+ 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 = new PhyloXmlParser();
+ 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" ) ) {
+ return false;
+ }
+ br = iter.next();
+ if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
+ return false;
+ }
+ if ( iter.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
+ final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
+ final Iterator<PhylogenyBranch> iter1 = l1.iterator();
+ br = iter1.next();
+ if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
+ return false;
+ }
+ if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
+ return false;
+ }
+ br = iter1.next();
+ if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {