+ final String p3_str = "((A,B),C)abc";
+ p.setSource( p3_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p3_0 = p.next();
+ if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p4_str = "((A,B)ab,C)abc";
+ p.setSource( p4_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p4_0 = p.next();
+ if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p5_str = "(((A,B)ab,C)abc,D)abcd";
+ p.setSource( p5_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p5_0 = p.next();
+ if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ p.setSource( p6_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p6_0 = p.next();
+ if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p6_0 = p.next();
+ if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ p.setSource( p7_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p7_0 = p.next();
+ if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p7_0 = p.next();
+ if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
+ p.setSource( p8_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p8_0 = p.next();
+ if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p8_1 = p.next();
+ if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p8_0 = p.next();
+ if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p8_1 = p.next();
+ if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ p.reset();
+ //
+ p.setSource( "" );
+ if ( p.hasNext() ) {
+ return false;
+ }
+ //
+ p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p_27 = p.next();
+ if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
+ System.out.println( p_27.toNewHampshireX() );
+ System.exit( -1 );
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p_27 = p.next();
+ if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
+ System.out.println( p_27.toNewHampshireX() );
+ System.exit( -1 );
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHXconversion() {
+ try {
+ final PhylogenyNode n1 = new PhylogenyNode();
+ final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
+ final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
+ final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
+ final PhylogenyNode n5 = PhylogenyNode
+ .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
+ final PhylogenyNode n6 = PhylogenyNode
+ .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
+ if ( !n1.toNewHampshireX().equals( "" ) ) {
+ return false;
+ }
+ if ( !n2.toNewHampshireX().equals( "" ) ) {
+ return false;
+ }
+ if ( !n3.toNewHampshireX().equals( "n3" ) ) {
+ return false;
+ }
+ if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
+ return false;
+ }
+ if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
+ 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;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHXNodeParsing() {
+ try {
+ final PhylogenyNode n1 = new PhylogenyNode();
+ final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
+ final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
+ final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
+ final PhylogenyNode n5 = PhylogenyNode
+ .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" );
+ if ( !n3.getName().equals( "n3" ) ) {
+ return false;
+ }
+ if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
+ return false;
+ }
+ if ( n3.isDuplication() ) {
+ return false;
+ }
+ if ( n3.isHasAssignedEvent() ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
+ return false;
+ }
+ if ( !n4.getName().equals( "n4" ) ) {
+ return false;
+ }
+ if ( n4.getDistanceToParent() != 0.01 ) {
+ return false;
+ }
+ if ( !n5.getName().equals( "n5" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
+ return false;
+ }
+ if ( n5.getDistanceToParent() != 0.1 ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
+ return false;
+ }
+ if ( !n5.isDuplication() ) {
+ return false;
+ }
+ if ( !n5.isHasAssignedEvent() ) {
+ return false;
+ }
+ final PhylogenyNode n8 = PhylogenyNode
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
+ return false;
+ }
+ final PhylogenyNode n9 = PhylogenyNode
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
+ return false;
+ }
+ final PhylogenyNode n10 = PhylogenyNode
+ .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n10.getName().equals( "n10.ECOLI" ) ) {
+ return false;
+ }
+ final PhylogenyNode n20 = PhylogenyNode
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
+ return false;
+ }
+ final PhylogenyNode n20x = PhylogenyNode
+ .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
+ return false;
+ }
+ final PhylogenyNode n20xx = PhylogenyNode
+ .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
+ return false;
+ }
+ final PhylogenyNode n20xxx = PhylogenyNode
+ .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
+ return false;
+ }
+ final PhylogenyNode n20xxxx = PhylogenyNode
+ .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
+ return false;
+ }
+ 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_STRICT );
+ if ( !n21x.getName().equals( "n21_PIG" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
+ return false;
+ }
+ final PhylogenyNode n22 = PhylogenyNode
+ .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n22.getName().equals( "n22/PIG" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
+ return false;
+ }
+ final PhylogenyNode n23 = PhylogenyNode
+ .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n23.getName().equals( "n23/PIG_1" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
+ return false;
+ }
+ final PhylogenyNode a = PhylogenyNode
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
+ return false;
+ }
+ final PhylogenyNode c1 = PhylogenyNode
+ .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
+ return false;
+ }
+ final PhylogenyNode c2 = PhylogenyNode
+ .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
+ return false;
+ }
+ final PhylogenyNode e3 = PhylogenyNode
+ .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !e3.getName().equals( "n10_RAT~" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
+ return false;
+ }
+ final PhylogenyNode n11 = PhylogenyNode
+ .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
+ return false;
+ }
+ if ( n11.getDistanceToParent() != 0.4 ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
+ return false;
+ }
+ final PhylogenyNode n12 = PhylogenyNode
+ .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
+ return false;
+ }
+ if ( n12.getDistanceToParent() != 0.4 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
+ return false;
+ }
+ 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" ) ) {
+ return false;
+ }
+ if ( n1.getName().compareTo( "" ) != 0 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ return false;
+ }
+ if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
+ return false;
+ }
+ if ( n2.getName().compareTo( "" ) != 0 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ return false;
+ }
+ if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
+ return false;
+ }
+ final PhylogenyNode n00 = PhylogenyNode
+ .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
+ if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
+ return false;
+ }
+ if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
+ return false;
+ }
+ final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
+ if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
+ return false;
+ }
+ final PhylogenyNode n13 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
+ return false;
+ }
+ if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
+ return false;
+ }
+ if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
+ return false;
+ }
+ if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
+ return false;
+ }
+ final PhylogenyNode n14 = PhylogenyNode
+ .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
+ return false;
+ }
+ final PhylogenyNode n15 = PhylogenyNode
+ .createInstanceFromNhxString( "something_wicked[123]",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n15.getName().equals( "something_wicked" ) ) {
+ return false;
+ }
+ if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
+ return false;
+ }
+ if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
+ return false;
+ }
+ final PhylogenyNode n16 = PhylogenyNode
+ .createInstanceFromNhxString( "something_wicked2[9]",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n16.getName().equals( "something_wicked2" ) ) {
+ return false;
+ }
+ if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
+ return false;
+ }
+ if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
+ return false;
+ }
+ final PhylogenyNode n17 = PhylogenyNode
+ .createInstanceFromNhxString( "something_wicked3[a]",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n17.getName().equals( "something_wicked3" ) ) {
+ return false;
+ }
+ if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
+ return false;
+ }
+ final PhylogenyNode n18 = PhylogenyNode
+ .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
+ return false;
+ }
+ if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
+ return false;
+ }
+ if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
+ return false;
+ }
+ final PhylogenyNode n19 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
+ return false;
+ }
+ if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
+ return false;
+ }
+ final PhylogenyNode n30 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_1234567-roejojoej",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
+ return false;
+ }
+ if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
+ return false;
+ }
+ final PhylogenyNode n31 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_12345678-roejojoej",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n31.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n32 = PhylogenyNode
+ .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n32.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n40 = PhylogenyNode
+ .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
+ return false;
+ }
+ final PhylogenyNode n41 = PhylogenyNode
+ .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n41.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n42 = PhylogenyNode
+ .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( n42.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
+ NHXParser.TAXONOMY_EXTRACTION.NO );
+ if ( n43.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n44 = PhylogenyNode
+ .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n44.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHXParsing() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
+ if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
+ return false;
+ }
+ final String p2_S = "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]";
+ final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
+ if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
+ return false;
+ }
+ final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]";
+ final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
+ if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
+ return false;
+ }
+ final Phylogeny[] p3 = factory
+ .create( "[ comment&&NHX,())))](((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]",
+ new NHXParser() );
+ if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
+ return false;
+ }
+ final Phylogeny[] p4 = factory
+ .create( "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(]",
+ new NHXParser() );
+ if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
+ return false;
+ }
+ final Phylogeny[] p5 = factory
+ .create( "[] ( [][ ][ ] ([((( &&NHXcomment only![[[[[[]([]((((A:0.2[&&NHX:S=q[comment )))]werty][,,,,))]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=a[comment,,))]sdf])[comment(((]:0.4[&&NHX:S=zxc][comment(((][comment(((]):0.5[&&NHX:S=a]):0.6[&&NHX:S=a[comment(((]sd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(((]",
+ new NHXParser() );
+ if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
+ return false;
+ }
+ final String p6_S_C = "(A[][][][1][22][333][4444][55555][666666][&&NHX:S=Aspecies],B[))],C,(AA,BB,CC,(CCC,DDD,EEE,[comment](FFFF,GGGG)x)y,D[comment]D,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
+ final String p6_S_WO_C = "(A[&&NHX:S=Aspecies],B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
+ final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
+ if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
+ return false;
+ }
+ final String p7_S_C = "(((A [&&NHX:S=species_a], B [&&NHX:S=Vstorri] , C , D),(A,B,C,D[comment])[],[c][]([xxx]A[comment],[comment]B[comment][comment],[comment][comment]C[comment][comment],[comment][comment]D[comment][comment])[comment][comment],[comment] [comment](A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C[comment][comment][comment][comment][comment] [comment],D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),[comment][comment]((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
+ final String p7_S_WO_C = "(((A[&&NHX:S=species_a],B[&&NHX:S=Vstorri],C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
+ final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
+ if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
+ return false;
+ }
+ final String p8_S_C = "[cmt](((([]([))))))](((((A[&&NHX:S= [a comment] a])))))))[too many comments!:)])),(((((((((B[&&NHX[ a comment in a bad place]:S =b])))))[] [] )))),(((((((((C[&&NHX:S=c]) ))[,,, ])))))))";
+ final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
+ final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
+ if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
+ return false;
+ }
+ final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
+ if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
+ return false;
+ }
+ final Phylogeny p10 = factory
+ .create( " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]",
+ new NHXParser() )[ 0 ];
+ if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHXParsingMB() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
+ + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
+ + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
+ + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
+ + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
+ + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
+ + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
+ if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
+ return false;
+ }
+ if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
+ return false;
+ }
+ if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
+ 0.1100000000000000e+00 ) ) {
+ return false;
+ }
+ if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
+ return false;
+ }
+ if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
+ return false;
+ }
+ final Phylogeny p2 = factory
+ .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
+ + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
+ + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
+ + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
+ + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
+ + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
+ + "7.369400000000000e-02}])",
+ new NHXParser() )[ 0 ];
+ if ( p2.getNode( "1" ) == null ) {
+ return false;
+ }
+ if ( p2.getNode( "2" ) == null ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ System.exit( -1 );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHXParsingQuotes() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final NHXParser p = new NHXParser();
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
+ if ( phylogenies_0.length != 5 ) {
+ return false;
+ }
+ final Phylogeny phy = phylogenies_0[ 4 ];
+ if ( phy.getNumberOfExternalNodes() != 7 ) {
+ return false;
+ }
+ if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
+ return false;
+ }
+ if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
+ return false;
+ }
+ if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
+ .getScientificName().equals( "hsapiens" ) ) {
+ return false;
+ }
+ if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
+ return false;
+ }
+ if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
+ return false;
+ }
+ if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
+ return false;
+ }
+ if ( phy.getNodes( "noquotes" ).size() != 1 ) {
+ return false;
+ }
+ if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
+ return false;
+ }
+ final NHXParser p1p = new NHXParser();
+ p1p.setIgnoreQuotes( true );
+ final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
+ if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
+ return false;
+ }
+ final NHXParser p2p = new NHXParser();
+ p1p.setIgnoreQuotes( false );
+ final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
+ if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
+ return false;
+ }
+ final NHXParser p3p = new NHXParser();
+ p3p.setIgnoreQuotes( false );
+ final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
+ if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
+ return false;
+ }
+ final NHXParser p4p = new NHXParser();
+ p4p.setIgnoreQuotes( false );
+ final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
+ if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
+ return false;
+ }
+ final Phylogeny p10 = factory
+ .create( " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]",
+ new NHXParser() )[ 0 ];
+ final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
+ if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
+ return false;
+ }
+ final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
+ if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
+ return false;
+ }
+ //
+ final Phylogeny p12 = factory
+ .create( " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]",
+ new NHXParser() )[ 0 ];
+ final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
+ if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
+ return false;
+ }
+ final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
+ if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
+ return false;
+ }
+ final String p12_clean_str_nh = "(('A B':0.2,'BB B':0.03):0.5,'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1;";
+ if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
+ return false;
+ }
+ final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
+ if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNodeRemoval() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
+ if ( !t0.toNewHampshire().equals( "(a);" ) ) {
+ return false;
+ }
+ final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
+ if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
+ return false;
+ }
+ final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
+ if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testPhylogenyBranch() {
+ try {
+ final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
+ final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
+ final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
+ final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
+ if ( !a1b1.equals( a1b1 ) ) {
+ return false;
+ }
+ if ( !a1b1.equals( b1a1 ) ) {
+ return false;
+ }
+ if ( !b1a1.equals( a1b1 ) ) {
+ return false;
+ }
+ final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
+ final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
+ final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
+ if ( a1_b1.equals( b1_a1 ) ) {
+ return false;
+ }
+ if ( a1_b1.equals( a1_b1_ ) ) {
+ return false;
+ }
+ final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
+ if ( !a1_b1.equals( b1_a1_ ) ) {
+ return false;
+ }
+ if ( a1_b1_.equals( b1_a1_ ) ) {
+ return false;
+ }
+ if ( !a1_b1_.equals( b1_a1 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testPhyloXMLparsingOfDistributionElement() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ PhyloXmlParser xml_parser = null;
+ try {
+ xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
+ }
+ catch ( final Exception e ) {
+ // Do nothing -- means were not running from jar.
+ }
+ if ( xml_parser == null ) {
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();
+ if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
+ xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
+ }
+ else {
+ xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
+ }
+ }
+ final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
+ xml_parser );
+ if ( xml_parser.getErrorCount() > 0 ) {
+ System.out.println( xml_parser.getErrorMessages().toString() );
+ return false;
+ }
+ if ( phylogenies_0.length != 1 ) {
+ return false;
+ }
+ final Phylogeny t1 = phylogenies_0[ 0 ];
+ PhylogenyNode n = null;
+ Distribution d = null;
+ n = t1.getNode( "root node" );
+ if ( !n.getNodeData().isHasDistribution() ) {
+ return false;
+ }
+ if ( n.getNodeData().getDistributions().size() != 1 ) {
+ return false;
+ }
+ d = n.getNodeData().getDistribution();
+ if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
+ return false;
+ }
+ if ( d.getPoints().size() != 1 ) {
+ return false;
+ }
+ if ( d.getPolygons() != null ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
+ return false;
+ }
+ n = t1.getNode( "node a" );
+ if ( !n.getNodeData().isHasDistribution() ) {
+ return false;
+ }
+ if ( n.getNodeData().getDistributions().size() != 2 ) {
+ return false;
+ }
+ d = n.getNodeData().getDistribution( 1 );
+ if ( !d.getDesc().equals( "San Diego" ) ) {
+ return false;
+ }
+ if ( d.getPoints().size() != 1 ) {
+ return false;
+ }
+ if ( d.getPolygons() != null ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
+ return false;
+ }
+ n = t1.getNode( "node bb" );
+ if ( !n.getNodeData().isHasDistribution() ) {
+ return false;
+ }
+ if ( n.getNodeData().getDistributions().size() != 1 ) {
+ return false;
+ }
+ d = n.getNodeData().getDistribution( 0 );
+ if ( d.getPoints().size() != 3 ) {
+ return false;
+ }
+ if ( d.getPolygons().size() != 2 ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
+ return false;
+ }
+ Polygon p = d.getPolygons().get( 0 );
+ if ( p.getPoints().size() != 3 ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
+ return false;
+ }
+ p = d.getPolygons().get( 1 );
+ if ( p.getPoints().size() != 3 ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
+ return false;
+ }
+ // Roundtrip:
+ final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
+ final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
+ if ( rt.length != 1 ) {
+ return false;
+ }
+ final Phylogeny t1_rt = rt[ 0 ];
+ n = t1_rt.getNode( "root node" );
+ if ( !n.getNodeData().isHasDistribution() ) {
+ return false;
+ }
+ if ( n.getNodeData().getDistributions().size() != 1 ) {
+ return false;
+ }
+ d = n.getNodeData().getDistribution();
+ if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
+ return false;
+ }
+ if ( d.getPoints().size() != 1 ) {
+ return false;
+ }
+ if ( d.getPolygons() != null ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
+ return false;
+ }
+ n = t1_rt.getNode( "node a" );
+ if ( !n.getNodeData().isHasDistribution() ) {
+ return false;
+ }
+ if ( n.getNodeData().getDistributions().size() != 2 ) {
+ return false;
+ }
+ d = n.getNodeData().getDistribution( 1 );
+ if ( !d.getDesc().equals( "San Diego" ) ) {
+ return false;
+ }
+ if ( d.getPoints().size() != 1 ) {
+ return false;
+ }
+ if ( d.getPolygons() != null ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
+ return false;
+ }
+ n = t1_rt.getNode( "node bb" );
+ if ( !n.getNodeData().isHasDistribution() ) {
+ return false;
+ }
+ if ( n.getNodeData().getDistributions().size() != 1 ) {
+ return false;
+ }
+ d = n.getNodeData().getDistribution( 0 );
+ if ( d.getPoints().size() != 3 ) {
+ return false;
+ }
+ if ( d.getPolygons().size() != 2 ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
+ return false;
+ }
+ if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
+ return false;
+ }
+ p = d.getPolygons().get( 0 );
+ if ( p.getPoints().size() != 3 ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
+ return false;
+ }
+ p = d.getPolygons().get( 1 );
+ if ( p.getPoints().size() != 3 ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
+ return false;
+ }
+ if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testPostOrderIterator() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
+ PhylogenyNodeIterator it0;
+ for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
+ it0.next();
+ }
+ for( it0.reset(); it0.hasNext(); ) {
+ it0.next();
+ }
+ final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
+ final PhylogenyNodeIterator it = t1.iteratorPostorder();
+ if ( !it.next().getName().equals( "A" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "B" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "ab" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "C" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "D" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "cd" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "abcd" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "E" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "F" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "ef" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "G" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "H" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "gh" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "efgh" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "r" ) ) {
+ return false;
+ }
+ if ( it.hasNext() ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testPreOrderIterator() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
+ PhylogenyNodeIterator it0;
+ for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
+ it0.next();
+ }
+ for( it0.reset(); it0.hasNext(); ) {
+ it0.next();
+ }
+ PhylogenyNodeIterator it = t0.iteratorPreorder();
+ if ( !it.next().getName().equals( "r" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "ab" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "A" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "B" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "cd" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "C" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "D" ) ) {
+ return false;
+ }
+ if ( it.hasNext() ) {
+ return false;
+ }
+ final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
+ it = t1.iteratorPreorder();
+ if ( !it.next().getName().equals( "r" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "abcd" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "ab" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "A" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "B" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "cd" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "C" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "D" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "efgh" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "ef" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "E" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "F" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "gh" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "G" ) ) {
+ return false;
+ }
+ if ( !it.next().getName().equals( "H" ) ) {
+ return false;
+ }
+ if ( it.hasNext() ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testPropertiesMap() {
+ try {
+ final PropertiesMap pm = new PropertiesMap();
+ final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
+ final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
+ final Property p2 = new Property( "something:else",
+ "?",
+ "improbable:research",
+ "xsd:decimal",
+ AppliesTo.NODE );
+ pm.addProperty( p0 );
+ pm.addProperty( p1 );
+ pm.addProperty( p2 );
+ if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
+ return false;
+ }
+ if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
+ return false;
+ }
+ if ( pm.getProperties().size() != 3 ) {
+ return false;
+ }
+ if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
+ return false;
+ }
+ if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
+ return false;
+ }
+ if ( pm.getProperties().size() != 3 ) {
+ return false;
+ }
+ pm.removeProperty( "dimensions:diameter" );
+ if ( pm.getProperties().size() != 2 ) {
+ return false;
+ }
+ if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
+ return false;
+ }
+ if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testProteinId() {
+ try {
+ final ProteinId id1 = new ProteinId( "a" );
+ final ProteinId id2 = new ProteinId( "a" );
+ final ProteinId id3 = new ProteinId( "A" );
+ final ProteinId id4 = new ProteinId( "b" );
+ if ( !id1.equals( id1 ) ) {
+ return false;
+ }
+ if ( id1.getId().equals( "x" ) ) {
+ return false;
+ }
+ if ( id1.getId().equals( null ) ) {
+ return false;
+ }
+ if ( !id1.equals( id2 ) ) {
+ return false;
+ }
+ if ( id1.equals( id3 ) ) {
+ return false;
+ }
+ if ( id1.hashCode() != id1.hashCode() ) {
+ return false;
+ }
+ if ( id1.hashCode() != id2.hashCode() ) {
+ return false;
+ }
+ if ( id1.hashCode() == id3.hashCode() ) {
+ return false;
+ }
+ if ( id1.compareTo( id1 ) != 0 ) {
+ return false;
+ }
+ if ( id1.compareTo( id2 ) != 0 ) {
+ return false;
+ }
+ if ( id1.compareTo( id3 ) != 0 ) {
+ return false;
+ }
+ if ( id1.compareTo( id4 ) >= 0 ) {
+ return false;
+ }
+ if ( id4.compareTo( id1 ) <= 0 ) {
+ return false;
+ }
+ if ( !id4.getId().equals( "b" ) ) {
+ return false;
+ }
+ final ProteinId id5 = new ProteinId( " C " );
+ if ( !id5.getId().equals( "C" ) ) {
+ return false;
+ }
+ if ( id5.equals( id1 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testReIdMethods() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
+ final long count = PhylogenyNode.getNodeCount();
+ p.levelOrderReID();
+ if ( p.getNode( "r" ).getId() != count ) {
+ return false;
+ }
+ if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
+ return false;
+ }
+ if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
+ return false;
+ }
+ if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
+ return false;
+ }
+ if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
+ return false;
+ }
+ if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
+ return false;
+ }
+ if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
+ return false;
+ }
+ if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
+ return false;
+ }
+ if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
+ return false;
+ }
+ if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
+ return false;
+ }
+ if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
+ return false;
+ }
+ if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
+ return false;
+ }
+ if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
+ return false;
+ }
+ if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
+ return false;
+ }
+ if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testRerooting() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:5)CD:3[&&NHX:B=10])ABCD:0.5",
+ new NHXParser() )[ 0 ];
+ if ( !t1.isRooted() ) {
+ return false;
+ }
+ t1.reRoot( t1.getNode( "D" ) );
+ t1.reRoot( t1.getNode( "CD" ) );
+ t1.reRoot( t1.getNode( "A" ) );
+ t1.reRoot( t1.getNode( "B" ) );
+ t1.reRoot( t1.getNode( "AB" ) );
+ t1.reRoot( t1.getNode( "D" ) );
+ t1.reRoot( t1.getNode( "C" ) );
+ t1.reRoot( t1.getNode( "CD" ) );
+ t1.reRoot( t1.getNode( "A" ) );
+ t1.reRoot( t1.getNode( "B" ) );
+ t1.reRoot( t1.getNode( "AB" ) );
+ t1.reRoot( t1.getNode( "D" ) );
+ t1.reRoot( t1.getNode( "D" ) );
+ t1.reRoot( t1.getNode( "C" ) );
+ t1.reRoot( t1.getNode( "A" ) );
+ t1.reRoot( t1.getNode( "B" ) );
+ t1.reRoot( t1.getNode( "AB" ) );
+ t1.reRoot( t1.getNode( "C" ) );
+ t1.reRoot( t1.getNode( "D" ) );
+ t1.reRoot( t1.getNode( "CD" ) );
+ t1.reRoot( t1.getNode( "D" ) );
+ t1.reRoot( t1.getNode( "A" ) );
+ t1.reRoot( t1.getNode( "B" ) );
+ t1.reRoot( t1.getNode( "AB" ) );
+ t1.reRoot( t1.getNode( "C" ) );
+ t1.reRoot( t1.getNode( "D" ) );
+ t1.reRoot( t1.getNode( "CD" ) );
+ t1.reRoot( t1.getNode( "D" ) );
+ if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
+ return false;
+ }
+ final Phylogeny t2 = factory.create( "(((A:1,B:2)AB:10[&&NHX:B=55],C)ABC:3[&&NHX:B=33],D:5)ABCD:0.5",
+ new NHXParser() )[ 0 ];
+ t2.reRoot( t2.getNode( "A" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "ABC" ) );
+ t2.reRoot( t2.getNode( "A" ) );
+ t2.reRoot( t2.getNode( "B" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "C" ) );
+ t2.reRoot( t2.getNode( "ABC" ) );
+ t2.reRoot( t2.getNode( "A" ) );
+ t2.reRoot( t2.getNode( "B" ) );
+ t2.reRoot( t2.getNode( "AB" ) );
+ t2.reRoot( t2.getNode( "AB" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "C" ) );
+ t2.reRoot( t2.getNode( "B" ) );
+ t2.reRoot( t2.getNode( "AB" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "ABC" ) );
+ t2.reRoot( t2.getNode( "A" ) );
+ t2.reRoot( t2.getNode( "B" ) );
+ t2.reRoot( t2.getNode( "AB" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "C" ) );
+ t2.reRoot( t2.getNode( "ABC" ) );
+ t2.reRoot( t2.getNode( "A" ) );
+ t2.reRoot( t2.getNode( "B" ) );
+ t2.reRoot( t2.getNode( "AB" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "C" ) );
+ t2.reRoot( t2.getNode( "A" ) );
+ t2.reRoot( t2.getNode( "B" ) );
+ t2.reRoot( t2.getNode( "AB" ) );
+ t2.reRoot( t2.getNode( "C" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "ABC" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "A" ) );
+ t2.reRoot( t2.getNode( "B" ) );
+ t2.reRoot( t2.getNode( "AB" ) );
+ t2.reRoot( t2.getNode( "C" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ t2.reRoot( t2.getNode( "ABC" ) );
+ t2.reRoot( t2.getNode( "D" ) );
+ if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
+ return false;
+ }
+ if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
+ return false;
+ }
+ t2.reRoot( t2.getNode( "ABC" ) );
+ if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
+ return false;
+ }
+ if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
+ return false;
+ }
+ t2.reRoot( t2.getNode( "AB" ) );
+ if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
+ return false;
+ }
+ if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
+ return false;
+ }
+ if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
+ return false;
+ }
+ t2.reRoot( t2.getNode( "AB" ) );
+ if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
+ return false;
+ }
+ if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
+ return false;
+ }
+ if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
+ return false;
+ }
+ t2.reRoot( t2.getNode( "D" ) );
+ if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
+ return false;
+ }
+ if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
+ return false;
+ }
+ t2.reRoot( t2.getNode( "ABC" ) );
+ if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
+ return false;
+ }
+ if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
+ return false;
+ }
+ final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
+ new NHXParser() )[ 0 ];
+ t3.reRoot( t3.getNode( "B" ) );
+ if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
+ return false;
+ }
+ if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
+ return false;
+ }
+ if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
+ return false;
+ }
+ t3.reRoot( t3.getNode( "B" ) );
+ if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
+ return false;
+ }
+ if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
+ return false;
+ }
+ if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
+ return false;
+ }
+ t3.reRoot( t3.getRoot() );
+ if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
+ return false;
+ }
+ if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
+ return false;
+ }
+ if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testSDIse() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
+ final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
+ gene1.setRooted( true );
+ species1.setRooted( true );
+ final SDI sdi = new SDI( gene1, species1 );
+ if ( !gene1.getRoot().isDuplication() ) {
+ return false;
+ }
+ final Phylogeny species2 = factory
+ .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
+ new NHXParser() )[ 0 ];
+ final Phylogeny gene2 = factory
+ .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
+ new NHXParser() )[ 0 ];
+ species2.setRooted( true );
+ gene2.setRooted( true );
+ final SDI sdi2 = new SDI( gene2, species2 );
+ if ( sdi2.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( !gene2.getNode( "ab" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
+ return false;
+ }
+ if ( !gene2.getNode( "abc" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
+ return false;
+ }
+ if ( !gene2.getNode( "r" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
+ return false;
+ }
+ final Phylogeny species3 = factory
+ .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
+ new NHXParser() )[ 0 ];
+ final Phylogeny gene3 = factory
+ .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
+ new NHXParser() )[ 0 ];
+ species3.setRooted( true );
+ gene3.setRooted( true );
+ final SDI sdi3 = new SDI( gene3, species3 );
+ if ( sdi3.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( !gene3.getNode( "aa" ).isDuplication() ) {
+ return false;
+ }
+ if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
+ return false;
+ }
+ final Phylogeny species4 = factory
+ .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
+ new NHXParser() )[ 0 ];
+ final Phylogeny gene4 = factory
+ .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
+ new NHXParser() )[ 0 ];
+ species4.setRooted( true );
+ gene4.setRooted( true );
+ final SDI sdi4 = new SDI( gene4, species4 );
+ if ( sdi4.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( !gene4.getNode( "ac" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene4.getNode( "abc" ).isDuplication() ) {
+ return false;
+ }
+ if ( gene4.getNode( "abcd" ).isDuplication() ) {
+ return false;
+ }
+ if ( species4.getNumberOfExternalNodes() != 6 ) {
+ return false;
+ }
+ if ( gene4.getNumberOfExternalNodes() != 6 ) {
+ return false;
+ }
+ final Phylogeny species5 = factory
+ .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
+ new NHXParser() )[ 0 ];
+ final Phylogeny gene5 = factory
+ .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
+ new NHXParser() )[ 0 ];
+ species5.setRooted( true );
+ gene5.setRooted( true );
+ final SDI sdi5 = new SDI( gene5, species5 );
+ if ( sdi5.getDuplicationsSum() != 2 ) {
+ return false;
+ }
+ if ( !gene5.getNode( "ad" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene5.getNode( "adc" ).isDuplication() ) {
+ return false;
+ }
+ if ( !gene5.getNode( "abcd" ).isDuplication() ) {
+ return false;
+ }
+ if ( species5.getNumberOfExternalNodes() != 6 ) {
+ return false;
+ }
+ if ( gene5.getNumberOfExternalNodes() != 6 ) {
+ return false;
+ }
+ // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
+ // Conjecture for Comparing Molecular Phylogenies"
+ // J. of Comput Bio. Vol. 4, No 2, pp.177-187
+ final Phylogeny species6 = factory
+ .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
+ final Phylogeny gene6 = factory
+ .create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1,"
+ + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1,"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;",
+ new NHXParser() )[ 0 ];
+ species6.setRooted( true );
+ gene6.setRooted( true );
+ final SDI sdi6 = new SDI( gene6, species6 );
+ if ( sdi6.getDuplicationsSum() != 3 ) {
+ return false;
+ }
+ if ( !gene6.getNode( "r" ).isDuplication() ) {
+ return false;
+ }
+ if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
+ return false;
+ }
+ if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
+ return false;
+ }
+ if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
+ return false;
+ }
+ sdi6.computeMappingCostL();
+ if ( sdi6.computeMappingCostL() != 17 ) {
+ return false;
+ }
+ if ( species6.getNumberOfExternalNodes() != 9 ) {
+ return false;
+ }
+ if ( gene6.getNumberOfExternalNodes() != 9 ) {
+ return false;
+ }
+ final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
+ + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
+ + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
+ + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
+ + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
+ species7.setRooted( true );
+ final Phylogeny gene7_1 = Test
+ .createPhylogeny( "((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
+ gene7_1.setRooted( true );
+ final SDI sdi7 = new SDI( gene7_1, species7 );
+ if ( sdi7.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny gene7_2 = Test
+ .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
+ gene7_2.setRooted( true );
+ final SDI sdi7_2 = new SDI( gene7_2, species7 );
+ if ( sdi7_2.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testSDIunrooted() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
+ final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
+ final Iterator<PhylogenyBranch> iter = l.iterator();
+ PhylogenyBranch br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {