X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=fc210a55a0b6c8527dd415996daaa0326d6ad500;hb=83086d32cf5b8c98a5c8d045187e07e4fa9bb752;hp=f20c0b3f2df3b3a13479297e0f64cd418d409cbc;hpb=23e3f673b9ef683edbb2b76037e7e06ae79f616a;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index f20c0b3..fc210a5 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.test; @@ -36,9 +36,10 @@ import java.util.Iterator; import java.util.List; import java.util.Locale; import java.util.Set; +import java.util.SortedSet; import org.forester.application.support_transfer; -import org.forester.datastructures.IntMatrix; +import org.forester.archaeopteryx.TreePanelUtil; import org.forester.development.DevelopmentTools; import org.forester.evoinference.TestPhylogenyReconstruction; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -52,9 +53,12 @@ import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser; import org.forester.io.parsers.nexus.NexusCharactersParser; import org.forester.io.parsers.nexus.NexusPhylogeniesParser; import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.io.parsers.tol.TolParser; +import org.forester.io.parsers.util.ParserUtils; import org.forester.io.writers.PhylogenyWriter; +import org.forester.io.writers.SequenceWriter; import org.forester.msa.BasicMsa; import org.forester.msa.Mafft; import org.forester.msa.Msa; @@ -64,9 +68,10 @@ import org.forester.pccx.TestPccx; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyBranch; import org.forester.phylogeny.PhylogenyMethods; -import org.forester.phylogeny.PhylogenyMethods.TAXONOMY_EXTRACTION; import org.forester.phylogeny.PhylogenyNode; -import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.data.Accession; +import org.forester.phylogeny.data.Accession.Source; import org.forester.phylogeny.data.BinaryCharacters; import org.forester.phylogeny.data.BranchWidth; import org.forester.phylogeny.data.Confidence; @@ -85,15 +90,19 @@ import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; +import org.forester.protein.BasicDomain; +import org.forester.protein.BasicProtein; +import org.forester.protein.Domain; import org.forester.protein.Protein; -import org.forester.sdi.GSDI; -import org.forester.sdi.RIO; +import org.forester.protein.ProteinId; +import org.forester.rio.TestRIO; import org.forester.sdi.SDI; import org.forester.sdi.SDIR; -import org.forester.sdi.SDIse; import org.forester.sdi.TestGSDI; import org.forester.sequence.BasicSequence; import org.forester.sequence.Sequence; +import org.forester.species.BasicSpecies; +import org.forester.species.Species; import org.forester.surfacing.TestSurfacing; import org.forester.tools.ConfidenceAssessor; import org.forester.tools.SupportCount; @@ -106,7 +115,7 @@ import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; import org.forester.util.GeneralTable; -import org.forester.util.SequenceIdParser; +import org.forester.util.SequenceAccessionTools; import org.forester.ws.seqdb.SequenceDatabaseEntry; import org.forester.ws.seqdb.SequenceDbWsTools; import org.forester.ws.seqdb.UniProtTaxonomy; @@ -118,6 +127,7 @@ import org.forester.ws.wabi.TxSearch.TAX_RANK; @SuppressWarnings( "unused") public final class Test { + private final static boolean PERFORM_DB_TESTS = true; 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" @@ -133,14 +143,257 @@ public final class Test { + ForesterConstants.PHYLO_XML_VERSION + "/" + ForesterConstants.PHYLO_XML_XSD; - private final static Phylogeny createPhylogeny( final String nhx ) throws IOException { - final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ]; - return p; + 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, 0.01, 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( "a" ) ) { + 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; } - private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) { - final PhylogenyMethods pm = PhylogenyMethods.getInstance(); - return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent(); + 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; } public static boolean isEqual( final double a, final double b ) { @@ -174,6 +427,60 @@ public final class Test { System.exit( -1 ); } final long start_time = new Date().getTime(); + System.out.print( "Basic node methods: " ); + if ( Test.testBasicNodeMethods() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Protein id: " ); + if ( !testProteinId() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); + System.out.print( "Species: " ); + if ( !testSpecies() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); + System.out.print( "Basic domain: " ); + if ( !testBasicDomain() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); + System.out.print( "Basic protein: " ); + if ( !testBasicProtein() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); + System.out.print( "Sequence writer: " ); + if ( testSequenceWriter() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Sequence id parsing: " ); if ( testSequenceIdParsing() ) { System.out.println( "OK." ); @@ -181,9 +488,51 @@ public final class Test { } else { System.out.println( "failed." ); - System.exit( -1 ); //TODO FIXME remove me!! ~ failed++; } + System.out.print( "UniProtKB id extraction: " ); + if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Sequence DB tools 1: " ); + if ( testSequenceDbWsTools1() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + if ( PERFORM_DB_TESTS ) { + System.out.print( "Ebi Entry Retrieval: " ); + if ( Test.testEbiEntryRetrieval() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + } + // System.exit( 0 ); + if ( PERFORM_DB_TESTS ) { + System.out.print( "Sequence DB tools 2: " ); + if ( testSequenceDbWsTools2() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + System.exit( -1 ); + } + } + // System.exit( 0 ); System.out.print( "Hmmscan output parser: " ); if ( testHmmscanOutputParser() ) { System.out.println( "OK." ); @@ -193,8 +542,55 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "Basic node methods: " ); - if ( Test.testBasicNodeMethods() ) { + // + System.out.print( "Overlap removal: " ); + if ( !org.forester.test.Test.testOverlapRemoval() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); + System.out.print( "Engulfing overlap removal: " ); + if ( !Test.testEngulfingOverlapRemoval() ) { + System.out.println( "failed." ); + failed++; + } + else { + succeeded++; + } + System.out.println( "OK." ); + // + System.out.print( "Taxonomy code extraction: " ); + if ( Test.testExtractTaxonomyCodeFromNodeName() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "SN extraction: " ); + if ( Test.testExtractSNFromNodeName() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Taxonomy extraction (general): " ); + if ( Test.testTaxonomyExtraction() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Uri for Aptx web sequence accession: " ); + if ( Test.testCreateUriForSeqWeb() ) { System.out.println( "OK." ); succeeded++; } @@ -211,6 +607,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "NHX parsing iterating: " ); + if ( Test.testNHParsingIter() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "NH parsing: " ); if ( Test.testNHParsing() ) { System.out.println( "OK." ); @@ -265,6 +670,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Nexus tree parsing iterating: " ); + if ( Test.testNexusTreeParsingIterating() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Nexus tree parsing: " ); if ( Test.testNexusTreeParsing() ) { System.out.println( "OK." ); @@ -346,6 +760,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Tree copy: " ); + if ( Test.testTreeCopy() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Basic tree methods: " ); if ( Test.testBasicTreeMethods() ) { System.out.println( "OK." ); @@ -355,6 +778,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Tree methods: " ); + if ( Test.testTreeMethods() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Postorder Iterator: " ); if ( Test.testPostOrderIterator() ) { System.out.println( "OK." ); @@ -454,6 +886,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Node removal: " ); + if ( Test.testNodeRemoval() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Support count: " ); if ( Test.testSupportCount() ) { System.out.println( "OK." ); @@ -499,8 +940,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "SDIse: " ); - if ( Test.testSDIse() ) { + System.out.print( "Descriptive statistics: " ); + if ( Test.testDescriptiveStatistics() ) { System.out.println( "OK." ); succeeded++; } @@ -508,8 +949,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "SDIunrooted: " ); - if ( Test.testSDIunrooted() ) { + System.out.print( "Data objects and methods: " ); + if ( Test.testDataObjects() ) { System.out.println( "OK." ); succeeded++; } @@ -517,8 +958,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "GSDI: " ); - if ( TestGSDI.test() ) { + System.out.print( "Properties map: " ); + if ( Test.testPropertiesMap() ) { System.out.println( "OK." ); succeeded++; } @@ -526,8 +967,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "Ortholog table: " ); - if ( Test.testOrthologTable() ) { + System.out.print( "SDIse: " ); + if ( Test.testSDIse() ) { System.out.println( "OK." ); succeeded++; } @@ -535,8 +976,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "Descriptive statistics: " ); - if ( Test.testDescriptiveStatistics() ) { + System.out.print( "SDIunrooted: " ); + if ( Test.testSDIunrooted() ) { System.out.println( "OK." ); succeeded++; } @@ -544,8 +985,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "Data objects and methods: " ); - if ( Test.testDataObjects() ) { + System.out.print( "GSDI: " ); + if ( TestGSDI.test() ) { System.out.println( "OK." ); succeeded++; } @@ -553,8 +994,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "Properties map: " ); - if ( Test.testPropertiesMap() ) { + System.out.print( "RIO: " ); + if ( TestRIO.test() ) { System.out.println( "OK." ); succeeded++; } @@ -682,17 +1123,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "EMBL Entry Retrieval: " ); - if ( Test.testEmblEntryRetrieval() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } - System.out.print( "Uniprot Entry Retrieval: " ); - if ( Test.testUniprotEntryRetrieval() ) { + System.out.print( "Genbank accessor parsing: " ); + if ( Test.testGenbankAccessorParsing() ) { System.out.println( "OK." ); succeeded++; } @@ -700,14 +1132,27 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "Uniprot Taxonomy Search: " ); - if ( Test.testUniprotTaxonomySearch() ) { - System.out.println( "OK." ); - succeeded++; + if ( PERFORM_DB_TESTS ) { + System.out.print( "Uniprot Entry Retrieval: " ); + if ( Test.testUniprotEntryRetrieval() ) { + 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 = ""; @@ -756,15 +1201,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // System.out.print( "WABI TxSearch: " ); - // if ( Test.testWabiTxSearch() ) { - // System.out.println( "OK." ); - // succeeded++; - // } - // else { - // System.out - // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" ); - // } System.out.println(); final Runtime rt = java.lang.Runtime.getRuntime(); final long free_memory = rt.freeMemory() / 1000000; @@ -781,73 +1217,108 @@ public final class Test { else { System.out.println( "Not OK." ); } - // System.out.println(); - // Development.setTime( true ); - //try { - // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() - // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx"; - // final String multi = Test.PATH_TO_EXAMPLE_FILES + - // "multifurcations_ex_1.nhx"; - // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx"; - // final Phylogeny t1 = factory.create( new File( domains ), new - // NHXParser() )[ 0 ]; - // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ]; - // } - // catch ( final Exception e ) { - // e.printStackTrace(); - // } - // t1.getRoot().preorderPrint(); - // final PhylogenyFactory factory = ParserBasedPhylogenyFactory - // .getInstance(); - // try { - // - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\AtNBSpos.nhx" ) ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ), - // new NHXParser() ); - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\AtNBSpos.nhx" ) ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ), - // new NHXParser() ); - // - // - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\big_tree.nhx" ) ); - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\big_tree.nhx" ) ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ), - // new NHXParser() ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ), - // new NHXParser() ); - // - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\big_tree.nhx" ) ); - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\big_tree.nhx" ) ); - // - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ), - // new NHXParser() ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ), - // new NHXParser() ); - // - // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES - // + "\\AtNBSpos.nhx" ) ); - // factory.create( - // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ), - // new NHXParser() ); - // - // } - // catch ( IOException e ) { - // // TODO Auto-generated catch block - // e.printStackTrace(); - // } + } + + private final static Phylogeny createPhylogeny( final String nhx ) throws IOException { + final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ]; + return p; + } + + private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) { + return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent(); + } + + private static boolean testAminoAcidSequence() { + try { + final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" ); + if ( aa1.getLength() != 13 ) { + return false; + } + if ( aa1.getResidueAt( 0 ) != 'A' ) { + return false; + } + if ( aa1.getResidueAt( 2 ) != 'K' ) { + return false; + } + if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) { + return false; + } + final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" ); + if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) { + return false; + } + final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" ); + if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) { + return false; + } + final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" ); + if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testBasicDomain() { + try { + final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); + if ( !pd.getDomainId().equals( "id" ) ) { + return false; + } + if ( pd.getNumber() != 1 ) { + return false; + } + if ( pd.getTotalCount() != 4 ) { + return false; + } + if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) { + return false; + } + final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 ); + final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 ); + final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 ); + final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 ); + final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 ); + if ( !a1.equals( a1 ) ) { + return false; + } + if ( !a1.equals( a1_copy ) ) { + return false; + } + if ( !a1.equals( a1_equal ) ) { + return false; + } + if ( !a1.equals( a2 ) ) { + return false; + } + if ( a1.equals( a3 ) ) { + return false; + } + if ( a1.compareTo( a1 ) != 0 ) { + return false; + } + if ( a1.compareTo( a1_copy ) != 0 ) { + return false; + } + if ( a1.compareTo( a1_equal ) != 0 ) { + return false; + } + if ( a1.compareTo( a2 ) != 0 ) { + return false; + } + if ( a1.compareTo( a3 ) == 0 ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; } private static boolean testBasicNodeMethods() { @@ -857,11 +1328,11 @@ public final class Test { } final PhylogenyNode n1 = new PhylogenyNode(); final PhylogenyNode n2 = PhylogenyNode - .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); final PhylogenyNode n4 = PhylogenyNode - .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( n1.isHasAssignedEvent() ) { return false; } @@ -894,7 +1365,7 @@ public final class Test { private static boolean testBasicPhyloXMLparsing() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final PhyloXmlParser xml_parser = new PhyloXmlParser(); + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { @@ -986,67 +1457,67 @@ public final class Test { if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() .equals( "apoptosis" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef() .equals( "GO:0006915" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource() .equals( "UniProtKB" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence() .equals( "experimental" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType() .equals( "function" ) ) { return false; } - if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence() + if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() .getValue() != 1 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() .getType().equals( "ml" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() .equals( "apoptosis" ) ) { return false; } - if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() .equals( "GO:0005829" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc() .equals( "intracellular organelle" ) ) { return false; } @@ -1060,114 +1531,22 @@ public final class Test { if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) { return false; } - //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) { - // return false; - //} - // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) { - // return false; - // } - // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) { - // return false; - // } - // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) { - // return false; - // } - // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) { - // return false; - // } - // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) { - // return false; - // } - // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { - // return false; - // } - // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) { - // return false; - // } - // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) { - // return false; - // } - // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName() - // .equals( "B" ) ) { - // return false; - // } - // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) { - // return false; - // } - // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) { - // return false; - // } - // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) { - // return false; - // } - // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) - // .getConfidence() != 2144 ) { - // return false; - // } - // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId() - // .equals( "pfam" ) ) { - // return false; - // } - // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) { - // return false; - // } - // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) { - // return false; - // } - // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) { - // return false; - // } - // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) { - // return false; - // } - // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() ) - // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) { - // ; - // return false; - // } - // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) { - // return false; - // } - // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) { - // return false; - // } - // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) { - // return false; - // } - // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) { - // return false; - // } - // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) { - // return false; - // } - // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) { - // return false; - // } - // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) { - // return false; - // } - // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml", - // xml_parser ); - // if ( xml_parser.getErrorCount() > 0 ) { - // System.out.println( xml_parser.getErrorMessages().toString() ); - // return false; - // } - // if ( phylogenies_1.length != 2 ) { - // return false; - // } - // final Phylogeny a = phylogenies_1[ 0 ]; - // if ( !a.getName().equals( "tree 4" ) ) { - // return false; - // } - // if ( a.getNumberOfExternalNodes() != 3 ) { - // return false; - // } - // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) { - // return false; - // } - // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) { - // return false; - // } + final SortedSet x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences(); + if ( x.size() != 4 ) { + return false; + } + int c = 0; + for( final Accession acc : x ) { + if ( c == 0 ) { + if ( !acc.getSource().equals( "KEGG" ) ) { + return false; + } + if ( !acc.getValue().equals( "hsa:596" ) ) { + return false; + } + } + c++; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -1179,7 +1558,7 @@ public final class Test { private static boolean testBasicPhyloXMLparsingRoundtrip() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final PhyloXmlParser xml_parser = new PhyloXmlParser(); + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); if ( USE_LOCAL_PHYLOXML_SCHEMA ) { xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); } @@ -1273,67 +1652,67 @@ public final class Test { .equals( "UniProtKB" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() .equals( "apoptosis" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef() .equals( "GO:0006915" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource() .equals( "UniProtKB" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence() .equals( "experimental" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType() .equals( "function" ) ) { return false; } - if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence() + if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() .getValue() != 1 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() .getType().equals( "ml" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() .equals( "apoptosis" ) ) { return false; } - if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() .equals( "GO:0005829" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc() .equals( "intracellular organelle" ) ) { return false; } @@ -1447,7 +1826,6 @@ public final class Test { } if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() ) .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) { - ; return false; } if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) { @@ -1496,6 +1874,23 @@ public final class Test { .equalsIgnoreCase( "433" ) ) { return false; } + final SortedSet x = t3_rt.getNode( "root node" ).getNodeData().getSequence() + .getCrossReferences(); + if ( x.size() != 4 ) { + return false; + } + int c = 0; + for( final Accession acc : x ) { + if ( c == 0 ) { + if ( !acc.getSource().equals( "KEGG" ) ) { + return false; + } + if ( !acc.getValue().equals( "hsa:596" ) ) { + return false; + } + } + c++; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -1515,7 +1910,7 @@ public final class Test { // Do nothing -- means were not running from jar. } if ( xml_parser == null ) { - xml_parser = new PhyloXmlParser(); + xml_parser = PhyloXmlParser.createPhyloXmlParser(); if ( USE_LOCAL_PHYLOXML_SCHEMA ) { xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); } @@ -1629,104 +2024,367 @@ public final class Test { return true; } - private static boolean testBasicTable() { + private static boolean testBasicProtein() { try { - final BasicTable t0 = new BasicTable(); - if ( t0.getNumberOfColumns() != 0 ) { + final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 ); + final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 ); + p0.addProteinDomain( y ); + p0.addProteinDomain( e ); + p0.addProteinDomain( b ); + p0.addProteinDomain( c ); + p0.addProteinDomain( d ); + p0.addProteinDomain( a ); + p0.addProteinDomain( x ); + if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) { + return false; + } + if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) { return false; } - if ( t0.getNumberOfRows() != 0 ) { + // + final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 ); + final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 ); + aa0.addProteinDomain( a1 ); + if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) { return false; } - t0.setValue( 3, 2, "23" ); - t0.setValue( 10, 1, "error" ); - t0.setValue( 10, 1, "110" ); - t0.setValue( 9, 1, "19" ); - t0.setValue( 1, 10, "101" ); - t0.setValue( 10, 10, "1010" ); - t0.setValue( 100, 10, "10100" ); - t0.setValue( 0, 0, "00" ); - if ( !t0.getValue( 3, 2 ).equals( "23" ) ) { + if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) { return false; } - if ( !t0.getValue( 10, 1 ).equals( "110" ) ) { + // + final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 ); + final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 ); + aa1.addProteinDomain( a11 ); + aa1.addProteinDomain( a12 ); + if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) { return false; } - if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) { return false; } - if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) { + aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) ); + if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) { return false; } - if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) { return false; } - if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) { + if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) { return false; } - if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) { + aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) ); + if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) { return false; } - if ( t0.getNumberOfColumns() != 101 ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) { return false; } - if ( t0.getNumberOfRows() != 11 ) { + if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) { return false; } - if ( t0.getValueAsString( 49, 4 ) != null ) { + if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) { return false; } - final String l = ForesterUtil.getLineSeparator(); - final StringBuffer source = new StringBuffer(); - source.append( "" + l ); - source.append( "# 1 1 1 1 1 1 1 1" + l ); - source.append( " 00 01 02 03" + l ); - source.append( " 10 11 12 13 " + l ); - source.append( "20 21 22 23 " + l ); - source.append( " 30 31 32 33" + l ); - source.append( "40 41 42 43" + l ); - source.append( " # 1 1 1 1 1 " + l ); - source.append( "50 51 52 53 54" + l ); - final BasicTable t1 = BasicTableParser.parse( source.toString(), " " ); - if ( t1.getNumberOfColumns() != 5 ) { + aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) ); + if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) { return false; } - if ( t1.getNumberOfRows() != 6 ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) { return false; } - if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) { + if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) { return false; } - if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) { + if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) { return false; } - if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) { + aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) ); + if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) { return false; } - if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) { return false; } - final StringBuffer source1 = new StringBuffer(); - source1.append( "" + l ); - source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l ); - source1.append( " 00; 01 ;02;03" + l ); - source1.append( " 10; 11; 12; 13 " + l ); - source1.append( "20; 21; 22; 23 " + l ); - source1.append( " 30; 31; 32; 33" + l ); - source1.append( "40;41;42;43" + l ); - source1.append( " # 1 1 1 1 1 " + l ); - source1.append( ";;;50 ; ;52; 53;;54 " + l ); - final BasicTable t2 = BasicTableParser.parse( source1.toString(), ";" ); - if ( t2.getNumberOfColumns() != 5 ) { + if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) { return false; } - if ( t2.getNumberOfRows() != 6 ) { + if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) { return false; } - if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) { + // + final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 ); + final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 ); + final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 ); + p00.addProteinDomain( y0 ); + p00.addProteinDomain( e0 ); + p00.addProteinDomain( b0 ); + p00.addProteinDomain( c0 ); + p00.addProteinDomain( d0 ); + p00.addProteinDomain( a0 ); + p00.addProteinDomain( x0 ); + p00.addProteinDomain( y1 ); + p00.addProteinDomain( y2 ); + p00.addProteinDomain( y3 ); + p00.addProteinDomain( e1 ); + p00.addProteinDomain( e2 ); + p00.addProteinDomain( e3 ); + p00.addProteinDomain( e4 ); + p00.addProteinDomain( e5 ); + p00.addProteinDomain( z0 ); + p00.addProteinDomain( z1 ); + p00.addProteinDomain( z2 ); + p00.addProteinDomain( zz0 ); + p00.addProteinDomain( zz1 ); + if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) { + return false; + } + if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) { + return false; + } + if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) { + return false; + } + if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) { + return false; + } + if ( !p00.toDomainArchitectureString( "~", 7, "" ).equals( "a~b~c~d~e~e~e~e~e~e~x~y~y~y~y~z~z~z~Z~Z" ) ) { + return false; + } + // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80 + final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 ); + final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 ); + final BasicProtein p = new BasicProtein( "p", "owl", 0 ); + p.addProteinDomain( B15 ); + p.addProteinDomain( C50 ); + p.addProteinDomain( A60 ); + p.addProteinDomain( A30 ); + p.addProteinDomain( C70 ); + p.addProteinDomain( B35 ); + p.addProteinDomain( B40 ); + p.addProteinDomain( A0 ); + p.addProteinDomain( A10 ); + p.addProteinDomain( A20 ); + p.addProteinDomain( B25 ); + p.addProteinDomain( D80 ); + List domains_ids = new ArrayList(); + domains_ids.add( "A" ); + domains_ids.add( "B" ); + domains_ids.add( "C" ); + if ( !p.contains( domains_ids, false ) ) { + return false; + } + if ( !p.contains( domains_ids, true ) ) { + return false; + } + domains_ids.add( "X" ); + if ( p.contains( domains_ids, false ) ) { + return false; + } + if ( p.contains( domains_ids, true ) ) { + return false; + } + domains_ids = new ArrayList(); + domains_ids.add( "A" ); + domains_ids.add( "C" ); + domains_ids.add( "D" ); + if ( !p.contains( domains_ids, false ) ) { return false; } - if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) { + if ( !p.contains( domains_ids, true ) ) { + return false; + } + domains_ids = new ArrayList(); + domains_ids.add( "A" ); + domains_ids.add( "D" ); + domains_ids.add( "C" ); + if ( !p.contains( domains_ids, false ) ) { + return false; + } + if ( p.contains( domains_ids, true ) ) { + return false; + } + domains_ids = new ArrayList(); + domains_ids.add( "A" ); + domains_ids.add( "A" ); + domains_ids.add( "B" ); + if ( !p.contains( domains_ids, false ) ) { + return false; + } + if ( !p.contains( domains_ids, true ) ) { + return false; + } + domains_ids = new ArrayList(); + domains_ids.add( "A" ); + domains_ids.add( "A" ); + domains_ids.add( "A" ); + domains_ids.add( "B" ); + domains_ids.add( "B" ); + if ( !p.contains( domains_ids, false ) ) { + return false; + } + if ( !p.contains( domains_ids, true ) ) { + return false; + } + domains_ids = new ArrayList(); + domains_ids.add( "A" ); + domains_ids.add( "A" ); + domains_ids.add( "B" ); + domains_ids.add( "A" ); + domains_ids.add( "B" ); + domains_ids.add( "B" ); + domains_ids.add( "A" ); + domains_ids.add( "B" ); + domains_ids.add( "C" ); + domains_ids.add( "A" ); + domains_ids.add( "C" ); + domains_ids.add( "D" ); + if ( !p.contains( domains_ids, false ) ) { + return false; + } + if ( p.contains( domains_ids, true ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testBasicTable() { + try { + final BasicTable t0 = new BasicTable(); + if ( t0.getNumberOfColumns() != 0 ) { + return false; + } + if ( t0.getNumberOfRows() != 0 ) { + return false; + } + t0.setValue( 3, 2, "23" ); + t0.setValue( 10, 1, "error" ); + t0.setValue( 10, 1, "110" ); + t0.setValue( 9, 1, "19" ); + t0.setValue( 1, 10, "101" ); + t0.setValue( 10, 10, "1010" ); + t0.setValue( 100, 10, "10100" ); + t0.setValue( 0, 0, "00" ); + if ( !t0.getValue( 3, 2 ).equals( "23" ) ) { + return false; + } + if ( !t0.getValue( 10, 1 ).equals( "110" ) ) { + return false; + } + if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) { + return false; + } + if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) { + return false; + } + if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) { + return false; + } + if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) { + return false; + } + if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) { + return false; + } + if ( t0.getNumberOfColumns() != 101 ) { + return false; + } + if ( t0.getNumberOfRows() != 11 ) { + return false; + } + if ( t0.getValueAsString( 49, 4 ) != null ) { + return false; + } + final String l = ForesterUtil.getLineSeparator(); + final StringBuffer source = new StringBuffer(); + source.append( "" + l ); + source.append( "# 1 1 1 1 1 1 1 1" + l ); + source.append( " 00 01 02 03" + l ); + source.append( " 10 11 12 13 " + l ); + source.append( "20 21 22 23 " + l ); + source.append( " 30 31 32 33" + l ); + source.append( "40 41 42 43" + l ); + source.append( " # 1 1 1 1 1 " + l ); + source.append( "50 51 52 53 54" + l ); + final BasicTable t1 = BasicTableParser.parse( source.toString(), ' ' ); + if ( t1.getNumberOfColumns() != 5 ) { + return false; + } + if ( t1.getNumberOfRows() != 6 ) { + return false; + } + if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) { + return false; + } + if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) { + return false; + } + if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) { + return false; + } + if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) { + return false; + } + final StringBuffer source1 = new StringBuffer(); + source1.append( "" + l ); + source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l ); + source1.append( " 00; 01 ;02;03" + l ); + source1.append( " 10; 11; 12; 13 " + l ); + source1.append( "20; 21; 22; 23 " + l ); + source1.append( " 30; 31; 32; 33" + l ); + source1.append( "40;41;42;43" + l ); + source1.append( " # 1 1 1 1 1 " + l ); + source1.append( ";;;50 ; ;52; 53;;54 " + l ); + final BasicTable t2 = BasicTableParser.parse( source1.toString(), ';' ); + if ( t2.getNumberOfColumns() != 5 ) { + return false; + } + if ( t2.getNumberOfRows() != 6 ) { + return false; + } + if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) { + return false; + } + if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) { return false; } if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) { @@ -1753,7 +2411,7 @@ public final class Test { source2.append( " comment: 1 1 1 1 1 " + l ); source2.append( ";;;50 ; 52; 53;;54 " + l ); final List> tl = BasicTableParser.parse( source2.toString(), - ";", + ';', false, false, "comment:", @@ -1992,7 +2650,7 @@ public final class Test { if ( t8.getHeight() != 15 ) { return false; } - final char[] a9 = new char[] {}; + final char[] a9 = new char[] { 'a' }; final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ]; if ( t9.getHeight() != 0 ) { return false; @@ -2117,6 +2775,129 @@ 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 ); + if ( p0.getRoot().getNumberOfDescendants() != 5 ) { + return false; + } + if ( p0.getNumberOfExternalNodes() != 15625 ) { + return false; + } + final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 ); + if ( p1.getRoot().getNumberOfDescendants() != 10 ) { + return false; + } + if ( p1.getNumberOfExternalNodes() != 100 ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testCreateUriForSeqWeb() { + try { + final PhylogenyNode n = new PhylogenyNode(); + n.setName( "tr|B3RJ64" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) { + return false; + } + n.setName( "B0LM41_HUMAN" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) { + return false; + } + n.setName( "NP_001025424" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) { + return false; + } + n.setName( "_NM_001030253-" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) { + return false; + } + n.setName( "XM_002122186" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) { + return false; + } + n.setName( "dgh_AAA34956_gdg" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) { + return false; + } + n.setName( "AAA34956" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) { + return false; + } + n.setName( "GI:394892" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) { + System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) ); + return false; + } + n.setName( "gi_394892" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) { + System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) ); + return false; + } + n.setName( "gi6335_gi_394892_56635_Gi_43" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) { + System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) ); + return false; + } + n.setName( "P12345" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) { + System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) ); + return false; + } + n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) { + System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) ); + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testDataObjects() { try { final Confidence s0 = new Confidence(); @@ -2910,6 +3691,56 @@ 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 testExternalNodeRelatedMethods() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); @@ -2991,6 +3822,29 @@ public final class Test { for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) { final PhylogenyNode node = iter.next(); } + final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ]; + final PhylogenyNodeIterator iter = t6.iteratorExternalForward(); + if ( !iter.next().getName().equals( "A" ) ) { + return false; + } + if ( !iter.next().getName().equals( "B" ) ) { + return false; + } + if ( !iter.next().getName().equals( "C" ) ) { + return false; + } + if ( !iter.next().getName().equals( "D" ) ) { + return false; + } + if ( !iter.next().getName().equals( "E" ) ) { + return false; + } + if ( !iter.next().getName().equals( "F" ) ) { + return false; + } + if ( iter.hasNext() ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -2999,799 +3853,688 @@ public final class Test { return true; } - private static boolean testGeneralTable() { + private static boolean testExtractSNFromNodeName() { try { - final GeneralTable t0 = new GeneralTable(); - t0.setValue( 3, 2, "23" ); - t0.setValue( 10, 1, "error" ); - t0.setValue( 10, 1, "110" ); - t0.setValue( 9, 1, "19" ); - t0.setValue( 1, 10, "101" ); - t0.setValue( 10, 10, "1010" ); - t0.setValue( 100, 10, "10100" ); - t0.setValue( 0, 0, "00" ); - if ( !t0.getValue( 3, 2 ).equals( "23" ) ) { - return false; - } - if ( !t0.getValue( 10, 1 ).equals( "110" ) ) { - return false; - } - if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) { - return false; - } - if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) { return false; } - if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) { - return false; - } - if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" ) + .equals( "Mus musculus musculus" ) ) { return false; } - if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" ) + .equals( "Mus musculus musculus" ) ) { return false; } - if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) { return false; } - if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" ) + .equals( "Mus musculus" ) ) { return false; } - final GeneralTable t1 = new GeneralTable(); - t1.setValue( "3", "2", "23" ); - t1.setValue( "10", "1", "error" ); - t1.setValue( "10", "1", "110" ); - t1.setValue( "9", "1", "19" ); - t1.setValue( "1", "10", "101" ); - t1.setValue( "10", "10", "1010" ); - t1.setValue( "100", "10", "10100" ); - t1.setValue( "0", "0", "00" ); - t1.setValue( "qwerty", "zxcvbnm", "asdef" ); - if ( !t1.getValue( "3", "2" ).equals( "23" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testExtractTaxonomyCodeFromNodeName() { + try { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !t1.getValue( "10", "1" ).equals( "110" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "ARATH" ) ) { return false; } - if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "ARATH" ) ) { return false; } - if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { return false; } - if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { return false; } - if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testGetDistance() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r", - new NHXParser() )[ 0 ]; - final PhylogenyMethods pm = PhylogenyMethods.getInstance(); - if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "SOYBN" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) { return false; } - if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01", + TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "9YX45" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "RAT" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) + .equals( "PIG" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) { + if ( !ParserUtils + .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) + .equals( "MOUSE" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testExtractUniProtKbProteinSeqIdentifier() { + try { + PhylogenyNode n = new PhylogenyNode(); + n.setName( "tr|B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) { + n.setName( "tr.B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) { + n.setName( "tr=B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) { + n.setName( "tr-B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) { + n.setName( "tr/B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) { + n.setName( "tr\\B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) { + n.setName( "tr_B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r", - new NHXParser() )[ 0 ]; - if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) { + n.setName( " tr|B3RJ64 " ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) { + n.setName( "-tr|B3RJ64-" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) { + n.setName( "-tr=B3RJ64-" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) { + n.setName( "_tr=B3RJ64_" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) { + n.setName( " tr_tr|B3RJ64_sp|123 " ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) { + n.setName( "B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) { + n.setName( "sp|B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) { + n.setName( "sp|B3RJ64C" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { return false; } - if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) { + n.setName( "sp B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) { + n.setName( "sp|B3RJ6X" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { return false; } - if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) { + n.setName( "sp|B3RJ6" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testGetLCA() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh", - new NHXParser() )[ 0 ]; - final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) ); - if ( !A.getName().equals( "A" ) ) { + n.setName( "K1PYK7_CRAGI" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { return false; } - final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) ); - if ( !gh.getName().equals( "gh" ) ) { + n.setName( "K1PYK7_PEA" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) { return false; } - final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) ); - if ( !ab.getName().equals( "ab" ) ) { + n.setName( "K1PYK7_RAT" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) { return false; } - final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) ); - if ( !ab2.getName().equals( "ab" ) ) { + n.setName( "K1PYK7_PIG" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) { return false; } - final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) ); - if ( !gh2.getName().equals( "gh" ) ) { + n.setName( "~K1PYK7_PIG~" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) { return false; } - final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) ); - if ( !gh3.getName().equals( "gh" ) ) { + n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { return false; } - final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) ); - if ( !abc.getName().equals( "abc" ) ) { + n.setName( "K1PYKX_CRAGI" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { return false; } - final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) ); - if ( !abc2.getName().equals( "abc" ) ) { + n.setName( "XXXXX_CRAGI" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) { return false; } - final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) ); - if ( !abcd.getName().equals( "abcd" ) ) { + n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) { return false; } - final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) ); - if ( !abcd2.getName().equals( "abcd" ) ) { + n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { return false; } - final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) ); - if ( !abcdef.getName().equals( "abcdef" ) ) { + n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) { return false; } - final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) ); - if ( !abcdef2.getName().equals( "abcdef" ) ) { + n = new PhylogenyNode(); + org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence(); + seq.setSymbol( "K1PYK7_CRAGI" ); + n.getNodeData().addSequence( seq ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { return false; } - final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) ); - if ( !abcdef3.getName().equals( "abcdef" ) ) { + seq.setSymbol( "tr|B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) ); - if ( !abcdef4.getName().equals( "abcdef" ) ) { + n = new PhylogenyNode(); + seq = new org.forester.phylogeny.data.Sequence(); + seq.setName( "K1PYK7_CRAGI" ); + n.getNodeData().addSequence( seq ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { return false; } - final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) ); - if ( !abcde.getName().equals( "abcde" ) ) { + seq.setName( "tr|B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) ); - if ( !abcde2.getName().equals( "abcde" ) ) { + n = new PhylogenyNode(); + seq = new org.forester.phylogeny.data.Sequence(); + seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) ); + n.getNodeData().addSequence( seq ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) { return false; } - final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) ); - if ( !r.getName().equals( "abcdefgh" ) ) { + n = new PhylogenyNode(); + seq = new org.forester.phylogeny.data.Sequence(); + seq.setAccession( new Accession( "tr|B3RJ64", "?" ) ); + n.getNodeData().addSequence( seq ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) ); - if ( !r2.getName().equals( "abcdefgh" ) ) { + // + n = new PhylogenyNode(); + n.setName( "ACP19736" ); + if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) { return false; } - final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) ); - if ( !r3.getName().equals( "abcdefgh" ) ) { + n = new PhylogenyNode(); + n.setName( "|ACP19736|" ); + if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) { return false; } - final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) ); - if ( !abcde3.getName().equals( "abcde" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testFastaParser() { + try { + if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) { return false; } - final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) ); - if ( !abcde4.getName().equals( "abcde" ) ) { + if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) { return false; } - final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) ); - if ( !ab3.getName().equals( "ab" ) ) { + final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ); + if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) { return false; } - final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) ); - if ( !ab4.getName().equals( "ab" ) ) { + if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) { return false; } - final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ]; - final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) ); - if ( !cd.getName().equals( "cd" ) ) { + if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) { return false; } - final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) ); - if ( !cd2.getName().equals( "cd" ) ) { + if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) { return false; } - final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) ); - if ( !cde.getName().equals( "cde" ) ) { + if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) { return false; } - final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) ); - if ( !cde2.getName().equals( "cde" ) ) { + if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) { return false; } - final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) ); - if ( !cdef.getName().equals( "cdef" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testGeneralMsaParser() { + try { + final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n"; + final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) ); + final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n"; + final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) ); + final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n"; + final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) ); + final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n"; + final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) ); + if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { return false; } - final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) ); - if ( !cdef2.getName().equals( "cdef" ) ) { + if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { return false; } - final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) ); - if ( !cdef3.getName().equals( "cdef" ) ) { + if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) { return false; } - final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) ); - if ( !rt.getName().equals( "r" ) ) { + if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) { return false; } - final Phylogeny p3 = factory - .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", - new NHXParser() )[ 0 ]; - final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) ); - if ( !bc_3.getName().equals( "bc" ) ) { + if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { return false; } - final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) ); - if ( !ac_3.getName().equals( "abc" ) ) { + if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { return false; } - final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) ); - if ( !ad_3.getName().equals( "abcde" ) ) { + if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) { return false; } - final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) ); - if ( !af_3.getName().equals( "abcdef" ) ) { + if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) { return false; } - final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) ); - if ( !ag_3.getName().equals( "" ) ) { + if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { return false; } - if ( !ag_3.isRoot() ) { + if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { return false; } - final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) ); - if ( !al_3.getName().equals( "" ) ) { + if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) { return false; } - if ( !al_3.isRoot() ) { + if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) { return false; } - final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) ); - if ( !kl_3.getName().equals( "" ) ) { + final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) ); + if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) { return false; } - if ( !kl_3.isRoot() ) { + if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) { return false; } - final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) ); - if ( !fl_3.getName().equals( "" ) ) { + if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { return false; } - if ( !fl_3.isRoot() ) { + final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) ); + if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) { return false; } - final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) ); - if ( !gk_3.getName().equals( "ghijk" ) ) { + if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) { return false; } - final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ]; - final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) ); - if ( !r_4.getName().equals( "r" ) ) { + if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) { return false; } - final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ]; - final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) ); - if ( !r_5.getName().equals( "root" ) ) { + final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ); + if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) { return false; } - final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ]; - final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) ); - if ( !r_6.getName().equals( "rot" ) ) { + if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) { return false; } - final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ]; - final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) ); - if ( !r_7.getName().equals( "rott" ) ) { + if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { return false; } } catch ( final Exception e ) { - e.printStackTrace( System.out ); + e.printStackTrace(); return false; } return true; } - private static boolean testGetLCA2() { + private static boolean testGeneralTable() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh", - new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p1 ); - final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "A" ) ); - if ( !A.getName().equals( "A" ) ) { - return false; - } - final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ), - p1.getNode( "gh" ) ); - if ( !gh.getName().equals( "gh" ) ) { - return false; - } - final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "B" ) ); - if ( !ab.getName().equals( "ab" ) ) { - return false; - } - final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ), - p1.getNode( "A" ) ); - if ( !ab2.getName().equals( "ab" ) ) { + final GeneralTable t0 = new GeneralTable(); + t0.setValue( 3, 2, "23" ); + t0.setValue( 10, 1, "error" ); + t0.setValue( 10, 1, "110" ); + t0.setValue( 9, 1, "19" ); + t0.setValue( 1, 10, "101" ); + t0.setValue( 10, 10, "1010" ); + t0.setValue( 100, 10, "10100" ); + t0.setValue( 0, 0, "00" ); + if ( !t0.getValue( 3, 2 ).equals( "23" ) ) { return false; } - final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ), - p1.getNode( "G" ) ); - if ( !gh2.getName().equals( "gh" ) ) { + if ( !t0.getValue( 10, 1 ).equals( "110" ) ) { return false; } - final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ), - p1.getNode( "H" ) ); - if ( !gh3.getName().equals( "gh" ) ) { + if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) { return false; } - final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ), - p1.getNode( "A" ) ); - if ( !abc.getName().equals( "abc" ) ) { + if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) { return false; } - final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "C" ) ); - if ( !abc2.getName().equals( "abc" ) ) { + if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) { return false; } - final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "D" ) ); - if ( !abcd.getName().equals( "abcd" ) ) { + if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) { return false; } - final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ), - p1.getNode( "A" ) ); - if ( !abcd2.getName().equals( "abcd" ) ) { + if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) { return false; } - final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "F" ) ); - if ( !abcdef.getName().equals( "abcdef" ) ) { + if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) { return false; } - final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ), - p1.getNode( "A" ) ); - if ( !abcdef2.getName().equals( "abcdef" ) ) { + if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) { return false; } - final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ), - p1.getNode( "F" ) ); - if ( !abcdef3.getName().equals( "abcdef" ) ) { + final GeneralTable t1 = new GeneralTable(); + t1.setValue( "3", "2", "23" ); + t1.setValue( "10", "1", "error" ); + t1.setValue( "10", "1", "110" ); + t1.setValue( "9", "1", "19" ); + t1.setValue( "1", "10", "101" ); + t1.setValue( "10", "10", "1010" ); + t1.setValue( "100", "10", "10100" ); + t1.setValue( "0", "0", "00" ); + t1.setValue( "qwerty", "zxcvbnm", "asdef" ); + if ( !t1.getValue( "3", "2" ).equals( "23" ) ) { return false; } - final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ), - p1.getNode( "ab" ) ); - if ( !abcdef4.getName().equals( "abcdef" ) ) { + if ( !t1.getValue( "10", "1" ).equals( "110" ) ) { return false; } - final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "E" ) ); - if ( !abcde.getName().equals( "abcde" ) ) { + if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) { return false; } - final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ), - p1.getNode( "A" ) ); - if ( !abcde2.getName().equals( "abcde" ) ) { + if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) { return false; } - final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ), - p1.getNode( "abcdefgh" ) ); - if ( !r.getName().equals( "abcdefgh" ) ) { + if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) { return false; } - final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "H" ) ); - if ( !r2.getName().equals( "abcdefgh" ) ) { + if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) { return false; } - final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ), - p1.getNode( "A" ) ); - if ( !r3.getName().equals( "abcdefgh" ) ) { + if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) { return false; } - final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ), - p1.getNode( "abcde" ) ); - if ( !abcde3.getName().equals( "abcde" ) ) { + if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) { return false; } - final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ), - p1.getNode( "E" ) ); - if ( !abcde4.getName().equals( "abcde" ) ) { + if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) { return false; } - final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ), - p1.getNode( "B" ) ); - if ( !ab3.getName().equals( "ab" ) ) { + if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) { return false; } - final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ), - p1.getNode( "ab" ) ); - if ( !ab4.getName().equals( "ab" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testGetDistance() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r", + new NHXParser() )[ 0 ]; + if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) { return false; } - final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p2 ); - final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), - p2.getNode( "d" ) ); - if ( !cd.getName().equals( "cd" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) { return false; } - final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ), - p2.getNode( "c" ) ); - if ( !cd2.getName().equals( "cd" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) { return false; } - final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), - p2.getNode( "e" ) ); - if ( !cde.getName().equals( "cde" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) { return false; } - final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ), - p2.getNode( "c" ) ); - if ( !cde2.getName().equals( "cde" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) { return false; } - final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), - p2.getNode( "f" ) ); - if ( !cdef.getName().equals( "cdef" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) { return false; } - final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ), - p2.getNode( "f" ) ); - if ( !cdef2.getName().equals( "cdef" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) { return false; } - final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ), - p2.getNode( "d" ) ); - if ( !cdef3.getName().equals( "cdef" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) { return false; } - final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), - p2.getNode( "a" ) ); - if ( !rt.getName().equals( "r" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) { return false; } - final Phylogeny p3 = factory - .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", - new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p3 ); - final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ), - p3.getNode( "c" ) ); - if ( !bc_3.getName().equals( "bc" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) { return false; } - final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "c" ) ); - if ( !ac_3.getName().equals( "abc" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) { return false; } - final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "d" ) ); - if ( !ad_3.getName().equals( "abcde" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) { return false; } - final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "f" ) ); - if ( !af_3.getName().equals( "abcdef" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) { return false; } - final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "g" ) ); - if ( !ag_3.getName().equals( "" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) { return false; } - if ( !ag_3.isRoot() ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) { return false; } - final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "l" ) ); - if ( !al_3.getName().equals( "" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) { return false; } - if ( !al_3.isRoot() ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) { return false; } - final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ), - p3.getNode( "l" ) ); - if ( !kl_3.getName().equals( "" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) { return false; } - if ( !kl_3.isRoot() ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) { return false; } - final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ), - p3.getNode( "l" ) ); - if ( !fl_3.getName().equals( "" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) { return false; } - if ( !fl_3.isRoot() ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) { return false; } - final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ), - p3.getNode( "k" ) ); - if ( !gk_3.getName().equals( "ghijk" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) { return false; } - final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p4 ); - final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ), - p4.getNode( "c" ) ); - if ( !r_4.getName().equals( "r" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) { return false; } - final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p5 ); - final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ), - p5.getNode( "c" ) ); - if ( !r_5.getName().equals( "root" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) { return false; } - final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p6 ); - final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ), - p6.getNode( "a" ) ); - if ( !r_6.getName().equals( "rot" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) { return false; } - final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p7 ); - final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ), - p7.getNode( "e" ) ); - if ( !r_7.getName().equals( "rott" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) { return false; } - final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), - p7.getNode( "a" ) ); - if ( !r_71.getName().equals( "rott" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) { return false; } - final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), - p7.getNode( "rott" ) ); - if ( !r_72.getName().equals( "rott" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) { return false; } - final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ), - p7.getNode( "a" ) ); - if ( !r_73.getName().equals( "rott" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) { return false; } - final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ), - p7.getNode( "rott" ) ); - if ( !r_74.getName().equals( "rott" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) { return false; } - final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), - p7.getNode( "e" ) ); - if ( !r_75.getName().equals( "e" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testHmmscanOutputParser() { - final String test_dir = Test.PATH_TO_TEST_DATA; - try { - final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); - parser1.parse(); - final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); - final List proteins = parser2.parse(); - if ( parser2.getProteinsEncountered() != 4 ) { + final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r", + new NHXParser() )[ 0 ]; + if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) { return false; } - if ( proteins.size() != 4 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) { return false; } - if ( parser2.getDomainsEncountered() != 69 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) { return false; } - if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) { return false; } - if ( parser2.getDomainsIgnoredDueToEval() != 0 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) { return false; } - final Protein p1 = proteins.get( 0 ); - if ( p1.getNumberOfProteinDomains() != 15 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) { return false; } - if ( p1.getLength() != 850 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) { return false; } - final Protein p2 = proteins.get( 1 ); - if ( p2.getNumberOfProteinDomains() != 51 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) { return false; } - if ( p2.getLength() != 1291 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) { return false; } - final Protein p3 = proteins.get( 2 ); - if ( p3.getNumberOfProteinDomains() != 2 ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) { return false; } - final Protein p4 = proteins.get( 3 ); - if ( p4.getNumberOfProteinDomains() != 1 ) { - return false; - } - if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) { - return false; - } - if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) { - return false; - } - if ( p4.getProteinDomain( 0 ).getTo() != 395 ) { - return false; - } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) { - return false; - } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) { - return false; - } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) { - return false; - } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) { - return false; - } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) { - return false; - } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) { return false; } } @@ -3802,196 +4545,205 @@ public final class Test { return true; } - private static boolean testLastExternalNodeMethods() { + private static boolean testGetLCA() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', }; - final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ]; - final PhylogenyNode n1 = t0.getNode( "A" ); - if ( n1.isLastExternalNode() ) { + final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh", + new NHXParser() )[ 0 ]; + final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) ); + if ( !A.getName().equals( "A" ) ) { return false; } - final PhylogenyNode n2 = t0.getNode( "B" ); - if ( n2.isLastExternalNode() ) { + final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) ); + if ( !gh.getName().equals( "gh" ) ) { return false; } - final PhylogenyNode n3 = t0.getNode( "C" ); - if ( n3.isLastExternalNode() ) { + final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) ); + if ( !ab.getName().equals( "ab" ) ) { return false; } - final PhylogenyNode n4 = t0.getNode( "D" ); - if ( !n4.isLastExternalNode() ) { + final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) ); + if ( !ab2.getName().equals( "ab" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testLevelOrderIterator() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ]; - PhylogenyNodeIterator it0; - for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) { - it0.next(); - } - for( it0.reset(); it0.hasNext(); ) { - it0.next(); - } - final PhylogenyNodeIterator it = t0.iteratorLevelOrder(); - if ( !it.next().getName().equals( "r" ) ) { + final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) ); + if ( !gh2.getName().equals( "gh" ) ) { return false; } - if ( !it.next().getName().equals( "ab" ) ) { + final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) ); + if ( !gh3.getName().equals( "gh" ) ) { return false; } - if ( !it.next().getName().equals( "cd" ) ) { + final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) ); + if ( !abc.getName().equals( "abc" ) ) { return false; } - if ( !it.next().getName().equals( "A" ) ) { + final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) ); + if ( !abc2.getName().equals( "abc" ) ) { return false; } - if ( !it.next().getName().equals( "B" ) ) { + final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) ); + if ( !abcd.getName().equals( "abcd" ) ) { return false; } - if ( !it.next().getName().equals( "C" ) ) { + final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) ); + if ( !abcd2.getName().equals( "abcd" ) ) { return false; } - if ( !it.next().getName().equals( "D" ) ) { + final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) ); + if ( !abcdef.getName().equals( "abcdef" ) ) { return false; } - if ( it.hasNext() ) { + final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) ); + if ( !abcdef2.getName().equals( "abcdef" ) ) { return false; } - final Phylogeny t2 = factory.create( "(((1,2,(a,(X,Y,Z)b)3,4,5,6)A,B,C)abc,(D,E,(f1,(f21)f2,f3)F,G)defg)r", - new NHXParser() )[ 0 ]; - PhylogenyNodeIterator it2; - for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) { - it2.next(); - } - for( it2.reset(); it2.hasNext(); ) { - it2.next(); - } - final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder(); - if ( !it3.next().getName().equals( "r" ) ) { + final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) ); + if ( !abcdef3.getName().equals( "abcdef" ) ) { return false; } - if ( !it3.next().getName().equals( "abc" ) ) { + final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) ); + if ( !abcdef4.getName().equals( "abcdef" ) ) { return false; } - if ( !it3.next().getName().equals( "defg" ) ) { + final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) ); + if ( !abcde.getName().equals( "abcde" ) ) { return false; } - if ( !it3.next().getName().equals( "A" ) ) { + final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) ); + if ( !abcde2.getName().equals( "abcde" ) ) { return false; } - if ( !it3.next().getName().equals( "B" ) ) { + final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) ); + if ( !r.getName().equals( "abcdefgh" ) ) { return false; } - if ( !it3.next().getName().equals( "C" ) ) { + final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) ); + if ( !r2.getName().equals( "abcdefgh" ) ) { return false; } - if ( !it3.next().getName().equals( "D" ) ) { + final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) ); + if ( !r3.getName().equals( "abcdefgh" ) ) { return false; } - if ( !it3.next().getName().equals( "E" ) ) { + final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) ); + if ( !abcde3.getName().equals( "abcde" ) ) { return false; } - if ( !it3.next().getName().equals( "F" ) ) { + final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) ); + if ( !abcde4.getName().equals( "abcde" ) ) { return false; } - if ( !it3.next().getName().equals( "G" ) ) { + final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) ); + if ( !ab3.getName().equals( "ab" ) ) { return false; } - if ( !it3.next().getName().equals( "1" ) ) { + final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) ); + if ( !ab4.getName().equals( "ab" ) ) { return false; } - if ( !it3.next().getName().equals( "2" ) ) { + final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ]; + final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) ); + if ( !cd.getName().equals( "cd" ) ) { return false; } - if ( !it3.next().getName().equals( "3" ) ) { + final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) ); + if ( !cd2.getName().equals( "cd" ) ) { return false; } - if ( !it3.next().getName().equals( "4" ) ) { + final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) ); + if ( !cde.getName().equals( "cde" ) ) { return false; } - if ( !it3.next().getName().equals( "5" ) ) { + final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) ); + if ( !cde2.getName().equals( "cde" ) ) { return false; } - if ( !it3.next().getName().equals( "6" ) ) { + final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) ); + if ( !cdef.getName().equals( "cdef" ) ) { return false; } - if ( !it3.next().getName().equals( "f1" ) ) { + final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) ); + if ( !cdef2.getName().equals( "cdef" ) ) { return false; } - if ( !it3.next().getName().equals( "f2" ) ) { + final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) ); + if ( !cdef3.getName().equals( "cdef" ) ) { return false; } - if ( !it3.next().getName().equals( "f3" ) ) { + final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) ); + if ( !rt.getName().equals( "r" ) ) { return false; } - if ( !it3.next().getName().equals( "a" ) ) { + final Phylogeny p3 = factory + .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", + new NHXParser() )[ 0 ]; + final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) ); + if ( !bc_3.getName().equals( "bc" ) ) { return false; } - if ( !it3.next().getName().equals( "b" ) ) { + final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) ); + if ( !ac_3.getName().equals( "abc" ) ) { return false; } - if ( !it3.next().getName().equals( "f21" ) ) { + final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) ); + if ( !ad_3.getName().equals( "abcde" ) ) { return false; } - if ( !it3.next().getName().equals( "X" ) ) { + final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) ); + if ( !af_3.getName().equals( "abcdef" ) ) { return false; } - if ( !it3.next().getName().equals( "Y" ) ) { + final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) ); + if ( !ag_3.getName().equals( "" ) ) { return false; } - if ( !it3.next().getName().equals( "Z" ) ) { + if ( !ag_3.isRoot() ) { return false; } - if ( it3.hasNext() ) { + final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) ); + if ( !al_3.getName().equals( "" ) ) { return false; } - final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ]; - PhylogenyNodeIterator it4; - for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) { - it4.next(); - } - for( it4.reset(); it4.hasNext(); ) { - it4.next(); + if ( !al_3.isRoot() ) { + return false; } - final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder(); - if ( !it5.next().getName().equals( "r" ) ) { + final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) ); + if ( !kl_3.getName().equals( "" ) ) { return false; } - if ( !it5.next().getName().equals( "A" ) ) { + if ( !kl_3.isRoot() ) { return false; } - if ( !it5.next().getName().equals( "B" ) ) { + final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) ); + if ( !fl_3.getName().equals( "" ) ) { return false; } - if ( !it5.next().getName().equals( "C" ) ) { + if ( !fl_3.isRoot() ) { return false; } - if ( !it5.next().getName().equals( "D" ) ) { + final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) ); + if ( !gk_3.getName().equals( "ghijk" ) ) { return false; } - final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ]; - PhylogenyNodeIterator it6; - for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) { - it6.next(); + final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ]; + final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) ); + if ( !r_4.getName().equals( "r" ) ) { + return false; } - for( it6.reset(); it6.hasNext(); ) { - it6.next(); + final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ]; + final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) ); + if ( !r_5.getName().equals( "root" ) ) { + return false; } - final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder(); - if ( !it7.next().getName().equals( "A" ) ) { + final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ]; + final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) ); + if ( !r_6.getName().equals( "rot" ) ) { return false; } - if ( it.hasNext() ) { + final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ]; + final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) ); + if ( !r_7.getName().equals( "rott" ) ) { return false; } } @@ -4002,380 +4754,434 @@ public final class Test { return true; } - private static boolean testMidpointrooting() { + private static boolean testGetLCA2() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:4)CD:3[&&NHX:B=10])ABCD:0.5", - new NHXParser() )[ 0 ]; - if ( !t1.isRooted() ) { + final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p_a ); + final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ), + p_a.getNode( "a" ) ); + if ( !p_a_1.getName().equals( "a" ) ) { return false; } - PhylogenyMethods.midpointRoot( t1 ); - if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p_b ); + final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ), + p_b.getNode( "a" ) ); + if ( !p_b_1.getName().equals( "b" ) ) { return false; } - if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { + final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ), + p_b.getNode( "b" ) ); + if ( !p_b_2.getName().equals( "b" ) ) { return false; } - if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { + final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p_c ); + final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ), + p_c.getNode( "a" ) ); + if ( !p_c_1.getName().equals( "b" ) ) { return false; } - if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) { + final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ), + p_c.getNode( "c" ) ); + if ( !p_c_2.getName().equals( "c" ) ) { + System.out.println( p_c_2.getName() ); + System.exit( -1 ); return false; } - if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) { + final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ), + p_c.getNode( "b" ) ); + if ( !p_c_3.getName().equals( "b" ) ) { return false; } - if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) { + final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ), + p_c.getNode( "a" ) ); + if ( !p_c_4.getName().equals( "c" ) ) { return false; } - t1.reRoot( t1.getNode( "A" ) ); - PhylogenyMethods.midpointRoot( t1 ); - if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh", + new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p1 ); + final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "A" ) ); + if ( !A.getName().equals( "A" ) ) { return false; } - if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { + final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ), + p1.getNode( "gh" ) ); + if ( !gh.getName().equals( "gh" ) ) { return false; } - if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { - return false; + final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "B" ) ); + if ( !ab.getName().equals( "ab" ) ) { + return false; } - if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) { + final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ), + p1.getNode( "A" ) ); + if ( !ab2.getName().equals( "ab" ) ) { return false; } - if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) { + final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ), + p1.getNode( "G" ) ); + if ( !gh2.getName().equals( "gh" ) ) { return false; } - if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) { + final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ), + p1.getNode( "H" ) ); + if ( !gh3.getName().equals( "gh" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNexusCharactersParsing() { - try { - final NexusCharactersParser parser = new NexusCharactersParser(); - parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) ); - parser.parse(); - String[] labels = parser.getCharStateLabels(); - if ( labels.length != 7 ) { + final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ), + p1.getNode( "A" ) ); + if ( !abc.getName().equals( "abc" ) ) { return false; } - if ( !labels[ 0 ].equals( "14-3-3" ) ) { + final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "C" ) ); + if ( !abc2.getName().equals( "abc" ) ) { return false; } - if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { + final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "D" ) ); + if ( !abcd.getName().equals( "abcd" ) ) { return false; } - if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { + final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ), + p1.getNode( "A" ) ); + if ( !abcd2.getName().equals( "abcd" ) ) { return false; } - if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { + final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "F" ) ); + if ( !abcdef.getName().equals( "abcdef" ) ) { return false; } - if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { + final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ), + p1.getNode( "A" ) ); + if ( !abcdef2.getName().equals( "abcdef" ) ) { return false; } - if ( !labels[ 5 ].equals( "3-HAO" ) ) { + final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ), + p1.getNode( "F" ) ); + if ( !abcdef3.getName().equals( "abcdef" ) ) { return false; } - if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { + final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ), + p1.getNode( "ab" ) ); + if ( !abcdef4.getName().equals( "abcdef" ) ) { return false; } - parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) ); - parser.parse(); - labels = parser.getCharStateLabels(); - if ( labels.length != 7 ) { + final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "E" ) ); + if ( !abcde.getName().equals( "abcde" ) ) { return false; } - if ( !labels[ 0 ].equals( "14-3-3" ) ) { + final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ), + p1.getNode( "A" ) ); + if ( !abcde2.getName().equals( "abcde" ) ) { return false; } - if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { + final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ), + p1.getNode( "abcdefgh" ) ); + if ( !r.getName().equals( "abcdefgh" ) ) { return false; } - if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { + final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "H" ) ); + if ( !r2.getName().equals( "abcdefgh" ) ) { return false; } - if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { + final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ), + p1.getNode( "A" ) ); + if ( !r3.getName().equals( "abcdefgh" ) ) { return false; } - if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { + final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ), + p1.getNode( "abcde" ) ); + if ( !abcde3.getName().equals( "abcde" ) ) { return false; } - if ( !labels[ 5 ].equals( "3-HAO" ) ) { + final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ), + p1.getNode( "E" ) ); + if ( !abcde4.getName().equals( "abcde" ) ) { return false; } - if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { + final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ), + p1.getNode( "B" ) ); + if ( !ab3.getName().equals( "ab" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNexusMatrixParsing() { - try { - final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser(); - parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) ); - parser.parse(); - final CharacterStateMatrix m = parser.getMatrix(); - if ( m.getNumberOfCharacters() != 9 ) { + final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ), + p1.getNode( "ab" ) ); + if ( !ab4.getName().equals( "ab" ) ) { return false; } - if ( m.getNumberOfIdentifiers() != 5 ) { + final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p2 ); + final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), + p2.getNode( "d" ) ); + if ( !cd.getName().equals( "cd" ) ) { return false; } - if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) { + final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ), + p2.getNode( "c" ) ); + if ( !cd2.getName().equals( "cd" ) ) { return false; } - if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) { + final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), + p2.getNode( "e" ) ); + if ( !cde.getName().equals( "cde" ) ) { return false; } - if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) { + final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ), + p2.getNode( "c" ) ); + if ( !cde2.getName().equals( "cde" ) ) { return false; } - if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) { + final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), + p2.getNode( "f" ) ); + if ( !cdef.getName().equals( "cdef" ) ) { return false; } - if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) { + final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ), + p2.getNode( "f" ) ); + if ( !cdef2.getName().equals( "cdef" ) ) { return false; } - if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) { + final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ), + p2.getNode( "d" ) ); + if ( !cdef3.getName().equals( "cdef" ) ) { return false; } - if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) { + final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), + p2.getNode( "a" ) ); + if ( !rt.getName().equals( "r" ) ) { return false; } - // if ( labels.length != 7 ) { - // return false; - // } - // if ( !labels[ 0 ].equals( "14-3-3" ) ) { - // return false; - // } - // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { - // return false; - // } - // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { - // return false; - // } - // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { - // return false; - // } - // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { - // return false; - // } - // if ( !labels[ 5 ].equals( "3-HAO" ) ) { - // return false; - // } - // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { - // return false; - // } - // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) ); - // parser.parse(); - // labels = parser.getCharStateLabels(); - // if ( labels.length != 7 ) { - // return false; - // } - // if ( !labels[ 0 ].equals( "14-3-3" ) ) { - // return false; - // } - // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { - // return false; - // } - // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { - // return false; - // } - // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { - // return false; - // } - // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { - // return false; - // } - // if ( !labels[ 5 ].equals( "3-HAO" ) ) { - // return false; - // } - // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { - // return false; - // } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNexusTreeParsing() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); - Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser ); - if ( phylogenies.length != 1 ) { + final Phylogeny p3 = factory + .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", + new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p3 ); + final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ), + p3.getNode( "c" ) ); + if ( !bc_3.getName().equals( "bc" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) { + final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "c" ) ); + if ( !ac_3.getName().equals( "abc" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "" ) ) { + final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "d" ) ); + if ( !ad_3.getName().equals( "abcde" ) ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser ); - if ( phylogenies.length != 1 ) { + final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "f" ) ); + if ( !af_3.getName().equals( "abcdef" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) { + final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "g" ) ); + if ( !ag_3.getName().equals( "" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "name" ) ) { + if ( !ag_3.isRoot() ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser ); - if ( phylogenies.length != 1 ) { + final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "l" ) ); + if ( !al_3.getName().equals( "" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + if ( !al_3.isRoot() ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "" ) ) { + final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ), + p3.getNode( "l" ) ); + if ( !kl_3.getName().equals( "" ) ) { return false; } - if ( phylogenies[ 0 ].isRooted() ) { + if ( !kl_3.isRoot() ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser ); - if ( phylogenies.length != 18 ) { - return false; - } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) { - return false; - } - if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) { - return false; - } - if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) { - return false; - } - if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) { - return false; - } - if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ), + p3.getNode( "l" ) ); + if ( !fl_3.getName().equals( "" ) ) { return false; } - if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) { + if ( !fl_3.isRoot() ) { return false; } - if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) { + final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ), + p3.getNode( "k" ) ); + if ( !gk_3.getName().equals( "ghijk" ) ) { return false; } - if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) { + final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p4 ); + final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ), + p4.getNode( "c" ) ); + if ( !r_4.getName().equals( "r" ) ) { return false; } - if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) { + final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p5 ); + final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ), + p5.getNode( "c" ) ); + if ( !r_5.getName().equals( "root" ) ) { return false; } - if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) { + final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p6 ); + final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ), + p6.getNode( "a" ) ); + if ( !r_6.getName().equals( "rot" ) ) { return false; } - if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) { + final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ]; + PhylogenyMethods.preOrderReId( p7 ); + final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ), + p7.getNode( "e" ) ); + if ( !r_7.getName().equals( "rott" ) ) { return false; } - if ( phylogenies[ 8 ].isRooted() ) { + final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), + p7.getNode( "a" ) ); + if ( !r_71.getName().equals( "rott" ) ) { return false; } - if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) { + final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), + p7.getNode( "rott" ) ); + if ( !r_72.getName().equals( "rott" ) ) { return false; } - if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) { + final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ), + p7.getNode( "a" ) ); + if ( !r_73.getName().equals( "rott" ) ) { return false; } - if ( !phylogenies[ 9 ].isRooted() ) { + final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ), + p7.getNode( "rott" ) ); + if ( !r_74.getName().equals( "rott" ) ) { return false; } - if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) { + final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), + p7.getNode( "e" ) ); + if ( !r_75.getName().equals( "e" ) ) { return false; } - if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testHmmscanOutputParser() { + final String test_dir = Test.PATH_TO_TEST_DATA; + try { + final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir + + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); + parser1.parse(); + final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir + + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); + final List proteins = parser2.parse(); + if ( parser2.getProteinsEncountered() != 4 ) { return false; } - if ( !phylogenies[ 10 ].isRooted() ) { + if ( proteins.size() != 4 ) { return false; } - if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) { + if ( parser2.getDomainsEncountered() != 69 ) { return false; } - if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) { + if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) { return false; } - if ( phylogenies[ 11 ].isRooted() ) { + if ( parser2.getDomainsIgnoredDueToEval() != 0 ) { return false; } - if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) { + final Protein p1 = proteins.get( 0 ); + if ( p1.getNumberOfProteinDomains() != 15 ) { return false; } - if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) { + if ( p1.getLength() != 850 ) { return false; } - if ( !phylogenies[ 12 ].isRooted() ) { + final Protein p2 = proteins.get( 1 ); + if ( p2.getNumberOfProteinDomains() != 51 ) { return false; } - if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) { + if ( p2.getLength() != 1291 ) { return false; } - if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) { + final Protein p3 = proteins.get( 2 ); + if ( p3.getNumberOfProteinDomains() != 2 ) { return false; } - if ( !phylogenies[ 13 ].isRooted() ) { + final Protein p4 = proteins.get( 3 ); + if ( p4.getNumberOfProteinDomains() != 1 ) { return false; } - if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) { + if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) { return false; } - if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) { + if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) { return false; } - if ( !phylogenies[ 14 ].isRooted() ) { + if ( p4.getProteinDomain( 0 ).getTo() != 395 ) { return false; } - if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) { + if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) { return false; } - if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) { + if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) { return false; } - if ( phylogenies[ 15 ].isRooted() ) { + if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) { return false; } - if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) { + if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) { return false; } - if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) { + if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) { return false; } - if ( !phylogenies[ 16 ].isRooted() ) { + if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) { return false; } - if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testLastExternalNodeMethods() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', }; + final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ]; + final PhylogenyNode n1 = t0.getNode( "A" ); + if ( n1.isLastExternalNode() ) { return false; } - if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) { + final PhylogenyNode n2 = t0.getNode( "B" ); + if ( n2.isLastExternalNode() ) { return false; } - if ( phylogenies[ 17 ].isRooted() ) { + final PhylogenyNode n3 = t0.getNode( "C" ); + if ( n3.isLastExternalNode() ) { return false; } - if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) { + final PhylogenyNode n4 = t0.getNode( "D" ); + if ( !n4.isLastExternalNode() ) { return false; } } @@ -4386,152 +5192,167 @@ public final class Test { return true; } - private static boolean testNexusTreeParsingTranslating() { + private static boolean testLevelOrderIterator() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); - Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser ); - if ( phylogenies.length != 1 ) { - return false; + final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ]; + PhylogenyNodeIterator it0; + for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) { + it0.next(); } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { - return false; + for( it0.reset(); it0.hasNext(); ) { + it0.next(); } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + final PhylogenyNodeIterator it = t0.iteratorLevelOrder(); + if ( !it.next().getName().equals( "r" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !it.next().getName().equals( "ab" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !it.next().getName().equals( "cd" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( !it.next().getName().equals( "A" ) ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser ); - if ( phylogenies.length != 3 ) { + if ( !it.next().getName().equals( "B" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + if ( !it.next().getName().equals( "C" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( !it.next().getName().equals( "D" ) ) { return false; } - if ( phylogenies[ 0 ].isRooted() ) { + if ( it.hasNext() ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { - return false; + final Phylogeny t2 = factory.create( "(((1,2,(a,(X,Y,Z)b)3,4,5,6)A,B,C)abc,(D,E,(f1,(f21)f2,f3)F,G)defg)r", + new NHXParser() )[ 0 ]; + PhylogenyNodeIterator it2; + for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) { + it2.next(); } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { - return false; + for( it2.reset(); it2.hasNext(); ) { + it2.next(); } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder(); + if ( !it3.next().getName().equals( "r" ) ) { return false; } - if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "abc" ) ) { return false; } - if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { + if ( !it3.next().getName().equals( "defg" ) ) { return false; } - if ( phylogenies[ 1 ].isRooted() ) { + if ( !it3.next().getName().equals( "A" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !it3.next().getName().equals( "B" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !it3.next().getName().equals( "C" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( !it3.next().getName().equals( "D" ) ) { return false; } - if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "E" ) ) { return false; } - if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { + if ( !it3.next().getName().equals( "F" ) ) { return false; } - if ( !phylogenies[ 2 ].isRooted() ) { + if ( !it3.next().getName().equals( "G" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !it3.next().getName().equals( "1" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !it3.next().getName().equals( "2" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( !it3.next().getName().equals( "3" ) ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser ); - if ( phylogenies.length != 3 ) { + if ( !it3.next().getName().equals( "4" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "5" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( !it3.next().getName().equals( "6" ) ) { return false; } - if ( phylogenies[ 0 ].isRooted() ) { + if ( !it3.next().getName().equals( "f1" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !it3.next().getName().equals( "f2" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !it3.next().getName().equals( "f3" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( !it3.next().getName().equals( "a" ) ) { return false; } - if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "b" ) ) { return false; } - if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { + if ( !it3.next().getName().equals( "f21" ) ) { return false; } - if ( phylogenies[ 1 ].isRooted() ) { + if ( !it3.next().getName().equals( "X" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !it3.next().getName().equals( "Y" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !it3.next().getName().equals( "Z" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( it3.hasNext() ) { return false; } - if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ]; + PhylogenyNodeIterator it4; + for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) { + it4.next(); + } + for( it4.reset(); it4.hasNext(); ) { + it4.next(); + } + final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder(); + if ( !it5.next().getName().equals( "r" ) ) { return false; } - if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { + if ( !it5.next().getName().equals( "A" ) ) { return false; } - if ( !phylogenies[ 2 ].isRooted() ) { + if ( !it5.next().getName().equals( "B" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !it5.next().getName().equals( "C" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !it5.next().getName().equals( "D" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ]; + PhylogenyNodeIterator it6; + for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) { + it6.next(); + } + for( it6.reset(); it6.hasNext(); ) { + it6.next(); + } + final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder(); + if ( !it7.next().getName().equals( "A" ) ) { + return false; + } + if ( it.hasNext() ) { return false; } } @@ -4542,741 +5363,840 @@ public final class Test { return true; } - private static boolean testNHParsing() { + private static boolean testMafft( final String path ) { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ]; - if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) { + final List opts = new ArrayList(); + opts.add( "--maxiterate" ); + opts.add( "1000" ); + opts.add( "--localpair" ); + opts.add( "--quiet" ); + Msa msa = null; + final MsaInferrer mafft = Mafft.createInstance( path ); + msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts ); + if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) { return false; } - final NHXParser nhxp = new NHXParser(); - nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO ); - nhxp.setReplaceUnderscores( true ); - final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ]; - if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) { + if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) { return false; } - if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testMidpointrooting() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ]; + PhylogenyMethods.midpointRoot( t0 ); + if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) { return false; } - final Phylogeny p1b = factory - .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ", - new NHXParser() )[ 0 ]; - if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) { + if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) { return false; } - if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) { + if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(), + 1 ) ) { return false; } - final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ]; - final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ]; - final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ]; - final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ]; - final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() ); - final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() ); - final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() ); - final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() ); - final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() ); - final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() ); - final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;" - + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " - + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", - new NHXParser() ); - if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) { + final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:4)CD:3[&&NHX:B=10])ABCD:0.5", + new NHXParser() )[ 0 ]; + if ( !t1.isRooted() ) { return false; } - if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) { + PhylogenyMethods.midpointRoot( t1 ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { return false; } - if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) { + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { return false; } - if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) { + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { return false; } - final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() ); - final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() ); - final String p16_S = "((A,B),C)"; - final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() ); - if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) { + if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) { return false; } - final String p17_S = "(C,(A,B))"; - final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() ); - if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) { + if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) { return false; } - final String p18_S = "((A,B),(C,D))"; - final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() ); - if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) { + if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) { return false; } - final String p19_S = "(((A,B),C),D)"; - final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() ); - if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) { + t1.reRoot( t1.getNode( "A" ) ); + PhylogenyMethods.midpointRoot( t1 ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { return false; } - final String p20_S = "(A,(B,(C,D)))"; - final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() ); - if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) { + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { return false; } - final String p21_S = "(A,(B,(C,(D,E))))"; - final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() ); - if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) { + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { return false; } - final String p22_S = "((((A,B),C),D),E)"; - final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() ); - if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) { + if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) { return false; } - final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() ); - if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) { + if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) { + System.exit( -1 ); return false; } - final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() ); - if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) { + if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) { return false; } - final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() ); - if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + 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 List l = new ArrayList(); + l.add( s0 ); + l.add( s1 ); + l.add( s2 ); + l.add( s3 ); + final Msa msa = BasicMsa.createInstance( l ); + if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) { return false; } - if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) { + if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) { return false; } - final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)" - + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D," - + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)" - + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde," - + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd," - + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)" - + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde" - + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde"; - final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() ); - if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) { + if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) { return false; } - final String p26_S = "(A,B)ab"; - final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() ); - if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) { + if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) { return false; } - final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ), - new NHXParser() ); - if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) { - return false; + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNextNodeWithCollapsing() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + PhylogenyNode n; + List ext = new ArrayList(); + final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ]; + t0.getNode( "cd" ).setCollapse( true ); + t0.getNode( "cde" ).setCollapse( true ); + n = t0.getFirstExternalNode(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final String p28_S3 = "(A,B)ab"; - final String p28_S4 = "((((A,B),C),D),;E;)"; - final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ), - new NHXParser() ); - if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) { + if ( !ext.get( 2 ).getName().equals( "cde" ) ) { return false; } - if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) { + if ( !ext.get( 3 ).getName().equals( "f" ) ) { return false; } - final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345"; - final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() ); - if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) { + if ( !ext.get( 4 ).getName().equals( "g" ) ) { return false; } - final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72"; - final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() ); - if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) { + if ( !ext.get( 5 ).getName().equals( "h" ) ) { return false; } - final String p32_S = " ; ; \n \t \b \f \r ;;;;;; "; - final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() ); - if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) { - return false; + ext.clear(); + final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ]; + t1.getNode( "ab" ).setCollapse( true ); + t1.getNode( "cd" ).setCollapse( true ); + t1.getNode( "cde" ).setCollapse( true ); + n = t1.getNode( "ab" ); + ext = new ArrayList(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - final String p33_S = "A"; - final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() ); - if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - final String p34_S = "B;"; - final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() ); - if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) { + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { return false; } - final String p35_S = "B:0.2"; - final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() ); - if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) { + if ( !ext.get( 2 ).getName().equals( "f" ) ) { return false; } - final String p36_S = "(A)"; - final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() ); - if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) { + if ( !ext.get( 3 ).getName().equals( "g" ) ) { return false; } - final String p37_S = "((A))"; - final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() ); - if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) { + if ( !ext.get( 4 ).getName().equals( "h" ) ) { return false; } - final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; - final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() ); - if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) { - return false; + // + // + ext.clear(); + final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); + final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ]; + t2.getNode( "ab" ).setCollapse( true ); + t2.getNode( "cd" ).setCollapse( true ); + t2.getNode( "cde" ).setCollapse( true ); + t2.getNode( "c" ).setCollapse( true ); + t2.getNode( "d" ).setCollapse( true ); + t2.getNode( "e" ).setCollapse( true ); + t2.getNode( "gh" ).setCollapse( true ); + n = t2.getNode( "ab" ); + ext = new ArrayList(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; - final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() ); - if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - final String p40_S = "(A,B,C)"; - final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() ); - if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) { + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { return false; } - final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)"; - final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() ); - if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) { + if ( !ext.get( 2 ).getName().equals( "f" ) ) { return false; } - final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)"; - final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() ); - if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) { + if ( !ext.get( 3 ).getName().equals( "gh" ) ) { return false; } - final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; - final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() ); - if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) { - return false; + // + // + ext.clear(); + final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); + final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ]; + t3.getNode( "ab" ).setCollapse( true ); + t3.getNode( "cd" ).setCollapse( true ); + t3.getNode( "cde" ).setCollapse( true ); + t3.getNode( "c" ).setCollapse( true ); + t3.getNode( "d" ).setCollapse( true ); + t3.getNode( "e" ).setCollapse( true ); + t3.getNode( "gh" ).setCollapse( true ); + t3.getNode( "fgh" ).setCollapse( true ); + n = t3.getNode( "ab" ); + ext = new ArrayList(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; - final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() ); - if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))"; - final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() ); - if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) { + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { return false; } - final String p46_S = ""; - final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() ); - if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) { + if ( !ext.get( 2 ).getName().equals( "fgh" ) ) { return false; } - final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ]; - if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { + // + // + ext.clear(); + final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); + final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ]; + t4.getNode( "ab" ).setCollapse( true ); + t4.getNode( "cd" ).setCollapse( true ); + t4.getNode( "cde" ).setCollapse( true ); + t4.getNode( "c" ).setCollapse( true ); + t4.getNode( "d" ).setCollapse( true ); + t4.getNode( "e" ).setCollapse( true ); + t4.getNode( "gh" ).setCollapse( true ); + t4.getNode( "fgh" ).setCollapse( true ); + t4.getNode( "abcdefgh" ).setCollapse( true ); + n = t4.getNode( "abcdefgh" ); + if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) { return false; } - final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; - if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { - return false; + // + // + final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; + ext.clear(); + n = t5.getFirstExternalNode(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - final Phylogeny p49 = factory - .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ), - new NHXParser() )[ 0 ]; - if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { + if ( ext.size() != 8 ) { return false; } - final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; - if ( p50.getNode( "A" ) == null ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) - .equals( "((A,B)ab:2.0[88],C);" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ) - .equals( "((A,B)88:2.0,C);" ) ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; - if ( p51.getNode( "A(A" ) == null ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; - if ( p52.getNode( "A(A" ) == null ) { + if ( !ext.get( 5 ).getName().equals( "f" ) ) { return false; } - final Phylogeny p53 = factory - .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ), - new NHXParser() )[ 0 ]; - if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) { + if ( !ext.get( 6 ).getName().equals( "g" ) ) { return false; } - // - final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ]; - if ( p54.getNode( "A" ) == null ) { + if ( !ext.get( 7 ).getName().equals( "h" ) ) { return false; } - if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) - .equals( "((A,B)[88],C);" ) ) { - return false; + // + // + final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ]; + ext.clear(); + t6.getNode( "ab" ).setCollapse( true ); + n = t6.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNHXconversion() { - try { - final PhylogenyNode n1 = new PhylogenyNode(); - final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" ); - final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" ); - final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" ); - final PhylogenyNode n5 = PhylogenyNode - .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" ); - final PhylogenyNode n6 = PhylogenyNode - .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" ); - if ( !n1.toNewHampshireX().equals( "" ) ) { + if ( ext.size() != 7 ) { return false; } - if ( !n2.toNewHampshireX().equals( "" ) ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( !n3.toNewHampshireX().equals( "n3" ) ) { + if ( !ext.get( 1 ).getName().equals( "c" ) ) { return false; } - if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) { + if ( !ext.get( 2 ).getName().equals( "d" ) ) { return false; } - if ( !n5.toNewHampshireX() - .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) { + if ( !ext.get( 4 ).getName().equals( "f" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNHXNodeParsing() { - try { - final PhylogenyNode n1 = new PhylogenyNode(); - final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" ); - final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" ); - final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" ); - final PhylogenyNode n5 = PhylogenyNode - .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" ); - if ( !n3.getName().equals( "n3" ) ) { + if ( !ext.get( 5 ).getName().equals( "g" ) ) { return false; } - if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - if ( n3.isDuplication() ) { - return false; + // + // + final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ]; + ext.clear(); + t7.getNode( "cd" ).setCollapse( true ); + n = t7.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - if ( n3.isHasAssignedEvent() ) { + if ( ext.size() != 7 ) { return false; } - if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !n4.getName().equals( "n4" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( n4.getDistanceToParent() != 0.01 ) { + if ( !ext.get( 2 ).getName().equals( "cd" ) ) { return false; } - if ( !n5.getName().equals( "n5" ) ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) { + if ( !ext.get( 4 ).getName().equals( "f" ) ) { return false; } - if ( n5.getDistanceToParent() != 0.1 ) { + if ( !ext.get( 5 ).getName().equals( "g" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) { + if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - if ( !n5.isDuplication() ) { - return false; + // + // + final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ]; + ext.clear(); + t8.getNode( "cd" ).setCollapse( true ); + t8.getNode( "c" ).setCollapse( true ); + t8.getNode( "d" ).setCollapse( true ); + n = t8.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - if ( !n5.isHasAssignedEvent() ) { + if ( ext.size() != 7 ) { return false; } - if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - final PhylogenyNode n8 = PhylogenyNode - .createInstanceFromNhxString( "n8_ECOLI/12:0.01", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n8.getName().equals( "n8_ECOLI/12" ) ) { + if ( !ext.get( 2 ).getName().equals( "cd" ) ) { + System.out.println( "2 fail" ); return false; } - if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - final PhylogenyNode n9 = PhylogenyNode - .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) { + if ( !ext.get( 4 ).getName().equals( "f" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) { + if ( !ext.get( 5 ).getName().equals( "g" ) ) { return false; } - final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n10.getName().equals( "n10.ECOLI" ) ) { + if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - final PhylogenyNode n20 = PhylogenyNode - .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) { - return false; + // + // + final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); + final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ]; + ext.clear(); + t9.getNode( "gh" ).setCollapse( true ); + n = t9.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) { + if ( ext.size() != 7 ) { return false; } - final PhylogenyNode n20x = PhylogenyNode - .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); - if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - final PhylogenyNode n20xx = PhylogenyNode - .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - final PhylogenyNode n20xxx = PhylogenyNode - .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) { + if ( !ext.get( 5 ).getName().equals( "f" ) ) { return false; } - final PhylogenyNode n20xxxx = PhylogenyNode - .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) { + if ( !ext.get( 6 ).getName().equals( "gh" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) { - return false; + // + // + final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); + final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ]; + ext.clear(); + t10.getNode( "gh" ).setCollapse( true ); + t10.getNode( "g" ).setCollapse( true ); + t10.getNode( "h" ).setCollapse( true ); + n = t10.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - final PhylogenyNode n21 = PhylogenyNode - .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); - if ( !n21.getName().equals( "n21_PIG" ) ) { + if ( ext.size() != 7 ) { return false; } - if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - final PhylogenyNode n21x = PhylogenyNode - .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n21x.getName().equals( "n21_PIG" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - final PhylogenyNode n22 = PhylogenyNode - .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n22.getName().equals( "n22/PIG" ) ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - final PhylogenyNode n23 = PhylogenyNode - .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n23.getName().equals( "n23/PIG_1" ) ) { + if ( !ext.get( 5 ).getName().equals( "f" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) { + if ( !ext.get( 6 ).getName().equals( "gh" ) ) { return false; } - final PhylogenyNode a = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) { - return false; + // + // + final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); + final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ]; + ext.clear(); + t11.getNode( "gh" ).setCollapse( true ); + t11.getNode( "fgh" ).setCollapse( true ); + n = t11.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) { + if ( ext.size() != 6 ) { return false; } - final PhylogenyNode b = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI1/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - final PhylogenyNode c = PhylogenyNode - .createInstanceFromNhxString( "n10_RATAF12/1000-2000", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - final PhylogenyNode c1 = PhylogenyNode - .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { + if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - final PhylogenyNode c2 = PhylogenyNode - .createInstanceFromNhxString( "n10_Bovin_1/1000-2000", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) { - return false; + // + // + final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); + final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ]; + ext.clear(); + t12.getNode( "gh" ).setCollapse( true ); + t12.getNode( "fgh" ).setCollapse( true ); + t12.getNode( "g" ).setCollapse( true ); + t12.getNode( "h" ).setCollapse( true ); + t12.getNode( "f" ).setCollapse( true ); + n = t12.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) { + if ( ext.size() != 6 ) { return false; } - final PhylogenyNode d = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !d.getName().equals( "n10_RAT1/1-2" ) ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - final PhylogenyNode e = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !e.getName().equals( "n10_RAT1" ) ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - final PhylogenyNode e2 = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); - if ( !e2.getName().equals( "n10_RAT1" ) ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) { + if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - final PhylogenyNode e3 = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT~", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); - if ( !e3.getName().equals( "n10_RAT~" ) ) { - return false; + // + // + final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); + final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ]; + ext.clear(); + t13.getNode( "ab" ).setCollapse( true ); + t13.getNode( "b" ).setCollapse( true ); + t13.getNode( "fgh" ).setCollapse( true ); + t13.getNode( "gh" ).setCollapse( true ); + n = t13.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) { + if ( ext.size() != 5 ) { return false; } - final PhylogenyNode n11 = PhylogenyNode - .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( n11.getDistanceToParent() != 0.4 ) { + if ( !ext.get( 1 ).getName().equals( "c" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) { + if ( !ext.get( 2 ).getName().equals( "d" ) ) { return false; } - final PhylogenyNode n12 = PhylogenyNode - .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - if ( n12.getDistanceToParent() != 0.4 ) { + if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) { - return false; + // + // + final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); + final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ]; + ext.clear(); + t14.getNode( "ab" ).setCollapse( true ); + t14.getNode( "a" ).setCollapse( true ); + t14.getNode( "fgh" ).setCollapse( true ); + t14.getNode( "gh" ).setCollapse( true ); + n = t14.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - final PhylogenyNode m = PhylogenyNode - .createInstanceFromNhxString( "n10_MOUSEa", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); - if ( !m.getName().equals( "n10_MOUSEa" ) ) { + if ( ext.size() != 5 ) { return false; } - if ( !PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - final PhylogenyNode o = PhylogenyNode - .createInstanceFromNhxString( "n10_MOUSE_", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); - if ( !o.getName().equals( "n10_MOUSE_" ) ) { + if ( !ext.get( 1 ).getName().equals( "c" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) { + if ( !ext.get( 2 ).getName().equals( "d" ) ) { return false; } - final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" ); - final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" ); - if ( !tvu1.getRef().equals( "tag1" ) ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - if ( !tvu1.getDataType().equals( "xsd:string" ) ) { + if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { return false; } - if ( !tvu1.getUnit().equals( "unit1" ) ) { - return false; + // + // + final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); + final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ]; + ext.clear(); + t15.getNode( "ab" ).setCollapse( true ); + t15.getNode( "a" ).setCollapse( true ); + t15.getNode( "fgh" ).setCollapse( true ); + t15.getNode( "gh" ).setCollapse( true ); + n = t15.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - if ( !tvu1.getValue().equals( "value1" ) ) { + if ( ext.size() != 6 ) { return false; } - if ( !tvu3.getRef().equals( "tag3" ) ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( !tvu3.getDataType().equals( "xsd:string" ) ) { + if ( !ext.get( 1 ).getName().equals( "c" ) ) { return false; } - if ( !tvu3.getUnit().equals( "unit3" ) ) { + if ( !ext.get( 2 ).getName().equals( "d" ) ) { return false; } - if ( !tvu3.getValue().equals( "value3" ) ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - if ( n1.getName().compareTo( "" ) != 0 ) { + if ( !ext.get( 4 ).getName().equals( "x" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + // + // + final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); + final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ]; + ext.clear(); + t16.getNode( "ab" ).setCollapse( true ); + t16.getNode( "a" ).setCollapse( true ); + t16.getNode( "fgh" ).setCollapse( true ); + t16.getNode( "gh" ).setCollapse( true ); + t16.getNode( "cd" ).setCollapse( true ); + t16.getNode( "cde" ).setCollapse( true ); + t16.getNode( "d" ).setCollapse( true ); + t16.getNode( "x" ).setCollapse( true ); + n = t16.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 4 ) { return false; } - if ( n2.getName().compareTo( "" ) != 0 ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { return false; } - if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + if ( !ext.get( 2 ).getName().equals( "x" ) ) { return false; } - final PhylogenyNode n00 = PhylogenyNode - .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" ); - if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) { + if ( !ext.get( 3 ).getName().equals( "fgh" ) ) { return false; } - if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNexusCharactersParsing() { + try { + final NexusCharactersParser parser = new NexusCharactersParser(); + parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) ); + parser.parse(); + String[] labels = parser.getCharStateLabels(); + if ( labels.length != 7 ) { return false; } - if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) { + if ( !labels[ 0 ].equals( "14-3-3" ) ) { return false; } - if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) { + if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { return false; } - if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) { + if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { return false; } - if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) { + if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { return false; } - if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) { + if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { return false; } - if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) { + if ( !labels[ 5 ].equals( "3-HAO" ) ) { return false; } - final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" ); - if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) { + if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { return false; } - final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" ); - if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) { + parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) ); + parser.parse(); + labels = parser.getCharStateLabels(); + if ( labels.length != 7 ) { return false; } - final PhylogenyNode n13 = PhylogenyNode - .createInstanceFromNhxString( "blah_12345/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n13.getName().equals( "blah_12345/1-2" ) ) { + if ( !labels[ 0 ].equals( "14-3-3" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) { + if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { return false; } - final PhylogenyNode n14 = PhylogenyNode - .createInstanceFromNhxString( "blah_12X45/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n14.getName().equals( "blah_12X45/1-2" ) ) { + if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) { + if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { return false; } - final PhylogenyNode n15 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked[123]", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n15.getName().equals( "something_wicked" ) ) { + if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { return false; } - if ( n15.getBranchData().getNumberOfConfidences() != 1 ) { + if ( !labels[ 5 ].equals( "3-HAO" ) ) { return false; } - if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) { + if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { return false; } - final PhylogenyNode n16 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked2[9]", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n16.getName().equals( "something_wicked2" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNexusMatrixParsing() { + try { + final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser(); + parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) ); + parser.parse(); + final CharacterStateMatrix m = parser.getMatrix(); + if ( m.getNumberOfCharacters() != 9 ) { return false; } - if ( n16.getBranchData().getNumberOfConfidences() != 1 ) { + if ( m.getNumberOfIdentifiers() != 5 ) { return false; } - if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) { + if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) { return false; } - final PhylogenyNode n17 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked3[a]", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n17.getName().equals( "something_wicked3" ) ) { + if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) { return false; } - if ( n17.getBranchData().getNumberOfConfidences() != 0 ) { + if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) { return false; } - final PhylogenyNode n18 = PhylogenyNode - .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) { + if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) { return false; } - if ( n18.getBranchData().getNumberOfConfidences() != 1 ) { + if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) { return false; } - if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) { + if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) { + return false; + } + if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) { return false; } + // if ( labels.length != 7 ) { + // return false; + // } + // if ( !labels[ 0 ].equals( "14-3-3" ) ) { + // return false; + // } + // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { + // return false; + // } + // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { + // return false; + // } + // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { + // return false; + // } + // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { + // return false; + // } + // if ( !labels[ 5 ].equals( "3-HAO" ) ) { + // return false; + // } + // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { + // return false; + // } + // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) ); + // parser.parse(); + // labels = parser.getCharStateLabels(); + // if ( labels.length != 7 ) { + // return false; + // } + // if ( !labels[ 0 ].equals( "14-3-3" ) ) { + // return false; + // } + // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { + // return false; + // } + // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { + // return false; + // } + // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { + // return false; + // } + // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { + // return false; + // } + // if ( !labels[ 5 ].equals( "3-HAO" ) ) { + // return false; + // } + // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { + // return false; + // } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -5285,263 +6205,168 @@ public final class Test { return true; } - private static boolean testNHXParsing() { + private static boolean testNexusTreeParsing() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ]; - if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) { + final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); + Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser ); + if ( phylogenies.length != 1 ) { return false; } - final String p2_S = "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]"; - final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() ); - if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) { return false; } - final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]"; - final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() ); - if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) { + if ( !phylogenies[ 0 ].getName().equals( "" ) ) { return false; } - final Phylogeny[] p3 = factory - .create( "[ comment&&NHX,())))](((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]", - new NHXParser() ); - if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser ); + if ( phylogenies.length != 1 ) { return false; } - final Phylogeny[] p4 = factory - .create( "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(]", - new NHXParser() ); - if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) { return false; } - final Phylogeny[] p5 = factory - .create( "[] ( [][ ][ ] ([((( &&NHXcomment only![[[[[[]([]((((A:0.2[&&NHX:S=q[comment )))]werty][,,,,))]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=a[comment,,))]sdf])[comment(((]:0.4[&&NHX:S=zxc][comment(((][comment(((]):0.5[&&NHX:S=a]):0.6[&&NHX:S=a[comment(((]sd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(((]", - new NHXParser() ); - if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) { + if ( !phylogenies[ 0 ].getName().equals( "name" ) ) { return false; } - final String p6_S_C = "(A[][][][1][22][333][4444][55555][666666][&&NHX:S=Aspecies],B[))],C,(AA,BB,CC,(CCC,DDD,EEE,[comment](FFFF,GGGG)x)y,D[comment]D,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; - final String p6_S_WO_C = "(A[&&NHX:S=Aspecies],B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; - final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() ); - if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser ); + if ( phylogenies.length != 1 ) { return false; } - final String p7_S_C = "(((A [&&NHX:S=species_a], B [&&NHX:S=Vstorri] , C , D),(A,B,C,D[comment])[],[c][]([xxx]A[comment],[comment]B[comment][comment],[comment][comment]C[comment][comment],[comment][comment]D[comment][comment])[comment][comment],[comment] [comment](A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C[comment][comment][comment][comment][comment] [comment],D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),[comment][comment]((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; - final String p7_S_WO_C = "(((A[&&NHX:S=species_a],B[&&NHX:S=Vstorri],C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; - final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() ); - if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { return false; } - final String p8_S_C = "[cmt](((([]([))))))](((((A[&&NHX:S= [a comment] a])))))))[too many comments!:)])),(((((((((B[&&NHX[ a comment in a bad place]:S =b])))))[] [] )))),(((((((((C[&&NHX:S=c]) ))[,,, ])))))))"; - final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))"; - final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() ); - if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) { + if ( !phylogenies[ 0 ].getName().equals( "" ) ) { return false; } - final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ]; - if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { + if ( phylogenies[ 0 ].isRooted() ) { return false; } - final Phylogeny p10 = factory - .create( " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]", - new NHXParser() )[ 0 ]; - if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser ); + if ( phylogenies.length != 18 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNHXParsingQuotes() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final NHXParser p = new NHXParser(); - final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p ); - if ( phylogenies_0.length != 5 ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) { return false; } - final Phylogeny phy = phylogenies_0[ 4 ]; - if ( phy.getNumberOfExternalNodes() != 7 ) { + if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) { return false; } - if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) { + if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) { return false; } - if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) { + if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) { return false; } - if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy() - .getScientificName().equals( "hsapiens" ) ) { + if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) { + if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) { + if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) { + if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( phy.getNodes( "noquotes" ).size() != 1 ) { + if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( phy.getNodes( "A ( B C '" ).size() != 1 ) { + if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) { return false; } - final NHXParser p1p = new NHXParser(); - p1p.setIgnoreQuotes( true ); - final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ]; - if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) { + if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) { return false; } - final NHXParser p2p = new NHXParser(); - p1p.setIgnoreQuotes( false ); - final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ]; - if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) { + if ( phylogenies[ 8 ].isRooted() ) { return false; } - final NHXParser p3p = new NHXParser(); - p3p.setIgnoreQuotes( false ); - final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ]; - if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) { + if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) { return false; } - final NHXParser p4p = new NHXParser(); - p4p.setIgnoreQuotes( false ); - final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ]; - if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) { + if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) { return false; } - final Phylogeny p10 = factory - .create( " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]", - new NHXParser() )[ 0 ]; - final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]"; - if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) { + if ( !phylogenies[ 9 ].isRooted() ) { return false; } - final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ]; - if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) { + if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) { return false; } - // - final Phylogeny p12 = factory - .create( " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]", - new NHXParser() )[ 0 ]; - final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]"; - if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) { + if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) { return false; } - final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ]; - if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) { + if ( !phylogenies[ 10 ].isRooted() ) { return false; } - final String p12_clean_str_nh = "(('A B':0.2,'BB B':0.03):0.5,'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1;"; - if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) { + if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) { return false; } - final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ]; - if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) { + if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNHXParsingMB() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00," - + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," - + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02," - + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02," - + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00," - + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," - + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," - + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," - + "7.369400000000000e-02}])", new NHXParser() )[ 0 ]; - if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) { + if ( phylogenies[ 11 ].isRooted() ) { return false; } - if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) { + if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(), - 0.1100000000000000e+00 ) ) { + if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) { return false; } - if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) { + if ( !phylogenies[ 12 ].isRooted() ) { return false; } - if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) { + if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) { return false; } - final Phylogeny p2 = factory - .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00," - + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," - + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02," - + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02," - + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00," - + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," - + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," - + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," - + "7.369400000000000e-02}])", - new NHXParser() )[ 0 ]; - if ( p2.getNode( "1" ) == null ) { + if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) { return false; } - if ( p2.getNode( "2" ) == null ) { + if ( !phylogenies[ 13 ].isRooted() ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - System.exit( -1 ); - return false; - } - return true; - } - - private static boolean testPhylogenyBranch() { - try { - final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" ); - final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" ); - final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 ); - final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 ); - if ( !a1b1.equals( a1b1 ) ) { + if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !a1b1.equals( b1a1 ) ) { + if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) { return false; } - if ( !b1a1.equals( a1b1 ) ) { + if ( !phylogenies[ 14 ].isRooted() ) { return false; } - final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true ); - final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true ); - final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false ); - if ( a1_b1.equals( b1_a1 ) ) { + if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) { return false; } - if ( a1_b1.equals( a1_b1_ ) ) { + if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) { return false; } - final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false ); - if ( !a1_b1.equals( b1_a1_ ) ) { + if ( phylogenies[ 15 ].isRooted() ) { return false; } - if ( a1_b1_.equals( b1_a1_ ) ) { + if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) { return false; } - if ( !a1_b1_.equals( b1_a1 ) ) { + if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) { + return false; + } + if ( !phylogenies[ 16 ].isRooted() ) { + return false; + } + if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) { + return false; + } + if ( phylogenies[ 17 ].isRooted() ) { + return false; + } + if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) { return false; } } @@ -5552,575 +6377,560 @@ public final class Test { return true; } - private static boolean testPhyloXMLparsingOfDistributionElement() { + private static boolean testNexusTreeParsingIterating() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - PhyloXmlParser xml_parser = null; - try { - xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating(); + final NexusPhylogeniesParser p = new NexusPhylogeniesParser(); + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" ); + if ( !p.hasNext() ) { + return false; } - catch ( final Exception e ) { - // Do nothing -- means were not running from jar. + Phylogeny phy = p.next(); + if ( phy == null ) { + return false; } - if ( xml_parser == null ) { - xml_parser = new PhyloXmlParser(); - if ( USE_LOCAL_PHYLOXML_SCHEMA ) { - xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); - } - else { - xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); - } + if ( phy.getNumberOfExternalNodes() != 25 ) { + return false; } - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml", - xml_parser ); - if ( xml_parser.getErrorCount() > 0 ) { - System.out.println( xml_parser.getErrorMessages().toString() ); + if ( !phy.getName().equals( "" ) ) { return false; } - if ( phylogenies_0.length != 1 ) { + if ( p.hasNext() ) { return false; } - final Phylogeny t1 = phylogenies_0[ 0 ]; - PhylogenyNode n = null; - Distribution d = null; - n = t1.getNode( "root node" ); - if ( !n.getNodeData().isHasDistribution() ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( n.getNodeData().getDistributions().size() != 1 ) { + // + p.reset(); + if ( !p.hasNext() ) { return false; } - d = n.getNodeData().getDistribution(); - if ( !d.getDesc().equals( "Hirschweg 38" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( d.getPoints().size() != 1 ) { + if ( phy.getNumberOfExternalNodes() != 25 ) { return false; } - if ( d.getPolygons() != null ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) { + if ( p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" ); + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - n = t1.getNode( "node a" ); - if ( !n.getNodeData().isHasDistribution() ) { + if ( !phy.getName().equals( "name" ) ) { return false; } - if ( n.getNodeData().getDistributions().size() != 2 ) { + if ( p.hasNext() ) { return false; } - d = n.getNodeData().getDistribution( 1 ); - if ( !d.getDesc().equals( "San Diego" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( d.getPoints().size() != 1 ) { + // + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( d.getPolygons() != null ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + if ( !phy.getName().equals( "name" ) ) { return false; } - if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + if ( p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) { + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" ); + if ( !p.hasNext() ) { return false; } - n = t1.getNode( "node bb" ); - if ( !n.getNodeData().isHasDistribution() ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( n.getNodeData().getDistributions().size() != 1 ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - d = n.getNodeData().getDistribution( 0 ); - if ( d.getPoints().size() != 3 ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( d.getPolygons().size() != 2 ) { + if ( phy.isRooted() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) { + if ( p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) { + // + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - Polygon p = d.getPolygons().get( 0 ); - if ( p.getPoints().size() != 3 ) { + if ( p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) { + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" ); + // if ( phylogenies.length != 18 ) { + // return false; + // } + //0 + if ( !p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) { + if ( !phy.getName().equals( "tree 0" ) ) { return false; } - if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) { + //1 + if ( !p.hasNext() ) { return false; } - p = d.getPolygons().get( 1 ); - if ( p.getPoints().size() != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) { + if ( !phy.getName().equals( "tree 1" ) ) { return false; } - if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + //2 + if ( !p.hasNext() ) { return false; } - // Roundtrip: - final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) ); - final Phylogeny[] rt = factory.create( t1_sb, xml_parser ); - if ( rt.length != 1 ) { + phy = p.next(); + if ( phy == null ) { return false; } - final Phylogeny t1_rt = rt[ 0 ]; - n = t1_rt.getNode( "root node" ); - if ( !n.getNodeData().isHasDistribution() ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( n.getNodeData().getDistributions().size() != 1 ) { + if ( !phy.getName().equals( "" ) ) { return false; } - d = n.getNodeData().getDistribution(); - if ( !d.getDesc().equals( "Hirschweg 38" ) ) { + if ( phy.isRooted() ) { return false; } - if ( d.getPoints().size() != 1 ) { + //3 + if ( !p.hasNext() ) { return false; } - if ( d.getPolygons() != null ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) { + if ( phy.getNumberOfExternalNodes() != 4 ) { return false; } - if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + if ( !phy.isRooted() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) { + //4 + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - n = t1_rt.getNode( "node a" ); - if ( !n.getNodeData().isHasDistribution() ) { + if ( phy.getNumberOfExternalNodes() != 5 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( n.getNodeData().getDistributions().size() != 2 ) { + if ( !phy.getName().equals( "" ) ) { return false; } - d = n.getNodeData().getDistribution( 1 ); - if ( !d.getDesc().equals( "San Diego" ) ) { + if ( !phy.isRooted() ) { return false; } - if ( d.getPoints().size() != 1 ) { + //5 + if ( !p.hasNext() ) { return false; } - if ( d.getPolygons() != null ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + if ( phy.isRooted() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) { + //6 + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - n = t1_rt.getNode( "node bb" ); - if ( !n.getNodeData().isHasDistribution() ) { + if ( phy.getNumberOfExternalNodes() != 2 ) { return false; } - if ( n.getNodeData().getDistributions().size() != 1 ) { + if ( !phy.getName().equals( "" ) ) { return false; } - d = n.getNodeData().getDistribution( 0 ); - if ( d.getPoints().size() != 3 ) { + if ( !phy.isRooted() ) { return false; } - if ( d.getPolygons().size() != 2 ) { + //7 + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) { + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { return false; } - if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) { + if ( !phy.isRooted() ) { return false; } - if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) { + //8 + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) { + if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) { return false; } - p = d.getPolygons().get( 0 ); - if ( p.getPoints().size() != 3 ) { + if ( !phy.getName().equals( "tree 8" ) ) { return false; } - if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) { + //9 + if ( !p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) { return false; } - if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) { + if ( !phy.getName().equals( "tree 9" ) ) { return false; } - if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) { + //10 + if ( !p.hasNext() ) { return false; } - if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - p = d.getPolygons().get( 1 ); - if ( p.getPoints().size() != 3 ) { + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { return false; } - if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) { + if ( !phy.getName().equals( "tree 10" ) ) { return false; } - if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) { + if ( !phy.isRooted() ) { return false; } - if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + //11 + if ( !p.hasNext() ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testPostOrderIterator() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ]; - PhylogenyNodeIterator it0; - for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) { - it0.next(); + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; } - for( it0.reset(); it0.hasNext(); ) { - it0.next(); + if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) { + return false; } - final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ]; - final PhylogenyNodeIterator it = t1.iteratorPostorder(); - if ( !it.next().getName().equals( "A" ) ) { + if ( !phy.getName().equals( "tree 11" ) ) { return false; } - if ( !it.next().getName().equals( "B" ) ) { + if ( phy.isRooted() ) { return false; } - if ( !it.next().getName().equals( "ab" ) ) { + //12 + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "C" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !it.next().getName().equals( "D" ) ) { + if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) { return false; } - if ( !it.next().getName().equals( "cd" ) ) { + if ( !phy.getName().equals( "tree 12" ) ) { return false; } - if ( !it.next().getName().equals( "abcd" ) ) { + if ( !phy.isRooted() ) { return false; } - if ( !it.next().getName().equals( "E" ) ) { + //13 + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "F" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !it.next().getName().equals( "ef" ) ) { + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { return false; } - if ( !it.next().getName().equals( "G" ) ) { + if ( !phy.getName().equals( "tree 13" ) ) { return false; } - if ( !it.next().getName().equals( "H" ) ) { + if ( !phy.isRooted() ) { return false; } - if ( !it.next().getName().equals( "gh" ) ) { + //14 + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "efgh" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !it.next().getName().equals( "r" ) ) { + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); return false; } - if ( it.hasNext() ) { + if ( !phy.getName().equals( "tree 14" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testPreOrderIterator() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ]; - PhylogenyNodeIterator it0; - for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) { - it0.next(); + if ( !phy.isRooted() ) { + return false; } - for( it0.reset(); it0.hasNext(); ) { - it0.next(); - } - PhylogenyNodeIterator it = t0.iteratorPreorder(); - if ( !it.next().getName().equals( "r" ) ) { - return false; - } - if ( !it.next().getName().equals( "ab" ) ) { - return false; - } - if ( !it.next().getName().equals( "A" ) ) { - return false; - } - if ( !it.next().getName().equals( "B" ) ) { + //15 + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "cd" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !it.next().getName().equals( "C" ) ) { + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); return false; } - if ( !it.next().getName().equals( "D" ) ) { + if ( !phy.getName().equals( "tree 15" ) ) { return false; } - if ( it.hasNext() ) { + if ( phy.isRooted() ) { return false; } - final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ]; - it = t1.iteratorPreorder(); - if ( !it.next().getName().equals( "r" ) ) { + //16 + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "abcd" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !it.next().getName().equals( "ab" ) ) { + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); return false; } - if ( !it.next().getName().equals( "A" ) ) { + if ( !phy.getName().equals( "tree 16" ) ) { return false; } - if ( !it.next().getName().equals( "B" ) ) { + if ( !phy.isRooted() ) { return false; } - if ( !it.next().getName().equals( "cd" ) ) { + //17 + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "C" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !it.next().getName().equals( "D" ) ) { + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); return false; } - if ( !it.next().getName().equals( "efgh" ) ) { + if ( !phy.getName().equals( "tree 17" ) ) { return false; } - if ( !it.next().getName().equals( "ef" ) ) { + if ( phy.isRooted() ) { return false; } - if ( !it.next().getName().equals( "E" ) ) { + // + if ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "F" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !it.next().getName().equals( "gh" ) ) { + p.reset(); + //0 + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "G" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !it.next().getName().equals( "H" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( it.hasNext() ) { + if ( !phy.getName().equals( "tree 0" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testPropertiesMap() { - try { - final PropertiesMap pm = new PropertiesMap(); - final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE ); - final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE ); - final Property p2 = new Property( "something:else", - "?", - "improbable:research", - "xsd:decimal", - AppliesTo.NODE ); - pm.addProperty( p0 ); - pm.addProperty( p1 ); - pm.addProperty( p2 ); - if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) { + //1 + if ( !p.hasNext() ) { return false; } - if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( pm.getProperties().size() != 3 ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) { + if ( !phy.getName().equals( "tree 1" ) ) { return false; } - if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) { + //2 + if ( !p.hasNext() ) { return false; } - if ( pm.getProperties().size() != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - pm.removeProperty( "dimensions:diameter" ); - if ( pm.getProperties().size() != 2 ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) { + if ( phy.isRooted() ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testReIdMethods() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ]; - final int count = PhylogenyNode.getNodeCount(); - p.levelOrderReID(); - if ( p.getNode( "r" ).getId() != count ) { + //3 + if ( !p.hasNext() ) { return false; } - if ( p.getNode( "A" ).getId() != ( count + 1 ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( p.getNode( "B" ).getId() != ( count + 1 ) ) { + if ( phy.getNumberOfExternalNodes() != 4 ) { return false; } - if ( p.getNode( "C" ).getId() != ( count + 1 ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( p.getNode( "1" ).getId() != ( count + 2 ) ) { + if ( !phy.isRooted() ) { return false; } - if ( p.getNode( "2" ).getId() != ( count + 2 ) ) { + //4 + if ( !p.hasNext() ) { return false; } - if ( p.getNode( "3" ).getId() != ( count + 2 ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( p.getNode( "4" ).getId() != ( count + 2 ) ) { + if ( phy.getNumberOfExternalNodes() != 5 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( p.getNode( "5" ).getId() != ( count + 2 ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( p.getNode( "6" ).getId() != ( count + 2 ) ) { + if ( !phy.isRooted() ) { return false; } - if ( p.getNode( "a" ).getId() != ( count + 3 ) ) { + //5 + if ( !p.hasNext() ) { return false; } - if ( p.getNode( "b" ).getId() != ( count + 3 ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( p.getNode( "X" ).getId() != ( count + 4 ) ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) { + if ( phy.isRooted() ) { return false; } } @@ -6131,2180 +6941,4249 @@ public final class Test { return true; } - private static boolean testRerooting() { + private static boolean testNexusTreeParsingTranslating() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:5)CD:3[&&NHX:B=10])ABCD:0.5", - new NHXParser() )[ 0 ]; - if ( !t1.isRooted() ) { + final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); + Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser ); + if ( phylogenies.length != 1 ) { return false; } - t1.reRoot( t1.getNode( "D" ) ); - t1.reRoot( t1.getNode( "CD" ) ); - t1.reRoot( t1.getNode( "A" ) ); - t1.reRoot( t1.getNode( "B" ) ); - t1.reRoot( t1.getNode( "AB" ) ); - t1.reRoot( t1.getNode( "D" ) ); - t1.reRoot( t1.getNode( "C" ) ); - t1.reRoot( t1.getNode( "CD" ) ); - t1.reRoot( t1.getNode( "A" ) ); - t1.reRoot( t1.getNode( "B" ) ); - t1.reRoot( t1.getNode( "AB" ) ); - t1.reRoot( t1.getNode( "D" ) ); - t1.reRoot( t1.getNode( "D" ) ); - t1.reRoot( t1.getNode( "C" ) ); - t1.reRoot( t1.getNode( "A" ) ); - t1.reRoot( t1.getNode( "B" ) ); - t1.reRoot( t1.getNode( "AB" ) ); - t1.reRoot( t1.getNode( "C" ) ); - t1.reRoot( t1.getNode( "D" ) ); - t1.reRoot( t1.getNode( "CD" ) ); - t1.reRoot( t1.getNode( "D" ) ); - t1.reRoot( t1.getNode( "A" ) ); - t1.reRoot( t1.getNode( "B" ) ); - t1.reRoot( t1.getNode( "AB" ) ); - t1.reRoot( t1.getNode( "C" ) ); - t1.reRoot( t1.getNode( "D" ) ); - t1.reRoot( t1.getNode( "CD" ) ); - t1.reRoot( t1.getNode( "D" ) ); - if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { return false; } - if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser ); + if ( phylogenies.length != 3 ) { return false; } - final Phylogeny t2 = factory.create( "(((A:1,B:2)AB:10[&&NHX:B=55],C)ABC:3[&&NHX:B=33],D:5)ABCD:0.5", - new NHXParser() )[ 0 ]; - t2.reRoot( t2.getNode( "A" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "ABC" ) ); - t2.reRoot( t2.getNode( "A" ) ); - t2.reRoot( t2.getNode( "B" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "C" ) ); - t2.reRoot( t2.getNode( "ABC" ) ); - t2.reRoot( t2.getNode( "A" ) ); - t2.reRoot( t2.getNode( "B" ) ); - t2.reRoot( t2.getNode( "AB" ) ); - t2.reRoot( t2.getNode( "AB" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "C" ) ); - t2.reRoot( t2.getNode( "B" ) ); - t2.reRoot( t2.getNode( "AB" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "ABC" ) ); - t2.reRoot( t2.getNode( "A" ) ); - t2.reRoot( t2.getNode( "B" ) ); - t2.reRoot( t2.getNode( "AB" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "C" ) ); - t2.reRoot( t2.getNode( "ABC" ) ); - t2.reRoot( t2.getNode( "A" ) ); - t2.reRoot( t2.getNode( "B" ) ); - t2.reRoot( t2.getNode( "AB" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "C" ) ); - t2.reRoot( t2.getNode( "A" ) ); - t2.reRoot( t2.getNode( "B" ) ); - t2.reRoot( t2.getNode( "AB" ) ); - t2.reRoot( t2.getNode( "C" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "ABC" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "A" ) ); - t2.reRoot( t2.getNode( "B" ) ); - t2.reRoot( t2.getNode( "AB" ) ); - t2.reRoot( t2.getNode( "C" ) ); - t2.reRoot( t2.getNode( "D" ) ); - t2.reRoot( t2.getNode( "ABC" ) ); - t2.reRoot( t2.getNode( "D" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { return false; } - t2.reRoot( t2.getNode( "ABC" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( phylogenies[ 0 ].isRooted() ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - t2.reRoot( t2.getNode( "AB" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { return false; } - t2.reRoot( t2.getNode( "AB" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( phylogenies[ 1 ].isRooted() ) { return false; } - if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - t2.reRoot( t2.getNode( "D" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - t2.reRoot( t2.getNode( "ABC" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { return false; } - final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])", - new NHXParser() )[ 0 ]; - t3.reRoot( t3.getNode( "B" ) ); - if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) { + if ( !phylogenies[ 2 ].isRooted() ) { return false; } - if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - t3.reRoot( t3.getNode( "B" ) ); - if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser ); + if ( phylogenies.length != 3 ) { return false; } - if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { return false; } - t3.reRoot( t3.getRoot() ); - if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) { + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { return false; } - if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + if ( phylogenies[ 0 ].isRooted() ) { return false; } - if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSDIse() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ]; - final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ]; - gene1.setRooted( true ); - species1.setRooted( true ); - final SDI sdi = new SDIse( gene1, species1 ); - if ( !gene1.getRoot().isDuplication() ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - final Phylogeny species2 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene2 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", - new NHXParser() )[ 0 ]; - species2.setRooted( true ); - gene2.setRooted( true ); - final SDI sdi2 = new SDIse( gene2, species2 ); - if ( sdi2.getDuplicationsSum() != 0 ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( !gene2.getNode( "ab" ).isSpeciation() ) { + if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) { + if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { return false; } - if ( !gene2.getNode( "abc" ).isSpeciation() ) { + if ( phylogenies[ 1 ].isRooted() ) { return false; } - if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - if ( !gene2.getNode( "r" ).isSpeciation() ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - final Phylogeny species3 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene3 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", - new NHXParser() )[ 0 ]; - species3.setRooted( true ); - gene3.setRooted( true ); - final SDI sdi3 = new SDIse( gene3, species3 ); - if ( sdi3.getDuplicationsSum() != 1 ) { + if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !gene3.getNode( "aa" ).isDuplication() ) { + if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { return false; } - if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) { + if ( !phylogenies[ 2 ].isRooted() ) { return false; } - final Phylogeny species4 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene4 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", - new NHXParser() )[ 0 ]; - species4.setRooted( true ); - gene4.setRooted( true ); - final SDI sdi4 = new SDIse( gene4, species4 ); - if ( sdi4.getDuplicationsSum() != 1 ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - if ( !gene4.getNode( "ac" ).isSpeciation() ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - if ( !gene4.getNode( "abc" ).isDuplication() ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( gene4.getNode( "abcd" ).isDuplication() ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNHParsing() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ]; + if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) { return false; } - if ( species4.getNumberOfExternalNodes() != 6 ) { + final NHXParser nhxp = new NHXParser(); + nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO ); + nhxp.setReplaceUnderscores( true ); + final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ]; + if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) { return false; } - if ( gene4.getNumberOfExternalNodes() != 6 ) { + if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) { return false; } - final Phylogeny species5 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene5 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + final Phylogeny p1b = factory + .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ", new NHXParser() )[ 0 ]; - species5.setRooted( true ); - gene5.setRooted( true ); - final SDI sdi5 = new SDIse( gene5, species5 ); - if ( sdi5.getDuplicationsSum() != 2 ) { + if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) { return false; } - if ( !gene5.getNode( "ad" ).isSpeciation() ) { + if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) { return false; } - if ( !gene5.getNode( "adc" ).isDuplication() ) { + final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ]; + final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ]; + final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ]; + final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ]; + final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() ); + final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() ); + final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() ); + final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() ); + final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() ); + final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() ); + final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;" + + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " + + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", + new NHXParser() ); + if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) { return false; } - if ( !gene5.getNode( "abcd" ).isDuplication() ) { + if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) { return false; } - if ( species5.getNumberOfExternalNodes() != 6 ) { + if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) { return false; } - if ( gene5.getNumberOfExternalNodes() != 6 ) { + if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) { return false; } - // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith - // Conjecture for Comparing Molecular Phylogenies" - // J. of Comput Bio. Vol. 4, No 2, pp.177-187 - final Phylogeny species6 = factory - .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; - final Phylogeny gene6 = factory - .create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1," - + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;", - new NHXParser() )[ 0 ]; - species6.setRooted( true ); - gene6.setRooted( true ); - final SDI sdi6 = new SDIse( gene6, species6 ); - if ( sdi6.getDuplicationsSum() != 3 ) { + final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() ); + final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() ); + final String p16_S = "((A,B),C)"; + final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() ); + if ( p16.length != 1 ) { return false; } - if ( !gene6.getNode( "r" ).isDuplication() ) { + if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) { return false; } - if ( !gene6.getNode( "4-5-6" ).isDuplication() ) { + final String p17_S = "(C,(A,B))"; + final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() ); + if ( p17.length != 1 ) { return false; } - if ( !gene6.getNode( "7-8-9" ).isDuplication() ) { + if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) { return false; } - if ( !gene6.getNode( "1-2" ).isSpeciation() ) { + final String p18_S = "((A,B),(C,D))"; + final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() ); + if ( p18.length != 1 ) { return false; } - if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) { + if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) { return false; } - if ( !gene6.getNode( "5-6" ).isSpeciation() ) { + final String p19_S = "(((A,B),C),D)"; + final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() ); + if ( p19.length != 1 ) { return false; } - if ( !gene6.getNode( "8-9" ).isSpeciation() ) { + if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) { return false; } - if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) { + final String p20_S = "(A,(B,(C,D)))"; + final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() ); + if ( p20.length != 1 ) { return false; } - sdi6.computeMappingCostL(); - if ( sdi6.computeMappingCostL() != 17 ) { + if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) { return false; } - if ( species6.getNumberOfExternalNodes() != 9 ) { + final String p21_S = "(A,(B,(C,(D,E))))"; + final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() ); + if ( p21.length != 1 ) { return false; } - if ( gene6.getNumberOfExternalNodes() != 9 ) { + if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) { return false; } - final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2])," - + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2])," - + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2])," - + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2])," - + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" ); - species7.setRooted( true ); - final Phylogeny gene7_1 = Test - .createPhylogeny( "((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); - gene7_1.setRooted( true ); - final SDI sdi7 = new SDIse( gene7_1, species7 ); - if ( sdi7.getDuplicationsSum() != 0 ) { + final String p22_S = "((((A,B),C),D),E)"; + final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() ); + if ( p22.length != 1 ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) { + if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) { + final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() ); + if ( p23.length != 1 ) { + System.out.println( "xl=" + p23.length ); + System.exit( -1 ); return false; } - if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) { + if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) { + final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() ); + if ( p24.length != 1 ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) { + if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) { + final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() ); + if ( p241.length != 2 ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) { + if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) { + if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) { return false; } - final Phylogeny gene7_2 = Test - .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); - gene7_2.setRooted( true ); - final SDI sdi7_2 = new SDIse( gene7_2, species7 ); - if ( sdi7_2.getDuplicationsSum() != 1 ) { + final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)" + + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D," + + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)" + + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde," + + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd," + + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)" + + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde" + + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde"; + final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() ); + if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) { + final String p26_S = "(A,B)ab"; + final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() ); + if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) { + final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() ); + if ( p27s.length != 1 ) { + System.out.println( "xxl=" + p27s.length ); + System.exit( -1 ); return false; } - if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) { + if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) { + System.out.println( p27s[ 0 ].toNewHampshireX() ); + System.exit( -1 ); return false; } - if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) { + final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ), + new NHXParser() ); + if ( p27.length != 1 ) { + System.out.println( "yl=" + p27.length ); + System.exit( -1 ); return false; } - if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) { + if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) { + System.out.println( p27[ 0 ].toNewHampshireX() ); + System.exit( -1 ); return false; } - if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) { + final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + final String p28_S3 = "(A,B)ab"; + final String p28_S4 = "((((A,B),C),D),;E;)"; + final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ), + new NHXParser() ); + if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) { + if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) { + if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) { + if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) { return false; } - } - catch ( final Exception e ) { - return false; - } - return true; - } - - private static boolean testSDIunrooted() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ]; - final List l = SDIR.getBranchesInPreorder( p0 ); - final Iterator iter = l.iterator(); - PhylogenyBranch br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) { + if ( p28.length != 4 ) { return false; } - if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) { + final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345"; + final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() ); + if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) { + final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72"; + final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() ); + if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) { + final String p32_S = " ; ; \n \t \b \f \r ;;;;;; "; + final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() ); + if ( ( p32.length != 0 ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) { + final String p33_S = "A"; + final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() ); + if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) { + final String p34_S = "B;"; + final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() ); + if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { + final String p35_S = "B:0.2"; + final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() ); + if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + final String p36_S = "(A)"; + final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() ); + if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + final String p37_S = "((A))"; + final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() ); + if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { + final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; + final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() ); + if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) { + final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; + final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() ); + if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) { + final String p40_S = "(A,B,C)"; + final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() ); + if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)"; + final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() ); + if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)"; + final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() ); + if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; + final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() ); + if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; + final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() ); + if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))"; + final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() ); + if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + final String p46_S = ""; + final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() ); + if ( p46.length != 0 ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ]; + if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) { + final Phylogeny p49 = factory + .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ), + new NHXParser() )[ 0 ]; + if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) { + final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + if ( p50.getNode( "A" ) == null ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) { + if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) + .equals( "((A,B)ab:2.0[88],C);" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) { + if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) { + if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ) + .equals( "((A,B)88:2.0,C);" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) { + final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + if ( p51.getNode( "A(A" ) == null ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) { + final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + if ( p52.getNode( "A(A" ) == null ) { return false; } - if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) { + final Phylogeny p53 = factory + .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ), + new NHXParser() )[ 0 ]; + if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) { + // + final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ]; + if ( p54.getNode( "A" ) == null ) { return false; } - if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) { + if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) + .equals( "((A,B)[88],C);" ) ) { return false; } - if ( iter.hasNext() ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNHParsingIter() { + try { + final String p0_str = "(A,B);"; + final NHXParser p = new NHXParser(); + p.setSource( p0_str ); + if ( !p.hasNext() ) { return false; } - final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ]; - final List l1 = SDIR.getBranchesInPreorder( p1 ); - final Iterator iter1 = l1.iterator(); - br = iter1.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) { + final Phylogeny p0 = p.next(); + if ( !p0.toNewHampshire().equals( p0_str ) ) { + System.out.println( p0.toNewHampshire() ); return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) { + if ( p.hasNext() ) { return false; } - br = iter1.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { + if ( p.next() != null ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + // + final String p00_str = "(A,B)root;"; + p.setSource( p00_str ); + final Phylogeny p00 = p.next(); + if ( !p00.toNewHampshire().equals( p00_str ) ) { + System.out.println( p00.toNewHampshire() ); return false; } - br = iter1.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + // + final String p000_str = "A;"; + p.setSource( p000_str ); + final Phylogeny p000 = p.next(); + if ( !p000.toNewHampshire().equals( p000_str ) ) { + System.out.println( p000.toNewHampshire() ); return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { + // + final String p0000_str = "A"; + p.setSource( p0000_str ); + final Phylogeny p0000 = p.next(); + if ( !p0000.toNewHampshire().equals( "A;" ) ) { + System.out.println( p0000.toNewHampshire() ); return false; } - if ( iter1.hasNext() ) { + // + p.setSource( "(A)" ); + final Phylogeny p00000 = p.next(); + if ( !p00000.toNewHampshire().equals( "(A);" ) ) { + System.out.println( p00000.toNewHampshire() ); return false; } - final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ]; - final List l2 = SDIR.getBranchesInPreorder( p2 ); - final Iterator iter2 = l2.iterator(); - br = iter2.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) { + // + final String p1_str = "(A,B)(C,D)(E,F)(G,H)"; + p.setSource( p1_str ); + if ( !p.hasNext() ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) { + final Phylogeny p1_0 = p.next(); + if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) { + System.out.println( p1_0.toNewHampshire() ); return false; } - br = iter2.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { + if ( !p.hasNext() ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + final Phylogeny p1_1 = p.next(); + if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( "(C,D) != " + p1_1.toNewHampshire() ); return false; } - br = iter2.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + if ( !p.hasNext() ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { + final Phylogeny p1_2 = p.next(); + if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) { + System.out.println( "(E,F) != " + p1_2.toNewHampshire() ); return false; } - if ( iter2.hasNext() ) { + if ( !p.hasNext() ) { return false; } - final Phylogeny species0 = factory - .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", - new NHXParser() )[ 0 ]; - final Phylogeny gene1 = factory - .create( "(((((A:0.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])", - new NHXParser() )[ 0 ]; - species0.setRooted( true ); - gene1.setRooted( true ); - final SDIR sdi_unrooted = new SDIR(); - sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 ); - if ( sdi_unrooted.getCount() != 1 ) { + final Phylogeny p1_3 = p.next(); + if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) { + System.out.println( "(G,H) != " + p1_3.toNewHampshire() ); return false; } - if ( sdi_unrooted.getMinimalDuplications() != 0 ) { + if ( p.hasNext() ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) { + if ( p.next() != null ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) { + // + final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)"; + p.setSource( p2_str ); + if ( !p.hasNext() ) { return false; } - if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + Phylogeny p2_0 = p.next(); + if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) { + System.out.println( p2_0.toNewHampshire() ); return false; } - final Phylogeny gene2 = factory - .create( "(((((A:2.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])", - new NHXParser() )[ 0 ]; - gene2.setRooted( true ); - sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 ); - if ( sdi_unrooted.getCount() != 1 ) { + if ( !p.hasNext() ) { return false; } - if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + Phylogeny p2_1 = p.next(); + if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( "(C,D) != " + p2_1.toNewHampshire() ); return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + if ( !p.hasNext() ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) { + Phylogeny p2_2 = p.next(); + if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) { + System.out.println( "(E,F)root != " + p2_2.toNewHampshire() ); return false; } - if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + if ( !p.hasNext() ) { return false; } - final Phylogeny species6 = factory - .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; - final Phylogeny gene6 = factory - .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; - species6.setRooted( true ); - gene6.setRooted( true ); - Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 ); - if ( sdi_unrooted.getCount() != 1 ) { + Phylogeny p2_3 = p.next(); + if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) { + System.out.println( "(G,H) != " + p2_3.toNewHampshire() ); return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + if ( !p.hasNext() ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + Phylogeny p2_4 = p.next(); + if ( !p2_4.toNewHampshire().equals( "(X);" ) ) { + System.out.println( "(X) != " + p2_4.toNewHampshire() ); return false; } - if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + if ( p.hasNext() ) { return false; } - if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + if ( p.next() != null ) { return false; } - if ( !p6[ 0 ].getRoot().isDuplication() ) { + //// + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) { + p2_0 = p.next(); + if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) { + System.out.println( p2_0.toNewHampshire() ); return false; } - if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) { + if ( !p.hasNext() ) { return false; } - if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) { + p2_1 = p.next(); + if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( "(C,D) != " + p2_1.toNewHampshire() ); return false; } - if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) { + if ( !p.hasNext() ) { return false; } - if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) { + p2_2 = p.next(); + if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) { + System.out.println( "(E,F)root != " + p2_2.toNewHampshire() ); return false; } - if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) { + if ( !p.hasNext() ) { return false; } - if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { + p2_3 = p.next(); + if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) { + System.out.println( "(G,H) != " + p2_3.toNewHampshire() ); return false; } - p6 = null; - final Phylogeny species7 = factory - .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; - final Phylogeny gene7 = factory - .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; - species7.setRooted( true ); - gene7.setRooted( true ); - Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 ); - if ( sdi_unrooted.getCount() != 1 ) { + if ( !p.hasNext() ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + p2_4 = p.next(); + if ( !p2_4.toNewHampshire().equals( "(X);" ) ) { + System.out.println( "(X) != " + p2_4.toNewHampshire() ); return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + if ( p.hasNext() ) { return false; } - if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + if ( p.next() != null ) { return false; } - if ( sdi_unrooted.getMinimalMappingCost() != 17 ) { + // + final String p3_str = "((A,B),C)abc"; + p.setSource( p3_str ); + if ( !p.hasNext() ) { return false; } - if ( !p7[ 0 ].getRoot().isDuplication() ) { + final Phylogeny p3_0 = p.next(); + if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) { return false; } - if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) { + if ( p.hasNext() ) { return false; } - if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) { + if ( p.next() != null ) { return false; } - if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) { + // + final String p4_str = "((A,B)ab,C)abc"; + p.setSource( p4_str ); + if ( !p.hasNext() ) { return false; } - if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) { + final Phylogeny p4_0 = p.next(); + if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) { return false; } - if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) { + if ( p.hasNext() ) { return false; } - if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) { + if ( p.next() != null ) { return false; } - if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { + // + final String p5_str = "(((A,B)ab,C)abc,D)abcd"; + p.setSource( p5_str ); + if ( !p.hasNext() ) { return false; } - p7 = null; - final Phylogeny species8 = factory - .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; - final Phylogeny gene8 = factory - .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; - species8.setRooted( true ); - gene8.setRooted( true ); - Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 ); - if ( sdi_unrooted.getCount() != 1 ) { + final Phylogeny p5_0 = p.next(); + if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + if ( p.hasNext() ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + if ( p.next() != null ) { return false; } - if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + // + final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + p.setSource( p6_str ); + if ( !p.hasNext() ) { return false; } - if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + Phylogeny p6_0 = p.next(); + if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { return false; } - if ( !p8[ 0 ].getRoot().isDuplication() ) { + if ( p.hasNext() ) { return false; } - if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) { + if ( p.next() != null ) { return false; } - if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) { + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) { + p6_0 = p.next(); + if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { return false; } - if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) { + if ( p.hasNext() ) { return false; } - if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) { + if ( p.next() != null ) { return false; } - if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) { + // + final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + p.setSource( p7_str ); + if ( !p.hasNext() ) { return false; } - if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { + Phylogeny p7_0 = p.next(); + if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { return false; } - p8 = null; - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testOrthologTable() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny s1 = factory.create( Test.PATH_TO_TEST_DATA + "rio_species.xml", new PhyloXmlParser() )[ 0 ]; - final NHXParser p = new NHXParser(); - p.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES ); - final Phylogeny g1[] = factory.create( new File( Test.PATH_TO_TEST_DATA - + "rio_Bcl-2_e1_20_mafft_05_40_fme.mlt" ), p ); - for( final Phylogeny gt : g1 ) { - gt.setRooted( true ); - final GSDI sdi = new GSDI( gt, s1, true, true, true ); + if ( p.hasNext() ) { + return false; } - final IntMatrix m = RIO.calculateOrthologTable( g1 ); - System.out.println( m.toString() ); - } - catch ( final Exception e ) { - e.printStackTrace(); - return false; - } - return true; - } - - 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" ) ); - 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 ) ) { + if ( p.next() != null ) { 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 ) ) { + p.reset(); + if ( !p.hasNext() ) { 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 ) ) { + p7_0 = p.next(); + if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { 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 ( p.hasNext() ) { 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 ) ) { + if ( p.next() != null ) { 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 ) ) { + final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde"; + p.setSource( p8_str ); + if ( !p.hasNext() ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( !s0.match( query_nodes ) ) { + Phylogeny p8_0 = p.next(); + if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { 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 ( !p.hasNext() ) { 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 ) ) { + if ( !p.hasNext() ) { 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 ) ) { + Phylogeny p8_1 = p.next(); + if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - if ( s0.match( query_nodes ) ) { + if ( p.hasNext() ) { 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 ) ) { + if ( p.next() != null ) { 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 ) ) { + p.reset(); + if ( !p.hasNext() ) { 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 ) ) { + p8_0 = p.next(); + if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( s0.match( query_nodes ) ) { + if ( !p.hasNext() ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + p8_1 = p.next(); + if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( s0.match( query_nodes ) ) { + if ( p.hasNext() ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - if ( s0.match( query_nodes ) ) { + if ( p.next() != null ) { return false; } + p.reset(); // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - if ( s0.match( query_nodes ) ) { + p.setSource( "" ); + if ( p.hasNext() ) { return false; } // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) ); + if ( !p.hasNext() ) { 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 ) ) { + Phylogeny p_27 = p.next(); + if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { + System.out.println( p_27.toNewHampshireX() ); + System.exit( -1 ); return false; } - // - 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 ( p.hasNext() ) { 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 ( p.next() != null ) { 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 ) ) { + p.reset(); + if ( !p.hasNext() ) { 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 ) ) { - 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 ) ) { - 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 ) ) { - 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 ) ) { + p_27 = p.next(); + if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { + System.out.println( p_27.toNewHampshireX() ); + System.exit( -1 ); return false; } - // - 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 ( p.hasNext() ) { 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 ( p.next() != 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( "F" ) ); - if ( s0.match( query_nodes ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNHXconversion() { + try { + final PhylogenyNode n1 = new PhylogenyNode(); + final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" ); + final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" ); + final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" ); + final PhylogenyNode n5 = PhylogenyNode + .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" ); + final PhylogenyNode n6 = PhylogenyNode + .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" ); + if ( !n1.toNewHampshireX().equals( "" ) ) { return false; } - // - 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 ( !n2.toNewHampshireX().equals( "" ) ) { 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 ( !n3.toNewHampshireX().equals( "n3" ) ) { 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 ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) { 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 ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) { 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 ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) { + System.out.println( n6.toNewHampshireX() ); return false; } } catch ( final Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testSplitStrict() { + private static boolean testNHXNodeParsing() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ]; - final Set ex = new HashSet(); - 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 ) ) { + final PhylogenyNode n1 = new PhylogenyNode(); + final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" ); + final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" ); + final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" ); + final PhylogenyNode n5 = PhylogenyNode + .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" ); + if ( !n3.getName().equals( "n3" ) ) { 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 ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { 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 ( n3.isDuplication() ) { 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 ( n3.isHasAssignedEvent() ) { 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 ) ) { + if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) { 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 ( !n4.getName().equals( "n4" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( !s0.match( query_nodes ) ) { + if ( n4.getDistanceToParent() != 0.01 ) { 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 ( !n5.getName().equals( "n5" ) ) { 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 ) ) { + if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) { 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 ( n5.getDistanceToParent() != 0.1 ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - if ( s0.match( query_nodes ) ) { + if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) { 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 ) ) { + if ( !n5.isDuplication() ) { 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 ) ) { + if ( !n5.isHasAssignedEvent() ) { 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 ) ) { + final PhylogenyNode n8 = PhylogenyNode + .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( s0.match( query_nodes ) ) { + if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + final PhylogenyNode n9 = PhylogenyNode + .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( s0.match( query_nodes ) ) { + if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - if ( s0.match( query_nodes ) ) { + final PhylogenyNode n10 = PhylogenyNode + .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n10.getName().equals( "n10.ECOLI" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - if ( s0.match( query_nodes ) ) { + final PhylogenyNode n20 = PhylogenyNode + .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) { 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 ) ) { + final PhylogenyNode n20x = PhylogenyNode + .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) { return false; } - // - 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 ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) { 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 ) ) { + final PhylogenyNode n20xx = PhylogenyNode + .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) { 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 ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace(); - return false; - } - 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 ) { + final PhylogenyNode n20xxx = PhylogenyNode + .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) { return false; } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "E" ), false ); - if ( t1.getNumberOfExternalNodes() != 4 ) { + if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) { return false; } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "F" ), false ); - if ( t1.getNumberOfExternalNodes() != 3 ) { + final PhylogenyNode n20xxxx = PhylogenyNode + .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) { return false; } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "D" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 3 ) { + if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) { return false; } - t1.deleteSubtree( t1.getNode( "def" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 2 ) { + final PhylogenyNode n21 = PhylogenyNode + .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n21.getName().equals( "N21_PIG" ) ) { return false; } - t1.deleteSubtree( t1.getNode( "B" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { + if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) { return false; } - t1.deleteSubtree( t1.getNode( "C" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { + final PhylogenyNode n21x = PhylogenyNode + .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n21x.getName().equals( "n21_PIG" ) ) { return false; } - t1.deleteSubtree( t1.getNode( "abc" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { + if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) { return false; } - t1.deleteSubtree( t1.getNode( "r" ), false ); - if ( t1.getNumberOfExternalNodes() != 0 ) { + final PhylogenyNode n22 = PhylogenyNode + .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n22.getName().equals( "n22/PIG" ) ) { return false; } - if ( !t1.isEmpty() ) { + if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) { 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 ) { + final PhylogenyNode n23 = PhylogenyNode + .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n23.getName().equals( "n23/PIG_1" ) ) { return false; } - t2.deleteSubtree( t2.getNode( "abc" ), false ); - t2.toNewHampshireX(); - if ( t2.getNumberOfExternalNodes() != 3 ) { + if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) { return false; } - t2.deleteSubtree( t2.getNode( "def" ), false ); - t2.toNewHampshireX(); - if ( t2.getNumberOfExternalNodes() != 1 ) { + final PhylogenyNode a = PhylogenyNode + .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSupportCount() { - 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; - } + if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) { + 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 ) { + final PhylogenyNode c1 = PhylogenyNode + .createInstanceFromNhxString( "n10_BOVIN/1000-2000", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) { + if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) { + final PhylogenyNode c2 = PhylogenyNode + .createInstanceFromNhxString( "N10_Bovin_1/1000-2000", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) { + if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) { + final PhylogenyNode e3 = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !e3.getName().equals( "n10_RAT~" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) { + if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) { + final PhylogenyNode n11 = PhylogenyNode + .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) { + if ( n11.getDistanceToParent() != 0.4 ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) { + if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) { + final PhylogenyNode n12 = PhylogenyNode + .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) { 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 ) { + if ( n12.getDistanceToParent() != 0.4 ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) { + if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) { + final PhylogenyNode o = PhylogenyNode + .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !o.getName().equals( "ABCD_MOUSE" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) { + if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) { + if ( n1.getName().compareTo( "" ) != 0 ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) { + if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) { + if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) { + if ( n2.getName().compareTo( "" ) != 0 ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) { + if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + return false; + } + if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + return false; + } + final PhylogenyNode n00 = PhylogenyNode + .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" ); + if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) { + return false; + } + if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) { + return false; + } + final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" ); + if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) { + return false; + } + final PhylogenyNode n13 = PhylogenyNode + .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n13.getName().equals( "blah_12345/1-2" ) ) { + return false; + } + if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) { + return false; + } + if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + return false; + } + if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { + return false; + } + final PhylogenyNode n14 = PhylogenyNode + .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) { + return false; + } + final PhylogenyNode n15 = PhylogenyNode + .createInstanceFromNhxString( "something_wicked[123]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n15.getName().equals( "something_wicked" ) ) { + return false; + } + if ( n15.getBranchData().getNumberOfConfidences() != 1 ) { + return false; + } + if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) { + return false; + } + final PhylogenyNode n16 = PhylogenyNode + .createInstanceFromNhxString( "something_wicked2[9]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n16.getName().equals( "something_wicked2" ) ) { + return false; + } + if ( n16.getBranchData().getNumberOfConfidences() != 1 ) { + return false; + } + if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) { + return false; + } + final PhylogenyNode n17 = PhylogenyNode + .createInstanceFromNhxString( "something_wicked3[a]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n17.getName().equals( "something_wicked3" ) ) { + return false; + } + if ( n17.getBranchData().getNumberOfConfidences() != 0 ) { + return false; + } + final PhylogenyNode n18 = PhylogenyNode + .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( n18.getBranchData().getNumberOfConfidences() != 1 ) { + return false; + } + if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) { + return false; + } + final PhylogenyNode n19 = PhylogenyNode + .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { + return false; + } + if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { + return false; + } + final PhylogenyNode n30 = PhylogenyNode + .createInstanceFromNhxString( "blah_1234567-roejojoej", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) { + return false; + } + if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { + return false; + } + final PhylogenyNode n31 = PhylogenyNode + .createInstanceFromNhxString( "blah_12345678-roejojoej", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n31.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n32 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n32.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n40 = PhylogenyNode + .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + return false; + } + final PhylogenyNode n41 = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n41.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n42 = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( n42.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345", + NHXParser.TAXONOMY_EXTRACTION.NO ); + if ( n43.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n44 = PhylogenyNode + .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n44.getNodeData().isHasTaxonomy() ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNHXParsing() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ]; + if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) { + return false; + } + final String p2_S = "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]"; + final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() ); + if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) { + return false; + } + final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]"; + final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() ); + if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) { + return false; + } + final Phylogeny[] p3 = factory + .create( "[ comment&&NHX,())))](((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]", + new NHXParser() ); + if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) { + return false; + } + final Phylogeny[] p4 = factory + .create( "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(]", + new NHXParser() ); + if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) { + return false; + } + final Phylogeny[] p5 = factory + .create( "[] ( [][ ][ ] ([((( &&NHXcomment only![[[[[[]([]((((A:0.2[&&NHX:S=q[comment )))]werty][,,,,))]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=a[comment,,))]sdf])[comment(((]:0.4[&&NHX:S=zxc][comment(((][comment(((]):0.5[&&NHX:S=a]):0.6[&&NHX:S=a[comment(((]sd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(((]", + new NHXParser() ); + if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) { + return false; + } + final String p6_S_C = "(A[][][][1][22][333][4444][55555][666666][&&NHX:S=Aspecies],B[))],C,(AA,BB,CC,(CCC,DDD,EEE,[comment](FFFF,GGGG)x)y,D[comment]D,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; + final String p6_S_WO_C = "(A[&&NHX:S=Aspecies],B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; + final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() ); + if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) { + return false; + } + final String p7_S_C = "(((A [&&NHX:S=species_a], B [&&NHX:S=Vstorri] , C , D),(A,B,C,D[comment])[],[c][]([xxx]A[comment],[comment]B[comment][comment],[comment][comment]C[comment][comment],[comment][comment]D[comment][comment])[comment][comment],[comment] [comment](A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C[comment][comment][comment][comment][comment] [comment],D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),[comment][comment]((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; + final String p7_S_WO_C = "(((A[&&NHX:S=species_a],B[&&NHX:S=Vstorri],C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; + final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() ); + if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) { + return false; + } + final String p8_S_C = "[cmt](((([]([))))))](((((A[&&NHX:S= [a comment] a])))))))[too many comments!:)])),(((((((((B[&&NHX[ a comment in a bad place]:S =b])))))[] [] )))),(((((((((C[&&NHX:S=c]) ))[,,, ])))))))"; + final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))"; + final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() ); + if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) { + return false; + } + final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ]; + if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { + return false; + } + final Phylogeny p10 = factory + .create( " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]", + new NHXParser() )[ 0 ]; + if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNHXParsingMB() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02," + + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02," + + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," + + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," + + "7.369400000000000e-02}])", new NHXParser() )[ 0 ]; + if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) { + return false; + } + if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) { + return false; + } + if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(), + 0.1100000000000000e+00 ) ) { + return false; + } + if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) { + return false; + } + if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) { + return false; + } + final Phylogeny p2 = factory + .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02," + + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02," + + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," + + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," + + "7.369400000000000e-02}])", + new NHXParser() )[ 0 ]; + if ( p2.getNode( "1" ) == null ) { + return false; + } + if ( p2.getNode( "2" ) == null ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + System.exit( -1 ); + return false; + } + return true; + } + + private static boolean testNHXParsingQuotes() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final NHXParser p = new NHXParser(); + final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p ); + if ( phylogenies_0.length != 5 ) { + return false; + } + final Phylogeny phy = phylogenies_0[ 4 ]; + if ( phy.getNumberOfExternalNodes() != 7 ) { + return false; + } + if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) { + return false; + } + if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) { + return false; + } + if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy() + .getScientificName().equals( "hsapiens" ) ) { + return false; + } + if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) { + return false; + } + if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) { + return false; + } + if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) { + return false; + } + if ( phy.getNodes( "noquotes" ).size() != 1 ) { + return false; + } + if ( phy.getNodes( "A ( B C '" ).size() != 1 ) { + return false; + } + final NHXParser p1p = new NHXParser(); + p1p.setIgnoreQuotes( true ); + final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ]; + if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) { + return false; + } + final NHXParser p2p = new NHXParser(); + p1p.setIgnoreQuotes( false ); + final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ]; + if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) { + return false; + } + final NHXParser p3p = new NHXParser(); + p3p.setIgnoreQuotes( false ); + final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ]; + if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) { + return false; + } + final NHXParser p4p = new NHXParser(); + p4p.setIgnoreQuotes( false ); + final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ]; + if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) { + return false; + } + final Phylogeny p10 = factory + .create( " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]", + new NHXParser() )[ 0 ]; + final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]"; + if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) { + return false; + } + final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ]; + if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) { + return false; + } + // + final Phylogeny p12 = factory + .create( " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]", + new NHXParser() )[ 0 ]; + final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]"; + if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) { + return false; + } + final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ]; + if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) { + return false; + } + final String p12_clean_str_nh = "(('A B':0.2,'BB B':0.03):0.5,'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1;"; + if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) { + return false; + } + final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ]; + if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNodeRemoval() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ]; + PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 ); + if ( !t0.toNewHampshire().equals( "(a);" ) ) { + return false; + } + final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ]; + PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 ); + if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) { + return false; + } + final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ]; + PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 ); + if ( !t2.toNewHampshire().equals( "((a),c);" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testPhylogenyBranch() { + try { + final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" ); + final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" ); + final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 ); + final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 ); + if ( !a1b1.equals( a1b1 ) ) { + return false; + } + if ( !a1b1.equals( b1a1 ) ) { + return false; + } + if ( !b1a1.equals( a1b1 ) ) { + return false; + } + final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true ); + final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true ); + final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false ); + if ( a1_b1.equals( b1_a1 ) ) { + return false; + } + if ( a1_b1.equals( a1_b1_ ) ) { + return false; + } + final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false ); + if ( !a1_b1.equals( b1_a1_ ) ) { + return false; + } + if ( a1_b1_.equals( b1_a1_ ) ) { + return false; + } + if ( !a1_b1_.equals( b1_a1 ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testPhyloXMLparsingOfDistributionElement() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + PhyloXmlParser xml_parser = null; + try { + xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating(); + } + catch ( final Exception e ) { + // Do nothing -- means were not running from jar. + } + if ( xml_parser == null ) { + xml_parser = PhyloXmlParser.createPhyloXmlParser(); + if ( USE_LOCAL_PHYLOXML_SCHEMA ) { + xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); + } + else { + xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); + } + } + final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml", + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); + return false; + } + if ( phylogenies_0.length != 1 ) { + return false; + } + final Phylogeny t1 = phylogenies_0[ 0 ]; + PhylogenyNode n = null; + Distribution d = null; + n = t1.getNode( "root node" ); + if ( !n.getNodeData().isHasDistribution() ) { + return false; + } + if ( n.getNodeData().getDistributions().size() != 1 ) { + return false; + } + d = n.getNodeData().getDistribution(); + if ( !d.getDesc().equals( "Hirschweg 38" ) ) { + return false; + } + if ( d.getPoints().size() != 1 ) { + return false; + } + if ( d.getPolygons() != null ) { + return false; + } + if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) { + return false; + } + n = t1.getNode( "node a" ); + if ( !n.getNodeData().isHasDistribution() ) { + return false; + } + if ( n.getNodeData().getDistributions().size() != 2 ) { + return false; + } + d = n.getNodeData().getDistribution( 1 ); + if ( !d.getDesc().equals( "San Diego" ) ) { + return false; + } + if ( d.getPoints().size() != 1 ) { + return false; + } + if ( d.getPolygons() != null ) { + return false; + } + if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) { + return false; + } + n = t1.getNode( "node bb" ); + if ( !n.getNodeData().isHasDistribution() ) { + return false; + } + if ( n.getNodeData().getDistributions().size() != 1 ) { + return false; + } + d = n.getNodeData().getDistribution( 0 ); + if ( d.getPoints().size() != 3 ) { + return false; + } + if ( d.getPolygons().size() != 2 ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) { + return false; + } + if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) { + return false; + } + if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) { + return false; + } + if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) { + return false; + } + if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) { + return false; + } + Polygon p = d.getPolygons().get( 0 ); + if ( p.getPoints().size() != 3 ) { + return false; + } + if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) { + return false; + } + if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) { + return false; + } + if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + return false; + } + if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) { + return false; + } + if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) { + return false; + } + if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) { + return false; + } + p = d.getPolygons().get( 1 ); + if ( p.getPoints().size() != 3 ) { + return false; + } + if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) { + return false; + } + if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) { + return false; + } + if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + return false; + } + // Roundtrip: + final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) ); + final Phylogeny[] rt = factory.create( t1_sb, xml_parser ); + if ( rt.length != 1 ) { + return false; + } + final Phylogeny t1_rt = rt[ 0 ]; + n = t1_rt.getNode( "root node" ); + if ( !n.getNodeData().isHasDistribution() ) { + return false; + } + if ( n.getNodeData().getDistributions().size() != 1 ) { + return false; + } + d = n.getNodeData().getDistribution(); + if ( !d.getDesc().equals( "Hirschweg 38" ) ) { + return false; + } + if ( d.getPoints().size() != 1 ) { + return false; + } + if ( d.getPolygons() != null ) { + return false; + } + if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) { + return false; + } + n = t1_rt.getNode( "node a" ); + if ( !n.getNodeData().isHasDistribution() ) { + return false; + } + if ( n.getNodeData().getDistributions().size() != 2 ) { + return false; + } + d = n.getNodeData().getDistribution( 1 ); + if ( !d.getDesc().equals( "San Diego" ) ) { + return false; + } + if ( d.getPoints().size() != 1 ) { + return false; + } + if ( d.getPolygons() != null ) { + return false; + } + if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) { + return false; + } + n = t1_rt.getNode( "node bb" ); + if ( !n.getNodeData().isHasDistribution() ) { + return false; + } + if ( n.getNodeData().getDistributions().size() != 1 ) { + return false; + } + d = n.getNodeData().getDistribution( 0 ); + if ( d.getPoints().size() != 3 ) { + return false; + } + if ( d.getPolygons().size() != 2 ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) { + return false; + } + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) { + return false; + } + if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) { + return false; + } + if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) { + return false; + } + if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) { + return false; + } + if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) { + return false; + } + p = d.getPolygons().get( 0 ); + if ( p.getPoints().size() != 3 ) { + return false; + } + if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) { + return false; + } + if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) { + return false; + } + if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + return false; + } + if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) { + return false; + } + if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) { + return false; + } + if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) { + return false; + } + p = d.getPolygons().get( 1 ); + if ( p.getPoints().size() != 3 ) { + return false; + } + if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) { + return false; + } + if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) { + return false; + } + if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testPostOrderIterator() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ]; + PhylogenyNodeIterator it0; + for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) { + it0.next(); + } + for( it0.reset(); it0.hasNext(); ) { + it0.next(); + } + final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ]; + final PhylogenyNodeIterator it = t1.iteratorPostorder(); + if ( !it.next().getName().equals( "A" ) ) { + return false; + } + if ( !it.next().getName().equals( "B" ) ) { + return false; + } + if ( !it.next().getName().equals( "ab" ) ) { + return false; + } + if ( !it.next().getName().equals( "C" ) ) { + return false; + } + if ( !it.next().getName().equals( "D" ) ) { + return false; + } + if ( !it.next().getName().equals( "cd" ) ) { + return false; + } + if ( !it.next().getName().equals( "abcd" ) ) { + return false; + } + if ( !it.next().getName().equals( "E" ) ) { + return false; + } + if ( !it.next().getName().equals( "F" ) ) { + return false; + } + if ( !it.next().getName().equals( "ef" ) ) { + return false; + } + if ( !it.next().getName().equals( "G" ) ) { + return false; + } + if ( !it.next().getName().equals( "H" ) ) { + return false; + } + if ( !it.next().getName().equals( "gh" ) ) { + return false; + } + if ( !it.next().getName().equals( "efgh" ) ) { + return false; + } + if ( !it.next().getName().equals( "r" ) ) { + return false; + } + if ( it.hasNext() ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testPreOrderIterator() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ]; + PhylogenyNodeIterator it0; + for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) { + it0.next(); + } + for( it0.reset(); it0.hasNext(); ) { + it0.next(); + } + PhylogenyNodeIterator it = t0.iteratorPreorder(); + if ( !it.next().getName().equals( "r" ) ) { + return false; + } + if ( !it.next().getName().equals( "ab" ) ) { + return false; + } + if ( !it.next().getName().equals( "A" ) ) { + return false; + } + if ( !it.next().getName().equals( "B" ) ) { + return false; + } + if ( !it.next().getName().equals( "cd" ) ) { + return false; + } + if ( !it.next().getName().equals( "C" ) ) { + return false; + } + if ( !it.next().getName().equals( "D" ) ) { + return false; + } + if ( it.hasNext() ) { + return false; + } + final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ]; + it = t1.iteratorPreorder(); + if ( !it.next().getName().equals( "r" ) ) { + return false; + } + if ( !it.next().getName().equals( "abcd" ) ) { + return false; + } + if ( !it.next().getName().equals( "ab" ) ) { + return false; + } + if ( !it.next().getName().equals( "A" ) ) { + return false; + } + if ( !it.next().getName().equals( "B" ) ) { + return false; + } + if ( !it.next().getName().equals( "cd" ) ) { + return false; + } + if ( !it.next().getName().equals( "C" ) ) { + return false; + } + if ( !it.next().getName().equals( "D" ) ) { + return false; + } + if ( !it.next().getName().equals( "efgh" ) ) { + return false; + } + if ( !it.next().getName().equals( "ef" ) ) { + return false; + } + if ( !it.next().getName().equals( "E" ) ) { + return false; + } + if ( !it.next().getName().equals( "F" ) ) { + return false; + } + if ( !it.next().getName().equals( "gh" ) ) { + return false; + } + if ( !it.next().getName().equals( "G" ) ) { + return false; + } + if ( !it.next().getName().equals( "H" ) ) { + return false; + } + if ( it.hasNext() ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testPropertiesMap() { + try { + final PropertiesMap pm = new PropertiesMap(); + final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE ); + final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE ); + final Property p2 = new Property( "something:else", + "?", + "improbable:research", + "xsd:decimal", + AppliesTo.NODE ); + pm.addProperty( p0 ); + pm.addProperty( p1 ); + pm.addProperty( p2 ); + if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) { + return false; + } + if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) { + return false; + } + if ( pm.getProperties().size() != 3 ) { + return false; + } + if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) { + return false; + } + if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) { + return false; + } + if ( pm.getProperties().size() != 3 ) { + return false; + } + pm.removeProperty( "dimensions:diameter" ); + if ( pm.getProperties().size() != 2 ) { + return false; + } + if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) { + return false; + } + if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testProteinId() { + try { + final ProteinId id1 = new ProteinId( "a" ); + final ProteinId id2 = new ProteinId( "a" ); + final ProteinId id3 = new ProteinId( "A" ); + final ProteinId id4 = new ProteinId( "b" ); + if ( !id1.equals( id1 ) ) { + return false; + } + if ( id1.getId().equals( "x" ) ) { + return false; + } + if ( id1.getId().equals( null ) ) { + return false; + } + if ( !id1.equals( id2 ) ) { + return false; + } + if ( id1.equals( id3 ) ) { + return false; + } + if ( id1.hashCode() != id1.hashCode() ) { + return false; + } + if ( id1.hashCode() != id2.hashCode() ) { + return false; + } + if ( id1.hashCode() == id3.hashCode() ) { + return false; + } + if ( id1.compareTo( id1 ) != 0 ) { + return false; + } + if ( id1.compareTo( id2 ) != 0 ) { + return false; + } + if ( id1.compareTo( id3 ) != 0 ) { + return false; + } + if ( id1.compareTo( id4 ) >= 0 ) { + return false; + } + if ( id4.compareTo( id1 ) <= 0 ) { + return false; + } + if ( !id4.getId().equals( "b" ) ) { + return false; + } + final ProteinId id5 = new ProteinId( " C " ); + if ( !id5.getId().equals( "C" ) ) { + return false; + } + if ( id5.equals( id1 ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testReIdMethods() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ]; + final long count = PhylogenyNode.getNodeCount(); + p.levelOrderReID(); + if ( p.getNode( "r" ).getId() != count ) { + return false; + } + if ( p.getNode( "A" ).getId() != ( count + 1 ) ) { + return false; + } + if ( p.getNode( "B" ).getId() != ( count + 1 ) ) { + return false; + } + if ( p.getNode( "C" ).getId() != ( count + 1 ) ) { + return false; + } + if ( p.getNode( "1" ).getId() != ( count + 2 ) ) { + return false; + } + if ( p.getNode( "2" ).getId() != ( count + 2 ) ) { + return false; + } + if ( p.getNode( "3" ).getId() != ( count + 2 ) ) { + return false; + } + if ( p.getNode( "4" ).getId() != ( count + 2 ) ) { + return false; + } + if ( p.getNode( "5" ).getId() != ( count + 2 ) ) { + return false; + } + if ( p.getNode( "6" ).getId() != ( count + 2 ) ) { + return false; + } + if ( p.getNode( "a" ).getId() != ( count + 3 ) ) { + return false; + } + if ( p.getNode( "b" ).getId() != ( count + 3 ) ) { + return false; + } + if ( p.getNode( "X" ).getId() != ( count + 4 ) ) { + return false; + } + if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) { + return false; + } + if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testRerooting() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:5)CD:3[&&NHX:B=10])ABCD:0.5", + new NHXParser() )[ 0 ]; + if ( !t1.isRooted() ) { + return false; + } + t1.reRoot( t1.getNode( "D" ) ); + t1.reRoot( t1.getNode( "CD" ) ); + t1.reRoot( t1.getNode( "A" ) ); + t1.reRoot( t1.getNode( "B" ) ); + t1.reRoot( t1.getNode( "AB" ) ); + t1.reRoot( t1.getNode( "D" ) ); + t1.reRoot( t1.getNode( "C" ) ); + t1.reRoot( t1.getNode( "CD" ) ); + t1.reRoot( t1.getNode( "A" ) ); + t1.reRoot( t1.getNode( "B" ) ); + t1.reRoot( t1.getNode( "AB" ) ); + t1.reRoot( t1.getNode( "D" ) ); + t1.reRoot( t1.getNode( "D" ) ); + t1.reRoot( t1.getNode( "C" ) ); + t1.reRoot( t1.getNode( "A" ) ); + t1.reRoot( t1.getNode( "B" ) ); + t1.reRoot( t1.getNode( "AB" ) ); + t1.reRoot( t1.getNode( "C" ) ); + t1.reRoot( t1.getNode( "D" ) ); + t1.reRoot( t1.getNode( "CD" ) ); + t1.reRoot( t1.getNode( "D" ) ); + t1.reRoot( t1.getNode( "A" ) ); + t1.reRoot( t1.getNode( "B" ) ); + t1.reRoot( t1.getNode( "AB" ) ); + t1.reRoot( t1.getNode( "C" ) ); + t1.reRoot( t1.getNode( "D" ) ); + t1.reRoot( t1.getNode( "CD" ) ); + t1.reRoot( t1.getNode( "D" ) ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) { + return false; + } + final Phylogeny t2 = factory.create( "(((A:1,B:2)AB:10[&&NHX:B=55],C)ABC:3[&&NHX:B=33],D:5)ABCD:0.5", + new NHXParser() )[ 0 ]; + t2.reRoot( t2.getNode( "A" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "ABC" ) ); + t2.reRoot( t2.getNode( "A" ) ); + t2.reRoot( t2.getNode( "B" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "C" ) ); + t2.reRoot( t2.getNode( "ABC" ) ); + t2.reRoot( t2.getNode( "A" ) ); + t2.reRoot( t2.getNode( "B" ) ); + t2.reRoot( t2.getNode( "AB" ) ); + t2.reRoot( t2.getNode( "AB" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "C" ) ); + t2.reRoot( t2.getNode( "B" ) ); + t2.reRoot( t2.getNode( "AB" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "ABC" ) ); + t2.reRoot( t2.getNode( "A" ) ); + t2.reRoot( t2.getNode( "B" ) ); + t2.reRoot( t2.getNode( "AB" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "C" ) ); + t2.reRoot( t2.getNode( "ABC" ) ); + t2.reRoot( t2.getNode( "A" ) ); + t2.reRoot( t2.getNode( "B" ) ); + t2.reRoot( t2.getNode( "AB" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "C" ) ); + t2.reRoot( t2.getNode( "A" ) ); + t2.reRoot( t2.getNode( "B" ) ); + t2.reRoot( t2.getNode( "AB" ) ); + t2.reRoot( t2.getNode( "C" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "ABC" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "A" ) ); + t2.reRoot( t2.getNode( "B" ) ); + t2.reRoot( t2.getNode( "AB" ) ); + t2.reRoot( t2.getNode( "C" ) ); + t2.reRoot( t2.getNode( "D" ) ); + t2.reRoot( t2.getNode( "ABC" ) ); + t2.reRoot( t2.getNode( "D" ) ); + if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + return false; + } + if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + return false; + } + t2.reRoot( t2.getNode( "ABC" ) ); + if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + return false; + } + if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + return false; + } + t2.reRoot( t2.getNode( "AB" ) ); + if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + return false; + } + if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + return false; + } + if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + return false; + } + t2.reRoot( t2.getNode( "AB" ) ); + if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + return false; + } + if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + return false; + } + if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + return false; + } + t2.reRoot( t2.getNode( "D" ) ); + if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + return false; + } + if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + return false; + } + t2.reRoot( t2.getNode( "ABC" ) ); + if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + return false; + } + if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + return false; + } + final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])", + new NHXParser() )[ 0 ]; + t3.reRoot( t3.getNode( "B" ) ); + if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) { + return false; + } + if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + return false; + } + if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) { + return false; + } + t3.reRoot( t3.getNode( "B" ) ); + if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) { + return false; + } + if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + return false; + } + if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) { + return false; + } + t3.reRoot( t3.getRoot() ); + if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) { + return false; + } + if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + return false; + } + if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testSDIse() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ]; + final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ]; + gene1.setRooted( true ); + species1.setRooted( true ); + final SDI sdi = new SDI( gene1, species1 ); + if ( !gene1.getRoot().isDuplication() ) { + return false; + } + final Phylogeny species2 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene2 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + new NHXParser() )[ 0 ]; + species2.setRooted( true ); + gene2.setRooted( true ); + final SDI sdi2 = new SDI( gene2, species2 ); + if ( sdi2.getDuplicationsSum() != 0 ) { + return false; + } + if ( !gene2.getNode( "ab" ).isSpeciation() ) { + return false; + } + if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) { + return false; + } + if ( !gene2.getNode( "abc" ).isSpeciation() ) { + return false; + } + if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) { + return false; + } + if ( !gene2.getNode( "r" ).isSpeciation() ) { + return false; + } + if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) { + return false; + } + final Phylogeny species3 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene3 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + new NHXParser() )[ 0 ]; + species3.setRooted( true ); + gene3.setRooted( true ); + final SDI sdi3 = new SDI( gene3, species3 ); + if ( sdi3.getDuplicationsSum() != 1 ) { + return false; + } + if ( !gene3.getNode( "aa" ).isDuplication() ) { + return false; + } + if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) { + return false; + } + final Phylogeny species4 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene4 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + new NHXParser() )[ 0 ]; + species4.setRooted( true ); + gene4.setRooted( true ); + final SDI sdi4 = new SDI( gene4, species4 ); + if ( sdi4.getDuplicationsSum() != 1 ) { + return false; + } + if ( !gene4.getNode( "ac" ).isSpeciation() ) { + return false; + } + if ( !gene4.getNode( "abc" ).isDuplication() ) { + return false; + } + if ( gene4.getNode( "abcd" ).isDuplication() ) { + return false; + } + if ( species4.getNumberOfExternalNodes() != 6 ) { + return false; + } + if ( gene4.getNumberOfExternalNodes() != 6 ) { + return false; + } + final Phylogeny species5 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene5 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r", + new NHXParser() )[ 0 ]; + species5.setRooted( true ); + gene5.setRooted( true ); + final SDI sdi5 = new SDI( gene5, species5 ); + if ( sdi5.getDuplicationsSum() != 2 ) { + return false; + } + if ( !gene5.getNode( "ad" ).isSpeciation() ) { + return false; + } + if ( !gene5.getNode( "adc" ).isDuplication() ) { + return false; + } + if ( !gene5.getNode( "abcd" ).isDuplication() ) { + return false; + } + if ( species5.getNumberOfExternalNodes() != 6 ) { + return false; + } + if ( gene5.getNumberOfExternalNodes() != 6 ) { + return false; + } + // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith + // Conjecture for Comparing Molecular Phylogenies" + // J. of Comput Bio. Vol. 4, No 2, pp.177-187 + final Phylogeny species6 = factory + .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; + final Phylogeny gene6 = factory + .create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1," + + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;", + new NHXParser() )[ 0 ]; + species6.setRooted( true ); + gene6.setRooted( true ); + final SDI sdi6 = new SDI( gene6, species6 ); + if ( sdi6.getDuplicationsSum() != 3 ) { + return false; + } + if ( !gene6.getNode( "r" ).isDuplication() ) { + return false; + } + if ( !gene6.getNode( "4-5-6" ).isDuplication() ) { + return false; + } + if ( !gene6.getNode( "7-8-9" ).isDuplication() ) { + return false; + } + if ( !gene6.getNode( "1-2" ).isSpeciation() ) { + return false; + } + if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) { + return false; + } + if ( !gene6.getNode( "5-6" ).isSpeciation() ) { + return false; + } + if ( !gene6.getNode( "8-9" ).isSpeciation() ) { + return false; + } + if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) { + return false; + } + sdi6.computeMappingCostL(); + if ( sdi6.computeMappingCostL() != 17 ) { + return false; + } + if ( species6.getNumberOfExternalNodes() != 9 ) { + return false; + } + if ( gene6.getNumberOfExternalNodes() != 9 ) { + return false; + } + final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2])," + + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2])," + + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2])," + + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2])," + + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" ); + species7.setRooted( true ); + final Phylogeny gene7_1 = Test + .createPhylogeny( "((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); + gene7_1.setRooted( true ); + final SDI sdi7 = new SDI( gene7_1, species7 ); + if ( sdi7.getDuplicationsSum() != 0 ) { + return false; + } + if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) { + return false; + } + final Phylogeny gene7_2 = Test + .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); + gene7_2.setRooted( true ); + final SDI sdi7_2 = new SDI( gene7_2, species7 ); + if ( sdi7_2.getDuplicationsSum() != 1 ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) { + return false; + } + if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) { + return false; + } + } + catch ( final Exception e ) { + return false; + } + return true; + } + + private static boolean testSDIunrooted() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ]; + final List l = SDIR.getBranchesInPreorder( p0 ); + final Iterator iter = l.iterator(); + PhylogenyBranch br = iter.next(); + if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) { + return false; + } + br = iter.next(); + if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) { + return false; + } + if ( iter.hasNext() ) { + return false; + } + final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ]; + final List l1 = SDIR.getBranchesInPreorder( p1 ); + final Iterator iter1 = l1.iterator(); + br = iter1.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) { + return false; + } + br = iter1.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + return false; + } + br = iter1.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { + return false; + } + if ( iter1.hasNext() ) { + return false; + } + final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ]; + final List l2 = SDIR.getBranchesInPreorder( p2 ); + final Iterator iter2 = l2.iterator(); + br = iter2.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) { + return false; + } + br = iter2.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + return false; + } + br = iter2.next(); + if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + return false; + } + if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { + return false; + } + if ( iter2.hasNext() ) { + return false; + } + final Phylogeny species0 = factory + .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))", + new NHXParser() )[ 0 ]; + final Phylogeny gene1 = factory + .create( "(((((A:0.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])", + new NHXParser() )[ 0 ]; + species0.setRooted( true ); + gene1.setRooted( true ); + final SDIR sdi_unrooted = new SDIR(); + sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 ); + if ( sdi_unrooted.getCount() != 1 ) { + return false; + } + if ( sdi_unrooted.getMinimalDuplications() != 0 ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) { + return false; + } + if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + return false; + } + final Phylogeny gene2 = factory + .create( "(((((A:2.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])", + new NHXParser() )[ 0 ]; + gene2.setRooted( true ); + sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 ); + if ( sdi_unrooted.getCount() != 1 ) { + return false; + } + if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) { + return false; + } + if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + return false; + } + final Phylogeny species6 = factory + .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; + final Phylogeny gene6 = factory + .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; + species6.setRooted( true ); + gene6.setRooted( true ); + Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 ); + if ( sdi_unrooted.getCount() != 1 ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + return false; + } + if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + return false; + } + if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + return false; + } + if ( !p6[ 0 ].getRoot().isDuplication() ) { + return false; + } + if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) { + return false; + } + if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) { + return false; + } + if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) { + return false; + } + if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) { + return false; + } + if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) { + return false; + } + if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) { + return false; + } + if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { + return false; + } + p6 = null; + final Phylogeny species7 = factory + .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; + final Phylogeny gene7 = factory + .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; + species7.setRooted( true ); + gene7.setRooted( true ); + Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 ); + if ( sdi_unrooted.getCount() != 1 ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + return false; + } + if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + return false; + } + if ( sdi_unrooted.getMinimalMappingCost() != 17 ) { + return false; + } + if ( !p7[ 0 ].getRoot().isDuplication() ) { + return false; + } + if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) { + return false; + } + if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) { + return false; + } + if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) { + return false; + } + if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) { + return false; + } + if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) { + return false; + } + if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) { + return false; + } + if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { + return false; + } + p7 = null; + final Phylogeny species8 = factory + .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; + final Phylogeny gene8 = factory + .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; + species8.setRooted( true ); + gene8.setRooted( true ); + Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 ); + if ( sdi_unrooted.getCount() != 1 ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + return false; + } + if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + return false; + } + if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + return false; + } + if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + return false; + } + 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" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString() + .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString() + .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) { + return false; + } + } + 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; + } + if ( s1.getSpeciesId().equals( "x" ) ) { + return false; + } + if ( s1.getSpeciesId().equals( null ) ) { + return false; + } + if ( !s1.equals( s2 ) ) { + return false; + } + if ( s1.equals( s3 ) ) { + return false; + } + if ( s1.hashCode() != s1.hashCode() ) { + return false; + } + if ( s1.hashCode() != s2.hashCode() ) { + return false; + } + if ( s1.hashCode() == s3.hashCode() ) { + return false; + } + if ( s1.compareTo( s1 ) != 0 ) { + return false; + } + 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( System.out ); + return false; + } + return true; + } + + 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" ) ); + 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 ) ) { + 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 ) ) { + 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 ) ) { + 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 ) ) { + 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 ) ) { + 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 ) ) { + return false; + } + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( !s0.match( query_nodes ) ) { + return false; + } + // + query_nodes = new HashSet(); + query_nodes.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; + } + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + if ( !s0.match( query_nodes ) ) { + return false; + } + // + query_nodes = new HashSet(); + query_nodes.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; + } + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + if ( s0.match( query_nodes ) ) { + return false; + } + // + query_nodes = new HashSet(); + query_nodes.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( "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( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + 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 ) ) { + 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 ) ) { + 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 ) ) { + 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 ) ) { + 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 ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) { + // + 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 ) ) { 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( "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 ) ) { 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( "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; } - 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( "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 ) ) { 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( "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 ) ) { return false; } } catch ( final Exception e ) { - e.printStackTrace( System.out ); + e.printStackTrace(); return false; } return true; } - private static boolean testSupportTransfer() { + private static boolean testSplitStrict() { 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 ) { + 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( p2.getNode( "abc" ) ) >= 0.0 ) { + 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; } - 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( "B" ) ); + 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( "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 ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) { + // + 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( p2.getNode( "ab" ) ) != 97 ) { + // + 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( p2.getNode( "abc" ) ) != 57 ) { + // + 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( p2.getNode( "de" ) ) != 10 ) { + // + 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( p2.getNode( "fg" ) ) != 50 ) { + // + 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( p2.getNode( "hi" ) ) != 64 ) { + // + 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; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testUniprotTaxonomySearch() { - try { - List results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone", - 10 ); - if ( results.size() != 1 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) { + // + 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; } - if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) { + // + 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; } - if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) { + // + 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 ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + if ( s0.match( query_nodes ) ) { return false; } - results = null; - results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 ); - if ( results.size() != 1 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { + // + 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 ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { + // + 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; } - results = null; - results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 ); - if ( results.size() != 1 ) { + // + 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 ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) { + // + 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; } - if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + 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; } - if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) { + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "E" ), false ); + if ( t1.getNumberOfExternalNodes() != 4 ) { return false; } - if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "F" ), false ); + if ( t1.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "D" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 3 ) { return false; } - results = null; - results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 ); - if ( results.size() != 1 ) { + t1.deleteSubtree( t1.getNode( "def" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 2 ) { return false; } - if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) { + t1.deleteSubtree( t1.getNode( "B" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) { + t1.deleteSubtree( t1.getNode( "C" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) { + t1.deleteSubtree( t1.getNode( "abc" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { + t1.deleteSubtree( t1.getNode( "r" ), false ); + if ( t1.getNumberOfExternalNodes() != 0 ) { return false; } - if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { + if ( !t1.isEmpty() ) { return false; } - if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) { + 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 ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) { + t2.deleteSubtree( t2.getNode( "abc" ), false ); + t2.toNewHampshireX(); + if ( t2.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 ) - .equals( "Nematostella vectensis" ) ) { - System.out.println( results.get( 0 ).getLineage() ); + t2.deleteSubtree( t2.getNode( "def" ), false ); + t2.toNewHampshireX(); + if ( t2.getNumberOfExternalNodes() != 1 ) { 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( System.out ); return false; } return true; } - private static boolean testEmblEntryRetrieval() { - //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 ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) { - return false; - } - if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) { - return false; - } - if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) { - return false; - } - if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) { - return false; - } - if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) { - return false; - } - if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) { - return false; - } - if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) { - return false; - } - if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) { - return false; - } - if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) { - return false; - } - if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) { - return false; - } - if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) { - return false; - } - if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) { - return false; - } - if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) { - return false; - } - return true; - } - - private static boolean testUniprotEntryRetrieval() { - if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) { - return false; - } + private static boolean testSupportCount() { try { - final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 ); - if ( !entry.getAccession().equals( "P12345" ) ) { - 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; + } } - if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) { + 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 ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) { return false; } - if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) { return false; } - if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) { 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 ) { - return false; - } - return true; - } - - private static boolean testWabiTxSearch() { - try { - String result = ""; - result = TxSearch.searchSimple( "nematostella" ); - result = TxSearch.getTxId( "nematostella" ); - if ( !result.equals( "45350" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) { return false; } - result = TxSearch.getTxName( "45350" ); - if ( !result.equals( "Nematostella" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) { return false; } - result = TxSearch.getTxId( "nematostella vectensis" ); - if ( !result.equals( "45351" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) { return false; } - result = TxSearch.getTxName( "45351" ); - if ( !result.equals( "Nematostella vectensis" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) { return false; } - result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" ); - if ( !result.equals( "536089" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) { return false; } - result = TxSearch.getTxName( "536089" ); - if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) { return false; } - final List queries = new ArrayList(); - queries.add( "Campylobacter coli" ); - queries.add( "Escherichia coli" ); - queries.add( "Arabidopsis" ); - queries.add( "Trichoplax" ); - queries.add( "Samanea saman" ); - queries.add( "Kluyveromyces marxianus" ); - queries.add( "Bacillus subtilis subsp. subtilis str. N170" ); - queries.add( "Bornavirus parrot/PDD/2008" ); - final List ranks = new ArrayList(); - ranks.add( RANKS.SUPERKINGDOM ); - ranks.add( RANKS.KINGDOM ); - ranks.add( RANKS.FAMILY ); - ranks.add( RANKS.GENUS ); - ranks.add( RANKS.TRIBE ); - result = TxSearch.searchLineage( queries, ranks ); - result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true ); - result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true ); - } - catch ( final Exception e ) { - System.out.println(); - System.out.println( "the following might be due to absence internet connection:" ); - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testAminoAcidSequence() { - try { - final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" ); - if ( aa1.getLength() != 13 ) { + 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; } - if ( aa1.getResidueAt( 0 ) != 'A' ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) { return false; } - if ( aa1.getResidueAt( 2 ) != 'K' ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) { return false; } - if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) { return false; } - final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" ); - if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) { return false; } - final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" ); - if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) { return false; } - final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" ); - if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace(); - return false; - } - return true; - } - - private static boolean testCreateBalancedPhylogeny() { - try { - final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 ); - if ( p0.getRoot().getNumberOfDescendants() != 5 ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) { return false; } - if ( p0.getNumberOfExternalNodes() != 15625 ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) { return false; } - final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 ); - if ( p1.getRoot().getNumberOfDescendants() != 10 ) { + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) { return false; } - if ( p1.getNumberOfExternalNodes() != 100 ) { + 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; + } + 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; + } + 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; + } + 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 Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testFastaParser() { + private static boolean testSupportTransfer() { try { - if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) { + 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 ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) { return false; } - final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ); - if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) { + support_transfer.moveBranchLengthsToBootstrap( p1 ); + support_transfer.transferSupportValues( p1, p2 ); + if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) { return false; } - if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) { + if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) { return false; } - if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) { + if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) { return false; } - if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) { return false; } - if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) { return false; } - if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) { + return false; + } + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) { + return false; + } + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) { return false; } } catch ( final Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testGeneralMsaParser() { + private static boolean testTaxonomyExtraction() { try { - final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n"; - final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) ); - final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n"; - final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) ); - final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n"; - final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) ); - final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n"; - final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) ); - if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { - return false; - } - if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { - return false; - } - if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) { - return false; - } - if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) { - return false; - } - if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + final PhylogenyNode n0 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n0.getNodeData().isHasTaxonomy() ) { return false; } - if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { - return false; - } - if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + 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 ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + final PhylogenyNode n2x = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n2x.getNodeData().isHasTaxonomy() ) { return false; } - if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + 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 ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + 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 ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + 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 ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + 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 Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) ); - if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) { + 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 ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) { + 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; } - if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { + final PhylogenyNode n9 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + System.out.println( n9.toString() ); return false; } - final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) ); - if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) { + 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 ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) { + 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 ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) { + final PhylogenyNode n10 = PhylogenyNode + .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { + System.out.println( n10.toString() ); return false; } - final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ); - if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) { + 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 ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) { + 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 ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { + final PhylogenyNode n13 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( n13.getNodeData().isHasTaxonomy() ) { + System.out.println( n13.toString() ); return false; } } catch ( final Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testMafft( final String path ) { + private static boolean testTreeMethods() { try { - final List opts = new ArrayList(); - opts.add( "--maxiterate" ); - opts.add( "1000" ); - opts.add( "--localpair" ); - opts.add( "--quiet" ); - Msa msa = null; - final MsaInferrer mafft = Mafft.createInstance( path ); - msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts ); - if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) { + 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 ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) { + final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) { return false; } } @@ -8315,720 +11194,641 @@ public final class Test { return true; } - private static boolean testNextNodeWithCollapsing() { + private static boolean testSequenceDbWsTools1() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - PhylogenyNode n; - List ext = new ArrayList(); - final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ]; - t0.getNode( "cd" ).setCollapse( true ); - t0.getNode( "cde" ).setCollapse( true ); - n = t0.getFirstExternalNode(); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); - } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { - return false; - } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { - return false; - } - if ( !ext.get( 2 ).getName().equals( "cde" ) ) { - return false; - } - if ( !ext.get( 3 ).getName().equals( "f" ) ) { - return false; - } - if ( !ext.get( 4 ).getName().equals( "g" ) ) { + 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 ( !ext.get( 5 ).getName().equals( "h" ) ) { - return false; - } - ext.clear(); - final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ]; - t1.getNode( "ab" ).setCollapse( true ); - t1.getNode( "cd" ).setCollapse( true ); - t1.getNode( "cde" ).setCollapse( true ); - n = t1.getNode( "ab" ); - ext = new ArrayList(); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); - } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + 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 ( !ext.get( 1 ).getName().equals( "cde" ) ) { + 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 ( !ext.get( 2 ).getName().equals( "f" ) ) { + 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 ( !ext.get( 3 ).getName().equals( "g" ) ) { + 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 ( !ext.get( 4 ).getName().equals( "h" ) ) { + 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; } - // - // - ext.clear(); - final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ]; - t2.getNode( "ab" ).setCollapse( true ); - t2.getNode( "cd" ).setCollapse( true ); - t2.getNode( "cde" ).setCollapse( true ); - t2.getNode( "c" ).setCollapse( true ); - t2.getNode( "d" ).setCollapse( true ); - t2.getNode( "e" ).setCollapse( true ); - t2.getNode( "gh" ).setCollapse( true ); - n = t2.getNode( "ab" ); - ext = new ArrayList(); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); - } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + 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 ( !ext.get( 1 ).getName().equals( "cde" ) ) { + 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 ( !ext.get( 2 ).getName().equals( "f" ) ) { + 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 ( !ext.get( 3 ).getName().equals( "gh" ) ) { + 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; } - // - // - ext.clear(); - final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ]; - t3.getNode( "ab" ).setCollapse( true ); - t3.getNode( "cd" ).setCollapse( true ); - t3.getNode( "cde" ).setCollapse( true ); - t3.getNode( "c" ).setCollapse( true ); - t3.getNode( "d" ).setCollapse( true ); - t3.getNode( "e" ).setCollapse( true ); - t3.getNode( "gh" ).setCollapse( true ); - t3.getNode( "fgh" ).setCollapse( true ); - n = t3.getNode( "ab" ); - ext = new ArrayList(); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + 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 ( !ext.get( 0 ).getName().equals( "ab" ) ) { + 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 ( !ext.get( 1 ).getName().equals( "cde" ) ) { + 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 ( !ext.get( 2 ).getName().equals( "fgh" ) ) { + 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; } - // - // - ext.clear(); - final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ]; - t4.getNode( "ab" ).setCollapse( true ); - t4.getNode( "cd" ).setCollapse( true ); - t4.getNode( "cde" ).setCollapse( true ); - t4.getNode( "c" ).setCollapse( true ); - t4.getNode( "d" ).setCollapse( true ); - t4.getNode( "e" ).setCollapse( true ); - t4.getNode( "gh" ).setCollapse( true ); - t4.getNode( "fgh" ).setCollapse( true ); - t4.getNode( "abcdefgh" ).setCollapse( true ); - n = t4.getNode( "abcdefgh" ); - if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) { + 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; } - // - // - final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; - ext.clear(); - n = t5.getFirstExternalNode(); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + 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; } - if ( ext.size() != 8 ) { + 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; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + } + 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" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + 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; } - if ( !ext.get( 5 ).getName().equals( "f" ) ) { + if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { return false; } - if ( !ext.get( 6 ).getName().equals( "g" ) ) { + if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false; } - if ( !ext.get( 7 ).getName().equals( "h" ) ) { + if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) { return false; } - // - // - final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ]; - ext.clear(); - t6.getNode( "ab" ).setCollapse( true ); - n = t6.getNode( "ab" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + 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; } - if ( ext.size() != 7 ) { + if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "c" ) ) { + if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "d" ) ) { + } + 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 testEbiEntryRetrieval() { + try { + final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" ); + if ( !entry.getAccession().equals( "AAK41263" ) ) { + System.out.println( entry.getAccession() ); return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) { + System.out.println( entry.getTaxonomyScientificName() ); return false; } - if ( !ext.get( 4 ).getName().equals( "f" ) ) { + if ( !entry.getSequenceName() + .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) { + System.out.println( entry.getSequenceName() ); return false; } - if ( !ext.get( 5 ).getName().equals( "g" ) ) { + // 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 ( !ext.get( 6 ).getName().equals( "h" ) ) { + if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) { + System.out.println( entry.getTaxonomyIdentifier() ); return false; } - // - // - final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ]; - ext.clear(); - t7.getNode( "cd" ).setCollapse( true ); - n = t7.getNode( "a" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) { + System.out.println( entry.getAnnotations().first().getRefValue() ); + return false; } - if ( ext.size() != 7 ) { + if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) { + System.out.println( entry.getAnnotations().first().getRefSource() ); return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + if ( entry.getCrossReferences().size() != 5 ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + // + final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); + if ( !entry1.getAccession().equals( "ABJ16409" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "cd" ) ) { + if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) { + System.out.println( entry1.getTaxonomyScientificName() ); return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) { + System.out.println( entry1.getSequenceName() ); return false; } - if ( !ext.get( 4 ).getName().equals( "f" ) ) { + if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) { + System.out.println( entry1.getTaxonomyIdentifier() ); return false; } - if ( !ext.get( 5 ).getName().equals( "g" ) ) { + if ( !entry1.getGeneName().equals( "BCL2" ) ) { + System.out.println( entry1.getGeneName() ); return false; } - if ( !ext.get( 6 ).getName().equals( "h" ) ) { + if ( entry1.getCrossReferences().size() != 6 ) { return false; } // - // - final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ]; - ext.clear(); - t8.getNode( "cd" ).setCollapse( true ); - t8.getNode( "c" ).setCollapse( true ); - t8.getNode( "d" ).setCollapse( true ); - n = t8.getNode( "a" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); + if ( !entry2.getAccession().equals( "NM_184234" ) ) { + return false; } - if ( ext.size() != 7 ) { + if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + System.out.println( entry2.getTaxonomyScientificName() ); return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + if ( !entry2.getSequenceName() + .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { + System.out.println( entry2.getSequenceName() ); return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) { + System.out.println( entry2.getTaxonomyIdentifier() ); return false; } - if ( !ext.get( 2 ).getName().equals( "cd" ) ) { - System.out.println( "2 fail" ); + if ( !entry2.getGeneName().equals( "RBM39" ) ) { + System.out.println( entry2.getGeneName() ); return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + if ( entry2.getCrossReferences().size() != 3 ) { return false; } - if ( !ext.get( 4 ).getName().equals( "f" ) ) { + // + final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" ); + if ( !entry3.getAccession().equals( "HM043801" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "g" ) ) { + if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) { + System.out.println( entry3.getTaxonomyScientificName() ); return false; } - if ( !ext.get( 6 ).getName().equals( "h" ) ) { + if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) { + System.out.println( entry3.getSequenceName() ); return false; } - // - // - final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ]; - ext.clear(); - t9.getNode( "gh" ).setCollapse( true ); - n = t9.getNode( "a" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) { + System.out.println( entry3.getTaxonomyIdentifier() ); + return false; } - if ( ext.size() != 7 ) { + if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) { + System.out.println( entry3.getSequenceSymbol() ); return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + if ( entry3.getCrossReferences().size() != 8 ) { return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + // + // + final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); + if ( !entry4.getAccession().equals( "AAA36557" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + System.out.println( entry4.getTaxonomyScientificName() ); return false; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) { + System.out.println( entry4.getSequenceName() ); return false; } - if ( !ext.get( 5 ).getName().equals( "f" ) ) { + if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) { + System.out.println( entry4.getTaxonomyIdentifier() ); return false; } - if ( !ext.get( 6 ).getName().equals( "gh" ) ) { + 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... // - // - final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ]; - ext.clear(); - t10.getNode( "gh" ).setCollapse( true ); - t10.getNode( "g" ).setCollapse( true ); - t10.getNode( "h" ).setCollapse( true ); - n = t10.getNode( "a" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + //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 ( ext.size() != 7 ) { + if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) { + System.out.println( entry5.getTaxonomyScientificName() ); return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) { + System.out.println( entry5.getSequenceName() ); return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) { + System.out.println( entry5.getTaxonomyIdentifier() ); return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + } + 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 testUniprotEntryRetrieval() { + try { + final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 ); + if ( !entry.getAccession().equals( "P12345" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "f" ) ) { + if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) { return false; } - if ( !ext.get( 6 ).getName().equals( "gh" ) ) { + if ( !entry.getGeneName().equals( "GOT2" ) ) { return false; } - // - // - final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ]; - ext.clear(); - t11.getNode( "gh" ).setCollapse( true ); - t11.getNode( "fgh" ).setCollapse( true ); - n = t11.getNode( "a" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) { + return false; } - if ( ext.size() != 6 ) { + } + 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 ) { + return false; + } + return true; + } + + private static boolean testUniprotTaxonomySearch() { + try { + List results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone", + 10 ); + if ( results.size() != 1 ) { return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { + results = null; + results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 ); + if ( results.size() != 1 ) { return false; } - // - // - final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ]; - ext.clear(); - t12.getNode( "gh" ).setCollapse( true ); - t12.getNode( "fgh" ).setCollapse( true ); - t12.getNode( "g" ).setCollapse( true ); - t12.getNode( "h" ).setCollapse( true ); - t12.getNode( "f" ).setCollapse( true ); - n = t12.getNode( "a" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) { + return false; } - if ( ext.size() != 6 ) { + if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) { + return false; + } + if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + results = null; + results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 ); + if ( results.size() != 1 ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { + if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) { return false; } - // - // - final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ]; - ext.clear(); - t13.getNode( "ab" ).setCollapse( true ); - t13.getNode( "b" ).setCollapse( true ); - t13.getNode( "fgh" ).setCollapse( true ); - t13.getNode( "gh" ).setCollapse( true ); - n = t13.getNode( "ab" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { + return false; } - if ( ext.size() != 5 ) { + if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + results = null; + results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 ); + if ( results.size() != 1 ) { return false; } - if ( !ext.get( 1 ).getName().equals( "c" ) ) { + if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "d" ) ) { + if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { + if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { return false; } - // - // - final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ]; - ext.clear(); - t14.getNode( "ab" ).setCollapse( true ); - t14.getNode( "a" ).setCollapse( true ); - t14.getNode( "fgh" ).setCollapse( true ); - t14.getNode( "gh" ).setCollapse( true ); - n = t14.getNode( "ab" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { + return false; } - if ( ext.size() != 5 ) { + if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "c" ) ) { + if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 ) + .equals( "Nematostella vectensis" ) ) { + System.out.println( results.get( 0 ).getLineage() ); return false; } - if ( !ext.get( 2 ).getName().equals( "d" ) ) { + // + results = null; + results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 ); + if ( results.size() != 1 ) { return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { + if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) { return false; } - // - // - final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ]; - ext.clear(); - t15.getNode( "ab" ).setCollapse( true ); - t15.getNode( "a" ).setCollapse( true ); - t15.getNode( "fgh" ).setCollapse( true ); - t15.getNode( "gh" ).setCollapse( true ); - n = t15.getNode( "ab" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) { + return false; } - if ( ext.size() != 6 ) { + if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "c" ) ) { + if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 ) + .equals( "Xenopus tropicalis" ) ) { + System.out.println( results.get( 0 ).getLineage() ); return false; } - if ( !ext.get( 2 ).getName().equals( "d" ) ) { + // + results = null; + results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 ); + if ( results.size() != 1 ) { return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "x" ) ) { + if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { + if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) { return false; } - // - // - final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ]; - ext.clear(); - t16.getNode( "ab" ).setCollapse( true ); - t16.getNode( "a" ).setCollapse( true ); - t16.getNode( "fgh" ).setCollapse( true ); - t16.getNode( "gh" ).setCollapse( true ); - t16.getNode( "cd" ).setCollapse( true ); - t16.getNode( "cde" ).setCollapse( true ); - t16.getNode( "d" ).setCollapse( true ); - t16.getNode( "x" ).setCollapse( true ); - n = t16.getNode( "ab" ); - while ( n != null ) { - ext.add( n ); - n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { + return false; } - if ( ext.size() != 4 ) { + if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 ) + .equals( "Xenopus tropicalis" ) ) { + System.out.println( results.get( 0 ).getLineage() ); return false; } - if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + // + results = null; + results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 ); + if ( results.size() != 1 ) { return false; } - if ( !ext.get( 2 ).getName().equals( "x" ) ) { + if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "fgh" ) ) { + if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - 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 List l = new ArrayList(); - l.add( s0 ); - l.add( s1 ); - l.add( s2 ); - l.add( s3 ); - final Msa msa = BasicMsa.createInstance( l ); - if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) { + if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) { return false; } - if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) { + if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) { return false; } - if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) { + if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) { return false; } - if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) { + if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 ) + .equals( "Xenopus tropicalis" ) ) { + System.out.println( results.get( 0 ).getLineage() ); return false; } } - catch ( final Exception e ) { + 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 ) { return false; } return true; } - private static boolean testSequenceIdParsing() { + private static boolean testWabiTxSearch() { try { - Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } - return false; - } - // - id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } - return false; - } - // - id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } - return false; - } - // - id = SequenceIdParser.parse( "gb_AAA96518_1" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } - return false; - } - // - id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } - return false; - } - // - id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } - return false; - } - // - id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } + String result = ""; + result = TxSearch.searchSimple( "nematostella" ); + result = TxSearch.getTxId( "nematostella" ); + if ( !result.equals( "45350" ) ) { return false; } - // - id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } + result = TxSearch.getTxName( "45350" ); + if ( !result.equals( "Nematostella" ) ) { return false; } - // - id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } + result = TxSearch.getTxId( "nematostella vectensis" ); + if ( !result.equals( "45351" ) ) { return false; } - // - id = SequenceIdParser.parse( "P4A123" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } + result = TxSearch.getTxName( "45351" ); + if ( !result.equals( "Nematostella vectensis" ) ) { return false; } - // - id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" ); - if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) - || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) { - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); - } + result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" ); + if ( !result.equals( "536089" ) ) { return false; } - // - id = SequenceIdParser.parse( "XP_12345" ); - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getProvider() ); + result = TxSearch.getTxName( "536089" ); + if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) { return false; } - // lcl_91970_unknown_ + final List queries = new ArrayList(); + queries.add( "Campylobacter coli" ); + queries.add( "Escherichia coli" ); + queries.add( "Arabidopsis" ); + queries.add( "Trichoplax" ); + queries.add( "Samanea saman" ); + queries.add( "Kluyveromyces marxianus" ); + queries.add( "Bacillus subtilis subsp. subtilis str. N170" ); + queries.add( "Bornavirus parrot/PDD/2008" ); + final List ranks = new ArrayList(); + ranks.add( RANKS.SUPERKINGDOM ); + ranks.add( RANKS.KINGDOM ); + ranks.add( RANKS.FAMILY ); + ranks.add( RANKS.GENUS ); + ranks.add( RANKS.TRIBE ); + result = TxSearch.searchLineage( queries, ranks ); + result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true ); + result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true ); } catch ( final Exception e ) { + System.out.println(); + System.out.println( "the following might be due to absence internet connection:" ); e.printStackTrace( System.out ); return false; }