X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=1c76c8dee78a48bb18c929777c9631ac445f67e2;hb=803a2b32992b5944b73c6dfcb80ceb58c09b81c1;hp=66bff3d70843385d710f8107bd71ef34cd7b2b97;hpb=380f98efacccdaeff5a86ba6b9b05367df133b79;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 66bff3d..1c76c8d 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -2,8 +2,8 @@ // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // -// Copyright (C) 2008-2009 Christian M. Zmasek -// Copyright (C) 2008-2009 Burnham Institute for Medical Research +// Copyright (C) 2014 Christian M. Zmasek +// Copyright (C) 2014 Sanford-Burnham Medical Research Institute // All rights reserved // // This library is free software; you can redistribute it and/or @@ -20,7 +20,6 @@ // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // -// Contact: phylosoft @ gmail . com // WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.test; @@ -29,6 +28,9 @@ import java.io.ByteArrayInputStream; import java.io.File; import java.io.FileInputStream; import java.io.IOException; +import java.io.StringWriter; +import java.io.Writer; +import java.net.URL; import java.util.ArrayList; import java.util.Date; import java.util.HashSet; @@ -38,8 +40,13 @@ import java.util.Locale; import java.util.Set; import java.util.SortedSet; +import javax.net.ssl.HttpsURLConnection; +import javax.net.ssl.SSLContext; + import org.forester.application.support_transfer; +import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.TreePanelUtil; +import org.forester.archaeopteryx.webservices.WebserviceUtil; import org.forester.development.DevelopmentTools; import org.forester.evoinference.TestPhylogenyReconstruction; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -60,8 +67,10 @@ 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.DeleteableMsa; import org.forester.msa.Mafft; import org.forester.msa.Msa; +import org.forester.msa.Msa.MSA_FORMAT; import org.forester.msa.MsaInferrer; import org.forester.msa.MsaMethods; import org.forester.pccx.TestPccx; @@ -100,7 +109,7 @@ import org.forester.sdi.SDI; import org.forester.sdi.SDIR; import org.forester.sdi.TestGSDI; import org.forester.sequence.BasicSequence; -import org.forester.sequence.Sequence; +import org.forester.sequence.MolecularSequence; import org.forester.species.BasicSpecies; import org.forester.species.Species; import org.forester.surfacing.TestSurfacing; @@ -119,291 +128,36 @@ import org.forester.util.SequenceAccessionTools; import org.forester.ws.seqdb.SequenceDatabaseEntry; import org.forester.ws.seqdb.SequenceDbWsTools; import org.forester.ws.seqdb.UniProtTaxonomy; -import org.forester.ws.wabi.TxSearch; -import org.forester.ws.wabi.TxSearch.RANKS; -import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS; -import org.forester.ws.wabi.TxSearch.TAX_RANK; + @SuppressWarnings( "unused") public final class Test { - private final static boolean PERFORM_DB_TESTS = false; - private final static double ZERO_DIFF = 1.0E-9; - private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "test_data" - + ForesterUtil.getFileSeparator(); private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "resources" - + ForesterUtil.getFileSeparator(); - private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true; - private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/" - + ForesterConstants.PHYLO_XML_VERSION + "/" - + ForesterConstants.PHYLO_XML_XSD; + + ForesterUtil.getFileSeparator() + "resources" + + ForesterUtil.getFileSeparator(); + private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + + ForesterUtil.getFileSeparator() + "test_data" + + ForesterUtil.getFileSeparator(); + private final static boolean PERFORM_DB_TESTS = true; + private static final boolean PERFORM_WEB_TREE_ACCESS = true; private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/" - + ForesterConstants.PHYLO_XML_VERSION + "/" - + ForesterConstants.PHYLO_XML_XSD; + + ForesterConstants.PHYLO_XML_VERSION + "/" + + ForesterConstants.PHYLO_XML_XSD; + private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/" + + ForesterConstants.PHYLO_XML_VERSION + "/" + + ForesterConstants.PHYLO_XML_XSD; + private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true; + private final static double ZERO_DIFF = 1.0E-9; - 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; - } - - 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 ) { - return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF ); + private static boolean isEqual( final double a, final double b ) { + return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF ); } public static void main( final String[] args ) { System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION - + "]" ); + + "]" ); Locale.setDefault( Locale.US ); System.out.println( "[Locale: " + Locale.getDefault() + "]" ); int failed = 0; @@ -427,6 +181,7 @@ 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." ); @@ -490,18 +245,6 @@ public final class Test { 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 ); System.out.print( "UniProtKB id extraction: " ); if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) { System.out.println( "OK." ); @@ -520,18 +263,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - 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.out.print( "Hmmscan output parser: " ); if ( testHmmscanOutputParser() ) { System.out.println( "OK." ); @@ -541,7 +272,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // System.out.print( "Overlap removal: " ); if ( !org.forester.test.Test.testOverlapRemoval() ) { System.out.println( "failed." ); @@ -560,7 +290,15 @@ public final class Test { succeeded++; } System.out.println( "OK." ); - // + System.out.print( "Taxonomy data extraction: " ); + if ( Test.testExtractTaxonomyDataFromNodeName() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Taxonomy code extraction: " ); if ( Test.testExtractTaxonomyCodeFromNodeName() ) { System.out.println( "OK." ); @@ -606,6 +344,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Node construction and parsing of NHX (node level): " ); + if ( Test.testNHXNodeParsing2() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "NHX parsing iterating: " ); if ( Test.testNHParsingIter() ) { System.out.println( "OK." ); @@ -624,6 +371,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "NH parsing - special chars: " ); + if ( Test.testNHParsingSpecialChars() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Conversion to NHX (node level): " ); if ( Test.testNHXconversion() ) { System.out.println( "OK." ); @@ -750,6 +506,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "UTF-8 parsing from file: " ); + if ( Test.testUTF8ParsingFromFile() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Copying of node data: " ); if ( Test.testCopyOfNodeData() ) { System.out.println( "OK." ); @@ -1131,29 +896,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - if ( PERFORM_DB_TESTS ) { - System.out.print( "Uniprot Entry Retrieval: " ); - if ( Test.testUniprotEntryRetrieval() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } - } - if ( PERFORM_DB_TESTS ) { - System.out.print( "Uniprot Taxonomy Search: " ); - if ( Test.testUniprotTaxonomySearch() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } - } - //---- String path = ""; final String os = ForesterUtil.OS_NAME.toLowerCase(); if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) { @@ -1163,13 +905,13 @@ public final class Test { path = "C:\\Program Files\\mafft-win\\mafft.bat"; } else { - path = "/home/czmasek/bin/mafft"; - } - if ( !MsaInferrer.isInstalled( path ) ) { path = "mafft"; - } - if ( !MsaInferrer.isInstalled( path ) ) { - path = "/usr/local/bin/mafft"; + if ( !MsaInferrer.isInstalled( path ) ) { + path = "/usr/bin/mafft"; + } + if ( !MsaInferrer.isInstalled( path ) ) { + path = "/usr/local/bin/mafft"; + } } if ( MsaInferrer.isInstalled( path ) ) { System.out.print( "MAFFT (external program): " ); @@ -1181,7 +923,6 @@ public final class Test { System.out.println( "failed [will not count towards failed tests]" ); } } - //---- System.out.print( "Next nodes with collapsed: " ); if ( Test.testNextNodeWithCollapsing() ) { System.out.println( "OK." ); @@ -1200,6 +941,128 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Deleteable MSA: " ); + if ( Test.testDeleteableMsa() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "MSA entropy: " ); + if ( Test.testMsaEntropy() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + if ( PERFORM_DB_TESTS ) { + System.out.print( "Uniprot Entry Retrieval: " ); + if ( Test.testUniprotEntryRetrieval() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Ebi Entry Retrieval: " ); + if ( Test.testEbiEntryRetrieval() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Sequence DB tools 2: " ); + if ( testSequenceDbWsTools2() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + System.exit( -1 ); + } + System.out.print( "Uniprot Taxonomy Search: " ); + if ( Test.testUniprotTaxonomySearch() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + } + if ( PERFORM_WEB_TREE_ACCESS ) { + System.out.print( "TreeBase acccess: " ); + if ( Test.testTreeBaseReading() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "ToL access: " ); + if ( Test.testToLReading() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "NHX parsing from URL: " ); + if ( Test.testNHXparsingFromURL() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "NHX parsing from URL 2: " ); + if ( Test.testNHXparsingFromURL2() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "phyloXML parsing from URL: " ); + if ( Test.testPhyloXMLparsingFromURL() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "TreeFam access: " ); + if ( Test.testTreeFamReading() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Pfam tree access: " ); + if ( Test.testPfamTreeReading() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + } System.out.println(); final Runtime rt = java.lang.Runtime.getRuntime(); final long free_memory = rt.freeMemory() / 1000000; @@ -1218,98 +1081,95 @@ public final class Test { } } - 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() { + private static boolean testEngulfingOverlapRemoval() { try { - final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" ); - if ( aa1.getLength() != 13 ) { + 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 ( aa1.getResidueAt( 0 ) != 'A' ) { + if ( ForesterUtil.isEngulfed( d1, covered ) ) { return false; } - if ( aa1.getResidueAt( 2 ) != 'K' ) { + if ( ForesterUtil.isEngulfed( d2, covered ) ) { return false; } - if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) { + if ( !ForesterUtil.isEngulfed( d3, covered ) ) { return false; } - final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" ); - if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) { + if ( ForesterUtil.isEngulfed( d4, covered ) ) { return false; } - final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" ); - if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) { + if ( ForesterUtil.isEngulfed( d5, covered ) ) { return false; } - final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" ); - if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) { + if ( !ForesterUtil.isEngulfed( d6, covered ) ) { 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" ) ) { + 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 ( pd.getNumber() != 1 ) { + if ( abc_r1.getNumberOfProteinDomains() != 3 ) { return false; } - if ( pd.getTotalCount() != 4 ) { + if ( abc_r2.getNumberOfProteinDomains() != 2 ) { return false; } - if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) { + if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) { 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 ) ) { + if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) { return false; } - if ( a1.equals( a3 ) ) { + 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 ( a1.compareTo( a1 ) != 0 ) { + if ( def_r1.getNumberOfProteinDomains() != 3 ) { return false; } - if ( a1.compareTo( a1_copy ) != 0 ) { + if ( def_r2.getNumberOfProteinDomains() != 3 ) { return false; } - if ( a1.compareTo( a1_equal ) != 0 ) { + if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) { return false; } - if ( a1.compareTo( a2 ) != 0 ) { + if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) { return false; } - if ( a1.compareTo( a3 ) == 0 ) { + if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) { return false; } } @@ -1320,576 +1180,880 @@ public final class Test { return true; } - private static boolean testBasicNodeMethods() { + private static final boolean testNHXparsingFromURL2() { try { - if ( PhylogenyNode.getNodeCount() != 0 ) { + final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; + final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ), + false, + false, + false, + TAXONOMY_EXTRACTION.NO, + false ); + if ( ( phys == null ) || ( phys.length != 5 ) ) { return false; } - final PhylogenyNode n1 = new PhylogenyNode(); - final PhylogenyNode n2 = PhylogenyNode - .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - final PhylogenyNode n4 = PhylogenyNode - .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( n1.isHasAssignedEvent() ) { + if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + System.out.println( phys[ 0 ].toNewHampshire() ); return false; } - if ( PhylogenyNode.getNodeCount() != 4 ) { + if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) { + System.out.println( phys[ 1 ].toNewHampshire() ); return false; } - if ( n3.getIndicator() != 0 ) { + final Phylogeny phys2[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ), + false, + false, + false, + TAXONOMY_EXTRACTION.NO, + false ); + if ( ( phys2 == null ) || ( phys2.length != 5 ) ) { return false; } - if ( n3.getNumberOfExternalNodes() != 1 ) { + if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + System.out.println( phys2[ 0 ].toNewHampshire() ); return false; } - if ( !n3.isExternal() ) { + if ( !phys2[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) { + System.out.println( phys2[ 1 ].toNewHampshire() ); return false; } - if ( !n3.isRoot() ) { + final Phylogeny phys3[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/" + + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false ); + if ( ( phys3 == null ) || ( phys3.length != 1 ) ) { return false; } - if ( !n4.getName().equals( "n4" ) ) { + if ( !phys3[ 0 ] + .toNewHampshire() + .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) { + System.out.println( phys3[ 0 ].toNewHampshire() ); + return false; + } + final Phylogeny phys4[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/" + + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false ); + if ( ( phys4 == null ) || ( phys4.length != 1 ) ) { + return false; + } + if ( !phys4[ 0 ] + .toNewHampshire() + .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) { + System.out.println( phys4[ 0 ].toNewHampshire() ); return false; } } catch ( final Exception e ) { - e.printStackTrace( System.out ); + e.printStackTrace(); return false; } return true; } - private static boolean testBasicPhyloXMLparsing() { + private static final boolean testNHXparsingFromURL() { try { + final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; + final URL u = new URL( s ); final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final PhyloXmlParser xml_parser = new PhyloXmlParser(); - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", - xml_parser ); - if ( xml_parser.getErrorCount() > 0 ) { - System.out.println( xml_parser.getErrorMessages().toString() ); - return false; - } - if ( phylogenies_0.length != 4 ) { + final Phylogeny[] phys = factory.create( u, new NHXParser() ); + if ( ( phys == null ) || ( phys.length != 5 ) ) { return false; } - final Phylogeny t1 = phylogenies_0[ 0 ]; - final Phylogeny t2 = phylogenies_0[ 1 ]; - final Phylogeny t3 = phylogenies_0[ 2 ]; - final Phylogeny t4 = phylogenies_0[ 3 ]; - if ( t1.getNumberOfExternalNodes() != 1 ) { + if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + System.out.println( phys[ 0 ].toNewHampshire() ); return false; } - if ( !t1.isRooted() ) { + if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) { + System.out.println( phys[ 1 ].toNewHampshire() ); return false; } - if ( t1.isRerootable() ) { + final URL u2 = new URL( s ); + final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() ); + if ( ( phys2 == null ) || ( phys2.length != 5 ) ) { return false; } - if ( !t1.getType().equals( "gene_tree" ) ) { + if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { + System.out.println( phys2[ 0 ].toNewHampshire() ); return false; } - if ( t2.getNumberOfExternalNodes() != 2 ) { + final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance(); + final NHXParser p = new NHXParser(); + final URL u3 = new URL( s ); + p.setSource( u3 ); + if ( !p.hasNext() ) { return false; } - if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) { + if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { return false; } - if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) { + if ( !p.hasNext() ) { return false; } - if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) { + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) { + if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { return false; } - if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) { + if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) { return false; } - if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) { + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence() - .startsWith( "actgtgggggt" ) ) { + if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) { return false; } - if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence() - .startsWith( "ctgtgatgcat" ) ) { + if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) { return false; } - if ( t3.getNumberOfExternalNodes() != 4 ) { + } + catch ( final Exception e ) { + System.out.println( e.toString() ); + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testOverlapRemoval() { + try { + final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 ); + final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 ); + final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 ); + final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 ); + final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 ); + final List covered = new ArrayList(); + 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 ( !t1.getName().equals( "t1" ) ) { + if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) { return false; } - if ( !t2.getName().equals( "t2" ) ) { + if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) { return false; } - if ( !t3.getName().equals( "t3" ) ) { + if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) { return false; } - if ( !t4.getName().equals( "t4" ) ) { + if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) { return false; } - if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) { + final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 ); + final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 ); + final Protein ab = new BasicProtein( "ab", "varanus", 0 ); + ab.addProteinDomain( a ); + ab.addProteinDomain( b ); + final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab ); + if ( ab.getNumberOfProteinDomains() != 2 ) { return false; } - if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) { + if ( ab_s0.getNumberOfProteinDomains() != 1 ) { return false; } - if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) { + if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) { return false; } - if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName() - .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) { + final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab ); + if ( ab.getNumberOfProteinDomains() != 2 ) { return false; } - if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) { + if ( ab_s1.getNumberOfProteinDomains() != 2 ) { return false; } - if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) { + 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 ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) { + if ( cde_s0.getNumberOfProteinDomains() != 3 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() - .equals( "apoptosis" ) ) { + 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 ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef() - .equals( "GO:0006915" ) ) { + if ( fghi_s0.getNumberOfProteinDomains() != 1 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource() - .equals( "UniProtKB" ) ) { + if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence() - .equals( "experimental" ) ) { + final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi ); + if ( fghi.getNumberOfProteinDomains() != 7 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType() - .equals( "function" ) ) { + if ( fghi_s1.getNumberOfProteinDomains() != 7 ) { return false; } - if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() - .getValue() != 1 ) { + 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 ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() - .getType().equals( "ml" ) ) { + if ( jklm_s0.getNumberOfProteinDomains() != 1 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() - .equals( "apoptosis" ) ) { + if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) { return false; } - if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { + final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm ); + if ( jklm.getNumberOfProteinDomains() != 7 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { + if ( jklm_s1.getNumberOfProteinDomains() != 7 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { + 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 ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { + if ( od_s0.getNumberOfProteinDomains() != 1 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static final boolean testPfamTreeReading() { + try { + final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" ); + final NHXParser parser = new NHXParser(); + parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + parser.setReplaceUnderscores( false ); + parser.setGuessRootedness( true ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser); + if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { + if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() - .equals( "GO:0005829" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static final boolean testPhyloXMLparsingFromURL() { + try { + final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml"; + final URL u = new URL( s ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() ); + + if ( ( phys == null ) || ( phys.length != 2 ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc() - .equals( "intracellular organelle" ) ) { + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() ); + + if ( ( phys2 == null ) || ( phys2.length != 2 ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static final boolean testToLReading() { + try { + final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, new TolParser() ); + if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription() - .equals( "UniProt link" ) ) ) { + if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) { return false; } - if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) { + if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) { return false; } - final SortedSet x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences(); - if ( x.size() != 4 ) { + if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) { 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++; + // + final URL u2 = new URL( WebserviceUtil.TOL_URL_BASE + "17706" ); + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, new TolParser() ); + if ( ( phys2 == null ) || ( phys2.length != 1 ) ) { + return false; + } + if ( !phys2[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "17706" ) ) { + return false; + } + if ( phys2[ 0 ].getNumberOfExternalNodes() < 5 ) { + return false; } } catch ( final Exception e ) { - e.printStackTrace( System.out ); + e.printStackTrace(); return false; } return true; } - private static boolean testBasicPhyloXMLparsingRoundtrip() { + private static final boolean testTreeBaseReading() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final PhyloXmlParser xml_parser = new PhyloXmlParser(); - if ( USE_LOCAL_PHYLOXML_SCHEMA ) { - xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); - } - else { - xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); + final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "72557?format=nexus" ); + final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); + parser.setReplaceUnderscores( true ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); + if ( ( phys == null ) || ( phys.length != 1 ) ) { + return false; } - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", - xml_parser ); - if ( xml_parser.getErrorCount() > 0 ) { - System.out.println( xml_parser.getErrorMessages().toString() ); + final URL u_1 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2406?format=nexus" ); + final NexusPhylogeniesParser parser_1 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_1 = ForesterUtil.readPhylogeniesFromUrl( u_1, parser_1 ); + if ( ( phys_1 == null ) || ( phys_1.length != 1 ) ) { return false; } - if ( phylogenies_0.length != 4 ) { + final URL u_2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "422?format=nexus" ); + final NexusPhylogeniesParser parser_2 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_2 = ForesterUtil.readPhylogeniesFromUrl( u_2, parser_2 ); + if ( ( phys_2 == null ) || ( phys_2.length != 1 ) ) { return false; } - final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) ); - final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser ); - if ( phylogenies_t1.length != 1 ) { + final URL u_3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2654?format=nexus" ); + final NexusPhylogeniesParser parser_3 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_3 = ForesterUtil.readPhylogeniesFromUrl( u_3, parser_3 ); + if ( ( phys_3 == null ) || ( phys_3.length != 1 ) ) { return false; } - final Phylogeny t1_rt = phylogenies_t1[ 0 ]; - if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) { + final URL u_4 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" ); + final NexusPhylogeniesParser parser_4 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_4 = ForesterUtil.readPhylogeniesFromUrl( u_4, parser_4 ); + if ( ( phys_4 == null ) || ( phys_4.length != 1 ) ) { return false; } - if ( !t1_rt.isRooted() ) { + final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" ); + final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser(); + parser2.setReplaceUnderscores( true ); + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, parser2 ); + if ( ( phys2 == null ) || ( phys2.length != 9 ) ) { return false; } - if ( t1_rt.isRerootable() ) { + final URL u3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14909?format=nexus" ); + final NexusPhylogeniesParser parser3 = new NexusPhylogeniesParser(); + final Phylogeny[] phys3 = ForesterUtil.readPhylogeniesFromUrl( u3, parser3 ); + if ( ( phys3 == null ) || ( phys3.length != 2 ) ) { return false; } - if ( !t1_rt.getType().equals( "gene_tree" ) ) { + final Phylogeny[] phys4 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14525?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys4 == null ) || ( phys4.length != 1 ) ) { return false; } - final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) ); - final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser ); - final Phylogeny t2_rt = phylogenies_t2[ 0 ]; - if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) { + final Phylogeny[] phys5 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15632?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys5 == null ) || ( phys5.length != 1 ) ) { return false; } - if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) { + final Phylogeny[] phys6 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "10190?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys6 == null ) || ( phys6.length != 1 ) ) { return false; } - if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) { + final Phylogeny[] phys7 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "13246?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys7 == null ) || ( phys7.length != 2 ) ) { return false; } - if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) { + final Phylogeny[] phys8 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "11662?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys8 == null ) || ( phys8.length != 2 ) ) { return false; } - if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence() - .startsWith( "actgtgggggt" ) ) { + final Phylogeny[] phys9 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "562?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys9 == null ) || ( phys9.length != 4 ) ) { return false; } - if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence() - .startsWith( "ctgtgatgcat" ) ) { + final Phylogeny[] phys16424 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "16424?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys16424 == null ) || ( phys16424.length != 1 ) ) { return false; } - final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) ); - final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser ); - final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) ); - final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser ); - if ( phylogenies_1.length != 1 ) { + final Phylogeny[] phys17878 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "17878?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys17878 == null ) || ( phys17878.length != 17 ) ) { return false; } - final Phylogeny t3_rt = phylogenies_1[ 0 ]; - if ( !t3_rt.getName().equals( "t3" ) ) { + final Phylogeny[] phys18804 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "18804?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys18804 == null ) || ( phys18804.length != 2 ) ) { return false; } - if ( t3_rt.getNumberOfExternalNodes() != 4 ) { + final Phylogeny[] phys346 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "346?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys346 == null ) || ( phys346.length != 1 ) ) { return false; } - if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static final boolean testTreeFamReading() { + try { + final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" ); + final NHXParser parser = new NHXParser(); + parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO ); + parser.setReplaceUnderscores( false ); + parser.setGuessRootedness( true ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); + if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } - if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) { + if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + 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 MolecularSequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" ); + if ( aa1.getLength() != 13 ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName() - .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) { + if ( aa1.getResidueAt( 0 ) != 'A' ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) { + if ( aa1.getResidueAt( 2 ) != 'K' ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) { + if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource() - .equals( "UniProtKB" ) ) { + final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" ); + if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() - .equals( "apoptosis" ) ) { + final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" ); + if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef() - .equals( "GO:0006915" ) ) { + final MolecularSequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" ); + if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource() - .equals( "UniProtKB" ) ) { + } + 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 ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence() - .equals( "experimental" ) ) { + if ( pd.getNumber() != 1 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType() - .equals( "function" ) ) { + if ( pd.getTotalCount() != 4 ) { return false; } - if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() - .getValue() != 1 ) { + if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() - .getType().equals( "ml" ) ) { + 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 ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() - .equals( "apoptosis" ) ) { + if ( !a1.equals( a1_copy ) ) { return false; } - if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { + if ( !a1.equals( a1_equal ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { + if ( !a1.equals( a2 ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { + if ( a1.equals( a3 ) ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { + if ( a1.compareTo( a1 ) != 0 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { + if ( a1.compareTo( a1_copy ) != 0 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() - .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { + if ( a1.compareTo( a1_equal ) != 0 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() - .equals( "GO:0005829" ) ) { + if ( a1.compareTo( a2 ) != 0 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc() - .equals( "intracellular organelle" ) ) { + if ( a1.compareTo( a3 ) == 0 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testBasicNodeMethods() { + try { + if ( PhylogenyNode.getNodeCount() != 0 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription() - .equals( "UniProt link" ) ) ) { + final PhylogenyNode n1 = new PhylogenyNode(); + final PhylogenyNode n2 = PhylogenyNode + .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + final PhylogenyNode n3 = PhylogenyNode + .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + final PhylogenyNode n4 = PhylogenyNode + .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( n1.isHasAssignedEvent() ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) { + if ( PhylogenyNode.getNodeCount() != 4 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) { + if ( n3.getIndicator() != 0 ) { return false; } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() - .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) { + if ( n3.getNumberOfExternalNodes() != 1 ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) { + if ( !n3.isExternal() ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) { + if ( !n3.isRoot() ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) { + if ( !n4.getName().equals( "n4" ) ) { return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testUTF8ParsingFromFile() { + try { + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); + final Phylogeny[] phylogenies_xml = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.xml" ), + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); return false; } - if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider() - .equals( "ncbi" ) ) { + if ( phylogenies_xml.length != 1 ) { return false; } - if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) { + + final Phylogeny[] phylogenies_xml2 = ParserBasedPhylogenyFactory.getInstance().create( new StringBuffer( phylogenies_xml[0].toPhyloXML( 0 )), + xml_parser ); + + final Phylogeny[] phylogenies_nh = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nh" ), new NHXParser() ); + if ( phylogenies_nh.length != 1 ) { return false; } - if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) - .getName().equals( "B" ) ) { + + final Phylogeny[] phylogenies_nex = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nex" ), new NexusPhylogeniesParser() ); + if ( phylogenies_nex.length != 1 ) { return false; } - if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) - .getFrom() != 21 ) { + + final String[] xml_n = phylogenies_xml[0].getAllExternalNodeNames(); + final String[] xml_n2 = phylogenies_xml2[0].getAllExternalNodeNames(); + final String[] nh_n = phylogenies_nh[0].getAllExternalNodeNames(); + final String[] nex_n = phylogenies_nex[0].getAllExternalNodeNames(); + final String n0 = "AQ~!@#$%^&*()_+-=\\{}|;:\"<>?,./"; + final String n1 = "€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ"; + final String n2 = "漢字ひらがなカタカナ"; + final String n3 = "อักษรไทย"; + final String n4 = "繁體字"; + final String n5 = "한글"; + final String n6 = "देवनागरी"; + + final String n7 = "chữ Quốc ngữ"; + final String n8 = "ру́сский язы́к"; + final String n9 = "អក្សរខ្មែរ"; + + if ( !xml_n[0].equals( n0 ) ) { + System.out.println( xml_n[0] ); + System.out.println( n0 ); return false; } - if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) { + if ( !xml_n2[0].equals( n0 ) ) { + System.out.println( xml_n2[0] ); + System.out.println( n0 ); return false; } - if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) - .getLength() != 24 ) { + if ( !nh_n[0].equals( n0 ) ) { + System.out.println( nh_n[0] ); + System.out.println( n0 ); return false; } - if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) - .getConfidence() != 2144 ) { + if ( !nex_n[0].equals( n0 ) ) { + System.out.println( nex_n[0] ); + System.out.println( n0 ); return false; } - if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId() - .equals( "pfam" ) ) { + + if ( !xml_n[1].equals( n1 ) ) { + System.out.println( xml_n[1] ); + System.out.println( n1 ); return false; } - if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) { + if ( !xml_n2[1].equals( n1 ) ) { + System.out.println( xml_n2[1] ); + System.out.println( n1 ); return false; } - if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) { + if ( !nh_n[1].equals( n1 ) ) { + System.out.println( nh_n[1] ); + System.out.println( n1 ); return false; } - if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) { + if ( !nex_n[1].equals( n1 ) ) { + System.out.println( nex_n[1] ); + System.out.println( n1 ); return false; } - if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) { + + if ( !xml_n[2].equals( n2 ) ) { + System.out.println( xml_n[2] ); + System.out.println( n2 ); return false; } - final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy(); - if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) { + if ( !xml_n2[2].equals( n2 ) ) { + System.out.println( xml_n2[2] ); + System.out.println( n2 ); return false; } - if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) { + if ( !nh_n[2].equals( n2 ) ) { + System.out.println( nh_n[2] ); + System.out.println( n2 ); return false; } - if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) { + if ( !nex_n[2].equals( n2 ) ) { + System.out.println( nex_n[2] ); + System.out.println( n2 ); return false; } - if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) { + // + if ( !xml_n[3].equals( n3 ) ) { + System.out.println( xml_n[3] ); + System.out.println( n3 ); return false; } - if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) { + if ( !xml_n2[3].equals( n3 ) ) { + System.out.println( xml_n2[3] ); + System.out.println( n3 ); return false; } - if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) { + if ( !nh_n[3].equals( n3 ) ) { + System.out.println( nh_n[3] ); + System.out.println( n3 ); return false; } - if ( taxbb.getSynonyms().size() != 2 ) { + if ( !nex_n[3].equals( n3 ) ) { + System.out.println( nex_n[3] ); + System.out.println( n3 ); return false; } - if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) { + // + if ( !xml_n[4].equals( n4 ) ) { + System.out.println( xml_n[4] ); + System.out.println( n4 ); return false; } - if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) { + if ( !nh_n[4].equals( n4 ) ) { + System.out.println( nh_n[4] ); + System.out.println( n4 ); return false; } - if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) { + if ( !nex_n[4].equals( n4 ) ) { + System.out.println( nex_n[4] ); + System.out.println( n4 ); return false; } - if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) { + // + if ( !xml_n[5].equals( n5 ) ) { + System.out.println( xml_n[5] ); + System.out.println( n5 ); return false; } - if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) { + if ( !nh_n[5].equals( n5 ) ) { + System.out.println( nh_n[5] ); + System.out.println( n5 ); return false; } - if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() ) - .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) { + if ( !nex_n[5].equals( n5 ) ) { + System.out.println( nex_n[5] ); + System.out.println( n5 ); return false; } - if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) { + // + if ( !xml_n[6].equals( n6 ) ) { + System.out.println( xml_n[6] ); + System.out.println( n6 ); return false; } - if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) { + if ( !nh_n[6].equals( n6 ) ) { + System.out.println( nh_n[6] ); + System.out.println( n6 ); return false; } - if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) { + if ( !nex_n[6].equals( n6 ) ) { + System.out.println( nex_n[6] ); + System.out.println( n6 ); return false; } - if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) { + // + if ( !xml_n[7].equals( n7 ) ) { + System.out.println( xml_n[7] ); + System.out.println( n7 ); return false; } - if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) { + if ( !nh_n[7].equals( n7 ) ) { + System.out.println( nh_n[7] ); + System.out.println( n7 ); return false; } - if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) { + if ( !nex_n[7].equals( n7 ) ) { + System.out.println( nex_n[7] ); + System.out.println( n7 ); return false; } - if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) { + if ( !xml_n[8].equals( n8 ) ) { + System.out.println( xml_n[8] ); + System.out.println( n8 ); return false; } - // - if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) { + if ( !nh_n[8].equals( n8 ) ) { + System.out.println( nh_n[8] ); + System.out.println( n8 ); return false; } - if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString() - .equalsIgnoreCase( "435" ) ) { + if ( !nex_n[8].equals( n8 ) ) { + System.out.println( nex_n[8] ); + System.out.println( n8 ); return false; } - if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) { + if ( !xml_n[9].equals( n9 ) ) { + System.out.println( xml_n[9] ); + System.out.println( n9 ); return false; } - if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString() - .equalsIgnoreCase( "443.7" ) ) { + if ( !xml_n2[9].equals( n9 ) ) { + System.out.println( xml_n2[9] ); + System.out.println( n9 ); return false; } - if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) { + if ( !nh_n[9].equals( n9 ) ) { + System.out.println( nh_n[9] ); + System.out.println( n9 ); return false; } - if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) { + if ( !nex_n[9].equals( n9 ) ) { + System.out.println( nex_n[9] ); + System.out.println( n9 ); return false; } - if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString() - .equalsIgnoreCase( "433" ) ) { + if (!phylogenies_xml[0].toNewHampshire().equals( + phylogenies_nh[0].toNewHampshire() ) ) { + System.out.println( phylogenies_xml[0].toNewHampshire() ); + System.out.println( phylogenies_nh[0].toNewHampshire() ); return false; } - final SortedSet x = t3_rt.getNode( "root node" ).getNodeData().getSequence() - .getCrossReferences(); - if ( x.size() != 4 ) { + if (!phylogenies_xml[0].toNewHampshire().equals( + phylogenies_nex[0].toNewHampshire() ) ) { + System.out.println( phylogenies_xml[0].toNewHampshire() ); + System.out.println( phylogenies_nex[0].toNewHampshire() ); return false; } - 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 ); @@ -1897,27 +2061,14 @@ public final class Test { } return true; } + + - private static boolean testBasicPhyloXMLparsingValidating() { + private static boolean testBasicPhyloXMLparsing() { 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 = new PhyloXmlParser(); - 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_test_t1.xml", + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); + final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( xml_parser.getErrorMessages().toString() ); @@ -1930,650 +2081,533 @@ public final class Test { final Phylogeny t2 = phylogenies_0[ 1 ]; final Phylogeny t3 = phylogenies_0[ 2 ]; final Phylogeny t4 = phylogenies_0[ 3 ]; - if ( !t1.getName().equals( "t1" ) ) { + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - if ( !t2.getName().equals( "t2" ) ) { + if ( !t1.isRooted() ) { return false; } - if ( !t3.getName().equals( "t3" ) ) { + if ( t1.isRerootable() ) { return false; } - if ( !t4.getName().equals( "t4" ) ) { + if ( !t1.getType().equals( "gene_tree" ) ) { return false; } - if ( t1.getNumberOfExternalNodes() != 1 ) { + if ( t2.getNumberOfExternalNodes() != 2 ) { return false; } - if ( t2.getNumberOfExternalNodes() != 2 ) { + if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) { return false; } - if ( t3.getNumberOfExternalNodes() != 4 ) { + if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) { return false; } - final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml"; - final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser ); - if ( xml_parser.getErrorCount() > 0 ) { - System.out.println( "errors:" ); - System.out.println( xml_parser.getErrorMessages().toString() ); + if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) { return false; } - if ( phylogenies_1.length != 4 ) { + if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) { return false; } - final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml", - xml_parser ); - if ( xml_parser.getErrorCount() > 0 ) { - System.out.println( "errors:" ); - System.out.println( xml_parser.getErrorMessages().toString() ); + if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) { return false; } - if ( phylogenies_2.length != 1 ) { + if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) { return false; } - if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) { + if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence() + .startsWith( "actgtgggggt" ) ) { return false; } - final Phylogeny[] phylogenies_3 = 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() ); + if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence() + .startsWith( "ctgtgatgcat" ) ) { return false; } - if ( phylogenies_3.length != 2 ) { + if ( t3.getNumberOfExternalNodes() != 4 ) { return false; } - final Phylogeny a = phylogenies_3[ 0 ]; - if ( !a.getName().equals( "tree 4" ) ) { + if ( !t1.getName().equals( "t1" ) ) { return false; } - if ( a.getNumberOfExternalNodes() != 3 ) { + if ( !t2.getName().equals( "t2" ) ) { return false; } - if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) { + if ( !t3.getName().equals( "t3" ) ) { return false; } - if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) { + if ( !t4.getName().equals( "t4" ) ) { return false; } - final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml", - xml_parser ); - if ( xml_parser.getErrorCount() > 0 ) { - System.out.println( xml_parser.getErrorMessages().toString() ); + if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) { return false; } - if ( phylogenies_4.length != 1 ) { + if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) { return false; } - final Phylogeny s = phylogenies_4[ 0 ]; - if ( s.getNumberOfExternalNodes() != 6 ) { + if ( !t3.getNode( "root node" ).isDuplication() ) { return false; } - s.getNode( "first" ); - s.getNode( "<>" ); - s.getNode( "\"\"" ); - s.getNode( "'''\"" ); - s.getNode( "\"\"\"" ); - s.getNode( "dick & doof" ); - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testBasicProtein() { - try { - final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 ); - 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" ) ) { + if ( !t3.getNode( "node a" ).isDuplication() ) { return false; } - if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) { + if ( t3.getNode( "node a" ).isSpeciation() ) { return false; } - // - 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" ) ) { + if ( t3.getNode( "node bc" ).isDuplication() ) { return false; } - if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) { + if ( !t3.getNode( "node bc" ).isSpeciation() ) { return false; } - // - 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" ) ) { + if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) { + if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName() + .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) { return false; } - aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) ); - if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) { + if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) { + if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) { + if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) { return false; } - aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) ); - if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() + .equals( "apoptosis" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef() + .equals( "GO:0006915" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource() + .equals( "UniProtKB" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence() + .equals( "experimental" ) ) { return false; } - aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) ); - if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType() + .equals( "function" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) { + if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() + .getValue() != 1 ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() + .getType().equals( "ml" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() + .equals( "apoptosis" ) ) { return false; } - aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) ); - if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) { + if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { return false; } - if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { return false; } - // - 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" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { return false; } - if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { return false; } - if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() + .equals( "GO:0005829" ) ) { return false; } - if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc() + .equals( "intracellular organelle" ) ) { 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" ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) { 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 ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription() + .equals( "UniProt link" ) ) ) { return false; } - if ( !p.contains( domains_ids, true ) ) { + if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) { return false; } - domains_ids.add( "X" ); - if ( p.contains( domains_ids, false ) ) { + final SortedSet x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences(); + if ( x.size() != 4 ) { return false; } - if ( p.contains( domains_ids, true ) ) { + 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 ); + return false; + } + return true; + } + + private static boolean testBasicPhyloXMLparsingRoundtrip() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); + if ( USE_LOCAL_PHYLOXML_SCHEMA ) { + xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); + } + else { + xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); + } + final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ), + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); return false; } - domains_ids = new ArrayList(); - domains_ids.add( "A" ); - domains_ids.add( "C" ); - domains_ids.add( "D" ); - if ( !p.contains( domains_ids, false ) ) { + if ( phylogenies_0.length != 4 ) { return false; } - if ( !p.contains( domains_ids, true ) ) { + final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) ); + final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser ); + if ( phylogenies_t1.length != 1 ) { return false; } - domains_ids = new ArrayList(); - domains_ids.add( "A" ); - domains_ids.add( "D" ); - domains_ids.add( "C" ); - if ( !p.contains( domains_ids, false ) ) { + final Phylogeny t1_rt = phylogenies_t1[ 0 ]; + if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) { return false; } - if ( p.contains( domains_ids, true ) ) { + if ( !t1_rt.isRooted() ) { return false; } - domains_ids = new ArrayList(); - domains_ids.add( "A" ); - domains_ids.add( "A" ); - domains_ids.add( "B" ); - if ( !p.contains( domains_ids, false ) ) { + if ( t1_rt.isRerootable() ) { return false; } - if ( !p.contains( domains_ids, true ) ) { + if ( !t1_rt.getType().equals( "gene_tree" ) ) { 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 ) ) { + final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) ); + final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser ); + final Phylogeny t2_rt = phylogenies_t2[ 0 ]; + if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) { return false; } - if ( !p.contains( domains_ids, true ) ) { + if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) { 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 ) ) { + if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) { return false; } - if ( p.contains( domains_ids, true ) ) { + if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) { 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 ) { + if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence() + .startsWith( "actgtgggggt" ) ) { return false; } - if ( t0.getNumberOfRows() != 0 ) { + if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence() + .startsWith( "ctgtgatgcat" ) ) { 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" ) ) { + final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) ); + final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser ); + final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) ); + final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser ); + if ( phylogenies_1.length != 1 ) { return false; } - if ( !t0.getValue( 10, 1 ).equals( "110" ) ) { + final Phylogeny t3_rt = phylogenies_1[ 0 ]; + if ( !t3_rt.getName().equals( "t3" ) ) { return false; } - if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) { + if ( t3_rt.getNumberOfExternalNodes() != 4 ) { return false; } - if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) { + if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) { return false; } - if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) { + if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) { return false; } - if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) { return false; } - if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName() + .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) { return false; } - if ( t0.getNumberOfColumns() != 101 ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) { return false; } - if ( t0.getNumberOfRows() != 11 ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) { return false; } - if ( t0.getValueAsString( 49, 4 ) != null ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource() + .equals( "UniProtKB" ) ) { 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 ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() + .equals( "apoptosis" ) ) { return false; } - if ( t1.getNumberOfRows() != 6 ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef() + .equals( "GO:0006915" ) ) { return false; } - if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource() + .equals( "UniProtKB" ) ) { return false; } - if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence() + .equals( "experimental" ) ) { return false; } - if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType() + .equals( "function" ) ) { return false; } - if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) { + if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() + .getValue() != 1 ) { 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 ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence() + .getType().equals( "ml" ) ) { return false; } - if ( t2.getNumberOfRows() != 6 ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc() + .equals( "apoptosis" ) ) { return false; } - if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) { + if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) { return false; } - if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) { return false; } - if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) { return false; } - if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) { return false; } - if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) { return false; } - if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties() + .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) { return false; } - final StringBuffer source2 = new StringBuffer(); - source2.append( "" + l ); - source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l ); - source2.append( " 00; 01 ;02;03" + l ); - source2.append( " 10; 11; 12; 13 " + l ); - source2.append( "20; 21; 22; 23 " + l ); - source2.append( " " + l ); - source2.append( " 30; 31; 32; 33" + l ); - source2.append( "40;41;42;43" + l ); - 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:", - false ); - if ( tl.size() != 2 ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef() + .equals( "GO:0005829" ) ) { return false; } - final BasicTable t3 = tl.get( 0 ); - final BasicTable t4 = tl.get( 1 ); - if ( t3.getNumberOfColumns() != 4 ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc() + .equals( "intracellular organelle" ) ) { return false; } - if ( t3.getNumberOfRows() != 3 ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) { return false; } - if ( t4.getNumberOfColumns() != 4 ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription() + .equals( "UniProt link" ) ) ) { return false; } - if ( t4.getNumberOfRows() != 3 ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) { return false; } - if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) { return false; } - if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) { + if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() + .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) { + System.out.println( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() ); return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testBasicTolXMLparsing() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final TolParser parser = new TolParser(); - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser ); - if ( parser.getErrorCount() > 0 ) { - System.out.println( parser.getErrorMessages().toString() ); + if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) { return false; } - if ( phylogenies_0.length != 1 ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) { return false; } - final Phylogeny t1 = phylogenies_0[ 0 ]; - if ( t1.getNumberOfExternalNodes() != 5 ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) { return false; } - if ( !t1.isRooted() ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { return false; } - if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) { + if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider() + .equals( "ncbi" ) ) { return false; } - if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) { + if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) { return false; } - if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) { + if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) + .getName().equals( "B" ) ) { return false; } - if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) { + if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) + .getFrom() != 21 ) { return false; } - final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser ); - if ( parser.getErrorCount() > 0 ) { - System.out.println( parser.getErrorMessages().toString() ); + if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) { return false; } - if ( phylogenies_1.length != 1 ) { + if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) + .getLength() != 24 ) { return false; } - final Phylogeny t2 = phylogenies_1[ 0 ]; - if ( t2.getNumberOfExternalNodes() != 664 ) { + if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) + .getConfidence() != 0 ) { return false; } - if ( !t2.isRooted() ) { + if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId() + .equals( "pfam" ) ) { return false; } - if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) { + if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) { return false; } - if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) { + if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) { return false; } - if ( t2.getRoot().getNumberOfDescendants() != 24 ) { + if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) { return false; } - if ( t2.getRoot().getNumberOfDescendants() != 24 ) { + if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) { return false; } - if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) { + final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy(); + if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) { return false; } - if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName() - .equals( "Aquifex" ) ) { + if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) { return false; } - final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser ); - if ( parser.getErrorCount() > 0 ) { - System.out.println( parser.getErrorMessages().toString() ); + if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) { return false; } - if ( phylogenies_2.length != 1 ) { + if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) { return false; } - final Phylogeny t3 = phylogenies_2[ 0 ]; - if ( t3.getNumberOfExternalNodes() != 184 ) { + if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) { return false; } - if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) { + if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) { return false; } - if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) { + if ( taxbb.getSynonyms().size() != 2 ) { return false; } - if ( t3.getRoot().getNumberOfDescendants() != 6 ) { + if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) { return false; } - final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser ); - if ( parser.getErrorCount() > 0 ) { - System.out.println( parser.getErrorMessages().toString() ); + if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) { return false; } - if ( phylogenies_3.length != 1 ) { + if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) { return false; } - final Phylogeny t4 = phylogenies_3[ 0 ]; - if ( t4.getNumberOfExternalNodes() != 1 ) { + if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) { return false; } - if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) { + if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) { return false; } - if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) { + if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() ) + .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) { return false; } - if ( t4.getRoot().getNumberOfDescendants() != 0 ) { + if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) { return false; } - final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser ); - if ( parser.getErrorCount() > 0 ) { - System.out.println( parser.getErrorMessages().toString() ); + if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) { return false; } - if ( phylogenies_4.length != 1 ) { + if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) { return false; } - final Phylogeny t5 = phylogenies_4[ 0 ]; - if ( t5.getNumberOfExternalNodes() != 13 ) { + if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) { return false; } - if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) { + if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) { return false; } - if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) { + if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) { return false; } - if ( t5.getRoot().getNumberOfDescendants() != 2 ) { + if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) { + return false; + } + if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) { + return false; + } + if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString() + .equalsIgnoreCase( "435" ) ) { + return false; + } + if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) { + return false; + } + if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString() + .equalsIgnoreCase( "443.7" ) ) { + return false; + } + if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) { + return false; + } + if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) { + return false; + } + if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString() + .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 ); @@ -2582,83 +2616,123 @@ public final class Test { return true; } - private static boolean testBasicTreeMethods() { + private static boolean testBasicPhyloXMLparsingValidating() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t1 = factory.create(); - if ( !t1.isEmpty() ) { - return false; + PhyloXmlParser xml_parser = null; + try { + xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating(); } - final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ]; - if ( t2.getNumberOfExternalNodes() != 4 ) { + catch ( final Exception e ) { + // Do nothing -- means were not running from jar. + } + if ( xml_parser == null ) { + xml_parser = PhyloXmlParser.createPhyloXmlParser(); + if ( USE_LOCAL_PHYLOXML_SCHEMA ) { + xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); + } + else { + xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); + } + } + final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ), + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); return false; } - if ( t2.getHeight() != 8.5 ) { + if ( phylogenies_0.length != 4 ) { return false; } - if ( !t2.isCompletelyBinary() ) { + final Phylogeny t1 = phylogenies_0[ 0 ]; + final Phylogeny t2 = phylogenies_0[ 1 ]; + final Phylogeny t3 = phylogenies_0[ 2 ]; + final Phylogeny t4 = phylogenies_0[ 3 ]; + if ( !t1.getName().equals( "t1" ) ) { return false; } - if ( t2.isEmpty() ) { + if ( !t2.getName().equals( "t2" ) ) { return false; } - final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ]; - if ( t3.getNumberOfExternalNodes() != 5 ) { + if ( !t3.getName().equals( "t3" ) ) { return false; } - if ( t3.getHeight() != 11 ) { + if ( !t4.getName().equals( "t4" ) ) { return false; } - if ( t3.isCompletelyBinary() ) { + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - final PhylogenyNode n = t3.getNode( "ABC" ); - final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ]; - if ( t4.getNumberOfExternalNodes() != 9 ) { + if ( t2.getNumberOfExternalNodes() != 2 ) { return false; } - if ( t4.getHeight() != 11 ) { + if ( t3.getNumberOfExternalNodes() != 4 ) { return false; } - if ( t4.isCompletelyBinary() ) { + final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml"; + final Phylogeny[] phylogenies_1 = factory.create( new File( x2 ), xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( "errors:" ); + System.out.println( xml_parser.getErrorMessages().toString() ); return false; } - final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" ); - final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; - if ( t5.getNumberOfExternalNodes() != 8 ) { + if ( phylogenies_1.length != 4 ) { return false; } - if ( t5.getHeight() != 15 ) { + final Phylogeny[] phylogenies_2 = factory.create( new File(Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml" ), + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( "errors:" ); + System.out.println( xml_parser.getErrorMessages().toString() ); return false; } - final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" ); - final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ]; - if ( t6.getHeight() != 15 ) { + if ( phylogenies_2.length != 1 ) { return false; } - final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" ); - final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ]; - if ( t7.getHeight() != 15 ) { + if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) { return false; } - final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" ); - final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ]; - if ( t8.getNumberOfExternalNodes() != 10 ) { + final Phylogeny[] phylogenies_3 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml" ), + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); return false; } - if ( t8.getHeight() != 15 ) { + if ( phylogenies_3.length != 2 ) { return false; } - final char[] a9 = new char[] { 'a' }; - final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ]; - if ( t9.getHeight() != 0 ) { + final Phylogeny a = phylogenies_3[ 0 ]; + if ( !a.getName().equals( "tree 4" ) ) { return false; } - final char[] a10 = new char[] { 'a', ':', '6' }; - final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ]; - if ( t10.getHeight() != 6 ) { + 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 Phylogeny[] phylogenies_4 = factory.create( new File( Test.PATH_TO_TEST_DATA + "special_characters.xml") , + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); + return false; + } + if ( phylogenies_4.length != 1 ) { + return false; + } + final Phylogeny s = phylogenies_4[ 0 ]; + if ( s.getNumberOfExternalNodes() != 6 ) { return false; } + s.getNode( "first" ); + s.getNode( "<>" ); + s.getNode( "\"\"" ); + s.getNode( "'''\"" ); + s.getNode( "\"\"\"" ); + s.getNode( "dick & doof" ); } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -2667,224 +2741,259 @@ public final class Test { return true; } - private static boolean testConfidenceAssessor() { + private static boolean testBasicProtein() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev0 = factory - .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);", - new NHXParser() ); - ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 ); - if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) { + 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 ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) { + if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) { return false; } - final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev1 = factory - .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));", - new NHXParser() ); - ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 ); - if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) { + // + 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; } - if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) { + if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) { return false; } - final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev_b = factory - .create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd", - new NHXParser() ); - ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 ); - if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) { + // + 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 ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) { return false; } - // - final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev1x = factory - .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));", - new NHXParser() ); - ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 ); - if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) { + aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) ); + if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) { return false; } - if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) { return false; } - final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ]; - final Phylogeny[] ev_bx = factory - .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd", - new NHXParser() ); - ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 ); - if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { + if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) { return false; } - if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { + aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) ); + if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) { return false; } - // - final Phylogeny[] t2 = factory - .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);", - new NHXParser() ); - final Phylogeny[] ev2 = factory - .create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);", - new NHXParser() ); - for( final Phylogeny target : t2 ) { - ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 ); - } - // - final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg", - new NHXParser() )[ 0 ]; - final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() ); - ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 ); - if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) { return false; } - if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) { + if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) { return false; } - if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { + if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace(); - return false; - } - return true; - } - - private static boolean testCopyOfNodeData() { - try { - final PhylogenyNode n1 = PhylogenyNode - .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" ); - final PhylogenyNode n2 = n1.copyNodeData(); - if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) { + 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; } - } - catch ( final Exception e ) { - e.printStackTrace(); - return false; - } - return true; - } - - private static boolean testTreeCopy() { - try { - final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])"; - final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 ); - final Phylogeny t1 = t0.copy(); - if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) { return false; } - if ( !t1.toNewHampshireX().equals( str_0 ) ) { + if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) { return false; } - t0.deleteSubtree( t0.getNode( "c" ), true ); - t0.deleteSubtree( t0.getNode( "a" ), true ); - t0.deleteSubtree( t0.getNode( "e" ), true ); - if ( !t0.toNewHampshireX().equals( "(b,d)[&&NHX:S=lizards]" ) ) { + if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) { return false; } - if ( !t1.toNewHampshireX().equals( str_0 ) ) { + 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; } - t0.deleteSubtree( t0.getNode( "b" ), true ); - t0.deleteSubtree( t0.getNode( "d" ), true ); - if ( !t1.toNewHampshireX().equals( str_0 ) ) { + if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) { 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 ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) { return false; } - if ( p0.getNumberOfExternalNodes() != 15625 ) { + if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) { return false; } - final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 ); - if ( p1.getRoot().getNumberOfDescendants() != 10 ) { + // + 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 ( p1.getNumberOfExternalNodes() != 100 ) { + if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) { 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" ) ) { + if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) { return false; } - n.setName( "B0LM41_HUMAN" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) { + if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) { return false; } - n.setName( "NP_001025424" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) { + 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; } - n.setName( "_NM_001030253-" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) { - 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; } - n.setName( "XM_002122186" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) { + if ( !p.contains( domains_ids, true ) ) { return false; } - n.setName( "dgh_AAA34956_gdg" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) { + domains_ids.add( "X" ); + if ( p.contains( domains_ids, false ) ) { return false; } - n.setName( "AAA34956" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) { + if ( p.contains( domains_ids, true ) ) { 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 ) ); + domains_ids = new ArrayList(); + domains_ids.add( "A" ); + domains_ids.add( "C" ); + domains_ids.add( "D" ); + if ( !p.contains( domains_ids, false ) ) { 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 ) ); + if ( !p.contains( domains_ids, true ) ) { 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 ) ); + domains_ids = new ArrayList(); + domains_ids.add( "A" ); + domains_ids.add( "D" ); + domains_ids.add( "C" ); + if ( !p.contains( domains_ids, false ) ) { return false; } - n.setName( "P12345" ); - if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) { - System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) ); + if ( p.contains( domains_ids, true ) ) { 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 ) ); + 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; } } @@ -2895,1123 +3004,1153 @@ public final class Test { return true; } - private static boolean testDataObjects() { + private static boolean testBasicTable() { try { - final Confidence s0 = new Confidence(); - final Confidence s1 = new Confidence(); - if ( !s0.isEqual( s1 ) ) { + final BasicTable t0 = new BasicTable(); + if ( t0.getNumberOfColumns() != 0 ) { return false; } - final Confidence s2 = new Confidence( 0.23, "bootstrap" ); - final Confidence s3 = new Confidence( 0.23, "bootstrap" ); - if ( s2.isEqual( s1 ) ) { + if ( t0.getNumberOfRows() != 0 ) { return false; } - if ( !s2.isEqual( s3 ) ) { + 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 Confidence s4 = ( Confidence ) s3.copy(); - if ( !s4.isEqual( s3 ) ) { + if ( !t0.getValue( 10, 1 ).equals( "110" ) ) { return false; } - s3.asSimpleText(); - s3.asText(); - // Taxonomy - // ---------- - final Taxonomy t1 = new Taxonomy(); - final Taxonomy t2 = new Taxonomy(); - final Taxonomy t3 = new Taxonomy(); - final Taxonomy t4 = new Taxonomy(); - final Taxonomy t5 = new Taxonomy(); - t1.setIdentifier( new Identifier( "ecoli" ) ); - t1.setTaxonomyCode( "ECOLI" ); - t1.setScientificName( "E. coli" ); - t1.setCommonName( "coli" ); - final Taxonomy t0 = ( Taxonomy ) t1.copy(); - if ( !t1.isEqual( t0 ) ) { + if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) { return false; } - t2.setIdentifier( new Identifier( "ecoli" ) ); - t2.setTaxonomyCode( "OTHER" ); - t2.setScientificName( "what" ); - t2.setCommonName( "something" ); - if ( !t1.isEqual( t2 ) ) { + if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) { return false; } - t2.setIdentifier( new Identifier( "nemve" ) ); - if ( t1.isEqual( t2 ) ) { + if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) { return false; } - t1.setIdentifier( null ); - t3.setTaxonomyCode( "ECOLI" ); - t3.setScientificName( "what" ); - t3.setCommonName( "something" ); - if ( !t1.isEqual( t3 ) ) { + if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) { return false; } - t1.setIdentifier( null ); - t1.setTaxonomyCode( "" ); - t4.setScientificName( "E. ColI" ); - t4.setCommonName( "something" ); - if ( !t1.isEqual( t4 ) ) { + if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) { return false; } - t4.setScientificName( "B. subtilis" ); - t4.setCommonName( "something" ); - if ( t1.isEqual( t4 ) ) { + if ( t0.getNumberOfColumns() != 101 ) { return false; } - t1.setIdentifier( null ); - t1.setTaxonomyCode( "" ); - t1.setScientificName( "" ); - t5.setCommonName( "COLI" ); - if ( !t1.isEqual( t5 ) ) { + if ( t0.getNumberOfRows() != 11 ) { return false; } - t5.setCommonName( "vibrio" ); - if ( t1.isEqual( t5 ) ) { + if ( t0.getValueAsString( 49, 4 ) != null ) { return false; } - // Identifier - // ---------- - final Identifier id0 = new Identifier( "123", "pfam" ); - final Identifier id1 = ( Identifier ) id0.copy(); - if ( !id1.isEqual( id1 ) ) { + 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 ( !id1.isEqual( id0 ) ) { + if ( t1.getNumberOfRows() != 6 ) { return false; } - if ( !id0.isEqual( id1 ) ) { + if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) { return false; } - id1.asSimpleText(); - id1.asText(); - // ProteinDomain - // --------------- - final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 ); - final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy(); - if ( !pd1.isEqual( pd1 ) ) { + if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) { return false; } - if ( !pd1.isEqual( pd0 ) ) { + if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) { return false; } - pd1.asSimpleText(); - pd1.asText(); - final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" ); - final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy(); - if ( !pd3.isEqual( pd3 ) ) { + if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) { return false; } - if ( !pd2.isEqual( pd3 ) ) { + 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 ( !pd0.isEqual( pd3 ) ) { + if ( t2.getNumberOfRows() != 6 ) { return false; } - pd3.asSimpleText(); - pd3.asText(); - // DomainArchitecture - // ------------------ - final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 ); - final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 ); - final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 ); - final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 ); - final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 ); - final ArrayList domains0 = new ArrayList(); - domains0.add( d2 ); - domains0.add( d0 ); - domains0.add( d3 ); - domains0.add( d1 ); - final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 ); - if ( ds0.getNumberOfDomains() != 4 ) { + if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) { return false; } - final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy(); - if ( !ds0.isEqual( ds0 ) ) { + if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) { return false; } - if ( !ds0.isEqual( ds1 ) ) { + if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) { return false; } - if ( ds1.getNumberOfDomains() != 4 ) { + if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) { return false; } - final ArrayList domains1 = new ArrayList(); - domains1.add( d1 ); - domains1.add( d2 ); - domains1.add( d4 ); - domains1.add( d0 ); - final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 ); - if ( ds0.isEqual( ds2 ) ) { + if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) { return false; } - ds1.asSimpleText(); - ds1.asText(); - ds1.toNHX(); - final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" ); - if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) { - System.out.println( ds3.toNHX() ); + if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) { return false; } - if ( ds3.getNumberOfDomains() != 3 ) { + final StringBuffer source2 = new StringBuffer(); + source2.append( "" + l ); + source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l ); + source2.append( " 00; 01 ;02;03" + l ); + source2.append( " 10; 11; 12; 13 " + l ); + source2.append( "20; 21; 22; 23 " + l ); + source2.append( " " + l ); + source2.append( " 30; 31; 32; 33" + l ); + source2.append( "40;41;42;43" + l ); + 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:", + false ); + if ( tl.size() != 2 ) { return false; } - // Event - // ----- - final Event e1 = new Event( Event.EventType.fusion ); - if ( e1.isDuplication() ) { + final BasicTable t3 = tl.get( 0 ); + final BasicTable t4 = tl.get( 1 ); + if ( t3.getNumberOfColumns() != 4 ) { return false; } - if ( !e1.isFusion() ) { + if ( t3.getNumberOfRows() != 3 ) { return false; } - if ( !e1.asText().toString().equals( "fusion" ) ) { + if ( t4.getNumberOfColumns() != 4 ) { return false; } - if ( !e1.asSimpleText().toString().equals( "fusion" ) ) { + if ( t4.getNumberOfRows() != 3 ) { return false; } - final Event e11 = new Event( Event.EventType.fusion ); - if ( !e11.isEqual( e1 ) ) { + if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) { return false; } - if ( !e11.toNHX().toString().equals( "" ) ) { + if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) { return false; } - final Event e2 = new Event( Event.EventType.speciation_or_duplication ); - if ( e2.isDuplication() ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testBasicTolXMLparsing() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final TolParser parser = new TolParser(); + final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser ); + if ( parser.getErrorCount() > 0 ) { + System.out.println( parser.getErrorMessages().toString() ); return false; } - if ( !e2.isSpeciationOrDuplication() ) { + if ( phylogenies_0.length != 1 ) { return false; } - if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) { + final Phylogeny t1 = phylogenies_0[ 0 ]; + if ( t1.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !e2.asSimpleText().toString().equals( "?" ) ) { + if ( !t1.isRooted() ) { return false; } - if ( !e2.toNHX().toString().equals( ":D=?" ) ) { + if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) { return false; } - if ( e11.isEqual( e2 ) ) { + if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) { return false; } - final Event e2c = ( Event ) e2.copy(); - if ( !e2c.isEqual( e2 ) ) { + if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) { return false; } - Event e3 = new Event( 1, 2, 3 ); - if ( e3.isDuplication() ) { + if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) { return false; } - if ( e3.isSpeciation() ) { + final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser ); + if ( parser.getErrorCount() > 0 ) { + System.out.println( parser.getErrorMessages().toString() ); return false; } - if ( e3.isGeneLoss() ) { + if ( phylogenies_1.length != 1 ) { return false; } - if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) { + final Phylogeny t2 = phylogenies_1[ 0 ]; + if ( t2.getNumberOfExternalNodes() != 664 ) { return false; } - final Event e3c = ( Event ) e3.copy(); - final Event e3cc = ( Event ) e3c.copy(); - if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) { + if ( !t2.isRooted() ) { return false; } - e3 = null; - if ( !e3c.isEqual( e3cc ) ) { + if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) { return false; } - Event e4 = new Event( 1, 2, 3 ); - if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) { + if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) { return false; } - if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) { + if ( t2.getRoot().getNumberOfDescendants() != 24 ) { return false; } - final Event e4c = ( Event ) e4.copy(); - e4 = null; - final Event e4cc = ( Event ) e4c.copy(); - if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) { + if ( t2.getRoot().getNumberOfDescendants() != 24 ) { return false; } - if ( !e4c.isEqual( e4cc ) ) { + if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) { return false; } - final Event e5 = new Event(); - if ( !e5.isUnassigned() ) { + if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName() + .equals( "Aquifex" ) ) { return false; } - if ( !e5.asText().toString().equals( "unassigned" ) ) { + final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser ); + if ( parser.getErrorCount() > 0 ) { + System.out.println( parser.getErrorMessages().toString() ); return false; } - if ( !e5.asSimpleText().toString().equals( "" ) ) { + if ( phylogenies_2.length != 1 ) { return false; } - final Event e6 = new Event( 1, 0, 0 ); - if ( !e6.asText().toString().equals( "duplication" ) ) { + final Phylogeny t3 = phylogenies_2[ 0 ]; + if ( t3.getNumberOfExternalNodes() != 184 ) { return false; } - if ( !e6.asSimpleText().toString().equals( "D" ) ) { + if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) { return false; } - final Event e7 = new Event( 0, 1, 0 ); - if ( !e7.asText().toString().equals( "speciation" ) ) { + if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) { return false; } - if ( !e7.asSimpleText().toString().equals( "S" ) ) { + if ( t3.getRoot().getNumberOfDescendants() != 6 ) { return false; } - final Event e8 = new Event( 0, 0, 1 ); - if ( !e8.asText().toString().equals( "gene-loss" ) ) { + final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser ); + if ( parser.getErrorCount() > 0 ) { + System.out.println( parser.getErrorMessages().toString() ); return false; } - if ( !e8.asSimpleText().toString().equals( "L" ) ) { + if ( phylogenies_3.length != 1 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testDeletionOfExternalNodes() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ]; - final PhylogenyWriter w = new PhylogenyWriter(); - if ( t0.isEmpty() ) { + final Phylogeny t4 = phylogenies_3[ 0 ]; + if ( t4.getNumberOfExternalNodes() != 1 ) { return false; } - if ( t0.getNumberOfExternalNodes() != 1 ) { + if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) { return false; } - t0.deleteSubtree( t0.getNode( "A" ), false ); - if ( t0.getNumberOfExternalNodes() != 0 ) { + if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) { return false; } - if ( !t0.isEmpty() ) { + if ( t4.getRoot().getNumberOfDescendants() != 0 ) { return false; } - final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ]; - if ( t1.getNumberOfExternalNodes() != 2 ) { + final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser ); + if ( parser.getErrorCount() > 0 ) { + System.out.println( parser.getErrorMessages().toString() ); return false; } - t1.deleteSubtree( t1.getNode( "A" ), false ); - if ( t1.getNumberOfExternalNodes() != 1 ) { + if ( phylogenies_4.length != 1 ) { return false; } - if ( !t1.getNode( "B" ).getName().equals( "B" ) ) { + final Phylogeny t5 = phylogenies_4[ 0 ]; + if ( t5.getNumberOfExternalNodes() != 13 ) { return false; } - t1.deleteSubtree( t1.getNode( "B" ), false ); - if ( t1.getNumberOfExternalNodes() != 1 ) { + if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) { return false; } - t1.deleteSubtree( t1.getNode( "r" ), false ); - if ( !t1.isEmpty() ) { + if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) { return false; } - final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ]; - if ( t2.getNumberOfExternalNodes() != 3 ) { + if ( t5.getRoot().getNumberOfDescendants() != 2 ) { return false; } - t2.deleteSubtree( t2.getNode( "B" ), false ); - if ( t2.getNumberOfExternalNodes() != 2 ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testBasicTreeMethods() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ]; + if ( t2.getNumberOfExternalNodes() != 4 ) { return false; } - t2.toNewHampshireX(); - PhylogenyNode n = t2.getNode( "A" ); - if ( !n.getNextExternalNode().getName().equals( "C" ) ) { + if ( t2.getHeight() != 8.5 ) { return false; } - t2.deleteSubtree( t2.getNode( "A" ), false ); - if ( t2.getNumberOfExternalNodes() != 2 ) { + if ( !t2.isCompletelyBinary() ) { return false; } - t2.deleteSubtree( t2.getNode( "C" ), true ); - if ( t2.getNumberOfExternalNodes() != 1 ) { + if ( t2.isEmpty() ) { return false; } - final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ]; - if ( t3.getNumberOfExternalNodes() != 4 ) { + final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ]; + if ( t3.getNumberOfExternalNodes() != 5 ) { return false; } - t3.deleteSubtree( t3.getNode( "B" ), true ); - if ( t3.getNumberOfExternalNodes() != 3 ) { + if ( t3.getHeight() != 11 ) { return false; } - n = t3.getNode( "A" ); - if ( !n.getNextExternalNode().getName().equals( "C" ) ) { + if ( t3.isCompletelyBinary() ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getNextExternalNode().getName().equals( "D" ) ) { + final PhylogenyNode n = t3.getNode( "ABC" ); + final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ]; + if ( t4.getNumberOfExternalNodes() != 9 ) { return false; } - t3.deleteSubtree( t3.getNode( "A" ), true ); - if ( t3.getNumberOfExternalNodes() != 2 ) { + if ( t4.getHeight() != 11 ) { return false; } - n = t3.getNode( "C" ); - if ( !n.getNextExternalNode().getName().equals( "D" ) ) { + if ( t4.isCompletelyBinary() ) { return false; } - t3.deleteSubtree( t3.getNode( "C" ), true ); - if ( t3.getNumberOfExternalNodes() != 1 ) { + final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" ); + final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ]; + if ( t5.getNumberOfExternalNodes() != 8 ) { return false; } - t3.deleteSubtree( t3.getNode( "D" ), true ); - if ( t3.getNumberOfExternalNodes() != 0 ) { + if ( t5.getHeight() != 15 ) { return false; } - final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; - if ( t4.getNumberOfExternalNodes() != 6 ) { + final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" ); + final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ]; + if ( t6.getHeight() != 15 ) { return false; } - t4.deleteSubtree( t4.getNode( "B2" ), true ); - if ( t4.getNumberOfExternalNodes() != 5 ) { + final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" ); + final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ]; + if ( t7.getHeight() != 15 ) { return false; } - String s = w.toNewHampshire( t4, false, true ).toString(); - if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) { + final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" ); + final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ]; + if ( t8.getNumberOfExternalNodes() != 10 ) { return false; } - t4.deleteSubtree( t4.getNode( "B11" ), true ); - if ( t4.getNumberOfExternalNodes() != 4 ) { + if ( t8.getHeight() != 15 ) { return false; } - t4.deleteSubtree( t4.getNode( "C" ), true ); - if ( t4.getNumberOfExternalNodes() != 3 ) { + final char[] a9 = new char[] { 'a' }; + final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ]; + if ( t9.getHeight() != 0 ) { return false; } - n = t4.getNode( "A" ); - n = n.getNextExternalNode(); - if ( !n.getName().equals( "B12" ) ) { + final char[] a10 = new char[] { 'a', ':', '6' }; + final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ]; + if ( t10.getHeight() != 6 ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "D" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testConfidenceAssessor() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; + final Phylogeny[] ev0 = factory + .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);", + new NHXParser() ); + ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 ); + if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) { return false; } - s = w.toNewHampshire( t4, false, true ).toString(); - if ( !s.equals( "((A,B12),D);" ) ) { + if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) { return false; } - final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; - t5.deleteSubtree( t5.getNode( "A" ), true ); - if ( t5.getNumberOfExternalNodes() != 5 ) { + final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; + final Phylogeny[] ev1 = factory + .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));", + new NHXParser() ); + ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 ); + if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) { return false; } - s = w.toNewHampshire( t5, false, true ).toString(); - if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) { + if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) { return false; } - final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; - t6.deleteSubtree( t6.getNode( "B11" ), true ); - if ( t6.getNumberOfExternalNodes() != 5 ) { + final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ]; + final Phylogeny[] ev_b = factory + .create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd", + new NHXParser() ); + ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 ); + if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) { return false; } - s = w.toNewHampshire( t6, false, false ).toString(); - if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) { + if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; } - final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; - t7.deleteSubtree( t7.getNode( "B12" ), true ); - if ( t7.getNumberOfExternalNodes() != 5 ) { + // + final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ]; + final Phylogeny[] ev1x = factory + .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));", + new NHXParser() ); + ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 ); + if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) { return false; } - s = w.toNewHampshire( t7, false, true ).toString(); - if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) { + if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) { return false; } - final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; - t8.deleteSubtree( t8.getNode( "B2" ), true ); - if ( t8.getNumberOfExternalNodes() != 5 ) { + final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ]; + final Phylogeny[] ev_bx = factory + .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd", + new NHXParser() ); + ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 ); + if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; } - s = w.toNewHampshire( t8, false, false ).toString(); - if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) { + if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; } - final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; - t9.deleteSubtree( t9.getNode( "C" ), true ); - if ( t9.getNumberOfExternalNodes() != 5 ) { - return false; + final Phylogeny[] t2 = factory + .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);", + new NHXParser() ); + final Phylogeny[] ev2 = factory + .create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);", + new NHXParser() ); + for( final Phylogeny target : t2 ) { + ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 ); } - s = w.toNewHampshire( t9, false, true ).toString(); - if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) { + final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg", + new NHXParser() )[ 0 ]; + final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() ); + ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 ); + if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; } - final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; - t10.deleteSubtree( t10.getNode( "D" ), true ); - if ( t10.getNumberOfExternalNodes() != 5 ) { + if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) { return false; } - s = w.toNewHampshire( t10, false, true ).toString(); - if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) { + if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; } - final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ]; - t11.deleteSubtree( t11.getNode( "A" ), true ); - if ( t11.getNumberOfExternalNodes() != 2 ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testCopyOfNodeData() { + try { + final PhylogenyNode n1 = PhylogenyNode + .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" ); + final PhylogenyNode n2 = n1.copyNodeData(); + if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) { return false; } - s = w.toNewHampshire( t11, false, true ).toString(); - if ( !s.equals( "(B,C);" ) ) { + } + 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; } - t11.deleteSubtree( t11.getNode( "C" ), true ); - if ( t11.getNumberOfExternalNodes() != 1 ) { + if ( p0.getNumberOfExternalNodes() != 15625 ) { return false; } - s = w.toNewHampshire( t11, false, false ).toString(); - if ( !s.equals( "B;" ) ) { + final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 ); + if ( p1.getRoot().getNumberOfDescendants() != 10 ) { return false; } - final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ]; - t12.deleteSubtree( t12.getNode( "B2" ), true ); - if ( t12.getNumberOfExternalNodes() != 8 ) { + if ( p1.getNumberOfExternalNodes() != 100 ) { return false; } - s = w.toNewHampshire( t12, false, true ).toString(); - if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) { + } + 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; } - t12.deleteSubtree( t12.getNode( "B3" ), true ); - if ( t12.getNumberOfExternalNodes() != 7 ) { + n.setName( "B0LM41_HUMAN" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) { return false; } - s = w.toNewHampshire( t12, false, true ).toString(); - if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) { + n.setName( "NP_001025424" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) { return false; } - t12.deleteSubtree( t12.getNode( "C3" ), true ); - if ( t12.getNumberOfExternalNodes() != 6 ) { + n.setName( "_NM_001030253-" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) { return false; } - s = w.toNewHampshire( t12, false, true ).toString(); - if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) { + n.setName( "XM_002122186" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) { return false; } - t12.deleteSubtree( t12.getNode( "A1" ), true ); - if ( t12.getNumberOfExternalNodes() != 5 ) { + n.setName( "dgh_AAA34956_gdg" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) { return false; } - s = w.toNewHampshire( t12, false, true ).toString(); - if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) { + n.setName( "AAA34956" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) { return false; } - t12.deleteSubtree( t12.getNode( "B1" ), true ); - if ( t12.getNumberOfExternalNodes() != 4 ) { + 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; } - s = w.toNewHampshire( t12, false, true ).toString(); - if ( !s.equals( "((A2,A3),(C1,C2));" ) ) { + 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; } - t12.deleteSubtree( t12.getNode( "A3" ), true ); - if ( t12.getNumberOfExternalNodes() != 3 ) { + 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; } - s = w.toNewHampshire( t12, false, true ).toString(); - if ( !s.equals( "(A2,(C1,C2));" ) ) { + n.setName( "P12345" ); + if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) { + System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) ); return false; } - t12.deleteSubtree( t12.getNode( "A2" ), true ); - if ( t12.getNumberOfExternalNodes() != 2 ) { + 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; } - s = w.toNewHampshire( t12, false, true ).toString(); - if ( !s.equals( "(C1,C2);" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testDataObjects() { + try { + final Confidence s0 = new Confidence(); + final Confidence s1 = new Confidence(); + if ( !s0.isEqual( s1 ) ) { return false; } - final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ]; - t13.deleteSubtree( t13.getNode( "D" ), true ); - if ( t13.getNumberOfExternalNodes() != 4 ) { + final Confidence s2 = new Confidence( 0.23, "bootstrap" ); + final Confidence s3 = new Confidence( 0.23, "bootstrap" ); + if ( s2.isEqual( s1 ) ) { return false; } - s = w.toNewHampshire( t13, false, true ).toString(); - if ( !s.equals( "(A,B,C,E:5.0);" ) ) { + if ( !s2.isEqual( s3 ) ) { return false; } - final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ]; - t14.deleteSubtree( t14.getNode( "E" ), true ); - if ( t14.getNumberOfExternalNodes() != 5 ) { + final Confidence s4 = ( Confidence ) s3.copy(); + if ( !s4.isEqual( s3 ) ) { return false; } - s = w.toNewHampshire( t14, false, true ).toString(); - if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) { + s3.asSimpleText(); + s3.asText(); + // Taxonomy + // ---------- + final Taxonomy t1 = new Taxonomy(); + final Taxonomy t2 = new Taxonomy(); + final Taxonomy t3 = new Taxonomy(); + final Taxonomy t4 = new Taxonomy(); + final Taxonomy t5 = new Taxonomy(); + t1.setIdentifier( new Identifier( "ecoli" ) ); + t1.setTaxonomyCode( "ECOLI" ); + t1.setScientificName( "E. coli" ); + t1.setCommonName( "coli" ); + final Taxonomy t0 = ( Taxonomy ) t1.copy(); + if ( !t1.isEqual( t0 ) ) { return false; } - final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ]; - t15.deleteSubtree( t15.getNode( "B2" ), true ); - if ( t15.getNumberOfExternalNodes() != 11 ) { + t2.setIdentifier( new Identifier( "ecoli" ) ); + t2.setTaxonomyCode( "OTHER" ); + t2.setScientificName( "what" ); + t2.setCommonName( "something" ); + if ( !t1.isEqual( t2 ) ) { return false; } - t15.deleteSubtree( t15.getNode( "B1" ), true ); - if ( t15.getNumberOfExternalNodes() != 10 ) { + t2.setIdentifier( new Identifier( "nemve" ) ); + if ( t1.isEqual( t2 ) ) { return false; } - t15.deleteSubtree( t15.getNode( "B3" ), true ); - if ( t15.getNumberOfExternalNodes() != 9 ) { - return false; + t1.setIdentifier( null ); + t3.setTaxonomyCode( "ECOLI" ); + t3.setScientificName( "what" ); + t3.setCommonName( "something" ); + if ( !t1.isEqual( t3 ) ) { + return false; } - t15.deleteSubtree( t15.getNode( "B4" ), true ); - if ( t15.getNumberOfExternalNodes() != 8 ) { + t1.setIdentifier( null ); + t1.setTaxonomyCode( "" ); + t4.setScientificName( "E. ColI" ); + t4.setCommonName( "something" ); + if ( !t1.isEqual( t4 ) ) { return false; } - t15.deleteSubtree( t15.getNode( "A1" ), true ); - if ( t15.getNumberOfExternalNodes() != 7 ) { + t4.setScientificName( "B. subtilis" ); + t4.setCommonName( "something" ); + if ( t1.isEqual( t4 ) ) { return false; } - t15.deleteSubtree( t15.getNode( "C4" ), true ); - if ( t15.getNumberOfExternalNodes() != 6 ) { + t1.setIdentifier( null ); + t1.setTaxonomyCode( "" ); + t1.setScientificName( "" ); + t5.setCommonName( "COLI" ); + if ( !t1.isEqual( t5 ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testDescriptiveStatistics() { - try { - final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics(); - dss1.addValue( 82 ); - dss1.addValue( 78 ); - dss1.addValue( 70 ); - dss1.addValue( 58 ); - dss1.addValue( 42 ); - if ( dss1.getN() != 5 ) { + t5.setCommonName( "vibrio" ); + if ( t1.isEqual( t5 ) ) { return false; } - if ( !Test.isEqual( dss1.getMin(), 42 ) ) { + // Identifier + // ---------- + final Identifier id0 = new Identifier( "123", "pfam" ); + final Identifier id1 = ( Identifier ) id0.copy(); + if ( !id1.isEqual( id1 ) ) { return false; } - if ( !Test.isEqual( dss1.getMax(), 82 ) ) { + if ( !id1.isEqual( id0 ) ) { return false; } - if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) { + if ( !id0.isEqual( id1 ) ) { return false; } - if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) { + id1.asSimpleText(); + id1.asText(); + // ProteinDomain + // --------------- + final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 ); + final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy(); + if ( !pd1.isEqual( pd1 ) ) { return false; } - if ( !Test.isEqual( dss1.median(), 70 ) ) { + if ( !pd1.isEqual( pd0 ) ) { return false; } - if ( !Test.isEqual( dss1.midrange(), 62 ) ) { + pd1.asSimpleText(); + pd1.asText(); + final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" ); + final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy(); + if ( !pd3.isEqual( pd3 ) ) { return false; } - if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) { + if ( !pd2.isEqual( pd3 ) ) { return false; } - if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) { + if ( !pd0.isEqual( pd3 ) ) { return false; } - if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) { + pd3.asSimpleText(); + pd3.asText(); + // DomainArchitecture + // ------------------ + final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 ); + final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 ); + final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 ); + final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 ); + final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 ); + final ArrayList domains0 = new ArrayList(); + domains0.add( d2 ); + domains0.add( d0 ); + domains0.add( d3 ); + domains0.add( d1 ); + final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 ); + if ( ds0.getNumberOfDomains() != 4 ) { return false; } - if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) { + final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy(); + if ( !ds0.isEqual( ds0 ) ) { return false; } - if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) { + if ( !ds0.isEqual( ds1 ) ) { return false; } - dss1.addValue( 123 ); - if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) { + if ( ds1.getNumberOfDomains() != 4 ) { return false; } - if ( !Test.isEqual( dss1.getMax(), 123 ) ) { + final ArrayList domains1 = new ArrayList(); + domains1.add( d1 ); + domains1.add( d2 ); + domains1.add( d4 ); + domains1.add( d0 ); + final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 ); + if ( ds0.isEqual( ds2 ) ) { return false; } - if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) { + ds1.asSimpleText(); + ds1.asText(); + ds1.toNHX(); + final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" ); + if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) { + System.out.println( ds3.toNHX() ); return false; } - final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics(); - dss2.addValue( -1.85 ); - dss2.addValue( 57.5 ); - dss2.addValue( 92.78 ); - dss2.addValue( 57.78 ); - if ( !Test.isEqual( dss2.median(), 57.64 ) ) { + if ( ds3.getNumberOfDomains() != 3 ) { return false; } - if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) { + // Event + // ----- + final Event e1 = new Event( Event.EventType.fusion ); + if ( e1.isDuplication() ) { return false; } - final double[] a = dss2.getDataAsDoubleArray(); - if ( !Test.isEqual( a[ 3 ], 57.78 ) ) { + if ( !e1.isFusion() ) { return false; } - dss2.addValue( -100 ); - if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) { + if ( !e1.asText().toString().equals( "fusion" ) ) { return false; } - if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) { + if ( !e1.asSimpleText().toString().equals( "fusion" ) ) { return false; } - final double[] ds = new double[ 14 ]; - ds[ 0 ] = 34; - ds[ 1 ] = 23; - ds[ 2 ] = 1; - ds[ 3 ] = 32; - ds[ 4 ] = 11; - ds[ 5 ] = 2; - ds[ 6 ] = 12; - ds[ 7 ] = 33; - ds[ 8 ] = 13; - ds[ 9 ] = 22; - ds[ 10 ] = 21; - ds[ 11 ] = 35; - ds[ 12 ] = 24; - ds[ 13 ] = 31; - final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 ); - if ( bins.length != 4 ) { + final Event e11 = new Event( Event.EventType.fusion ); + if ( !e11.isEqual( e1 ) ) { return false; } - if ( bins[ 0 ] != 2 ) { + if ( !e11.toNHX().toString().equals( "" ) ) { return false; } - if ( bins[ 1 ] != 3 ) { + final Event e2 = new Event( Event.EventType.speciation_or_duplication ); + if ( e2.isDuplication() ) { return false; } - if ( bins[ 2 ] != 4 ) { + if ( !e2.isSpeciationOrDuplication() ) { return false; } - if ( bins[ 3 ] != 5 ) { + if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) { return false; } - final double[] ds1 = new double[ 9 ]; - ds1[ 0 ] = 10.0; - ds1[ 1 ] = 19.0; - ds1[ 2 ] = 9.999; - ds1[ 3 ] = 0.0; - ds1[ 4 ] = 39.9; - ds1[ 5 ] = 39.999; - ds1[ 6 ] = 30.0; - ds1[ 7 ] = 19.999; - ds1[ 8 ] = 30.1; - final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 ); - if ( bins1.length != 4 ) { + if ( !e2.asSimpleText().toString().equals( "?" ) ) { return false; } - if ( bins1[ 0 ] != 2 ) { + if ( !e2.toNHX().toString().equals( ":D=?" ) ) { return false; } - if ( bins1[ 1 ] != 3 ) { + if ( e11.isEqual( e2 ) ) { return false; } - if ( bins1[ 2 ] != 0 ) { + final Event e2c = ( Event ) e2.copy(); + if ( !e2c.isEqual( e2 ) ) { return false; } - if ( bins1[ 3 ] != 4 ) { + Event e3 = new Event( 1, 2, 3 ); + if ( e3.isDuplication() ) { return false; } - final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 ); - if ( bins1_1.length != 3 ) { + if ( e3.isSpeciation() ) { return false; } - if ( bins1_1[ 0 ] != 3 ) { + if ( e3.isGeneLoss() ) { return false; } - if ( bins1_1[ 1 ] != 2 ) { + if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) { return false; } - if ( bins1_1[ 2 ] != 4 ) { + final Event e3c = ( Event ) e3.copy(); + final Event e3cc = ( Event ) e3c.copy(); + if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) { return false; } - final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 ); - if ( bins1_2.length != 3 ) { + e3 = null; + if ( !e3c.isEqual( e3cc ) ) { return false; } - if ( bins1_2[ 0 ] != 2 ) { + Event e4 = new Event( 1, 2, 3 ); + if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) { return false; } - if ( bins1_2[ 1 ] != 2 ) { + if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) { return false; } - if ( bins1_2[ 2 ] != 2 ) { + final Event e4c = ( Event ) e4.copy(); + e4 = null; + final Event e4cc = ( Event ) e4c.copy(); + if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) { return false; } - final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics(); - dss3.addValue( 1 ); - dss3.addValue( 1 ); - dss3.addValue( 1 ); - dss3.addValue( 2 ); - dss3.addValue( 3 ); - dss3.addValue( 4 ); - dss3.addValue( 5 ); - dss3.addValue( 5 ); - dss3.addValue( 5 ); - dss3.addValue( 6 ); - dss3.addValue( 7 ); - dss3.addValue( 8 ); - dss3.addValue( 9 ); - dss3.addValue( 10 ); - dss3.addValue( 10 ); - dss3.addValue( 10 ); - final AsciiHistogram histo = new AsciiHistogram( dss3 ); - histo.toStringBuffer( 10, '=', 40, 5 ); - histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null ); - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testDir( final String file ) { - try { - final File f = new File( file ); - if ( !f.exists() ) { + if ( !e4c.isEqual( e4cc ) ) { return false; } - if ( !f.isDirectory() ) { + final Event e5 = new Event(); + if ( !e5.isUnassigned() ) { return false; } - if ( !f.canRead() ) { + if ( !e5.asText().toString().equals( "unassigned" ) ) { + return false; + } + if ( !e5.asSimpleText().toString().equals( "" ) ) { + return false; + } + final Event e6 = new Event( 1, 0, 0 ); + if ( !e6.asText().toString().equals( "duplication" ) ) { + return false; + } + if ( !e6.asSimpleText().toString().equals( "D" ) ) { + return false; + } + final Event e7 = new Event( 0, 1, 0 ); + if ( !e7.asText().toString().equals( "speciation" ) ) { + return false; + } + if ( !e7.asSimpleText().toString().equals( "S" ) ) { + return false; + } + final Event e8 = new Event( 0, 0, 1 ); + if ( !e8.asText().toString().equals( "gene-loss" ) ) { + return false; + } + if ( !e8.asSimpleText().toString().equals( "L" ) ) { return false; } } - catch ( final Exception e ) { - return false; - } - 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 ) { + catch ( final Exception e ) { + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testExternalNodeRelatedMethods() { + private static boolean testDeletionOfExternalNodes() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ]; - PhylogenyNode n = t1.getNode( "A" ); - n = n.getNextExternalNode(); - if ( !n.getName().equals( "B" ) ) { + final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ]; + final PhylogenyWriter w = new PhylogenyWriter(); + if ( t0.isEmpty() ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "C" ) ) { + if ( t0.getNumberOfExternalNodes() != 1 ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "D" ) ) { + t0.deleteSubtree( t0.getNode( "A" ), false ); + if ( t0.getNumberOfExternalNodes() != 0 ) { return false; } - n = t1.getNode( "B" ); - while ( !n.isLastExternalNode() ) { - n = n.getNextExternalNode(); - } - final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ]; - n = t2.getNode( "A" ); - n = n.getNextExternalNode(); - if ( !n.getName().equals( "B" ) ) { + if ( !t0.isEmpty() ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "C" ) ) { + final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ]; + if ( t1.getNumberOfExternalNodes() != 2 ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "D" ) ) { + t1.deleteSubtree( t1.getNode( "A" ), false ); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - n = t2.getNode( "B" ); - while ( !n.isLastExternalNode() ) { - n = n.getNextExternalNode(); - } - final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ]; - n = t3.getNode( "A" ); - n = n.getNextExternalNode(); - if ( !n.getName().equals( "B" ) ) { + if ( !t1.getNode( "B" ).getName().equals( "B" ) ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "C" ) ) { + t1.deleteSubtree( t1.getNode( "B" ), false ); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "D" ) ) { + t1.deleteSubtree( t1.getNode( "r" ), false ); + if ( !t1.isEmpty() ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "E" ) ) { + final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ]; + if ( t2.getNumberOfExternalNodes() != 3 ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "F" ) ) { + t2.deleteSubtree( t2.getNode( "B" ), false ); + if ( t2.getNumberOfExternalNodes() != 2 ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "G" ) ) { + t2.toNewHampshireX(); + PhylogenyNode n = t2.getNode( "A" ); + if ( !n.getNextExternalNode().getName().equals( "C" ) ) { return false; } - n = n.getNextExternalNode(); - if ( !n.getName().equals( "H" ) ) { + t2.deleteSubtree( t2.getNode( "A" ), false ); + if ( t2.getNumberOfExternalNodes() != 2 ) { return false; } - n = t3.getNode( "B" ); - while ( !n.isLastExternalNode() ) { - n = n.getNextExternalNode(); - } - final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ]; - for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); + t2.deleteSubtree( t2.getNode( "C" ), true ); + if ( t2.getNumberOfExternalNodes() != 1 ) { + return false; } - final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ]; - for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); + final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ]; + if ( t3.getNumberOfExternalNodes() != 4 ) { + return false; } - 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" ) ) { + t3.deleteSubtree( t3.getNode( "B" ), true ); + if ( t3.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !iter.next().getName().equals( "B" ) ) { + n = t3.getNode( "A" ); + if ( !n.getNextExternalNode().getName().equals( "C" ) ) { return false; } - if ( !iter.next().getName().equals( "C" ) ) { + n = n.getNextExternalNode(); + if ( !n.getNextExternalNode().getName().equals( "D" ) ) { return false; } - if ( !iter.next().getName().equals( "D" ) ) { + t3.deleteSubtree( t3.getNode( "A" ), true ); + if ( t3.getNumberOfExternalNodes() != 2 ) { return false; } - if ( !iter.next().getName().equals( "E" ) ) { + n = t3.getNode( "C" ); + if ( !n.getNextExternalNode().getName().equals( "D" ) ) { return false; } - if ( !iter.next().getName().equals( "F" ) ) { + t3.deleteSubtree( t3.getNode( "C" ), true ); + if ( t3.getNumberOfExternalNodes() != 1 ) { return false; } - if ( iter.hasNext() ) { + t3.deleteSubtree( t3.getNode( "D" ), true ); + if ( t3.getNumberOfExternalNodes() != 0 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testExtractSNFromNodeName() { - try { - if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) { + final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; + if ( t4.getNumberOfExternalNodes() != 6 ) { return false; } - if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" ) - .equals( "Mus musculus musculus" ) ) { + t4.deleteSubtree( t4.getNode( "B2" ), true ); + if ( t4.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" ) - .equals( "Mus musculus musculus" ) ) { + String s = w.toNewHampshire( t4, true ).toString(); + if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) { return false; } - if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) { + t4.deleteSubtree( t4.getNode( "B11" ), true ); + if ( t4.getNumberOfExternalNodes() != 4 ) { return false; } - if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" ) - .equals( "Mus musculus" ) ) { + t4.deleteSubtree( t4.getNode( "C" ), true ); + if ( t4.getNumberOfExternalNodes() != 3 ) { return false; } - } - 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 ) { + n = t4.getNode( "A" ); + n = n.getNextExternalNode(); + if ( !n.getName().equals( "B12" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "D" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "ARATH" ) ) { + s = w.toNewHampshire( t4, true ).toString(); + if ( !s.equals( "((A,B12),D);" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "ARATH" ) ) { + final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; + t5.deleteSubtree( t5.getNode( "A" ), true ); + if ( t5.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { + s = w.toNewHampshire( t5, true ).toString(); + if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { + final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; + t6.deleteSubtree( t6.getNode( "B11" ), true ); + if ( t6.getNumberOfExternalNodes() != 5 ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + s = w.toNewHampshire( t6, false ).toString(); + if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; + t7.deleteSubtree( t7.getNode( "B12" ), true ); + if ( t7.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + s = w.toNewHampshire( t7, true ).toString(); + if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; + t8.deleteSubtree( t8.getNode( "B2" ), true ); + if ( t8.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + s = w.toNewHampshire( t8, false ).toString(); + if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "SOYBN" ) ) { + final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; + t9.deleteSubtree( t9.getNode( "C" ), true ); + if ( t9.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + s = w.toNewHampshire( t9, true ).toString(); + if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ]; + t10.deleteSubtree( t10.getNode( "D" ), true ); + if ( t10.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + s = w.toNewHampshire( t10, true ).toString(); + if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) { + final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ]; + t11.deleteSubtree( t11.getNode( "A" ), true ); + if ( t11.getNumberOfExternalNodes() != 2 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "SOYBN" ) ) { + s = w.toNewHampshire( t11, true ).toString(); + if ( !s.equals( "(B,C);" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01", - TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) { + t11.deleteSubtree( t11.getNode( "C" ), true ); + if ( t11.getNumberOfExternalNodes() != 1 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE ) - .equals( "9YX45" ) ) { + s = w.toNewHampshire( t11, false ).toString(); + if ( !s.equals( "B;" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ]; + t12.deleteSubtree( t12.getNode( "B2" ), true ); + if ( t12.getNumberOfExternalNodes() != 8 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + s = w.toNewHampshire( t12, true ).toString(); + if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + t12.deleteSubtree( t12.getNode( "B3" ), true ); + if ( t12.getNumberOfExternalNodes() != 7 ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + s = w.toNewHampshire( t12, true ).toString(); + if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + t12.deleteSubtree( t12.getNode( "C3" ), true ); + if ( t12.getNumberOfExternalNodes() != 6 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { + s = w.toNewHampshire( t12, true ).toString(); + if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { + t12.deleteSubtree( t12.getNode( "A1" ), true ); + if ( t12.getNumberOfExternalNodes() != 5 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { + s = w.toNewHampshire( t12, true ).toString(); + if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + t12.deleteSubtree( t12.getNode( "B1" ), true ); + if ( t12.getNumberOfExternalNodes() != 4 ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", - TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + s = w.toNewHampshire( t12, true ).toString(); + if ( !s.equals( "((A2,A3),(C1,C2));" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "RAT" ) ) { + t12.deleteSubtree( t12.getNode( "A3" ), true ); + if ( t12.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) - .equals( "PIG" ) ) { + s = w.toNewHampshire( t12, true ).toString(); + if ( !s.equals( "(A2,(C1,C2));" ) ) { return false; } - if ( !ParserUtils - .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + t12.deleteSubtree( t12.getNode( "A2" ), true ); + if ( t12.getNumberOfExternalNodes() != 2 ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) - .equals( "MOUSE" ) ) { + s = w.toNewHampshire( t12, true ).toString(); + if ( !s.equals( "(C1,C2);" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ]; + t13.deleteSubtree( t13.getNode( "D" ), true ); + if ( t13.getNumberOfExternalNodes() != 4 ) { + return false; + } + s = w.toNewHampshire( t13, true ).toString(); + if ( !s.equals( "(A,B,C,E:5.0);" ) ) { + return false; + } + final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ]; + t14.deleteSubtree( t14.getNode( "E" ), true ); + if ( t14.getNumberOfExternalNodes() != 5 ) { + return false; + } + s = w.toNewHampshire( t14, true ).toString(); + if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) { + return false; + } + final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ]; + t15.deleteSubtree( t15.getNode( "B2" ), true ); + if ( t15.getNumberOfExternalNodes() != 11 ) { + return false; + } + t15.deleteSubtree( t15.getNode( "B1" ), true ); + if ( t15.getNumberOfExternalNodes() != 10 ) { + return false; + } + t15.deleteSubtree( t15.getNode( "B3" ), true ); + if ( t15.getNumberOfExternalNodes() != 9 ) { + return false; + } + t15.deleteSubtree( t15.getNode( "B4" ), true ); + if ( t15.getNumberOfExternalNodes() != 8 ) { + return false; + } + t15.deleteSubtree( t15.getNode( "A1" ), true ); + if ( t15.getNumberOfExternalNodes() != 7 ) { + return false; + } + t15.deleteSubtree( t15.getNode( "C4" ), true ); + if ( t15.getNumberOfExternalNodes() != 6 ) { return false; } } @@ -4022,172 +4161,185 @@ public final class Test { return true; } - private static boolean testExtractUniProtKbProteinSeqIdentifier() { + private static boolean testDescriptiveStatistics() { try { - PhylogenyNode n = new PhylogenyNode(); - n.setName( "tr|B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics(); + dss1.addValue( 82 ); + dss1.addValue( 78 ); + dss1.addValue( 70 ); + dss1.addValue( 58 ); + dss1.addValue( 42 ); + if ( dss1.getN() != 5 ) { return false; } - n.setName( "tr.B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.getMin(), 42 ) ) { return false; } - n.setName( "tr=B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.getMax(), 82 ) ) { return false; } - n.setName( "tr-B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) { return false; } - n.setName( "tr/B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) { return false; } - n.setName( "tr\\B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.median(), 70 ) ) { return false; } - n.setName( "tr_B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.midrange(), 62 ) ) { return false; } - n.setName( " tr|B3RJ64 " ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) { return false; } - n.setName( "-tr|B3RJ64-" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) { return false; } - n.setName( "-tr=B3RJ64-" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) { return false; } - n.setName( "_tr=B3RJ64_" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) { return false; } - n.setName( " tr_tr|B3RJ64_sp|123 " ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) { return false; } - n.setName( "B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + dss1.addValue( 123 ); + if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) { return false; } - n.setName( "sp|B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( !Test.isEqual( dss1.getMax(), 123 ) ) { return false; } - n.setName( "sp|B3RJ64C" ); - if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { + if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) { return false; } - n.setName( "sp B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics(); + dss2.addValue( -1.85 ); + dss2.addValue( 57.5 ); + dss2.addValue( 92.78 ); + dss2.addValue( 57.78 ); + if ( !Test.isEqual( dss2.median(), 57.64 ) ) { return false; } - n.setName( "sp|B3RJ6X" ); - if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { + if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) { return false; } - n.setName( "sp|B3RJ6" ); - if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { + final double[] a = dss2.getDataAsDoubleArray(); + if ( !Test.isEqual( a[ 3 ], 57.78 ) ) { return false; } - n.setName( "K1PYK7_CRAGI" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { + dss2.addValue( -100 ); + if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) { return false; } - n.setName( "K1PYK7_PEA" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) { + if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) { return false; } - n.setName( "K1PYK7_RAT" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) { + final double[] ds = new double[ 14 ]; + ds[ 0 ] = 34; + ds[ 1 ] = 23; + ds[ 2 ] = 1; + ds[ 3 ] = 32; + ds[ 4 ] = 11; + ds[ 5 ] = 2; + ds[ 6 ] = 12; + ds[ 7 ] = 33; + ds[ 8 ] = 13; + ds[ 9 ] = 22; + ds[ 10 ] = 21; + ds[ 11 ] = 35; + ds[ 12 ] = 24; + ds[ 13 ] = 31; + final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 ); + if ( bins.length != 4 ) { return false; } - n.setName( "K1PYK7_PIG" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) { + if ( bins[ 0 ] != 2 ) { return false; } - n.setName( "~K1PYK7_PIG~" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) { + if ( bins[ 1 ] != 3 ) { return false; } - n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { + if ( bins[ 2 ] != 4 ) { return false; } - n.setName( "K1PYKX_CRAGI" ); - if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { + if ( bins[ 3 ] != 5 ) { return false; } - n.setName( "XXXXX_CRAGI" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) { + final double[] ds1 = new double[ 9 ]; + ds1[ 0 ] = 10.0; + ds1[ 1 ] = 19.0; + ds1[ 2 ] = 9.999; + ds1[ 3 ] = 0.0; + ds1[ 4 ] = 39.9; + ds1[ 5 ] = 39.999; + ds1[ 6 ] = 30.0; + ds1[ 7 ] = 19.999; + ds1[ 8 ] = 30.1; + final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 ); + if ( bins1.length != 4 ) { return false; } - n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) { + if ( bins1[ 0 ] != 2 ) { return false; } - n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" ); - if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { + if ( bins1[ 1 ] != 3 ) { return false; } - n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) { + if ( bins1[ 2 ] != 0 ) { return false; } - 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" ) ) { + if ( bins1[ 3 ] != 4 ) { return false; } - seq.setSymbol( "tr|B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { - return false; + final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 ); + if ( bins1_1.length != 3 ) { + return false; } - 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" ) ) { + if ( bins1_1[ 0 ] != 3 ) { return false; } - seq.setName( "tr|B3RJ64" ); - if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { + if ( bins1_1[ 1 ] != 2 ) { return false; } - 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" ) ) { + if ( bins1_1[ 2 ] != 4 ) { return false; } - 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" ) ) { + final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 ); + if ( bins1_2.length != 3 ) { return false; } - // - n = new PhylogenyNode(); - n.setName( "ACP19736" ); - if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) { + if ( bins1_2[ 0 ] != 2 ) { return false; } - n = new PhylogenyNode(); - n.setName( "|ACP19736|" ); - if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) { + if ( bins1_2[ 1 ] != 2 ) { + return false; + } + if ( bins1_2[ 2 ] != 2 ) { return false; } + final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics(); + dss3.addValue( 1 ); + dss3.addValue( 1 ); + dss3.addValue( 1 ); + dss3.addValue( 2 ); + dss3.addValue( 3 ); + dss3.addValue( 4 ); + dss3.addValue( 5 ); + dss3.addValue( 5 ); + dss3.addValue( 5 ); + dss3.addValue( 6 ); + dss3.addValue( 7 ); + dss3.addValue( 8 ); + dss3.addValue( 9 ); + dss3.addValue( 10 ); + dss3.addValue( 10 ); + dss3.addValue( 10 ); + final AsciiHistogram histo = new AsciiHistogram( dss3 ); + histo.toStringBuffer( 10, '=', 40, 5 ); + histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null ); } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -4196,551 +4348,590 @@ public final class Test { return true; } - private static boolean testFastaParser() { + private static boolean testDir( final String file ) { try { - if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) { - return false; - } - if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) { - 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" ) ) { - return false; - } - if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) { - return false; - } - if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) { - return false; - } - if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) { + final File f = new File( file ); + if ( !f.exists() ) { return false; } - if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) { + if ( !f.isDirectory() ) { return false; } - if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) { + if ( !f.canRead() ) { return false; } } catch ( final Exception e ) { - e.printStackTrace(); return false; } return true; } - private static boolean testGeneralMsaParser() { + private static boolean testEbiEntryRetrieval() { 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" ) ) { + final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" ); + if ( !entry.getAccession().equals( "AAK41263" ) ) { + System.out.println( entry.getAccession() ); return false; } - if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) { + System.out.println( entry.getTaxonomyScientificName() ); return false; } - if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + if ( !entry.getSequenceName() + .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) { + System.out.println( entry.getSequenceName() ); return false; } - if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + if ( !entry.getGeneName().equals( "treX-like" ) ) { + System.out.println( entry.getGeneName() ); return false; } - if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) { + System.out.println( entry.getTaxonomyIdentifier() ); return false; } - if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) { + System.out.println( entry.getAnnotations().first().getRefValue() ); return false; } - if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) { + System.out.println( entry.getAnnotations().first().getRefSource() ); return false; } - if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + if ( entry.getCrossReferences().size() < 1 ) { return false; } - if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); + if ( !entry1.getAccession().equals( "ABJ16409" ) ) { return false; } - if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) { + System.out.println( entry1.getTaxonomyScientificName() ); return false; } - if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) { + System.out.println( entry1.getSequenceName() ); return false; } - if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) { + System.out.println( entry1.getTaxonomyIdentifier() ); 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" ) ) { + if ( !entry1.getGeneName().equals( "BCL2" ) ) { + System.out.println( entry1.getGeneName() ); return false; } - if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) { + if ( entry1.getCrossReferences().size() < 1 ) { return false; } - if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { + final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); + if ( !entry2.getAccession().equals( "NM_184234" ) ) { 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" ) ) { + if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + System.out.println( entry2.getTaxonomyScientificName() ); return false; } - if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) { + if ( !entry2.getSequenceName() + .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { + System.out.println( entry2.getSequenceName() ); return false; } - if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) { + if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) { + System.out.println( entry2.getTaxonomyIdentifier() ); 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" ) ) { + if ( !entry2.getGeneName().equals( "RBM39" ) ) { + System.out.println( entry2.getGeneName() ); return false; } - if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) { + if ( entry2.getCrossReferences().size() < 1 ) { return false; } - if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { + if ( !entry2.getChromosome().equals( "20" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace(); - return false; - } - return true; - } - - private static boolean testGeneralTable() { - 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" ) ) { + if ( !entry2.getMap().equals( "20q11.22" ) ) { return false; } - if ( !t0.getValue( 10, 1 ).equals( "110" ) ) { + final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" ); + if ( !entry3.getAccession().equals( "HM043801" ) ) { return false; } - if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) { + if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) { + System.out.println( entry3.getTaxonomyScientificName() ); return false; } - if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) { + if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) { + System.out.println( entry3.getSequenceName() ); return false; } - if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) { + if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) { + System.out.println( entry3.getTaxonomyIdentifier() ); return false; } - if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) { + if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) { + System.out.println( entry3.getSequenceSymbol() ); return false; } - if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) { + if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { return false; } - if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) { + if ( entry3.getCrossReferences().size() < 1 ) { return false; } - if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) { + final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); + if ( !entry4.getAccession().equals( "AAA36557" ) ) { 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" ) ) { + if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + System.out.println( entry4.getTaxonomyScientificName() ); return false; } - if ( !t1.getValue( "10", "1" ).equals( "110" ) ) { + if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) { + System.out.println( entry4.getSequenceName() ); return false; } - if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) { + if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) { + System.out.println( entry4.getTaxonomyIdentifier() ); return false; } - if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) { + if ( !entry4.getGeneName().equals( "ras" ) ) { + System.out.println( entry4.getGeneName() ); return false; } - if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) { + final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" ); + if ( !entry5.getAccession().equals( "AAZ45343" ) ) { return false; } - if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) { + if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) { + System.out.println( entry5.getTaxonomyScientificName() ); return false; } - if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) { + if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) { + System.out.println( entry5.getSequenceName() ); return false; } - if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) { + if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) { + System.out.println( entry5.getTaxonomyIdentifier() ); return false; } - if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) { + final SequenceDatabaseEntry entry6 = SequenceDbWsTools.obtainEntry( "M30539" ); + if ( !entry6.getAccession().equals( "M30539" ) ) { return false; } - if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) { + if ( !entry6.getGeneName().equals( "ras" ) ) { + return false; + } + if ( !entry6.getSequenceName().equals( "Human SK2 c-Ha-ras-1 oncogene-encoded protein gene, exon 1" ) ) { + return false; + } + if ( !entry6.getTaxonomyIdentifier().equals( "9606" ) ) { + return false; + } + if ( !entry6.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + return false; + } + if ( entry6.getCrossReferences().size() < 1 ) { return false; } } - catch ( final 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 ) { + e.printStackTrace(); return false; } return true; } - private static boolean testGetDistance() { + private static boolean testExternalNodeRelatedMethods() { 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 ) { + final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ]; + PhylogenyNode n = t1.getNode( "A" ); + n = n.getNextExternalNode(); + if ( !n.getName().equals( "B" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "C" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "D" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) { - return false; + n = t1.getNode( "B" ); + while ( !n.isLastExternalNode() ) { + n = n.getNextExternalNode(); } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) { + final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ]; + n = t2.getNode( "A" ); + n = n.getNextExternalNode(); + if ( !n.getName().equals( "B" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "C" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "D" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) { + n = t2.getNode( "B" ); + while ( !n.isLastExternalNode() ) { + n = n.getNextExternalNode(); + } + final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ]; + n = t3.getNode( "A" ); + n = n.getNextExternalNode(); + if ( !n.getName().equals( "B" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "C" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "D" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "E" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "F" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "G" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) { + n = n.getNextExternalNode(); + if ( !n.getName().equals( "H" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) { + n = t3.getNode( "B" ); + while ( !n.isLastExternalNode() ) { + n = n.getNextExternalNode(); + } + final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ]; + for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + } + final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ]; + 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 ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) { + if ( !iter.next().getName().equals( "B" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) { + if ( !iter.next().getName().equals( "C" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) { + if ( !iter.next().getName().equals( "D" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) { + if ( !iter.next().getName().equals( "E" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) { + if ( !iter.next().getName().equals( "F" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) { + if ( iter.hasNext() ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testExtractSNFromNodeName() { + try { + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus" ).equals( "Mus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCDO2" ).equals( "Mus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus musculus BCDO2" ) + .equals( "Mus musculus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_BCDO2" ) + .equals( "Mus musculus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus musculus" ) + .equals( "Mus musculus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Bcl Mus musculus musculus" ) + .equals( "Mus musculus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) { + if ( ParserUtils.extractScientificNameFromNodeName( "vcl Mus musculus musculus" ) != null ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_BCDO2" ) + .equals( "Mus musculus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_Musculus" ) + .equals( "Mus musculus musculus" ) ) { 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 ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) { + if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) { + if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) { + if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus" ) != null ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) { + if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus_musculus" ) != null ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_1" ) + .equals( "Mus musculus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_1" ).equals( "Mus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) { + if ( ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_bcl" ) != null ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCL" ).equals( "Mus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) { + if ( ParserUtils.extractScientificNameFromNodeName( "Mus musculus bcl" ) != null ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus BCL" ).equals( "Mus musculus" ) ) { return false; } - if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus xBCL" ).equals( "Mus musculus" ) ) { 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" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus x1" ).equals( "Mus musculus" ) ) { return false; } - final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) ); - if ( !gh.getName().equals( "gh" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus_12" ).equals( "Mus musculus" ) ) { return false; } - final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) ); - if ( !ab.getName().equals( "ab" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12 affrre e" ) + .equals( "Mus musculus" ) ) { return false; } - final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) ); - if ( !ab2.getName().equals( "ab" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12_affrre_e" ) + .equals( "Mus musculus" ) ) { return false; } - final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) ); - if ( !gh2.getName().equals( "gh" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) { return false; } - final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) ); - if ( !gh3.getName().equals( "gh" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" ) + .equals( "Mus musculus musculus" ) ) { return false; } - final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) ); - if ( !abc.getName().equals( "abc" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" ) + .equals( "Mus musculus musculus" ) ) { return false; } - final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) ); - if ( !abc2.getName().equals( "abc" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_bcl2" ) + .equals( "Mus musculus musculus" ) ) { return false; } - final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) ); - if ( !abcd.getName().equals( "abcd" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) { return false; } - final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) ); - if ( !abcd2.getName().equals( "abcd" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Pilostyles mexicana Mexico Breedlove 27233" ) + .equals( "Pilostyles mexicana" ) ) { return false; } - final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) ); - if ( !abcdef.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_strain_K12/DH10B" ) + .equals( "Escherichia coli strain K12/DH10B" ) ) { return false; } - final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) ); - if ( !abcdef2.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K12/DH10B" ) + .equals( "Escherichia coli str. K12/DH10B" ) ) { return false; } - final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) ); - if ( !abcdef3.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K12/DH10B" ) + .equals( "Escherichia coli str. K12/DH10B" ) ) { return false; } - final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) ); - if ( !abcdef4.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis_lyrata_subsp_lyrata" ) + .equals( "Arabidopsis lyrata subsp. lyrata" ) ) { return false; } - final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) ); - if ( !abcde.getName().equals( "abcde" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata" ) + .equals( "Arabidopsis lyrata subsp. lyrata" ) ) { return false; } - final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) ); - if ( !abcde2.getName().equals( "abcde" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata 395" ) + .equals( "Arabidopsis lyrata subsp. lyrata" ) ) { return false; } - final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) ); - if ( !r.getName().equals( "abcdefgh" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata bcl2" ) + .equals( "Arabidopsis lyrata subsp. lyrata" ) ) { return false; } - final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) ); - if ( !r2.getName().equals( "abcdefgh" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp lyrata bcl2" ) + .equals( "Arabidopsis lyrata subsp. lyrata" ) ) { return false; } - final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) ); - if ( !r3.getName().equals( "abcdefgh" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subspecies lyrata bcl2" ) + .equals( "Arabidopsis lyrata subspecies lyrata" ) ) { return false; } - final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) ); - if ( !abcde3.getName().equals( "abcde" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Verbascum sinuatum var. adenosepalum bcl2" ) + .equals( "Verbascum sinuatum var. adenosepalum" ) ) { return false; } - final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) ); - if ( !abcde4.getName().equals( "abcde" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12)" ) + .equals( "Escherichia coli (strain K12)" ) ) { return false; } - final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) ); - if ( !ab3.getName().equals( "ab" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12) bcl2" ) + .equals( "Escherichia coli (strain K12)" ) ) { return false; } - final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) ); - if ( !ab4.getName().equals( "ab" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12)" ) + .equals( "Escherichia coli (str. K12)" ) ) { 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 ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str K12)" ) + .equals( "Escherichia coli (str. K12)" ) ) { return false; } - final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) ); - if ( !cd2.getName().equals( "cd" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12) bcl2" ) + .equals( "Escherichia coli (str. K12)" ) ) { return false; } - final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) ); - if ( !cde.getName().equals( "cde" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (var K12) bcl2" ) + .equals( "Escherichia coli (var. K12)" ) ) { return false; } - final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) ); - if ( !cde2.getName().equals( "cde" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K-12 substr. MG1655star" ) + .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) { return false; } - final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) ); - if ( !cdef.getName().equals( "cdef" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star" ) + .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) { return false; } - final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) ); - if ( !cdef2.getName().equals( "cdef" ) ) { + if ( !ParserUtils + .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star" ) + .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) { return false; } - final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) ); - if ( !cdef3.getName().equals( "cdef" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star gene1" ) + .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) { return false; } - final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) ); - if ( !rt.getName().equals( "r" ) ) { + if ( !ParserUtils + .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star GENE1" ) + .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) { 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 ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" ) + .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) { return false; } - final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) ); - if ( !ac_3.getName().equals( "abc" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" ) + .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) { return false; } - final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) ); - if ( !ad_3.getName().equals( "abcde" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp." ).equals( "Macrocera sp." ) ) { return false; } - final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) ); - if ( !af_3.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. 123" ).equals( "Macrocera sp." ) ) { return false; } - final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) ); - if ( !ag_3.getName().equals( "" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. K12" ).equals( "Macrocera sp." ) ) { return false; } - if ( !ag_3.isRoot() ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "something Macrocera sp. K12" ) + .equals( "Macrocera sp." ) ) { return false; } - final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) ); - if ( !al_3.getName().equals( "" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) { return false; } - if ( !al_3.isRoot() ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" ) + .equals( "Sesamum rigidum subsp. merenskyanum" ) ) { return false; } - final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) ); - if ( !kl_3.getName().equals( "" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" ) + .equals( "Sesamum rigidum subsp. merenskyanum" ) ) { return false; } - if ( !kl_3.isRoot() ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp. merenskyanum)" ) + .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) { return false; } - final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) ); - if ( !fl_3.getName().equals( "" ) ) { + if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp merenskyanum)" ) + .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) { return false; } - if ( !fl_3.isRoot() ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testExtractTaxonomyDataFromNodeName() { + try { + PhylogenyNode n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { return false; } - final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) ); - if ( !gk_3.getName().equals( "ghijk" ) ) { + n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { 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" ) ) { + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { 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" ) ) { + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN|" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { 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" ) ) { + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN~12" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { 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" ) ) { + n = new PhylogenyNode( "HNRPR_HUMAN" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "HNRPR_HUMAN_X" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { return false; } } @@ -4751,605 +4942,579 @@ public final class Test { return true; } - private static boolean testGetLCA2() { + private static boolean testExtractTaxonomyCodeFromNodeName() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p_a ); - final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ), - p_a.getNode( "a" ) ); - if ( !p_a_1.getName().equals( "a" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p_b ); - final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ), - p_b.getNode( "a" ) ); - if ( !p_b_1.getName().equals( "b" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ), - p_b.getNode( "b" ) ); - if ( !p_b_2.getName().equals( "b" ) ) { - return false; + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "ARATH" ) ) { + return false; } - final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p_c ); - final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ), - p_c.getNode( "a" ) ); - if ( !p_c_1.getName().equals( "b" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "ARATH" ) ) { return false; } - final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ), - p_c.getNode( "c" ) ); - if ( !p_c_2.getName().equals( "c" ) ) { - System.out.println( p_c_2.getName() ); - System.exit( -1 ); + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { return false; } - final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ), - p_c.getNode( "b" ) ); - if ( !p_c_3.getName().equals( "b" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { return false; } - final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ), - p_c.getNode( "a" ) ); - if ( !p_c_4.getName().equals( "c" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh", - new NHXParser() )[ 0 ]; - PhylogenyMethods.preOrderReId( p1 ); - final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "A" ) ); - if ( !A.getName().equals( "A" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ), - p1.getNode( "gh" ) ); - if ( !gh.getName().equals( "gh" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "B" ) ); - if ( !ab.getName().equals( "ab" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ), - p1.getNode( "A" ) ); - if ( !ab2.getName().equals( "ab" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ), - p1.getNode( "G" ) ); - if ( !gh2.getName().equals( "gh" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ), - p1.getNode( "H" ) ); - if ( !gh3.getName().equals( "gh" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ), - p1.getNode( "A" ) ); - if ( !abc.getName().equals( "abc" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "C" ) ); - if ( !abc2.getName().equals( "abc" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "D" ) ); - if ( !abcd.getName().equals( "abcd" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) { return false; } - final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ), - p1.getNode( "A" ) ); - if ( !abcd2.getName().equals( "abcd" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "F" ) ); - if ( !abcdef.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01", + TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) { return false; } - final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ), - p1.getNode( "A" ) ); - if ( !abcdef2.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "9YX45" ) ) { return false; } - final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ), - p1.getNode( "F" ) ); - if ( !abcdef3.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ), - p1.getNode( "ab" ) ); - if ( !abcdef4.getName().equals( "abcdef" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "E" ) ); - if ( !abcde.getName().equals( "abcde" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ), - p1.getNode( "A" ) ); - if ( !abcde2.getName().equals( "abcde" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ), - p1.getNode( "abcdefgh" ) ); - if ( !r.getName().equals( "abcdefgh" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), - p1.getNode( "H" ) ); - if ( !r2.getName().equals( "abcdefgh" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ), - p1.getNode( "A" ) ); - if ( !r3.getName().equals( "abcdefgh" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ), - p1.getNode( "abcde" ) ); - if ( !abcde3.getName().equals( "abcde" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ), - p1.getNode( "E" ) ); - if ( !abcde4.getName().equals( "abcde" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ), - p1.getNode( "B" ) ); - if ( !ab3.getName().equals( "ab" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ), - p1.getNode( "ab" ) ); - if ( !ab4.getName().equals( "ab" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "RAT" ) ) { 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 ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) + .equals( "PIG" ) ) { return false; } - final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ), - p2.getNode( "c" ) ); - if ( !cd2.getName().equals( "cd" ) ) { + if ( !ParserUtils + .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "MOUSE" ) ) { return false; } - final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), - p2.getNode( "e" ) ); - if ( !cde.getName().equals( "cde" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) + .equals( "MOUSE" ) ) { return false; } - final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ), - p2.getNode( "c" ) ); - if ( !cde2.getName().equals( "cde" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), - p2.getNode( "f" ) ); - if ( !cdef.getName().equals( "cdef" ) ) { + } + 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; } - final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ), - p2.getNode( "f" ) ); - if ( !cdef2.getName().equals( "cdef" ) ) { + n.setName( "tr.B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ), - p2.getNode( "d" ) ); - if ( !cdef3.getName().equals( "cdef" ) ) { + n.setName( "tr=B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), - p2.getNode( "a" ) ); - if ( !rt.getName().equals( "r" ) ) { + n.setName( "tr-B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { 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" ) ) { + n.setName( "tr/B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "c" ) ); - if ( !ac_3.getName().equals( "abc" ) ) { + n.setName( "tr\\B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "d" ) ); - if ( !ad_3.getName().equals( "abcde" ) ) { + n.setName( "tr_B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "f" ) ); - if ( !af_3.getName().equals( "abcdef" ) ) { + n.setName( " tr|B3RJ64 " ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "g" ) ); - if ( !ag_3.getName().equals( "" ) ) { + n.setName( "-tr|B3RJ64-" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( !ag_3.isRoot() ) { + n.setName( "-tr=B3RJ64-" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), - p3.getNode( "l" ) ); - if ( !al_3.getName().equals( "" ) ) { + n.setName( "_tr=B3RJ64_" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( !al_3.isRoot() ) { + n.setName( " tr_tr|B3RJ64_sp|123 " ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ), - p3.getNode( "l" ) ); - if ( !kl_3.getName().equals( "" ) ) { + n.setName( "B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - if ( !kl_3.isRoot() ) { + n.setName( "sp|B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ), - p3.getNode( "l" ) ); - if ( !fl_3.getName().equals( "" ) ) { + n.setName( "sp|B3RJ64C" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { return false; } - if ( !fl_3.isRoot() ) { + n.setName( "sp B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ), - p3.getNode( "k" ) ); - if ( !gk_3.getName().equals( "ghijk" ) ) { + n.setName( "sp|B3RJ6X" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { 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" ) ) { + n.setName( "sp|B3RJ6" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { 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" ) ) { + n.setName( "K1PYK7_CRAGI" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { 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" ) ) { + n.setName( "K1PYK7_PEA" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) { 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" ) ) { + n.setName( "K1PYK7_RAT" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) { return false; } - final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), - p7.getNode( "a" ) ); - if ( !r_71.getName().equals( "rott" ) ) { + n.setName( "K1PYK7_PIG" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) { return false; } - final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), - p7.getNode( "rott" ) ); - if ( !r_72.getName().equals( "rott" ) ) { + n.setName( "~K1PYK7_PIG~" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) { return false; } - final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ), - p7.getNode( "a" ) ); - if ( !r_73.getName().equals( "rott" ) ) { + n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { return false; } - final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ), - p7.getNode( "rott" ) ); - if ( !r_74.getName().equals( "rott" ) ) { + n.setName( "K1PYKX_CRAGI" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { return false; } - final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), - p7.getNode( "e" ) ); - if ( !r_75.getName().equals( "e" ) ) { + n.setName( "XXXXX_CRAGI" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) { 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 ) { + n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) { return false; } - if ( proteins.size() != 4 ) { + n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" ); + if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) { return false; } - if ( parser2.getDomainsEncountered() != 69 ) { + n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) { return false; } - if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) { + 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; } - if ( parser2.getDomainsIgnoredDueToEval() != 0 ) { + seq.setSymbol( "tr|B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final Protein p1 = proteins.get( 0 ); - if ( p1.getNumberOfProteinDomains() != 15 ) { + 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; } - if ( p1.getLength() != 850 ) { + seq.setName( "tr|B3RJ64" ); + if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false; } - final Protein p2 = proteins.get( 1 ); - if ( p2.getNumberOfProteinDomains() != 51 ) { + 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; } - if ( p2.getLength() != 1291 ) { + 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 Protein p3 = proteins.get( 2 ); - if ( p3.getNumberOfProteinDomains() != 2 ) { + // + n = new PhylogenyNode(); + n.setName( "ACP19736" ); + if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) { return false; } - final Protein p4 = proteins.get( 3 ); - if ( p4.getNumberOfProteinDomains() != 1 ) { + n = new PhylogenyNode(); + n.setName( "|ACP19736|" ); + if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) { return false; } - if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testFastaParser() { + try { + FileInputStream fis1 = new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ); + if ( !FastaParser.isLikelyFasta( fis1 ) ) { + fis1.close(); return false; } - if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) { - return false; + else { + fis1.close(); } - if ( p4.getProteinDomain( 0 ).getTo() != 395 ) { + FileInputStream fis2 = new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ); + if ( FastaParser.isLikelyFasta( fis2 ) ) { + fis2.close(); return false; } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) { + else { + fis2.close(); + } + final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ); + if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) { return false; } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) { + if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) { return false; } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) { + if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) { return false; } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) { + if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) { return false; } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) { + if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) { return false; } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) { + if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) { return false; } } catch ( final Exception e ) { - e.printStackTrace( System.out ); + e.printStackTrace(); 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; - } - final PhylogenyNode n2 = t0.getNode( "B" ); - if ( n2.isLastExternalNode() ) { - return false; - } - final PhylogenyNode n3 = t0.getNode( "C" ); - if ( n3.isLastExternalNode() ) { - return false; - } - final PhylogenyNode n4 = t0.getNode( "D" ); - if ( !n4.isLastExternalNode() ) { - return false; - } + 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; } - catch ( final Exception e ) { - e.printStackTrace( System.out ); + 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 testLevelOrderIterator() { + private static boolean testGeneralMsaParser() { 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(); + 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; } - for( it0.reset(); it0.hasNext(); ) { - it0.next(); + if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + return false; } - final PhylogenyNodeIterator it = t0.iteratorLevelOrder(); - if ( !it.next().getName().equals( "r" ) ) { + if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) { return false; } - if ( !it.next().getName().equals( "ab" ) ) { + if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) { return false; } - if ( !it.next().getName().equals( "cd" ) ) { + if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { return false; } - if ( !it.next().getName().equals( "A" ) ) { + if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { return false; } - if ( !it.next().getName().equals( "B" ) ) { + if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) { return false; } - if ( !it.next().getName().equals( "C" ) ) { + if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) { return false; } - if ( !it.next().getName().equals( "D" ) ) { + if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { return false; } - if ( it.hasNext() ) { + if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { 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" ) ) { - return false; - } - if ( !it3.next().getName().equals( "abc" ) ) { - return false; - } - if ( !it3.next().getName().equals( "defg" ) ) { - return false; - } - if ( !it3.next().getName().equals( "A" ) ) { + if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) { return false; } - if ( !it3.next().getName().equals( "B" ) ) { + if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) { return false; } - if ( !it3.next().getName().equals( "C" ) ) { + 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 ( !it3.next().getName().equals( "D" ) ) { + if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) { return false; } - if ( !it3.next().getName().equals( "E" ) ) { + if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { return false; } - if ( !it3.next().getName().equals( "F" ) ) { + 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; } - if ( !it3.next().getName().equals( "G" ) ) { + if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) { return false; } - if ( !it3.next().getName().equals( "1" ) ) { + if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) { return false; } - if ( !it3.next().getName().equals( "2" ) ) { + 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; } - if ( !it3.next().getName().equals( "3" ) ) { + if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) { return false; } - if ( !it3.next().getName().equals( "4" ) ) { + if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) { return false; } - if ( !it3.next().getName().equals( "5" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testGeneralTable() { + 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 ( !it3.next().getName().equals( "6" ) ) { + if ( !t0.getValue( 10, 1 ).equals( "110" ) ) { return false; } - if ( !it3.next().getName().equals( "f1" ) ) { + if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) { return false; } - if ( !it3.next().getName().equals( "f2" ) ) { + if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) { return false; } - if ( !it3.next().getName().equals( "f3" ) ) { + if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) { return false; } - if ( !it3.next().getName().equals( "a" ) ) { + if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) { return false; } - if ( !it3.next().getName().equals( "b" ) ) { + if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) { return false; } - if ( !it3.next().getName().equals( "f21" ) ) { + if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) { return false; } - if ( !it3.next().getName().equals( "X" ) ) { + if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) { return false; } - if ( !it3.next().getName().equals( "Y" ) ) { + 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; } - if ( !it3.next().getName().equals( "Z" ) ) { + if ( !t1.getValue( "10", "1" ).equals( "110" ) ) { return false; } - if ( it3.hasNext() ) { + if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) { 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(); - } - final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder(); - if ( !it5.next().getName().equals( "r" ) ) { + if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) { return false; } - if ( !it5.next().getName().equals( "A" ) ) { + if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) { return false; } - if ( !it5.next().getName().equals( "B" ) ) { + if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) { return false; } - if ( !it5.next().getName().equals( "C" ) ) { + if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) { return false; } - if ( !it5.next().getName().equals( "D" ) ) { + if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) { return false; } - 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" ) ) { + if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) { return false; } - if ( it.hasNext() ) { + if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) { return false; } } @@ -5360,681 +5525,675 @@ public final class Test { return true; } - private static boolean testMafft( final String path ) { + private static boolean testGetDistance() { 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 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; } - if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) { return false; } - } - 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 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) { return false; } - if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) { return false; } - if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(), - 1 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) { return false; } - 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() ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) { return false; } - PhylogenyMethods.midpointRoot( t1 ); - if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) { return false; } - if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) { return false; } - if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) { return false; } - if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) { return false; } - if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) { return false; } - if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) { return false; } - t1.reRoot( t1.getNode( "A" ) ); - PhylogenyMethods.midpointRoot( t1 ); - if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) { return false; } - if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) { return false; } - if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) { return false; } - if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) { return false; } - if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) { - System.exit( -1 ); + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) { return false; } - if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) { 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 ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) { return false; } - if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) { return false; } - if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) { return false; } - if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) { 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(); + if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) { + return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) { return false; } - if ( !ext.get( 2 ).getName().equals( "cde" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) { return false; } - if ( !ext.get( 3 ).getName().equals( "f" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) { return false; } - if ( !ext.get( 4 ).getName().equals( "g" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) { return false; } - if ( !ext.get( 5 ).getName().equals( "h" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) { 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 ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) { + return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) { return false; } - if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + 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 ( !ext.get( 2 ).getName().equals( "f" ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) { return false; } - if ( !ext.get( 3 ).getName().equals( "g" ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) { return false; } - if ( !ext.get( 4 ).getName().equals( "h" ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) { 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 ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) { + return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) { return false; } - if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) { return false; } - if ( !ext.get( 2 ).getName().equals( "f" ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) { return false; } - if ( !ext.get( 3 ).getName().equals( "gh" ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) { 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(); + if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) { + return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) { return false; } - if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + } + 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" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "fgh" ) ) { + final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) ); + if ( !gh.getName().equals( "gh" ) ) { 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 ) { + final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) ); + if ( !ab.getName().equals( "ab" ) ) { 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 PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) ); + if ( !ab2.getName().equals( "ab" ) ) { + return false; } - if ( ext.size() != 8 ) { + final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) ); + if ( !gh2.getName().equals( "gh" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) ); + if ( !gh3.getName().equals( "gh" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) ); + if ( !abc.getName().equals( "abc" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) ); + if ( !abc2.getName().equals( "abc" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) ); + if ( !abcd.getName().equals( "abcd" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) ); + if ( !abcd2.getName().equals( "abcd" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "f" ) ) { + final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) ); + if ( !abcdef.getName().equals( "abcdef" ) ) { return false; } - if ( !ext.get( 6 ).getName().equals( "g" ) ) { + final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) ); + if ( !abcdef2.getName().equals( "abcdef" ) ) { return false; } - if ( !ext.get( 7 ).getName().equals( "h" ) ) { + final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) ); + if ( !abcdef3.getName().equals( "abcdef" ) ) { 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 abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) ); + if ( !abcdef4.getName().equals( "abcdef" ) ) { + return false; } - if ( ext.size() != 7 ) { + final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) ); + if ( !abcde.getName().equals( "abcde" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) ); + if ( !abcde2.getName().equals( "abcde" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "c" ) ) { + final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) ); + if ( !r.getName().equals( "abcdefgh" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "d" ) ) { + final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) ); + if ( !r2.getName().equals( "abcdefgh" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) ); + if ( !r3.getName().equals( "abcdefgh" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "f" ) ) { + final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) ); + if ( !abcde3.getName().equals( "abcde" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "g" ) ) { + final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) ); + if ( !abcde4.getName().equals( "abcde" ) ) { return false; } - if ( !ext.get( 6 ).getName().equals( "h" ) ) { + final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) ); + if ( !ab3.getName().equals( "ab" ) ) { 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(); + final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) ); + if ( !ab4.getName().equals( "ab" ) ) { + return false; } - if ( ext.size() != 7 ) { + 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 ( !ext.get( 0 ).getName().equals( "a" ) ) { + final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) ); + if ( !cd2.getName().equals( "cd" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) ); + if ( !cde.getName().equals( "cde" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "cd" ) ) { + final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) ); + if ( !cde2.getName().equals( "cde" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) ); + if ( !cdef.getName().equals( "cdef" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "f" ) ) { + final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) ); + if ( !cdef2.getName().equals( "cdef" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "g" ) ) { + final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) ); + if ( !cdef3.getName().equals( "cdef" ) ) { return false; } - if ( !ext.get( 6 ).getName().equals( "h" ) ) { + final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) ); + if ( !rt.getName().equals( "r" ) ) { 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 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 ( ext.size() != 7 ) { + final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) ); + if ( !ac_3.getName().equals( "abc" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) ); + if ( !ad_3.getName().equals( "abcde" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) ); + if ( !af_3.getName().equals( "abcdef" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "cd" ) ) { - System.out.println( "2 fail" ); + final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) ); + if ( !ag_3.getName().equals( "" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + if ( !ag_3.isRoot() ) { return false; } - if ( !ext.get( 4 ).getName().equals( "f" ) ) { + final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) ); + if ( !al_3.getName().equals( "" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "g" ) ) { + if ( !al_3.isRoot() ) { return false; } - if ( !ext.get( 6 ).getName().equals( "h" ) ) { + final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) ); + if ( !kl_3.getName().equals( "" ) ) { 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 ( ext.size() != 7 ) { + if ( !kl_3.isRoot() ) { return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) ); + if ( !fl_3.getName().equals( "" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + if ( !fl_3.isRoot() ) { return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) ); + if ( !gk_3.getName().equals( "ghijk" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + 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; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + 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; } - if ( !ext.get( 5 ).getName().equals( "f" ) ) { + 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 ( !ext.get( 6 ).getName().equals( "gh" ) ) { + 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; } - // - // - 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(); - } - if ( ext.size() != 7 ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testGetLCA2() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ]; + final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ]; + PhylogenyMethods.preOrderReId( p_a ); + final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ), + p_a.getNode( "a" ) ); + if ( !p_a_1.getName().equals( "a" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ]; + PhylogenyMethods.preOrderReId( p_b ); + final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ), + p_b.getNode( "a" ) ); + if ( !p_b_1.getName().equals( "b" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + 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 ( !ext.get( 2 ).getName().equals( "c" ) ) { + 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 ( !ext.get( 3 ).getName().equals( "d" ) ) { + 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 ( !ext.get( 4 ).getName().equals( "e" ) ) { + 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 ( !ext.get( 5 ).getName().equals( "f" ) ) { + final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ), + p_c.getNode( "a" ) ); + if ( !p_c_4.getName().equals( "c" ) ) { return false; } - if ( !ext.get( 6 ).getName().equals( "gh" ) ) { + 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 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 ( ext.size() != 6 ) { + final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ), + p1.getNode( "gh" ) ); + if ( !gh.getName().equals( "gh" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "B" ) ); + if ( !ab.getName().equals( "ab" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ), + p1.getNode( "A" ) ); + if ( !ab2.getName().equals( "ab" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ), + p1.getNode( "G" ) ); + if ( !gh2.getName().equals( "gh" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ), + p1.getNode( "H" ) ); + if ( !gh3.getName().equals( "gh" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ), + p1.getNode( "A" ) ); + if ( !abc.getName().equals( "abc" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { + final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "C" ) ); + if ( !abc2.getName().equals( "abc" ) ) { 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 ( ext.size() != 6 ) { + final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "D" ) ); + if ( !abcd.getName().equals( "abcd" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "a" ) ) { + final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ), + p1.getNode( "A" ) ); + if ( !abcd2.getName().equals( "abcd" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "b" ) ) { + final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "F" ) ); + if ( !abcdef.getName().equals( "abcdef" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "c" ) ) { + final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ), + p1.getNode( "A" ) ); + if ( !abcdef2.getName().equals( "abcdef" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "d" ) ) { + final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ), + p1.getNode( "F" ) ); + if ( !abcdef3.getName().equals( "abcdef" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "e" ) ) { + final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ), + p1.getNode( "ab" ) ); + if ( !abcdef4.getName().equals( "abcdef" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { + final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "E" ) ); + if ( !abcde.getName().equals( "abcde" ) ) { 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 ( ext.size() != 5 ) { + final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ), + p1.getNode( "A" ) ); + if ( !abcde2.getName().equals( "abcde" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ), + p1.getNode( "abcdefgh" ) ); + if ( !r.getName().equals( "abcdefgh" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "c" ) ) { + final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ), + p1.getNode( "H" ) ); + if ( !r2.getName().equals( "abcdefgh" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "d" ) ) { + final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ), + p1.getNode( "A" ) ); + if ( !r3.getName().equals( "abcdefgh" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ), + p1.getNode( "abcde" ) ); + if ( !abcde3.getName().equals( "abcde" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { + final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ), + p1.getNode( "E" ) ); + if ( !abcde4.getName().equals( "abcde" ) ) { 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 ( ext.size() != 5 ) { + final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ), + p1.getNode( "B" ) ); + if ( !ab3.getName().equals( "ab" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ), + p1.getNode( "ab" ) ); + if ( !ab4.getName().equals( "ab" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "c" ) ) { + 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 ( !ext.get( 2 ).getName().equals( "d" ) ) { + final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ), + p2.getNode( "c" ) ); + if ( !cd2.getName().equals( "cd" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "e" ) ) { + final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), + p2.getNode( "e" ) ); + if ( !cde.getName().equals( "cde" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { + final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ), + p2.getNode( "c" ) ); + if ( !cde2.getName().equals( "cde" ) ) { 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(); + final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), + p2.getNode( "f" ) ); + if ( !cdef.getName().equals( "cdef" ) ) { + return false; } - if ( ext.size() != 6 ) { + final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ), + p2.getNode( "f" ) ); + if ( !cdef2.getName().equals( "cdef" ) ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ), + p2.getNode( "d" ) ); + if ( !cdef3.getName().equals( "cdef" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "c" ) ) { + final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ), + p2.getNode( "a" ) ); + if ( !rt.getName().equals( "r" ) ) { return false; } - if ( !ext.get( 2 ).getName().equals( "d" ) ) { + 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 ( !ext.get( 3 ).getName().equals( "e" ) ) { + final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "c" ) ); + if ( !ac_3.getName().equals( "abc" ) ) { return false; } - if ( !ext.get( 4 ).getName().equals( "x" ) ) { + final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "d" ) ); + if ( !ad_3.getName().equals( "abcde" ) ) { return false; } - if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { + final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "f" ) ); + if ( !af_3.getName().equals( "abcdef" ) ) { 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(); + final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "g" ) ); + if ( !ag_3.getName().equals( "" ) ) { + return false; } - if ( ext.size() != 4 ) { + if ( !ag_3.isRoot() ) { return false; } - if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ), + p3.getNode( "l" ) ); + if ( !al_3.getName().equals( "" ) ) { return false; } - if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + if ( !al_3.isRoot() ) { return false; } - if ( !ext.get( 2 ).getName().equals( "x" ) ) { + final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ), + p3.getNode( "l" ) ); + if ( !kl_3.getName().equals( "" ) ) { return false; } - if ( !ext.get( 3 ).getName().equals( "fgh" ) ) { + if ( !kl_3.isRoot() ) { + return false; + } + final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ), + p3.getNode( "l" ) ); + if ( !fl_3.getName().equals( "" ) ) { + return false; + } + if ( !fl_3.isRoot() ) { + return false; + } + final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ), + p3.getNode( "k" ) ); + if ( !gk_3.getName().equals( "ghijk" ) ) { + 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" ) ) { + 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" ) ) { + 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" ) ) { + 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" ) ) { + return false; + } + final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), + p7.getNode( "a" ) ); + if ( !r_71.getName().equals( "rott" ) ) { + return false; + } + final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), + p7.getNode( "rott" ) ); + if ( !r_72.getName().equals( "rott" ) ) { + return false; + } + final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ), + p7.getNode( "a" ) ); + if ( !r_73.getName().equals( "rott" ) ) { + return false; + } + final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ), + p7.getNode( "rott" ) ); + if ( !r_74.getName().equals( "rott" ) ) { + return false; + } + final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ), + p7.getNode( "e" ) ); + if ( !r_75.getName().equals( "e" ) ) { return false; } } @@ -6045,61 +6204,74 @@ public final class Test { return true; } - private static boolean testNexusCharactersParsing() { + private static boolean testHmmscanOutputParser() { + final String test_dir = Test.PATH_TO_TEST_DATA; 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 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 ( !labels[ 0 ].equals( "14-3-3" ) ) { + if ( proteins.size() != 4 ) { return false; } - if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { + if ( parser2.getDomainsEncountered() != 69 ) { return false; } - if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { + if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) { return false; } - if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { + if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) { return false; } - if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { + if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) { return false; } - if ( !labels[ 5 ].equals( "3-HAO" ) ) { + final Protein p1 = proteins.get( 0 ); + if ( p1.getNumberOfProteinDomains() != 15 ) { return false; } - if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { + if ( p1.getLength() != 850 ) { 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 Protein p2 = proteins.get( 1 ); + if ( p2.getNumberOfProteinDomains() != 51 ) { return false; } - if ( !labels[ 0 ].equals( "14-3-3" ) ) { + if ( p2.getLength() != 1291 ) { return false; } - if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { + final Protein p3 = proteins.get( 2 ); + if ( p3.getNumberOfProteinDomains() != 2 ) { return false; } - if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { + final Protein p4 = proteins.get( 3 ); + if ( p4.getNumberOfProteinDomains() != 1 ) { return false; } - if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { + if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) { return false; } - if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { + if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) { return false; } - if ( !labels[ 5 ].equals( "3-HAO" ) ) { + if ( p4.getProteinDomain( 0 ).getTo() != 395 ) { return false; } - if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { + 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 ).getNumber(), 1 ) ) { + return false; + } + if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) { return false; } } @@ -6110,260 +6282,288 @@ public final class Test { return true; } - private static boolean testNexusMatrixParsing() { + private static boolean testLastExternalNodeMethods() { 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 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 ( m.getNumberOfIdentifiers() != 5 ) { + final PhylogenyNode n2 = t0.getNode( "B" ); + if ( n2.isLastExternalNode() ) { return false; } - if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) { + final PhylogenyNode n3 = t0.getNode( "C" ); + if ( n3.isLastExternalNode() ) { return false; } - if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) { + final PhylogenyNode n4 = t0.getNode( "D" ); + if ( !n4.isLastExternalNode() ) { return false; } - if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) { + } + 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" ) ) { return false; } - if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) { + if ( !it.next().getName().equals( "ab" ) ) { return false; } - if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) { + if ( !it.next().getName().equals( "cd" ) ) { return false; } - if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) { + if ( !it.next().getName().equals( "A" ) ) { return false; } - if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) { + if ( !it.next().getName().equals( "B" ) ) { 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 ) { + if ( !it.next().getName().equals( "C" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) { + if ( !it.next().getName().equals( "D" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "" ) ) { + if ( it.hasNext() ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser ); - if ( phylogenies.length != 1 ) { + 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" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) { + if ( !it3.next().getName().equals( "abc" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "name" ) ) { + if ( !it3.next().getName().equals( "defg" ) ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser ); - if ( phylogenies.length != 1 ) { + if ( !it3.next().getName().equals( "A" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "B" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "" ) ) { + if ( !it3.next().getName().equals( "C" ) ) { return false; } - if ( phylogenies[ 0 ].isRooted() ) { + if ( !it3.next().getName().equals( "D" ) ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser ); - if ( phylogenies.length != 18 ) { + if ( !it3.next().getName().equals( "E" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) { + if ( !it3.next().getName().equals( "F" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) { + if ( !it3.next().getName().equals( "G" ) ) { return false; } - if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) { + if ( !it3.next().getName().equals( "1" ) ) { return false; } - if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) { + if ( !it3.next().getName().equals( "2" ) ) { return false; } - if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "3" ) ) { return false; } - if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "4" ) ) { return false; } - if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "5" ) ) { return false; } - if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "6" ) ) { return false; } - if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "f1" ) ) { return false; } - if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "f2" ) ) { return false; } - if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) { + if ( !it3.next().getName().equals( "f3" ) ) { return false; } - if ( phylogenies[ 8 ].isRooted() ) { + if ( !it3.next().getName().equals( "a" ) ) { return false; } - if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "b" ) ) { return false; } - if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) { + if ( !it3.next().getName().equals( "f21" ) ) { return false; } - if ( !phylogenies[ 9 ].isRooted() ) { + if ( !it3.next().getName().equals( "X" ) ) { return false; } - if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) { + if ( !it3.next().getName().equals( "Y" ) ) { return false; } - if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) { + if ( !it3.next().getName().equals( "Z" ) ) { return false; } - if ( !phylogenies[ 10 ].isRooted() ) { + if ( it3.hasNext() ) { return false; } - if ( phylogenies[ 10 ].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[ 11 ].getName().equals( "tree 11" ) ) { + if ( !it5.next().getName().equals( "A" ) ) { return false; } - if ( phylogenies[ 11 ].isRooted() ) { + if ( !it5.next().getName().equals( "B" ) ) { return false; } - if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) { + if ( !it5.next().getName().equals( "C" ) ) { return false; } - if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) { + if ( !it5.next().getName().equals( "D" ) ) { return false; } - if ( !phylogenies[ 12 ].isRooted() ) { + 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 ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) { + if ( it.hasNext() ) { return false; } - if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testMafft( final String path ) { + 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 ) ) { return false; } - if ( !phylogenies[ 13 ].isRooted() ) { + if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) { return false; } - if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) { + } + 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; } - if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) { + if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) { return false; } - if ( !phylogenies[ 14 ].isRooted() ) { + if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(), + 1 ) ) { return false; } - if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) { + 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 ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) { + PhylogenyMethods.midpointRoot( t1 ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { return false; } - if ( phylogenies[ 15 ].isRooted() ) { + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { return false; } - if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) { + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { return false; } - if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) { + if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) { return false; } - if ( !phylogenies[ 16 ].isRooted() ) { + if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) { return false; } - if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) { + if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) { return false; } - if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) { + t1.reRoot( t1.getNode( "A" ) ); + PhylogenyMethods.midpointRoot( t1 ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) { return false; } - if ( phylogenies[ 17 ].isRooted() ) { + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { return false; } - if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) { + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) { + System.exit( -1 ); + return false; + } + if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) { return false; } } @@ -6374,560 +6574,793 @@ public final class Test { return true; } - private static boolean testNexusTreeParsingIterating() { + private static boolean testMsaQualityMethod() { try { - final NexusPhylogeniesParser p = new NexusPhylogeniesParser(); - p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" ); - if ( !p.hasNext() ) { + final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" ); + final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" ); + final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" ); + final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" ); + final List l = new ArrayList(); + 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; } - Phylogeny phy = p.next(); - if ( phy == null ) { + if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 25 ) { + if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) { return false; } - if ( p.hasNext() ) { + if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) { return false; } - phy = p.next(); - if ( phy != null ) { + if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) { return false; } - // - p.reset(); - if ( !p.hasNext() ) { + if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testMsaEntropy() { + try { + final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" ); + final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" ); + final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" ); + final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" ); + final List l = new ArrayList(); + l.add( s0 ); + l.add( s1 ); + l.add( s2 ); + l.add( s3 ); + final Msa msa = BasicMsa.createInstance( l ); + //TODO need to DO the tests!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + //FIXME + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) ); + // System.out.println(); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) ); + final List l2 = new ArrayList(); + l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) ); + l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) ); + l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) ); + l2.add( BasicSequence.createAaSequence( "4", "AIIIVVW" ) ); + l2.add( BasicSequence.createAaSequence( "5", "AAAAAAA" ) ); + l2.add( BasicSequence.createAaSequence( "6", "AAAIACC" ) ); + l2.add( BasicSequence.createAaSequence( "7", "AAIIIIF" ) ); + l2.add( BasicSequence.createAaSequence( "8", "AIIIVVW" ) ); + l2.add( BasicSequence.createAaSequence( "9", "AAAAAAA" ) ); + l2.add( BasicSequence.createAaSequence( "10", "AAAIACC" ) ); + l2.add( BasicSequence.createAaSequence( "11", "AAIIIIF" ) ); + l2.add( BasicSequence.createAaSequence( "12", "AIIIVVW" ) ); + l2.add( BasicSequence.createAaSequence( "13", "AAIIIIF" ) ); + l2.add( BasicSequence.createAaSequence( "14", "AIIIVVW" ) ); + l2.add( BasicSequence.createAaSequence( "15", "AAAAAAA" ) ); + l2.add( BasicSequence.createAaSequence( "16", "AAAIACC" ) ); + l2.add( BasicSequence.createAaSequence( "17", "AAIIIIF" ) ); + l2.add( BasicSequence.createAaSequence( "18", "AIIIVVW" ) ); + l2.add( BasicSequence.createAaSequence( "19", "AAAAAAA" ) ); + l2.add( BasicSequence.createAaSequence( "20", "AAAIACC" ) ); + l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) ); + l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) ); + final Msa msa2 = BasicMsa.createInstance( l2 ); + // System.out.println(); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) ); + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testDeleteableMsa() { + try { + final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAA" ); + final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "BAAA" ); + final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "CAAA" ); + final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" ); + final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" ); + final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" ); + final List l0 = new ArrayList(); + l0.add( s0 ); + l0.add( s1 ); + l0.add( s2 ); + l0.add( s3 ); + l0.add( s4 ); + l0.add( s5 ); + final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 ); + dmsa0.deleteRow( "b", false ); + if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 25 ) { + dmsa0.deleteRow( "e", false ); + dmsa0.deleteRow( "a", false ); + dmsa0.deleteRow( "f", false ); + if ( dmsa0.getLength() != 4 ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( dmsa0.getNumberOfSequences() != 2 ) { return false; } - if ( p.hasNext() ) { + if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) { return false; } - phy = p.next(); - if ( phy != null ) { + if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) { return false; } - //// - p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" ); - if ( !p.hasNext() ) { + if ( dmsa0.getResidueAt( 0, 0 ) != 'C' ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 10 ) { + if ( dmsa0.getColumnAt( 0 ).size() != 2 ) { return false; } - if ( !phy.getName().equals( "name" ) ) { + dmsa0.deleteRow( "c", false ); + dmsa0.deleteRow( "d", false ); + if ( dmsa0.getNumberOfSequences() != 0 ) { return false; } - if ( p.hasNext() ) { + // + final MolecularSequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" ); + final MolecularSequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" ); + final MolecularSequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" ); + final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" ); + final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" ); + final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" ); + final List l1 = new ArrayList(); + l1.add( s_0 ); + l1.add( s_1 ); + l1.add( s_2 ); + l1.add( s_3 ); + l1.add( s_4 ); + l1.add( s_5 ); + final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 ); + dmsa1.deleteGapOnlyColumns(); + dmsa1.deleteRow( "a", false ); + dmsa1.deleteRow( "f", false ); + dmsa1.deleteRow( "d", false ); + dmsa1.deleteGapOnlyColumns(); + if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) { return false; } - phy = p.next(); - if ( phy != null ) { + if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "CABCZ" ) ) { return false; } - // - p.reset(); - if ( !p.hasNext() ) { + if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + dmsa1.deleteRow( "c", false ); + dmsa1.deleteGapOnlyColumns(); + final Writer w0 = new StringWriter(); + dmsa1.write( w0, MSA_FORMAT.FASTA ); + final Writer w1 = new StringWriter(); + dmsa1.write( w1, MSA_FORMAT.PHYLIP ); + if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 10 ) { + if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) { return false; } - if ( !phy.getName().equals( "name" ) ) { + final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" ); + final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" ); + final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" ); + final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" ); + final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" ); + final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" ); + final List l2 = new ArrayList(); + l2.add( s__0 ); + l2.add( s__1 ); + l2.add( s__2 ); + l2.add( s__3 ); + l2.add( s__4 ); + l2.add( s__5 ); + final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 ); + dmsa2.deleteGapColumns( 0.5 ); + if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) { return false; } - if ( p.hasNext() ) { + if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) { return false; } - phy = p.next(); - if ( phy != null ) { + if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) { return false; } - //// - p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" ); - if ( !p.hasNext() ) { + dmsa2.deleteGapColumns( 0.2 ); + if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + dmsa2.deleteGapColumns( 0 ); + dmsa2.deleteRow( "a", false ); + dmsa2.deleteRow( "b", false ); + dmsa2.deleteRow( "f", false ); + dmsa2.deleteRow( "e", false ); + dmsa2.setIdentifier( 0, "new_c" ); + dmsa2.setIdentifier( 1, "new_d" ); + dmsa2.setResidueAt( 0, 0, 'x' ); + final MolecularSequence s = dmsa2.deleteRow( "new_d", true ); + if ( !s.getMolecularSequenceAsString().equals( "D" ) ) { return false; } - if ( phy.isRooted() ) { + final Writer w = new StringWriter(); + dmsa2.write( w, MSA_FORMAT.PHYLIP ); + final String phylip = w.toString(); + if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) { + System.out.println( phylip ); return false; } - if ( p.hasNext() ) { + final Writer w2 = new StringWriter(); + dmsa2.write( w2, MSA_FORMAT.FASTA ); + final String fasta = w2.toString(); + if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) { + System.out.println( fasta ); return false; } - phy = p.next(); - if ( phy != null ) { - 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.toString(), 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(); } - // - p.reset(); - if ( !p.hasNext() ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 2 ).getName().equals( "cde" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !ext.get( 3 ).getName().equals( "f" ) ) { return false; } - if ( p.hasNext() ) { + if ( !ext.get( 4 ).getName().equals( "g" ) ) { return false; } - phy = p.next(); - if ( phy != null ) { + if ( !ext.get( 5 ).getName().equals( "h" ) ) { return false; } - //// - p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" ); - // if ( phylogenies.length != 18 ) { - // return false; - // } - //0 - if ( !p.hasNext() ) { - 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.toString(), new NHXParser() )[ 0 ]; + t1.getNode( "ab" ).setCollapse( true ); + t1.getNode( "cd" ).setCollapse( true ); + t1.getNode( "cde" ).setCollapse( true ); + n = t1.getNode( "ab" ); + ext = new ArrayList(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 10 ) { + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { return false; } - if ( !phy.getName().equals( "tree 0" ) ) { + if ( !ext.get( 2 ).getName().equals( "f" ) ) { return false; } - //1 - if ( !p.hasNext() ) { + if ( !ext.get( 3 ).getName().equals( "g" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 4 ).getName().equals( "h" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 10 ) { + 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.toString(), 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" ) ) { return false; } - if ( !phy.getName().equals( "tree 1" ) ) { + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { return false; } - //2 - if ( !p.hasNext() ) { + if ( !ext.get( 2 ).getName().equals( "f" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 3 ).getName().equals( "gh" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 3 ) { + 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.toString(), 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(); + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { return false; } - if ( phy.isRooted() ) { + if ( !ext.get( 2 ).getName().equals( "fgh" ) ) { return false; } - //3 - if ( !p.hasNext() ) { + 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.toString(), 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; } - phy = p.next(); - if ( phy == null ) { + 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.toString(), new NHXParser() )[ 0 ]; + ext.clear(); + n = t5.getFirstExternalNode(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 8 ) { return false; } - if ( phy.getNumberOfExternalNodes() != 4 ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( !phy.isRooted() ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - //4 - if ( !p.hasNext() ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 5 ) { - System.out.println( phy.getNumberOfExternalNodes() ); + if ( !ext.get( 5 ).getName().equals( "f" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !ext.get( 6 ).getName().equals( "g" ) ) { return false; } - if ( !phy.isRooted() ) { + if ( !ext.get( 7 ).getName().equals( "h" ) ) { return false; } - //5 - if ( !p.hasNext() ) { + 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.toString(), new NHXParser() )[ 0 ]; + ext.clear(); + t6.getNode( "ab" ).setCollapse( true ); + n = t6.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 7 ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 1 ).getName().equals( "c" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !ext.get( 2 ).getName().equals( "d" ) ) { return false; } - if ( phy.isRooted() ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - //6 - if ( !p.hasNext() ) { + if ( !ext.get( 4 ).getName().equals( "f" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 5 ).getName().equals( "g" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 2 ) { + if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { - 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.toString(), new NHXParser() )[ 0 ]; + ext.clear(); + t7.getNode( "cd" ).setCollapse( true ); + n = t7.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - if ( !phy.isRooted() ) { + if ( ext.size() != 7 ) { return false; } - //7 - if ( !p.hasNext() ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { + if ( !ext.get( 2 ).getName().equals( "cd" ) ) { return false; } - if ( !phy.isRooted() ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - //8 - if ( !p.hasNext() ) { + if ( !ext.get( 4 ).getName().equals( "f" ) ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 5 ).getName().equals( "g" ) ) { return false; } - if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) { + if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - if ( !phy.getName().equals( "tree 8" ) ) { - 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.toString(), 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(); } - //9 - if ( !p.hasNext() ) { + if ( ext.size() != 7 ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( !phy.getName().equals( "tree 9" ) ) { + if ( !ext.get( 2 ).getName().equals( "cd" ) ) { + System.out.println( "2 fail" ); return false; } - //10 - if ( !p.hasNext() ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 4 ).getName().equals( "f" ) ) { return false; } - if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { + if ( !ext.get( 5 ).getName().equals( "g" ) ) { return false; } - if ( !phy.getName().equals( "tree 10" ) ) { + if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - if ( !phy.isRooted() ) { - 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.toString(), new NHXParser() )[ 0 ]; + ext.clear(); + t9.getNode( "gh" ).setCollapse( true ); + n = t9.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); } - //11 - if ( !p.hasNext() ) { + if ( ext.size() != 7 ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( !phy.getName().equals( "tree 11" ) ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - if ( phy.isRooted() ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - //12 - if ( !p.hasNext() ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 5 ).getName().equals( "f" ) ) { return false; } - if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) { + if ( !ext.get( 6 ).getName().equals( "gh" ) ) { return false; } - if ( !phy.getName().equals( "tree 12" ) ) { - 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.toString(), 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(); } - if ( !phy.isRooted() ) { + if ( ext.size() != 7 ) { return false; } - //13 - if ( !p.hasNext() ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - if ( !phy.getName().equals( "tree 13" ) ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - if ( !phy.isRooted() ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - //14 - if ( !p.hasNext() ) { + if ( !ext.get( 5 ).getName().equals( "f" ) ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 10 ) { - System.out.println( phy.getNumberOfExternalNodes() ); + if ( !ext.get( 6 ).getName().equals( "gh" ) ) { return false; } - if ( !phy - .toNewHampshire() - .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { - System.out.println( phy.toNewHampshire() ); - return false; + 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.toString(), 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 ( !phy.getName().equals( "tree 14" ) ) { + if ( ext.size() != 6 ) { return false; } - if ( !phy.isRooted() ) { + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - //15 - if ( !p.hasNext() ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 10 ) { - System.out.println( phy.getNumberOfExternalNodes() ); + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - if ( !phy - .toNewHampshire() - .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { - System.out.println( phy.toNewHampshire() ); + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - if ( !phy.getName().equals( "tree 15" ) ) { + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - if ( phy.isRooted() ) { + if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - //16 - if ( !p.hasNext() ) { - 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.toString(), 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(); } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 10 ) { - System.out.println( phy.getNumberOfExternalNodes() ); + if ( ext.size() != 6 ) { return false; } - if ( !phy - .toNewHampshire() - .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { - System.out.println( phy.toNewHampshire() ); + if ( !ext.get( 0 ).getName().equals( "a" ) ) { return false; } - if ( !phy.getName().equals( "tree 16" ) ) { + if ( !ext.get( 1 ).getName().equals( "b" ) ) { return false; } - if ( !phy.isRooted() ) { + if ( !ext.get( 2 ).getName().equals( "c" ) ) { return false; } - //17 - if ( !p.hasNext() ) { + if ( !ext.get( 3 ).getName().equals( "d" ) ) { return false; } - phy = p.next(); - if ( phy.getNumberOfExternalNodes() != 10 ) { - System.out.println( phy.getNumberOfExternalNodes() ); + if ( !ext.get( 4 ).getName().equals( "e" ) ) { return false; } - if ( !phy - .toNewHampshire() - .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { - System.out.println( phy.toNewHampshire() ); + if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - if ( !phy.getName().equals( "tree 17" ) ) { - 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.toString(), 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 ( phy.isRooted() ) { + if ( ext.size() != 5 ) { return false; } - // - if ( p.hasNext() ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - phy = p.next(); - if ( phy != null ) { + if ( !ext.get( 1 ).getName().equals( "c" ) ) { return false; } - p.reset(); - //0 - if ( !p.hasNext() ) { + if ( !ext.get( 2 ).getName().equals( "d" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 10 ) { + if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { return false; } - if ( !phy.getName().equals( "tree 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.toString(), 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(); } - //1 - if ( !p.hasNext() ) { + if ( ext.size() != 5 ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 10 ) { + if ( !ext.get( 1 ).getName().equals( "c" ) ) { return false; } - if ( !phy.getName().equals( "tree 1" ) ) { + if ( !ext.get( 2 ).getName().equals( "d" ) ) { return false; } - //2 - if ( !p.hasNext() ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 3 ) { - return false; - } - if ( !phy.getName().equals( "" ) ) { - return false; - } - if ( phy.isRooted() ) { - return false; - } - //3 - if ( !p.hasNext() ) { - return false; - } - phy = p.next(); - if ( phy == null ) { - return false; + 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.toString(), 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 ( phy.getNumberOfExternalNodes() != 4 ) { + if ( ext.size() != 6 ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( !phy.isRooted() ) { + if ( !ext.get( 1 ).getName().equals( "c" ) ) { return false; } - //4 - if ( !p.hasNext() ) { + if ( !ext.get( 2 ).getName().equals( "d" ) ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 3 ).getName().equals( "e" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 5 ) { - System.out.println( phy.getNumberOfExternalNodes() ); + if ( !ext.get( 4 ).getName().equals( "x" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - if ( !phy.isRooted() ) { - 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.toString(), 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(); } - //5 - if ( !p.hasNext() ) { + if ( ext.size() != 4 ) { return false; } - phy = p.next(); - if ( phy == null ) { + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { return false; } - if ( phy.getNumberOfExternalNodes() != 3 ) { + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { return false; } - if ( !phy.getName().equals( "" ) ) { + if ( !ext.get( 2 ).getName().equals( "x" ) ) { return false; } - if ( phy.isRooted() ) { + if ( !ext.get( 3 ).getName().equals( "fgh" ) ) { return false; } } @@ -6938,1291 +7371,1152 @@ public final class Test { return true; } - private static boolean testNexusTreeParsingTranslating() { + private static boolean testNexusCharactersParsing() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); - Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser ); - if ( phylogenies.length != 1 ) { + final 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 ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + if ( !labels[ 0 ].equals( "14-3-3" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser ); - if ( phylogenies.length != 3 ) { + if ( !labels[ 5 ].equals( "3-HAO" ) ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + 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 ( phylogenies[ 0 ].isRooted() ) { + if ( !labels[ 0 ].equals( "14-3-3" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) { return false; } - if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { + if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) { return false; } - if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { + if ( !labels[ 5 ].equals( "3-HAO" ) ) { return false; } - if ( phylogenies[ 1 ].isRooted() ) { + if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + } + 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 ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( m.getNumberOfIdentifiers() != 5 ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) { return false; } - if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) { return false; } - if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { + if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) { return false; } - if ( !phylogenies[ 2 ].isRooted() ) { + if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser ); - if ( phylogenies.length != 3 ) { + // 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 ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( !phylogenies[ 0 ].getName().equals( "" ) ) { return false; } - if ( phylogenies[ 0 ].isRooted() ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser ); + if ( phylogenies.length != 1 ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( !phylogenies[ 0 ].getName().equals( "name" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser ); + if ( phylogenies.length != 1 ) { return false; } - if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { + if ( !phylogenies[ 0 ].getName().equals( "" ) ) { return false; } - if ( phylogenies[ 1 ].isRooted() ) { + if ( phylogenies[ 0 ].isRooted() ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser ); + if ( phylogenies.length != 18 ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) { return false; } - if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) { return false; } - if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { + if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) { return false; } - if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { + if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) { return false; } - if ( !phylogenies[ 2 ].isRooted() ) { + if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testNHParsing() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ]; - if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) { + if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) { return false; } - final NHXParser nhxp = new NHXParser(); - nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO ); - nhxp.setReplaceUnderscores( true ); - final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ]; - if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) { + if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) { + if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) { 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 ( phylogenies[ 8 ].isRooted() ) { return false; } - if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) { + if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) { return false; } - final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ]; - final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ]; - final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ]; - final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ]; - final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() ); - final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() ); - final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() ); - final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() ); - final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() ); - final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() ); - final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;" - + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " - + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", - new NHXParser() ); - if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) { + if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) { return false; } - if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) { + if ( !phylogenies[ 9 ].isRooted() ) { return false; } - if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) { + if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) { + if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) { return false; } - final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() ); - final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() ); - final String p16_S = "((A,B),C)"; - final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() ); - if ( p16.length != 1 ) { + if ( !phylogenies[ 10 ].isRooted() ) { return false; } - if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) { + if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) { return false; } - final String p17_S = "(C,(A,B))"; - final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() ); - if ( p17.length != 1 ) { + if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) { return false; } - if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) { + if ( phylogenies[ 11 ].isRooted() ) { return false; } - final String p18_S = "((A,B),(C,D))"; - final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() ); - if ( p18.length != 1 ) { + if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) { + if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) { return false; } - final String p19_S = "(((A,B),C),D)"; - final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() ); - if ( p19.length != 1 ) { + if ( !phylogenies[ 12 ].isRooted() ) { return false; } - if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) { + if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) { return false; } - final String p20_S = "(A,(B,(C,D)))"; - final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() ); - if ( p20.length != 1 ) { + if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) { return false; } - if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) { + if ( !phylogenies[ 13 ].isRooted() ) { return false; } - final String p21_S = "(A,(B,(C,(D,E))))"; - final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() ); - if ( p21.length != 1 ) { + if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) { + if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) { return false; } - final String p22_S = "((((A,B),C),D),E)"; - final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() ); - if ( p22.length != 1 ) { + if ( !phylogenies[ 14 ].isRooted() ) { return false; } - if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) { + if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) { return false; } - final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() ); - if ( p23.length != 1 ) { - System.out.println( "xl=" + p23.length ); - System.exit( -1 ); + if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) { return false; } - if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) { + if ( phylogenies[ 15 ].isRooted() ) { return false; } - final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() ); - if ( p24.length != 1 ) { + if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) { return false; } - if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) { + if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) { return false; } - final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() ); - if ( p241.length != 2 ) { + if ( !phylogenies[ 16 ].isRooted() ) { return false; } - if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) { + if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) { return false; } - if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) { + if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) { 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 ( phylogenies[ 17 ].isRooted() ) { return false; } - final String p26_S = "(A,B)ab"; - final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() ); - if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) { + if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) { return false; } - final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() ); - if ( p27s.length != 1 ) { - System.out.println( "xxl=" + p27s.length ); - System.exit( -1 ); + final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser(); + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 ); + if ( phylogenies.length != 9 ) { return false; } - if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) { - System.out.println( p27s[ 0 ].toNewHampshireX() ); - System.exit( -1 ); + if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" ) + .getDistanceToParent() ) ) { return false; } - final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ), - new NHXParser() ); - if ( p27.length != 1 ) { - System.out.println( "yl=" + p27.length ); - System.exit( -1 ); + if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" ) + .getDistanceToParent() ) ) { return false; } - if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) { - System.out.println( p27[ 0 ].toNewHampshireX() ); - System.exit( -1 ); + if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) { return false; } - final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - final String p28_S3 = "(A,B)ab"; - final String p28_S4 = "((((A,B),C),D),;E;)"; - final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ), - new NHXParser() ); - if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) { + if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) { return false; } - if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) { + if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) { return false; } - if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) { + if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) { return false; } - if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) { + if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) { return false; } - if ( p28.length != 4 ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNexusTreeParsingIterating() { + try { + final NexusPhylogeniesParser p = new NexusPhylogeniesParser(); + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" ); + if ( !p.hasNext() ) { return false; } - final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345"; - final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() ); - if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) { + Phylogeny phy = p.next(); + if ( phy == null ) { return false; } - final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72"; - final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() ); - if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) { + if ( phy.getNumberOfExternalNodes() != 25 ) { return false; } - final String p32_S = " ; ; \n \t \b \f \r ;;;;;; "; - final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() ); - if ( ( p32.length != 0 ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - final String p33_S = "A"; - final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() ); - if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) { + if ( p.hasNext() ) { return false; } - final String p34_S = "B;"; - final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() ); - if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) { + phy = p.next(); + if ( phy != null ) { 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 ) ) { + p.reset(); + if ( !p.hasNext() ) { return false; } - final String p36_S = "(A)"; - final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() ); - if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - final String p37_S = "((A))"; - final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() ); - if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) { + if ( phy.getNumberOfExternalNodes() != 25 ) { 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 ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; - final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() ); - if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) { + if ( p.hasNext() ) { 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 ) ) { + phy = p.next(); + if ( phy != null ) { 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 ) ) { + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" ); + if ( !p.hasNext() ) { return false; } - final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)"; - final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() ); - if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)"; - final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() ); - if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))"; - final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() ); - if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) { + if ( !phy.getName().equals( "name" ) ) { 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 ( p.hasNext() ) { return false; } - final String p46_S = ""; - final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() ); - if ( p46.length != 0 ) { + phy = p.next(); + if ( phy != null ) { 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() ) ) { + p.reset(); + if ( !p.hasNext() ) { 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() ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - final Phylogeny p49 = factory - .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ), - new NHXParser() )[ 0 ]; - if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; - if ( p50.getNode( "A" ) == null ) { + if ( !phy.getName().equals( "name" ) ) { return false; } - if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) - .equals( "((A,B)ab:2.0[88],C);" ) ) { + if ( p.hasNext() ) { return false; } - if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ) - .equals( "((A,B)88:2.0,C);" ) ) { + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" ); + if ( !p.hasNext() ) { 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 ) { + phy = p.next(); + if ( phy == null ) { 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 ( phy.getNumberOfExternalNodes() != 3 ) { 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 ( !phy.getName().equals( "" ) ) { return false; } - // - final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ]; - if ( p54.getNode( "A" ) == null ) { + if ( phy.isRooted() ) { return false; } - if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) - .equals( "((A,B)[88],C);" ) ) { + if ( p.hasNext() ) { return false; } - } - 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 ); + phy = p.next(); + if ( phy != null ) { + return false; + } + // + p.reset(); if ( !p.hasNext() ) { return false; } - final Phylogeny p0 = p.next(); - if ( !p0.toNewHampshire().equals( p0_str ) ) { - System.out.println( p0.toNewHampshire() ); + phy = p.next(); + if ( phy == null ) { return false; } - if ( p.hasNext() ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.next() != null ) { + if ( !phy.getName().equals( "" ) ) { return false; } - // - 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() ); + if ( p.hasNext() ) { return false; } - // - 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() ); + phy = p.next(); + if ( phy != null ) { return false; } // - final String p0000_str = "A"; - p.setSource( p0000_str ); - final Phylogeny p0000 = p.next(); - if ( !p0000.toNewHampshire().equals( "A;" ) ) { - System.out.println( p0000.toNewHampshire() ); + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" ); + if ( !p.hasNext() ) { return false; } - // - p.setSource( "(A)" ); - final Phylogeny p00000 = p.next(); - if ( !p00000.toNewHampshire().equals( "(A);" ) ) { - System.out.println( p00000.toNewHampshire() ); + //0 + phy = p.next(); + if ( phy == null ) { return false; } - // - final String p1_str = "(A,B)(C,D)(E,F)(G,H)"; - p.setSource( p1_str ); - if ( !p.hasNext() ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - final Phylogeny p1_0 = p.next(); - if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) { - System.out.println( p1_0.toNewHampshire() ); + if ( !phy.getName().equals( "tree 0" ) ) { return false; } + //1 if ( !p.hasNext() ) { return false; } - final Phylogeny p1_1 = p.next(); - if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) { - System.out.println( "(C,D) != " + p1_1.toNewHampshire() ); + phy = p.next(); + if ( phy == null ) { return false; } - if ( !p.hasNext() ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - final Phylogeny p1_2 = p.next(); - if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) { - System.out.println( "(E,F) != " + p1_2.toNewHampshire() ); + if ( !phy.getName().equals( "tree 1" ) ) { return false; } + //2 if ( !p.hasNext() ) { return false; } - final Phylogeny p1_3 = p.next(); - if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) { - System.out.println( "(G,H) != " + p1_3.toNewHampshire() ); + phy = p.next(); + if ( phy == null ) { return false; } - if ( p.hasNext() ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { + System.out.println( phy.toString() ); return false; } - if ( p.next() != null ) { + if ( !phy.getName().equals( "" ) ) { return false; } - // - final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)"; - p.setSource( p2_str ); - if ( !p.hasNext() ) { + if ( phy.isRooted() ) { return false; } - Phylogeny p2_0 = p.next(); - if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) { - System.out.println( p2_0.toNewHampshire() ); + //3 + if ( !p.hasNext() ) { return false; } - if ( !p.hasNext() ) { + phy = p.next(); + if ( phy == null ) { return false; } - Phylogeny p2_1 = p.next(); - if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) { - System.out.println( "(C,D) != " + p2_1.toNewHampshire() ); + if ( phy.getNumberOfExternalNodes() != 4 ) { return false; } - if ( !p.hasNext() ) { + if ( !phy.getName().equals( "" ) ) { return false; } - Phylogeny p2_2 = p.next(); - if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) { - System.out.println( "(E,F)root != " + p2_2.toNewHampshire() ); + if ( !phy.isRooted() ) { return false; } + //4 if ( !p.hasNext() ) { return false; } - Phylogeny p2_3 = p.next(); - if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) { - System.out.println( "(G,H) != " + p2_3.toNewHampshire() ); + phy = p.next(); + if ( phy == null ) { return false; } - if ( !p.hasNext() ) { + if ( phy.getNumberOfExternalNodes() != 5 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - Phylogeny p2_4 = p.next(); - if ( !p2_4.toNewHampshire().equals( "(X);" ) ) { - System.out.println( "(X) != " + p2_4.toNewHampshire() ); + if ( !phy.getName().equals( "" ) ) { return false; } - if ( p.hasNext() ) { + if ( !phy.isRooted() ) { return false; } - if ( p.next() != null ) { + //5 + if ( !p.hasNext() ) { return false; } - //// - p.reset(); - if ( !p.hasNext() ) { + phy = p.next(); + if ( phy == null ) { return false; } - p2_0 = p.next(); - if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) { - System.out.println( p2_0.toNewHampshire() ); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !p.hasNext() ) { + if ( !phy.getName().equals( "" ) ) { return false; } - p2_1 = p.next(); - if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) { - System.out.println( "(C,D) != " + p2_1.toNewHampshire() ); + if ( phy.isRooted() ) { return false; } + //6 if ( !p.hasNext() ) { return false; } - p2_2 = p.next(); - if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) { - System.out.println( "(E,F)root != " + p2_2.toNewHampshire() ); + phy = p.next(); + if ( phy == null ) { return false; } - if ( !p.hasNext() ) { + if ( phy.getNumberOfExternalNodes() != 2 ) { return false; } - p2_3 = p.next(); - if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) { - System.out.println( "(G,H) != " + p2_3.toNewHampshire() ); + if ( !phy.getName().equals( "" ) ) { return false; } + if ( !phy.isRooted() ) { + return false; + } + //7 if ( !p.hasNext() ) { return false; } - p2_4 = p.next(); - if ( !p2_4.toNewHampshire().equals( "(X);" ) ) { - System.out.println( "(X) != " + p2_4.toNewHampshire() ); + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.hasNext() ) { + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { return false; } - if ( p.next() != null ) { + if ( !phy.isRooted() ) { return false; } - // - final String p3_str = "((A,B),C)abc"; - p.setSource( p3_str ); + //8 if ( !p.hasNext() ) { return false; } - final Phylogeny p3_0 = p.next(); - if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.hasNext() ) { + if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) { return false; } - if ( p.next() != null ) { + if ( !phy.getName().equals( "tree 8" ) ) { return false; } - // - final String p4_str = "((A,B)ab,C)abc"; - p.setSource( p4_str ); + //9 if ( !p.hasNext() ) { return false; } - final Phylogeny p4_0 = p.next(); - if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.hasNext() ) { + if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) { return false; } - if ( p.next() != null ) { + if ( !phy.getName().equals( "tree 9" ) ) { return false; } - // - final String p5_str = "(((A,B)ab,C)abc,D)abcd"; - p.setSource( p5_str ); + //10 if ( !p.hasNext() ) { return false; } - final Phylogeny p5_0 = p.next(); - if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.hasNext() ) { + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { return false; } - if ( p.next() != null ) { + if ( !phy.getName().equals( "tree 10" ) ) { return false; } - // - final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; - p.setSource( p6_str ); + if ( !phy.isRooted() ) { + return false; + } + //11 if ( !p.hasNext() ) { return false; } - Phylogeny p6_0 = p.next(); - if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.hasNext() ) { + if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) { return false; } - if ( p.next() != null ) { + if ( !phy.getName().equals( "tree 11" ) ) { return false; } - p.reset(); - if ( !p.hasNext() ) { + if ( phy.isRooted() ) { return false; } - p6_0 = p.next(); - if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { + //12 + if ( !p.hasNext() ) { return false; } - if ( p.hasNext() ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.next() != null ) { + if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) { return false; } - // - final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde"; - p.setSource( p7_str ); + if ( !phy.getName().equals( "tree 12" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //13 if ( !p.hasNext() ) { return false; } - Phylogeny p7_0 = p.next(); - if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( p.hasNext() ) { + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { return false; } - if ( p.next() != null ) { + if ( !phy.getName().equals( "tree 13" ) ) { return false; } - p.reset(); - if ( !p.hasNext() ) { + if ( !phy.isRooted() ) { return false; } - p7_0 = p.next(); - if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + //14 + if ( !p.hasNext() ) { return false; } - if ( p.hasNext() ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( p.next() != null ) { + 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; } - // - 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() ) { + if ( !phy.getName().equals( "tree 14" ) ) { return false; } - Phylogeny p8_0 = p.next(); - if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + if ( !phy.isRooted() ) { return false; } + //15 if ( !p.hasNext() ) { return false; } - if ( !p.hasNext() ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - Phylogeny p8_1 = p.next(); - if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { + 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 ( p.hasNext() ) { + if ( !phy.getName().equals( "tree 15" ) ) { return false; } - if ( p.next() != null ) { + if ( phy.isRooted() ) { return false; } - p.reset(); + //16 if ( !p.hasNext() ) { return false; } - p8_0 = p.next(); - if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !p.hasNext() ) { + 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; } - p8_1 = p.next(); - if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { + if ( !phy.getName().equals( "tree 16" ) ) { return false; } - if ( p.hasNext() ) { + if ( !phy.isRooted() ) { return false; } - if ( p.next() != null ) { + //17 + if ( !p.hasNext() ) { return false; } - p.reset(); - // - p.setSource( "" ); - if ( p.hasNext() ) { + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - // - p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) ); - if ( !p.hasNext() ) { + 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; } - 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 ); + if ( !phy.getName().equals( "tree 17" ) ) { return false; } + if ( phy.isRooted() ) { + return false; + } + // if ( p.hasNext() ) { return false; } - if ( p.next() != null ) { + phy = p.next(); + if ( phy != null ) { return false; } p.reset(); + //0 if ( !p.hasNext() ) { return false; } - p_27 = p.next(); - if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { - System.out.println( p_27.toNewHampshireX() ); - System.exit( -1 ); + phy = p.next(); + if ( phy == null ) { return false; } - if ( p.hasNext() ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( p.next() != null ) { + if ( !phy.getName().equals( "tree 0" ) ) { return false; } - } - 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( "" ) ) { + //1 + if ( !p.hasNext() ) { return false; } - if ( !n2.toNewHampshireX().equals( "" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !n3.toNewHampshireX().equals( "n3" ) ) { + if ( phy.getNumberOfExternalNodes() != 10 ) { return false; } - if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) { + if ( !phy.getName().equals( "tree 1" ) ) { return false; } - if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) { + //2 + if ( !p.hasNext() ) { return false; } - if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) { - System.out.println( n6.toNewHampshireX() ); + phy = p.next(); + if ( phy == null ) { 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 ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( n3.isDuplication() ) { + if ( phy.isRooted() ) { return false; } - if ( n3.isHasAssignedEvent() ) { + //3 + if ( !p.hasNext() ) { return false; } - if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !n4.getName().equals( "n4" ) ) { + if ( phy.getNumberOfExternalNodes() != 4 ) { return false; } - if ( n4.getDistanceToParent() != 0.01 ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !n5.getName().equals( "n5" ) ) { + if ( !phy.isRooted() ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) { + //4 + if ( !p.hasNext() ) { return false; } - if ( n5.getDistanceToParent() != 0.1 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) { + if ( phy.getNumberOfExternalNodes() != 5 ) { + System.out.println( phy.getNumberOfExternalNodes() ); return false; } - if ( !n5.isDuplication() ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !n5.isHasAssignedEvent() ) { + if ( !phy.isRooted() ) { return false; } - 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" ) ) { + //5 + if ( !p.hasNext() ) { return false; } - if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) { + phy = p.next(); + if ( phy == null ) { return false; } - 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" ) ) { + if ( phy.getNumberOfExternalNodes() != 3 ) { return false; } - if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n10.getName().equals( "n10.ECOLI" ) ) { + if ( phy.isRooted() ) { return false; } - final PhylogenyNode n20 = PhylogenyNode - .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) { + // + final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser(); + p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" ); + // 0 + if ( !p2.hasNext() ) { return false; } - if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) { + phy = p2.next(); + if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) { return false; } - final PhylogenyNode n20x = PhylogenyNode - .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) { + if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) { + // 1 + if ( !p2.hasNext() ) { return false; } - final PhylogenyNode n20xx = PhylogenyNode - .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) { + phy = p2.next(); + // 2 + if ( !p2.hasNext() ) { return false; } - if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) { + phy = p2.next(); + // 3 + if ( !p2.hasNext() ) { return false; } - final PhylogenyNode n20xxx = PhylogenyNode - .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) { + phy = p2.next(); + // 4 + if ( !p2.hasNext() ) { return false; } - if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) { + phy = p2.next(); + // 5 + if ( !p2.hasNext() ) { return false; } - final PhylogenyNode n20xxxx = PhylogenyNode - .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) { + phy = p2.next(); + // 6 + if ( !p2.hasNext() ) { return false; } - if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) { + phy = p2.next(); + // 7 + if ( !p2.hasNext() ) { return false; } - final PhylogenyNode n21 = PhylogenyNode - .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n21.getName().equals( "N21_PIG" ) ) { + phy = p2.next(); + // 8 + if ( !p2.hasNext() ) { return false; } - if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) { + phy = p2.next(); + if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) { return false; } - final PhylogenyNode n21x = PhylogenyNode - .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n21x.getName().equals( "n21_PIG" ) ) { + if ( p2.hasNext() ) { return false; } - if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) { + phy = p2.next(); + if ( phy != null ) { return false; } - final PhylogenyNode n22 = PhylogenyNode - .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n22.getName().equals( "n22/PIG" ) ) { - return false; - } - if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) { - return false; - } - final PhylogenyNode n23 = PhylogenyNode - .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n23.getName().equals( "n23/PIG_1" ) ) { - return false; - } - if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) { - return false; - } - 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; - } - if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) { - return false; - } - 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.getSpecies( c1 ).equals( "BOVIN" ) ) { - return false; - } - 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" ) ) { + // 0 + p2.reset(); + if ( !p2.hasNext() ) { return false; } - if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) { + phy = p2.next(); + if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) { return false; } - final PhylogenyNode e3 = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !e3.getName().equals( "n10_RAT~" ) ) { + if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNexusTreeParsingTranslating() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); + Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser ); + if ( phylogenies.length != 1 ) { return false; } - 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" ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( n11.getDistanceToParent() != 0.4 ) { + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - final PhylogenyNode n12 = PhylogenyNode - .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - if ( n12.getDistanceToParent() != 0.4 ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser ); + if ( phylogenies.length != 3 ) { return false; } - final PhylogenyNode o = PhylogenyNode - .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !o.getName().equals( "ABCD_MOUSE" ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) { + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { return false; } - if ( n1.getName().compareTo( "" ) != 0 ) { + if ( phylogenies[ 0 ].isRooted() ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - if ( n2.getName().compareTo( "" ) != 0 ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { 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" ) ) { + if ( phylogenies[ 1 ].isRooted() ) { return false; } - if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { 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 ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { 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" ) ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) { + if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { return false; } - if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { + if ( !phylogenies[ 2 ].isRooted() ) { 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" ) ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - final PhylogenyNode n15 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked[123]", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n15.getName().equals( "something_wicked" ) ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( n15.getBranchData().getNumberOfConfidences() != 1 ) { + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser ); + if ( phylogenies.length != 3 ) { return false; } - if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) { + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { return false; } - final PhylogenyNode n16 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked2[9]", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n16.getName().equals( "something_wicked2" ) ) { + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { return false; } - if ( n16.getBranchData().getNumberOfConfidences() != 1 ) { + if ( phylogenies[ 0 ].isRooted() ) { return false; } - if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - final PhylogenyNode n17 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked3[a]", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !n17.getName().equals( "something_wicked3" ) ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - if ( n17.getBranchData().getNumberOfConfidences() != 0 ) { + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - final PhylogenyNode n18 = PhylogenyNode - .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) { + if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) { return false; } - if ( n18.getBranchData().getNumberOfConfidences() != 1 ) { + if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) { return false; } - if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) { + if ( phylogenies[ 1 ].isRooted() ) { return false; } - final PhylogenyNode n19 = PhylogenyNode - .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - final PhylogenyNode n30 = PhylogenyNode - .createInstanceFromNhxString( "blah_1234567-roejojoej", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) { + if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { + if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) { return false; } - final PhylogenyNode n31 = PhylogenyNode - .createInstanceFromNhxString( "blah_12345678-roejojoej", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n31.getNodeData().isHasTaxonomy() ) { + if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) { return false; } - final PhylogenyNode n32 = PhylogenyNode - .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n32.getNodeData().isHasTaxonomy() ) { + if ( !phylogenies[ 2 ].isRooted() ) { return false; } - final PhylogenyNode n40 = PhylogenyNode - .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { return false; } - final PhylogenyNode n41 = PhylogenyNode - .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n41.getNodeData().isHasTaxonomy() ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { return false; } - final PhylogenyNode n42 = PhylogenyNode - .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - if ( n42.getNodeData().isHasTaxonomy() ) { + if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { return false; } - final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345", - NHXParser.TAXONOMY_EXTRACTION.NO ); - if ( n43.getNodeData().isHasTaxonomy() ) { + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser ); + if ( phylogenies.length != 3 ) { return false; } - final PhylogenyNode n44 = PhylogenyNode - .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n44.getNodeData().isHasTaxonomy() ) { + if ( !isEqual( phylogenies[ 2 ].getNode( "Aloysia lycioides 251-76-02169" ).getDistanceToParent(), + 0.00100049 ) ) { return false; } } @@ -8233,809 +8527,873 @@ public final class Test { return true; } - private static boolean testNHXParsing() { + private static boolean testNHParsing() { 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 ) ) { + final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ]; + if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) { 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" ) ) { + 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; } - 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 ) ) { + if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( "B B" ) ) { 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 ) ) { + final Phylogeny p1b = factory + .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ", + new NHXParser() )[ 0 ]; + if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) { return false; } - 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 ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) { 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 ) ) { + final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ).toString(), new NHXParser() )[ 0 ]; + final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ]; + final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ]; + final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ).toString(), new NHXParser() )[ 0 ]; + final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() ); + final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() ); + final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() ); + 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; } - 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 ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) { 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 ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) { 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 ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) { 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]" ) ) { + 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; } - } - 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 ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) { return false; } - if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) { + final String p17_S = "(C,(A,B))"; + final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() ); + if ( p17.length != 1 ) { return false; } - if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(), - 0.1100000000000000e+00 ) ) { + if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) { return false; } - if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) { + final String p18_S = "((A,B),(C,D))"; + final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() ); + if ( p18.length != 1 ) { return false; } - if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) { + if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) { 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 ) { + final String p19_S = "(((A,B),C),D)"; + final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() ); + if ( p19.length != 1 ) { return false; } - if ( p2.getNode( "2" ) == null ) { + if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) { 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 ) { + final String p20_S = "(A,(B,(C,D)))"; + final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() ); + if ( p20.length != 1 ) { return false; } - final Phylogeny phy = phylogenies_0[ 4 ]; - if ( phy.getNumberOfExternalNodes() != 7 ) { + if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) { return false; } - if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) { + 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 ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) { + if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) { return false; } - if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy() - .getScientificName().equals( "hsapiens" ) ) { + 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 ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) { + if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) { return false; } - if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) { + 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 ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) { + if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) { return false; } - if ( phy.getNodes( "noquotes" ).size() != 1 ) { + 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 ( phy.getNodes( "A ( B C '" ).size() != 1 ) { + if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) { 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);" ) ) { + 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; } - final NHXParser p2p = new NHXParser(); - p1p.setIgnoreQuotes( false ); - final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ]; - if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) { + if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) { 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 ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) { 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');" ) ) { + final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)" + + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D," + + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)" + + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde," + + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd," + + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)" + + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde" + + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde"; + final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() ); + if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) { return false; } - final 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 ) ) { + final String p26_S = "(A,B)ab"; + final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() ); + if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) { return false; } - final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ]; - if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) { + 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; } - // - 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 ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) { + System.out.println( p27s[ 0 ].toNewHampshireX() ); + System.exit( -1 ); return false; } - final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ]; - if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) { + 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; } - 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 ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) { + System.out.println( p27[ 0 ].toNewHampshireX() ); + System.exit( -1 ); return false; } - final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ]; - if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) { + 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; } - } - 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);" ) ) { + if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) { 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);" ) ) { + if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) { 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);" ) ) { + if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) { 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 ) ) { + if ( p28.length != 4 ) { return false; } - if ( !a1b1.equals( b1a1 ) ) { + 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; } - if ( !b1a1.equals( a1b1 ) ) { + final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72"; + final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() ); + if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) { return false; } - final 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 ) ) { + final String p32_S = " ; ; \n \t \b \f \r ;;;;;; "; + final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() ); + if ( ( p32.length != 0 ) ) { return false; } - if ( a1_b1.equals( a1_b1_ ) ) { + final String p33_S = "A"; + final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() ); + if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) { return false; } - final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false ); - if ( !a1_b1.equals( b1_a1_ ) ) { + final String p34_S = "B;"; + final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() ); + if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) { return false; } - if ( a1_b1_.equals( b1_a1_ ) ) { + 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 ( !a1_b1_.equals( b1_a1 ) ) { + final String p36_S = "(A)"; + final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() ); + if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) { 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 = new PhyloXmlParser(); - 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() ); + final String p37_S = "((A))"; + final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() ); + if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) { return false; } - if ( phylogenies_0.length != 1 ) { + final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8"; + final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() ); + if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) { return false; } - final Phylogeny t1 = phylogenies_0[ 0 ]; - PhylogenyNode n = null; - Distribution d = null; - n = t1.getNode( "root node" ); - if ( !n.getNodeData().isHasDistribution() ) { + 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 ( n.getNodeData().getDistributions().size() != 1 ) { + 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; } - d = n.getNodeData().getDistribution(); - if ( !d.getDesc().equals( "Hirschweg 38" ) ) { + 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 ( d.getPoints().size() != 1 ) { + 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; } - if ( d.getPolygons() != null ) { + 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 ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) { + 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; } - if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + 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 ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + final String p46_S = ""; + final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() ); + if ( p46.length != 0 ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) { + final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ).toString(), new NHXParser() )[ 0 ]; + if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) { + final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; + if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - n = t1.getNode( "node a" ); - if ( !n.getNodeData().isHasDistribution() ) { + final Phylogeny p49 = factory + .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ).toString(), + new NHXParser() )[ 0 ]; + if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - if ( n.getNodeData().getDistributions().size() != 2 ) { + final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; + if ( p50.getNode( "A" ) == null ) { return false; } - d = n.getNodeData().getDistribution( 1 ); - if ( !d.getDesc().equals( "San Diego" ) ) { + if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) + .equals( "((A,B)ab:2.0[88],C);" ) ) { return false; } - if ( d.getPoints().size() != 1 ) { + if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) { return false; } - if ( d.getPolygons() != null ) { + if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ) + .equals( "((A,B)88:2.0,C);" ) ) { return false; } - if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) { + final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; + if ( p51.getNode( "A(A" ) == null ) { return false; } - if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; + if ( p52.getNode( "A(A" ) == null ) { return false; } - if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + final Phylogeny p53 = factory + .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ).toString(), + new NHXParser() )[ 0 ]; + if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) { + final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ).toString(), new NHXParser() )[ 0 ]; + if ( p54.getNode( "A" ) == null ) { return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) { + if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) { return false; } - n = t1.getNode( "node bb" ); - if ( !n.getNodeData().isHasDistribution() ) { + final Phylogeny p55 = factory + .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ).toString(), + new NHXParser() )[ 0 ]; + if ( !p55 + .toNewHampshire() + .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,lcl|HPV66_L1.1x:0.0798012);" ) ) { + System.out.println( p55.toNewHampshire() ); return false; } - if ( n.getNodeData().getDistributions().size() != 1 ) { + final Phylogeny p56 = factory + .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ).toString(), + new NHXParser() )[ 0 ]; + if ( !p56 + .toNewHampshire() + .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) { + System.out.println( p56.toNewHampshire() ); return false; } - d = n.getNodeData().getDistribution( 0 ); - if ( d.getPoints().size() != 3 ) { + final Phylogeny p57 = factory + .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ).toString(), + new NHXParser() )[ 0 ]; + if ( !p57 + .toNewHampshire() + .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) { + System.out.println( p56.toNewHampshire() ); return false; } - if ( d.getPolygons().size() != 2 ) { + final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';"; + final Phylogeny p58 = factory.create( s58, new NHXParser() )[ 0 ]; + if ( !p58.toNewHampshire().equals( s58 ) ) { + System.out.println( p58.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) { + final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";"; + final Phylogeny p59 = factory.create( s59 , new NHXParser() )[ 0 ]; + if ( !p59.toNewHampshire().equals( s59 ) ) { + System.out.println( p59.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) { + final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');"; + final Phylogeny p60 = factory.create( s60, new NHXParser() )[ 0 ]; + if ( !p60.toNewHampshire().equals( s60 ) ) { + System.out.println( p60.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) { + final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';"; + final Phylogeny p61 = factory.create( s61, new NHXParser() )[ 0 ]; + if ( !p61.toNewHampshire() + .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) { + System.out.println( p61.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNHParsingSpecialChars() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final String i0 = "(A!+=~QWERTY!@#$%^&*-,€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ)"; + final Phylogeny p0 = factory.create( i0, new NHXParser() )[ 0 ]; + if ( !p0.toNewHampshireX().equals( i0 ) ) { + System.out.println(); + System.out.println( p0.toNewHampshireX() ); + System.out.println( i0 ); return false; } - if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) { + final String i1 = "(हिंदी,한글,ไทย,'Tiếng Việt',ひらがなカタカナ漢字,繁體字,русский)"; + final Phylogeny p1 = factory.create( i1, new NHXParser() )[ 0 ]; + if ( !p1.toNewHampshireX().equals( i1 ) ) { + System.out.println(); + System.out.println( p1.toNewHampshireX() ); + System.out.println( i1 ); return false; } - if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) { + } + 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; } - Polygon p = d.getPolygons().get( 0 ); - if ( p.getPoints().size() != 3 ) { + final Phylogeny p0 = p.next(); + if ( !p0.toNewHampshire().equals( p0_str ) ) { + System.out.println( p0.toNewHampshire() ); return false; } - if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) { + if ( p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) { + if ( p.next() != null ) { return false; } - if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + // + 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; } - if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) { + // + 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 ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) { + // + 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 ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) { + // + p.setSource( "(A)" ); + final Phylogeny p00000 = p.next(); + if ( !p00000.toNewHampshire().equals( "(A);" ) ) { + System.out.println( p00000.toNewHampshire() ); return false; } - p = d.getPolygons().get( 1 ); - if ( p.getPoints().size() != 3 ) { + // + final String p1_str = "(A,B)(C,D)(E,F)(G,H)"; + p.setSource( p1_str ); + if ( !p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) { + final Phylogeny p1_0 = p.next(); + if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) { + System.out.println( p1_0.toNewHampshire() ); return false; } - if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) { + if ( !p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + final Phylogeny p1_1 = p.next(); + if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( "(C,D) != " + p1_1.toNewHampshire() ); 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 ) { + if ( !p.hasNext() ) { return false; } - final Phylogeny t1_rt = rt[ 0 ]; - n = t1_rt.getNode( "root node" ); - if ( !n.getNodeData().isHasDistribution() ) { + final Phylogeny p1_2 = p.next(); + if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) { + System.out.println( "(E,F) != " + p1_2.toNewHampshire() ); return false; } - if ( n.getNodeData().getDistributions().size() != 1 ) { + if ( !p.hasNext() ) { return false; } - d = n.getNodeData().getDistribution(); - if ( !d.getDesc().equals( "Hirschweg 38" ) ) { + final Phylogeny p1_3 = p.next(); + if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) { + System.out.println( "(G,H) != " + p1_3.toNewHampshire() ); return false; } - if ( d.getPoints().size() != 1 ) { + if ( p.hasNext() ) { return false; } - if ( d.getPolygons() != null ) { + if ( p.next() != null ) { return false; } - if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) { + // + 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 ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + Phylogeny p2_0 = p.next(); + if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) { + System.out.println( p2_0.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) { + Phylogeny p2_1 = p.next(); + if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( "(C,D) != " + p2_1.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) { + if ( !p.hasNext() ) { return false; } - n = t1_rt.getNode( "node a" ); - if ( !n.getNodeData().isHasDistribution() ) { + 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 ( n.getNodeData().getDistributions().size() != 2 ) { + if ( !p.hasNext() ) { return false; } - d = n.getNodeData().getDistribution( 1 ); - if ( !d.getDesc().equals( "San Diego" ) ) { + Phylogeny p2_3 = p.next(); + if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) { + System.out.println( "(G,H) != " + p2_3.toNewHampshire() ); return false; } - if ( d.getPoints().size() != 1 ) { + if ( !p.hasNext() ) { return false; } - if ( d.getPolygons() != null ) { + Phylogeny p2_4 = p.next(); + if ( !p2_4.toNewHampshire().equals( "(X);" ) ) { + System.out.println( "(X) != " + p2_4.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) { + if ( p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { + if ( p.next() != null ) { return false; } - if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { + //// + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) { + p2_0 = p.next(); + if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) { + System.out.println( p2_0.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) { + if ( !p.hasNext() ) { return false; } - n = t1_rt.getNode( "node bb" ); - if ( !n.getNodeData().isHasDistribution() ) { + p2_1 = p.next(); + if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( "(C,D) != " + p2_1.toNewHampshire() ); return false; } - if ( n.getNodeData().getDistributions().size() != 1 ) { + if ( !p.hasNext() ) { return false; } - d = n.getNodeData().getDistribution( 0 ); - if ( d.getPoints().size() != 3 ) { + p2_2 = p.next(); + if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) { + System.out.println( "(E,F)root != " + p2_2.toNewHampshire() ); return false; } - if ( d.getPolygons().size() != 2 ) { + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) { + p2_3 = p.next(); + if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) { + System.out.println( "(G,H) != " + p2_3.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) { + if ( !p.hasNext() ) { return false; } - if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) { + p2_4 = p.next(); + if ( !p2_4.toNewHampshire().equals( "(X);" ) ) { + System.out.println( "(X) != " + p2_4.toNewHampshire() ); return false; } - if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) { + if ( p.hasNext() ) { return false; } - if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) { + if ( p.next() != null ) { return false; } - if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) { + // + final String p3_str = "((A,B),C)abc"; + p.setSource( p3_str ); + if ( !p.hasNext() ) { return false; } - p = d.getPolygons().get( 0 ); - if ( p.getPoints().size() != 3 ) { + final Phylogeny p3_0 = p.next(); + if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) { return false; } - if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) { + if ( p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) { + if ( p.next() != null ) { return false; } - if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + // + final String p4_str = "((A,B)ab,C)abc"; + p.setSource( p4_str ); + if ( !p.hasNext() ) { return false; } - if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) { + final Phylogeny p4_0 = p.next(); + if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) { return false; } - if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) { + if ( p.hasNext() ) { return false; } - if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) { + if ( p.next() != null ) { return false; } - p = d.getPolygons().get( 1 ); - if ( p.getPoints().size() != 3 ) { + // + final String p5_str = "(((A,B)ab,C)abc,D)abcd"; + p.setSource( p5_str ); + if ( !p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) { + final Phylogeny p5_0 = p.next(); + if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) { return false; } - if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) { + if ( p.hasNext() ) { return false; } - if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { + if ( p.next() != null ) { 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(); + // + final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + p.setSource( p6_str ); + if ( !p.hasNext() ) { + return false; } - for( it0.reset(); it0.hasNext(); ) { - it0.next(); + Phylogeny p6_0 = p.next(); + if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { + 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 ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "B" ) ) { + if ( p.next() != null ) { return false; } - if ( !it.next().getName().equals( "ab" ) ) { + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "C" ) ) { + p6_0 = p.next(); + if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { return false; } - if ( !it.next().getName().equals( "D" ) ) { + if ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "cd" ) ) { + if ( p.next() != null ) { return false; } - if ( !it.next().getName().equals( "abcd" ) ) { + // + final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + p.setSource( p7_str ); + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "E" ) ) { + Phylogeny p7_0 = p.next(); + if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { return false; } - if ( !it.next().getName().equals( "F" ) ) { + if ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "ef" ) ) { + if ( p.next() != null ) { return false; } - if ( !it.next().getName().equals( "G" ) ) { + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "H" ) ) { + p7_0 = p.next(); + if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { return false; } - if ( !it.next().getName().equals( "gh" ) ) { + if ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "efgh" ) ) { + if ( p.next() != null ) { return false; } - if ( !it.next().getName().equals( "r" ) ) { + // + 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; } - if ( it.hasNext() ) { + Phylogeny p8_0 = p.next(); + if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { 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 ( !p.hasNext() ) { + return false; } - for( it0.reset(); it0.hasNext(); ) { - it0.next(); + if ( !p.hasNext() ) { + return false; } - PhylogenyNodeIterator it = t0.iteratorPreorder(); - if ( !it.next().getName().equals( "r" ) ) { + Phylogeny p8_1 = p.next(); + if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { return false; } - if ( !it.next().getName().equals( "ab" ) ) { + if ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "A" ) ) { + if ( p.next() != null ) { return false; } - if ( !it.next().getName().equals( "B" ) ) { + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "cd" ) ) { + p8_0 = p.next(); + if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { return false; } - if ( !it.next().getName().equals( "C" ) ) { + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "D" ) ) { + p8_1 = p.next(); + if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { return false; } - if ( it.hasNext() ) { + if ( p.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" ) ) { + if ( p.next() != null ) { return false; } - if ( !it.next().getName().equals( "abcd" ) ) { + p.reset(); + // + p.setSource( "" ); + if ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "ab" ) ) { + // + p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) ); + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "A" ) ) { + Phylogeny p_27 = p.next(); + if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { + System.out.println( p_27.toNewHampshireX() ); + System.exit( -1 ); return false; } - if ( !it.next().getName().equals( "B" ) ) { + if ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "cd" ) ) { + if ( p.next() != null ) { return false; } - if ( !it.next().getName().equals( "C" ) ) { + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "D" ) ) { + p_27 = p.next(); + if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { + System.out.println( p_27.toNewHampshireX() ); + System.exit( -1 ); return false; } - if ( !it.next().getName().equals( "efgh" ) ) { + if ( p.hasNext() ) { return false; } - if ( !it.next().getName().equals( "ef" ) ) { + if ( p.next() != null ) { return false; } - if ( !it.next().getName().equals( "E" ) ) { + // + final String p30_str = "(A,B);(C,D)"; + final NHXParser p30 = new NHXParser(); + p30.setSource( p30_str ); + if ( !p30.hasNext() ) { return false; } - if ( !it.next().getName().equals( "F" ) ) { + Phylogeny phy30 = p30.next(); + if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) { + System.out.println( phy30.toNewHampshire() ); return false; } - if ( !it.next().getName().equals( "gh" ) ) { + if ( !p30.hasNext() ) { return false; } - if ( !it.next().getName().equals( "G" ) ) { + Phylogeny phy301 = p30.next(); + if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( phy301.toNewHampshire() ); return false; } - if ( !it.next().getName().equals( "H" ) ) { + if ( p30.hasNext() ) { return false; } - if ( it.hasNext() ) { + if ( p30.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" ) ) { + if ( p30.next() != null ) { return false; } - if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) { + if ( p30.next() != null ) { return false; } - if ( pm.getProperties().size() != 3 ) { + p30.reset(); + if ( !p30.hasNext() ) { return false; } - if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) { + phy30 = p30.next(); + if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) { + System.out.println( phy30.toNewHampshire() ); return false; } - if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) { + if ( !p30.hasNext() ) { return false; } - if ( pm.getProperties().size() != 3 ) { + phy301 = p30.next(); + if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) { + System.out.println( phy301.toNewHampshire() ); return false; } - pm.removeProperty( "dimensions:diameter" ); - if ( pm.getProperties().size() != 2 ) { + if ( p30.hasNext() ) { return false; } - if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) { + if ( p30.hasNext() ) { return false; } - if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) { + if ( p30.next() != null ) { + return false; + } + if ( p30.next() != null ) { return false; } } @@ -9046,59 +9404,41 @@ public final class Test { return true; } - private static boolean testProteinId() { + private static boolean testNHXconversion() { 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 ) { + 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; } - if ( id1.compareTo( id3 ) != 0 ) { + if ( !n2.toNewHampshireX().equals( "" ) ) { return false; } - if ( id1.compareTo( id4 ) >= 0 ) { + if ( !n3.toNewHampshireX().equals( "n3" ) ) { return false; } - if ( id4.compareTo( id1 ) <= 0 ) { + if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) { return false; } - if ( !id4.getId().equals( "b" ) ) { + if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) { return false; } - final ProteinId id5 = new ProteinId( " C " ); - if ( !id5.getId().equals( "C" ) ) { + if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) { + System.out.println( n6.toNewHampshireX() ); return false; } - if ( id5.equals( id1 ) ) { + final PhylogenyNode n7 = new PhylogenyNode(); + n7.setName( " gks:dr-m4 \" ' `@:[]sadq04 " ); + if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) + .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) { + System.out.println( n7 + .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) ); return false; } } @@ -9109,1489 +9449,2697 @@ public final class Test { return true; } - private static boolean testReIdMethods() { + private static boolean testNHXNodeParsing() { 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 ) { + 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; } - if ( p.getNode( "A" ).getId() != ( count + 1 ) ) { + if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { return false; } - if ( p.getNode( "B" ).getId() != ( count + 1 ) ) { + if ( n3.isDuplication() ) { return false; } - if ( p.getNode( "C" ).getId() != ( count + 1 ) ) { + if ( n3.isHasAssignedEvent() ) { return false; } - if ( p.getNode( "1" ).getId() != ( count + 2 ) ) { + if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) { return false; } - if ( p.getNode( "2" ).getId() != ( count + 2 ) ) { + if ( !n4.getName().equals( "n4" ) ) { return false; } - if ( p.getNode( "3" ).getId() != ( count + 2 ) ) { + if ( n4.getDistanceToParent() != 0.01 ) { return false; } - if ( p.getNode( "4" ).getId() != ( count + 2 ) ) { + if ( !n5.getName().equals( "n5" ) ) { return false; } - if ( p.getNode( "5" ).getId() != ( count + 2 ) ) { + if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) { return false; } - if ( p.getNode( "6" ).getId() != ( count + 2 ) ) { + if ( n5.getDistanceToParent() != 0.1 ) { return false; } - if ( p.getNode( "a" ).getId() != ( count + 3 ) ) { + if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) { return false; } - if ( p.getNode( "b" ).getId() != ( count + 3 ) ) { + if ( !n5.isDuplication() ) { return false; } - if ( p.getNode( "X" ).getId() != ( count + 4 ) ) { + if ( !n5.isHasAssignedEvent() ) { return false; } - if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) { + 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; } - if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) { + if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) { 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() ) { + 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; } - 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 ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) { return false; } - if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) { + final PhylogenyNode n10 = PhylogenyNode + .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n10.getName().equals( "n10.ECOLI" ) ) { return false; } - if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) { + 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; } - if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { + if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) { return false; } - if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) { + 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; } - if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) { + if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) { 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 ) ) { + 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; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) { return false; } - t2.reRoot( t2.getNode( "ABC" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + 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; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) { return false; } - t2.reRoot( t2.getNode( "AB" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + 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; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) { return false; } - if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + final PhylogenyNode n21 = PhylogenyNode + .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n21.getName().equals( "N21_PIG" ) ) { return false; } - t2.reRoot( t2.getNode( "AB" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + final PhylogenyNode n21x = PhylogenyNode + .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n21x.getName().equals( "n21_PIG" ) ) { return false; } - if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) { return false; } - t2.reRoot( t2.getNode( "D" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + final PhylogenyNode n22 = PhylogenyNode + .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n22.getName().equals( "n22/PIG" ) ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) { return false; } - t2.reRoot( t2.getNode( "ABC" ) ); - if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) { + final PhylogenyNode n23 = PhylogenyNode + .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n23.getName().equals( "n23/PIG_1" ) ) { return false; } - if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) { + if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) { 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; + 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; } - if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) { return false; } - if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 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; } - t3.reRoot( t3.getNode( "B" ) ); - if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) { + if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { return false; } - if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + 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 ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) { + if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) { return false; } - t3.reRoot( t3.getRoot() ); - if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) { + final PhylogenyNode e3 = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !e3.getName().equals( "n10_RAT~" ) ) { return false; } - if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) { + if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) { return false; } - if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) { + 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; } - } - 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() ) { + if ( n11.getDistanceToParent() != 0.4 ) { 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 ) { + if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) { return false; } - if ( !gene2.getNode( "ab" ).isSpeciation() ) { + 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; } - if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) { + if ( n12.getDistanceToParent() != 0.4 ) { return false; } - if ( !gene2.getNode( "abc" ).isSpeciation() ) { + if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) { return false; } - if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) { + final PhylogenyNode o = PhylogenyNode + .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !o.getName().equals( "ABCD_MOUSE" ) ) { return false; } - if ( !gene2.getNode( "r" ).isSpeciation() ) { + if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) { return false; } - if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) { + if ( n1.getName().compareTo( "" ) != 0 ) { 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 ) { + if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { return false; } - if ( !gene3.getNode( "aa" ).isDuplication() ) { + if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { return false; } - if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) { + if ( n2.getName().compareTo( "" ) != 0 ) { 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 ) { + if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { return false; } - if ( !gene4.getNode( "ac" ).isSpeciation() ) { + if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { return false; } - if ( !gene4.getNode( "abc" ).isDuplication() ) { + 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 ( gene4.getNode( "abcd" ).isDuplication() ) { + if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) { return false; } - if ( species4.getNumberOfExternalNodes() != 6 ) { + final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" ); + if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) { return false; } - if ( gene4.getNumberOfExternalNodes() != 6 ) { + 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; } - 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 ) { + if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) { return false; } - if ( !gene5.getNode( "ad" ).isSpeciation() ) { + if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { return false; } - if ( !gene5.getNode( "adc" ).isDuplication() ) { + if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { return false; } - if ( !gene5.getNode( "abcd" ).isDuplication() ) { + 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 ( species5.getNumberOfExternalNodes() != 6 ) { + if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) { return false; } - if ( gene5.getNumberOfExternalNodes() != 6 ) { + final PhylogenyNode n15 = PhylogenyNode + .createInstanceFromNhxString( "something_wicked[123]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n15.getName().equals( "something_wicked" ) ) { 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 ) { + if ( n15.getBranchData().getNumberOfConfidences() != 1 ) { return false; } - if ( !gene6.getNode( "r" ).isDuplication() ) { + if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) { return false; } - if ( !gene6.getNode( "4-5-6" ).isDuplication() ) { + final PhylogenyNode n16 = PhylogenyNode + .createInstanceFromNhxString( "something_wicked2[9]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n16.getName().equals( "something_wicked2" ) ) { return false; } - if ( !gene6.getNode( "7-8-9" ).isDuplication() ) { + if ( n16.getBranchData().getNumberOfConfidences() != 1 ) { return false; } - if ( !gene6.getNode( "1-2" ).isSpeciation() ) { + if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) { return false; } - if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) { + final PhylogenyNode n17 = PhylogenyNode + .createInstanceFromNhxString( "something_wicked3[a]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n17.getName().equals( "something_wicked3" ) ) { return false; } - if ( !gene6.getNode( "5-6" ).isSpeciation() ) { + if ( n17.getBranchData().getNumberOfConfidences() != 0 ) { return false; } - if ( !gene6.getNode( "8-9" ).isSpeciation() ) { + final PhylogenyNode n18 = PhylogenyNode + .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) { return false; } - if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) { + if ( n18.getBranchData().getNumberOfConfidences() != 1 ) { return false; } - sdi6.computeMappingCostL(); - if ( sdi6.computeMappingCostL() != 17 ) { + if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) { return false; } - if ( species6.getNumberOfExternalNodes() != 9 ) { + 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 ( gene6.getNumberOfExternalNodes() != 9 ) { + if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { 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 ) { + 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 ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) { + if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) { + final PhylogenyNode n31 = PhylogenyNode + .createInstanceFromNhxString( "BLAH_12345678-roejojoej", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n31.getNodeData().isHasTaxonomy() ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) { + final PhylogenyNode n32 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n32.getNodeData().isHasTaxonomy() ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) { + final PhylogenyNode n40 = PhylogenyNode + .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) { + final PhylogenyNode n41 = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n41.getNodeData().isHasTaxonomy() ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) { + final PhylogenyNode n42 = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( n42.getNodeData().isHasTaxonomy() ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) { + final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345", + NHXParser.TAXONOMY_EXTRACTION.NO ); + if ( n43.getNodeData().isHasTaxonomy() ) { return false; } - if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) { + final PhylogenyNode n44 = PhylogenyNode + .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n44.getNodeData().isHasTaxonomy() ) { 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 ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + + private static boolean testNHXNodeParsing2() { + try { + + final PhylogenyNode n0_0 = PhylogenyNode + .createInstanceFromNhxString( "n0:[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_0.getName().equals( "n0" ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) { + if ( !isEqual( n0_0.getDistanceToParent(), 0.001 ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) { + final PhylogenyNode n0_1 = PhylogenyNode + .createInstanceFromNhxString( "n0[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_1.getName().equals( "n0" ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) { + if ( !isEqual( n0_1.getDistanceToParent(), 0.001 ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) { + final PhylogenyNode n0_2 = PhylogenyNode + .createInstanceFromNhxString( "n0:1E-3[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_2.getName().equals( "n0" ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) { + if ( !isEqual( n0_2.getDistanceToParent(), 0.001 ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) { + final PhylogenyNode n0_3 = PhylogenyNode + .createInstanceFromNhxString( "n0:1E-3:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_3.getName().equals( "n0" ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) { + if ( !isEqual( n0_3.getDistanceToParent(), 0.001 ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) { + final PhylogenyNode n0_4 = PhylogenyNode + .createInstanceFromNhxString( "n0:0.001:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_4.getName().equals( "n0" ) ) { return false; } - if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) { + if ( !isEqual( n0_4.getDistanceToParent(), 0.001 ) ) { 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" ) ) { + final PhylogenyNode n1_0 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_0.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) { - return false; + if ( n1_0.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) { + final PhylogenyNode n1_1 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]:0.001", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_1.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) { - return false; + if ( n1_1.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) { + if ( !isEqual( n1_1.getDistanceToParent(), 0.001 ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) { + final PhylogenyNode n1_2 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:0.001[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_2.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { - return false; + if ( n1_2.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + if ( !isEqual( n1_2.getDistanceToParent(), 0.001 ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + final PhylogenyNode n1_3 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[&boostrap=69,&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_3.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { - return false; + if ( n1_3.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) { + if ( !isEqual( n1_3.getDistanceToParent(), 0.001 ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) { + if ( !isEqual( n1_3.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + if ( !n1_3.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + final PhylogenyNode n1_4 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&bootstrap=69,&!colour=#FFFFFF]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_4.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) { - return false; + if ( n1_4.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; } - if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + if ( !isEqual( n1_4.getDistanceToParent(), 0.001 ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + if ( !isEqual( n1_4.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + if ( !n1_4.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) { + final PhylogenyNode n1_5 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[69.0]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_5.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) { + if ( !isEqual( n1_5.getDistanceToParent(), 0.001 ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) { + if ( !isEqual( n1_5.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + final PhylogenyNode n1_6 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_6.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) { + + if ( !isEqual( n1_6.getDistanceToParent(), 0.001 ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) { + if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.11 ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) { + if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getValue(), 0.95 ) ) { return false; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) { + if ( !n1_6.getBranchData().getConfidence( 0 ).getType().equals( "posterior probability" ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) { + } + 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; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) { + 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; } - if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) { + 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; } - br = iter.next(); - if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) { + 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; } - if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) { + 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; } - if ( iter.hasNext() ) { + 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 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 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; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) { + 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; } - br = iter1.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { + 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; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + 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; } - br = iter1.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + 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; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { + final Phylogeny p11 = factory + .create( " [79] ( ('A: \" ' [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]", + new NHXParser() )[ 0 ]; + if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } - if ( iter1.hasNext() ) { + final Phylogeny p12 = factory.create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]", + new NHXParser() )[ 0 ]; + if ( !p12.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 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" ) ) { + } + 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 ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) { + if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) { return false; } - br = iter2.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) { + if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(), + 0.1100000000000000e+00 ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) { + if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) { return false; } - br = iter2.next(); - if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) { + if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) { return false; } - if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) { + 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 ( iter2.hasNext() ) { + if ( p2.getNode( "2" ) == null ) { 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 ) { + } + 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; } - if ( sdi_unrooted.getMinimalDuplications() != 0 ) { + final Phylogeny phy = phylogenies_0[ 4 ]; + if ( phy.getNumberOfExternalNodes() != 7 ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) { + if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) { + if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) { return false; } - if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy() + .getScientificName().equals( "hsapiens" ) ) { 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 ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) { return false; } - if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + if ( phy.getNodes( "\"double quotes\" inside single quotes" ).size() != 1 ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) { + if ( phy.getNodes( "noquotes" ).size() != 1 ) { return false; } - if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + if ( phy.getNodes( "A ( B C '" ).size() != 1 ) { 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 ) { + 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; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + 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; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + 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; } - if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + 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; } - if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + 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; } - if ( !p6[ 0 ].getRoot().isDuplication() ) { + final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ]; + if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) { return false; } - if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) { + 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; } - if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) { + final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ]; + if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) { return false; } - if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) { + 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; } - if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) { + final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ]; + if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) { return false; } - if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) { + } + 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; } - if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) { + 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; } - if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { + 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; } - 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 ) { + } + 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 ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + if ( !a1b1.equals( b1a1 ) ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + if ( !b1a1.equals( a1b1 ) ) { return false; } - if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + 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 ( sdi_unrooted.getMinimalMappingCost() != 17 ) { + if ( a1_b1.equals( a1_b1_ ) ) { return false; } - if ( !p7[ 0 ].getRoot().isDuplication() ) { + final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false ); + if ( !a1_b1.equals( b1_a1_ ) ) { return false; } - if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) { + if ( a1_b1_.equals( b1_a1_ ) ) { return false; } - if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) { + if ( !a1_b1_.equals( b1_a1 ) ) { return false; } - if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) { + } + 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( new File( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml" ), + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); return false; } - if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) { + if ( phylogenies_0.length != 1 ) { return false; } - if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) { + final Phylogeny t1 = phylogenies_0[ 0 ]; + PhylogenyNode n = null; + Distribution d = null; + n = t1.getNode( "root node" ); + if ( !n.getNodeData().isHasDistribution() ) { return false; } - if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) { + if ( n.getNodeData().getDistributions().size() != 1 ) { return false; } - if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { + d = n.getNodeData().getDistribution(); + if ( !d.getDesc().equals( "Hirschweg 38" ) ) { 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 ) { + if ( d.getPoints().size() != 1 ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) { + if ( d.getPolygons() != null ) { return false; } - if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) { + if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) { return false; } - if ( sdi_unrooted.getMinimalDuplications() != 3 ) { + if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { return false; } - if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) { + if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { return false; } - if ( !p8[ 0 ].getRoot().isDuplication() ) { + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) { return false; } - if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) { + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) { return false; } - if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) { + n = t1.getNode( "node a" ); + if ( !n.getNodeData().isHasDistribution() ) { return false; } - if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) { + if ( n.getNodeData().getDistributions().size() != 2 ) { return false; } - if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) { + d = n.getNodeData().getDistribution( 1 ); + if ( !d.getDesc().equals( "San Diego" ) ) { return false; } - if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) { + if ( d.getPoints().size() != 1 ) { return false; } - if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) { + if ( d.getPolygons() != null ) { return false; } - if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) { + if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) { 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() ); - } + if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { 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() ); - } + if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { 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() ); - } + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) { 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() ); - } + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) { 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() ); - } + n = t1.getNode( "node bb" ); + if ( !n.getNodeData().isHasDistribution() ) { 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() ); - } + if ( n.getNodeData().getDistributions().size() != 1 ) { 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() ); - } + d = n.getNodeData().getDistribution( 0 ); + if ( d.getPoints().size() != 3 ) { 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() ); - } + if ( d.getPolygons().size() != 2 ) { 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() ); - } + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) { 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() ); - } + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) { return false; } - id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" ); - if ( id != null ) { - System.out.println( "value =" + id.getValue() ); - System.out.println( "provider=" + id.getSource() ); + if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSequenceWriter() { - try { - final String n = ForesterUtil.LINE_SEPARATOR; - if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) { + if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) { return false; } - if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) { + if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) { return false; } - if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) { + if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) { return false; } - if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) { + Polygon p = d.getPolygons().get( 0 ); + if ( p.getPoints().size() != 3 ) { return false; } - if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString() - .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) { + if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) { return false; } - if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString() - .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) { + if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) { 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 ) ) { + if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { return false; } - if ( s1.getSpeciesId().equals( "x" ) ) { + if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) { return false; } - if ( s1.getSpeciesId().equals( null ) ) { + if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) { return false; } - if ( !s1.equals( s2 ) ) { + if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) { return false; } - if ( s1.equals( s3 ) ) { + p = d.getPolygons().get( 1 ); + if ( p.getPoints().size() != 3 ) { return false; } - if ( s1.hashCode() != s1.hashCode() ) { + if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) { return false; } - if ( s1.hashCode() != s2.hashCode() ) { + if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) { return false; } - if ( s1.hashCode() == s3.hashCode() ) { + if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) { return false; } - if ( s1.compareTo( s1 ) != 0 ) { + // 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; } - if ( s1.compareTo( s2 ) != 0 ) { + final Phylogeny t1_rt = rt[ 0 ]; + n = t1_rt.getNode( "root node" ); + if ( !n.getNodeData().isHasDistribution() ) { return false; } - if ( s1.compareTo( s3 ) != 0 ) { + if ( n.getNodeData().getDistributions().size() != 1 ) { return false; } - if ( s1.compareTo( s4 ) >= 0 ) { + d = n.getNodeData().getDistribution(); + if ( !d.getDesc().equals( "Hirschweg 38" ) ) { return false; } - if ( s4.compareTo( s1 ) <= 0 ) { + if ( d.getPoints().size() != 1 ) { return false; } - if ( !s4.getSpeciesId().equals( "b" ) ) { + if ( d.getPolygons() != null ) { return false; } - final Species s5 = new BasicSpecies( " C " ); - if ( !s5.getSpeciesId().equals( "C" ) ) { + if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) { return false; } - if ( s5.equals( s1 ) ) { + if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { 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 ) ) { + if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { 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 ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) { 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 ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) { 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 ) ) { + n = t1_rt.getNode( "node a" ); + if ( !n.getNodeData().isHasDistribution() ) { 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 ( n.getNodeData().getDistributions().size() != 2 ) { 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 ) ) { + d = n.getNodeData().getDistribution( 1 ); + if ( !d.getDesc().equals( "San Diego" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( !s0.match( query_nodes ) ) { + if ( d.getPoints().size() != 1 ) { 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 ( d.getPolygons() != 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" ) ); - if ( !s0.match( query_nodes ) ) { + if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) { 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 ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - if ( s0.match( query_nodes ) ) { + if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) { 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 ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) { 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 ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) { 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 ) ) { + n = t1_rt.getNode( "node bb" ); + if ( !n.getNodeData().isHasDistribution() ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( s0.match( query_nodes ) ) { + if ( n.getNodeData().getDistributions().size() != 1 ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + d = n.getNodeData().getDistribution( 0 ); + if ( d.getPoints().size() != 3 ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); - if ( s0.match( query_nodes ) ) { + if ( d.getPolygons().size() != 2 ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - if ( s0.match( query_nodes ) ) { + if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - if ( s0.match( query_nodes ) ) { + if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "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 ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) { 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 ) ) { + 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 testSequenceDbWsTools1() { + try { + final PhylogenyNode n = new PhylogenyNode(); + n.setName( "NP_001025424" ); + Accession acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) + || !acc.getValue().equals( "NP_001025424" ) ) { + return false; + } + n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) + || !acc.getValue().equals( "NP_001025424" ) ) { + return false; + } + n.setName( "NP_001025424.1" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) + || !acc.getValue().equals( "NP_001025424" ) ) { + return false; + } + n.setName( "NM_001030253" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) + || !acc.getValue().equals( "NM_001030253" ) ) { + return false; + } + n.setName( "BCL2_HUMAN" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) + || !acc.getValue().equals( "BCL2_HUMAN" ) ) { + System.out.println( acc.toString() ); + return false; + } + 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; + } + 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; + } + 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; + } + 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; + } + 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; + } + 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; + } + 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; + } + 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; + } + 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; + } + 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; + } + n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() ) + || !acc.getValue().equals( "71845847" ) ) { + System.out.println( acc.toString() ); + return false; + } + n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AAZ45343.1" ) ) { + System.out.println( acc.toString() ); + return false; + } + } + catch ( final Exception e ) { + 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; } - // - 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 ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { 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 ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) { return false; } - ///////// - // query_nodes = new HashSet(); - // query_nodes.add( 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 ) ) { + final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" ); + SequenceDbWsTools.obtainSeqInformation( n2 ); + if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) { + return false; + } + if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { + return false; + } + if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + return false; + } + if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) { + return false; + } + final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" ); + SequenceDbWsTools.obtainSeqInformation( n3 ); + if ( !n3.getNodeData().getSequence().getName() + .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { + return false; + } + if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) { + return false; + } + if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + return false; + } + if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) { + return false; + } + } + catch ( final IOException e ) { + System.out.println(); + System.out.println( "the following might be due to absence internet connection:" ); + e.printStackTrace( System.out ); + return true; + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testSequenceIdParsing() { + try { + Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } + return false; + } + 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; + } + id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } + return false; + } + id = SequenceAccessionTools.parseAccessorFromString( "A4CAA4ZBB9" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } + return false; + } + id = SequenceAccessionTools.parseAccessorFromString( "ecoli_A4CAA4ZBB9_rt" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) + || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + } return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" ); + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); return false; } - /////////////////////////// - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( s0.match( query_nodes ) ) { + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testSequenceWriter() { + try { + final String n = ForesterUtil.LINE_SEPARATOR; + if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - if ( s0.match( query_nodes ) ) { + if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) { 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 ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - if ( s0.match( query_nodes ) ) { + if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - if ( s0.match( query_nodes ) ) { + if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString() + .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString() + .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testSpecies() { + try { + final Species s1 = new BasicSpecies( "a" ); + final Species s2 = new BasicSpecies( "a" ); + final Species s3 = new BasicSpecies( "A" ); + final Species s4 = new BasicSpecies( "b" ); + if ( !s1.equals( s1 ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.getSpeciesId().equals( "x" ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - if ( s0.match( query_nodes ) ) { + if ( s1.getSpeciesId().equals( null ) ) { return false; } - // - query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { + if ( !s1.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(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testSplitStrict() { + private static boolean testSplit() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ]; + //Archaeopteryx.createApplication( p0 ); final Set ex = new HashSet(); ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -10600,7 +12148,11 @@ public final class Test { ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); + final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex ); + // System.out.println( s0.toString() ); + // Set query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -10652,14 +12204,12 @@ public final class Test { 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" ) ); @@ -10669,7 +12219,6 @@ public final class Test { if ( !s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -10677,51 +12226,196 @@ public final class Test { 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( "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 ) ) { + if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + 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( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + 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( "F" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + 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( "C" ) ); + 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" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); if ( s0.match( query_nodes ) ) { return false; } + /////////////////////////// // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); if ( s0.match( query_nodes ) ) { @@ -10729,6 +12423,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); if ( s0.match( query_nodes ) ) { @@ -10736,6 +12432,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); if ( s0.match( query_nodes ) ) { @@ -10743,6 +12441,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); if ( s0.match( query_nodes ) ) { @@ -10750,6 +12450,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); if ( s0.match( query_nodes ) ) { @@ -10757,6 +12459,7 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( s0.match( query_nodes ) ) { @@ -10764,6 +12467,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -10772,6 +12477,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -10780,6 +12487,8 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); @@ -10788,371 +12497,303 @@ public final class Test { } // query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); - query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); - if ( s0.match( query_nodes ) ) { - 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 ) { - return false; - } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "E" ), false ); - if ( t1.getNumberOfExternalNodes() != 4 ) { - return false; - } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "F" ), false ); - if ( t1.getNumberOfExternalNodes() != 3 ) { - return false; - } - t1.toNewHampshireX(); - t1.deleteSubtree( t1.getNode( "D" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 3 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "def" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 2 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "B" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "C" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "abc" ), false ); - t1.toNewHampshireX(); - if ( t1.getNumberOfExternalNodes() != 1 ) { - return false; - } - t1.deleteSubtree( t1.getNode( "r" ), false ); - if ( t1.getNumberOfExternalNodes() != 0 ) { - return false; - } - if ( !t1.isEmpty() ) { - return false; - } - final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ]; - t2.deleteSubtree( t2.getNode( "A" ), false ); - t2.toNewHampshireX(); - if ( t2.getNumberOfExternalNodes() != 5 ) { - return false; - } - t2.deleteSubtree( t2.getNode( "abc" ), false ); - t2.toNewHampshireX(); - if ( t2.getNumberOfExternalNodes() != 3 ) { - return false; - } - t2.deleteSubtree( t2.getNode( "def" ), false ); - t2.toNewHampshireX(); - if ( t2.getNumberOfExternalNodes() != 1 ) { - return false; - } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSupportCount() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ]; - final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))" - + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))" - + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))" - + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))" - + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))", - new NHXParser() ); - SupportCount.count( t0_1, phylogenies_1, true, false ); - final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ]; - final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),((F,G),X))" - + "(((((A,Y),B),C),D),((F,G),E))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G),Z)" - + "(((((A,B),C),D),E),(F,G))" - + "((((((A,B),C),D),E),F),G)" - + "(((((X,Y),F,G),E),((A,B),C)),D)", - new NHXParser() ); - SupportCount.count( t0_2, phylogenies_2, true, false ); - final PhylogenyNodeIterator it = t0_2.iteratorPostorder(); - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) { - return false; - } - } - final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ]; - final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))" - + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() ); - SupportCount.count( t0_3, phylogenies_3, true, false ); - t0_3.reRoot( t0_3.getNode( "def" ).getId() ); - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) { - return false; - } - if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) { - return false; - } - final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) " - + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() ); - SupportCount.count( t0_4, phylogenies_4, true, false ); - t0_4.reRoot( t0_4.getNode( "F" ).getId() ); - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) { + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) { + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + + private static boolean testSplitStrict() { + 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 ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) { + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + if ( !s0.match( query_nodes ) ) { return false; } - Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - double d = SupportCount.compare( b1, a, true, true, true ); - if ( !Test.isEqual( d, 5.0 / 5.0 ) ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + 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 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( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + if ( s0.match( query_nodes ) ) { return false; } - a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; - final Phylogeny 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( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + if ( s0.match( query_nodes ) ) { return false; } - a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)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( "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; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSupportTransfer() { - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny p1 = factory.create( "(((A,B)ab:97,C)abc:57,((D,E)de:10,(F,G)fg:50,(H,I)hi:64)defghi)", - new NHXParser() )[ 0 ]; - final Phylogeny p2 = factory - .create( "(((A:0.1,B:0.3)ab:0.4,C)abc:0.5,((D,E)de,(F,G)fg,(H,I)hi:0.59)defghi)", new NHXParser() )[ 0 ]; - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + 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" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); + 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( "E" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) { + // + query_nodes = new HashSet(); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); + query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); + if ( s0.match( query_nodes ) ) { return false; } - if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) { + // + 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; } } catch ( final Exception e ) { - e.printStackTrace( System.out ); + e.printStackTrace(); return false; } return true; } - private static boolean testTaxonomyExtraction() { + private static boolean testSubtreeDeletion() { try { - final PhylogenyNode n0 = PhylogenyNode - .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n0.getNodeData().isHasTaxonomy() ) { - return false; - } - final PhylogenyNode n1 = PhylogenyNode - .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n1.getNodeData().isHasTaxonomy() ) { - System.out.println( n1.toString() ); - return false; - } - final PhylogenyNode n2x = PhylogenyNode - .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n2x.getNodeData().isHasTaxonomy() ) { - return false; - } - final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { - System.out.println( n3.toString() ); + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ]; + t1.deleteSubtree( t1.getNode( "A" ), false ); + if ( t1.getNumberOfExternalNodes() != 5 ) { return false; } - final PhylogenyNode n4 = PhylogenyNode - .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n4.getNodeData().isHasTaxonomy() ) { - System.out.println( n4.toString() ); + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "E" ), false ); + if ( t1.getNumberOfExternalNodes() != 4 ) { return false; } - final PhylogenyNode n5 = PhylogenyNode - .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n5.getNodeData().isHasTaxonomy() ) { - System.out.println( n5.toString() ); + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "F" ), false ); + if ( t1.getNumberOfExternalNodes() != 3 ) { return false; } - final PhylogenyNode n6 = PhylogenyNode - .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n6.getNodeData().isHasTaxonomy() ) { - System.out.println( n6.toString() ); + t1.toNewHampshireX(); + t1.deleteSubtree( t1.getNode( "D" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 3 ) { return false; } - final PhylogenyNode n7 = PhylogenyNode - .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n7.getNodeData().isHasTaxonomy() ) { - System.out.println( n7.toString() ); + t1.deleteSubtree( t1.getNode( "def" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 2 ) { return false; } - final PhylogenyNode n8 = PhylogenyNode - .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { - System.out.println( n8.toString() ); + t1.deleteSubtree( t1.getNode( "B" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - final PhylogenyNode n9 = PhylogenyNode - .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { - System.out.println( n9.toString() ); + t1.deleteSubtree( t1.getNode( "C" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - final PhylogenyNode n10x = PhylogenyNode - .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n10x.getNodeData().isHasTaxonomy() ) { - System.out.println( n10x.toString() ); + t1.deleteSubtree( t1.getNode( "abc" ), false ); + t1.toNewHampshireX(); + if ( t1.getNumberOfExternalNodes() != 1 ) { return false; } - final PhylogenyNode n10xx = PhylogenyNode - .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( n10xx.getNodeData().isHasTaxonomy() ) { - System.out.println( n10xx.toString() ); + t1.deleteSubtree( t1.getNode( "r" ), false ); + if ( t1.getNumberOfExternalNodes() != 0 ) { return false; } - final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { - System.out.println( n10.toString() ); + if ( !t1.isEmpty() ) { return false; } - final PhylogenyNode n11 = PhylogenyNode - .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { - System.out.println( n11.toString() ); + 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; } - 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() ); + t2.deleteSubtree( t2.getNode( "abc" ), false ); + t2.toNewHampshireX(); + if ( t2.getNumberOfExternalNodes() != 3 ) { return false; } - final PhylogenyNode n13 = PhylogenyNode - .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( n13.getNodeData().isHasTaxonomy() ) { - System.out.println( n13.toString() ); + t2.deleteSubtree( t2.getNode( "def" ), false ); + t2.toNewHampshireX(); + if ( t2.getNumberOfExternalNodes() != 1 ) { return false; } } @@ -11163,364 +12804,402 @@ public final class Test { return true; } - private static boolean testTreeMethods() { + private static boolean testSupportCount() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ]; - PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) ); - if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) { - System.out.println( t0.toNewHampshireX() ); + final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ]; + final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))" + + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))" + + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))" + + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))" + + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))", + new NHXParser() ); + SupportCount.count( t0_1, phylogenies_1, true, false ); + final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ]; + final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),((F,G),X))" + + "(((((A,Y),B),C),D),((F,G),E))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G),Z)" + + "(((((A,B),C),D),E),(F,G))" + + "((((((A,B),C),D),E),F),G)" + + "(((((X,Y),F,G),E),((A,B),C)),D)", + new NHXParser() ); + SupportCount.count( t0_2, phylogenies_2, true, false ); + final PhylogenyNodeIterator it = t0_2.iteratorPostorder(); + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) { + return false; + } + } + final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ]; + final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))" + + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() ); + SupportCount.count( t0_3, phylogenies_3, true, false ); + t0_3.reRoot( t0_3.getNode( "def" ).getId() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) { return false; } - 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 ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) { return false; } - if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) { return false; } - if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) { return false; } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - - private static boolean testSequenceDbWsTools1() { - try { - final PhylogenyNode n = new PhylogenyNode(); - n.setName( "NP_001025424" ); - Accession acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) - || !acc.getValue().equals( "NP_001025424" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) { return false; } - n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) - || !acc.getValue().equals( "NP_001025424" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) { return false; } - n.setName( "NP_001025424.1" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) - || !acc.getValue().equals( "NP_001025424" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) { return false; } - n.setName( "NM_001030253" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) - || !acc.getValue().equals( "NM_001030253" ) ) { + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) { return false; } - n.setName( "BCL2_HUMAN" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) - || !acc.getValue().equals( "BCL2_HUMAN" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) { return false; } - n.setName( "P10415" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) - || !acc.getValue().equals( "P10415" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) { return false; } - n.setName( " P10415 " ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) - || !acc.getValue().equals( "P10415" ) ) { - System.out.println( acc.toString() ); + final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ]; + final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) " + + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() ); + SupportCount.count( t0_4, phylogenies_4, true, false ); + t0_4.reRoot( t0_4.getNode( "F" ).getId() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) { return false; } - n.setName( "_P10415|" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) - || !acc.getValue().equals( "P10415" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) { return false; } - n.setName( "AY695820" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AY695820" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) { return false; } - n.setName( "_AY695820_" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AY695820" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) { return false; } - n.setName( "AAA59452" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAA59452" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) { return false; } - n.setName( "_AAA59452_" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAA59452" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) { return false; } - n.setName( "AAA59452.1" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAA59452.1" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) { return false; } - n.setName( "_AAA59452.1_" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) - || !acc.getValue().equals( "AAA59452.1" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) { return false; } - n.setName( "GI:94894583" ); - acc = SequenceDbWsTools.obtainSeqAccession( n ); - if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() ) - || !acc.getValue().equals( "94894583" ) ) { - System.out.println( acc.toString() ); + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) { + return false; + } + if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) { + 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 ) ) { + 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( System.out ); return false; } return true; } - private static boolean testSequenceDbWsTools2() { + private static boolean testSupportTransfer() { try { - final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" ); - SequenceDbWsTools.obtainSeqInformation( n1 ); - if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) { - return false; - } - if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { - return false; - } - if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + 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 ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) { return false; } - final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" ); - SequenceDbWsTools.obtainSeqInformation( n2 ); - System.out.println( n2.toString() ); - if ( !n2.getNodeData().getSequence().getName() - .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) { + support_transfer.moveBranchLengthsToBootstrap( p1 ); + support_transfer.transferSupportValues( p1, p2 ); + if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) { return false; } - if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { + if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) { return false; } - if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) { return false; } - if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) { return false; } - final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" ); - SequenceDbWsTools.obtainSeqInformation( n3 ); - System.out.println( "n=" + n3.toString() ); - if ( !n3.getNodeData().getSequence().getName() - .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) { return false; } - if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) { return false; } - if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) { return false; } - if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) { + if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) { return false; } } - catch ( final IOException e ) { - System.out.println(); - System.out.println( "the following might be due to absence internet connection:" ); - e.printStackTrace( System.out ); - return true; - } catch ( final Exception e ) { - e.printStackTrace(); + e.printStackTrace( System.out ); return false; } return true; } - private static boolean testEbiEntryRetrieval() { + private static boolean testTaxonomyExtraction() { try { - final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" ); - if ( !entry.getAccession().equals( "AAK41263" ) ) { - System.out.println( entry.getAccession() ); + final PhylogenyNode n0 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n0.getNodeData().isHasTaxonomy() ) { return false; } - if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) { - System.out.println( entry.getTaxonomyScientificName() ); + 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 ( !entry.getSequenceName() - .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) { - System.out.println( entry.getSequenceName() ); + final PhylogenyNode n2x = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n2x.getNodeData().isHasTaxonomy() ) { return false; } - // if ( !entry.getSequenceSymbol().equals( "" ) ) { - // System.out.println( entry.getSequenceSymbol() ); - // return false; - // } - if ( !entry.getGeneName().equals( "treX-like" ) ) { - System.out.println( entry.getGeneName() ); + 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 ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) { - System.out.println( entry.getTaxonomyIdentifier() ); + 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 ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) { - System.out.println( entry.getAnnotations().first().getRefValue() ); + 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 ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) { - System.out.println( entry.getAnnotations().first().getRefSource() ); + final PhylogenyNode n6 = PhylogenyNode + .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n6.getNodeData().isHasTaxonomy() ) { + System.out.println( n6.toString() ); return false; } - if ( entry.getCrossReferences().size() != 5 ) { + final PhylogenyNode n7 = PhylogenyNode + .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n7.getNodeData().isHasTaxonomy() ) { + System.out.println( n7.toString() ); return false; } - // - final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); - if ( !entry1.getAccession().equals( "ABJ16409" ) ) { + 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 ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) { - System.out.println( entry1.getTaxonomyScientificName() ); + final PhylogenyNode n9 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + System.out.println( n9.toString() ); return false; } - if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) { - System.out.println( entry1.getSequenceName() ); + 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 ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) { - System.out.println( entry1.getTaxonomyIdentifier() ); + 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 ( !entry1.getGeneName().equals( "BCL2" ) ) { - System.out.println( entry1.getGeneName() ); + final PhylogenyNode n10 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { + System.out.println( n10.toString() ); return false; } - if ( entry1.getCrossReferences().size() != 6 ) { + 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; } - // - final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); - if ( !entry2.getAccession().equals( "NM_184234" ) ) { + 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 ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { - System.out.println( entry2.getTaxonomyScientificName() ); + final PhylogenyNode n13 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( n13.getNodeData().isHasTaxonomy() ) { + System.out.println( n13.toString() ); return false; } - if ( !entry2.getSequenceName() - .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { - System.out.println( entry2.getSequenceName() ); + final PhylogenyNode n14 = PhylogenyNode + .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { + System.out.println( n14.toString() ); return false; } - if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) { - System.out.println( entry2.getTaxonomyIdentifier() ); + final PhylogenyNode n15 = PhylogenyNode + .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { + System.out.println( n15.toString() ); return false; } - if ( !entry2.getGeneName().equals( "RBM39" ) ) { - System.out.println( entry2.getGeneName() ); + final PhylogenyNode n16 = PhylogenyNode + .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { + System.out.println( n16.toString() ); return false; } - if ( entry2.getCrossReferences().size() != 3 ) { + final PhylogenyNode n17 = PhylogenyNode + .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { + System.out.println( n17.toString() ); return false; } - // - final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" ); - if ( !entry3.getAccession().equals( "HM043801" ) ) { + final PhylogenyNode n18 = PhylogenyNode + .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { + System.out.println( n18.toString() ); return false; } - if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) { - System.out.println( entry3.getTaxonomyScientificName() ); + final PhylogenyNode n19 = PhylogenyNode + .createInstanceFromNhxString( "Mus_musculus_musculus_K392", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { + System.out.println( n19.toString() ); return false; } - if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) { - System.out.println( entry3.getSequenceName() ); + final PhylogenyNode n20 = PhylogenyNode + .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { + System.out.println( n20.toString() ); return false; } - if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) { - System.out.println( entry3.getTaxonomyIdentifier() ); + final PhylogenyNode n21 = PhylogenyNode + .createInstanceFromNhxString( "Mus musculus musculus K392", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { + System.out.println( n21.toString() ); return false; } - if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) { - System.out.println( entry3.getSequenceSymbol() ); + final PhylogenyNode n23 = PhylogenyNode + .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n23.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) { + System.out.println( n23.toString() ); return false; } - if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { + final PhylogenyNode n24 = PhylogenyNode + .createInstanceFromNhxString( "9EMVE_Nematostella", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n24.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) { + System.out.println( n24.toString() ); return false; } - if ( entry3.getCrossReferences().size() != 8 ) { + // + final PhylogenyNode n25 = PhylogenyNode + .createInstanceFromNhxString( "Nematostella_vectensis_NEMVE", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n25.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) { + System.out.println( n25.toString() ); return false; } - // - // - final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); - if ( !entry4.getAccession().equals( "AAA36557" ) ) { + final PhylogenyNode n26 = PhylogenyNode + .createInstanceFromNhxString( "Nematostella_vectensis_9EMVE", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n26.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) { + System.out.println( n26.toString() ); return false; } - if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { - System.out.println( entry4.getTaxonomyScientificName() ); + final PhylogenyNode n27 = PhylogenyNode + .createInstanceFromNhxString( "Nematostella_9EMVE", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !n27.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) { + System.out.println( n27.toString() ); return false; } - if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) { - System.out.println( entry4.getSequenceName() ); + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testTreeCopy() { + try { + final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]"; + final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 ); + final Phylogeny t1 = t0.copy(); + if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) { return false; } - if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) { - System.out.println( entry4.getTaxonomyIdentifier() ); + if ( !t1.toNewHampshireX().equals( str_0 ) ) { return false; } - if ( !entry4.getGeneName().equals( "ras" ) ) { - System.out.println( entry4.getGeneName() ); + t0.deleteSubtree( t0.getNode( "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; } - // 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 fails: - // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" ); - // if ( !entry5.getAccession().equals( "HM043801" ) ) { - // 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(); @@ -11529,9 +13208,37 @@ public final class Test { return true; } + private static boolean testTreeMethods() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) ); + if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) { + System.out.println( t0.toNewHampshireX() ); + return false; + } + final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testUniprotEntryRetrieval() { try { - final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 ); + final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 ); if ( !entry.getAccession().equals( "P12345" ) ) { return false; } @@ -11550,6 +13257,18 @@ public final class Test { if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) { return false; } + if ( entry.getMolecularSequence() == null ) { + return false; + } + if ( !entry + .getMolecularSequence() + .getMolecularSequenceAsString() + .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" ) + || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) { + System.out.println( "got: " + entry.getMolecularSequence().getMolecularSequenceAsString() ); + System.out.println( "expected something else." ); + return false; + } } catch ( final IOException e ) { System.out.println(); @@ -11557,6 +13276,10 @@ public final class Test { e.printStackTrace( System.out ); return true; } + catch ( final NullPointerException f ) { + f.printStackTrace( System.out ); + return false; + } catch ( final Exception e ) { return false; } @@ -11746,60 +13469,6 @@ public final class Test { } return true; } - - private static boolean testWabiTxSearch() { - try { - String result = ""; - result = TxSearch.searchSimple( "nematostella" ); - result = TxSearch.getTxId( "nematostella" ); - if ( !result.equals( "45350" ) ) { - return false; - } - result = TxSearch.getTxName( "45350" ); - if ( !result.equals( "Nematostella" ) ) { - return false; - } - result = TxSearch.getTxId( "nematostella vectensis" ); - if ( !result.equals( "45351" ) ) { - return false; - } - result = TxSearch.getTxName( "45351" ); - if ( !result.equals( "Nematostella vectensis" ) ) { - return false; - } - result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" ); - if ( !result.equals( "536089" ) ) { - return false; - } - result = TxSearch.getTxName( "536089" ); - if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) { - return false; - } - final List queries = new ArrayList(); - queries.add( "Campylobacter coli" ); - queries.add( "Escherichia coli" ); - queries.add( "Arabidopsis" ); - queries.add( "Trichoplax" ); - queries.add( "Samanea saman" ); - queries.add( "Kluyveromyces marxianus" ); - queries.add( "Bacillus subtilis subsp. subtilis str. N170" ); - queries.add( "Bornavirus parrot/PDD/2008" ); - final List ranks = new ArrayList(); - ranks.add( RANKS.SUPERKINGDOM ); - ranks.add( RANKS.KINGDOM ); - ranks.add( RANKS.FAMILY ); - ranks.add( RANKS.GENUS ); - ranks.add( RANKS.TRIBE ); - result = TxSearch.searchLineage( queries, ranks ); - result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true ); - result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true ); - } - catch ( final Exception e ) { - System.out.println(); - System.out.println( "the following might be due to absence internet connection:" ); - e.printStackTrace( System.out ); - return false; - } - return true; - } + + }