+ if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
+ return false;
+ }
+ final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
+ + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
+ + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
+ + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
+ + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
+ + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
+ + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
+ + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
+ final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
+ if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
+ return false;
+ }
+ final String p26_S = "(A,B)ab";
+ final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
+ if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
+ return false;
+ }
+ final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
+ if ( p27s.length != 1 ) {
+ System.out.println( "xxl=" + p27s.length );
+ System.exit( -1 );
+ return false;
+ }
+ if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
+ System.out.println( p27s[ 0 ].toNewHampshireX() );
+ System.exit( -1 );
+ return false;
+ }
+ final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
+ new NHXParser() );
+ if ( p27.length != 1 ) {
+ System.out.println( "yl=" + p27.length );
+ System.exit( -1 );
+ return false;
+ }
+ if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
+ System.out.println( p27[ 0 ].toNewHampshireX() );
+ System.exit( -1 );
+ return false;
+ }
+ final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ final String p28_S3 = "(A,B)ab";
+ final String p28_S4 = "((((A,B),C),D),;E;)";
+ final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
+ new NHXParser() );
+ if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
+ return false;
+ }
+ if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
+ return false;
+ }
+ if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
+ return false;
+ }
+ if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
+ return false;
+ }
+ if ( p28.length != 4 ) {
+ return false;
+ }
+ final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345";
+ final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
+ if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
+ return false;
+ }
+ final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72";
+ final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
+ if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
+ return false;
+ }
+ final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
+ final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
+ if ( ( p32.length != 0 ) ) {
+ return false;
+ }
+ final String p33_S = "A";
+ final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
+ if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
+ return false;
+ }
+ final String p34_S = "B;";
+ final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
+ if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
+ return false;
+ }
+ final String p35_S = "B:0.2";
+ final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
+ if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
+ return false;
+ }
+ final String p36_S = "(A)";
+ final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
+ if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
+ return false;
+ }
+ final String p37_S = "((A))";
+ final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
+ if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
+ return false;
+ }
+ final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
+ final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
+ if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
+ return false;
+ }
+ final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
+ final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
+ if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
+ return false;
+ }
+ final String p40_S = "(A,B,C)";
+ final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
+ if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
+ return false;
+ }
+ final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
+ final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
+ if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
+ return false;
+ }
+ final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
+ final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
+ if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
+ return false;
+ }
+ final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
+ final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
+ if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
+ return false;
+ }
+ final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
+ final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
+ if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
+ return false;
+ }
+ final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
+ final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
+ if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
+ return false;
+ }
+ final String p46_S = "";
+ final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
+ if ( p46.length != 0 ) {
+ return false;
+ }
+ final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
+ if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ return false;
+ }
+ final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ return false;
+ }
+ final Phylogeny p49 = factory
+ .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
+ new NHXParser() )[ 0 ];
+ if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ return false;
+ }
+ final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p50.getNode( "A" ) == null ) {
+ return false;
+ }
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
+ .equals( "((A,B)ab:2.0[88],C);" ) ) {
+ return false;
+ }
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
+ return false;
+ }
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
+ .equals( "((A,B)88:2.0,C);" ) ) {
+ return false;
+ }
+ final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p51.getNode( "A(A" ) == null ) {
+ return false;
+ }
+ final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p52.getNode( "A(A" ) == null ) {
+ return false;
+ }
+ final Phylogeny p53 = factory
+ .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
+ new NHXParser() )[ 0 ];
+ if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
+ return false;
+ }
+ //
+ final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p54.getNode( "A" ) == null ) {
+ return false;
+ }
+ if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
+ .equals( "((A,B)[88],C);" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHParsingIter() {
+ try {
+ final String p0_str = "(A,B);";
+ final NHXParser p = new NHXParser();
+ p.setSource( p0_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p0 = p.next();
+ if ( !p0.toNewHampshire().equals( p0_str ) ) {
+ System.out.println( p0.toNewHampshire() );
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p00_str = "(A,B)root;";
+ p.setSource( p00_str );
+ final Phylogeny p00 = p.next();
+ if ( !p00.toNewHampshire().equals( p00_str ) ) {
+ System.out.println( p00.toNewHampshire() );
+ return false;
+ }
+ //
+ final String p000_str = "A;";
+ p.setSource( p000_str );
+ final Phylogeny p000 = p.next();
+ if ( !p000.toNewHampshire().equals( p000_str ) ) {
+ System.out.println( p000.toNewHampshire() );
+ return false;
+ }
+ //
+ final String p0000_str = "A";
+ p.setSource( p0000_str );
+ final Phylogeny p0000 = p.next();
+ if ( !p0000.toNewHampshire().equals( "A;" ) ) {
+ System.out.println( p0000.toNewHampshire() );
+ return false;
+ }
+ //
+ p.setSource( "(A)" );
+ final Phylogeny p00000 = p.next();
+ if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
+ System.out.println( p00000.toNewHampshire() );
+ return false;
+ }
+ //
+ final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
+ p.setSource( p1_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p1_0 = p.next();
+ if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
+ System.out.println( p1_0.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p1_1 = p.next();
+ if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p1_2 = p.next();
+ if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
+ System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p1_3 = p.next();
+ if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
+ p.setSource( p2_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p2_0 = p.next();
+ if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
+ System.out.println( p2_0.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p2_1 = p.next();
+ if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p2_2 = p.next();
+ if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
+ System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p2_3 = p.next();
+ if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p2_4 = p.next();
+ if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
+ System.out.println( "(X) != " + p2_4.toNewHampshire() );
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ ////
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p2_0 = p.next();
+ if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
+ System.out.println( p2_0.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p2_1 = p.next();
+ if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p2_2 = p.next();
+ if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
+ System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p2_3 = p.next();
+ if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p2_4 = p.next();
+ if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
+ System.out.println( "(X) != " + p2_4.toNewHampshire() );
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p3_str = "((A,B),C)abc";
+ p.setSource( p3_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p3_0 = p.next();
+ if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p4_str = "((A,B)ab,C)abc";
+ p.setSource( p4_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p4_0 = p.next();
+ if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {