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.protein.DomainId;
47 import org.forester.species.Species;
48 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
49 import org.forester.util.DescriptiveStatistics;
50 import org.forester.util.ForesterUtil;
52 public class PairwiseGenomeComparator {
54 private List<DistanceMatrix> _domain_distance_scores_means;
55 private List<DistanceMatrix> _shared_domains_based_distances;
56 private List<DistanceMatrix> _shared_binary_combinations_based_distances;
58 //private List<HistogramData> _histogram_datas;
59 public PairwiseGenomeComparator() {
63 public List<DistanceMatrix> getDomainDistanceScoresMeans() {
64 return _domain_distance_scores_means;
67 //public List<HistogramData> getHistogramDatas() {
68 // return _histogram_datas;
70 public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances() {
71 return _shared_binary_combinations_based_distances;
74 public List<DistanceMatrix> getSharedDomainsBasedDistances() {
75 return _shared_domains_based_distances;
79 //_histogram_datas = new ArrayList<HistogramData>();
80 _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
81 _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
82 _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
85 public void performPairwiseComparisons( final StringBuilder html_desc,
86 final boolean sort_by_species_count_first,
87 final Detailedness detailedness,
88 final boolean ignore_domains_without_combs_in_all_spec,
89 final boolean ignore_domains_specific_to_one_species,
90 final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
91 final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
92 final DomainSimilarity.DomainSimilarityScoring scoring,
93 final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
94 final Map<GoId, GoTerm> go_id_to_term_map,
95 final GoNameSpace go_namespace_limit,
96 final Species[] species,
97 final int number_of_genomes,
98 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
99 final PairwiseDomainSimilarityCalculator pw_calc,
100 final String automated_pairwise_comparison_suffix,
101 final boolean verbose,
102 final String automated_pairwise_comparison_prefix,
103 final String command_line_prg_name,
105 final boolean write_pairwise_comparisons,
106 final Map<String, Integer> tax_code_to_id_map ) {
108 final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
109 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
110 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
112 System.out.println();
113 System.out.println( "Pairwise genome distances:" );
114 System.out.print( "[species-i - species-j:" );
115 System.out.print( " mean-score-based" );
116 System.out.print( " (sd)" );
117 System.out.print( " [N]" );
118 System.out.print( " | shared-domains-based" );
119 System.out.println( " | shared-binary-combinations-based]" );
120 System.out.println();
122 for( int i = 0; i < number_of_genomes; ++i ) {
123 final String species_i = species[ i ].getSpeciesId();
124 domain_distance_scores_means.setIdentifier( i, species_i );
125 shared_domains_based_distances.setIdentifier( i, species_i );
126 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
128 System.out.println( ( i + 1 ) + "/" + number_of_genomes );
130 for( int j = 0; j < i; ++j ) {
131 if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
132 || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
133 domain_distance_scores_means
134 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
135 shared_domains_based_distances
136 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
137 shared_binary_combinations_based_distances
138 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
141 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
142 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
143 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
144 DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
145 if ( domain_id_to_go_ids_map != null ) {
146 go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
148 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
149 sort_by_species_count_first,
151 final SortedSet<DomainSimilarity> similarities = calc
152 .calculateSimilarities( pw_calc,
154 ignore_domains_without_combs_in_all_spec,
155 ignore_domains_specific_to_one_species );
156 SurfacingUtil.decoratePrintableDomainSimilarities( similarities,
158 go_annotation_output,
160 go_namespace_limit );
161 final DescriptiveStatistics stats = SurfacingUtil
162 .calculateDescriptiveStatisticsForMeanValues( similarities );
163 final String species_j = species[ j ].getSpeciesId();
164 final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
166 list_of_genome_wide_combinable_domains
168 genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
169 double dissimilarity_score_mean;
170 if ( stats.getN() < 1 ) {
171 // No domains in common
172 dissimilarity_score_mean = 1.0;
175 dissimilarity_score_mean = 1.0 - stats.arithmeticMean();
177 final double shared_domains_based_genome_distance = 1.0 - genome_similarity_calculator
178 .calculateSharedDomainsBasedGenomeSimilarityScore();
179 final double shared_binary_combinations_based_genome_distance = 1.0 - genome_similarity_calculator
180 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore();
181 domain_distance_scores_means.setValue( i, j, dissimilarity_score_mean );
182 shared_domains_based_distances.setValue( i, j, shared_domains_based_genome_distance );
183 shared_binary_combinations_based_distances.setValue( i,
185 shared_binary_combinations_based_genome_distance );
187 System.out.print( species_i + "-" );
188 System.out.print( species_j + ": " );
189 System.out.print( ForesterUtil.round( dissimilarity_score_mean, 2 ) );
190 if ( stats.getN() > 1 ) {
191 System.out.print( " (" + ForesterUtil.round( stats.sampleStandardDeviation(), 2 ) + ")" );
194 System.out.print( " (n/a)" );
196 System.out.print( " [" + stats.getN() + "]" );
197 System.out.print( " | " );
198 System.out.print( ForesterUtil.round( shared_domains_based_genome_distance, 2 ) );
199 System.out.print( " | " );
200 System.out.println( ForesterUtil.round( shared_binary_combinations_based_genome_distance, 2 ) );
202 String pairwise_similarities_output_file_str = automated_pairwise_comparison_prefix + species_i + "_"
203 + species_j + automated_pairwise_comparison_suffix;
204 switch ( domain_similarity_print_option ) {
206 if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
207 pairwise_similarities_output_file_str += ".html";
211 DescriptiveStatistics pw_stats = null;
212 if ( write_pairwise_comparisons ) {
214 final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
215 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
216 pw_stats = SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
217 new StringBuilder( species_i + "-"
224 domain_similarity_print_option,
225 domain_similarity_sort_field,
228 tax_code_to_id_map );
230 catch ( final IOException e ) {
231 ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
232 + pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
235 if ( pw_stats != null ) {
236 if ( pw_stats.getMin() >= pw_stats.getMax() ) {
238 .printWarningMessage( command_line_prg_name, "for [" + species_i + "-" + species_j
239 + "] score minimum is [" + pw_stats.getMin() + "] while score maximum is ["
241 + "], possibly indicating that a genome is compared to itself" );
246 getDomainDistanceScoresMeans().add( domain_distance_scores_means );
247 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
248 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
250 System.out.println();
254 public void performPairwiseComparisonsJacknifed( final Species[] species,
255 final int number_of_genomes,
256 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
257 final boolean verbose,
258 final int number_of_resamplings,
259 final double jacknife_ratio,
260 final long random_seed ) {
262 if ( number_of_resamplings < 2 ) {
263 throw new IllegalArgumentException( "attempt to perform jacknife resampling with less than 2 resamplings" );
265 if ( jacknife_ratio <= 0.0 ) {
266 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio of 0.0 or less" );
268 else if ( jacknife_ratio >= 1.0 ) {
269 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio 1.0 or more" );
271 final DomainId[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
273 System.out.println();
274 System.out.println( "Jacknife: total of domains: " + all_unique_domain_ids.length );
277 System.out.print( "resampling " );
279 final Random generator = new Random( random_seed );
280 for( int r = 0; r < number_of_resamplings; ++r ) {
282 System.out.print( " " + r );
284 final SortedSet<DomainId> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
287 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
288 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
289 for( int i = 0; i < number_of_genomes; ++i ) {
290 final String species_i = species[ i ].getSpeciesId();
291 shared_domains_based_distances.setIdentifier( i, species_i );
292 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
293 for( int j = 0; j < i; ++j ) {
294 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
295 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
296 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
297 final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
299 list_of_genome_wide_combinable_domains
301 genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
302 genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
303 shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
304 .calculateSharedDomainsBasedGenomeSimilarityScore() );
305 shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
306 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
309 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
310 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
313 System.out.println();
317 static private DomainId[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
318 DomainId[] all_domain_ids_array;
319 final SortedSet<DomainId> all_domain_ids = new TreeSet<DomainId>();
320 for( final GenomeWideCombinableDomains genome_wide_combinable_domains : list_of_genome_wide_combinable_domains ) {
321 final SortedSet<DomainId> all_domains = genome_wide_combinable_domains.getAllDomainIds();
322 for( final DomainId domain : all_domains ) {
323 all_domain_ids.add( domain );
326 all_domain_ids_array = new DomainId[ all_domain_ids.size() ];
328 for( final DomainId domain_id : all_domain_ids ) {
329 all_domain_ids_array[ n++ ] = domain_id;
331 return all_domain_ids_array;
334 static private SortedSet<DomainId> randomlyPickDomainIds( final DomainId[] all_domain_ids_array,
335 final double jacknife_ratio,
336 final Random generator ) {
337 final int size = all_domain_ids_array.length;
338 final SortedSet<DomainId> random_domain_ids = new TreeSet<DomainId>();
339 final int number_of_ids_pick = ForesterUtil.roundToInt( jacknife_ratio * size );
340 while ( random_domain_ids.size() < number_of_ids_pick ) {
341 final int r = generator.nextInt( size );
342 random_domain_ids.add( all_domain_ids_array[ r ] );
344 return random_domain_ids;