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.phylogeny.Phylogeny;
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 public PairwiseGenomeComparator() {
62 public List<DistanceMatrix> getDomainDistanceScoresMeans() {
63 return _domain_distance_scores_means;
66 public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances() {
67 return _shared_binary_combinations_based_distances;
70 public List<DistanceMatrix> getSharedDomainsBasedDistances() {
71 return _shared_domains_based_distances;
75 _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
76 _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
77 _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
80 public void performPairwiseComparisons( final StringBuilder html_desc,
81 final boolean sort_by_species_count_first,
82 final Detailedness detailedness,
83 final boolean ignore_domains_without_combs_in_all_spec,
84 final boolean ignore_domains_specific_to_one_species,
85 final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
86 final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
87 final DomainSimilarity.DomainSimilarityScoring scoring,
88 final Map<String, List<GoId>> domain_id_to_go_ids_map,
89 final Map<GoId, GoTerm> go_id_to_term_map,
90 final GoNameSpace go_namespace_limit,
91 final Species[] species,
92 final int number_of_genomes,
93 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
94 final PairwiseDomainSimilarityCalculator pw_calc,
95 final String automated_pairwise_comparison_suffix,
96 final boolean verbose,
97 final String automated_pairwise_comparison_prefix,
98 final String command_line_prg_name,
100 final boolean write_pairwise_comparisons,
101 final Map<String, Integer> tax_code_to_id_map,
102 final boolean calc_similarity_scores,
103 final Phylogeny phy ) {
105 final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
106 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
107 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
109 System.out.println();
110 System.out.println( "Pairwise genome distances:" );
111 System.out.print( "[species-i - species-j:" );
112 System.out.print( " mean-score-based" );
113 System.out.print( " (sd)" );
114 System.out.print( " [N]" );
115 System.out.print( " | shared-domains-based" );
116 System.out.println( " | shared-binary-combinations-based]" );
117 System.out.println();
119 for( int i = 0; i < number_of_genomes; ++i ) {
120 final String species_i = species[ i ].getSpeciesId();
121 domain_distance_scores_means.setIdentifier( i, species_i );
122 shared_domains_based_distances.setIdentifier( i, species_i );
123 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
125 System.out.println( ( i + 1 ) + "/" + number_of_genomes );
127 for( int j = 0; j < i; ++j ) {
128 if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
129 || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
130 domain_distance_scores_means
131 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
132 shared_domains_based_distances
133 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
134 shared_binary_combinations_based_distances
135 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
138 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
139 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
140 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
141 DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
142 if ( domain_id_to_go_ids_map != null ) {
143 go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
145 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
146 sort_by_species_count_first,
148 calc_similarity_scores );
149 final SortedSet<DomainSimilarity> similarities = calc
150 .calculateSimilarities( pw_calc,
152 ignore_domains_without_combs_in_all_spec,
153 ignore_domains_specific_to_one_species );
154 SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness );
155 final DescriptiveStatistics stats = SurfacingUtil
156 .calculateDescriptiveStatisticsForMeanValues( similarities );
157 final String species_j = species[ j ].getSpeciesId();
158 final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
160 list_of_genome_wide_combinable_domains
162 genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
163 double dissimilarity_score_mean;
164 if ( stats.getN() < 1 ) {
165 // No domains in common
166 dissimilarity_score_mean = 1.0;
169 dissimilarity_score_mean = 1.0 - stats.arithmeticMean();
171 final double shared_domains_based_genome_distance = 1.0 - genome_similarity_calculator
172 .calculateSharedDomainsBasedGenomeSimilarityScore();
173 final double shared_binary_combinations_based_genome_distance = 1.0 - genome_similarity_calculator
174 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore();
175 domain_distance_scores_means.setValue( i, j, dissimilarity_score_mean );
176 shared_domains_based_distances.setValue( i, j, shared_domains_based_genome_distance );
177 shared_binary_combinations_based_distances.setValue( i,
179 shared_binary_combinations_based_genome_distance );
181 System.out.print( species_i + "-" );
182 System.out.print( species_j + ": " );
183 System.out.print( ForesterUtil.round( dissimilarity_score_mean, 2 ) );
184 if ( stats.getN() > 1 ) {
185 System.out.print( " (" + ForesterUtil.round( stats.sampleStandardDeviation(), 2 ) + ")" );
188 System.out.print( " (n/a)" );
190 System.out.print( " [" + stats.getN() + "]" );
191 System.out.print( " | " );
192 System.out.print( ForesterUtil.round( shared_domains_based_genome_distance, 2 ) );
193 System.out.print( " | " );
194 System.out.println( ForesterUtil.round( shared_binary_combinations_based_genome_distance, 2 ) );
196 String pairwise_similarities_output_file_str = automated_pairwise_comparison_prefix + species_i + "_"
197 + species_j + automated_pairwise_comparison_suffix;
198 switch ( domain_similarity_print_option ) {
200 if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
201 pairwise_similarities_output_file_str += ".html";
205 if ( write_pairwise_comparisons ) {
207 final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
208 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
209 SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
210 new StringBuilder( species_i + "-" + species_j ),
217 domain_similarity_print_option,
223 catch ( final IOException e ) {
224 ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
225 + pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
230 getDomainDistanceScoresMeans().add( domain_distance_scores_means );
231 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
232 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
234 System.out.println();
238 public void performPairwiseComparisonsJacknifed( final Species[] species,
239 final int number_of_genomes,
240 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
241 final boolean verbose,
242 final int number_of_resamplings,
243 final double jacknife_ratio,
244 final long random_seed ) {
246 if ( number_of_resamplings < 2 ) {
247 throw new IllegalArgumentException( "attempt to perform jacknife resampling with less than 2 resamplings" );
249 if ( jacknife_ratio <= 0.0 ) {
250 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio of 0.0 or less" );
252 else if ( jacknife_ratio >= 1.0 ) {
253 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio 1.0 or more" );
255 final String[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
257 System.out.println();
258 System.out.println( "Jacknife: total of domains: " + all_unique_domain_ids.length );
261 System.out.print( "resampling " );
263 final Random generator = new Random( random_seed );
264 for( int r = 0; r < number_of_resamplings; ++r ) {
266 System.out.print( " " + r );
268 final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
271 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
272 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
273 for( int i = 0; i < number_of_genomes; ++i ) {
274 final String species_i = species[ i ].getSpeciesId();
275 shared_domains_based_distances.setIdentifier( i, species_i );
276 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
277 for( int j = 0; j < i; ++j ) {
278 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
279 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
280 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
281 final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
283 list_of_genome_wide_combinable_domains
285 genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
286 genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
287 shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
288 .calculateSharedDomainsBasedGenomeSimilarityScore() );
289 shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
290 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
293 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
294 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
297 System.out.println();
301 static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
302 String[] all_domain_ids_array;
303 final SortedSet<String> all_domain_ids = new TreeSet<String>();
304 for( final GenomeWideCombinableDomains genome_wide_combinable_domains : list_of_genome_wide_combinable_domains ) {
305 final SortedSet<String> all_domains = genome_wide_combinable_domains.getAllDomainIds();
306 for( final String domain : all_domains ) {
307 all_domain_ids.add( domain );
310 all_domain_ids_array = new String[ all_domain_ids.size() ];
312 for( final String domain_id : all_domain_ids ) {
313 all_domain_ids_array[ n++ ] = domain_id;
315 return all_domain_ids_array;
318 static private SortedSet<String> randomlyPickDomainIds( final String[] all_domain_ids_array,
319 final double jacknife_ratio,
320 final Random generator ) {
321 final int size = all_domain_ids_array.length;
322 final SortedSet<String> random_domain_ids = new TreeSet<String>();
323 final int number_of_ids_pick = ForesterUtil.roundToInt( jacknife_ratio * size );
324 while ( random_domain_ids.size() < number_of_ids_pick ) {
325 final int r = generator.nextInt( size );
326 random_domain_ids.add( all_domain_ids_array[ r ] );
328 return random_domain_ids;