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;
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;
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." );
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( "WABI TxSearch: " );
// if ( Test.testWabiTxSearch() ) {
// System.out.println( "OK." );
}
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;
}
parser1.parse();
final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
+ ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
- final List<Protein> domain_collections = parser2.parse();
+ final List<Protein> proteins = parser2.parse();
if ( parser2.getProteinsEncountered() != 4 ) {
return false;
}
- if ( domain_collections.size() != 4 ) {
+ if ( proteins.size() != 4 ) {
return false;
}
if ( parser2.getDomainsEncountered() != 69 ) {
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 );
+ final Protein p2 = proteins.get( 1 );
+ if ( p2.getNumberOfProteinDomains() != 51 ) {
+ 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;
}
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 " ) ) {
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[88.0],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)88.0:2.0,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;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
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() ) {
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;
}
}
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;
}
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;
}
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;
}
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;
}
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;
}
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;
}
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;
}
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;
}
}
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;
}
}
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;
}
}
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;
}
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;
}
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;
}
}
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;
}
}
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;
}
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 ) {
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
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;
}
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;
}
}
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;
}
}
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;
}
}
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;
}
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;
}
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;
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" );
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;
}
}
}
return true;
}
+
+ private static boolean testNextNodeWithCollapsing() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ PhylogenyNode n;
+ List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
+ 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<PhylogenyNode>();
+ 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<PhylogenyNode>();
+ 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<PhylogenyNode>();
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff