final boolean replace_undescores_in_nhx_trees,
final boolean ignore_quotes_in_nhx_trees,
final TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees )
- throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException {
+ throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException {
Phylogeny species_tree;
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
switch ( comp_base ) {
case SCIENTIFIC_NAME:
PhylogenyMethods
- .transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
- true );
+ .transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ true );
break;
case CODE:
PhylogenyMethods.transferNodeNameToField( species_tree,