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: www.phylosoft.org/forester
  27
  28 package org.forester.surfacing;
  29
  30 import java.util.ArrayList;
  31 import java.util.List;
  32 import java.util.SortedMap;
  33 import java.util.SortedSet;
  34 import java.util.TreeMap;
  35 import java.util.TreeSet;
  36
  37 import org.forester.util.BasicDescriptiveStatistics;
  38 import org.forester.util.DescriptiveStatistics;
  39
  40 public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculator {
  41
  42     final DomainSimilarity.DomainSimilaritySortField _sort;
  43     private final boolean                            _sort_by_species_count_first;
  44     private final boolean                            _treat_as_binary_comparison;
  45
  46     public BasicDomainSimilarityCalculator( final DomainSimilarity.DomainSimilaritySortField sort,
  47                                             final boolean sort_by_species_count_first,
  48                                             final boolean treat_as_binary_comparison ) {
  49         _sort = sort;
  50         _sort_by_species_count_first = sort_by_species_count_first;
  51         _treat_as_binary_comparison = treat_as_binary_comparison;
  52     }
  53
  54     @Override
  55     public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
  56                                                               final List<GenomeWideCombinableDomains> cdc_list,
  57                                                               final boolean ignore_domains_without_combinations_in_any_genome,
  58                                                               final boolean ignore_domains_specific_to_one_genome ) {
  59         if ( cdc_list.size() < 2 ) {
  60             throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinale domains collections" );
  61         }
  62         final SortedSet<DomainSimilarity> similarities = new TreeSet<DomainSimilarity>();
  63         final SortedSet<DomainId> keys = new TreeSet<DomainId>();
  64         for( final GenomeWideCombinableDomains cdc : cdc_list ) {
  65             keys.addAll( ( cdc ).getAllCombinableDomainsIds().keySet() );
  66         }
  67         for( final DomainId key : keys ) {
  68             final List<CombinableDomains> same_id_cd_list = new ArrayList<CombinableDomains>( cdc_list.size() );
  69             final List<Species> species_with_key_id_domain = new ArrayList<Species>();
  70             for( final GenomeWideCombinableDomains cdc : cdc_list ) {
  71                 if ( cdc.contains( key ) ) {
  72                     same_id_cd_list.add( cdc.get( key ) );
  73                     species_with_key_id_domain.add( cdc.getSpecies() );
  74                 }
  75             }
  76             if ( ignore_domains_without_combinations_in_any_genome ) { //TODO: test me..........................................<<<<<<<<<<<<<
  77                 boolean without_combinations = true;
  78                 for( final CombinableDomains cd : same_id_cd_list ) {
  79                     if ( cd.getNumberOfCombinableDomains() > 0 ) {
  80                         without_combinations = false;
  81                         break;
  82                     }
  83                 }
  84                 if ( without_combinations ) {
  85                     continue;
  86                 }
  87             }
  88             // BIG CHANGE IN LOGIC: Tuesday July 08, 0;55
  89             // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  90             // OLD: if ( same_id_cd_list.size() > 1 ) {
  91             if ( same_id_cd_list.size() > 0 ) {
  92                 if ( !ignore_domains_specific_to_one_genome || ( same_id_cd_list.size() > 1 ) ) {
  93                     final DomainSimilarity s = calculateSimilarity( pairwise_calculator, same_id_cd_list );
  94                     if ( s != null ) {
  95                         similarities.add( s );
  96                     }
  97                     else {
  98                         throw new RuntimeException( "similarity is null: this should not have happened" );
  99                     }
 100                 }
 101             }
 102             // ~~~ NEW:
 103             else {
 104                 throw new RuntimeException( "this should not have happened" );
 105             }
 106             // ~~~ OLD:
 107             // else if ( same_id_cd_list.size() == 1 ) {
 108             // TODO need to go in file
 109             // System.out.println( "only in one species [" +
 110             // species_with_key_id_domain.get( 0 ) + "]: " + key_id );
 111             //}
 112             //else {
 113             //    throw new RuntimeException( "this should not have happened" );
 114             // }
 115         }
 116         return similarities;
 117     }
 118
 119     private DomainSimilarity calculateSimilarity( final PairwiseDomainSimilarityCalculator pairwise_calculator,
 120                                                   final List<CombinableDomains> domains_list ) {
 121         if ( domains_list.size() == 1 ) {
 122             // BIG CHANGE IN LOGIC: Tuesday July 08, 0;55
 123             // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 124             // ~~~OLD:
 125             //throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinable domains" );
 126             // ~~~new:
 127             final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
 128             species_data.put( domains_list.get( 0 ).getSpecies(),
 129                               createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
 130             return new PrintableDomainSimilarity( domains_list.get( 0 ),
 131                                                   1.0,
 132                                                   1.0,
 133                                                   1.0,
 134                                                   1.0,
 135                                                   0.0,
 136                                                   0,
 137                                                   0,
 138                                                   0,
 139                                                   species_data,
 140                                                   getSort(),
 141                                                   isSortBySpeciesCountFirst(),
 142                                                   isTreatAsBinaryComparison() );
 143         }
 144         final DescriptiveStatistics stat = new BasicDescriptiveStatistics();
 145         final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
 146         species_data.put( domains_list.get( 0 ).getSpecies(),
 147                           createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
 148         int max_difference_in_counts = 0;
 149         int max_difference = 0;
 150         final boolean is_domain_combination_based = pairwise_calculator instanceof CombinationsBasedPairwiseDomainSimilarityCalculator;
 151         for( int i = 1; i < domains_list.size(); ++i ) {
 152             species_data.put( domains_list.get( i ).getSpecies(),
 153                               createSpeciesSpecificDomainSimilariyData( domains_list.get( i ) ) );
 154             final CombinableDomains domains_i = domains_list.get( i );
 155             for( int j = 0; j < i; ++j ) {
 156                 final PairwiseDomainSimilarity pairwise_similarity = pairwise_calculator
 157                         .calculateSimilarity( domains_i, domains_list.get( j ) );
 158                 final int difference_in_counts = pairwise_similarity.getDifferenceInCounts();
 159                 int difference = 0;
 160                 if ( is_domain_combination_based ) {
 161                     difference = ( ( CombinationsBasedPairwiseDomainSimilarity ) pairwise_similarity )
 162                             .getNumberOfDifferentDomains();
 163                 }
 164                 else {
 165                     difference = difference_in_counts;
 166                 }
 167                 if ( Math.abs( difference_in_counts ) > Math.abs( max_difference_in_counts ) ) {
 168                     max_difference_in_counts = difference_in_counts;
 169                 }
 170                 if ( Math.abs( difference ) > Math.abs( max_difference ) ) {
 171                     max_difference = difference;
 172                 }
 173                 stat.addValue( pairwise_similarity.getSimilarityScore() );
 174             }
 175         }
 176         if ( stat.getN() < 1 ) {
 177             throw new AssertionError( "empty descriptive statistics: this should not have happened" );
 178         }
 179         if ( ( stat.getN() != 1 ) && isTreatAsBinaryComparison() ) {
 180             throw new IllegalArgumentException( "attmpt to treat similarity with N not equal to one as binary comparison" );
 181         }
 182         if ( ( /*stat.getN() != 1 ||*/!isTreatAsBinaryComparison() ) && ( max_difference_in_counts < 0 ) ) {
 183             max_difference_in_counts = Math.abs( max_difference_in_counts );
 184             if ( !is_domain_combination_based ) {
 185                 max_difference = Math.abs( max_difference ); //=max_difference_in_counts for !is_domain_combination_based.
 186             }
 187         }
 188         DomainSimilarity similarity = null;
 189         if ( stat.getN() == 1 ) {
 190             similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
 191                                                         stat.getMin(),
 192                                                         stat.getMax(),
 193                                                         stat.arithmeticMean(),
 194                                                         stat.median(),
 195                                                         0.0,
 196                                                         stat.getN(),
 197                                                         max_difference_in_counts,
 198                                                         max_difference,
 199                                                         species_data,
 200                                                         getSort(),
 201                                                         isSortBySpeciesCountFirst(),
 202                                                         isTreatAsBinaryComparison() );
 203         }
 204         else {
 205             similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
 206                                                         stat.getMin(),
 207                                                         stat.getMax(),
 208                                                         stat.arithmeticMean(),
 209                                                         stat.median(),
 210                                                         stat.sampleStandardDeviation(),
 211                                                         stat.getN(),
 212                                                         max_difference_in_counts,
 213                                                         max_difference,
 214                                                         species_data,
 215                                                         getSort(),
 216                                                         isSortBySpeciesCountFirst(),
 217                                                         isTreatAsBinaryComparison() );
 218         }
 219         return similarity;
 220     }
 221
 222     private DomainSimilarity.DomainSimilaritySortField getSort() {
 223         return _sort;
 224     }
 225
 226     private boolean isSortBySpeciesCountFirst() {
 227         return _sort_by_species_count_first;
 228     }
 229
 230     private boolean isTreatAsBinaryComparison() {
 231         return _treat_as_binary_comparison;
 232     }
 233
 234     private static SpeciesSpecificDomainSimilariyData createSpeciesSpecificDomainSimilariyData( final CombinableDomains cd ) {
 235         final SpeciesSpecificDomainSimilariyData sd = new PrintableSpeciesSpecificDomainSimilariyData( cd.getKeyDomainProteinsCount(),
 236                                                                                                        cd.getKeyDomainCount(),
 237                                                                                                        cd.getNumberOfCombinableDomains(),
 238                                                                                                        cd.getKeyDomainConfidenceDescriptiveStatistics() );
 239         for( final DomainId domain : cd.getCombinableDomains() ) {
 240             sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );
 241         }
 242         return sd;
 243     }
 244 }