import org.forester.phylogeny.iterators.PreorderTreeIterator;
import org.forester.sdi.DistanceCalculator;
import org.forester.sdi.RIO;
+import org.forester.sdi.SDIException;
import org.forester.sdi.SDIR;
import org.forester.util.ForesterUtil;
final int warn_no_orthos,
final double warn_one_ortho,
final int bootstraps,
- final double t_orthologs_dc ) throws IOException {
+ final double t_orthologs_dc ) throws IOException, SDIException {
Phylogeny consensus_tree = null;
Phylogeny
// to be a consensus tree.
output.append( rio_instance
.inferredUltraParalogsToString( seq_name, sort > 2, threshold_ultra_paralogs ) );
}
+ rio_instance.inferredOrthologTableToFile( new File( "table" ) );
output.append( "\n\nSort priority: " + RIO.getOrder( sort ) );
output.append( "\nExt nodes : " + rio_instance.getExtNodesOfAnalyzedGeneTrees() );
output.append( "\nSamples : " + rio_instance.getBootstraps() + "\n" );