4 // FORESTER -- software libraries and applications
5 // for evolutionary biology research and applications.
7 // Copyright (C) 2008-2009 Christian M. Zmasek
8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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.
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.
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
25 // Contact: phylosoft @ gmail . com
26 // WWW: www.phylosoft.org/forester
28 package org.forester.surfacing;
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;
37 import org.forester.util.BasicDescriptiveStatistics;
38 import org.forester.util.DescriptiveStatistics;
40 public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculator {
42 final DomainSimilarity.DomainSimilaritySortField _sort;
43 private final boolean _sort_by_species_count_first;
44 private final boolean _treat_as_binary_comparison;
46 public BasicDomainSimilarityCalculator( final DomainSimilarity.DomainSimilaritySortField sort,
47 final boolean sort_by_species_count_first,
48 final boolean treat_as_binary_comparison ) {
50 _sort_by_species_count_first = sort_by_species_count_first;
51 _treat_as_binary_comparison = treat_as_binary_comparison;
54 public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
55 final List<GenomeWideCombinableDomains> cdc_list,
56 final boolean ignore_domains_without_combinations_in_any_genome,
57 final boolean ignore_domains_specific_to_one_genome ) {
58 if ( cdc_list.size() < 2 ) {
59 throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinale domains collections" );
61 final SortedSet<DomainSimilarity> similarities = new TreeSet<DomainSimilarity>();
62 final SortedSet<DomainId> keys = new TreeSet<DomainId>();
63 for( final GenomeWideCombinableDomains cdc : cdc_list ) {
64 keys.addAll( ( cdc ).getAllCombinableDomainsIds().keySet() );
66 for( final DomainId key : keys ) {
67 final List<CombinableDomains> same_id_cd_list = new ArrayList<CombinableDomains>( cdc_list.size() );
68 final List<Species> species_with_key_id_domain = new ArrayList<Species>();
69 for( final GenomeWideCombinableDomains cdc : cdc_list ) {
70 if ( cdc.contains( key ) ) {
71 same_id_cd_list.add( cdc.get( key ) );
72 species_with_key_id_domain.add( cdc.getSpecies() );
75 if ( ignore_domains_without_combinations_in_any_genome ) { //TODO: test me..........................................<<<<<<<<<<<<<
76 boolean without_combinations = true;
77 for( final CombinableDomains cd : same_id_cd_list ) {
78 if ( cd.getNumberOfCombinableDomains() > 0 ) {
79 without_combinations = false;
83 if ( without_combinations ) {
87 // BIG CHANGE IN LOGIC: Tuesday July 08, 0;55
88 // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
89 // OLD: if ( same_id_cd_list.size() > 1 ) {
90 if ( same_id_cd_list.size() > 0 ) {
91 if ( !ignore_domains_specific_to_one_genome || ( same_id_cd_list.size() > 1 ) ) {
92 final DomainSimilarity s = calculateSimilarity( pairwise_calculator, same_id_cd_list );
94 similarities.add( s );
97 throw new RuntimeException( "similarity is null: this should not have happened" );
103 throw new RuntimeException( "this should not have happened" );
106 // else if ( same_id_cd_list.size() == 1 ) {
107 // TODO need to go in file
108 // System.out.println( "only in one species [" +
109 // species_with_key_id_domain.get( 0 ) + "]: " + key_id );
112 // throw new RuntimeException( "this should not have happened" );
118 private DomainSimilarity calculateSimilarity( final PairwiseDomainSimilarityCalculator pairwise_calculator,
119 final List<CombinableDomains> domains_list ) {
120 if ( domains_list.size() == 1 ) {
121 // BIG CHANGE IN LOGIC: Tuesday July 08, 0;55
122 // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
124 //throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinable domains" );
126 final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
127 species_data.put( domains_list.get( 0 ).getSpecies(),
128 createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
129 return new PrintableDomainSimilarity( domains_list.get( 0 ),
140 isSortBySpeciesCountFirst(),
141 isTreatAsBinaryComparison() );
143 final DescriptiveStatistics stat = new BasicDescriptiveStatistics();
144 final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
145 species_data.put( domains_list.get( 0 ).getSpecies(), createSpeciesSpecificDomainSimilariyData( domains_list
147 int max_difference_in_counts = 0;
148 int max_difference = 0;
149 final boolean is_domain_combination_based = pairwise_calculator instanceof CombinationsBasedPairwiseDomainSimilarityCalculator;
150 for( int i = 1; i < domains_list.size(); ++i ) {
151 species_data.put( domains_list.get( i ).getSpecies(),
152 createSpeciesSpecificDomainSimilariyData( domains_list.get( i ) ) );
153 final CombinableDomains domains_i = domains_list.get( i );
154 for( int j = 0; j < i; ++j ) {
155 final PairwiseDomainSimilarity pairwise_similarity = pairwise_calculator
156 .calculateSimilarity( domains_i, domains_list.get( j ) );
157 final int difference_in_counts = pairwise_similarity.getDifferenceInCounts();
159 if ( is_domain_combination_based ) {
160 difference = ( ( CombinationsBasedPairwiseDomainSimilarity ) pairwise_similarity )
161 .getNumberOfDifferentDomains();
164 difference = difference_in_counts;
166 if ( Math.abs( difference_in_counts ) > Math.abs( max_difference_in_counts ) ) {
167 max_difference_in_counts = difference_in_counts;
169 if ( Math.abs( difference ) > Math.abs( max_difference ) ) {
170 max_difference = difference;
172 stat.addValue( pairwise_similarity.getSimilarityScore() );
175 if ( stat.getN() < 1 ) {
176 throw new AssertionError( "empty descriptive statistics: this should not have happened" );
178 if ( ( stat.getN() != 1 ) && isTreatAsBinaryComparison() ) {
179 throw new IllegalArgumentException( "attmpt to treat similarity with N not equal to one as binary comparison" );
181 if ( ( /*stat.getN() != 1 ||*/!isTreatAsBinaryComparison() ) && ( max_difference_in_counts < 0 ) ) {
182 max_difference_in_counts = Math.abs( max_difference_in_counts );
183 if ( !is_domain_combination_based ) {
184 max_difference = Math.abs( max_difference ); //=max_difference_in_counts for !is_domain_combination_based.
187 DomainSimilarity similarity = null;
188 if ( stat.getN() == 1 ) {
189 similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
192 stat.arithmeticMean(),
196 max_difference_in_counts,
200 isSortBySpeciesCountFirst(),
201 isTreatAsBinaryComparison() );
204 similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
207 stat.arithmeticMean(),
209 stat.sampleStandardDeviation(),
211 max_difference_in_counts,
215 isSortBySpeciesCountFirst(),
216 isTreatAsBinaryComparison() );
221 private DomainSimilarity.DomainSimilaritySortField getSort() {
225 private boolean isSortBySpeciesCountFirst() {
226 return _sort_by_species_count_first;
229 private boolean isTreatAsBinaryComparison() {
230 return _treat_as_binary_comparison;
233 private static SpeciesSpecificDomainSimilariyData createSpeciesSpecificDomainSimilariyData( final CombinableDomains cd ) {
234 final SpeciesSpecificDomainSimilariyData sd = new PrintableSpeciesSpecificDomainSimilariyData( cd
235 .getKeyDomainProteinsCount(), cd.getKeyDomainCount(), cd.getNumberOfCombinableDomains(), cd
236 .getKeyDomainConfidenceDescriptiveStatistics() );
237 for( final DomainId domain : cd.getCombinableDomains() ) {
238 sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );