forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java

   1 // $Id:
   2 // 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 java.awt.Color;
  30 import java.util.List;
  31 import java.util.Map;
  32 import java.util.SortedMap;
  33
  34 import org.forester.phylogeny.Phylogeny;
  35 import org.forester.phylogeny.PhylogenyMethods;
  36 import org.forester.phylogeny.PhylogenyNode;
  37 import org.forester.util.BasicDescriptiveStatistics;
  38 import org.forester.util.DescriptiveStatistics;
  39 import org.forester.util.ForesterUtil;
  40
  41 /*
  42  * @author Christian M. Zmasek
  43  */
  44 public class ExternalNodeBasedCoverageMethod implements CoverageCalculationMethod {
  45
  46     private static final Color MEAN_COVERAGE_COLOR = new Color( 0, 0, 0 );
  47     private static final Color MAXIMAL_COV_COLOR   = new Color( 0, 255, 0 );
  48     private static final Color MINIMAL_COV_COLOR   = new Color( 255, 0, 0 );
  49
  50     @Override
  51     public Coverage calculateCoverage( final List<Phylogeny> phylogenies,
  52                                        final List<String> names,
  53                                        final CoverageCalculationOptions options,
  54                                        final boolean annotate_phylogenies ) {
  55         final DescriptiveStatistics normalized_score_stats = new BasicDescriptiveStatistics();
  56         final DescriptiveStatistics raw_score_stats = new BasicDescriptiveStatistics();
  57         final ExternalNodeBasedCoverageMethodOptions my_options = ( ExternalNodeBasedCoverageMethodOptions ) options;
  58         if ( ( my_options == null ) || ForesterUtil.isEmpty( my_options.getScoringMethod() ) ) {
  59             throw new IllegalArgumentException( "options for external node based coverage method appear to not have been set" );
  60         }
  61         BranchCountingBasedScoringMethod scoring_method;
  62         try {
  63             scoring_method = ( BranchCountingBasedScoringMethod ) ( Class.forName( my_options.getScoringMethod() ) )
  64                     .newInstance();
  65         }
  66         catch ( final Exception e ) {
  67             throw new IllegalArgumentException( "could not create scoring method class \""
  68                     + my_options.getScoringMethod() + "\"" );
  69         }
  70         final double normalization_factor = scoring_method.getNormalizationFactor( phylogenies.get( 0 ) );
  71         for( final Object element : phylogenies ) {
  72             final double raw_score = calculateCoverage( ( Phylogeny ) element,
  73                                                         names,
  74                                                         options,
  75                                                         scoring_method,
  76                                                         annotate_phylogenies,
  77                                                         normalization_factor );
  78             normalized_score_stats.addValue( raw_score * normalization_factor );
  79             raw_score_stats.addValue( raw_score );
  80         }
  81         return new ExternalNodeBasedCoverage( normalized_score_stats, raw_score_stats.arithmeticMean(), options );
  82     }
  83
  84     private double calculateCoverage( final Phylogeny phylogeny,
  85                                       final List<String> names,
  86                                       final CoverageCalculationOptions options,
  87                                       final BranchCountingBasedScoringMethod scoring_method,
  88                                       final boolean annotate_phylogeny,
  89                                       final double normalization_factor ) {
  90         final SortedMap<PhylogenyNode, Double> external_node_scores = ModelingUtils
  91                 .setUpExternalCoverageHashMap( phylogeny );
  92         for( final Object element : names ) {
  93             scoring_method.calculateScoreForExternalNode( external_node_scores,
  94                                                           phylogeny,
  95                                                           phylogeny.getNode( ( String ) element ),
  96                                                           options );
  97         }
  98         if ( annotate_phylogeny ) {
  99             colorizePhylogenyAccordingToCoverage( external_node_scores, phylogeny, normalization_factor );
 100         }
 101         double score = 0.0;
 102         for( final Object element : external_node_scores.values() ) {
 103             score += ( ( Double ) element ).doubleValue();
 104         }
 105         return score;
 106     }
 107
 108     private void colorizePhylogenyAccordingToCoverage( final SortedMap<PhylogenyNode, Double> external_node_scores,
 109                                                        final Phylogeny phylogeny,
 110                                                        final double normalization_factor ) {
 111         final DescriptiveStatistics ds = new BasicDescriptiveStatistics();
 112         for( final Object element : external_node_scores.entrySet() ) {
 113             ds.addValue( ( Double ) ( ( Map.Entry ) element ).getValue() * normalization_factor );
 114         }
 115         final double min = ds.getMin();
 116         final double max = ds.getMax();
 117         final double median = ds.median();
 118         for( final Object element2 : external_node_scores.entrySet() ) {
 119             final Map.Entry element = ( Map.Entry ) element2;
 120             final PhylogenyNode node = ( PhylogenyNode ) element.getKey();
 121             final double normalized_value = ( Double ) element.getValue() * normalization_factor;
 122             PhylogenyMethods.setBranchColorValue( node, ForesterUtil
 123                     .calcColor( normalized_value,
 124                                 min,
 125                                 max,
 126                                 median,
 127                                 ExternalNodeBasedCoverageMethod.MINIMAL_COV_COLOR,
 128                                 ExternalNodeBasedCoverageMethod.MAXIMAL_COV_COLOR,
 129                                 ExternalNodeBasedCoverageMethod.MEAN_COVERAGE_COLOR ) );
 130         }
 131         PhylogenyMethods.postorderBranchColorAveragingExternalNodeBased( phylogeny );
 132     }
 133 }