// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
if ( strip_evaluator_phylogenies ) {
unstripped_evaluator_phylogeny = evaluator_phylogeny.copy();
SupportCount.strip( seq_names_to_keep, evaluator_phylogeny );
- evaluator_phylogeny.orderAppearance( true ); // This is for
+ PhylogenyMethods.orderAppearance( evaluator_phylogeny.getRoot(),
+ true,
+ true,
+ DESCENDANT_SORT_PRIORITY.TAXONOMY ); // This is for
// easer
// comparison if
// phylos are saved
// to file.
+ evaluator_phylogeny.externalNodesHaveChanged();
+ evaluator_phylogeny.hashIDs();
+ evaluator_phylogeny.recalculateNumberOfExternalDescendants( true );
}
final double s = SupportCount.compare( phylogeny,
evaluator_phylogenies[ i ],
true,
similarity_threshold );
if ( ( similarity_threshold < 0.0 ) || ( s >= similarity_threshold ) ) {
- unstripped_evaluator_phylogeny.orderAppearance( true );
+ PhylogenyMethods.orderAppearance( unstripped_evaluator_phylogeny.getRoot(),
+ true,
+ true,
+ DESCENDANT_SORT_PRIORITY.TAXONOMY );
evaluator_phylogenies_above_threshold.add( unstripped_evaluator_phylogeny );
}
if ( verbose ) {