+ 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" ) ) {