X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=80a20b6939784166e02f09d83f4806c4c098bb8e;hb=6479c35c4734850f517a6ef8de0fce500fdd6693;hp=e7aa418afe69e580803288c5183667ed8c98971b;hpb=b59302eba1039cb46f634ffe77cebc1b5c9bbcbf;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index e7aa418..80a20b6 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -50,7 +50,6 @@ import org.forester.io.parsers.FastaParser; import org.forester.io.parsers.GeneralMsaParser; import org.forester.io.parsers.HmmscanPerDomainTableParser; import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF; -import org.forester.io.parsers.PhylogenyParser; import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser; import org.forester.io.parsers.nexus.NexusCharactersParser; import org.forester.io.parsers.nexus.NexusPhylogeniesParser; @@ -129,301 +128,27 @@ import org.forester.ws.wabi.TxSearch.TAX_RANK; @SuppressWarnings( "unused") public final class Test { - private final static boolean PERFORM_DB_TESTS = false; - private final static double ZERO_DIFF = 1.0E-9; - private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "test_data" - + ForesterUtil.getFileSeparator(); private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() + "resources" + ForesterUtil.getFileSeparator(); - private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true; - private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/" + 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 = false; + private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/" + ForesterConstants.PHYLO_XML_VERSION + "/" + ForesterConstants.PHYLO_XML_XSD; - private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/" + private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/" + ForesterConstants.PHYLO_XML_VERSION + "/" + ForesterConstants.PHYLO_XML_XSD; - - public 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(); - covered.add( true ); // 0 - covered.add( false ); // 1 - covered.add( true ); // 2 - covered.add( false ); // 3 - covered.add( true ); // 4 - covered.add( true ); // 5 - covered.add( false ); // 6 - covered.add( true ); // 7 - covered.add( true ); // 8 - if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) { - return false; - } - if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) { - return false; - } - if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) { - return false; - } - if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) { - return false; - } - if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) { - return false; - } - final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 ); - final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 ); - final Protein ab = new BasicProtein( "ab", "varanus", 0 ); - ab.addProteinDomain( a ); - ab.addProteinDomain( b ); - final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab ); - if ( ab.getNumberOfProteinDomains() != 2 ) { - return false; - } - if ( ab_s0.getNumberOfProteinDomains() != 1 ) { - return false; - } - if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) { - return false; - } - final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab ); - if ( ab.getNumberOfProteinDomains() != 2 ) { - return false; - } - if ( ab_s1.getNumberOfProteinDomains() != 2 ) { - return false; - } - final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 ); - final Domain d = new BasicDomain( "d", - ( short ) 10000, - ( short ) 10500, - ( short ) 1, - ( short ) 1, - 0.0000001, - 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 ); - cde.addProteinDomain( e ); - final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde ); - if ( cde.getNumberOfProteinDomains() != 3 ) { - return false; - } - if ( cde_s0.getNumberOfProteinDomains() != 3 ) { - return false; - } - final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 ); - final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 ); - final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 ); - final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 ); - final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 ); - final Protein fghi = new BasicProtein( "fghi", "varanus", 0 ); - fghi.addProteinDomain( f ); - fghi.addProteinDomain( g ); - fghi.addProteinDomain( h ); - fghi.addProteinDomain( i ); - fghi.addProteinDomain( i ); - fghi.addProteinDomain( i ); - fghi.addProteinDomain( i2 ); - final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi ); - if ( fghi.getNumberOfProteinDomains() != 7 ) { - return false; - } - if ( fghi_s0.getNumberOfProteinDomains() != 1 ) { - return false; - } - if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) { - return false; - } - final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi ); - if ( fghi.getNumberOfProteinDomains() != 7 ) { - return false; - } - if ( fghi_s1.getNumberOfProteinDomains() != 7 ) { - return false; - } - final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 ); - final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 ); - final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 ); - final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 ); - final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 ); - final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 ); - final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 ); - final Protein jklm = new BasicProtein( "jklm", "varanus", 0 ); - jklm.addProteinDomain( j ); - jklm.addProteinDomain( k ); - jklm.addProteinDomain( l ); - jklm.addProteinDomain( m ); - jklm.addProteinDomain( m0 ); - jklm.addProteinDomain( m1 ); - jklm.addProteinDomain( m2 ); - final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm ); - if ( jklm.getNumberOfProteinDomains() != 7 ) { - return false; - } - if ( jklm_s0.getNumberOfProteinDomains() != 1 ) { - return false; - } - if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) { - return false; - } - final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm ); - if ( jklm.getNumberOfProteinDomains() != 7 ) { - return false; - } - if ( jklm_s1.getNumberOfProteinDomains() != 7 ) { - return false; - } - final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 ); - final Protein od = new BasicProtein( "od", "varanus", 0 ); - od.addProteinDomain( only ); - final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od ); - if ( od.getNumberOfProteinDomains() != 1 ) { - return false; - } - if ( od_s0.getNumberOfProteinDomains() != 1 ) { - return false; - } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - public 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 ); - final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 ); - final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 ); - 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(); - covered.add( true ); // 0 - covered.add( false ); // 1 - covered.add( true ); // 2 - covered.add( false ); // 3 - covered.add( true ); // 4 - covered.add( true ); // 5 - covered.add( false ); // 6 - covered.add( true ); // 7 - covered.add( true ); // 8 - if ( ForesterUtil.isEngulfed( d0, covered ) ) { - return false; - } - if ( ForesterUtil.isEngulfed( d1, covered ) ) { - return false; - } - if ( ForesterUtil.isEngulfed( d2, covered ) ) { - return false; - } - if ( !ForesterUtil.isEngulfed( d3, covered ) ) { - return false; - } - if ( ForesterUtil.isEngulfed( d4, covered ) ) { - return false; - } - if ( ForesterUtil.isEngulfed( d5, covered ) ) { - return false; - } - if ( !ForesterUtil.isEngulfed( d6, covered ) ) { - return false; - } - final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 ); - final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 ); - final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 ); - final Protein abc = new BasicProtein( "abc", "nemve", 0 ); - abc.addProteinDomain( a ); - abc.addProteinDomain( b ); - abc.addProteinDomain( c ); - final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc ); - final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc ); - if ( abc.getNumberOfProteinDomains() != 3 ) { - return false; - } - if ( abc_r1.getNumberOfProteinDomains() != 3 ) { - return false; - } - if ( abc_r2.getNumberOfProteinDomains() != 2 ) { - return false; - } - if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) { - return false; - } - if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) { - return false; - } - final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 ); - final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 ); - final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 ); - final Protein def = new BasicProtein( "def", "nemve", 0 ); - def.addProteinDomain( d ); - def.addProteinDomain( e ); - def.addProteinDomain( f ); - final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def ); - final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def ); - if ( def.getNumberOfProteinDomains() != 3 ) { - return false; - } - if ( def_r1.getNumberOfProteinDomains() != 3 ) { - return false; - } - if ( def_r2.getNumberOfProteinDomains() != 3 ) { - return false; - } - if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) { - return false; - } - if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) { - return false; - } - if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) { - return false; - } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } + 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 ) { return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF ); } public static void main( final String[] args ) { - try { - String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; - final URL u = new URL( s ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final PhylogenyParser parser = ParserUtils.createParserDependingOnUrlContents( u, true ); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); - System.out.println( "results 1:" ); - for( final Phylogeny phy : phys ) { - System.out.println( phy.toString() ); - } - System.out.println( "" ); - final Phylogeny[] phys3 = factory.create( "((a,b),c)", parser ); - System.out.println( "results 3:" ); - for( final Phylogeny phy : phys3 ) { - System.out.println( phy.toString() ); - } - } - catch ( Exception e ) { - e.printStackTrace(); - } - System.exit( 0 ); System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION + "]" ); @@ -1161,85 +886,437 @@ public final class Test { System.out.println( "OK." ); succeeded++; } - else { - System.out.println( "failed." ); - failed++; + else { + System.out.println( "failed." ); + failed++; + } + } + if ( PERFORM_DB_TESTS ) { + System.out.print( "Uniprot Taxonomy Search: " ); + if ( Test.testUniprotTaxonomySearch() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + } + //---- + String path = ""; + final String os = ForesterUtil.OS_NAME.toLowerCase(); + if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) { + path = "/usr/local/bin/mafft"; + } + else if ( os.indexOf( "win" ) >= 0 ) { + path = "C:\\Program Files\\mafft-win\\mafft.bat"; + } + else { + path = "mafft"; + if ( !MsaInferrer.isInstalled( path ) ) { + path = "/usr/bin/mafft"; + } + if ( !MsaInferrer.isInstalled( path ) ) { + path = "/usr/local/bin/mafft"; + } + } + if ( MsaInferrer.isInstalled( path ) ) { + System.out.print( "MAFFT (external program): " ); + if ( Test.testMafft( path ) ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed [will not count towards failed tests]" ); + } + } + //---- + System.out.print( "Next nodes with collapsed: " ); + if ( Test.testNextNodeWithCollapsing() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Simple MSA quality: " ); + if ( Test.testMsaQualityMethod() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "NHX parsing from URL: " ); + if ( Test.testNHXparsingFromURL() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "phyloXML parsing from URL: " ); + if ( Test.testPhyloXMLparsingFromURL() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.println(); + final Runtime rt = java.lang.Runtime.getRuntime(); + final long free_memory = rt.freeMemory() / 1000000; + final long total_memory = rt.totalMemory() / 1000000; + System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: " + + free_memory + "MB, total memory: " + total_memory + "MB)" ); + System.out.println(); + System.out.println( "Successful tests: " + succeeded ); + System.out.println( "Failed tests: " + failed ); + System.out.println(); + if ( failed < 1 ) { + System.out.println( "OK." ); + } + else { + System.out.println( "Not OK." ); + } + } + + public 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 ); + final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 ); + final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 ); + 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(); + covered.add( true ); // 0 + covered.add( false ); // 1 + covered.add( true ); // 2 + covered.add( false ); // 3 + covered.add( true ); // 4 + covered.add( true ); // 5 + covered.add( false ); // 6 + covered.add( true ); // 7 + covered.add( true ); // 8 + if ( ForesterUtil.isEngulfed( d0, covered ) ) { + return false; + } + if ( ForesterUtil.isEngulfed( d1, covered ) ) { + return false; + } + if ( ForesterUtil.isEngulfed( d2, covered ) ) { + return false; + } + if ( !ForesterUtil.isEngulfed( d3, covered ) ) { + return false; + } + if ( ForesterUtil.isEngulfed( d4, covered ) ) { + return false; + } + if ( ForesterUtil.isEngulfed( d5, covered ) ) { + return false; + } + if ( !ForesterUtil.isEngulfed( d6, covered ) ) { + return false; + } + final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 ); + final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 ); + final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 ); + final Protein abc = new BasicProtein( "abc", "nemve", 0 ); + abc.addProteinDomain( a ); + abc.addProteinDomain( b ); + abc.addProteinDomain( c ); + final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc ); + final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc ); + if ( abc.getNumberOfProteinDomains() != 3 ) { + return false; + } + if ( abc_r1.getNumberOfProteinDomains() != 3 ) { + return false; + } + if ( abc_r2.getNumberOfProteinDomains() != 2 ) { + return false; + } + if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) { + return false; + } + if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) { + return false; + } + final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 ); + final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 ); + final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 ); + final Protein def = new BasicProtein( "def", "nemve", 0 ); + def.addProteinDomain( d ); + def.addProteinDomain( e ); + def.addProteinDomain( f ); + final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def ); + final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def ); + if ( def.getNumberOfProteinDomains() != 3 ) { + return false; + } + if ( def_r1.getNumberOfProteinDomains() != 3 ) { + return false; } - } - if ( PERFORM_DB_TESTS ) { - System.out.print( "Uniprot Taxonomy Search: " ); - if ( Test.testUniprotTaxonomySearch() ) { - System.out.println( "OK." ); - succeeded++; + if ( def_r2.getNumberOfProteinDomains() != 3 ) { + return false; } - else { - System.out.println( "failed." ); - failed++; + if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) { + return false; + } + if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) { + return false; + } + if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) { + return false; } } - //---- - String path = ""; - final String os = ForesterUtil.OS_NAME.toLowerCase(); - if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) { - path = "/usr/local/bin/mafft"; - } - else if ( os.indexOf( "win" ) >= 0 ) { - path = "C:\\Program Files\\mafft-win\\mafft.bat"; - } - else { - path = "/home/czmasek/bin/mafft"; + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; } - if ( !MsaInferrer.isInstalled( path ) ) { - path = "mafft"; + return true; + } + + public 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() ); + if ( ( phys == null ) || ( phys.length != 2 ) ) { + return false; + } } - if ( !MsaInferrer.isInstalled( path ) ) { - path = "/usr/local/bin/mafft"; + catch ( final Exception e ) { + e.printStackTrace(); } - if ( MsaInferrer.isInstalled( path ) ) { - System.out.print( "MAFFT (external program): " ); - if ( Test.testMafft( path ) ) { - System.out.println( "OK." ); - succeeded++; + return true; + } + + public 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 ); + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny[] phys = factory.create( u, new NHXParser() ); + if ( ( phys == null ) || ( phys.length != 5 ) ) { + return false; } - else { - System.out.println( "failed [will not count towards failed tests]" ); + if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + System.out.println( phys[ 0 ].toNewHampshire() ); + return false; + } + if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) { + System.out.println( phys[ 1 ].toNewHampshire() ); + return false; + } + final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() ); + if ( ( phys2 == null ) || ( phys2.length != 5 ) ) { + return false; + } + if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + System.out.println( phys2[ 0 ].toNewHampshire() ); + return false; + } + final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance(); + final NHXParser p = new NHXParser(); + final URL u2 = new URL( s ); + p.setSource( u2 ); + if ( !p.hasNext() ) { + return false; + } + if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + return false; + } + if ( !p.hasNext() ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + return false; + } + if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + return false; + } + if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) { + return false; } } - //---- - System.out.print( "Next nodes with collapsed: " ); - if ( Test.testNextNodeWithCollapsing() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } - System.out.print( "Simple MSA quality: " ); - if ( Test.testMsaQualityMethod() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; + catch ( final Exception e ) { + e.printStackTrace(); } - System.out.println(); - final Runtime rt = java.lang.Runtime.getRuntime(); - final long free_memory = rt.freeMemory() / 1000000; - final long total_memory = rt.totalMemory() / 1000000; - System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: " - + free_memory + "MB, total memory: " + total_memory + "MB)" ); - System.out.println(); - System.out.println( "Successful tests: " + succeeded ); - System.out.println( "Failed tests: " + failed ); - System.out.println(); - if ( failed < 1 ) { - System.out.println( "OK." ); + return true; + } + + public 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(); + covered.add( true ); // 0 + covered.add( false ); // 1 + covered.add( true ); // 2 + covered.add( false ); // 3 + covered.add( true ); // 4 + covered.add( true ); // 5 + covered.add( false ); // 6 + covered.add( true ); // 7 + covered.add( true ); // 8 + if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) { + return false; + } + if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) { + return false; + } + if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) { + return false; + } + if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) { + return false; + } + if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) { + return false; + } + final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 ); + final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 ); + final Protein ab = new BasicProtein( "ab", "varanus", 0 ); + ab.addProteinDomain( a ); + ab.addProteinDomain( b ); + final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab ); + if ( ab.getNumberOfProteinDomains() != 2 ) { + return false; + } + if ( ab_s0.getNumberOfProteinDomains() != 1 ) { + return false; + } + if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) { + return false; + } + final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab ); + if ( ab.getNumberOfProteinDomains() != 2 ) { + return false; + } + if ( ab_s1.getNumberOfProteinDomains() != 2 ) { + return false; + } + final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 ); + final Domain d = new BasicDomain( "d", + ( short ) 10000, + ( short ) 10500, + ( short ) 1, + ( short ) 1, + 0.0000001, + 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 ); + cde.addProteinDomain( e ); + final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde ); + if ( cde.getNumberOfProteinDomains() != 3 ) { + return false; + } + if ( cde_s0.getNumberOfProteinDomains() != 3 ) { + return false; + } + final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 ); + final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 ); + final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 ); + final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 ); + final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 ); + final Protein fghi = new BasicProtein( "fghi", "varanus", 0 ); + fghi.addProteinDomain( f ); + fghi.addProteinDomain( g ); + fghi.addProteinDomain( h ); + fghi.addProteinDomain( i ); + fghi.addProteinDomain( i ); + fghi.addProteinDomain( i ); + fghi.addProteinDomain( i2 ); + final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi ); + if ( fghi.getNumberOfProteinDomains() != 7 ) { + return false; + } + if ( fghi_s0.getNumberOfProteinDomains() != 1 ) { + return false; + } + if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) { + return false; + } + final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi ); + if ( fghi.getNumberOfProteinDomains() != 7 ) { + return false; + } + if ( fghi_s1.getNumberOfProteinDomains() != 7 ) { + return false; + } + final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 ); + final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 ); + final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 ); + final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 ); + final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 ); + final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 ); + final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 ); + final Protein jklm = new BasicProtein( "jklm", "varanus", 0 ); + jklm.addProteinDomain( j ); + jklm.addProteinDomain( k ); + jklm.addProteinDomain( l ); + jklm.addProteinDomain( m ); + jklm.addProteinDomain( m0 ); + jklm.addProteinDomain( m1 ); + jklm.addProteinDomain( m2 ); + final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm ); + if ( jklm.getNumberOfProteinDomains() != 7 ) { + return false; + } + if ( jklm_s0.getNumberOfProteinDomains() != 1 ) { + return false; + } + if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) { + return false; + } + final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm ); + if ( jklm.getNumberOfProteinDomains() != 7 ) { + return false; + } + if ( jklm_s1.getNumberOfProteinDomains() != 7 ) { + return false; + } + final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 ); + final Protein od = new BasicProtein( "od", "varanus", 0 ); + od.addProteinDomain( only ); + final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od ); + if ( od.getNumberOfProteinDomains() != 1 ) { + return false; + } + if ( od_s0.getNumberOfProteinDomains() != 1 ) { + return false; + } } - else { - System.out.println( "Not OK." ); + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; } + return true; } private final static Phylogeny createPhylogeny( final String nhx ) throws IOException { @@ -2794,41 +2871,6 @@ public final class Test { return true; } - private static boolean testTreeCopy() { - try { - final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]"; - final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 ); - final Phylogeny t1 = t0.copy(); - if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) { - return false; - } - if ( !t1.toNewHampshireX().equals( str_0 ) ) { - return false; - } - t0.deleteSubtree( t0.getNode( "c" ), true ); - t0.deleteSubtree( t0.getNode( "a" ), true ); - t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" ); - t0.getNode( "b" ).setName( "Bee" ); - if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) { - return false; - } - if ( !t1.toNewHampshireX().equals( str_0 ) ) { - return false; - } - t0.deleteSubtree( t0.getNode( "e" ), true ); - t0.deleteSubtree( t0.getNode( "Bee" ), true ); - t0.deleteSubtree( t0.getNode( "d" ), true ); - if ( !t1.toNewHampshireX().equals( str_0 ) ) { - return false; - } - } - catch ( final Exception e ) { - e.printStackTrace(); - return false; - } - return true; - } - private static boolean testCreateBalancedPhylogeny() { try { final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 ); @@ -3710,51 +3752,183 @@ public final class Test { return true; } - private static boolean testGenbankAccessorParsing() { - //The format for GenBank Accession numbers are: - //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals - //Protein: 3 letters + 5 numerals - //http://www.ncbi.nlm.nih.gov/Sequin/acc.html - if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) { - return false; - } - if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) { - return false; - } - if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) { - return false; - } - if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) { - return false; - } - if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) { - return false; - } - if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) { - return false; - } - if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) { - return false; - } - if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) { - return false; - } - if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) { - return false; - } - if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) { - return false; - } - if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) { - return false; - } - if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) { - return false; + private static boolean testEbiEntryRetrieval() { + try { + final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" ); + if ( !entry.getAccession().equals( "AAK41263" ) ) { + System.out.println( entry.getAccession() ); + return false; + } + if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) { + System.out.println( entry.getTaxonomyScientificName() ); + return false; + } + if ( !entry.getSequenceName() + .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) { + System.out.println( entry.getSequenceName() ); + return false; + } + // if ( !entry.getSequenceSymbol().equals( "" ) ) { + // System.out.println( entry.getSequenceSymbol() ); + // return false; + // } + if ( !entry.getGeneName().equals( "treX-like" ) ) { + System.out.println( entry.getGeneName() ); + return false; + } + if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) { + System.out.println( entry.getTaxonomyIdentifier() ); + return false; + } + if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) { + System.out.println( entry.getAnnotations().first().getRefValue() ); + return false; + } + if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) { + System.out.println( entry.getAnnotations().first().getRefSource() ); + return false; + } + if ( entry.getCrossReferences().size() != 5 ) { + return false; + } + // + final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); + if ( !entry1.getAccession().equals( "ABJ16409" ) ) { + return false; + } + if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) { + System.out.println( entry1.getTaxonomyScientificName() ); + return false; + } + if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) { + System.out.println( entry1.getSequenceName() ); + return false; + } + if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) { + System.out.println( entry1.getTaxonomyIdentifier() ); + return false; + } + if ( !entry1.getGeneName().equals( "BCL2" ) ) { + System.out.println( entry1.getGeneName() ); + return false; + } + if ( entry1.getCrossReferences().size() != 6 ) { + return false; + } + // + final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); + if ( !entry2.getAccession().equals( "NM_184234" ) ) { + return false; + } + if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + System.out.println( entry2.getTaxonomyScientificName() ); + return false; + } + if ( !entry2.getSequenceName() + .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { + System.out.println( entry2.getSequenceName() ); + return false; + } + if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) { + System.out.println( entry2.getTaxonomyIdentifier() ); + return false; + } + if ( !entry2.getGeneName().equals( "RBM39" ) ) { + System.out.println( entry2.getGeneName() ); + return false; + } + if ( entry2.getCrossReferences().size() != 3 ) { + return false; + } + // + final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" ); + if ( !entry3.getAccession().equals( "HM043801" ) ) { + return false; + } + if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) { + System.out.println( entry3.getTaxonomyScientificName() ); + return false; + } + if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) { + System.out.println( entry3.getSequenceName() ); + return false; + } + if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) { + System.out.println( entry3.getTaxonomyIdentifier() ); + return false; + } + if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) { + System.out.println( entry3.getSequenceSymbol() ); + return false; + } + if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { + return false; + } + if ( entry3.getCrossReferences().size() != 8 ) { + return false; + } + // + // + final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); + if ( !entry4.getAccession().equals( "AAA36557" ) ) { + return false; + } + if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + System.out.println( entry4.getTaxonomyScientificName() ); + return false; + } + if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) { + System.out.println( entry4.getSequenceName() ); + return false; + } + if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) { + System.out.println( entry4.getTaxonomyIdentifier() ); + return false; + } + if ( !entry4.getGeneName().equals( "ras" ) ) { + 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; + } + if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) { + System.out.println( entry5.getTaxonomyScientificName() ); + return false; + } + if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) { + System.out.println( entry5.getSequenceName() ); + return false; + } + if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) { + System.out.println( entry5.getTaxonomyIdentifier() ); + return false; + } } - if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) { - return false; + catch ( final IOException e ) { + System.out.println(); + System.out.println( "the following might be due to absence internet connection:" ); + e.printStackTrace( System.out ); + return true; } - if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) { + catch ( final Exception e ) { + e.printStackTrace(); return false; } return true; @@ -4253,6 +4427,56 @@ public final class Test { return true; } + private static boolean testGenbankAccessorParsing() { + //The format for GenBank Accession numbers are: + //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals + //Protein: 3 letters + 5 numerals + //http://www.ncbi.nlm.nih.gov/Sequin/acc.html + if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) { + return false; + } + if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) { + return false; + } + if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) { + return false; + } + if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) { + return false; + } + if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) { + return false; + } + if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) { + return false; + } + if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) { + return false; + } + if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) { + return false; + } + if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) { + return false; + } + if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) { + return false; + } + if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) { + return false; + } + if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) { + return false; + } + if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) { + return false; + } + if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) { + return false; + } + return true; + } + private static boolean testGeneralMsaParser() { try { final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n"; @@ -4776,14 +5000,15 @@ public final class Test { private static boolean testGetLCA2() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ]; + // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ]; + final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ]; PhylogenyMethods.preOrderReId( p_a ); final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ), p_a.getNode( "a" ) ); if ( !p_a_1.getName().equals( "a" ) ) { return false; } - final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ]; + final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ]; PhylogenyMethods.preOrderReId( p_b ); final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ), p_b.getNode( "a" ) ); @@ -5473,10 +5698,10 @@ public final class Test { private static boolean testMsaQualityMethod() { try { - final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" ); - final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" ); - final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" ); - final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" ); + final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" ); + final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" ); + final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" ); + final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" ); final List l = new ArrayList(); l.add( s0 ); l.add( s1 ); @@ -5495,6 +5720,15 @@ public final class Test { if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) { return false; } + if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) { + return false; + } + if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) { + return false; + } + if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -7842,6 +8076,67 @@ public final class Test { if ( p.next() != null ) { return false; } + // + final String p30_str = "(A,B);(C,D)"; + final NHXParser p30 = new NHXParser(); + p30.setSource( p30_str ); + if ( !p30.hasNext() ) { + return false; + } + Phylogeny phy30 = p30.next(); + if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) { + System.out.println( phy30.toNewHampshire() ); + return false; + } + if ( !p30.hasNext() ) { + return false; + } + Phylogeny phy301 = p30.next(); + if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( phy301.toNewHampshire() ); + return false; + } + if ( p30.hasNext() ) { + return false; + } + if ( p30.hasNext() ) { + return false; + } + if ( p30.next() != null ) { + return false; + } + if ( p30.next() != null ) { + return false; + } + p30.reset(); + if ( !p30.hasNext() ) { + return false; + } + phy30 = p30.next(); + if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) { + System.out.println( phy30.toNewHampshire() ); + return false; + } + if ( !p30.hasNext() ) { + return false; + } + phy301 = p30.next(); + if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( phy301.toNewHampshire() ); + return false; + } + if ( p30.hasNext() ) { + return false; + } + if ( p30.hasNext() ) { + return false; + } + if ( p30.next() != null ) { + return false; + } + if ( p30.next() != null ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -9971,646 +10266,435 @@ public final class Test { if ( !p8[ 0 ].getRoot().isDuplication() ) { return false; } - if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) { - return false; - } - if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) { - return false; - } - if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) { - return false; - } - if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) { - return false; - } - if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) { - return false; - } - if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) { - return false; - } - if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { - return false; - } - p8 = null; - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSequenceIdParsing() { - try { - Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - // - id = SequenceAccessionTools.parseAccessorFromString( "P4A123" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) - || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - } - return false; - } - id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" ); - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); - return false; - } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSequenceWriter() { - try { - final String n = ForesterUtil.LINE_SEPARATOR; - if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) { + if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) { return false; } - if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) { + if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) { return false; } - if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) { + if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) { return false; } - if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) { + if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) { return false; } - if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString() - .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) { + if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) { return false; } - if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString() - .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) { + if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) { + return false; + } + if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { return false; } + p8 = null; } catch ( final Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testSpecies() { + private static boolean testSequenceDbWsTools1() { try { - final Species s1 = new BasicSpecies( "a" ); - final Species s2 = new BasicSpecies( "a" ); - final Species s3 = new BasicSpecies( "A" ); - final Species s4 = new BasicSpecies( "b" ); - if ( !s1.equals( s1 ) ) { + final PhylogenyNode n = new PhylogenyNode(); + n.setName( "NP_001025424" ); + Accession acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) + || !acc.getValue().equals( "NP_001025424" ) ) { return false; } - if ( s1.getSpeciesId().equals( "x" ) ) { + n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) + || !acc.getValue().equals( "NP_001025424" ) ) { return false; } - if ( s1.getSpeciesId().equals( null ) ) { + n.setName( "NP_001025424.1" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) + || !acc.getValue().equals( "NP_001025424" ) ) { return false; } - if ( !s1.equals( s2 ) ) { + n.setName( "NM_001030253" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) + || !acc.getValue().equals( "NM_001030253" ) ) { return false; } - if ( s1.equals( s3 ) ) { + n.setName( "BCL2_HUMAN" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) + || !acc.getValue().equals( "BCL2_HUMAN" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s1.hashCode() != s1.hashCode() ) { + n.setName( "P10415" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) + || !acc.getValue().equals( "P10415" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s1.hashCode() != s2.hashCode() ) { + n.setName( " P10415 " ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) + || !acc.getValue().equals( "P10415" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s1.hashCode() == s3.hashCode() ) { + n.setName( "_P10415|" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) + || !acc.getValue().equals( "P10415" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s1.compareTo( s1 ) != 0 ) { + n.setName( "AY695820" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AY695820" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s1.compareTo( s2 ) != 0 ) { + n.setName( "_AY695820_" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AY695820" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s1.compareTo( s3 ) != 0 ) { + n.setName( "AAA59452" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AAA59452" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s1.compareTo( s4 ) >= 0 ) { + n.setName( "_AAA59452_" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AAA59452" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s4.compareTo( s1 ) <= 0 ) { + n.setName( "AAA59452.1" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AAA59452.1" ) ) { + System.out.println( acc.toString() ); return false; } - if ( !s4.getSpeciesId().equals( "b" ) ) { + n.setName( "_AAA59452.1_" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AAA59452.1" ) ) { + System.out.println( acc.toString() ); return false; } - final Species s5 = new BasicSpecies( " C " ); - if ( !s5.getSpeciesId().equals( "C" ) ) { + n.setName( "GI:94894583" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() ) + || !acc.getValue().equals( "94894583" ) ) { + System.out.println( acc.toString() ); return false; } - if ( s5.equals( s1 ) ) { + n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() ) + || !acc.getValue().equals( "71845847" ) ) { + System.out.println( acc.toString() ); + return false; + } + n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AAZ45343.1" ) ) { + System.out.println( acc.toString() ); return false; } } catch ( final Exception e ) { - e.printStackTrace( System.out ); return false; } return true; } - private static boolean testSplit() { + private static boolean testSequenceDbWsTools2() { try { - 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(); - ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex ); - // System.out.println( s0.toString() ); - // - Set query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" ); + SequenceDbWsTools.obtainSeqInformation( n1 ); + if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) { return false; } - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( !s0.match( query_nodes ) ) { + if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( !s0.match( query_nodes ) ) { + if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( !s0.match( query_nodes ) ) { + if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( !s0.match( query_nodes ) ) { + final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" ); + SequenceDbWsTools.obtainSeqInformation( n2 ); + if ( !n2.getNodeData().getSequence().getName() + .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) { return false; } - // - 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 ) ) { + if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( !s0.match( query_nodes ) ) { + if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - if ( !s0.match( query_nodes ) ) { + if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) { return false; } - // - 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 ) ) { + final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" ); + SequenceDbWsTools.obtainSeqInformation( n3 ); + if ( !n3.getNodeData().getSequence().getName() + .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( !s0.match( query_nodes ) ) { + if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) { + return false; + } + if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + return false; + } + if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) { + return false; + } + } + catch ( final IOException e ) { + System.out.println(); + System.out.println( "the following might be due to absence internet connection:" ); + e.printStackTrace( System.out ); + return true; + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testSequenceIdParsing() { + try { + Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - if ( s0.match( query_nodes ) ) { + id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( s0.match( query_nodes ) ) { + id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( s0.match( query_nodes ) ) { + // + id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - 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 ) ) { + // + id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( s0.match( query_nodes ) ) { + // + id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + // + id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( s0.match( query_nodes ) ) { + // + id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - if ( s0.match( query_nodes ) ) { + // + id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - if ( s0.match( query_nodes ) ) { + // + id = SequenceAccessionTools.parseAccessorFromString( "P4A123" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" ); + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); return false; } - // - 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 ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testSequenceWriter() { + try { + final String n = ForesterUtil.LINE_SEPARATOR; + if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) { return false; } - // - 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 ) ) { + if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) { return false; } - // - 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 ) ) { + if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) { return false; } - ///////// - // query_nodes = new HashSet(); - // query_nodes.add( new PhylogenyNode( "X" ) ); - // query_nodes.add( new PhylogenyNode( "Y" ) ); - // query_nodes.add( new PhylogenyNode( "A" ) ); - // query_nodes.add( new PhylogenyNode( "B" ) ); - // query_nodes.add( new PhylogenyNode( "C" ) ); - // query_nodes.add( new PhylogenyNode( "D" ) ); - // query_nodes.add( new PhylogenyNode( "E" ) ); - // query_nodes.add( new PhylogenyNode( "F" ) ); - // query_nodes.add( new PhylogenyNode( "G" ) ); - // if ( !s0.match( query_nodes ) ) { - // return false; - // } - // query_nodes = new HashSet(); - // query_nodes.add( new PhylogenyNode( "X" ) ); - // query_nodes.add( new PhylogenyNode( "Y" ) ); - // query_nodes.add( new PhylogenyNode( "A" ) ); - // query_nodes.add( new PhylogenyNode( "B" ) ); - // query_nodes.add( new PhylogenyNode( "C" ) ); - // if ( !s0.match( query_nodes ) ) { - // return false; - // } - // // - // query_nodes = new HashSet(); - // query_nodes.add( new PhylogenyNode( "X" ) ); - // query_nodes.add( new PhylogenyNode( "Y" ) ); - // query_nodes.add( new PhylogenyNode( "D" ) ); - // query_nodes.add( new PhylogenyNode( "E" ) ); - // query_nodes.add( new PhylogenyNode( "F" ) ); - // query_nodes.add( new PhylogenyNode( "G" ) ); - // if ( !s0.match( query_nodes ) ) { - // return false; - // } - // // - // query_nodes = new HashSet(); - // query_nodes.add( new PhylogenyNode( "X" ) ); - // query_nodes.add( new PhylogenyNode( "Y" ) ); - // query_nodes.add( new PhylogenyNode( "A" ) ); - // query_nodes.add( new PhylogenyNode( "B" ) ); - // query_nodes.add( new PhylogenyNode( "C" ) ); - // query_nodes.add( new PhylogenyNode( "D" ) ); - // if ( !s0.match( query_nodes ) ) { - // return false; - // } - // // - // query_nodes = new HashSet(); - // query_nodes.add( new PhylogenyNode( "X" ) ); - // query_nodes.add( new PhylogenyNode( "Y" ) ); - // query_nodes.add( new PhylogenyNode( "E" ) ); - // query_nodes.add( new PhylogenyNode( "F" ) ); - // query_nodes.add( new PhylogenyNode( "G" ) ); - // if ( !s0.match( query_nodes ) ) { - // return false; - // } - // // - // query_nodes = new HashSet(); - // query_nodes.add( new PhylogenyNode( "X" ) ); - // query_nodes.add( new PhylogenyNode( "Y" ) ); - // query_nodes.add( new PhylogenyNode( "F" ) ); - // query_nodes.add( new PhylogenyNode( "G" ) ); - // if ( !s0.match( query_nodes ) ) { - // return false; - // } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString() + .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString() + .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) { return false; } - /////////////////////////// - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( s0.match( query_nodes ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testSpecies() { + try { + final Species s1 = new BasicSpecies( "a" ); + final Species s2 = new BasicSpecies( "a" ); + final Species s3 = new BasicSpecies( "A" ); + final Species s4 = new BasicSpecies( "b" ); + if ( !s1.equals( s1 ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.getSpeciesId().equals( "x" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.getSpeciesId().equals( null ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - if ( s0.match( query_nodes ) ) { + if ( !s1.equals( s2 ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.equals( s3 ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.hashCode() != s1.hashCode() ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.hashCode() != s2.hashCode() ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.hashCode() == s3.hashCode() ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.compareTo( s1 ) != 0 ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.compareTo( s2 ) != 0 ) { + return false; + } + if ( s1.compareTo( s3 ) != 0 ) { + return false; + } + if ( s1.compareTo( s4 ) >= 0 ) { + return false; + } + if ( s4.compareTo( s1 ) <= 0 ) { + return false; + } + if ( !s4.getSpeciesId().equals( "b" ) ) { + return false; + } + final Species s5 = new BasicSpecies( " C " ); + if ( !s5.getSpeciesId().equals( "C" ) ) { + return false; + } + if ( s5.equals( s1 ) ) { return false; } } catch ( final Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testSplitStrict() { + private static boolean testSplit() { try { 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(); ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -10619,7 +10703,11 @@ public final class Test { ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); + final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex ); + // System.out.println( s0.toString() ); + // Set query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -10714,33 +10802,193 @@ public final class Test { } // query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( s0.match( query_nodes ) ) { + return false; + } + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( s0.match( query_nodes ) ) { + return false; + } + // + 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.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + if ( s0.match( query_nodes ) ) { + return false; + } + // + 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.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( s0.match( query_nodes ) ) { + return false; + } + // + 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.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + if ( s0.match( query_nodes ) ) { + return false; + } + // + 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.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.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.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.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + 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.add( new PhylogenyNode( "X" ) ); + // query_nodes.add( new PhylogenyNode( "Y" ) ); + // query_nodes.add( new PhylogenyNode( "A" ) ); + // query_nodes.add( new PhylogenyNode( "B" ) ); + // query_nodes.add( new PhylogenyNode( "C" ) ); + // query_nodes.add( new PhylogenyNode( "D" ) ); + // query_nodes.add( new PhylogenyNode( "E" ) ); + // query_nodes.add( new PhylogenyNode( "F" ) ); + // query_nodes.add( new PhylogenyNode( "G" ) ); + // if ( !s0.match( query_nodes ) ) { + // return false; + // } + // query_nodes = new HashSet(); + // query_nodes.add( new PhylogenyNode( "X" ) ); + // query_nodes.add( new PhylogenyNode( "Y" ) ); + // query_nodes.add( new PhylogenyNode( "A" ) ); + // query_nodes.add( new PhylogenyNode( "B" ) ); + // query_nodes.add( new PhylogenyNode( "C" ) ); + // if ( !s0.match( query_nodes ) ) { + // return false; + // } + // // + // query_nodes = new HashSet(); + // query_nodes.add( new PhylogenyNode( "X" ) ); + // query_nodes.add( new PhylogenyNode( "Y" ) ); + // query_nodes.add( new PhylogenyNode( "D" ) ); + // query_nodes.add( new PhylogenyNode( "E" ) ); + // query_nodes.add( new PhylogenyNode( "F" ) ); + // query_nodes.add( new PhylogenyNode( "G" ) ); + // if ( !s0.match( query_nodes ) ) { + // return false; + // } + // // + // query_nodes = new HashSet(); + // query_nodes.add( new PhylogenyNode( "X" ) ); + // query_nodes.add( new PhylogenyNode( "Y" ) ); + // query_nodes.add( new PhylogenyNode( "A" ) ); + // query_nodes.add( new PhylogenyNode( "B" ) ); + // query_nodes.add( new PhylogenyNode( "C" ) ); + // query_nodes.add( new PhylogenyNode( "D" ) ); + // if ( !s0.match( query_nodes ) ) { + // return false; + // } + // // + // query_nodes = new HashSet(); + // query_nodes.add( new PhylogenyNode( "X" ) ); + // query_nodes.add( new PhylogenyNode( "Y" ) ); + // query_nodes.add( new PhylogenyNode( "E" ) ); + // query_nodes.add( new PhylogenyNode( "F" ) ); + // query_nodes.add( new PhylogenyNode( "G" ) ); + // if ( !s0.match( query_nodes ) ) { + // return false; + // } + // // + // query_nodes = new HashSet(); + // query_nodes.add( new PhylogenyNode( "X" ) ); + // query_nodes.add( new PhylogenyNode( "Y" ) ); + // query_nodes.add( new PhylogenyNode( "F" ) ); + // query_nodes.add( new PhylogenyNode( "G" ) ); + // if ( !s0.match( query_nodes ) ) { + // return false; + // } + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( s0.match( query_nodes ) ) { - return false; - } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); if ( s0.match( query_nodes ) ) { return false; } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); 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.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); if ( s0.match( query_nodes ) ) { @@ -10748,6 +10996,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); if ( s0.match( query_nodes ) ) { @@ -10755,6 +11005,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); if ( s0.match( query_nodes ) ) { @@ -10762,6 +11014,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); if ( s0.match( query_nodes ) ) { @@ -10769,6 +11023,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); if ( s0.match( query_nodes ) ) { @@ -10776,6 +11032,7 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( s0.match( query_nodes ) ) { @@ -10783,6 +11040,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -10791,6 +11050,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -10799,6 +11060,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -10807,6 +11070,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -10822,384 +11087,286 @@ public final class Test { return true; } - private static boolean testSubtreeDeletion() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ]; - t1.deleteSubtree( t1.getNode( "A" ), false ); - if ( t1.getNumberOfExternalNodes() != 5 ) { - return false; - } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "E" ), false ); - if ( t1.getNumberOfExternalNodes() != 4 ) { - return false; - } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "F" ), false ); - if ( t1.getNumberOfExternalNodes() != 3 ) { - return false; - } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "D" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 3 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "def" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 2 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "B" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "C" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "abc" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "r" ), false ); - if ( t1.getNumberOfExternalNodes() != 0 ) { - return false; - } - if ( !t1.isEmpty() ) { - return false; - } - final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ]; - t2.deleteSubtree( t2.getNode( "A" ), false ); - t2.toNewHampshireX(); - if ( t2.getNumberOfExternalNodes() != 5 ) { - return false; - } - t2.deleteSubtree( t2.getNode( "abc" ), false ); - t2.toNewHampshireX(); - if ( t2.getNumberOfExternalNodes() != 3 ) { - return false; - } - t2.deleteSubtree( t2.getNode( "def" ), false ); - t2.toNewHampshireX(); - if ( t2.getNumberOfExternalNodes() != 1 ) { - return false; - } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSupportCount() { + private static boolean testSplitStrict() { try { 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() ); - 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() ); - SupportCount.count( t0_2, phylogenies_2, true, false ); - final PhylogenyNodeIterator it = t0_2.iteratorPostorder(); - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) { - return false; - } - } - final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ]; - final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))" - + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() ); - SupportCount.count( t0_3, phylogenies_3, true, false ); - t0_3.reRoot( t0_3.getNode( "def" ).getId() ); - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) { - 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() ); - SupportCount.count( t0_4, phylogenies_4, true, false ); - t0_4.reRoot( t0_4.getNode( "F" ).getId() ); - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) { + final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ]; + final Set ex = new HashSet(); + ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex ); + Set query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) { + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + 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; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + 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; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) { + // + 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; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) { + // + 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; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - double d = SupportCount.compare( b1, a, true, true, true ); - if ( !Test.isEqual( d, 5.0 / 5.0 ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + if ( s0.match( query_nodes ) ) { return false; } - a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - d = SupportCount.compare( b2, a, true, true, true ); - if ( !Test.isEqual( d, 4.0 / 5.0 ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( s0.match( query_nodes ) ) { return false; } - a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ]; - d = SupportCount.compare( b3, a, true, true, true ); - if ( !Test.isEqual( d, 2.0 / 5.0 ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( s0.match( query_nodes ) ) { return false; } - a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ]; - final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ]; - d = SupportCount.compare( b4, a, true, true, false ); - if ( !Test.isEqual( d, 1.0 / 5.0 ) ) { + // + 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; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSupportTransfer() { - try { - 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 ]; - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + if ( s0.match( query_nodes ) ) { return false; } - support_transfer.moveBranchLengthsToBootstrap( p1 ); - support_transfer.transferSupportValues( p1, p2 ); - if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) { + // + 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; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) { + // + 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; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) { + // + 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; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( s0.match( query_nodes ) ) { return false; } } catch ( final Exception e ) { - e.printStackTrace( System.out ); + e.printStackTrace(); return false; } return true; } - private static boolean testTaxonomyExtraction() { + private static boolean testSubtreeDeletion() { try { - final PhylogenyNode n0 = PhylogenyNode - .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n0.getNodeData().isHasTaxonomy() ) { - return false; - } - final PhylogenyNode n1 = PhylogenyNode - .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n1.getNodeData().isHasTaxonomy() ) { - System.out.println( n1.toString() ); - return false; - } - final PhylogenyNode n2x = PhylogenyNode - .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n2x.getNodeData().isHasTaxonomy() ) { - return false; - } - final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { - System.out.println( n3.toString() ); - return false; - } - final PhylogenyNode n4 = PhylogenyNode - .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n4.getNodeData().isHasTaxonomy() ) { - System.out.println( n4.toString() ); - return false; - } - final PhylogenyNode n5 = PhylogenyNode - .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n5.getNodeData().isHasTaxonomy() ) { - System.out.println( n5.toString() ); - return false; - } - final PhylogenyNode n6 = PhylogenyNode - .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.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 ); - if ( n7.getNodeData().isHasTaxonomy() ) { - System.out.println( n7.toString() ); + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ]; + t1.deleteSubtree( t1.getNode( "A" ), false ); + if ( t1.getNumberOfExternalNodes() != 5 ) { return false; } - final PhylogenyNode n8 = PhylogenyNode - .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { - System.out.println( n8.toString() ); + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "E" ), false ); + if ( t1.getNumberOfExternalNodes() != 4 ) { return false; } - final PhylogenyNode n9 = PhylogenyNode - .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { - System.out.println( n9.toString() ); + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "F" ), false ); + if ( t1.getNumberOfExternalNodes() != 3 ) { return false; } - final PhylogenyNode n10x = PhylogenyNode - .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n10x.getNodeData().isHasTaxonomy() ) { - System.out.println( n10x.toString() ); + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "D" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 3 ) { return false; } - final PhylogenyNode n10xx = PhylogenyNode - .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n10xx.getNodeData().isHasTaxonomy() ) { - System.out.println( n10xx.toString() ); + t1.deleteSubtree( t1.getNode( "def" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 2 ) { return false; } - final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { - System.out.println( n10.toString() ); + t1.deleteSubtree( t1.getNode( "B" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - final PhylogenyNode n11 = PhylogenyNode - .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { - System.out.println( n11.toString() ); + t1.deleteSubtree( t1.getNode( "C" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - final PhylogenyNode n12 = PhylogenyNode - .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus", - NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { - System.out.println( n12.toString() ); + t1.deleteSubtree( t1.getNode( "abc" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - final PhylogenyNode n13 = PhylogenyNode - .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( n13.getNodeData().isHasTaxonomy() ) { - System.out.println( n13.toString() ); + t1.deleteSubtree( t1.getNode( "r" ), false ); + if ( t1.getNumberOfExternalNodes() != 0 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testTreeMethods() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ]; - PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) ); - if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) { - System.out.println( t0.toNewHampshireX() ); + if ( !t1.isEmpty() ) { return false; } - final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ]; - PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) ); - if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) { + final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ]; + t2.deleteSubtree( t2.getNode( "A" ), false ); + t2.toNewHampshireX(); + if ( t2.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) { + t2.deleteSubtree( t2.getNode( "abc" ), false ); + t2.toNewHampshireX(); + if ( t2.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) { + t2.deleteSubtree( t2.getNode( "def" ), false ); + t2.toNewHampshireX(); + if ( t2.getNumberOfExternalNodes() != 1 ) { return false; } } @@ -11210,368 +11377,349 @@ public final class Test { return true; } - private static boolean testSequenceDbWsTools1() { + private static boolean testSupportCount() { try { - final PhylogenyNode n = new PhylogenyNode(); - n.setName( "NP_001025424" ); - Accession acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) - || !acc.getValue().equals( "NP_001025424" ) ) { - return false; - } - n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) - || !acc.getValue().equals( "NP_001025424" ) ) { - return false; - } - n.setName( "NP_001025424.1" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) - || !acc.getValue().equals( "NP_001025424" ) ) { - return false; - } - n.setName( "NM_001030253" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) - || !acc.getValue().equals( "NM_001030253" ) ) { - return false; - } - n.setName( "BCL2_HUMAN" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) - || !acc.getValue().equals( "BCL2_HUMAN" ) ) { - System.out.println( acc.toString() ); - return false; + 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() ); + 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() ); + SupportCount.count( t0_2, phylogenies_2, true, false ); + final PhylogenyNodeIterator it = t0_2.iteratorPostorder(); + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) { + return false; + } } - n.setName( "P10415" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) - || !acc.getValue().equals( "P10415" ) ) { - System.out.println( acc.toString() ); + final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ]; + final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))" + + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() ); + SupportCount.count( t0_3, phylogenies_3, true, false ); + t0_3.reRoot( t0_3.getNode( "def" ).getId() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) { return false; } - n.setName( " P10415 " ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) - || !acc.getValue().equals( "P10415" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) { return false; } - n.setName( "_P10415|" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) - || !acc.getValue().equals( "P10415" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) { return false; } - n.setName( "AY695820" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AY695820" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) { return false; } - n.setName( "_AY695820_" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AY695820" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) { return false; } - n.setName( "AAA59452" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAA59452" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) { return false; } - n.setName( "_AAA59452_" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAA59452" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) { return false; } - n.setName( "AAA59452.1" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAA59452.1" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) { return false; } - n.setName( "_AAA59452.1_" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAA59452.1" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) { return false; } - n.setName( "GI:94894583" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() ) - || !acc.getValue().equals( "94894583" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) { return false; } - n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() ) - || !acc.getValue().equals( "71845847" ) ) { - System.out.println( acc.toString() ); + 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() ); + SupportCount.count( t0_4, phylogenies_4, true, false ); + t0_4.reRoot( t0_4.getNode( "F" ).getId() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) { return false; } - n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAZ45343.1" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) { return false; } - } - catch ( final Exception e ) { - return false; - } - return true; - } - - private static boolean testSequenceDbWsTools2() { - try { - final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" ); - SequenceDbWsTools.obtainSeqInformation( n1 ); - if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) { return false; } - if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) { return false; } - if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) { return false; } - if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) { return false; } - final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" ); - SequenceDbWsTools.obtainSeqInformation( n2 ); - if ( !n2.getNodeData().getSequence().getName() - .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) { return false; } - if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) { return false; } - if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) { return false; } - if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) { return false; } - final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" ); - SequenceDbWsTools.obtainSeqInformation( n3 ); - if ( !n3.getNodeData().getSequence().getName() - .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { + Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; + final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; + double d = SupportCount.compare( b1, a, true, true, true ); + if ( !Test.isEqual( d, 5.0 / 5.0 ) ) { return false; } - if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) { + a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; + final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; + d = SupportCount.compare( b2, a, true, true, true ); + if ( !Test.isEqual( d, 4.0 / 5.0 ) ) { return false; } - if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; + final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ]; + d = SupportCount.compare( b3, a, true, true, true ); + if ( !Test.isEqual( d, 2.0 / 5.0 ) ) { return false; } - if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) { + a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ]; + final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ]; + d = SupportCount.compare( b4, a, true, true, false ); + if ( !Test.isEqual( d, 1.0 / 5.0 ) ) { return false; } } - catch ( final IOException e ) { - System.out.println(); - System.out.println( "the following might be due to absence internet connection:" ); - e.printStackTrace( System.out ); - return true; - } catch ( final Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testEbiEntryRetrieval() { + private static boolean testSupportTransfer() { try { - final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" ); - if ( !entry.getAccession().equals( "AAK41263" ) ) { - System.out.println( entry.getAccession() ); - return false; - } - if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) { - System.out.println( entry.getTaxonomyScientificName() ); + 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 ]; + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) { return false; } - if ( !entry.getSequenceName() - .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) { - System.out.println( entry.getSequenceName() ); + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) { return false; } - // if ( !entry.getSequenceSymbol().equals( "" ) ) { - // System.out.println( entry.getSequenceSymbol() ); - // return false; - // } - if ( !entry.getGeneName().equals( "treX-like" ) ) { - System.out.println( entry.getGeneName() ); + support_transfer.moveBranchLengthsToBootstrap( p1 ); + support_transfer.transferSupportValues( p1, p2 ); + if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) { return false; } - if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) { - System.out.println( entry.getTaxonomyIdentifier() ); + if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) { return false; } - if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) { - System.out.println( entry.getAnnotations().first().getRefValue() ); + if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) { return false; } - if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) { - System.out.println( entry.getAnnotations().first().getRefSource() ); + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) { return false; } - if ( entry.getCrossReferences().size() != 5 ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) { return false; } - // - final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); - if ( !entry1.getAccession().equals( "ABJ16409" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) { return false; } - if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) { - System.out.println( entry1.getTaxonomyScientificName() ); + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) { return false; } - if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) { - System.out.println( entry1.getSequenceName() ); + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) { return false; } - if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) { - System.out.println( entry1.getTaxonomyIdentifier() ); + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testTaxonomyExtraction() { + try { + final PhylogenyNode n0 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n0.getNodeData().isHasTaxonomy() ) { return false; } - if ( !entry1.getGeneName().equals( "BCL2" ) ) { - System.out.println( entry1.getGeneName() ); + final PhylogenyNode n1 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n1.getNodeData().isHasTaxonomy() ) { + System.out.println( n1.toString() ); return false; } - if ( entry1.getCrossReferences().size() != 6 ) { + final PhylogenyNode n2x = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n2x.getNodeData().isHasTaxonomy() ) { return false; } - // - final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); - if ( !entry2.getAccession().equals( "NM_184234" ) ) { + final PhylogenyNode n3 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + System.out.println( n3.toString() ); return false; } - if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { - System.out.println( entry2.getTaxonomyScientificName() ); + final PhylogenyNode n4 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n4.getNodeData().isHasTaxonomy() ) { + System.out.println( n4.toString() ); return false; } - if ( !entry2.getSequenceName() - .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { - System.out.println( entry2.getSequenceName() ); + final PhylogenyNode n5 = PhylogenyNode + .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n5.getNodeData().isHasTaxonomy() ) { + System.out.println( n5.toString() ); return false; } - if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) { - System.out.println( entry2.getTaxonomyIdentifier() ); + final PhylogenyNode n6 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n6.getNodeData().isHasTaxonomy() ) { + System.out.println( n6.toString() ); return false; } - if ( !entry2.getGeneName().equals( "RBM39" ) ) { - System.out.println( entry2.getGeneName() ); + final PhylogenyNode n7 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n7.getNodeData().isHasTaxonomy() ) { + System.out.println( n7.toString() ); return false; } - if ( entry2.getCrossReferences().size() != 3 ) { + final PhylogenyNode n8 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + System.out.println( n8.toString() ); return false; } - // - final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" ); - if ( !entry3.getAccession().equals( "HM043801" ) ) { + final PhylogenyNode n9 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + System.out.println( n9.toString() ); return false; } - if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) { - System.out.println( entry3.getTaxonomyScientificName() ); + final PhylogenyNode n10x = PhylogenyNode + .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n10x.getNodeData().isHasTaxonomy() ) { + System.out.println( n10x.toString() ); return false; } - if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) { - System.out.println( entry3.getSequenceName() ); + final PhylogenyNode n10xx = PhylogenyNode + .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n10xx.getNodeData().isHasTaxonomy() ) { + System.out.println( n10xx.toString() ); return false; } - if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) { - System.out.println( entry3.getTaxonomyIdentifier() ); + final PhylogenyNode n10 = PhylogenyNode + .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { + System.out.println( n10.toString() ); return false; } - if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) { - System.out.println( entry3.getSequenceSymbol() ); + final PhylogenyNode n11 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { + System.out.println( n11.toString() ); return false; } - if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { + final PhylogenyNode n12 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { + System.out.println( n12.toString() ); return false; } - if ( entry3.getCrossReferences().size() != 8 ) { + final PhylogenyNode n13 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( n13.getNodeData().isHasTaxonomy() ) { + System.out.println( n13.toString() ); return false; } - // - // - final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); - if ( !entry4.getAccession().equals( "AAA36557" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testTreeCopy() { + try { + final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]"; + final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 ); + final Phylogeny t1 = t0.copy(); + if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) { return false; } - if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { - System.out.println( entry4.getTaxonomyScientificName() ); + if ( !t1.toNewHampshireX().equals( str_0 ) ) { return false; } - if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) { - System.out.println( entry4.getSequenceName() ); + t0.deleteSubtree( t0.getNode( "c" ), true ); + t0.deleteSubtree( t0.getNode( "a" ), true ); + t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" ); + t0.getNode( "b" ).setName( "Bee" ); + if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) { return false; } - if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) { - System.out.println( entry4.getTaxonomyIdentifier() ); + if ( !t1.toNewHampshireX().equals( str_0 ) ) { return false; } - if ( !entry4.getGeneName().equals( "ras" ) ) { - System.out.println( entry4.getGeneName() ); + t0.deleteSubtree( t0.getNode( "e" ), true ); + t0.deleteSubtree( t0.getNode( "Bee" ), true ); + t0.deleteSubtree( t0.getNode( "d" ), true ); + if ( !t1.toNewHampshireX().equals( str_0 ) ) { 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" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testTreeMethods() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) ); + if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) { + System.out.println( t0.toNewHampshireX() ); return false; } - if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) { - System.out.println( entry5.getTaxonomyScientificName() ); + final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) { return false; } - if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) { - System.out.println( entry5.getSequenceName() ); + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) { return false; } - if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) { - System.out.println( entry5.getTaxonomyIdentifier() ); + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) { return false; } } - catch ( final IOException e ) { - System.out.println(); - System.out.println( "the following might be due to absence internet connection:" ); - e.printStackTrace( System.out ); - return true; - } catch ( final Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true;