3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.pccx;
29 import org.forester.phylogeny.Phylogeny;
30 import org.forester.phylogeny.PhylogenyNode;
31 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
35 * @author Christian M. Zmasek
37 public class LogBranchLengthBasedScoringMethod extends BranchCountingBasedScoringMethod {
39 public static final double MIN_ALLOWED_BL_VALUE = 0.0001;
40 public static final double MAX_ALLOWED_BL_VALUE = 1.0;
43 double calculateScoreContributionPerExternalNode( final PhylogenyNode external_node,
44 final PhylogenyNode current_node ) {
45 double score_contribution = 0.0;
46 if ( current_node == external_node ) {
47 score_contribution = external_node.getDistanceToParent();
48 // This, of course, is completely /ad hoc/.
51 score_contribution = ModelingUtils.calculateBranchLengthSum( external_node, current_node );
53 if ( score_contribution > LogBranchLengthBasedScoringMethod.MAX_ALLOWED_BL_VALUE ) {
54 score_contribution = LogBranchLengthBasedScoringMethod.MAX_ALLOWED_BL_VALUE;
56 else if ( score_contribution < LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE ) {
57 score_contribution = LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE;
59 return ( -Math.log( score_contribution ) );
63 public String getDesciption() {
64 return "sum of -ln(branch-length-sum) [for self: -ln(branch-length)] [min branch length: "
65 + LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE + ", max branch length: "
66 + LogBranchLengthBasedScoringMethod.MAX_ALLOWED_BL_VALUE + "]";
70 public double getNormalizationFactor( final Phylogeny phylogeny ) {
73 for( final PhylogenyNodeIterator iter = phylogeny.iteratorExternalForward(); iter.hasNext(); ) {
74 d = iter.next().getDistanceToParent();
75 if ( d > LogBranchLengthBasedScoringMethod.MAX_ALLOWED_BL_VALUE ) {
76 d = LogBranchLengthBasedScoringMethod.MAX_ALLOWED_BL_VALUE;
78 else if ( d < LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE ) {
79 d = LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE;
81 s += ( -Math.log( d ) );