forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java

   1 // $Id:
   2 // Exp $
   3 //
   4 // FORESTER -- software libraries and applications
   5 // for evolutionary biology research and applications.
   6 //
   7 // Copyright (C) 2008-2009 Christian M. Zmasek
   8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   9 // All rights reserved
  10 //
  11 // This library is free software; you can redistribute it and/or
  12 // modify it under the terms of the GNU Lesser General Public
  13 // License as published by the Free Software Foundation; either
  14 // version 2.1 of the License, or (at your option) any later version.
  15 //
  16 // This library is distributed in the hope that it will be useful,
  17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  19 // Lesser General Public License for more details.
  20 //
  21 // You should have received a copy of the GNU Lesser General Public
  22 // License along with this library; if not, write to the Free Software
  23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  24 //
  25 // Contact: phylosoft @ gmail . com
  26 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  27
  28 package org.forester.surfacing;
  29
  30 import java.text.DecimalFormat;
  31 import java.util.ArrayList;
  32 import java.util.List;
  33 import java.util.SortedMap;
  34 import java.util.SortedSet;
  35 import java.util.TreeMap;
  36 import java.util.TreeSet;
  37
  38 import org.forester.species.Species;
  39 import org.forester.util.BasicDescriptiveStatistics;
  40 import org.forester.util.DescriptiveStatistics;
  41 import org.forester.util.ForesterUtil;
  42
  43 public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculator {
  44
  45     final DomainSimilarity.DomainSimilaritySortField _sort;
  46     private final boolean                            _calc_similarity_score;
  47     private final boolean                            _sort_by_species_count_first;
  48     private final boolean                            _treat_as_binary_comparison;
  49
  50     public BasicDomainSimilarityCalculator( final DomainSimilarity.DomainSimilaritySortField sort,
  51                                             final boolean sort_by_species_count_first,
  52                                             final boolean treat_as_binary_comparison,
  53                                             final boolean calc_similarity_score ) {
  54         _sort = sort;
  55         _sort_by_species_count_first = sort_by_species_count_first;
  56         _treat_as_binary_comparison = treat_as_binary_comparison;
  57         _calc_similarity_score = calc_similarity_score;
  58     }
  59
  60     @Override
  61     public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
  62                                                               final List<GenomeWideCombinableDomains> cdc_list,
  63                                                               final boolean ignore_domains_without_combinations_in_any_genome,
  64                                                               final boolean ignore_domains_specific_to_one_genome ) {
  65         if ( cdc_list.size() < 2 ) {
  66             throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinale domains collections" );
  67         }
  68         final SortedSet<DomainSimilarity> similarities = new TreeSet<DomainSimilarity>();
  69         final SortedSet<String> keys = new TreeSet<String>();
  70         for( final GenomeWideCombinableDomains cdc : cdc_list ) {
  71             keys.addAll( ( cdc ).getAllCombinableDomainsIds().keySet() );
  72         }
  73         final DecimalFormat pf = new java.text.DecimalFormat( "000000" );
  74         int counter = 1;
  75         System.out.println( keys.size() );
  76         for( final String key : keys ) {
  77             ForesterUtil.updateProgress( counter, pf );
  78             counter++;
  79             final List<CombinableDomains> same_id_cd_list = new ArrayList<CombinableDomains>( cdc_list.size() );
  80             final List<Species> species_with_key_id_domain = new ArrayList<Species>();
  81             for( final GenomeWideCombinableDomains cdc : cdc_list ) {
  82                 if ( cdc.contains( key ) ) {
  83                     same_id_cd_list.add( cdc.get( key ) );
  84                     species_with_key_id_domain.add( cdc.getSpecies() );
  85                 }
  86             }
  87             if ( ignore_domains_without_combinations_in_any_genome ) { //TODO: test me..........................................<<<<<<<<<<<<<
  88                 boolean without_combinations = true;
  89                 for( final CombinableDomains cd : same_id_cd_list ) {
  90                     if ( cd.getNumberOfCombinableDomains() > 0 ) {
  91                         without_combinations = false;
  92                         break;
  93                     }
  94                 }
  95                 if ( without_combinations ) {
  96                     continue;
  97                 }
  98             }
  99             if ( same_id_cd_list.size() > 0 ) {
 100                 if ( !ignore_domains_specific_to_one_genome || ( same_id_cd_list.size() > 1 ) ) {
 101                     final DomainSimilarity s = calculateSimilarity( pairwise_calculator, same_id_cd_list );
 102                     if ( s != null ) {
 103                         similarities.add( s );
 104                     }
 105                     else {
 106                         throw new RuntimeException( "similarity is null: this should not have happened" );
 107                     }
 108                 }
 109             }
 110             else {
 111                 throw new RuntimeException( "this should not have happened" );
 112             }
 113         }
 114         System.out.println();
 115         return similarities;
 116     }
 117
 118     public boolean isCalcSimilarityScore() {
 119         return _calc_similarity_score;
 120     }
 121
 122     private DomainSimilarity calculateSimilarity( final PairwiseDomainSimilarityCalculator pairwise_calculator,
 123                                                   final List<CombinableDomains> domains_list ) {
 124         if ( domains_list.size() == 1 ) {
 125             final SortedMap<Species, SpeciesSpecificDcData> species_data = new TreeMap<Species, SpeciesSpecificDcData>();
 126             species_data.put( domains_list.get( 0 ).getSpecies(),
 127                               createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
 128             if ( !isCalcSimilarityScore() ) {
 129                 return new DomainSimilarity( domains_list.get( 0 ),
 130                                              0,
 131                                              0,
 132                                              species_data,
 133                                              isSortBySpeciesCountFirst(),
 134                                              isTreatAsBinaryComparison() );
 135             }
 136             else {
 137                 return new DomainSimilarity( domains_list.get( 0 ),
 138                                              1.0,
 139                                              1.0,
 140                                              1.0,
 141                                              1.0,
 142                                              0.0,
 143                                              0,
 144                                              0,
 145                                              0,
 146                                              species_data,
 147                                              isSortBySpeciesCountFirst(),
 148                                              isTreatAsBinaryComparison() );
 149             }
 150         }
 151         DescriptiveStatistics stat = null;
 152         if ( isCalcSimilarityScore() ) {
 153             stat = new BasicDescriptiveStatistics();
 154         }
 155         final SortedMap<Species, SpeciesSpecificDcData> species_data = new TreeMap<Species, SpeciesSpecificDcData>();
 156         species_data.put( domains_list.get( 0 ).getSpecies(),
 157                           createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
 158         int max_difference_in_counts = 0;
 159         int max_difference = 0;
 160         final boolean is_domain_combination_based = pairwise_calculator instanceof CombinationsBasedPairwiseDomainSimilarityCalculator;
 161         for( int i = 1; i < domains_list.size(); ++i ) {
 162             species_data.put( domains_list.get( i ).getSpecies(),
 163                               createSpeciesSpecificDomainSimilariyData( domains_list.get( i ) ) );
 164             final CombinableDomains domains_i = domains_list.get( i );
 165             for( int j = 0; j < i; ++j ) {
 166                 final PairwiseDomainSimilarity pairwise_similarity = pairwise_calculator
 167                         .calculateSimilarity( domains_i, domains_list.get( j ) );
 168                 final int difference_in_counts = pairwise_similarity.getDifferenceInCounts();
 169                 int difference = 0;
 170                 if ( is_domain_combination_based ) {
 171                     difference = ( ( CombinationsBasedPairwiseDomainSimilarity ) pairwise_similarity )
 172                             .getNumberOfDifferentDomains();
 173                 }
 174                 else {
 175                     difference = difference_in_counts;
 176                 }
 177                 if ( Math.abs( difference_in_counts ) > Math.abs( max_difference_in_counts ) ) {
 178                     max_difference_in_counts = difference_in_counts;
 179                 }
 180                 if ( Math.abs( difference ) > Math.abs( max_difference ) ) {
 181                     max_difference = difference;
 182                 }
 183                 if ( isCalcSimilarityScore() ) {
 184                     stat.addValue( pairwise_similarity.getSimilarityScore() );
 185                 }
 186             }
 187         }
 188         if ( isCalcSimilarityScore() ) {
 189             if ( stat.getN() < 1 ) {
 190                 throw new RuntimeException( "empty descriptive statistics: this should not have happened" );
 191             }
 192             if ( ( stat.getN() != 1 ) && isTreatAsBinaryComparison() ) {
 193                 throw new IllegalArgumentException( "attmpt to treat similarity with N not equal to one as binary comparison" );
 194             }
 195         }
 196         if ( !isTreatAsBinaryComparison() && ( max_difference_in_counts < 0 ) ) {
 197             max_difference_in_counts = Math.abs( max_difference_in_counts );
 198             if ( !is_domain_combination_based ) {
 199                 max_difference = Math.abs( max_difference );
 200             }
 201         }
 202         DomainSimilarity similarity = null;
 203         if ( !isCalcSimilarityScore() ) {
 204             similarity = new DomainSimilarity( domains_list.get( 0 ),
 205                                                max_difference_in_counts,
 206                                                max_difference,
 207                                                species_data,
 208                                                isSortBySpeciesCountFirst(),
 209                                                isTreatAsBinaryComparison() );
 210         }
 211         else {
 212             if ( stat.getN() == 1 ) {
 213                 similarity = new DomainSimilarity( domains_list.get( 0 ),
 214                                                    stat.getMin(),
 215                                                    stat.getMax(),
 216                                                    stat.arithmeticMean(),
 217                                                    stat.median(),
 218                                                    0.0,
 219                                                    stat.getN(),
 220                                                    max_difference_in_counts,
 221                                                    max_difference,
 222                                                    species_data,
 223                                                    isSortBySpeciesCountFirst(),
 224                                                    isTreatAsBinaryComparison() );
 225             }
 226             else {
 227                 similarity = new DomainSimilarity( domains_list.get( 0 ),
 228                                                    stat.getMin(),
 229                                                    stat.getMax(),
 230                                                    stat.arithmeticMean(),
 231                                                    stat.median(),
 232                                                    stat.sampleStandardDeviation(),
 233                                                    stat.getN(),
 234                                                    max_difference_in_counts,
 235                                                    max_difference,
 236                                                    species_data,
 237                                                    isSortBySpeciesCountFirst(),
 238                                                    isTreatAsBinaryComparison() );
 239             }
 240         }
 241         return similarity;
 242     }
 243
 244     private boolean isSortBySpeciesCountFirst() {
 245         return _sort_by_species_count_first;
 246     }
 247
 248     private boolean isTreatAsBinaryComparison() {
 249         return _treat_as_binary_comparison;
 250     }
 251
 252     private static SpeciesSpecificDcData createSpeciesSpecificDomainSimilariyData( final CombinableDomains cd ) {
 253         final SpeciesSpecificDcData sd = new PrintableSpeciesSpecificDcData( cd.getKeyDomainCount(),
 254                                                                              cd.getNumberOfCombinableDomains() );
 255         for( final String prot : cd.getKeyDomainProteins() ) {
 256             sd.addKeyDomainProtein( prot );
 257         }
 258         for( final String domain : cd.getCombinableDomains() ) {
 259             sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );
 260         }
 261         return sd;
 262     }
 263 }