoplax" ); - queries.add( "Samanea saman" ); - queries.add( "Kluyveromyces marxianus" ); - queries.add( "Bacillus subtilis subsp. subtilis str. N170" ); - queries.add( "Bornavirus parrot/PDD/2008" ); - final List ranks = new ArrayList(); - ranks.add( RANKS.SUPERKINGDOM ); - ranks.add( RANKS.KINGDOM ); - ranks.add( RANKS.FAMILY ); - ranks.add( RANKS.GENUS ); - ranks.add( RANKS.TRIBE ); - result = TxSearch.searchLineage( queries, ranks ); - result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true ); - result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true ); - } - catch ( final Exception e ) { - System.out.println(); - System.out.println( "the following might be due to absence internet connection:" ); - e.printStackTrace( System.out ); - return false; - } - return true; - } }