X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=598ad3a1e09f07e39af60d55f5bf9e03d41fe62d;hb=6062dfb954cafb6af22e01af89222888d9d5ba66;hp=b74c3e1e74053f43a6ec57db52441702b1c54b83;hpb=37cb4c1bc15ea30a6f64953d5e23e09694083f06;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index b74c3e1..598ad3a 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -38,6 +38,7 @@ import java.util.Locale; import java.util.Set; import org.forester.application.support_transfer; +import org.forester.archaeopteryx.AptxUtil; import org.forester.development.DevelopmentTools; import org.forester.evoinference.TestPhylogenyReconstruction; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -56,6 +57,7 @@ import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.io.parsers.tol.TolParser; import org.forester.io.parsers.util.ParserUtils; import org.forester.io.writers.PhylogenyWriter; +import org.forester.io.writers.SequenceWriter; import org.forester.msa.BasicMsa; import org.forester.msa.Mafft; import org.forester.msa.Msa; @@ -67,6 +69,7 @@ import org.forester.phylogeny.PhylogenyBranch; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.data.Accession; import org.forester.phylogeny.data.BinaryCharacters; import org.forester.phylogeny.data.BranchWidth; import org.forester.phylogeny.data.Confidence; @@ -171,6 +174,15 @@ public final class Test { System.exit( -1 ); } final long start_time = new Date().getTime(); + System.out.print( "Sequence writer: " ); + if ( testSequenceWriter() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Sequence id parsing: " ); if ( testSequenceIdParsing() ) { System.out.println( "OK." ); @@ -207,6 +219,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "SN extraction: " ); + if ( Test.testExtractSNFromNodeName() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Taxonomy extraction (general): " ); if ( Test.testTaxonomyExtraction() ) { System.out.println( "OK." ); @@ -216,6 +237,24 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "UniProtKB id extraction: " ); + if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Uri for Aptx web sequence accession: " ); + if ( Test.testCreateUriForSeqWeb() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Basic node construction and parsing of NHX (node level): " ); if ( Test.testNHXNodeParsing() ) { System.out.println( "OK." ); @@ -288,6 +327,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Nexus tree parsing iterating: " ); + if ( Test.testNexusTreeParsingIterating() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Nexus tree parsing: " ); if ( Test.testNexusTreeParsing() ) { System.out.println( "OK." ); @@ -378,6 +426,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Tree methods: " ); + if ( Test.testTreeMethods() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Postorder Iterator: " ); if ( Test.testPostOrderIterator() ) { System.out.println( "OK." ); @@ -806,68 +863,398 @@ public final class Test { } } + private static boolean testExtractUniProtKbProteinSeqIdentifier() { + try { + PhylogenyNode n = new PhylogenyNode(); + n.setName( "tr|B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "tr.B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "tr=B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "tr-B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "tr/B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "tr\\B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "tr_B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( " tr|B3RJ64 " ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "-tr|B3RJ64-" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "-tr=B3RJ64-" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "_tr=B3RJ64_" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( " tr_tr|B3RJ64_sp|123 " ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "sp|B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n.setName( "ssp|B3RJ64" ); + if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) { + return false; + } + n.setName( "sp|B3RJ64C" ); + if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) { + return false; + } + n.setName( "sp B3RJ64" ); + if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) { + return false; + } + n.setName( "sp|B3RJ6X" ); + if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) { + return false; + } + n.setName( "sp|B3RJ6" ); + if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) { + return false; + } + n.setName( "K1PYK7_CRAGI" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) { + return false; + } + n.setName( "K1PYK7_PEA" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PEA" ) ) { + return false; + } + n.setName( "K1PYK7_RAT" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_RAT" ) ) { + return false; + } + n.setName( "K1PYK7_PIG" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) { + return false; + } + n.setName( "~K1PYK7_PIG~" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) { + return false; + } + n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) { + return false; + } + n.setName( "K1PYKX_CRAGI" ); + if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) { + return false; + } + n.setName( "XXXXX_CRAGI" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "XXXXX_CRAGI" ) ) { + return false; + } + n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "H3IB65" ) ) { + return false; + } + n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" ); + if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) { + return false; + } + n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "Q86U06" ) ) { + return false; + } + n = new PhylogenyNode(); + org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence(); + seq.setSymbol( "K1PYK7_CRAGI" ); + n.getNodeData().addSequence( seq ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) { + return false; + } + seq.setSymbol( "tr|B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n = new PhylogenyNode(); + seq = new org.forester.phylogeny.data.Sequence(); + seq.setName( "K1PYK7_CRAGI" ); + n.getNodeData().addSequence( seq ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) { + return false; + } + seq.setName( "tr|B3RJ64" ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + n = new PhylogenyNode(); + seq = new org.forester.phylogeny.data.Sequence(); + seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) ); + n.getNodeData().addSequence( seq ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK8_CRAGI" ) ) { + return false; + } + n = new PhylogenyNode(); + seq = new org.forester.phylogeny.data.Sequence(); + seq.setAccession( new Accession( "tr|B3RJ64", "?" ) ); + n.getNodeData().addSequence( seq ); + if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) { + return false; + } + // + n = new PhylogenyNode(); + n.setName( "ACP19736" ); + if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) { + return false; + } + n = new PhylogenyNode(); + n.setName( "_ACP19736_" ); + if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testCreateUriForSeqWeb() { + try { + final PhylogenyNode n = new PhylogenyNode(); + n.setName( "tr|B3RJ64" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) { + return false; + } + n.setName( "B0LM41_HUMAN" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) { + return false; + } + n.setName( "NP_001025424" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) { + return false; + } + n.setName( "_NM_001030253-" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) { + return false; + } + n.setName( "XM_002122186" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) { + return false; + } + n.setName( "dgh_AAA34956_gdg" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) { + return false; + } + n.setName( "j40f4_Q06891.1_fndn2 fnr3" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "Q06891.1" ) ) { + return false; + } + n.setName( "GI:394892" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) { + System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) ); + return false; + } + n.setName( "gi_394892" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) { + System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) ); + return false; + } + n.setName( "gi6335_gi_394892_56635_Gi_43" ); + if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) { + System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) ); + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testExtractSNFromNodeName() { + try { + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) { + return false; + } + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" ) + .equals( "Mus musculus musculus" ) ) { + return false; + } + if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" ) + .equals( "Mus musculus musculus" ) ) { + return false; + } + if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) { + return false; + } + if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" ) + .equals( "Mus musculus" ) ) { + 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.YES ).equals( "MOUSE" ) ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "ARATH" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "ARATH" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) { + return false; + } + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "SOYBN" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { + return false; + } + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "SOYBN" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01", + TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE ) + .equals( "9YX45" ) ) { + return false; + } + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES ) - .equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES ) - .equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES ) - .equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", + TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) { + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + .equals( "RAT" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) .equals( "PIG" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES ) + if ( !ParserUtils + .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) .equals( "MOUSE" ) ) { return false; } + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -883,11 +1270,11 @@ public final class Test { } final PhylogenyNode n1 = new PhylogenyNode(); final PhylogenyNode n2 = PhylogenyNode - .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); final PhylogenyNode n4 = PhylogenyNode - .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( n1.isHasAssignedEvent() ) { return false; } @@ -1605,7 +1992,7 @@ public final class Test { source.append( "40 41 42 43" + l ); source.append( " # 1 1 1 1 1 " + l ); source.append( "50 51 52 53 54" + l ); - final BasicTable t1 = BasicTableParser.parse( source.toString(), " " ); + final BasicTable t1 = BasicTableParser.parse( source.toString(), ' ' ); if ( t1.getNumberOfColumns() != 5 ) { return false; } @@ -1634,7 +2021,7 @@ public final class Test { source1.append( "40;41;42;43" + l ); source1.append( " # 1 1 1 1 1 " + l ); source1.append( ";;;50 ; ;52; 53;;54 " + l ); - final BasicTable t2 = BasicTableParser.parse( source1.toString(), ";" ); + final BasicTable t2 = BasicTableParser.parse( source1.toString(), ';' ); if ( t2.getNumberOfColumns() != 5 ) { return false; } @@ -1671,7 +2058,7 @@ public final class Test { source2.append( " comment: 1 1 1 1 1 " + l ); source2.append( ";;;50 ; 52; 53;;54 " + l ); final List> tl = BasicTableParser.parse( source2.toString(), - ";", + ';', false, false, "comment:", @@ -1928,6 +2315,34 @@ public final class Test { return true; } + private static boolean testTreeMethods() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) ); + if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) { + System.out.println( t0.toNewHampshireX() ); + return false; + } + final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ]; + PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) ); + if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testConfidenceAssessor() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); @@ -4408,51 +4823,615 @@ public final class Test { return true; } - private static boolean testNexusTreeParsingTranslating() { + private static boolean testNexusTreeParsingIterating() { try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); - Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser ); - if ( phylogenies.length != 1 ) { + final NexusPhylogeniesParser p = new NexusPhylogeniesParser(); + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" ); + if ( !p.hasNext() ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + Phylogeny phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( phy.getNumberOfExternalNodes() != 25 ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + if ( p.hasNext() ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() - .equals( "Aranaeus" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - phylogenies = null; - phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser ); - if ( phylogenies.length != 3 ) { + // + p.reset(); + if ( !p.hasNext() ) { return false; } - if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + phy = p.next(); + if ( phy == null ) { return false; } - if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + if ( phy.getNumberOfExternalNodes() != 25 ) { return false; } - if ( phylogenies[ 0 ].isRooted() ) { + if ( !phy.getName().equals( "" ) ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + if ( p.hasNext() ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + phy = p.next(); + if ( phy != null ) { return false; } - if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" ); + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phy.getName().equals( "name" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy != null ) { + return false; + } + // + p.reset(); + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phy.getName().equals( "name" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy != null ) { + return false; + } + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" ); + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy != null ) { + return false; + } + // + p.reset(); + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy != null ) { + return false; + } + //// + p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" ); + // if ( phylogenies.length != 18 ) { + // return false; + // } + //0 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phy.getName().equals( "tree 0" ) ) { + return false; + } + //1 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phy.getName().equals( "tree 1" ) ) { + return false; + } + //2 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + //3 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 4 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //4 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 5 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //5 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + //6 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 2 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //7 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //8 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 8" ) ) { + return false; + } + //9 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 9" ) ) { + return false; + } + //10 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 10" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //11 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 11" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + //12 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 12" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //13 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) { + return false; + } + if ( !phy.getName().equals( "tree 13" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //14 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); + return false; + } + if ( !phy.getName().equals( "tree 14" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //15 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); + return false; + } + if ( !phy.getName().equals( "tree 15" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + //16 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); + return false; + } + if ( !phy.getName().equals( "tree 16" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //17 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy.getNumberOfExternalNodes() != 10 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy + .toNewHampshire() + .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) { + System.out.println( phy.toNewHampshire() ); + return false; + } + if ( !phy.getName().equals( "tree 17" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + // + if ( p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy != null ) { + return false; + } + p.reset(); + //0 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phy.getName().equals( "tree 0" ) ) { + return false; + } + //1 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 10 ) { + return false; + } + if ( !phy.getName().equals( "tree 1" ) ) { + return false; + } + //2 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + //3 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 4 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //4 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 5 ) { + System.out.println( phy.getNumberOfExternalNodes() ); + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( !phy.isRooted() ) { + return false; + } + //5 + if ( !p.hasNext() ) { + return false; + } + phy = p.next(); + if ( phy == null ) { + return false; + } + if ( phy.getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phy.getName().equals( "" ) ) { + return false; + } + if ( phy.isRooted() ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNexusTreeParsingTranslating() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); + Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser ); + if ( phylogenies.length != 1 ) { + return false; + } + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() + .equals( "Aranaeus" ) ) { + return false; + } + phylogenies = null; + phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser ); + if ( phylogenies.length != 3 ) { + return false; + } + if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) { + return false; + } + if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) { + return false; + } + if ( phylogenies[ 0 ].isRooted() ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) { + return false; + } + if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName() .equals( "Aranaeus" ) ) { return false; } @@ -5327,6 +6306,7 @@ public final class Test { return false; } if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) { + System.out.println( n6.toNewHampshireX() ); return false; } } @@ -5339,113 +6319,101 @@ public final class Test { private static boolean testTaxonomyExtraction() { try { - final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n0 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n0.getNodeData().isHasTaxonomy() ) { return false; } - final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n1 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n1.getNodeData().isHasTaxonomy() ) { System.out.println( n1.toString() ); return false; } - final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { - System.out.println( n2.toString() ); + final PhylogenyNode n2x = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n2x.getNodeData().isHasTaxonomy() ) { return false; } - final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n3 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n3.toString() ); return false; } - final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n4 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n4.getNodeData().isHasTaxonomy() ) { System.out.println( n4.toString() ); return false; } - final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n5 = PhylogenyNode + .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n5.getNodeData().isHasTaxonomy() ) { System.out.println( n5.toString() ); return false; } - final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n6 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n6.getNodeData().isHasTaxonomy() ) { System.out.println( n6.toString() ); return false; } - final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n7 = PhylogenyNode + .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n7.getNodeData().isHasTaxonomy() ) { System.out.println( n7.toString() ); return false; } - final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n8 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n8.toString() ); return false; } - final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n9 = PhylogenyNode + .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n9.toString() ); return false; } - final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) { + final PhylogenyNode n10x = PhylogenyNode + .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n10x.getNodeData().isHasTaxonomy() ) { + System.out.println( n10x.toString() ); + return false; + } + final PhylogenyNode n10xx = PhylogenyNode + .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n10xx.getNodeData().isHasTaxonomy() ) { + System.out.println( n10xx.toString() ); + return false; + } + final PhylogenyNode n10 = PhylogenyNode + .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { System.out.println( n10.toString() ); return false; } - final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n11 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) { System.out.println( n11.toString() ); return false; } - final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n12 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus", + NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { System.out.println( n12.toString() ); return false; } - final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n13 = PhylogenyNode + .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( n13.getNodeData().isHasTaxonomy() ) { System.out.println( n13.toString() ); return false; } - final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( n14.getNodeData().isHasTaxonomy() ) { - System.out.println( n14.toString() ); - return false; - } - final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) { - System.out.println( n15.toString() ); - return false; - } - final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( n16.getNodeData().isHasTaxonomy() ) { - System.out.println( n16.toString() ); - return false; - } - final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( n17.getNodeData().isHasTaxonomy() ) { - System.out.println( n17.toString() ); - return false; - } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -5502,52 +6470,54 @@ public final class Test { return false; } final PhylogenyNode n8 = PhylogenyNode - .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n8.getName().equals( "n8_ECOLI/12" ) ) { + .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) { + if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) { return false; } final PhylogenyNode n9 = PhylogenyNode - .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) { + .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) { + if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) { return false; } final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n10.getName().equals( "n10.ECOLI" ) ) { return false; } final PhylogenyNode n20 = PhylogenyNode - .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) { + .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) { return false; } if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) { return false; } - final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) { + final PhylogenyNode n20x = PhylogenyNode + .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) { return false; } if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) { return false; } final PhylogenyNode n20xx = PhylogenyNode - .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) { + .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) { return false; } if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) { return false; } final PhylogenyNode n20xxx = PhylogenyNode - .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) { return false; } @@ -5555,23 +6525,23 @@ public final class Test { return false; } final PhylogenyNode n20xxxx = PhylogenyNode - .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) { return false; } if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) { return false; } - final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !n21.getName().equals( "n21_PIG" ) ) { + final PhylogenyNode n21 = PhylogenyNode + .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n21.getName().equals( "N21_PIG" ) ) { return false; } if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) { return false; } final PhylogenyNode n21x = PhylogenyNode - .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n21x.getName().equals( "n21_PIG" ) ) { return false; } @@ -5579,7 +6549,7 @@ public final class Test { return false; } final PhylogenyNode n22 = PhylogenyNode - .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n22.getName().equals( "n22/PIG" ) ) { return false; } @@ -5587,7 +6557,7 @@ public final class Test { return false; } final PhylogenyNode n23 = PhylogenyNode - .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n23.getName().equals( "n23/PIG_1" ) ) { return false; } @@ -5595,74 +6565,33 @@ public final class Test { return false; } final PhylogenyNode a = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) { + .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) { return false; } if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) { return false; } - final PhylogenyNode b = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) { - return false; - } - if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) { - return false; - } - final PhylogenyNode c = PhylogenyNode - .createInstanceFromNhxString( "n10_RATAF12/1000-2000", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) { - return false; - } - if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) { - return false; - } final PhylogenyNode c1 = PhylogenyNode - .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) { + .createInstanceFromNhxString( "n10_BOVIN/1000-2000", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) { return false; } - if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { + if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { return false; } final PhylogenyNode c2 = PhylogenyNode - .createInstanceFromNhxString( "n10_Bovin_1/1000-2000", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) { - return false; - } - if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) { + .createInstanceFromNhxString( "N10_Bovin_1/1000-2000", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) { return false; } - final PhylogenyNode d = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !d.getName().equals( "n10_RAT1/1-2" ) ) { + if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) { return false; } - if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) { - return false; - } - final PhylogenyNode e = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !e.getName().equals( "n10_RAT1" ) ) { - return false; - } - if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) { - return false; - } - final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !e2.getName().equals( "n10_RAT1" ) ) { - return false; - } - if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) { - return false; - } - final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode e3 = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !e3.getName().equals( "n10_RAT~" ) ) { return false; } @@ -5670,21 +6599,21 @@ public final class Test { return false; } final PhylogenyNode n11 = PhylogenyNode - .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) { + .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) { return false; } if ( n11.getDistanceToParent() != 0.4 ) { return false; } - if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) { + if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) { return false; } final PhylogenyNode n12 = PhylogenyNode - .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) { + .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) { return false; } if ( n12.getDistanceToParent() != 0.4 ) { @@ -5693,17 +6622,9 @@ public final class Test { if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) { return false; } - final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !m.getName().equals( "n10_MOUSEa" ) ) { - return false; - } - if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) { - return false; - } - final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_", - NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !o.getName().equals( "n10_MOUSE_" ) ) { + final PhylogenyNode o = PhylogenyNode + .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !o.getName().equals( "ABCD_MOUSE" ) ) { return false; } if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) { @@ -5740,7 +6661,7 @@ public final class Test { return false; } final PhylogenyNode n13 = PhylogenyNode - .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n13.getName().equals( "blah_12345/1-2" ) ) { return false; } @@ -5754,16 +6675,16 @@ public final class Test { return false; } final PhylogenyNode n14 = PhylogenyNode - .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !n14.getName().equals( "blah_12X45/1-2" ) ) { + .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) { + if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) { return false; } final PhylogenyNode n15 = PhylogenyNode .createInstanceFromNhxString( "something_wicked[123]", - NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n15.getName().equals( "something_wicked" ) ) { return false; } @@ -5774,7 +6695,8 @@ public final class Test { return false; } final PhylogenyNode n16 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "something_wicked2[9]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n16.getName().equals( "something_wicked2" ) ) { return false; } @@ -5785,7 +6707,8 @@ public final class Test { return false; } final PhylogenyNode n17 = PhylogenyNode - .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "something_wicked3[a]", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !n17.getName().equals( "something_wicked3" ) ) { return false; } @@ -5793,7 +6716,7 @@ public final class Test { return false; } final PhylogenyNode n18 = PhylogenyNode - .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) { return false; } @@ -5803,32 +6726,59 @@ public final class Test { if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) { return false; } - final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n19 = PhylogenyNode + .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) { return false; } if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { return false; } - final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n30 = PhylogenyNode + .createInstanceFromNhxString( "blah_1234567-roejojoej", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) { return false; } if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) { return false; } - final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n31 = PhylogenyNode + .createInstanceFromNhxString( "blah_12345678-roejojoej", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n31.getNodeData().isHasTaxonomy() ) { return false; } - final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678", - NHXParser.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n32 = PhylogenyNode + .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n32.getNodeData().isHasTaxonomy() ) { return false; } + final PhylogenyNode n40 = PhylogenyNode + .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { + return false; + } + final PhylogenyNode n41 = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n41.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n42 = PhylogenyNode + .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + if ( n42.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345", + NHXParser.TAXONOMY_EXTRACTION.NO ); + if ( n43.getNodeData().isHasTaxonomy() ) { + return false; + } + final PhylogenyNode n44 = PhylogenyNode + .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( n44.getNodeData().isHasTaxonomy() ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -6628,7 +7578,7 @@ public final class Test { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ]; - final int count = PhylogenyNode.getNodeCount(); + final long count = PhylogenyNode.getNodeCount(); p.levelOrderReID(); if ( p.getNode( "r" ).getId() != count ) { return false; @@ -8478,7 +9428,10 @@ public final class Test { if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) { return false; } - if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) { + if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861.2" ).equals( "AY423861.2" ) ) { + return false; + } + if ( !SequenceIdParser.parseGenbankAccessor( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) { return false; } if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) { @@ -8518,45 +9471,6 @@ public final class Test { } private static boolean testUniprotEntryRetrieval() { - if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) { - return false; - } - if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) { - return false; - } - if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) { - return false; - } try { final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 ); if ( !entry.getAccession().equals( "P12345" ) ) { @@ -8568,9 +9482,6 @@ public final class Test { if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) { return false; } - if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) { - return false; - } if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) { return false; } @@ -8678,6 +9589,37 @@ public final class Test { return true; } + private static boolean testSequenceWriter() { + try { + final String n = ForesterUtil.LINE_SEPARATOR; + if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString() + .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) { + return false; + } + if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString() + .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace(); + return false; + } + return true; + } + private static boolean testCreateBalancedPhylogeny() { try { final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );