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=5864f613fb7646998751832cab65a30ca980f8b2;hpb=ff79eee1cd2e65925ada2e6fd484010122c74d22;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 5864f61..1c76c8d 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -40,6 +40,9 @@ 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; @@ -106,7 +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; @@ -125,39 +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 String PATH_TO_RESOURCES = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "resources" - + ForesterUtil.getFileSeparator(); + + ForesterUtil.getFileSeparator() + "resources" + + ForesterUtil.getFileSeparator(); private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "test_data" - + ForesterUtil.getFileSeparator(); - private final static boolean PERFORM_DB_TESTS = false; + + 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; + + ForesterConstants.PHYLO_XML_VERSION + "/" + + ForesterConstants.PHYLO_XML_XSD; private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true; private final static double ZERO_DIFF = 1.0E-9; - public static boolean isEqual( final double a, final double b ) { + private static boolean isEqual( final double a, final double b ) { return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF ); } public static void main( final String[] args ) { System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION - + "]" ); + + "]" ); Locale.setDefault( Locale.US ); System.out.println( "[Locale: " + Locale.getDefault() + "]" ); int failed = 0; @@ -181,15 +181,7 @@ public final class Test { System.exit( -1 ); } final long start_time = new Date().getTime(); - System.out.print( "MSA entropy: " ); - if ( Test.testMsaEntropy() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } + System.out.print( "Basic node methods: " ); if ( Test.testBasicNodeMethods() ) { System.out.println( "OK." ); @@ -298,6 +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." ); @@ -343,6 +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." ); @@ -361,6 +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." ); @@ -487,6 +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." ); @@ -922,6 +950,15 @@ public final class Test { 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() ) { @@ -962,8 +999,8 @@ public final class Test { } } if ( PERFORM_WEB_TREE_ACCESS ) { - System.out.print( "NHX parsing from URL: " ); - if ( Test.testNHXparsingFromURL() ) { + System.out.print( "TreeBase acccess: " ); + if ( Test.testTreeBaseReading() ) { System.out.println( "OK." ); succeeded++; } @@ -971,8 +1008,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "NHX parsing from URL 2: " ); - if ( Test.testNHXparsingFromURL2() ) { + System.out.print( "ToL access: " ); + if ( Test.testToLReading() ) { System.out.println( "OK." ); succeeded++; } @@ -980,8 +1017,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "phyloXML parsing from URL: " ); - if ( Test.testPhyloXMLparsingFromURL() ) { + System.out.print( "NHX parsing from URL: " ); + if ( Test.testNHXparsingFromURL() ) { System.out.println( "OK." ); succeeded++; } @@ -989,8 +1026,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "TreeBase acccess: " ); - if ( Test.testTreeBaseReading() ) { + System.out.print( "NHX parsing from URL 2: " ); + if ( Test.testNHXparsingFromURL2() ) { System.out.println( "OK." ); succeeded++; } @@ -998,9 +1035,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - // - System.out.print( "ToL access: " ); - if ( Test.testToLReading() ) { + System.out.print( "phyloXML parsing from URL: " ); + if ( Test.testPhyloXMLparsingFromURL() ) { System.out.println( "OK." ); succeeded++; } @@ -1008,7 +1044,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // System.out.print( "TreeFam access: " ); if ( Test.testTreeFamReading() ) { System.out.println( "OK." ); @@ -1018,8 +1053,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // - // System.out.print( "Pfam tree access: " ); if ( Test.testPfamTreeReading() ) { System.out.println( "OK." ); @@ -1048,7 +1081,7 @@ public final class Test { } } - public static boolean testEngulfingOverlapRemoval() { + private static boolean testEngulfingOverlapRemoval() { try { final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 ); @@ -1147,7 +1180,7 @@ public final class Test { return true; } - public static final boolean testNHXparsingFromURL2() { + private static final boolean testNHXparsingFromURL2() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ), @@ -1209,11 +1242,12 @@ public final class Test { } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testNHXparsingFromURL() { + private static final boolean testNHXparsingFromURL() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; final URL u = new URL( s ); @@ -1230,7 +1264,8 @@ public final class Test { System.out.println( phys[ 1 ].toNewHampshire() ); return false; } - final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() ); + final URL u2 = new URL( s ); + final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() ); if ( ( phys2 == null ) || ( phys2.length != 5 ) ) { return false; } @@ -1240,8 +1275,8 @@ public final class Test { } final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance(); final NHXParser p = new NHXParser(); - final URL u2 = new URL( s ); - p.setSource( u2 ); + final URL u3 = new URL( s ); + p.setSource( u3 ); if ( !p.hasNext() ) { return false; } @@ -1273,12 +1308,14 @@ public final class Test { } } catch ( final Exception e ) { + System.out.println( e.toString() ); e.printStackTrace(); + return false; } return true; } - public static boolean testOverlapRemoval() { + private static boolean testOverlapRemoval() { try { final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 ); @@ -1432,15 +1469,14 @@ public final class Test { return true; } - public static final boolean testPfamTreeReading() { + private static final boolean testPfamTreeReading() { try { final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" ); final NHXParser parser = new NHXParser(); parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); parser.setReplaceUnderscores( false ); parser.setGuessRootedness( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } @@ -1450,31 +1486,37 @@ public final class Test { } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testPhyloXMLparsingFromURL() { + private static final boolean testPhyloXMLparsingFromURL() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml"; final URL u = new URL( s ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() ); + if ( ( phys == null ) || ( phys.length != 2 ) ) { return false; } + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() ); + + if ( ( phys2 == null ) || ( phys2.length != 2 ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testToLReading() { + private static final boolean testToLReading() { try { final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, new TolParser() ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } @@ -1487,47 +1529,138 @@ public final class Test { if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) { return false; } + // + final URL u2 = new URL( WebserviceUtil.TOL_URL_BASE + "17706" ); + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, new TolParser() ); + if ( ( phys2 == null ) || ( phys2.length != 1 ) ) { + return false; + } + if ( !phys2[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "17706" ) ) { + return false; + } + if ( phys2[ 0 ].getNumberOfExternalNodes() < 5 ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testTreeBaseReading() { + private static final boolean testTreeBaseReading() { try { - final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" ); + final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "72557?format=nexus" ); final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); parser.setReplaceUnderscores( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } + final URL u_1 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2406?format=nexus" ); + final NexusPhylogeniesParser parser_1 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_1 = ForesterUtil.readPhylogeniesFromUrl( u_1, parser_1 ); + if ( ( phys_1 == null ) || ( phys_1.length != 1 ) ) { + return false; + } + final URL u_2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "422?format=nexus" ); + final NexusPhylogeniesParser parser_2 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_2 = ForesterUtil.readPhylogeniesFromUrl( u_2, parser_2 ); + if ( ( phys_2 == null ) || ( phys_2.length != 1 ) ) { + return false; + } + final URL u_3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2654?format=nexus" ); + final NexusPhylogeniesParser parser_3 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_3 = ForesterUtil.readPhylogeniesFromUrl( u_3, parser_3 ); + if ( ( phys_3 == null ) || ( phys_3.length != 1 ) ) { + return false; + } + final URL u_4 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" ); + final NexusPhylogeniesParser parser_4 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_4 = ForesterUtil.readPhylogeniesFromUrl( u_4, parser_4 ); + if ( ( phys_4 == null ) || ( phys_4.length != 1 ) ) { + return false; + } final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" ); final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser(); parser2.setReplaceUnderscores( true ); - final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 ); + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, parser2 ); if ( ( phys2 == null ) || ( phys2.length != 9 ) ) { return false; } + final URL u3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14909?format=nexus" ); + final NexusPhylogeniesParser parser3 = new NexusPhylogeniesParser(); + final Phylogeny[] phys3 = ForesterUtil.readPhylogeniesFromUrl( u3, parser3 ); + if ( ( phys3 == null ) || ( phys3.length != 2 ) ) { + return false; + } + final Phylogeny[] phys4 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14525?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys4 == null ) || ( phys4.length != 1 ) ) { + return false; + } + final Phylogeny[] phys5 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15632?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys5 == null ) || ( phys5.length != 1 ) ) { + return false; + } + final Phylogeny[] phys6 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "10190?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys6 == null ) || ( phys6.length != 1 ) ) { + return false; + } + final Phylogeny[] phys7 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "13246?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys7 == null ) || ( phys7.length != 2 ) ) { + return false; + } + final Phylogeny[] phys8 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "11662?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys8 == null ) || ( phys8.length != 2 ) ) { + return false; + } + final Phylogeny[] phys9 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "562?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys9 == null ) || ( phys9.length != 4 ) ) { + return false; + } + final Phylogeny[] phys16424 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "16424?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys16424 == null ) || ( phys16424.length != 1 ) ) { + return false; + } + final Phylogeny[] phys17878 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "17878?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys17878 == null ) || ( phys17878.length != 17 ) ) { + return false; + } + final Phylogeny[] phys18804 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "18804?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys18804 == null ) || ( phys18804.length != 2 ) ) { + return false; + } + final Phylogeny[] phys346 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "346?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys346 == null ) || ( phys346.length != 1 ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testTreeFamReading() { + private static final boolean testTreeFamReading() { try { final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" ); final NHXParser parser = new NHXParser(); parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO ); parser.setReplaceUnderscores( false ); parser.setGuessRootedness( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } @@ -1537,6 +1670,7 @@ public final class Test { } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } @@ -1552,7 +1686,7 @@ public final class Test { private static boolean testAminoAcidSequence() { try { - final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" ); + final MolecularSequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" ); if ( aa1.getLength() != 13 ) { return false; } @@ -1565,15 +1699,15 @@ public final class Test { if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) { return false; } - final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" ); - if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) { + final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" ); + if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) { return false; } - final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" ); + final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" ); if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) { return false; } - final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" ); + final MolecularSequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" ); if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) { return false; } @@ -1683,12 +1817,258 @@ public final class Test { } return true; } + + private static boolean testUTF8ParsingFromFile() { + try { + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); + final Phylogeny[] phylogenies_xml = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.xml" ), + xml_parser ); + if ( xml_parser.getErrorCount() > 0 ) { + System.out.println( xml_parser.getErrorMessages().toString() ); + return false; + } + if ( phylogenies_xml.length != 1 ) { + return false; + } + + final Phylogeny[] phylogenies_xml2 = ParserBasedPhylogenyFactory.getInstance().create( new StringBuffer( phylogenies_xml[0].toPhyloXML( 0 )), + xml_parser ); + + final Phylogeny[] phylogenies_nh = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nh" ), new NHXParser() ); + if ( phylogenies_nh.length != 1 ) { + return false; + } + + final Phylogeny[] phylogenies_nex = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nex" ), new NexusPhylogeniesParser() ); + if ( phylogenies_nex.length != 1 ) { + return false; + } + + final String[] xml_n = phylogenies_xml[0].getAllExternalNodeNames(); + final String[] xml_n2 = phylogenies_xml2[0].getAllExternalNodeNames(); + final String[] nh_n = phylogenies_nh[0].getAllExternalNodeNames(); + final String[] nex_n = phylogenies_nex[0].getAllExternalNodeNames(); + final String n0 = "AQ~!@#$%^&*()_+-=\\{}|;:\"<>?,./"; + final String n1 = "€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ"; + final String n2 = "漢字ひらがなカタカナ"; + final String n3 = "อักษรไทย"; + final String n4 = "繁體字"; + final String n5 = "한글"; + final String n6 = "देवनागरी"; + + final String n7 = "chữ Quốc ngữ"; + final String n8 = "ру́сский язы́к"; + final String n9 = "អក្សរខ្មែរ"; + + if ( !xml_n[0].equals( n0 ) ) { + System.out.println( xml_n[0] ); + System.out.println( n0 ); + return false; + } + if ( !xml_n2[0].equals( n0 ) ) { + System.out.println( xml_n2[0] ); + System.out.println( n0 ); + return false; + } + if ( !nh_n[0].equals( n0 ) ) { + System.out.println( nh_n[0] ); + System.out.println( n0 ); + return false; + } + if ( !nex_n[0].equals( n0 ) ) { + System.out.println( nex_n[0] ); + System.out.println( n0 ); + return false; + } + + if ( !xml_n[1].equals( n1 ) ) { + System.out.println( xml_n[1] ); + System.out.println( n1 ); + return false; + } + if ( !xml_n2[1].equals( n1 ) ) { + System.out.println( xml_n2[1] ); + System.out.println( n1 ); + return false; + } + if ( !nh_n[1].equals( n1 ) ) { + System.out.println( nh_n[1] ); + System.out.println( n1 ); + return false; + } + if ( !nex_n[1].equals( n1 ) ) { + System.out.println( nex_n[1] ); + System.out.println( n1 ); + return false; + } + + if ( !xml_n[2].equals( n2 ) ) { + System.out.println( xml_n[2] ); + System.out.println( n2 ); + return false; + } + if ( !xml_n2[2].equals( n2 ) ) { + System.out.println( xml_n2[2] ); + System.out.println( n2 ); + return false; + } + if ( !nh_n[2].equals( n2 ) ) { + System.out.println( nh_n[2] ); + System.out.println( n2 ); + return false; + } + if ( !nex_n[2].equals( n2 ) ) { + System.out.println( nex_n[2] ); + System.out.println( n2 ); + return false; + } + // + if ( !xml_n[3].equals( n3 ) ) { + System.out.println( xml_n[3] ); + System.out.println( n3 ); + return false; + } + if ( !xml_n2[3].equals( n3 ) ) { + System.out.println( xml_n2[3] ); + System.out.println( n3 ); + return false; + } + if ( !nh_n[3].equals( n3 ) ) { + System.out.println( nh_n[3] ); + System.out.println( n3 ); + return false; + } + if ( !nex_n[3].equals( n3 ) ) { + System.out.println( nex_n[3] ); + System.out.println( n3 ); + return false; + } + // + if ( !xml_n[4].equals( n4 ) ) { + System.out.println( xml_n[4] ); + System.out.println( n4 ); + return false; + } + if ( !nh_n[4].equals( n4 ) ) { + System.out.println( nh_n[4] ); + System.out.println( n4 ); + return false; + } + if ( !nex_n[4].equals( n4 ) ) { + System.out.println( nex_n[4] ); + System.out.println( n4 ); + return false; + } + // + if ( !xml_n[5].equals( n5 ) ) { + System.out.println( xml_n[5] ); + System.out.println( n5 ); + return false; + } + if ( !nh_n[5].equals( n5 ) ) { + System.out.println( nh_n[5] ); + System.out.println( n5 ); + return false; + } + if ( !nex_n[5].equals( n5 ) ) { + System.out.println( nex_n[5] ); + System.out.println( n5 ); + return false; + } + // + if ( !xml_n[6].equals( n6 ) ) { + System.out.println( xml_n[6] ); + System.out.println( n6 ); + return false; + } + if ( !nh_n[6].equals( n6 ) ) { + System.out.println( nh_n[6] ); + System.out.println( n6 ); + return false; + } + if ( !nex_n[6].equals( n6 ) ) { + System.out.println( nex_n[6] ); + System.out.println( n6 ); + return false; + } + // + if ( !xml_n[7].equals( n7 ) ) { + System.out.println( xml_n[7] ); + System.out.println( n7 ); + return false; + } + if ( !nh_n[7].equals( n7 ) ) { + System.out.println( nh_n[7] ); + System.out.println( n7 ); + return false; + } + if ( !nex_n[7].equals( n7 ) ) { + System.out.println( nex_n[7] ); + System.out.println( n7 ); + return false; + } + if ( !xml_n[8].equals( n8 ) ) { + System.out.println( xml_n[8] ); + System.out.println( n8 ); + return false; + } + if ( !nh_n[8].equals( n8 ) ) { + System.out.println( nh_n[8] ); + System.out.println( n8 ); + return false; + } + if ( !nex_n[8].equals( n8 ) ) { + System.out.println( nex_n[8] ); + System.out.println( n8 ); + return false; + } + if ( !xml_n[9].equals( n9 ) ) { + System.out.println( xml_n[9] ); + System.out.println( n9 ); + return false; + } + if ( !xml_n2[9].equals( n9 ) ) { + System.out.println( xml_n2[9] ); + System.out.println( n9 ); + return false; + } + if ( !nh_n[9].equals( n9 ) ) { + System.out.println( nh_n[9] ); + System.out.println( n9 ); + return false; + } + if ( !nex_n[9].equals( n9 ) ) { + System.out.println( nex_n[9] ); + System.out.println( n9 ); + return false; + } + if (!phylogenies_xml[0].toNewHampshire().equals( + phylogenies_nh[0].toNewHampshire() ) ) { + System.out.println( phylogenies_xml[0].toNewHampshire() ); + System.out.println( phylogenies_nh[0].toNewHampshire() ); + return false; + } + if (!phylogenies_xml[0].toNewHampshire().equals( + phylogenies_nex[0].toNewHampshire() ) ) { + System.out.println( phylogenies_xml[0].toNewHampshire() ); + System.out.println( phylogenies_nex[0].toNewHampshire() ); + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testBasicPhyloXMLparsing() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", + 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() ); @@ -1763,6 +2143,21 @@ public final class Test { if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) { return false; } + if ( !t3.getNode( "root node" ).isDuplication() ) { + return false; + } + if ( !t3.getNode( "node a" ).isDuplication() ) { + return false; + } + if ( t3.getNode( "node a" ).isSpeciation() ) { + return false; + } + if ( t3.getNode( "node bc" ).isDuplication() ) { + return false; + } + if ( !t3.getNode( "node bc" ).isSpeciation() ) { + return false; + } if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) { return false; } @@ -1887,7 +2282,7 @@ public final class Test { else { xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); } - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", + 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() ); @@ -2053,6 +2448,7 @@ public final class Test { } if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) { + System.out.println( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() ); return false; } if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) { @@ -2090,7 +2486,7 @@ public final class Test { return false; } if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) - .getConfidence() != 2144 ) { + .getConfidence() != 0 ) { return false; } if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId() @@ -2171,7 +2567,6 @@ public final class Test { 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; } @@ -2240,7 +2635,7 @@ public final class Test { xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); } } - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", + 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() ); @@ -2275,7 +2670,7 @@ public final class Test { return false; } final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml"; - final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser ); + final Phylogeny[] phylogenies_1 = factory.create( new File( x2 ), xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { System.out.println( "errors:" ); System.out.println( xml_parser.getErrorMessages().toString() ); @@ -2284,7 +2679,7 @@ public final class Test { if ( phylogenies_1.length != 4 ) { return false; } - final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml", + 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:" ); @@ -2297,7 +2692,7 @@ public final class Test { if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) { return false; } - final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml", + 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() ); @@ -2319,7 +2714,7 @@ public final class Test { if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) { return false; } - final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml", + 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() ); @@ -2943,7 +3338,7 @@ public final class Test { return false; } final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" ); - final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; + final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ]; if ( t5.getNumberOfExternalNodes() != 8 ) { return false; } @@ -2951,17 +3346,17 @@ public final class Test { 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 ]; + final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ]; if ( t6.getHeight() != 15 ) { return false; } final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" ); - final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ]; + final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ]; if ( t7.getHeight() != 15 ) { return false; } final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" ); - final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ]; + final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ]; if ( t8.getNumberOfExternalNodes() != 10 ) { return false; } @@ -3045,7 +3440,6 @@ public final class Test { if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; } - // final Phylogeny[] t2 = factory .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);", new NHXParser() ); @@ -3055,7 +3449,6 @@ public final class Test { 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() ); @@ -3990,10 +4383,6 @@ public final class Test { System.out.println( entry.getSequenceName() ); return false; } - // if ( !entry.getSequenceSymbol().equals( "" ) ) { - // System.out.println( entry.getSequenceSymbol() ); - // return false; - // } if ( !entry.getGeneName().equals( "treX-like" ) ) { System.out.println( entry.getGeneName() ); return false; @@ -4010,10 +4399,9 @@ public final class Test { System.out.println( entry.getAnnotations().first().getRefSource() ); return false; } - if ( entry.getCrossReferences().size() != 5 ) { + if ( entry.getCrossReferences().size() < 1 ) { return false; } - // final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); if ( !entry1.getAccession().equals( "ABJ16409" ) ) { return false; @@ -4034,10 +4422,9 @@ public final class Test { System.out.println( entry1.getGeneName() ); return false; } - if ( entry1.getCrossReferences().size() != 6 ) { + if ( entry1.getCrossReferences().size() < 1 ) { return false; } - // final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); if ( !entry2.getAccession().equals( "NM_184234" ) ) { return false; @@ -4059,10 +4446,15 @@ public final class Test { System.out.println( entry2.getGeneName() ); return false; } - if ( entry2.getCrossReferences().size() != 3 ) { + if ( entry2.getCrossReferences().size() < 1 ) { + return false; + } + if ( !entry2.getChromosome().equals( "20" ) ) { + return false; + } + if ( !entry2.getMap().equals( "20q11.22" ) ) { return false; } - // final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" ); if ( !entry3.getAccession().equals( "HM043801" ) ) { return false; @@ -4086,11 +4478,9 @@ public final class Test { if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { return false; } - if ( entry3.getCrossReferences().size() != 8 ) { + if ( entry3.getCrossReferences().size() < 1 ) { return false; } - // - // final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); if ( !entry4.getAccession().equals( "AAA36557" ) ) { return false; @@ -4111,21 +4501,6 @@ public final class Test { System.out.println( entry4.getGeneName() ); return false; } - // if ( !entry4.getChromosome().equals( "ras" ) ) { - // System.out.println( entry4.getChromosome() ); - // return false; - // } - // if ( !entry4.getMap().equals( "ras" ) ) { - // System.out.println( entry4.getMap() ); - // return false; - // } - //TODO FIXME gi... - // - //TODO fails: - // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" ); - // if ( !entry5.getAccession().equals( "HM043801" ) ) { - // return false; - // } final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" ); if ( !entry5.getAccession().equals( "AAZ45343" ) ) { return false; @@ -4142,6 +4517,25 @@ public final class Test { System.out.println( entry5.getTaxonomyIdentifier() ); return false; } + final SequenceDatabaseEntry entry6 = SequenceDbWsTools.obtainEntry( "M30539" ); + if ( !entry6.getAccession().equals( "M30539" ) ) { + return false; + } + if ( !entry6.getGeneName().equals( "ras" ) ) { + return false; + } + if ( !entry6.getSequenceName().equals( "Human SK2 c-Ha-ras-1 oncogene-encoded protein gene, exon 1" ) ) { + return false; + } + if ( !entry6.getTaxonomyIdentifier().equals( "9606" ) ) { + return false; + } + if ( !entry6.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + return false; + } + if ( entry6.getCrossReferences().size() < 1 ) { + return false; + } } catch ( final IOException e ) { System.out.println(); @@ -4510,6 +4904,44 @@ public final class Test { 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; + } + n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN|" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN~12" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + 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; + } + } + 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 ) { @@ -4585,17 +5017,17 @@ public final class Test { } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", @@ -4830,12 +5262,22 @@ public final class Test { private static boolean testFastaParser() { try { - if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) { + FileInputStream fis1 = new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ); + if ( !FastaParser.isLikelyFasta( fis1 ) ) { + fis1.close(); return false; } - if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) { + else { + fis1.close(); + } + FileInputStream fis2 = new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ); + if ( FastaParser.isLikelyFasta( fis2 ) ) { + fis2.close(); return false; } + else { + fis2.close(); + } final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ); if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) { return false; @@ -4846,7 +5288,7 @@ public final class Test { if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) { return false; } - if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) { + if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) { return false; } if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) { @@ -5766,10 +6208,10 @@ public final class Test { final String test_dir = Test.PATH_TO_TEST_DATA; try { final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); + + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); parser1.parse(); final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); + + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); final List proteins = parser2.parse(); if ( parser2.getProteinsEncountered() != 4 ) { return false; @@ -6134,11 +6576,11 @@ public final class Test { private static boolean testMsaQualityMethod() { try { - final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" ); - final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" ); - final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" ); - final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" ); - final List l = new ArrayList(); + 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 ); @@ -6175,32 +6617,34 @@ public final class Test { private static boolean testMsaEntropy() { try { - final Sequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" ); - final Sequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" ); - final Sequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" ); - final Sequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" ); - final List l = new ArrayList(); + 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 ); - 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(); + //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" ) ); @@ -6224,10 +6668,10 @@ public final class Test { 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 ) ); + // 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 ); @@ -6238,13 +6682,13 @@ public final class Test { private static boolean testDeleteableMsa() { try { - final Sequence s0 = BasicSequence.createAaSequence( "a", "AAAA" ); - final Sequence s1 = BasicSequence.createAaSequence( "b", "BAAA" ); - final Sequence s2 = BasicSequence.createAaSequence( "c", "CAAA" ); - final Sequence s3 = BasicSequence.createAaSequence( "d", "DAAA" ); - final Sequence s4 = BasicSequence.createAaSequence( "e", "EAAA" ); - final Sequence s5 = BasicSequence.createAaSequence( "f", "FAAA" ); - final List l0 = new ArrayList(); + 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 ); @@ -6286,13 +6730,13 @@ public final class Test { return false; } // - final Sequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" ); - final Sequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" ); - final Sequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" ); - final Sequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" ); - final Sequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" ); - final Sequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" ); - final List l1 = new ArrayList(); + 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 ); @@ -6326,14 +6770,13 @@ public final class Test { if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) { return false; } - // - final Sequence s__0 = BasicSequence.createAaSequence( "a", "A------" ); - final Sequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" ); - final Sequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" ); - final Sequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" ); - final Sequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" ); - final Sequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" ); - final List l2 = new ArrayList(); + 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 ); @@ -6369,20 +6812,22 @@ public final class Test { dmsa2.setIdentifier( 0, "new_c" ); dmsa2.setIdentifier( 1, "new_d" ); dmsa2.setResidueAt( 0, 0, 'x' ); - final Sequence s = dmsa2.deleteRow( "new_d", true ); + final MolecularSequence s = dmsa2.deleteRow( "new_d", true ); if ( !s.getMolecularSequenceAsString().equals( "D" ) ) { return false; } final Writer w = new StringWriter(); dmsa2.write( w, MSA_FORMAT.PHYLIP ); final String phylip = w.toString(); - if ( !phylip.equals( "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) { + if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) { + System.out.println( phylip ); return false; } 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; } } @@ -6399,7 +6844,7 @@ public final class Test { 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 ]; + final Phylogeny t0 = factory.create( sb0.toString(), new NHXParser() )[ 0 ]; t0.getNode( "cd" ).setCollapse( true ); t0.getNode( "cde" ).setCollapse( true ); n = t0.getFirstExternalNode(); @@ -6427,7 +6872,7 @@ public final class Test { } ext.clear(); final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ]; + final Phylogeny t1 = factory.create( sb1.toString(), new NHXParser() )[ 0 ]; t1.getNode( "ab" ).setCollapse( true ); t1.getNode( "cd" ).setCollapse( true ); t1.getNode( "cde" ).setCollapse( true ); @@ -6452,11 +6897,9 @@ public final class Test { if ( !ext.get( 4 ).getName().equals( "h" ) ) { 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 ]; + 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 ); @@ -6482,11 +6925,9 @@ public final class Test { if ( !ext.get( 3 ).getName().equals( "gh" ) ) { 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 ]; + 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 ); @@ -6510,11 +6951,9 @@ public final class Test { if ( !ext.get( 2 ).getName().equals( "fgh" ) ) { 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 ]; + 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 ); @@ -6528,10 +6967,8 @@ public final class Test { if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) { return false; } - // - // final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; + final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ]; ext.clear(); n = t5.getFirstExternalNode(); while ( n != null ) { @@ -6565,10 +7002,8 @@ public final class Test { if ( !ext.get( 7 ).getName().equals( "h" ) ) { return false; } - // - // final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ]; + final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ]; ext.clear(); t6.getNode( "ab" ).setCollapse( true ); n = t6.getNode( "ab" ); @@ -6600,10 +7035,8 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - // - // final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ]; + final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ]; ext.clear(); t7.getNode( "cd" ).setCollapse( true ); n = t7.getNode( "a" ); @@ -6635,10 +7068,8 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - // - // final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); - final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ]; + final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ]; ext.clear(); t8.getNode( "cd" ).setCollapse( true ); t8.getNode( "c" ).setCollapse( true ); @@ -6673,10 +7104,8 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - // - // final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ]; + final Phylogeny t9 = factory.create( sb9.toString(), new NHXParser() )[ 0 ]; ext.clear(); t9.getNode( "gh" ).setCollapse( true ); n = t9.getNode( "a" ); @@ -6708,10 +7137,8 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "gh" ) ) { return false; } - // - // final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ]; + final Phylogeny t10 = factory.create( sb10.toString(), new NHXParser() )[ 0 ]; ext.clear(); t10.getNode( "gh" ).setCollapse( true ); t10.getNode( "g" ).setCollapse( true ); @@ -6745,10 +7172,8 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "gh" ) ) { return false; } - // - // final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ]; + final Phylogeny t11 = factory.create( sb11.toString(), new NHXParser() )[ 0 ]; ext.clear(); t11.getNode( "gh" ).setCollapse( true ); t11.getNode( "fgh" ).setCollapse( true ); @@ -6778,10 +7203,8 @@ public final class Test { if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - // - // final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ]; + final Phylogeny t12 = factory.create( sb12.toString(), new NHXParser() )[ 0 ]; ext.clear(); t12.getNode( "gh" ).setCollapse( true ); t12.getNode( "fgh" ).setCollapse( true ); @@ -6814,10 +7237,8 @@ public final class Test { if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - // - // final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); - final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ]; + final Phylogeny t13 = factory.create( sb13.toString(), new NHXParser() )[ 0 ]; ext.clear(); t13.getNode( "ab" ).setCollapse( true ); t13.getNode( "b" ).setCollapse( true ); @@ -6846,10 +7267,8 @@ public final class Test { if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { return false; } - // - // final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ]; + final Phylogeny t14 = factory.create( sb14.toString(), new NHXParser() )[ 0 ]; ext.clear(); t14.getNode( "ab" ).setCollapse( true ); t14.getNode( "a" ).setCollapse( true ); @@ -6878,10 +7297,8 @@ public final class Test { if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { return false; } - // - // final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ]; + final Phylogeny t15 = factory.create( sb15.toString(), new NHXParser() )[ 0 ]; ext.clear(); t15.getNode( "ab" ).setCollapse( true ); t15.getNode( "a" ).setCollapse( true ); @@ -6916,7 +7333,7 @@ public final class Test { // // final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); - final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ]; + final Phylogeny t16 = factory.create( sb16.toString(), new NHXParser() )[ 0 ]; ext.clear(); t16.getNode( "ab" ).setCollapse( true ); t16.getNode( "a" ).setCollapse( true ); @@ -7282,11 +7699,11 @@ public final class Test { return false; } if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" ) - .getDistanceToParent() ) ) { + .getDistanceToParent() ) ) { return false; } if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" ) - .getDistanceToParent() ) ) { + .getDistanceToParent() ) ) { return false; } if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) { @@ -7336,7 +7753,6 @@ public final class Test { if ( phy != null ) { return false; } - // p.reset(); if ( !p.hasNext() ) { return false; @@ -7358,7 +7774,6 @@ public final class Test { if ( phy != null ) { return false; } - //// p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" ); if ( !p.hasNext() ) { return false; @@ -7380,7 +7795,6 @@ public final class Test { if ( phy != null ) { return false; } - // p.reset(); if ( !p.hasNext() ) { return false; @@ -7402,7 +7816,6 @@ public final class Test { if ( phy != null ) { return false; } - // p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" ); if ( !p.hasNext() ) { return false; @@ -8140,10 +8553,10 @@ public final class Test { if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) { return false; } - final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ]; + final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ).toString(), new NHXParser() )[ 0 ]; final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ]; final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ]; - final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ]; + final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ).toString(), new NHXParser() )[ 0 ]; final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() ); final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() ); final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() ); @@ -8151,9 +8564,9 @@ public final class Test { final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() ); final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() ); final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;" - + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " - + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", - new NHXParser() ); + + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " + + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", + new NHXParser() ); if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) { return false; } @@ -8401,21 +8814,21 @@ public final class Test { if ( p46.length != 0 ) { return false; } - final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ).toString(), new NHXParser() )[ 0 ]; if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } final Phylogeny p49 = factory - .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ), + .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ).toString(), new NHXParser() )[ 0 ]; if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { return false; } - final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; if ( p50.getNode( "A" ) == null ) { return false; } @@ -8430,21 +8843,21 @@ public final class Test { .equals( "((A,B)88:2.0,C);" ) ) { return false; } - final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; if ( p51.getNode( "A(A" ) == null ) { return false; } - final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; if ( p52.getNode( "A(A" ) == null ) { return false; } final Phylogeny p53 = factory - .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ), + .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ]; if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) { return false; } - final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ).toString(), new NHXParser() )[ 0 ]; if ( p54.getNode( "A" ) == null ) { return false; } @@ -8452,7 +8865,7 @@ public final class Test { return false; } final Phylogeny p55 = factory - .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ), + .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() @@ -8461,7 +8874,7 @@ public final class Test { return false; } final Phylogeny p56 = factory - .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ), + .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() @@ -8470,7 +8883,7 @@ public final class Test { return false; } final Phylogeny p57 = factory - .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ), + .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() @@ -8479,25 +8892,25 @@ public final class Test { return false; } final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';"; - final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ]; + final Phylogeny p58 = factory.create( s58, new NHXParser() )[ 0 ]; if ( !p58.toNewHampshire().equals( s58 ) ) { System.out.println( p58.toNewHampshire() ); return false; } final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";"; - final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ]; + final Phylogeny p59 = factory.create( s59 , new NHXParser() )[ 0 ]; if ( !p59.toNewHampshire().equals( s59 ) ) { System.out.println( p59.toNewHampshire() ); return false; } final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');"; - final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ]; + final Phylogeny p60 = factory.create( s60, new NHXParser() )[ 0 ]; if ( !p60.toNewHampshire().equals( s60 ) ) { System.out.println( p60.toNewHampshire() ); return false; } final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';"; - final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ]; + final Phylogeny p61 = factory.create( s61, new NHXParser() )[ 0 ]; if ( !p61.toNewHampshire() .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) { System.out.println( p61.toNewHampshire() ); @@ -8510,7 +8923,36 @@ public final class Test { } return true; } - + + private static boolean testNHParsingSpecialChars() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final String i0 = "(A!+=~QWERTY!@#$%^&*-,€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ)"; + final Phylogeny p0 = factory.create( i0, new NHXParser() )[ 0 ]; + if ( !p0.toNewHampshireX().equals( i0 ) ) { + System.out.println(); + System.out.println( p0.toNewHampshireX() ); + System.out.println( i0 ); + return false; + } + final String i1 = "(हिंदी,한글,ไทย,'Tiếng Việt',ひらがなカタカナ漢字,繁體字,русский)"; + final Phylogeny p1 = factory.create( i1, new NHXParser() )[ 0 ]; + if ( !p1.toNewHampshireX().equals( i1 ) ) { + System.out.println(); + System.out.println( p1.toNewHampshireX() ); + System.out.println( i1 ); + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + + private static boolean testNHParsingIter() { try { final String p0_str = "(A,B);"; @@ -8996,7 +9438,7 @@ public final class Test { if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) { System.out.println( n7 - .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) ); + .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) ); return false; } } @@ -9372,6 +9814,151 @@ public final class Test { return true; } + + private static boolean testNHXNodeParsing2() { + try { + + final PhylogenyNode n0_0 = PhylogenyNode + .createInstanceFromNhxString( "n0:[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_0.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_0.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_1 = PhylogenyNode + .createInstanceFromNhxString( "n0[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_1.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_1.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_2 = PhylogenyNode + .createInstanceFromNhxString( "n0:1E-3[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_2.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_2.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_3 = PhylogenyNode + .createInstanceFromNhxString( "n0:1E-3:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_3.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_3.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_4 = PhylogenyNode + .createInstanceFromNhxString( "n0:0.001:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_4.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_4.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_0 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_0.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_0.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + final PhylogenyNode n1_1 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]:0.001", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_1.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_1.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + if ( !isEqual( n1_1.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_2 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:0.001[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_2.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_2.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + if ( !isEqual( n1_2.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_3 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[&boostrap=69,&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_3.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_3.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + if ( !isEqual( n1_3.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_3.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + if ( !n1_3.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) { + return false; + } + final PhylogenyNode n1_4 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&bootstrap=69,&!colour=#FFFFFF]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_4.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_4.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + if ( !isEqual( n1_4.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_4.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + if ( !n1_4.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) { + return false; + } + final PhylogenyNode n1_5 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[69.0]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_5.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( !isEqual( n1_5.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_5.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + final PhylogenyNode n1_6 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_6.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + + if ( !isEqual( n1_6.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.11 ) ) { + return false; + } + if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getValue(), 0.95 ) ) { + return false; + } + if ( !n1_6.getBranchData().getConfidence( 0 ).getType().equals( "posterior probability" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testNHXParsing() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); @@ -9441,6 +10028,11 @@ public final class Test { 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; } + 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; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -9479,15 +10071,15 @@ public final class Test { } 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 ]; + + "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; } @@ -9689,7 +10281,7 @@ public final class Test { xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD ); } } - final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml", + 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() ); @@ -10618,13 +11210,13 @@ public final class Test { // 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 ]; + + "((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 ]; + + "((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 ); @@ -10958,15 +11550,15 @@ public final class Test { } 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 ]; + + "((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 ]; + + "(((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 ); @@ -11012,15 +11604,15 @@ public final class Test { 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 ]; + + "((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 ]; + + "(((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 ); @@ -11066,15 +11658,15 @@ public final class Test { 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 ]; + + "((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 ]; + + "(((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 ); @@ -11269,8 +11861,7 @@ public final class Test { } final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" ); SequenceDbWsTools.obtainSeqInformation( n2 ); - if ( !n2.getNodeData().getSequence().getName() - .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) { + if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) { return false; } if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { @@ -11322,7 +11913,6 @@ public final class Test { } 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" ) ) { @@ -11332,7 +11922,6 @@ public final class Test { } 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" ) ) { @@ -11342,7 +11931,6 @@ public final class Test { } 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" ) ) { @@ -11352,7 +11940,6 @@ public final class Test { } 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" ) ) { @@ -11362,7 +11949,6 @@ public final class Test { } 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" ) ) { @@ -11372,7 +11958,6 @@ public final class Test { } 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" ) ) { @@ -11382,7 +11967,6 @@ public final class Test { } 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" ) ) { @@ -11392,7 +11976,6 @@ public final class Test { } 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" ) ) { @@ -11402,7 +11985,6 @@ public final class Test { } 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" ) ) { @@ -11418,6 +12000,39 @@ public final class Test { 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; + } + id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" ); + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getSource() ); + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -11589,14 +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" ) ); @@ -11606,7 +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" ) ); @@ -11614,7 +12226,6 @@ 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" ) ); @@ -11623,14 +12234,12 @@ 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( "A" ) ); if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -11639,7 +12248,6 @@ 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" ) ); @@ -11649,7 +12257,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -11657,49 +12264,42 @@ public final class Test { 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" ) ); @@ -11707,7 +12307,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -11715,7 +12314,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -11723,7 +12321,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -12212,24 +12809,24 @@ public final class Test { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ]; final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))" - + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))" - + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))" - + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))" - + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))", - new NHXParser() ); + + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))" + + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))" + + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))" + + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))", + new NHXParser() ); SupportCount.count( t0_1, phylogenies_1, true, false ); final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ]; final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),((F,G),X))" - + "(((((A,Y),B),C),D),((F,G),E))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G),Z)" - + "(((((A,B),C),D),E),(F,G))" - + "((((((A,B),C),D),E),F),G)" - + "(((((X,Y),F,G),E),((A,B),C)),D)", - new NHXParser() ); + + "(((((A,B),C),D),E),((F,G),X))" + + "(((((A,Y),B),C),D),((F,G),E))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G),Z)" + + "(((((A,B),C),D),E),(F,G))" + + "((((((A,B),C),D),E),F),G)" + + "(((((X,Y),F,G),E),((A,B),C)),D)", + new NHXParser() ); SupportCount.count( t0_2, phylogenies_2, true, false ); final PhylogenyNodeIterator it = t0_2.iteratorPostorder(); while ( it.hasNext() ) { @@ -12508,7 +13105,6 @@ public final class Test { System.out.println( n17.toString() ); return false; } - // final PhylogenyNode n18 = PhylogenyNode .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { @@ -12535,13 +13131,6 @@ public final class Test { System.out.println( n21.toString() ); return false; } - final PhylogenyNode n22 = PhylogenyNode - .createInstanceFromNhxString( "NEMVE_Nematostella_vectensis", - NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( !n22.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) { - System.out.println( n22.toString() ); - return false; - } final PhylogenyNode n23 = PhylogenyNode .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); @@ -12649,7 +13238,7 @@ public final class Test { 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; } @@ -12668,6 +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(); @@ -12675,6 +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; } @@ -12864,60 +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; - } + + }