not_found.add( tax.toString() );
}
else {
- not_found.add(node.getName() );
+ not_found.add( node.getName() );
}
if ( delete && node.isExternal() ) {
not_found_external_nodes.add( node );
phy.deleteSubtree( node, true );
}
phy.externalNodesHaveChanged();
- phy.hashIDs();
+ phy.clearHashIdToNodeMap();
phy.recalculateNumberOfExternalDescendants( true );
}
return not_found;
synchronized final private static void updateTaxonomy( final QUERY_TYPE qt,
final PhylogenyNode node,
final Taxonomy tax,
- final UniProtTaxonomy up_tax ) {
+ final UniProtTaxonomy up_tax )
+ throws PhyloXmlDataFormatException {
if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() )
&& ForesterUtil.isEmpty( tax.getScientificName() ) ) {
tax.setScientificName( up_tax.getScientificName() );