3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.surfacing;
29 import java.io.BufferedWriter;
31 import java.io.FileWriter;
32 import java.io.IOException;
33 import java.io.Writer;
34 import java.util.ArrayList;
35 import java.util.List;
37 import java.util.Random;
38 import java.util.SortedSet;
39 import java.util.TreeSet;
41 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
42 import org.forester.evoinference.matrix.distance.DistanceMatrix;
43 import org.forester.go.GoId;
44 import org.forester.go.GoNameSpace;
45 import org.forester.go.GoTerm;
46 import org.forester.species.Species;
47 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
48 import org.forester.util.DescriptiveStatistics;
49 import org.forester.util.ForesterUtil;
51 public class PairwiseGenomeComparator {
53 private List<DistanceMatrix> _domain_distance_scores_means;
54 private List<DistanceMatrix> _shared_domains_based_distances;
55 private List<DistanceMatrix> _shared_binary_combinations_based_distances;
57 public PairwiseGenomeComparator() {
61 public List<DistanceMatrix> getDomainDistanceScoresMeans() {
62 return _domain_distance_scores_means;
65 public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances() {
66 return _shared_binary_combinations_based_distances;
69 public List<DistanceMatrix> getSharedDomainsBasedDistances() {
70 return _shared_domains_based_distances;
74 _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
75 _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
76 _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
79 public void performPairwiseComparisons( final StringBuilder html_desc,
80 final boolean sort_by_species_count_first,
81 final Detailedness detailedness,
82 final boolean ignore_domains_without_combs_in_all_spec,
83 final boolean ignore_domains_specific_to_one_species,
84 final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
85 final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
86 final DomainSimilarity.DomainSimilarityScoring scoring,
87 final Map<String, List<GoId>> domain_id_to_go_ids_map,
88 final Map<GoId, GoTerm> go_id_to_term_map,
89 final GoNameSpace go_namespace_limit,
90 final Species[] species,
91 final int number_of_genomes,
92 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
93 final PairwiseDomainSimilarityCalculator pw_calc,
94 final String automated_pairwise_comparison_suffix,
95 final boolean verbose,
96 final String automated_pairwise_comparison_prefix,
97 final String command_line_prg_name,
99 final boolean write_pairwise_comparisons,
100 final Map<String, Integer> tax_code_to_id_map,
101 final boolean calc_similarity_scores ) {
103 final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
104 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
105 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
107 System.out.println();
108 System.out.println( "Pairwise genome distances:" );
109 System.out.print( "[species-i - species-j:" );
110 System.out.print( " mean-score-based" );
111 System.out.print( " (sd)" );
112 System.out.print( " [N]" );
113 System.out.print( " | shared-domains-based" );
114 System.out.println( " | shared-binary-combinations-based]" );
115 System.out.println();
117 for( int i = 0; i < number_of_genomes; ++i ) {
118 final String species_i = species[ i ].getSpeciesId();
119 domain_distance_scores_means.setIdentifier( i, species_i );
120 shared_domains_based_distances.setIdentifier( i, species_i );
121 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
123 System.out.println( ( i + 1 ) + "/" + number_of_genomes );
125 for( int j = 0; j < i; ++j ) {
126 if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
127 || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
128 domain_distance_scores_means
129 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
130 shared_domains_based_distances
131 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
132 shared_binary_combinations_based_distances
133 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
136 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
137 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
138 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
139 DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
140 if ( domain_id_to_go_ids_map != null ) {
141 go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
143 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
144 sort_by_species_count_first,
146 calc_similarity_scores );
147 final SortedSet<DomainSimilarity> similarities = calc
148 .calculateSimilarities( pw_calc,
150 ignore_domains_without_combs_in_all_spec,
151 ignore_domains_specific_to_one_species );
152 SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness );
153 final DescriptiveStatistics stats = SurfacingUtil
154 .calculateDescriptiveStatisticsForMeanValues( similarities );
155 final String species_j = species[ j ].getSpeciesId();
156 final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
158 list_of_genome_wide_combinable_domains
160 genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
161 double dissimilarity_score_mean;
162 if ( stats.getN() < 1 ) {
163 // No domains in common
164 dissimilarity_score_mean = 1.0;
167 dissimilarity_score_mean = 1.0 - stats.arithmeticMean();
169 final double shared_domains_based_genome_distance = 1.0 - genome_similarity_calculator
170 .calculateSharedDomainsBasedGenomeSimilarityScore();
171 final double shared_binary_combinations_based_genome_distance = 1.0 - genome_similarity_calculator
172 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore();
173 domain_distance_scores_means.setValue( i, j, dissimilarity_score_mean );
174 shared_domains_based_distances.setValue( i, j, shared_domains_based_genome_distance );
175 shared_binary_combinations_based_distances.setValue( i,
177 shared_binary_combinations_based_genome_distance );
179 System.out.print( species_i + "-" );
180 System.out.print( species_j + ": " );
181 System.out.print( ForesterUtil.round( dissimilarity_score_mean, 2 ) );
182 if ( stats.getN() > 1 ) {
183 System.out.print( " (" + ForesterUtil.round( stats.sampleStandardDeviation(), 2 ) + ")" );
186 System.out.print( " (n/a)" );
188 System.out.print( " [" + stats.getN() + "]" );
189 System.out.print( " | " );
190 System.out.print( ForesterUtil.round( shared_domains_based_genome_distance, 2 ) );
191 System.out.print( " | " );
192 System.out.println( ForesterUtil.round( shared_binary_combinations_based_genome_distance, 2 ) );
194 String pairwise_similarities_output_file_str = automated_pairwise_comparison_prefix + species_i + "_"
195 + species_j + automated_pairwise_comparison_suffix;
196 switch ( domain_similarity_print_option ) {
198 if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
199 pairwise_similarities_output_file_str += ".html";
203 if ( write_pairwise_comparisons ) {
205 final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
206 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
207 SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
208 new StringBuilder( species_i + "-" + species_j ),
215 domain_similarity_print_option,
218 tax_code_to_id_map );
220 catch ( final IOException e ) {
221 ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
222 + pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
227 getDomainDistanceScoresMeans().add( domain_distance_scores_means );
228 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
229 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
231 System.out.println();
235 public void performPairwiseComparisonsJacknifed( final Species[] species,
236 final int number_of_genomes,
237 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
238 final boolean verbose,
239 final int number_of_resamplings,
240 final double jacknife_ratio,
241 final long random_seed ) {
243 if ( number_of_resamplings < 2 ) {
244 throw new IllegalArgumentException( "attempt to perform jacknife resampling with less than 2 resamplings" );
246 if ( jacknife_ratio <= 0.0 ) {
247 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio of 0.0 or less" );
249 else if ( jacknife_ratio >= 1.0 ) {
250 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio 1.0 or more" );
252 final String[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
254 System.out.println();
255 System.out.println( "Jacknife: total of domains: " + all_unique_domain_ids.length );
258 System.out.print( "resampling " );
260 final Random generator = new Random( random_seed );
261 for( int r = 0; r < number_of_resamplings; ++r ) {
263 System.out.print( " " + r );
265 final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
268 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
269 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
270 for( int i = 0; i < number_of_genomes; ++i ) {
271 final String species_i = species[ i ].getSpeciesId();
272 shared_domains_based_distances.setIdentifier( i, species_i );
273 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
274 for( int j = 0; j < i; ++j ) {
275 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
276 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
277 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
278 final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
280 list_of_genome_wide_combinable_domains
282 genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
283 genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
284 shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
285 .calculateSharedDomainsBasedGenomeSimilarityScore() );
286 shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
287 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
290 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
291 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
294 System.out.println();
298 static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
299 String[] all_domain_ids_array;
300 final SortedSet<String> all_domain_ids = new TreeSet<String>();
301 for( final GenomeWideCombinableDomains genome_wide_combinable_domains : list_of_genome_wide_combinable_domains ) {
302 final SortedSet<String> all_domains = genome_wide_combinable_domains.getAllDomainIds();
303 for( final String domain : all_domains ) {
304 all_domain_ids.add( domain );
307 all_domain_ids_array = new String[ all_domain_ids.size() ];
309 for( final String domain_id : all_domain_ids ) {
310 all_domain_ids_array[ n++ ] = domain_id;
312 return all_domain_ids_array;
315 static private SortedSet<String> randomlyPickDomainIds( final String[] all_domain_ids_array,
316 final double jacknife_ratio,
317 final Random generator ) {
318 final int size = all_domain_ids_array.length;
319 final SortedSet<String> random_domain_ids = new TreeSet<String>();
320 final int number_of_ids_pick = ForesterUtil.roundToInt( jacknife_ratio * size );
321 while ( random_domain_ids.size() < number_of_ids_pick ) {
322 final int r = generator.nextInt( size );
323 random_domain_ids.add( all_domain_ids_array[ r ] );
325 return random_domain_ids;