import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
final static private byte BUFFERED_READER = 3;
final static private byte STRING_BUILDER = 4;
private boolean _guess_rootedness;
- private boolean _has_next;
private boolean _ignore_quotes;
private byte _input_type;
private int _source_length;
char[] _my_source_charary = null;
BufferedReader _my_source_br = null;
int _i;
+ private Phylogeny _next;
public NHXParser2() {
init();
}
- public Phylogeny getNext() throws IOException, NHXFormatException {
- while ( true ) {
- char c = '\b';
- if ( getInputType() == BUFFERED_READER ) {
- final int ci = _my_source_br.read();
- if ( ci >= 0 ) {
- c = ( char ) ci;
- }
- else {
- break;
- }
- }
- else {
- if ( _i >= getSourceLength() ) {
- break;
- }
- else {
- switch ( getInputType() ) {
- case STRING:
- c = _my_source_str.charAt( _i );
- break;
- case STRING_BUFFER:
- c = _my_source_sbuff.charAt( _i );
- break;
- case STRING_BUILDER:
- c = _my_source_sbuil.charAt( _i );
- break;
- case CHAR_ARRAY:
- c = _my_source_charary[ _i ];
- break;
- }
- }
- }
- if ( !_in_single_quote && !_in_double_quote ) {
- if ( c == ':' ) {
- _saw_colon = true;
- }
- else if ( !( ( c < 33 ) || ( c > 126 ) ) && _saw_colon
- && ( ( c != '[' ) && ( c != '.' ) && ( ( c < 48 ) || ( c > 57 ) ) ) ) {
- _saw_colon = false;
- }
- if ( _in_open_bracket && ( c == ']' ) ) {
- _in_open_bracket = false;
- }
- }
- // \n\t is always ignored,
- // as is " (34) and ' (39) (space is 32):
- if ( ( isIgnoreQuotes() && ( ( c < 33 ) || ( c > 126 ) || ( c == 34 ) || ( c == 39 ) || ( ( getCladeLevel() == 0 ) && ( c == ';' ) ) ) )
- || ( !isIgnoreQuotes() && ( ( c < 32 ) || ( c > 126 ) || ( ( getCladeLevel() == 0 ) && ( c == ';' ) ) ) ) ) {
- // Do nothing.
- }
- else if ( ( c == 32 ) && ( !_in_single_quote && !_in_double_quote ) ) {
- // Do nothing.
- }
- else if ( _in_comment ) {
- if ( c == ']' ) {
- _in_comment = false;
- }
- }
- else if ( _in_double_quote ) {
- if ( c == '"' ) {
- _in_double_quote = false;
- }
- else {
- getCurrentAnotation().append( c );
- }
- }
- else if ( c == '"' ) {
- _in_double_quote = true;
- }
- else if ( _in_single_quote ) {
- if ( c == 39 ) {
- _in_single_quote = false;
- }
- else {
- getCurrentAnotation().append( c );
- }
- }
- else if ( c == 39 ) {
- _in_single_quote = true;
- }
- else if ( c == '[' ) {
- _saw_open_bracket = true;
- _in_open_bracket = true;
- }
- else if ( _saw_open_bracket ) {
- if ( c != ']' ) {
- // everything not starting with "[&" is considered a comment
- // unless ":digits and/or . [bootstrap]":
- if ( c == '&' ) {
- getCurrentAnotation().append( "[&" );
- }
- else if ( _saw_colon ) {
- getCurrentAnotation().append( "[" + c );
- }
- else {
- _in_comment = true;
- }
- }
- // comment consisting just of "[]":
- _saw_open_bracket = false;
- }
- else if ( ( c == '(' ) && !_in_open_bracket ) {
- Phylogeny phy = processOpenParen2();
- if ( phy != null ) {
- ++_i;
- return phy;
- }
- }
- else if ( ( c == ')' ) && !_in_open_bracket ) {
- processCloseParen();
- }
- else if ( ( c == ',' ) && !_in_open_bracket ) {
- processComma();
- }
- else {
- getCurrentAnotation().append( c );
- }
- ++_i;
- } // while ( true )
- System.out.println( "done with loop" );
- if ( getCladeLevel() != 0 ) {
- throw new PhylogenyParserException( "error in NH (Newick)/NHX formatted data: most likely cause: number of open parens does not equal number of close parens" );
- }
- if ( getCurrentPhylogeny() != null ) {
- return finishPhylogeny2();
- }
- else if ( getCurrentAnotation().length() > 0 ) {
- System.out.println( "1node=" + getCurrentAnotation() );
- return finishSingleNodePhylogeny2();
- }
- else {
- return null;
- }
- } // parse()
-
public TAXONOMY_EXTRACTION getTaxonomyExtraction() {
return _taxonomy_extraction;
}
public boolean hasNext() {
- return _has_next;
+ return _next != null;
+ }
+
+ public Phylogeny next() throws NHXFormatException, IOException {
+ final Phylogeny phy = _next;
+ getNext();
+ return phy;
+ }
+
+ @Override
+ public Phylogeny[] parse() throws IOException {
+ reset();
+ List<Phylogeny> l = new ArrayList<Phylogeny>();
+ while ( hasNext() ) {
+ l.add( next() );
+ }
+ final Phylogeny[] p = new Phylogeny[ l.size() ];
+ for( int i = 0; i < l.size(); ++i ) {
+ p[ i ] = l.get( i );
+ }
+ return p;
+ }
+
+ public void reset() throws NHXFormatException, IOException {
+ _i = 0;
+ _in_comment = false;
+ _saw_colon = false;
+ _saw_open_bracket = false;
+ _in_open_bracket = false;
+ _in_double_quote = false;
+ _in_single_quote = false;
+ setCladeLevel( 0 );
+ newCurrentAnotation();
+ setCurrentPhylogeny( null );
+ setCurrentNode( null );
+ _my_source_str = null;
+ _my_source_sbuff = null;
+ _my_source_sbuil = null;
+ _my_source_charary = null;
+ _my_source_br = null;
+ switch ( getInputType() ) {
+ case STRING:
+ _my_source_str = ( String ) getNhxSource();
+ break;
+ case STRING_BUFFER:
+ _my_source_sbuff = ( StringBuffer ) getNhxSource();
+ break;
+ case STRING_BUILDER:
+ _my_source_sbuil = ( StringBuilder ) getNhxSource();
+ break;
+ case CHAR_ARRAY:
+ _my_source_charary = ( char[] ) getNhxSource();
+ break;
+ case BUFFERED_READER:
+ _my_source_br = ( BufferedReader ) getNhxSource();
+ break;
+ default:
+ throw new RuntimeException( "unknown input type" );
+ }
+ getNext();
}
public void setGuessRootedness( final boolean guess_rootedness ) {
}
else {
throw new IllegalArgumentException( getClass() + " can only parse objects of type String,"
- + " StringBuffer, char[], File," + " or InputStream " + " [attempt to parse object of "
- + nhx_source.getClass() + "]." );
+ + " StringBuffer, StringBuilder, char[], File," + " or InputStream "
+ + " [attempt to parse object of " + nhx_source.getClass() + "]." );
}
- setHasNext( true );
reset();
}
_taxonomy_extraction = taxonomy_extraction;
}
- public void reset() {
- setHasNext( false );
- _i = 0;
- _in_comment = false;
- _saw_colon = false;
- _saw_open_bracket = false;
- _in_open_bracket = false;
- _in_double_quote = false;
- _in_single_quote = false;
- setCladeLevel( 0 );
- newCurrentAnotation();
- setCurrentPhylogeny( null );
- setCurrentNode( null );
- _my_source_str = null;
- _my_source_sbuff = null;
- _my_source_sbuil = null;
- _my_source_charary = null;
- _my_source_br = null;
- switch ( getInputType() ) {
- case STRING:
- _my_source_str = ( String ) getNhxSource();
- break;
- case STRING_BUFFER:
- _my_source_sbuff = ( StringBuffer ) getNhxSource();
- break;
- case STRING_BUILDER:
- _my_source_sbuil = ( StringBuilder ) getNhxSource();
- break;
- case CHAR_ARRAY:
- _my_source_charary = ( char[] ) getNhxSource();
- break;
- case BUFFERED_READER:
- _my_source_br = ( BufferedReader ) getNhxSource();
- break;
- default:
- throw new RuntimeException( "unknown input type" );
- }
- }
-
/**
* Decreases the clade level by one.
*
//setCladeLevel( 0 );
if ( getCurrentPhylogeny() != null ) {
System.out.println( "cp=" + getCurrentPhylogeny() );
- System.out.println( "ca=" + getCurrentAnotation().toString() );
- parseNHX( getCurrentAnotation().toString(),
- getCurrentPhylogeny().getRoot(),
- getTaxonomyExtraction(),
- isReplaceUnderscores() );
+ if ( getCurrentAnotation() != null ) {
+ System.out.println( "ca=" + getCurrentAnotation().toString() );
+ }
+ else {
+ System.out.println( "ca=null" );
+ }
+ parseNHX( getCurrentAnotation() != null ? getCurrentAnotation().toString() : "", getCurrentPhylogeny()
+ .getRoot(), getTaxonomyExtraction(), isReplaceUnderscores() );
if ( GUESS_IF_SUPPORT_VALUES ) {
if ( isBranchLengthsLikeBootstrapValues( getCurrentPhylogeny() ) ) {
moveBranchLengthsToConfidenceValues( getCurrentPhylogeny() );
return _input_type;
}
+ private void getNext() throws IOException, NHXFormatException {
+ while ( true ) {
+ char c = '\b';
+ if ( getInputType() == BUFFERED_READER ) {
+ final int ci = _my_source_br.read();
+ if ( ci >= 0 ) {
+ c = ( char ) ci;
+ }
+ else {
+ break;
+ }
+ }
+ else {
+ if ( _i >= getSourceLength() ) {
+ break;
+ }
+ else {
+ switch ( getInputType() ) {
+ case STRING:
+ c = _my_source_str.charAt( _i );
+ break;
+ case STRING_BUFFER:
+ c = _my_source_sbuff.charAt( _i );
+ break;
+ case STRING_BUILDER:
+ c = _my_source_sbuil.charAt( _i );
+ break;
+ case CHAR_ARRAY:
+ c = _my_source_charary[ _i ];
+ break;
+ }
+ }
+ }
+ if ( !_in_single_quote && !_in_double_quote ) {
+ if ( c == ':' ) {
+ _saw_colon = true;
+ }
+ else if ( !( ( c < 33 ) || ( c > 126 ) ) && _saw_colon
+ && ( ( c != '[' ) && ( c != '.' ) && ( ( c < 48 ) || ( c > 57 ) ) ) ) {
+ _saw_colon = false;
+ }
+ if ( _in_open_bracket && ( c == ']' ) ) {
+ _in_open_bracket = false;
+ }
+ }
+ // \n\t is always ignored,
+ // as is " (34) and ' (39) (space is 32):
+ if ( ( isIgnoreQuotes() && ( ( c < 33 ) || ( c > 126 ) || ( c == 34 ) || ( c == 39 ) || ( ( getCladeLevel() == 0 ) && ( c == ';' ) ) ) )
+ || ( !isIgnoreQuotes() && ( ( c < 32 ) || ( c > 126 ) || ( ( getCladeLevel() == 0 ) && ( c == ';' ) ) ) ) ) {
+ // Do nothing.
+ }
+ else if ( ( c == 32 ) && ( !_in_single_quote && !_in_double_quote ) ) {
+ // Do nothing.
+ }
+ else if ( _in_comment ) {
+ if ( c == ']' ) {
+ _in_comment = false;
+ }
+ }
+ else if ( _in_double_quote ) {
+ if ( c == '"' ) {
+ _in_double_quote = false;
+ }
+ else {
+ getCurrentAnotation().append( c );
+ }
+ }
+ else if ( c == '"' ) {
+ _in_double_quote = true;
+ }
+ else if ( _in_single_quote ) {
+ if ( c == 39 ) {
+ _in_single_quote = false;
+ }
+ else {
+ getCurrentAnotation().append( c );
+ }
+ }
+ else if ( c == 39 ) {
+ _in_single_quote = true;
+ }
+ else if ( c == '[' ) {
+ _saw_open_bracket = true;
+ _in_open_bracket = true;
+ }
+ else if ( _saw_open_bracket ) {
+ if ( c != ']' ) {
+ // everything not starting with "[&" is considered a comment
+ // unless ":digits and/or . [bootstrap]":
+ if ( c == '&' ) {
+ getCurrentAnotation().append( "[&" );
+ }
+ else if ( _saw_colon ) {
+ getCurrentAnotation().append( "[" + c );
+ }
+ else {
+ _in_comment = true;
+ }
+ }
+ // comment consisting just of "[]":
+ _saw_open_bracket = false;
+ }
+ else if ( ( c == '(' ) && !_in_open_bracket ) {
+ final Phylogeny phy = processOpenParen2();
+ if ( phy != null ) {
+ ++_i;
+ // return phy;
+ _next = phy;
+ return;
+ }
+ }
+ else if ( ( c == ')' ) && !_in_open_bracket ) {
+ processCloseParen();
+ }
+ else if ( ( c == ',' ) && !_in_open_bracket ) {
+ processComma();
+ }
+ else {
+ getCurrentAnotation().append( c );
+ }
+ ++_i;
+ } // while ( true )
+ System.out.println( "done with loop" );
+ 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() );
+ _next = finishPhylogeny2();
+ setCurrentPhylogeny( null );
+ //return finishPhylogeny2();
+ }
+ else if ( ( getCurrentAnotation() != null ) && ( getCurrentAnotation().length() > 0 ) ) {
+ System.out.println( "1node=" + getCurrentAnotation() );
+ _next = finishSingleNodePhylogeny2();
+ setCurrentAnotation( null );
+ //return finishSingleNodePhylogeny2();
+ }
+ else {
+ _next = null;
+ //return null;
+ }
+ }
+
private Object getNhxSource() {
return _nhx_source;
}
setReplaceUnderscores( REPLACE_UNDERSCORES_DEFAULT );
setGuessRootedness( GUESS_ROOTEDNESS_DEFAULT );
setIgnoreQuotes( IGNORE_QUOTES_DEFAULT );
- setHasNext( false );
}
private boolean isGuessRootedness() {
_current_phylogeny = current_phylogeny;
}
- private void setHasNext( final boolean has_next ) {
- _has_next = has_next;
- }
-
private void setInputType( final byte input_type ) {
_input_type = input_type;
}
final int blu = ForesterUtil.limitRangeForColor( Integer.parseInt( st.nextToken() ) );
return new Color( red, green, blu );
}
-
- @Override
- public Phylogeny[] parse() throws IOException {
- // TODO Auto-generated method stub
- return null;
- }
}
System.out.println( "failed." );
failed++;
}
- System.exit( 0 );
System.out.print( "Nexus characters parsing: " );
if ( Test.testNexusCharactersParsing() ) {
System.out.println( "OK." );
private static boolean testNHParsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
+ final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser2() )[ 0 ];
if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
return false;
}
if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
return false;
}
- final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
- final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
- final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
- final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
- final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
- final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
- final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
- final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
- final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
- final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
+ final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser2() )[ 0 ];
+ final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser2() )[ 0 ];
+ final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser2() )[ 0 ];
+ final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser2() )[ 0 ];
+ final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser2() );
+ final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser2() );
+ final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser2() );
+ final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser2() );
+ final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser2() );
+ final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser2() );
final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
+ " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
+ "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
- new NHXParser() );
+ new NHXParser2() );
if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
return false;
}
if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
return false;
}
- final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
- final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
+ final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser2() );
+ 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 NHXParser() );
+ final Phylogeny[] p16 = factory.create( p16_S, new NHXParser2() );
if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
return false;
}
final String p17_S = "(C,(A,B))";
- final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
+ final Phylogeny[] p17 = factory.create( p17_S, new NHXParser2() );
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 NHXParser() );
+ final Phylogeny[] p18 = factory.create( p18_S, new NHXParser2() );
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 NHXParser() );
+ final Phylogeny[] p19 = factory.create( p19_S, new NHXParser2() );
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 NHXParser() );
+ final Phylogeny[] p20 = factory.create( p20_S, new NHXParser2() );
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 NHXParser() );
+ final Phylogeny[] p21 = factory.create( p21_S, new NHXParser2() );
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 NHXParser() );
+ final Phylogeny[] p22 = factory.create( p22_S, new NHXParser2() );
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 NHXParser() );
+ final Phylogeny[] p23 = factory.create( p23_S, new NHXParser2() );
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 NHXParser() );
+ final Phylogeny[] p24 = factory.create( p24_S, new NHXParser2() );
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 NHXParser() );
+ final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser2() );
if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
return false;
}
+ "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() );
+ final Phylogeny[] p25 = factory.create( p25_S, new NHXParser2() );
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() );
+ final Phylogeny[] p26 = factory.create( p26_S, new NHXParser2() );
if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
return false;
}
final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
- new NHXParser() );
+ new NHXParser2() );
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";
String p0_str = "(A,B);";
NHXParser2 p = new NHXParser2();
p.setSource( p0_str );
- Phylogeny p0 = p.getNext();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p0 = p.next();
if ( !p0.toNewHampshire().equals( p0_str ) ) {
System.out.println( p0.toNewHampshire() );
return false;
}
- //if ( p.getNext() != null ) {
- // return false;
- //}
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
//
String p00_str = "(A,B)root;";
- //p = new NHXParser2();
p.setSource( p00_str );
- Phylogeny p00 = p.getNext();
+ Phylogeny p00 = p.next();
if ( !p00.toNewHampshire().equals( p00_str ) ) {
System.out.println( p00.toNewHampshire() );
return false;
//
String p000_str = "A;";
p.setSource( p000_str );
- Phylogeny p000 = p.getNext();
+ Phylogeny p000 = p.next();
if ( !p000.toNewHampshire().equals( p000_str ) ) {
System.out.println( p000.toNewHampshire() );
return false;
//
String p0000_str = "A";
p.setSource( p0000_str );
- Phylogeny p0000 = p.getNext();
+ Phylogeny p0000 = p.next();
if ( !p0000.toNewHampshire().equals( "A;" ) ) {
System.out.println( p0000.toNewHampshire() );
return false;
}
//
p.setSource( "(A)" );
- Phylogeny p00000 = p.getNext();
+ Phylogeny p00000 = p.next();
if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
System.out.println( p00000.toNewHampshire() );
return false;
}
//
- // p.setSource( " " );
- // Phylogeny p000000 = p.getNext();
- // if ( !p000000.toNewHampshire().equals( "(A);" ) ) {
- // System.out.println( p000000.toNewHampshire() );
- // return false;
- // }
- //
String p1_str = "(A,B)(C,D)(E,F)(G,H)";
p.setSource( p1_str );
- Phylogeny p1_0 = p.getNext();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p1_0 = p.next();
if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
System.out.println( p1_0.toNewHampshire() );
return false;
}
- Phylogeny p1_1 = p.getNext();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p1_1 = p.next();
if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
return false;
}
- Phylogeny p1_2 = p.getNext();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny p1_2 = p.next();
if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
return false;
}
- Phylogeny p1_3 = p.getNext();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ 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;
+ }
//
String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
p.setSource( p2_str );
- Phylogeny p2_0 = p.getNext();
+ 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;
}
- Phylogeny p2_1 = p.getNext();
+ 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;
}
- Phylogeny p2_2 = p.getNext();
+ 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;
}
- Phylogeny p2_3 = p.getNext();
+ 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;
}
- Phylogeny p2_4 = p.getNext();
+ 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;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
final PhylogenyNode n5 = PhylogenyNode
- .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
+ .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30]" );
final PhylogenyNode n6 = PhylogenyNode
- .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
+ .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0]" );
if ( !n1.toNewHampshireX().equals( "" ) ) {
return false;
}
if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
return false;
}
- if ( !n5.toNewHampshireX()
- .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
+ if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56:W=2.0:C=10.20.30]" ) ) {
return false;
}
- if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
+ if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100:W=2.0:C=0.0.0]" ) ) {
return false;
}
}
return false;
}
final PhylogenyNode n00 = PhylogenyNode
- .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
+ .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1:W=2:C=0.0.0]" );
if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
return false;
}
+ "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
+ "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
- + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
+ + "7.369400000000000e-02}])", new NHXParser2() )[ 0 ];
if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
return false;
}
+ "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
+ "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
+ "7.369400000000000e-02}])",
- new NHXParser() )[ 0 ];
+ new NHXParser2() )[ 0 ];
if ( p2.getNode( "1" ) == null ) {
return false;
}
git://source.jalview.org / jalview.git / commitdiff