final NHXParser nhx = new NHXParser();
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );
- nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
//
final String gene_trees_00_str = "(MOUSE,RAT);(MOUSE,RAT);(MOUSE,RAT);(RAT,MOUSE);";
final Phylogeny[] gene_trees_00 = factory.create( gene_trees_00_str, nhx );
final NHXParser nhx = new NHXParser();
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );
- nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
+ "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
+ "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";