import java.io.IOException;
import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.util.ParserUtils;
final File species_tree_file,
final boolean replace_undescores_in_nhx_trees,
final boolean ignore_quotes_in_nhx_trees,
- final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees )
+ final TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees )
throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException {
Phylogeny species_tree;
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
nhx.setIgnoreQuotes( ignore_quotes_in_nhx_trees );
nhx.setTaxonomyExtraction( taxonomy_extraction_in_nhx_trees );
}
+ else if ( p instanceof NexusPhylogeniesParser ) {
+ final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
+ nex.setReplaceUnderscores( replace_undescores_in_nhx_trees );
+ nex.setIgnoreQuotes( ignore_quotes_in_nhx_trees );
+ nex.setTaxonomyExtraction( taxonomy_extraction_in_nhx_trees );
+ }
species_tree = factory.create( species_tree_file, p )[ 0 ];
species_tree.setRooted( true );
final TaxonomyComparisonBase comp_base = determineTaxonomyComparisonBase( gene_tree );