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: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.pccx;
28 import java.util.SortedMap;
29 import java.util.TreeMap;
31 import org.forester.phylogeny.Phylogeny;
32 import org.forester.phylogeny.PhylogenyMethods;
33 import org.forester.phylogeny.PhylogenyNode;
34 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
37 * @author Christian M. Zmasek
39 public final class ModelingUtils {
41 static double calculateBranchLengthSum( final PhylogenyNode n1, final PhylogenyNode n2 ) {
42 final PhylogenyNode lca = PhylogenyMethods.calculateLCA( n1, n2 );
43 return ModelingUtils.calculateBranchLengthSumHelper( n1, lca )
44 + ModelingUtils.calculateBranchLengthSumHelper( n2, lca );
47 private static double calculateBranchLengthSumHelper( final PhylogenyNode outer, final PhylogenyNode inner ) {
48 PhylogenyNode my_outer = outer;
50 while ( my_outer != inner ) {
51 if ( my_outer.getDistanceToParent() > 0.0 ) {
52 l += my_outer.getDistanceToParent();
54 my_outer = my_outer.getParent();
59 static int calculateBranchSum( final PhylogenyNode n1, final PhylogenyNode n2 ) {
60 final PhylogenyNode lca = PhylogenyMethods.calculateLCA( n1, n2 );
61 return ModelingUtils.calculateBranchSumHelper( n1, lca ) + ModelingUtils.calculateBranchSumHelper( n2, lca );
64 private static int calculateBranchSumHelper( final PhylogenyNode outer, final PhylogenyNode inner ) {
65 PhylogenyNode my_outer = outer;
67 while ( my_outer != inner ) {
69 my_outer = my_outer.getParent();
74 static SortedMap<PhylogenyNode, Double> setUpExternalCoverageHashMap( final Phylogeny phylogeny ) {
75 final SortedMap<PhylogenyNode, Double> external_node_coverage = new TreeMap<PhylogenyNode, Double>();
76 for( final PhylogenyNodeIterator iter = phylogeny.iteratorExternalForward(); iter.hasNext(); ) {
77 external_node_coverage.put( iter.next(), 0.0 );
79 return external_node_coverage;