package org.forester.io.parsers.nhx;
import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
import java.io.File;
-import java.io.FileReader;
+import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
final static private boolean GUESS_IF_SUPPORT_VALUES = true;
final static private boolean GUESS_ROOTEDNESS_DEFAULT = true;
final static private boolean IGNORE_QUOTES_DEFAULT = false;
- final static private byte STRING = 0;
- final static private byte STRING_BUFFER = 1;
- final static private byte STRING_BUILDER = 4;
+
final static private char BELL = 7;
+ public final static String UTF_8 = "UTF-8";
+ public final static String ISO_8859_1 = "ISO-8859-1";
+ private final static String ENCODING_DEFAULT = UTF_8;
private boolean _allow_errors_in_distance_to_parent;
private int _clade_level;
private StringBuilder _current_anotation;
private byte _input_type;
private BufferedReader _my_source_br = null;
private char[] _my_source_charary = null;
- private StringBuffer _my_source_sbuff = null;
- private StringBuilder _my_source_sbuil = null;
- private String _my_source_str = null;
private Phylogeny _next;
private Object _nhx_source;
private boolean _replace_underscores;
private Object _source;
private int _source_length;
private TAXONOMY_EXTRACTION _taxonomy_extraction;
+ private final String _encoding;
public NHXParser() {
+ _encoding = ENCODING_DEFAULT;
+ init();
+ }
+
+ public NHXParser( final String encoding ) {
+ _encoding = encoding;
init();
}
@Override
public final Phylogeny[] parse() throws IOException {
final List<Phylogeny> l = new ArrayList<Phylogeny>();
- //int c = 0;
while ( hasNext() ) {
l.add( next() );
- // c++;
}
final Phylogeny[] p = new Phylogeny[ l.size() ];
for( int i = 0; i < l.size(); ++i ) {
_current_anotation = new StringBuilder();
_current_phylogeny = null;
_current_node = null;
- _my_source_str = null;
- _my_source_sbuff = null;
- _my_source_sbuil = null;
_my_source_charary = null;
determineAndProcessSourceType( _source );
switch ( _input_type ) {
- case STRING:
- _my_source_br = null;
- _my_source_str = ( String ) _nhx_source;
- break;
- case STRING_BUFFER:
- _my_source_br = null;
- _my_source_sbuff = ( StringBuffer ) _nhx_source;
- break;
- case STRING_BUILDER:
- _my_source_br = null;
- _my_source_sbuil = ( StringBuilder ) _nhx_source;
- break;
case CHAR_ARRAY:
_my_source_br = null;
_my_source_charary = ( char[] ) _nhx_source;
throw new PhylogenyParserException( getClass() + ": attempt to parse null object." );
}
else if ( nhx_source instanceof String ) {
- _input_type = NHXParser.STRING;
- _source_length = ( ( String ) nhx_source ).length();
- _nhx_source = nhx_source;
- }
- else if ( nhx_source instanceof StringBuilder ) {
- _input_type = NHXParser.STRING_BUILDER;
- _source_length = ( ( StringBuilder ) nhx_source ).length();
- _nhx_source = nhx_source;
- }
- else if ( nhx_source instanceof StringBuffer ) {
- _input_type = NHXParser.STRING_BUFFER;
- _source_length = ( ( StringBuffer ) nhx_source ).length();
- _nhx_source = nhx_source;
- }
- else if ( nhx_source instanceof StringBuilder ) {
- _input_type = NHXParser.STRING_BUILDER;
- _source_length = ( ( StringBuilder ) nhx_source ).length();
_nhx_source = nhx_source;
+ _input_type = NHXParser.BUFFERED_READER;
+ _source_length = 0;
+ InputStream is = new ByteArrayInputStream( (( String ) nhx_source ).getBytes(getEncoding()));
+ final InputStreamReader isr = new InputStreamReader( is, getEncoding() );
+ _nhx_source = new BufferedReader( isr );
}
else if ( nhx_source instanceof char[] ) {
_input_type = NHXParser.CHAR_ARRAY;
if ( !ForesterUtil.isEmpty( error ) ) {
throw new PhylogenyParserException( error );
}
- _nhx_source = new BufferedReader( new FileReader( f ) );
+ final InputStream is = new FileInputStream( f );
+ final InputStreamReader isr = new InputStreamReader( is, getEncoding() );
+ _nhx_source = new BufferedReader( isr );
}
else if ( nhx_source instanceof URL ) {
_input_type = NHXParser.BUFFERED_READER;
// catch ( final IOException e ) {
// }
}
- final InputStreamReader isr = new InputStreamReader( ( ( URL ) nhx_source ).openStream() );
+ final InputStream is = ( ( URL ) nhx_source ).openStream();
+ final InputStreamReader isr = new InputStreamReader( is, getEncoding() );
_nhx_source = new BufferedReader( isr );
}
else if ( nhx_source instanceof InputStream ) {
// catch ( final IOException e ) {
// }
}
- final InputStreamReader isr = new InputStreamReader( ( InputStream ) nhx_source );
- _nhx_source = new BufferedReader( isr );
+ final InputStream is = ( InputStream ) nhx_source;
+ final InputStreamReader isr = new InputStreamReader( is, getEncoding() );
+ _nhx_source = new BufferedReader( isr );
}
else {
throw new IllegalArgumentException( getClass() + " can only parse objects of type String,"
- + " StringBuffer, StringBuilder, char[], File, InputStream, or URL "
+ + " char[], File, InputStream, or URL "
+ " [attempt to parse object of " + nhx_source.getClass() + "]." );
}
}
if ( _i >= _source_length ) {
break;
}
- else {
- switch ( _input_type ) {
- 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;
- }
- }
+ c = _my_source_charary[ _i ];
}
if ( !_in_single_quote && !_in_double_quote ) {
if ( c == ':' ) {
}
// \n\t is always ignored,
// "=34 '=39 space=32
- if ( ( c < 32 ) || ( c > 126 ) || ( isIgnoreQuotes() && ( ( c == 32 ) || ( c == 34 ) || ( c == 39 ) ) )
+ if ( ( c < 32 ) || ( c == 127 ) || ( isIgnoreQuotes() && ( ( c == 32 ) || ( c == 34 ) || ( c == 39 ) ) )
|| ( ( c == 32 ) && ( !_in_single_quote && !_in_double_quote ) )
|| ( ( _clade_level == 0 ) && ( c == ';' ) && ( !_in_single_quote && !_in_double_quote ) ) ) {
//do nothing
final Phylogeny phy = processOpenParen();
if ( phy != null ) {
++_i;
- // return phy;
_next = phy;
return;
}
}
}
+ public String getEncoding() {
+ return _encoding;
+ }
+
public static enum TAXONOMY_EXTRACTION {
AGGRESSIVE, NO, PFAM_STYLE_RELAXED, PFAM_STYLE_STRICT;
}
System.out.println( "failed." );
failed++;
}
+ System.out.print( "NH parsing - special chars: " );
+ if ( Test.testNHParsingSpecialChars() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Conversion to NHX (node level): " );
if ( Test.testNHXconversion() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "UTF-8 parsing from file: " );
+ if ( Test.testUTF8ParsingFromFile() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Copying of node data: " );
if ( Test.testCopyOfNodeData() ) {
System.out.println( "OK." );
}
return true;
}
+
+ private static boolean testUTF8ParsingFromFile() {
+ try {
+ final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
+ final Phylogeny[] phylogenies_xml = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.xml" ),
+ xml_parser );
+ if ( xml_parser.getErrorCount() > 0 ) {
+ System.out.println( xml_parser.getErrorMessages().toString() );
+ return false;
+ }
+ if ( phylogenies_xml.length != 1 ) {
+ return false;
+ }
+
+ final Phylogeny[] phylogenies_xml2 = ParserBasedPhylogenyFactory.getInstance().create( new StringBuffer( phylogenies_xml[0].toPhyloXML( 0 )),
+ xml_parser );
+
+ final Phylogeny[] phylogenies_nh = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nh" ), new NHXParser() );
+ if ( phylogenies_nh.length != 1 ) {
+ return false;
+ }
+
+ final Phylogeny[] phylogenies_nex = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nex" ), new NexusPhylogeniesParser() );
+ if ( phylogenies_nex.length != 1 ) {
+ return false;
+ }
+
+ final String[] xml_n = phylogenies_xml[0].getAllExternalNodeNames();
+ final String[] xml_n2 = phylogenies_xml2[0].getAllExternalNodeNames();
+ final String[] nh_n = phylogenies_nh[0].getAllExternalNodeNames();
+ final String[] nex_n = phylogenies_nex[0].getAllExternalNodeNames();
+ final String n0 = "AQ~!@#$%^&*()_+-=\\{}|;:\"<>?,./";
+ final String n1 = "€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ";
+ final String n2 = "漢字ひらがなカタカナ";
+ final String n3 = "อักษรไทย";
+ final String n4 = "繁體字";
+ final String n5 = "한글";
+ final String n6 = "देवनागरी";
+
+ final String n7 = "chữ Quốc ngữ";
+ final String n8 = "ру́сский язы́к";
+ final String n9 = "អក្សរខ្មែរ";
+
+ if ( !xml_n[0].equals( n0 ) ) {
+ System.out.println( xml_n[0] );
+ System.out.println( n0 );
+ return false;
+ }
+ if ( !xml_n2[0].equals( n0 ) ) {
+ System.out.println( xml_n2[0] );
+ System.out.println( n0 );
+ return false;
+ }
+ if ( !nh_n[0].equals( n0 ) ) {
+ System.out.println( nh_n[0] );
+ System.out.println( n0 );
+ return false;
+ }
+ if ( !nex_n[0].equals( n0 ) ) {
+ System.out.println( nex_n[0] );
+ System.out.println( n0 );
+ return false;
+ }
+
+ if ( !xml_n[1].equals( n1 ) ) {
+ System.out.println( xml_n[1] );
+ System.out.println( n1 );
+ return false;
+ }
+ if ( !xml_n2[1].equals( n1 ) ) {
+ System.out.println( xml_n2[1] );
+ System.out.println( n1 );
+ return false;
+ }
+ if ( !nh_n[1].equals( n1 ) ) {
+ System.out.println( nh_n[1] );
+ System.out.println( n1 );
+ return false;
+ }
+ if ( !nex_n[1].equals( n1 ) ) {
+ System.out.println( nex_n[1] );
+ System.out.println( n1 );
+ return false;
+ }
+
+ if ( !xml_n[2].equals( n2 ) ) {
+ System.out.println( xml_n[2] );
+ System.out.println( n2 );
+ return false;
+ }
+ if ( !xml_n2[2].equals( n2 ) ) {
+ System.out.println( xml_n2[2] );
+ System.out.println( n2 );
+ return false;
+ }
+ if ( !nh_n[2].equals( n2 ) ) {
+ System.out.println( nh_n[2] );
+ System.out.println( n2 );
+ return false;
+ }
+ if ( !nex_n[2].equals( n2 ) ) {
+ System.out.println( nex_n[2] );
+ System.out.println( n2 );
+ return false;
+ }
+ //
+ if ( !xml_n[3].equals( n3 ) ) {
+ System.out.println( xml_n[3] );
+ System.out.println( n3 );
+ return false;
+ }
+ if ( !xml_n2[3].equals( n3 ) ) {
+ System.out.println( xml_n2[3] );
+ System.out.println( n3 );
+ return false;
+ }
+ if ( !nh_n[3].equals( n3 ) ) {
+ System.out.println( nh_n[3] );
+ System.out.println( n3 );
+ return false;
+ }
+ if ( !nex_n[3].equals( n3 ) ) {
+ System.out.println( nex_n[3] );
+ System.out.println( n3 );
+ return false;
+ }
+ //
+ if ( !xml_n[4].equals( n4 ) ) {
+ System.out.println( xml_n[4] );
+ System.out.println( n4 );
+ return false;
+ }
+ if ( !nh_n[4].equals( n4 ) ) {
+ System.out.println( nh_n[4] );
+ System.out.println( n4 );
+ return false;
+ }
+ if ( !nex_n[4].equals( n4 ) ) {
+ System.out.println( nex_n[4] );
+ System.out.println( n4 );
+ return false;
+ }
+ //
+ if ( !xml_n[5].equals( n5 ) ) {
+ System.out.println( xml_n[5] );
+ System.out.println( n5 );
+ return false;
+ }
+ if ( !nh_n[5].equals( n5 ) ) {
+ System.out.println( nh_n[5] );
+ System.out.println( n5 );
+ return false;
+ }
+ if ( !nex_n[5].equals( n5 ) ) {
+ System.out.println( nex_n[5] );
+ System.out.println( n5 );
+ return false;
+ }
+ //
+ if ( !xml_n[6].equals( n6 ) ) {
+ System.out.println( xml_n[6] );
+ System.out.println( n6 );
+ return false;
+ }
+ if ( !nh_n[6].equals( n6 ) ) {
+ System.out.println( nh_n[6] );
+ System.out.println( n6 );
+ return false;
+ }
+ if ( !nex_n[6].equals( n6 ) ) {
+ System.out.println( nex_n[6] );
+ System.out.println( n6 );
+ return false;
+ }
+ //
+ if ( !xml_n[7].equals( n7 ) ) {
+ System.out.println( xml_n[7] );
+ System.out.println( n7 );
+ return false;
+ }
+ if ( !nh_n[7].equals( n7 ) ) {
+ System.out.println( nh_n[7] );
+ System.out.println( n7 );
+ return false;
+ }
+ if ( !nex_n[7].equals( n7 ) ) {
+ System.out.println( nex_n[7] );
+ System.out.println( n7 );
+ return false;
+ }
+ if ( !xml_n[8].equals( n8 ) ) {
+ System.out.println( xml_n[8] );
+ System.out.println( n8 );
+ return false;
+ }
+ if ( !nh_n[8].equals( n8 ) ) {
+ System.out.println( nh_n[8] );
+ System.out.println( n8 );
+ return false;
+ }
+ if ( !nex_n[8].equals( n8 ) ) {
+ System.out.println( nex_n[8] );
+ System.out.println( n8 );
+ return false;
+ }
+ if ( !xml_n[9].equals( n9 ) ) {
+ System.out.println( xml_n[9] );
+ System.out.println( n9 );
+ return false;
+ }
+ if ( !xml_n2[9].equals( n9 ) ) {
+ System.out.println( xml_n2[9] );
+ System.out.println( n9 );
+ return false;
+ }
+ if ( !nh_n[9].equals( n9 ) ) {
+ System.out.println( nh_n[9] );
+ System.out.println( n9 );
+ return false;
+ }
+ if ( !nex_n[9].equals( n9 ) ) {
+ System.out.println( nex_n[9] );
+ System.out.println( n9 );
+ return false;
+ }
+ if (!phylogenies_xml[0].toNewHampshire().equals(
+ phylogenies_nh[0].toNewHampshire() ) ) {
+ System.out.println( phylogenies_xml[0].toNewHampshire() );
+ System.out.println( phylogenies_nh[0].toNewHampshire() );
+ return false;
+ }
+ if (!phylogenies_xml[0].toNewHampshire().equals(
+ phylogenies_nex[0].toNewHampshire() ) ) {
+ System.out.println( phylogenies_xml[0].toNewHampshire() );
+ System.out.println( phylogenies_nex[0].toNewHampshire() );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+
private static boolean testBasicPhyloXMLparsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
else {
xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
}
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
.equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
+ System.out.println( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() );
return false;
}
if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
}
}
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
- final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
+ final Phylogeny[] phylogenies_1 = factory.create( new File( x2 ), xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( "errors:" );
System.out.println( xml_parser.getErrorMessages().toString() );
if ( phylogenies_1.length != 4 ) {
return false;
}
- final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
+ final Phylogeny[] phylogenies_2 = factory.create( new File(Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( "errors:" );
if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
return false;
}
- final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
+ final Phylogeny[] phylogenies_3 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
return false;
}
- final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
+ final Phylogeny[] phylogenies_4 = factory.create( new File( Test.PATH_TO_TEST_DATA + "special_characters.xml") ,
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
- final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
+ final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ];
if ( t5.getNumberOfExternalNodes() != 8 ) {
return false;
}
return false;
}
final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
- final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
+ final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ];
if ( t6.getHeight() != 15 ) {
return false;
}
final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
- final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
+ final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ];
if ( t7.getHeight() != 15 ) {
return false;
}
final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
- final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
+ final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ];
if ( t8.getNumberOfExternalNodes() != 10 ) {
return false;
}
PhylogenyNode n;
List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
+ final Phylogeny t0 = factory.create( sb0.toString(), new NHXParser() )[ 0 ];
t0.getNode( "cd" ).setCollapse( true );
t0.getNode( "cde" ).setCollapse( true );
n = t0.getFirstExternalNode();
}
ext.clear();
final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
+ final Phylogeny t1 = factory.create( sb1.toString(), new NHXParser() )[ 0 ];
t1.getNode( "ab" ).setCollapse( true );
t1.getNode( "cd" ).setCollapse( true );
t1.getNode( "cde" ).setCollapse( true );
}
ext.clear();
final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
+ final Phylogeny t2 = factory.create( sb2.toString(), new NHXParser() )[ 0 ];
t2.getNode( "ab" ).setCollapse( true );
t2.getNode( "cd" ).setCollapse( true );
t2.getNode( "cde" ).setCollapse( true );
}
ext.clear();
final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
+ final Phylogeny t3 = factory.create( sb3.toString(), new NHXParser() )[ 0 ];
t3.getNode( "ab" ).setCollapse( true );
t3.getNode( "cd" ).setCollapse( true );
t3.getNode( "cde" ).setCollapse( true );
}
ext.clear();
final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
+ final Phylogeny t4 = factory.create( sb4.toString(), new NHXParser() )[ 0 ];
t4.getNode( "ab" ).setCollapse( true );
t4.getNode( "cd" ).setCollapse( true );
t4.getNode( "cde" ).setCollapse( true );
return false;
}
final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
+ final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ];
ext.clear();
n = t5.getFirstExternalNode();
while ( n != null ) {
return false;
}
final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
+ final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ];
ext.clear();
t6.getNode( "ab" ).setCollapse( true );
n = t6.getNode( "ab" );
return false;
}
final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
+ final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ];
ext.clear();
t7.getNode( "cd" ).setCollapse( true );
n = t7.getNode( "a" );
return false;
}
final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
+ final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ];
ext.clear();
t8.getNode( "cd" ).setCollapse( true );
t8.getNode( "c" ).setCollapse( true );
return false;
}
final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
+ final Phylogeny t9 = factory.create( sb9.toString(), new NHXParser() )[ 0 ];
ext.clear();
t9.getNode( "gh" ).setCollapse( true );
n = t9.getNode( "a" );
return false;
}
final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
+ final Phylogeny t10 = factory.create( sb10.toString(), new NHXParser() )[ 0 ];
ext.clear();
t10.getNode( "gh" ).setCollapse( true );
t10.getNode( "g" ).setCollapse( true );
return false;
}
final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
+ final Phylogeny t11 = factory.create( sb11.toString(), new NHXParser() )[ 0 ];
ext.clear();
t11.getNode( "gh" ).setCollapse( true );
t11.getNode( "fgh" ).setCollapse( true );
return false;
}
final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
+ final Phylogeny t12 = factory.create( sb12.toString(), new NHXParser() )[ 0 ];
ext.clear();
t12.getNode( "gh" ).setCollapse( true );
t12.getNode( "fgh" ).setCollapse( true );
return false;
}
final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
+ final Phylogeny t13 = factory.create( sb13.toString(), new NHXParser() )[ 0 ];
ext.clear();
t13.getNode( "ab" ).setCollapse( true );
t13.getNode( "b" ).setCollapse( true );
return false;
}
final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
- final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
+ final Phylogeny t14 = factory.create( sb14.toString(), new NHXParser() )[ 0 ];
ext.clear();
t14.getNode( "ab" ).setCollapse( true );
t14.getNode( "a" ).setCollapse( true );
return false;
}
final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
- final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
+ final Phylogeny t15 = factory.create( sb15.toString(), new NHXParser() )[ 0 ];
ext.clear();
t15.getNode( "ab" ).setCollapse( true );
t15.getNode( "a" ).setCollapse( true );
//
//
final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
- final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
+ final Phylogeny t16 = factory.create( sb16.toString(), new NHXParser() )[ 0 ];
ext.clear();
t16.getNode( "ab" ).setCollapse( true );
t16.getNode( "a" ).setCollapse( true );
if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
return false;
}
- final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ).toString(), 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 p5 = factory.create( new StringBuffer( "(A,B5);" ).toString(), 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() );
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)" ).toString(), 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 ];
+ final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ).toString(), 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)" ),
+ .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ).toString(),
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 ];
+ final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 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)" ).toString(), 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 ];
+ final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ).toString(), 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)" ),
+ .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ).toString(),
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 ];
+ final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ).toString(), new NHXParser() )[ 0 ];
if ( p54.getNode( "A" ) == null ) {
return false;
}
return false;
}
final Phylogeny p55 = factory
- .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ),
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ).toString(),
new NHXParser() )[ 0 ];
if ( !p55
.toNewHampshire()
return false;
}
final Phylogeny p56 = factory
- .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ).toString(),
new NHXParser() )[ 0 ];
if ( !p56
.toNewHampshire()
return false;
}
final Phylogeny p57 = factory
- .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ).toString(),
new NHXParser() )[ 0 ];
if ( !p57
.toNewHampshire()
return false;
}
final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
- final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
+ final Phylogeny p58 = factory.create( s58, new NHXParser() )[ 0 ];
if ( !p58.toNewHampshire().equals( s58 ) ) {
System.out.println( p58.toNewHampshire() );
return false;
}
final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
- final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
+ final Phylogeny p59 = factory.create( s59 , new NHXParser() )[ 0 ];
if ( !p59.toNewHampshire().equals( s59 ) ) {
System.out.println( p59.toNewHampshire() );
return false;
}
final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
- final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
+ final Phylogeny p60 = factory.create( s60, new NHXParser() )[ 0 ];
if ( !p60.toNewHampshire().equals( s60 ) ) {
System.out.println( p60.toNewHampshire() );
return false;
}
final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
- final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
+ final Phylogeny p61 = factory.create( s61, new NHXParser() )[ 0 ];
if ( !p61.toNewHampshire()
.equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
System.out.println( p61.toNewHampshire() );
}
return true;
}
-
+
+ private static boolean testNHParsingSpecialChars() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final String i0 = "(A!+=~QWERTY!@#$%^&*-,€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ)";
+ final Phylogeny p0 = factory.create( i0, new NHXParser() )[ 0 ];
+ if ( !p0.toNewHampshireX().equals( i0 ) ) {
+ System.out.println();
+ System.out.println( p0.toNewHampshireX() );
+ System.out.println( i0 );
+ return false;
+ }
+ final String i1 = "(हिंदी,한글,ไทย,'Tiếng Việt',ひらがなカタカナ漢字,繁體字,русский)";
+ final Phylogeny p1 = factory.create( i1, new NHXParser() )[ 0 ];
+ if ( !p1.toNewHampshireX().equals( i1 ) ) {
+ System.out.println();
+ System.out.println( p1.toNewHampshireX() );
+ System.out.println( i1 );
+ 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);";
xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
}
}
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
git://source.jalview.org / jalview.git / commitdiff