2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.sdi;
28 import org.forester.phylogeny.Phylogeny;
29 import org.forester.phylogeny.PhylogenyNode;
30 import org.forester.phylogeny.data.Taxonomy;
32 public class TaxonomyAssigner extends SDI {
34 public TaxonomyAssigner( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SdiException {
35 super( gene_tree, species_tree );
36 getSpeciesTree().preOrderReId();
38 geneTreePostOrderTraversal( getGeneTree().getRoot() );
41 void geneTreePostOrderTraversal( final PhylogenyNode g ) {
42 if ( !g.isExternal() ) {
43 for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
44 geneTreePostOrderTraversal( g.getChildNode( i ) );
46 final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
47 for( int i = 0; i < linked_nodes.length; ++i ) {
48 linked_nodes[ i ] = g.getChildNode( i ).getLink();
50 final int[] min_max = GSDI.obtainMinMaxIdIndices( linked_nodes );
51 int min_i = min_max[ 0 ];
52 int max_i = min_max[ 1 ];
53 while ( linked_nodes[ min_i ] != linked_nodes[ max_i ] ) {
54 linked_nodes[ max_i ] = linked_nodes[ max_i ].getParent();
55 final int[] min_max_ = GSDI.obtainMinMaxIdIndices( linked_nodes );
56 min_i = min_max_[ 0 ];
57 max_i = min_max_[ 1 ];
59 final PhylogenyNode s = linked_nodes[ max_i ];
61 if ( s.getNodeData().isHasTaxonomy() ) {
62 g.getNodeData().setTaxonomy( ( Taxonomy ) s.getNodeData().getTaxonomy().copy() );
67 public static void execute( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SdiException {
68 new TaxonomyAssigner( gene_tree, species_tree );