* @param query
* the sequence name of the squence whose orthologs are to be
* inferred
+ * @throws SDIException
*/
public void inferOrthologs( final File gene_trees_file, final Phylogeny species_tree, final String query )
- throws IOException {
+ throws IOException, SDIException {
int bs = 0;
if ( RIO.TIME ) {
_time = System.currentTimeMillis();
// Helper method which performs the actual ortholog inference for
// the external node with seqname query.
- private void inferOrthologsHelper( final Phylogeny gene_tree, final Phylogeny species_tree, final String query ) {
+ private void inferOrthologsHelper( final Phylogeny gene_tree, final Phylogeny species_tree, final String query )
+ throws SDIException {
Phylogeny assigned_tree = null;
List<PhylogenyNode> nodes = null;
final SDIR sdiunrooted = new SDIR();