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: https://sites.google.com/site/cmzmasek/home/software/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.species.Species;
38 import org.forester.util.BasicDescriptiveStatistics;
39 import org.forester.util.DescriptiveStatistics;
41 public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculator {
43 final DomainSimilarity.DomainSimilaritySortField _sort;
44 private final boolean _sort_by_species_count_first;
45 private final boolean _treat_as_binary_comparison;
47 public BasicDomainSimilarityCalculator( final DomainSimilarity.DomainSimilaritySortField sort,
48 final boolean sort_by_species_count_first,
49 final boolean treat_as_binary_comparison ) {
51 _sort_by_species_count_first = sort_by_species_count_first;
52 _treat_as_binary_comparison = treat_as_binary_comparison;
56 public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
57 final List<GenomeWideCombinableDomains> cdc_list,
58 final boolean ignore_domains_without_combinations_in_any_genome,
59 final boolean ignore_domains_specific_to_one_genome ) {
60 if ( cdc_list.size() < 2 ) {
61 throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinale domains collections" );
63 final SortedSet<DomainSimilarity> similarities = new TreeSet<DomainSimilarity>();
64 final SortedSet<String> keys = new TreeSet<String>();
65 for( final GenomeWideCombinableDomains cdc : cdc_list ) {
66 keys.addAll( ( cdc ).getAllCombinableDomainsIds().keySet() );
68 for( final String key : keys ) {
69 final List<CombinableDomains> same_id_cd_list = new ArrayList<CombinableDomains>( cdc_list.size() );
70 final List<Species> species_with_key_id_domain = new ArrayList<Species>();
71 for( final GenomeWideCombinableDomains cdc : cdc_list ) {
72 if ( cdc.contains( key ) ) {
73 same_id_cd_list.add( cdc.get( key ) );
74 species_with_key_id_domain.add( cdc.getSpecies() );
77 if ( ignore_domains_without_combinations_in_any_genome ) { //TODO: test me..........................................<<<<<<<<<<<<<
78 boolean without_combinations = true;
79 for( final CombinableDomains cd : same_id_cd_list ) {
80 if ( cd.getNumberOfCombinableDomains() > 0 ) {
81 without_combinations = false;
85 if ( without_combinations ) {
89 // BIG CHANGE IN LOGIC: Tuesday July 08, 0;55
90 // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 // OLD: if ( same_id_cd_list.size() > 1 ) {
92 if ( same_id_cd_list.size() > 0 ) {
93 if ( !ignore_domains_specific_to_one_genome || ( same_id_cd_list.size() > 1 ) ) {
94 final DomainSimilarity s = calculateSimilarity( pairwise_calculator, same_id_cd_list );
96 similarities.add( s );
99 throw new RuntimeException( "similarity is null: this should not have happened" );
105 throw new RuntimeException( "this should not have happened" );
108 // else if ( same_id_cd_list.size() == 1 ) {
109 // TODO need to go in file
110 // System.out.println( "only in one species [" +
111 // species_with_key_id_domain.get( 0 ) + "]: " + key_id );
114 // throw new RuntimeException( "this should not have happened" );
120 private DomainSimilarity calculateSimilarity( final PairwiseDomainSimilarityCalculator pairwise_calculator,
121 final List<CombinableDomains> domains_list ) {
122 if ( domains_list.size() == 1 ) {
123 // BIG CHANGE IN LOGIC: Tuesday July 08, 0;55
124 // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
126 //throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinable domains" );
128 final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
129 species_data.put( domains_list.get( 0 ).getSpecies(),
130 createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
131 return new PrintableDomainSimilarity( domains_list.get( 0 ),
142 isSortBySpeciesCountFirst(),
143 isTreatAsBinaryComparison() );
145 final DescriptiveStatistics stat = new BasicDescriptiveStatistics();
146 final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
147 species_data.put( domains_list.get( 0 ).getSpecies(),
148 createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
149 int max_difference_in_counts = 0;
150 int max_difference = 0;
151 final boolean is_domain_combination_based = pairwise_calculator instanceof CombinationsBasedPairwiseDomainSimilarityCalculator;
152 for( int i = 1; i < domains_list.size(); ++i ) {
153 species_data.put( domains_list.get( i ).getSpecies(),
154 createSpeciesSpecificDomainSimilariyData( domains_list.get( i ) ) );
155 final CombinableDomains domains_i = domains_list.get( i );
156 for( int j = 0; j < i; ++j ) {
157 final PairwiseDomainSimilarity pairwise_similarity = pairwise_calculator
158 .calculateSimilarity( domains_i, domains_list.get( j ) );
159 final int difference_in_counts = pairwise_similarity.getDifferenceInCounts();
161 if ( is_domain_combination_based ) {
162 difference = ( ( CombinationsBasedPairwiseDomainSimilarity ) pairwise_similarity )
163 .getNumberOfDifferentDomains();
166 difference = difference_in_counts;
168 if ( Math.abs( difference_in_counts ) > Math.abs( max_difference_in_counts ) ) {
169 max_difference_in_counts = difference_in_counts;
171 if ( Math.abs( difference ) > Math.abs( max_difference ) ) {
172 max_difference = difference;
174 stat.addValue( pairwise_similarity.getSimilarityScore() );
177 if ( stat.getN() < 1 ) {
178 throw new AssertionError( "empty descriptive statistics: this should not have happened" );
180 if ( ( stat.getN() != 1 ) && isTreatAsBinaryComparison() ) {
181 throw new IllegalArgumentException( "attmpt to treat similarity with N not equal to one as binary comparison" );
183 if ( ( /*stat.getN() != 1 ||*/!isTreatAsBinaryComparison() ) && ( max_difference_in_counts < 0 ) ) {
184 max_difference_in_counts = Math.abs( max_difference_in_counts );
185 if ( !is_domain_combination_based ) {
186 max_difference = Math.abs( max_difference ); //=max_difference_in_counts for !is_domain_combination_based.
189 DomainSimilarity similarity = null;
190 if ( stat.getN() == 1 ) {
191 similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
194 stat.arithmeticMean(),
198 max_difference_in_counts,
202 isSortBySpeciesCountFirst(),
203 isTreatAsBinaryComparison() );
206 similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
209 stat.arithmeticMean(),
211 stat.sampleStandardDeviation(),
213 max_difference_in_counts,
217 isSortBySpeciesCountFirst(),
218 isTreatAsBinaryComparison() );
223 private DomainSimilarity.DomainSimilaritySortField getSort() {
227 private boolean isSortBySpeciesCountFirst() {
228 return _sort_by_species_count_first;
231 private boolean isTreatAsBinaryComparison() {
232 return _treat_as_binary_comparison;
235 private static SpeciesSpecificDomainSimilariyData createSpeciesSpecificDomainSimilariyData( final CombinableDomains cd ) {
236 final SpeciesSpecificDomainSimilariyData sd = new PrintableSpeciesSpecificDomainSimilariyData( cd.getKeyDomainProteinsCount(),
237 cd.getKeyDomainCount(),
238 cd.getNumberOfCombinableDomains(),
239 cd.getKeyDomainConfidenceDescriptiveStatistics() );
240 for( final String domain : cd.getCombinableDomains() ) {
241 sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );