final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );
- nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+ nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
}
else if ( p instanceof NexusPhylogeniesParser ) {
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
nex.setReplaceUnderscores( false );
nex.setIgnoreQuotes( true );
- nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+ nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
}
return factory.create( gene_trees_file, p );
}