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.protein.DomainId;
  38 import org.forester.species.Species;
  39 import org.forester.util.BasicDescriptiveStatistics;
  40 import org.forester.util.DescriptiveStatistics;
  41
  42 public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculator {
  43
  44     final DomainSimilarity.DomainSimilaritySortField _sort;
  45     private final boolean                            _sort_by_species_count_first;
  46     private final boolean                            _treat_as_binary_comparison;
  47
  48     public BasicDomainSimilarityCalculator( final DomainSimilarity.DomainSimilaritySortField sort,
  49                                             final boolean sort_by_species_count_first,
  50                                             final boolean treat_as_binary_comparison ) {
  51         _sort = sort;
  52         _sort_by_species_count_first = sort_by_species_count_first;
  53         _treat_as_binary_comparison = treat_as_binary_comparison;
  54     }
  55
  56     @Override
  57     public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
  58                                                               final List<GenomeWideCombinableDomains> cdc_list,
  59                                                               final boolean ignore_domains_without_combinations_in_any_genome,
  60                                                               final boolean ignore_domains_specific_to_one_genome ) {
  61         if ( cdc_list.size() < 2 ) {
  62             throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinale domains collections" );
  63         }
  64         final SortedSet<DomainSimilarity> similarities = new TreeSet<DomainSimilarity>();
  65         final SortedSet<DomainId> keys = new TreeSet<DomainId>();
  66         for( final GenomeWideCombinableDomains cdc : cdc_list ) {
  67             keys.addAll( ( cdc ).getAllCombinableDomainsIds().keySet() );
  68         }
  69         for( final DomainId key : keys ) {
  70             final List<CombinableDomains> same_id_cd_list = new ArrayList<CombinableDomains>( cdc_list.size() );
  71             final List<Species> species_with_key_id_domain = new ArrayList<Species>();
  72             for( final GenomeWideCombinableDomains cdc : cdc_list ) {
  73                 if ( cdc.contains( key ) ) {
  74                     same_id_cd_list.add( cdc.get( key ) );
  75                     species_with_key_id_domain.add( cdc.getSpecies() );
  76                 }
  77             }
  78             if ( ignore_domains_without_combinations_in_any_genome ) { //TODO: test me..........................................<<<<<<<<<<<<<
  79                 boolean without_combinations = true;
  80                 for( final CombinableDomains cd : same_id_cd_list ) {
  81                     if ( cd.getNumberOfCombinableDomains() > 0 ) {
  82                         without_combinations = false;
  83                         break;
  84                     }
  85                 }
  86                 if ( without_combinations ) {
  87                     continue;
  88                 }
  89             }
  90             // BIG CHANGE IN LOGIC: Tuesday July 08, 0;55
  91             // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  92             // OLD: if ( same_id_cd_list.size() > 1 ) {
  93             if ( same_id_cd_list.size() > 0 ) {
  94                 if ( !ignore_domains_specific_to_one_genome || ( same_id_cd_list.size() > 1 ) ) {
  95                     final DomainSimilarity s = calculateSimilarity( pairwise_calculator, same_id_cd_list );
  96                     if ( s != null ) {
  97                         similarities.add( s );
  98                     }
  99                     else {
 100                         throw new RuntimeException( "similarity is null: this should not have happened" );
 101                     }
 102                 }
 103             }
 104             // ~~~ NEW:
 105             else {
 106                 throw new RuntimeException( "this should not have happened" );
 107             }
 108             // ~~~ OLD:
 109             // else if ( same_id_cd_list.size() == 1 ) {
 110             // TODO need to go in file
 111             // System.out.println( "only in one species [" +
 112             // species_with_key_id_domain.get( 0 ) + "]: " + key_id );
 113             //}
 114             //else {
 115             //    throw new RuntimeException( "this should not have happened" );
 116             // }
 117         }
 118         return similarities;
 119     }
 120
 121     private DomainSimilarity calculateSimilarity( final PairwiseDomainSimilarityCalculator pairwise_calculator,
 122                                                   final List<CombinableDomains> domains_list ) {
 123         if ( domains_list.size() == 1 ) {
 124             // BIG CHANGE IN LOGIC: Tuesday July 08, 0;55
 125             // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 126             // ~~~OLD:
 127             //throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinable domains" );
 128             // ~~~new:
 129             final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
 130             species_data.put( domains_list.get( 0 ).getSpecies(),
 131                               createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
 132             return new PrintableDomainSimilarity( domains_list.get( 0 ),
 133                                                   1.0,
 134                                                   1.0,
 135                                                   1.0,
 136                                                   1.0,
 137                                                   0.0,
 138                                                   0,
 139                                                   0,
 140                                                   0,
 141                                                   species_data,
 142                                                   getSort(),
 143                                                   isSortBySpeciesCountFirst(),
 144                                                   isTreatAsBinaryComparison() );
 145         }
 146         final DescriptiveStatistics stat = new BasicDescriptiveStatistics();
 147         final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
 148         species_data.put( domains_list.get( 0 ).getSpecies(),
 149                           createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
 150         int max_difference_in_counts = 0;
 151         int max_difference = 0;
 152         final boolean is_domain_combination_based = pairwise_calculator instanceof CombinationsBasedPairwiseDomainSimilarityCalculator;
 153         for( int i = 1; i < domains_list.size(); ++i ) {
 154             species_data.put( domains_list.get( i ).getSpecies(),
 155                               createSpeciesSpecificDomainSimilariyData( domains_list.get( i ) ) );
 156             final CombinableDomains domains_i = domains_list.get( i );
 157             for( int j = 0; j < i; ++j ) {
 158                 final PairwiseDomainSimilarity pairwise_similarity = pairwise_calculator
 159                         .calculateSimilarity( domains_i, domains_list.get( j ) );
 160                 final int difference_in_counts = pairwise_similarity.getDifferenceInCounts();
 161                 int difference = 0;
 162                 if ( is_domain_combination_based ) {
 163                     difference = ( ( CombinationsBasedPairwiseDomainSimilarity ) pairwise_similarity )
 164                             .getNumberOfDifferentDomains();
 165                 }
 166                 else {
 167                     difference = difference_in_counts;
 168                 }
 169                 if ( Math.abs( difference_in_counts ) > Math.abs( max_difference_in_counts ) ) {
 170                     max_difference_in_counts = difference_in_counts;
 171                 }
 172                 if ( Math.abs( difference ) > Math.abs( max_difference ) ) {
 173                     max_difference = difference;
 174                 }
 175                 stat.addValue( pairwise_similarity.getSimilarityScore() );
 176             }
 177         }
 178         if ( stat.getN() < 1 ) {
 179             throw new AssertionError( "empty descriptive statistics: this should not have happened" );
 180         }
 181         if ( ( stat.getN() != 1 ) && isTreatAsBinaryComparison() ) {
 182             throw new IllegalArgumentException( "attmpt to treat similarity with N not equal to one as binary comparison" );
 183         }
 184         if ( ( /*stat.getN() != 1 ||*/!isTreatAsBinaryComparison() ) && ( max_difference_in_counts < 0 ) ) {
 185             max_difference_in_counts = Math.abs( max_difference_in_counts );
 186             if ( !is_domain_combination_based ) {
 187                 max_difference = Math.abs( max_difference ); //=max_difference_in_counts for !is_domain_combination_based.
 188             }
 189         }
 190         DomainSimilarity similarity = null;
 191         if ( stat.getN() == 1 ) {
 192             similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
 193                                                         stat.getMin(),
 194                                                         stat.getMax(),
 195                                                         stat.arithmeticMean(),
 196                                                         stat.median(),
 197                                                         0.0,
 198                                                         stat.getN(),
 199                                                         max_difference_in_counts,
 200                                                         max_difference,
 201                                                         species_data,
 202                                                         getSort(),
 203                                                         isSortBySpeciesCountFirst(),
 204                                                         isTreatAsBinaryComparison() );
 205         }
 206         else {
 207             similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
 208                                                         stat.getMin(),
 209                                                         stat.getMax(),
 210                                                         stat.arithmeticMean(),
 211                                                         stat.median(),
 212                                                         stat.sampleStandardDeviation(),
 213                                                         stat.getN(),
 214                                                         max_difference_in_counts,
 215                                                         max_difference,
 216                                                         species_data,
 217                                                         getSort(),
 218                                                         isSortBySpeciesCountFirst(),
 219                                                         isTreatAsBinaryComparison() );
 220         }
 221         return similarity;
 222     }
 223
 224     private DomainSimilarity.DomainSimilaritySortField getSort() {
 225         return _sort;
 226     }
 227
 228     private boolean isSortBySpeciesCountFirst() {
 229         return _sort_by_species_count_first;
 230     }
 231
 232     private boolean isTreatAsBinaryComparison() {
 233         return _treat_as_binary_comparison;
 234     }
 235
 236     private static SpeciesSpecificDomainSimilariyData createSpeciesSpecificDomainSimilariyData( final CombinableDomains cd ) {
 237         final SpeciesSpecificDomainSimilariyData sd = new PrintableSpeciesSpecificDomainSimilariyData( cd.getKeyDomainProteinsCount(),
 238                                                                                                        cd.getKeyDomainCount(),
 239                                                                                                        cd.getNumberOfCombinableDomains(),
 240                                                                                                        cd.getKeyDomainConfidenceDescriptiveStatistics() );
 241         for( final DomainId domain : cd.getCombinableDomains() ) {
 242             sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );
 243         }
 244         return sd;
 245     }
 246 }