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 //private List<HistogramData> _histogram_datas;
58 public PairwiseGenomeComparator() {
62 public List<DistanceMatrix> getDomainDistanceScoresMeans() {
63 return _domain_distance_scores_means;
66 //public List<HistogramData> getHistogramDatas() {
67 // return _histogram_datas;
69 public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances() {
70 return _shared_binary_combinations_based_distances;
73 public List<DistanceMatrix> getSharedDomainsBasedDistances() {
74 return _shared_domains_based_distances;
78 //_histogram_datas = new ArrayList<HistogramData>();
79 _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
80 _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
81 _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
84 public void performPairwiseComparisons( final StringBuilder html_desc,
85 final boolean sort_by_species_count_first,
86 final Detailedness detailedness,
87 final boolean ignore_domains_without_combs_in_all_spec,
88 final boolean ignore_domains_specific_to_one_species,
89 final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
90 final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
91 final DomainSimilarity.DomainSimilarityScoring scoring,
92 final Map<String, List<GoId>> domain_id_to_go_ids_map,
93 final Map<GoId, GoTerm> go_id_to_term_map,
94 final GoNameSpace go_namespace_limit,
95 final Species[] species,
96 final int number_of_genomes,
97 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
98 final PairwiseDomainSimilarityCalculator pw_calc,
99 final String automated_pairwise_comparison_suffix,
100 final boolean verbose,
101 final String automated_pairwise_comparison_prefix,
102 final String command_line_prg_name,
104 final boolean write_pairwise_comparisons,
105 final Map<String, Integer> tax_code_to_id_map ) {
107 final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
108 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
109 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
111 System.out.println();
112 System.out.println( "Pairwise genome distances:" );
113 System.out.print( "[species-i - species-j:" );
114 System.out.print( " mean-score-based" );
115 System.out.print( " (sd)" );
116 System.out.print( " [N]" );
117 System.out.print( " | shared-domains-based" );
118 System.out.println( " | shared-binary-combinations-based]" );
119 System.out.println();
121 for( int i = 0; i < number_of_genomes; ++i ) {
122 final String species_i = species[ i ].getSpeciesId();
123 domain_distance_scores_means.setIdentifier( i, species_i );
124 shared_domains_based_distances.setIdentifier( i, species_i );
125 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
127 System.out.println( ( i + 1 ) + "/" + number_of_genomes );
129 for( int j = 0; j < i; ++j ) {
130 if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
131 || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
132 domain_distance_scores_means
133 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
134 shared_domains_based_distances
135 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
136 shared_binary_combinations_based_distances
137 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
140 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
141 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
142 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
143 DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
144 if ( domain_id_to_go_ids_map != null ) {
145 go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
147 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
148 sort_by_species_count_first,
150 final SortedSet<DomainSimilarity> similarities = calc
151 .calculateSimilarities( pw_calc,
153 ignore_domains_without_combs_in_all_spec,
154 ignore_domains_specific_to_one_species );
155 SurfacingUtil.decoratePrintableDomainSimilarities( similarities,
157 go_annotation_output,
159 go_namespace_limit );
160 final DescriptiveStatistics stats = SurfacingUtil
161 .calculateDescriptiveStatisticsForMeanValues( similarities );
162 final String species_j = species[ j ].getSpeciesId();
163 final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
165 list_of_genome_wide_combinable_domains
167 genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
168 double dissimilarity_score_mean;
169 if ( stats.getN() < 1 ) {
170 // No domains in common
171 dissimilarity_score_mean = 1.0;
174 dissimilarity_score_mean = 1.0 - stats.arithmeticMean();
176 final double shared_domains_based_genome_distance = 1.0 - genome_similarity_calculator
177 .calculateSharedDomainsBasedGenomeSimilarityScore();
178 final double shared_binary_combinations_based_genome_distance = 1.0 - genome_similarity_calculator
179 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore();
180 domain_distance_scores_means.setValue( i, j, dissimilarity_score_mean );
181 shared_domains_based_distances.setValue( i, j, shared_domains_based_genome_distance );
182 shared_binary_combinations_based_distances.setValue( i,
184 shared_binary_combinations_based_genome_distance );
186 System.out.print( species_i + "-" );
187 System.out.print( species_j + ": " );
188 System.out.print( ForesterUtil.round( dissimilarity_score_mean, 2 ) );
189 if ( stats.getN() > 1 ) {
190 System.out.print( " (" + ForesterUtil.round( stats.sampleStandardDeviation(), 2 ) + ")" );
193 System.out.print( " (n/a)" );
195 System.out.print( " [" + stats.getN() + "]" );
196 System.out.print( " | " );
197 System.out.print( ForesterUtil.round( shared_domains_based_genome_distance, 2 ) );
198 System.out.print( " | " );
199 System.out.println( ForesterUtil.round( shared_binary_combinations_based_genome_distance, 2 ) );
201 String pairwise_similarities_output_file_str = automated_pairwise_comparison_prefix + species_i + "_"
202 + species_j + automated_pairwise_comparison_suffix;
203 switch ( domain_similarity_print_option ) {
205 if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
206 pairwise_similarities_output_file_str += ".html";
210 DescriptiveStatistics pw_stats = null;
211 if ( write_pairwise_comparisons ) {
213 final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
214 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
215 pw_stats = SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
216 new StringBuilder( species_i + "-"
223 domain_similarity_print_option,
224 domain_similarity_sort_field,
227 tax_code_to_id_map );
229 catch ( final IOException e ) {
230 ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
231 + pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
234 if ( pw_stats != null ) {
235 if ( pw_stats.getMin() >= pw_stats.getMax() ) {
237 .printWarningMessage( command_line_prg_name, "for [" + species_i + "-" + species_j
238 + "] score minimum is [" + pw_stats.getMin() + "] while score maximum is ["
240 + "], possibly indicating that a genome is compared to itself" );
245 getDomainDistanceScoresMeans().add( domain_distance_scores_means );
246 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
247 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
249 System.out.println();
253 public void performPairwiseComparisonsJacknifed( final Species[] species,
254 final int number_of_genomes,
255 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
256 final boolean verbose,
257 final int number_of_resamplings,
258 final double jacknife_ratio,
259 final long random_seed ) {
261 if ( number_of_resamplings < 2 ) {
262 throw new IllegalArgumentException( "attempt to perform jacknife resampling with less than 2 resamplings" );
264 if ( jacknife_ratio <= 0.0 ) {
265 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio of 0.0 or less" );
267 else if ( jacknife_ratio >= 1.0 ) {
268 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio 1.0 or more" );
270 final String[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
272 System.out.println();
273 System.out.println( "Jacknife: total of domains: " + all_unique_domain_ids.length );
276 System.out.print( "resampling " );
278 final Random generator = new Random( random_seed );
279 for( int r = 0; r < number_of_resamplings; ++r ) {
281 System.out.print( " " + r );
283 final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
286 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
287 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
288 for( int i = 0; i < number_of_genomes; ++i ) {
289 final String species_i = species[ i ].getSpeciesId();
290 shared_domains_based_distances.setIdentifier( i, species_i );
291 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
292 for( int j = 0; j < i; ++j ) {
293 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
294 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
295 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
296 final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
298 list_of_genome_wide_combinable_domains
300 genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
301 genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
302 shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
303 .calculateSharedDomainsBasedGenomeSimilarityScore() );
304 shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
305 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
308 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
309 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
312 System.out.println();
316 static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
317 String[] all_domain_ids_array;
318 final SortedSet<String> all_domain_ids = new TreeSet<String>();
319 for( final GenomeWideCombinableDomains genome_wide_combinable_domains : list_of_genome_wide_combinable_domains ) {
320 final SortedSet<String> all_domains = genome_wide_combinable_domains.getAllDomainIds();
321 for( final String domain : all_domains ) {
322 all_domain_ids.add( domain );
325 all_domain_ids_array = new String[ all_domain_ids.size() ];
327 for( final String domain_id : all_domain_ids ) {
328 all_domain_ids_array[ n++ ] = domain_id;
330 return all_domain_ids_array;
333 static private SortedSet<String> randomlyPickDomainIds( final String[] all_domain_ids_array,
334 final double jacknife_ratio,
335 final Random generator ) {
336 final int size = all_domain_ids_array.length;
337 final SortedSet<String> random_domain_ids = new TreeSet<String>();
338 final int number_of_ids_pick = ForesterUtil.roundToInt( jacknife_ratio * size );
339 while ( random_domain_ids.size() < number_of_ids_pick ) {
340 final int r = generator.nextInt( size );
341 random_domain_ids.add( all_domain_ids_array[ r ] );
343 return random_domain_ids;