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;
31 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
33 public class TaxonomyAssigner extends SDI {
35 public TaxonomyAssigner( final Phylogeny gene_tree, final Phylogeny species_tree ) {
36 super( gene_tree, species_tree );
37 getSpeciesTree().preOrderReId();
39 geneTreePostOrderTraversal( getGeneTree().getRoot() );
42 void geneTreePostOrderTraversal( final PhylogenyNode g ) {
43 if ( !g.isExternal() ) {
44 for( final PhylogenyNodeIterator iter = g.iterateChildNodesForward(); iter.hasNext(); ) {
45 geneTreePostOrderTraversal( iter.next() );
47 final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
48 for( int i = 0; i < linked_nodes.length; ++i ) {
49 linked_nodes[ i ] = g.getChildNode( i ).getLink();
51 final int[] min_max = GSDI.obtainMinMaxIdIndices( linked_nodes );
52 int min_i = min_max[ 0 ];
53 int max_i = min_max[ 1 ];
54 while ( linked_nodes[ min_i ] != linked_nodes[ max_i ] ) {
55 linked_nodes[ max_i ] = linked_nodes[ max_i ].getParent();
56 final int[] min_max_ = GSDI.obtainMinMaxIdIndices( linked_nodes );
57 min_i = min_max_[ 0 ];
58 max_i = min_max_[ 1 ];
60 final PhylogenyNode s = linked_nodes[ max_i ];
62 if ( s.getNodeData().isHasTaxonomy() ) {
63 g.getNodeData().setTaxonomy( ( Taxonomy ) s.getNodeData().getTaxonomy().copy() );
68 public static void execute( final Phylogeny gene_tree, final Phylogeny species_tree ) {
69 new TaxonomyAssigner( gene_tree, species_tree );