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;
BufferedReader _my_source_br = null;
int _i;
private Phylogeny _next;
+ private Object _source;
public NHXParser2() {
init();
public Phylogeny[] parse() throws IOException {
reset();
List<Phylogeny> l = new ArrayList<Phylogeny>();
+ 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 ) {
public void reset() throws NHXFormatException, IOException {
_i = 0;
+ _next = null;
_in_comment = false;
_saw_colon = false;
_saw_open_bracket = false;
_my_source_sbuil = null;
_my_source_charary = null;
_my_source_br = null;
+ determineSourceType( _source );
switch ( getInputType() ) {
case STRING:
_my_source_str = ( String ) getNhxSource();
_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:
* @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." );
}
+ " StringBuffer, StringBuilder, char[], File," + " or InputStream "
+ " [attempt to parse object of " + nhx_source.getClass() + "]." );
}
- reset();
}
public void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
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() );
++_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 ) ) {
PhyloXmlDataFormatException {
Phylogeny phy = null;
final PhylogenyNode new_node = new PhylogenyNode();
+ System.out.println( "level=" + getCladeLevel() );
if ( getCladeLevel() == 0 ) {
if ( getCurrentPhylogeny() != null ) {
phy = finishPhylogeny2();
}
setCurrentNode( new_node );
setSawClosingParen( false );
+ if ( phy != null ) {
+ System.out.println( "processOpenParen2 returns " + phy.toString() );
+ }
+ else {
+ System.out.println( "processOpenParen2 returns null" );
+ }
return phy;
}
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." );
System.out.println( "failed." );
failed++;
}
+ System.exit( 0 );
System.out.print( "Conversion to NHX (node level): " );
if ( Test.testNHXconversion() ) {
System.out.println( "OK." );
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." );
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;
}
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 );
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;
}
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;
}
.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;
}
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 );
git://source.jalview.org / jalview.git / commitdiff