From 16324fd2269d168c1a0cf15396169e4f8800bee6 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 5 Jan 2013 04:02:53 +0000 Subject: [PATCH] iterating nh parser --- .../org/forester/io/parsers/nhx/NHXParser2.java | 46 ++- forester/java/src/org/forester/test/Test.java | 320 +++++++++++++++++--- 2 files changed, 322 insertions(+), 44 deletions(-) diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser2.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser2.java index b3b764a..d30c5d0 100644 --- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser2.java +++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser2.java @@ -28,6 +28,7 @@ package org.forester.io.parsers.nhx; import java.awt.Color; import java.io.BufferedReader; import java.io.File; +import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.io.InputStream; @@ -99,6 +100,7 @@ public final class NHXParser2 implements PhylogenyParser { BufferedReader _my_source_br = null; int _i; private Phylogeny _next; + private Object _source; public NHXParser2() { init(); @@ -122,8 +124,11 @@ public final class NHXParser2 implements PhylogenyParser { public Phylogeny[] parse() throws IOException { reset(); List l = new ArrayList(); + System.out.println( ">> _next=" + _next ); while ( hasNext() ) { - l.add( next() ); + Phylogeny n = next(); + System.out.println( ">> going to add " + n ); + l.add( n ); } final Phylogeny[] p = new Phylogeny[ l.size() ]; for( int i = 0; i < l.size(); ++i ) { @@ -134,6 +139,7 @@ public final class NHXParser2 implements PhylogenyParser { public void reset() throws NHXFormatException, IOException { _i = 0; + _next = null; _in_comment = false; _saw_colon = false; _saw_open_bracket = false; @@ -149,6 +155,7 @@ public final class NHXParser2 implements PhylogenyParser { _my_source_sbuil = null; _my_source_charary = null; _my_source_br = null; + determineSourceType( _source ); switch ( getInputType() ) { case STRING: _my_source_str = ( String ) getNhxSource(); @@ -163,6 +170,14 @@ public final class NHXParser2 implements PhylogenyParser { _my_source_charary = ( char[] ) getNhxSource(); break; case BUFFERED_READER: + if ( _my_source_br != null ) { + try { + _my_source_br.close(); + } + catch ( IOException e ) { + //do nothing + } + } _my_source_br = ( BufferedReader ) getNhxSource(); break; default: @@ -203,11 +218,17 @@ public final class NHXParser2 implements PhylogenyParser { * @param nhx_source * the source to be parsed (String, StringBuffer, char[], File, * or InputStream) + * @throws NHXFormatException * @throws IOException * @throws PhylogenyParserException */ @Override - public void setSource( final Object nhx_source ) throws PhylogenyParserException, IOException { + public void setSource( final Object nhx_source ) throws NHXFormatException, IOException { + _source = nhx_source; + reset(); + } + + private void determineSourceType( final Object nhx_source ) throws PhylogenyParserException, FileNotFoundException { if ( nhx_source == null ) { throw new PhylogenyParserException( getClass() + ": attempt to parse null object." ); } @@ -257,7 +278,6 @@ public final class NHXParser2 implements PhylogenyParser { + " StringBuffer, StringBuilder, char[], File," + " or InputStream " + " [attempt to parse object of " + nhx_source.getClass() + "]." ); } - reset(); } public void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { @@ -281,12 +301,12 @@ public final class NHXParser2 implements PhylogenyParser { PhyloXmlDataFormatException { //setCladeLevel( 0 ); if ( getCurrentPhylogeny() != null ) { - System.out.println( "cp=" + getCurrentPhylogeny() ); + System.out.println( "fp: cp=" + getCurrentPhylogeny() ); if ( getCurrentAnotation() != null ) { - System.out.println( "ca=" + getCurrentAnotation().toString() ); + System.out.println( "fp: ca=" + getCurrentAnotation().toString() ); } else { - System.out.println( "ca=null" ); + System.out.println( "fp: ca=null" ); } parseNHX( getCurrentAnotation() != null ? getCurrentAnotation().toString() : "", getCurrentPhylogeny() .getRoot(), getTaxonomyExtraction(), isReplaceUnderscores() ); @@ -460,13 +480,18 @@ public final class NHXParser2 implements PhylogenyParser { ++_i; } // while ( true ) System.out.println( "done with loop" ); + if ( getCurrentPhylogeny() == null ) { + System.out.println( "... but is null" ); + } if ( getCladeLevel() != 0 ) { throw new PhylogenyParserException( "error in NH (Newick) formatted data: most likely cause: number of open parens does not equal number of close parens" ); } if ( getCurrentPhylogeny() != null ) { - System.out.println( "current=" + getCurrentPhylogeny() ); + System.out.println( "... and current=" + getCurrentPhylogeny() ); _next = finishPhylogeny2(); + System.out.println( "... _next=" + _next ); setCurrentPhylogeny( null ); + setCurrentAnotation( null ); //return finishPhylogeny2(); } else if ( ( getCurrentAnotation() != null ) && ( getCurrentAnotation().length() > 0 ) ) { @@ -581,6 +606,7 @@ public final class NHXParser2 implements PhylogenyParser { PhyloXmlDataFormatException { Phylogeny phy = null; final PhylogenyNode new_node = new PhylogenyNode(); + System.out.println( "level=" + getCladeLevel() ); if ( getCladeLevel() == 0 ) { if ( getCurrentPhylogeny() != null ) { phy = finishPhylogeny2(); @@ -596,6 +622,12 @@ public final class NHXParser2 implements PhylogenyParser { } setCurrentNode( new_node ); setSawClosingParen( false ); + if ( phy != null ) { + System.out.println( "processOpenParen2 returns " + phy.toString() ); + } + else { + System.out.println( "processOpenParen2 returns null" ); + } return phy; } diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index dff58d6..6a1744d 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -226,6 +226,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "NHX parsing iterating: " ); + if ( Test.testNHParsingIter() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "NH parsing: " ); if ( Test.testNHParsing() ) { System.out.println( "OK." ); @@ -235,6 +244,7 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.exit( 0 ); System.out.print( "Conversion to NHX (node level): " ); if ( Test.testNHXconversion() ) { System.out.println( "OK." ); @@ -271,15 +281,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "NHX parsing iterating: " ); - if ( Test.testNHParsingIter() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } System.out.print( "Nexus characters parsing: " ); if ( Test.testNexusCharactersParsing() ) { System.out.println( "OK." ); @@ -4621,52 +4622,84 @@ public final class Test { final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser2() ); final String p16_S = "((A,B),C)"; final Phylogeny[] p16 = factory.create( p16_S, new NHXParser2() ); + if ( p16.length != 1 ) { + return false; + } if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) { return false; } final String p17_S = "(C,(A,B))"; final Phylogeny[] p17 = factory.create( p17_S, new NHXParser2() ); + if ( p17.length != 1 ) { + return false; + } if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) { return false; } final String p18_S = "((A,B),(C,D))"; final Phylogeny[] p18 = factory.create( p18_S, new NHXParser2() ); + if ( p18.length != 1 ) { + return false; + } if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) { return false; } final String p19_S = "(((A,B),C),D)"; final Phylogeny[] p19 = factory.create( p19_S, new NHXParser2() ); + if ( p19.length != 1 ) { + return false; + } if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) { return false; } final String p20_S = "(A,(B,(C,D)))"; final Phylogeny[] p20 = factory.create( p20_S, new NHXParser2() ); + if ( p20.length != 1 ) { + return false; + } if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) { return false; } final String p21_S = "(A,(B,(C,(D,E))))"; final Phylogeny[] p21 = factory.create( p21_S, new NHXParser2() ); + if ( p21.length != 1 ) { + return false; + } if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) { return false; } final String p22_S = "((((A,B),C),D),E)"; final Phylogeny[] p22 = factory.create( p22_S, new NHXParser2() ); + if ( p22.length != 1 ) { + return false; + } if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) { return false; } final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; final Phylogeny[] p23 = factory.create( p23_S, new NHXParser2() ); + if ( p23.length != 1 ) { + System.out.println( "xl=" + p23.length ); + System.exit( -1 ); + return false; + } if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) { return false; } final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; final Phylogeny[] p24 = factory.create( p24_S, new NHXParser2() ); + if ( p24.length != 1 ) { + return false; + } if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) { return false; } final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde"; final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser2() ); + if ( p241.length != 2 ) { + return false; + } if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) { return false; } @@ -4691,8 +4724,24 @@ public final class Test { return false; } final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + final Phylogeny[] p27s = factory.create( p27_S, new NHXParser2() ); + 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 NHXParser2() ); + 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 ); @@ -4703,7 +4752,7 @@ public final class Test { 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() ); + new NHXParser2() ); if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) { return false; } @@ -4716,106 +4765,109 @@ public final class Test { 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() ); + final Phylogeny[] p29 = factory.create( p29_S, new NHXParser2() ); 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() ); + final Phylogeny[] p30 = factory.create( p30_S, new NHXParser2() ); 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 != 1 ) || !p32[ 0 ].isEmpty() ) { + final Phylogeny[] p32 = factory.create( p32_S, new NHXParser2() ); + if ( ( p32.length != 0 ) ) { return false; } final String p33_S = "A"; - final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() ); + final Phylogeny[] p33 = factory.create( p33_S, new NHXParser2() ); if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) { return false; } final String p34_S = "B;"; - final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() ); + final Phylogeny[] p34 = factory.create( p34_S, new NHXParser2() ); if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) { return false; } final String p35_S = "B:0.2"; - final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() ); + final Phylogeny[] p35 = factory.create( p35_S, new NHXParser2() ); if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) { return false; } final String p36_S = "(A)"; - final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() ); + final Phylogeny[] p36 = factory.create( p36_S, new NHXParser2() ); if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) { return false; } final String p37_S = "((A))"; - final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() ); + final Phylogeny[] p37 = factory.create( p37_S, new NHXParser2() ); 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() ); + final Phylogeny[] p38 = factory.create( p38_S, new NHXParser2() ); 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() ); + final Phylogeny[] p39 = factory.create( p39_S, new NHXParser2() ); 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() ); + final Phylogeny[] p40 = factory.create( p40_S, new NHXParser2() ); 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() ); + final Phylogeny[] p41 = factory.create( p41_S, new NHXParser2() ); 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() ); + final Phylogeny[] p42 = factory.create( p42_S, new NHXParser2() ); 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() ); + final Phylogeny[] p43 = factory.create( p43_S, new NHXParser2() ); 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() ); + final Phylogeny[] p44 = factory.create( p44_S, new NHXParser2() ); 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() ); + final Phylogeny[] p45 = factory.create( p45_S, new NHXParser2() ); 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 != 1 ) || !p46[ 0 ].isEmpty() ) { + final Phylogeny[] p46 = factory.create( p46_S, new NHXParser2() ); + if ( p46.length != 0 ) { return false; } - final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ]; + final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser2() )[ 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 ]; + final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser2() )[ 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 ]; + new NHXParser2() )[ 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 ]; + final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser2() )[ 0 ]; if ( p50.getNode( "A" ) == null ) { return false; } @@ -4830,22 +4882,22 @@ public final class Test { .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 ]; + final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser2() )[ 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 ]; + final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser2() )[ 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 ]; + new NHXParser2() )[ 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 ]; + final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser2() )[ 0 ]; if ( p54.getNode( "A" ) == null ) { return false; } @@ -5049,6 +5101,200 @@ public final class Test { if ( p.next() != null ) { return false; } + // + String p3_str = "((A,B),C)abc"; + p.setSource( p3_str ); + if ( !p.hasNext() ) { + return false; + } + 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; + } + // + String p4_str = "((A,B)ab,C)abc"; + p.setSource( p4_str ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p4_0 = p.next(); + if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + String p5_str = "(((A,B)ab,C)abc,D)abcd"; + p.setSource( p5_str ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p5_0 = p.next(); + if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde"; + p.setSource( p6_str ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p6_0 = p.next(); + if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p6_0 = p.next(); + if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde"; + p.setSource( p7_str ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p7_0 = p.next(); + if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p7_0 = p.next(); + if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + // + String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde"; + p.setSource( p8_str ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p8_0 = p.next(); + if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + return false; + } + if ( !p.hasNext() ) { + return false; + } + if ( !p.hasNext() ) { + return false; + } + Phylogeny p8_1 = p.next(); + if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p8_0 = p.next(); + if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) { + return false; + } + if ( !p.hasNext() ) { + return false; + } + p8_1 = p.next(); + if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) { + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + // + p.setSource( "" ); + if ( p.hasNext() ) { + return false; + } + // + p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) ); + if ( !p.hasNext() ) { + return false; + } + Phylogeny p_27 = p.next(); + if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { + System.out.println( p_27.toNewHampshireX() ); + System.exit( -1 ); + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } + p.reset(); + if ( !p.hasNext() ) { + return false; + } + p_27 = p.next(); + if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) { + System.out.println( p_27.toNewHampshireX() ); + System.exit( -1 ); + return false; + } + if ( p.hasNext() ) { + return false; + } + if ( p.next() != null ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); -- 1.7.10.2