forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java

   1 // $Id:
   2 // cmzmasek Exp $
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  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.
  14 //
  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.
  19 //
  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
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.pccx;
  28
  29 import org.forester.phylogeny.Phylogeny;
  30 import org.forester.phylogeny.PhylogenyNode;
  31 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  32
  33 /*
  34  *
  35  * @author Christian M. Zmasek
  36  */
  37 public class LogBranchLengthBasedScoringMethod extends BranchCountingBasedScoringMethod {
  38
  39     public static final double MIN_ALLOWED_BL_VALUE = 0.0001;
  40     public static final double MAX_ALLOWED_BL_VALUE = 1.0;
  41
  42     @Override
  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/.
  49         }
  50         else {
  51             score_contribution = ModelingUtils.calculateBranchLengthSum( external_node, current_node );
  52         }
  53         if ( score_contribution > LogBranchLengthBasedScoringMethod.MAX_ALLOWED_BL_VALUE ) {
  54             score_contribution = LogBranchLengthBasedScoringMethod.MAX_ALLOWED_BL_VALUE;
  55         }
  56         else if ( score_contribution < LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE ) {
  57             score_contribution = LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE;
  58         }
  59         return ( -Math.log( score_contribution ) );
  60     }
  61
  62     @Override
  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 + "]";
  67     }
  68
  69     @Override
  70     public double getNormalizationFactor( final Phylogeny phylogeny ) {
  71         double s = 0.0;
  72         double d = 0.0;
  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;
  77             }
  78             else if ( d < LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE ) {
  79                 d = LogBranchLengthBasedScoringMethod.MIN_ALLOWED_BL_VALUE;
  80             }
  81             s += ( -Math.log( d ) );
  82         }
  83         return 1 / s;
  84     }
  85 }