X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=adcbac9e48a9d51d1c95b682f5c3af3f2d326d8b;hb=d4af4e66f7aee7d99deecc7b3a3125eb3748884e;hp=637d05cdd5bb4c6211e123125aac1928e633c923;hpb=ebaa3f63d0dc201b9b5a5cd91e2cfa3c7157f143;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 637d05c..adcbac9 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -54,14 +54,17 @@ import org.forester.io.parsers.nhx.NHXParser; import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.io.parsers.tol.TolParser; import org.forester.io.writers.PhylogenyWriter; +import org.forester.msa.BasicMsa; import org.forester.msa.Mafft; import org.forester.msa.Msa; import org.forester.msa.MsaInferrer; +import org.forester.msa.MsaMethods; import org.forester.pccx.TestPccx; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyBranch; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE; import org.forester.phylogeny.data.BinaryCharacters; import org.forester.phylogeny.data.BranchWidth; import org.forester.phylogeny.data.Confidence; @@ -70,6 +73,7 @@ import org.forester.phylogeny.data.DomainArchitecture; import org.forester.phylogeny.data.Event; import org.forester.phylogeny.data.Identifier; import org.forester.phylogeny.data.PhylogenyData; +import org.forester.phylogeny.data.PhylogenyDataUtil; import org.forester.phylogeny.data.Polygon; import org.forester.phylogeny.data.PropertiesMap; import org.forester.phylogeny.data.Property; @@ -79,6 +83,7 @@ import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; +import org.forester.protein.Protein; import org.forester.sdi.SDI; import org.forester.sdi.SDIR; import org.forester.sdi.SDIse; @@ -86,7 +91,6 @@ import org.forester.sdi.TaxonomyAssigner; import org.forester.sdi.TestGSDI; import org.forester.sequence.BasicSequence; import org.forester.sequence.Sequence; -import org.forester.surfacing.Protein; import org.forester.surfacing.TestSurfacing; import org.forester.tools.ConfidenceAssessor; import org.forester.tools.SupportCount; @@ -230,6 +234,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "NHX parsing (MrBayes): " ); + if ( Test.testNHXParsingMB() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Nexus characters parsing: " ); if ( Test.testNexusCharactersParsing() ) { System.out.println( "OK." ); @@ -684,6 +697,24 @@ public final class Test { System.out.println( "failed [will not count towards failed tests]" ); } } + System.out.print( "Next nodes with collapsed: " ); + if ( Test.testNextNodeWithCollapsing() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + System.out.print( "Simple MSA quality: " ); + if ( Test.testMsaQualityMethod() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } // System.out.print( "WABI TxSearch: " ); // if ( Test.testWabiTxSearch() ) { // System.out.println( "OK." ); @@ -785,11 +816,11 @@ public final class Test { } final PhylogenyNode n1 = new PhylogenyNode(); final PhylogenyNode n2 = PhylogenyNode - .createInstanceFromNhxString( "", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); final PhylogenyNode n3 = PhylogenyNode - .createInstanceFromNhxString( "n3", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); final PhylogenyNode n4 = PhylogenyNode - .createInstanceFromNhxString( "n4:0.01", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( n1.isHasAssignedEvent() ) { return false; } @@ -2830,7 +2861,7 @@ public final class Test { dss3.addValue( 10 ); final AsciiHistogram histo = new AsciiHistogram( dss3 ); histo.toStringBuffer( 10, '=', 40, 5 ); - histo.toStringBuffer( 3, 8, 10, '=', 40, 5 ); + histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null ); } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -3393,11 +3424,11 @@ public final class Test { parser1.parse(); final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); - final List domain_collections = parser2.parse(); + final List proteins = parser2.parse(); if ( parser2.getProteinsEncountered() != 4 ) { return false; } - if ( domain_collections.size() != 4 ) { + if ( proteins.size() != 4 ) { return false; } if ( parser2.getDomainsEncountered() != 69 ) { @@ -3409,11 +3440,25 @@ public final class Test { if ( parser2.getDomainsIgnoredDueToEval() != 0 ) { return false; } - final Protein p1 = domain_collections.get( 0 ); + final Protein p1 = proteins.get( 0 ); if ( p1.getNumberOfProteinDomains() != 15 ) { return false; } - final Protein p4 = domain_collections.get( 3 ); + if ( p1.getLength() != 850 ) { + return false; + } + final Protein p2 = proteins.get( 1 ); + if ( p2.getNumberOfProteinDomains() != 51 ) { + return false; + } + if ( p2.getLength() != 1291 ) { + return false; + } + final Protein p3 = proteins.get( 2 ); + if ( p3.getNumberOfProteinDomains() != 2 ) { + return false; + } + final Protein p4 = proteins.get( 3 ); if ( p4.getNumberOfProteinDomains() != 1 ) { return false; } @@ -4200,7 +4245,7 @@ public final class Test { return false; } final NHXParser nhxp = new NHXParser(); - nhxp.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO ); + nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO ); nhxp.setReplaceUnderscores( true ); final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ]; if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) { @@ -4426,6 +4471,58 @@ public final class Test { if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) { return false; } + final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ]; + if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p49 = factory + .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ), + new NHXParser() )[ 0 ]; + if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) { + return false; + } + final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ]; + if ( p50.getNode( "A" ) == null ) { + return false; + } + if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) + .equals( "((A,B)ab:2.0[88],C);" ) ) { + return false; + } + if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) { + return false; + } + if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ) + .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 ]; + 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 ]; + 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)" ), + 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 ]; + if ( p54.getNode( "A" ) == null ) { + return false; + } + if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) + .equals( "((A,B)[88],C);" ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -4457,11 +4554,10 @@ public final class Test { return false; } if ( !n5.toNewHampshireX() - .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56.0:W=2.0:C=10.20.30]" ) ) { + .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) { return false; } - if ( !n6.toNewHampshireX() - .equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100.0:W=2.0:C=0.0.0]" ) ) { + if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) { return false; } } @@ -4483,7 +4579,7 @@ public final class Test { if ( !n3.getName().equals( "n3" ) ) { return false; } - if ( n3.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) { + if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { return false; } if ( n3.isDuplication() ) { @@ -4526,7 +4622,8 @@ public final class Test { return false; } final PhylogenyNode n8 = PhylogenyNode - .createInstanceFromNhxString( "n8_ECOLI/12:0.01", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n8_ECOLI/12:0.01", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n8.getName().equals( "n8_ECOLI/12" ) ) { return false; } @@ -4535,7 +4632,7 @@ public final class Test { } final PhylogenyNode n9 = PhylogenyNode .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", - ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) { return false; } @@ -4543,20 +4640,20 @@ public final class Test { return false; } final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "n10.ECOLI", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n10.getName().equals( "n10.ECOLI" ) ) { return false; } final PhylogenyNode n20 = PhylogenyNode - .createInstanceFromNhxString( "n20_ECOLI/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) { return false; } if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) { return false; } - final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2", - ForesterUtil.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n20x = PhylogenyNode + .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) { return false; } @@ -4564,7 +4661,7 @@ public final class Test { return false; } final PhylogenyNode n20xx = PhylogenyNode - .createInstanceFromNhxString( "n20_eCOL1/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) { return false; } @@ -4572,7 +4669,7 @@ public final class Test { return false; } final PhylogenyNode n20xxx = PhylogenyNode - .createInstanceFromNhxString( "n20_ecoli/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) { return false; } @@ -4580,15 +4677,15 @@ public final class Test { return false; } final PhylogenyNode n20xxxx = PhylogenyNode - .createInstanceFromNhxString( "n20_Ecoli/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); 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", - ForesterUtil.TAXONOMY_EXTRACTION.YES ); + final PhylogenyNode n21 = PhylogenyNode + .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); if ( !n21.getName().equals( "n21_PIG" ) ) { return false; } @@ -4596,7 +4693,7 @@ public final class Test { return false; } final PhylogenyNode n21x = PhylogenyNode - .createInstanceFromNhxString( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n21x.getName().equals( "n21_PIG" ) ) { return false; } @@ -4604,7 +4701,7 @@ public final class Test { return false; } final PhylogenyNode n22 = PhylogenyNode - .createInstanceFromNhxString( "n22/PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n22.getName().equals( "n22/PIG" ) ) { return false; } @@ -4612,7 +4709,7 @@ public final class Test { return false; } final PhylogenyNode n23 = PhylogenyNode - .createInstanceFromNhxString( "n23/PIG_1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n23.getName().equals( "n23/PIG_1" ) ) { return false; } @@ -4621,7 +4718,8 @@ public final class Test { } if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) { final PhylogenyNode a = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_ECOLI/1-2", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) { return false; } @@ -4630,24 +4728,43 @@ public final class Test { } final PhylogenyNode b = PhylogenyNode .createInstanceFromNhxString( "n10_ECOLI1/1-2", - ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) { + if ( !PhylogenyMethods.getSpecies( b ).equals( "" ) ) { return false; } final PhylogenyNode c = PhylogenyNode .createInstanceFromNhxString( "n10_RATAF12/1000-2000", - ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) { + if ( !PhylogenyMethods.getSpecies( c ).equals( "" ) ) { + return false; + } + final PhylogenyNode c1 = PhylogenyNode + .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { + return false; + } + final PhylogenyNode c2 = PhylogenyNode + .createInstanceFromNhxString( "n10_Bovin_1/1000-2000", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) { return false; } final PhylogenyNode d = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_RAT1/1-2", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !d.getName().equals( "n10_RAT1/1-2" ) ) { return false; } @@ -4655,7 +4772,7 @@ public final class Test { return false; } final PhylogenyNode e = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !e.getName().equals( "n10_RAT1" ) ) { return false; } @@ -4665,7 +4782,7 @@ public final class Test { } final PhylogenyNode n11 = PhylogenyNode .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4", - ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) { return false; } @@ -4677,7 +4794,7 @@ public final class Test { } final PhylogenyNode n12 = PhylogenyNode .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4", - ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) { return false; } @@ -4719,7 +4836,7 @@ public final class Test { if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { return false; } - if ( n1.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) { + if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { return false; } if ( n2.getName().compareTo( "" ) != 0 ) { @@ -4728,7 +4845,7 @@ public final class Test { if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) { return false; } - if ( n2.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) { + if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { return false; } final PhylogenyNode n00 = PhylogenyNode @@ -4766,7 +4883,8 @@ public final class Test { return false; } final PhylogenyNode n13 = PhylogenyNode - .createInstanceFromNhxString( "blah_12345/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "blah_12345/1-2", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n13.getName().equals( "blah_12345/1-2" ) ) { return false; } @@ -4774,7 +4892,8 @@ public final class Test { return false; } final PhylogenyNode n14 = PhylogenyNode - .createInstanceFromNhxString( "blah_12X45/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( "blah_12X45/1-2", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n14.getName().equals( "blah_12X45/1-2" ) ) { return false; } @@ -4783,7 +4902,7 @@ public final class Test { } final PhylogenyNode n15 = PhylogenyNode .createInstanceFromNhxString( "something_wicked[123]", - ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n15.getName().equals( "something_wicked" ) ) { return false; } @@ -4795,7 +4914,7 @@ public final class Test { } final PhylogenyNode n16 = PhylogenyNode .createInstanceFromNhxString( "something_wicked2[9]", - ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n16.getName().equals( "something_wicked2" ) ) { return false; } @@ -4807,7 +4926,7 @@ public final class Test { } final PhylogenyNode n17 = PhylogenyNode .createInstanceFromNhxString( "something_wicked3[a]", - ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !n17.getName().equals( "something_wicked3" ) ) { return false; } @@ -4815,7 +4934,7 @@ public final class Test { return false; } final PhylogenyNode n18 = PhylogenyNode - .createInstanceFromNhxString( ":0.5[91]", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) { return false; } @@ -4845,7 +4964,7 @@ public final class Test { if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) { return false; } - final String p2b_S = "(((((((A:0.2[&NHX:S=qwerty]):0.2[&:S=uiop]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]"; + final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]"; final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() ); if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) { return false; @@ -4887,13 +5006,13 @@ public final class Test { return false; } final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ]; - if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91.0],C:0.1)root:0.1[&&NHX:B=100.0]" ) ) { + if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } final Phylogeny p10 = factory .create( " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]", new NHXParser() )[ 0 ]; - if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91.0],C:0.1)root:0.1[&&NHX:B=100.0]" ) ) { + if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } } @@ -4968,7 +5087,7 @@ public final class Test { final Phylogeny p10 = factory .create( " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]", new NHXParser() )[ 0 ]; - final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91.0],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100.0]"; + final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]"; if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) { return false; } @@ -4980,7 +5099,7 @@ public final class Test { final Phylogeny p12 = factory .create( " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]", new NHXParser() )[ 0 ]; - final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91.0],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100.0]"; + final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]"; if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) { return false; } @@ -5004,6 +5123,60 @@ public final class Test { return true; } + private static boolean testNHXParsingMB() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02," + + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02," + + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," + + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," + + "7.369400000000000e-02}])", new NHXParser() )[ 0 ]; + if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) { + return false; + } + if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) { + return false; + } + if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(), + 0.1100000000000000e+00 ) ) { + return false; + } + if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) { + return false; + } + if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) { + return false; + } + final Phylogeny p2 = factory + .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02," + + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02," + + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," + + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," + + "7.369400000000000e-02}])", + new NHXParser() )[ 0 ]; + if ( p2.getNode( "1" ) == null ) { + return false; + } + if ( p2.getNode( "2" ) == null ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + System.exit( -1 ); + return false; + } + return true; + } + private static boolean testPhylogenyBranch() { try { final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" ); @@ -7743,13 +7916,15 @@ public final class Test { if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) { return false; } - if ( !results.get( 0 ).getLineage()[ 0 ].equals( "Eukaryota" ) ) { + if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) { return false; } - if ( !results.get( 0 ).getLineage()[ 1 ].equals( "Metazoa" ) ) { + if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) { return false; } - if ( !results.get( 0 ).getLineage()[ results.get( 0 ).getLineage().length - 1 ].equals( "Nematostella" ) ) { + if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 ) + .equals( "Nematostella vectensis" ) ) { + System.out.println( results.get( 0 ).getLineage() ); return false; } } @@ -8036,12 +8211,48 @@ public final class Test { try { final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n"; final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) ); - final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n"; + final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n"; final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) ); final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n"; final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) ); final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n"; final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) ); + if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + return false; + } + if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + return false; + } + if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + return false; + } + if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + return false; + } + if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + return false; + } + if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + return false; + } + if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + return false; + } + if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + return false; + } + if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + return false; + } + if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + return false; + } + if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + return false; + } + if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + return false; + } final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) ); if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) { return false; @@ -8089,8 +8300,604 @@ public final class Test { opts.add( "--quiet" ); Msa msa = null; final MsaInferrer mafft = Mafft.createInstance(); - msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts ); - if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) { + msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts ); + if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) { + return false; + } + if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNextNodeWithCollapsing() { + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + PhylogenyNode n; + List ext = new ArrayList(); + final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ]; + t0.getNode( "cd" ).setCollapse( true ); + t0.getNode( "cde" ).setCollapse( true ); + n = t0.getFirstExternalNode(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( !ext.get( 0 ).getName().equals( "a" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "b" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "cde" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "f" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "g" ) ) { + return false; + } + if ( !ext.get( 5 ).getName().equals( "h" ) ) { + return false; + } + ext.clear(); + final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ]; + t1.getNode( "ab" ).setCollapse( true ); + t1.getNode( "cd" ).setCollapse( true ); + t1.getNode( "cde" ).setCollapse( true ); + n = t1.getNode( "ab" ); + ext = new ArrayList(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "f" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "g" ) ) { + return false; + } + 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 ]; + t2.getNode( "ab" ).setCollapse( true ); + t2.getNode( "cd" ).setCollapse( true ); + t2.getNode( "cde" ).setCollapse( true ); + t2.getNode( "c" ).setCollapse( true ); + t2.getNode( "d" ).setCollapse( true ); + t2.getNode( "e" ).setCollapse( true ); + t2.getNode( "gh" ).setCollapse( true ); + n = t2.getNode( "ab" ); + ext = new ArrayList(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "f" ) ) { + return false; + } + 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 ]; + t3.getNode( "ab" ).setCollapse( true ); + t3.getNode( "cd" ).setCollapse( true ); + t3.getNode( "cde" ).setCollapse( true ); + t3.getNode( "c" ).setCollapse( true ); + t3.getNode( "d" ).setCollapse( true ); + t3.getNode( "e" ).setCollapse( true ); + t3.getNode( "gh" ).setCollapse( true ); + t3.getNode( "fgh" ).setCollapse( true ); + n = t3.getNode( "ab" ); + ext = new ArrayList(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + return false; + } + 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 ]; + t4.getNode( "ab" ).setCollapse( true ); + t4.getNode( "cd" ).setCollapse( true ); + t4.getNode( "cde" ).setCollapse( true ); + t4.getNode( "c" ).setCollapse( true ); + t4.getNode( "d" ).setCollapse( true ); + t4.getNode( "e" ).setCollapse( true ); + t4.getNode( "gh" ).setCollapse( true ); + t4.getNode( "fgh" ).setCollapse( true ); + t4.getNode( "abcdefgh" ).setCollapse( true ); + n = t4.getNode( "abcdefgh" ); + if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) { + return false; + } + // + // + final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); + final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; + ext.clear(); + n = t5.getFirstExternalNode(); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 8 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "a" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "b" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "e" ) ) { + return false; + } + if ( !ext.get( 5 ).getName().equals( "f" ) ) { + return false; + } + if ( !ext.get( 6 ).getName().equals( "g" ) ) { + return false; + } + 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 ]; + ext.clear(); + t6.getNode( "ab" ).setCollapse( true ); + n = t6.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 7 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "e" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "f" ) ) { + return false; + } + if ( !ext.get( 5 ).getName().equals( "g" ) ) { + return false; + } + 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 ]; + ext.clear(); + t7.getNode( "cd" ).setCollapse( true ); + n = t7.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 7 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "a" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "b" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "cd" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "e" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "f" ) ) { + return false; + } + if ( !ext.get( 5 ).getName().equals( "g" ) ) { + return false; + } + 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 ]; + ext.clear(); + t8.getNode( "cd" ).setCollapse( true ); + t8.getNode( "c" ).setCollapse( true ); + t8.getNode( "d" ).setCollapse( true ); + n = t8.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 7 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "a" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "b" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "cd" ) ) { + System.out.println( "2 fail" ); + return false; + } + if ( !ext.get( 3 ).getName().equals( "e" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "f" ) ) { + return false; + } + if ( !ext.get( 5 ).getName().equals( "g" ) ) { + return false; + } + 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 ]; + ext.clear(); + t9.getNode( "gh" ).setCollapse( true ); + n = t9.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 7 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "a" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "b" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "e" ) ) { + return false; + } + if ( !ext.get( 5 ).getName().equals( "f" ) ) { + return false; + } + 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 ]; + ext.clear(); + t10.getNode( "gh" ).setCollapse( true ); + t10.getNode( "g" ).setCollapse( true ); + t10.getNode( "h" ).setCollapse( true ); + n = t10.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 7 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "a" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "b" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "e" ) ) { + return false; + } + if ( !ext.get( 5 ).getName().equals( "f" ) ) { + return false; + } + 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 ]; + ext.clear(); + t11.getNode( "gh" ).setCollapse( true ); + t11.getNode( "fgh" ).setCollapse( true ); + n = t11.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 6 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "a" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "b" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "e" ) ) { + return false; + } + 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 ]; + ext.clear(); + t12.getNode( "gh" ).setCollapse( true ); + t12.getNode( "fgh" ).setCollapse( true ); + t12.getNode( "g" ).setCollapse( true ); + t12.getNode( "h" ).setCollapse( true ); + t12.getNode( "f" ).setCollapse( true ); + n = t12.getNode( "a" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 6 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "a" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "b" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "e" ) ) { + return false; + } + 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 ]; + ext.clear(); + t13.getNode( "ab" ).setCollapse( true ); + t13.getNode( "b" ).setCollapse( true ); + t13.getNode( "fgh" ).setCollapse( true ); + t13.getNode( "gh" ).setCollapse( true ); + n = t13.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 5 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "e" ) ) { + return false; + } + 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 ]; + ext.clear(); + t14.getNode( "ab" ).setCollapse( true ); + t14.getNode( "a" ).setCollapse( true ); + t14.getNode( "fgh" ).setCollapse( true ); + t14.getNode( "gh" ).setCollapse( true ); + n = t14.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 5 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "e" ) ) { + return false; + } + 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 ]; + ext.clear(); + t15.getNode( "ab" ).setCollapse( true ); + t15.getNode( "a" ).setCollapse( true ); + t15.getNode( "fgh" ).setCollapse( true ); + t15.getNode( "gh" ).setCollapse( true ); + n = t15.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 6 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "c" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "d" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "e" ) ) { + return false; + } + if ( !ext.get( 4 ).getName().equals( "x" ) ) { + return false; + } + if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { + return false; + } + // + // + final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); + final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ]; + ext.clear(); + t16.getNode( "ab" ).setCollapse( true ); + t16.getNode( "a" ).setCollapse( true ); + t16.getNode( "fgh" ).setCollapse( true ); + t16.getNode( "gh" ).setCollapse( true ); + t16.getNode( "cd" ).setCollapse( true ); + t16.getNode( "cde" ).setCollapse( true ); + t16.getNode( "d" ).setCollapse( true ); + t16.getNode( "x" ).setCollapse( true ); + n = t16.getNode( "ab" ); + while ( n != null ) { + ext.add( n ); + n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes(); + } + if ( ext.size() != 4 ) { + return false; + } + if ( !ext.get( 0 ).getName().equals( "ab" ) ) { + return false; + } + if ( !ext.get( 1 ).getName().equals( "cde" ) ) { + return false; + } + if ( !ext.get( 2 ).getName().equals( "x" ) ) { + return false; + } + if ( !ext.get( 3 ).getName().equals( "fgh" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testMsaQualityMethod() { + try { + final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" ); + final Sequence s1 = BasicSequence.createAaSequence( "a", "ABBXEFGHIJ" ); + final Sequence s2 = BasicSequence.createAaSequence( "a", "AXCXEFGHIJ" ); + final Sequence s3 = BasicSequence.createAaSequence( "a", "AXDDEFGHIJ" ); + final List l = new ArrayList(); + l.add( s0 ); + l.add( s1 ); + l.add( s2 ); + l.add( s3 ); + final Msa msa = BasicMsa.createInstance( l ); + if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) { + return false; + } + if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) { + return false; + } + if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) { + return false; + } + if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) { return false; } }