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_binary_combinations_based_distances;
56 private List<DistanceMatrix> _shared_domains_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;
74 public void performPairwiseComparisons( final StringBuilder html_desc,
75 final boolean sort_by_species_count_first,
76 final Detailedness detailedness,
77 final boolean ignore_domains_without_combs_in_all_spec,
78 final boolean ignore_domains_specific_to_one_species,
79 final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
80 final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
81 final DomainSimilarity.DomainSimilarityScoring scoring,
82 final Map<String, List<GoId>> domain_id_to_go_ids_map,
83 final Map<GoId, GoTerm> go_id_to_term_map,
84 final GoNameSpace go_namespace_limit,
85 final Species[] species,
86 final int number_of_genomes,
87 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
88 final PairwiseDomainSimilarityCalculator pw_calc,
89 final String automated_pairwise_comparison_suffix,
90 final boolean verbose,
91 final String automated_pairwise_comparison_prefix,
92 final String command_line_prg_name,
94 final boolean write_pairwise_comparisons,
95 final Map<String, Integer> tax_code_to_id_map,
96 final boolean calc_similarity_scores,
97 final Phylogeny phy ) {
99 final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
100 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
101 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
103 System.out.println();
104 System.out.println( "Pairwise genome distances:" );
105 System.out.print( "[species-i - species-j:" );
106 System.out.print( " mean-score-based" );
107 System.out.print( " (sd)" );
108 System.out.print( " [N]" );
109 System.out.print( " | shared-domains-based" );
110 System.out.println( " | shared-binary-combinations-based]" );
111 System.out.println();
113 for( int i = 0; i < number_of_genomes; ++i ) {
114 final String species_i = species[ i ].getSpeciesId();
115 domain_distance_scores_means.setIdentifier( i, species_i );
116 shared_domains_based_distances.setIdentifier( i, species_i );
117 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
119 System.out.println( ( i + 1 ) + "/" + number_of_genomes );
121 for( int j = 0; j < i; ++j ) {
122 if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
123 || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
124 domain_distance_scores_means
125 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
126 shared_domains_based_distances
127 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
128 shared_binary_combinations_based_distances
129 .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
132 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
133 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
134 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
135 DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
136 if ( domain_id_to_go_ids_map != null ) {
137 go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
139 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
140 sort_by_species_count_first,
142 calc_similarity_scores );
143 final SortedSet<DomainSimilarity> similarities = calc
144 .calculateSimilarities( pw_calc,
146 ignore_domains_without_combs_in_all_spec,
147 ignore_domains_specific_to_one_species );
148 SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness );
149 final DescriptiveStatistics stats = SurfacingUtil
150 .calculateDescriptiveStatisticsForMeanValues( similarities );
151 final String species_j = species[ j ].getSpeciesId();
152 final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
154 list_of_genome_wide_combinable_domains
156 genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
157 double dissimilarity_score_mean;
158 if ( stats.getN() < 1 ) {
159 // No domains in common
160 dissimilarity_score_mean = 1.0;
163 dissimilarity_score_mean = 1.0 - stats.arithmeticMean();
165 final double shared_domains_based_genome_distance = 1.0 - genome_similarity_calculator
166 .calculateSharedDomainsBasedGenomeSimilarityScore();
167 final double shared_binary_combinations_based_genome_distance = 1.0 - genome_similarity_calculator
168 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore();
169 domain_distance_scores_means.setValue( i, j, dissimilarity_score_mean );
170 shared_domains_based_distances.setValue( i, j, shared_domains_based_genome_distance );
171 shared_binary_combinations_based_distances.setValue( i,
173 shared_binary_combinations_based_genome_distance );
175 System.out.print( species_i + "-" );
176 System.out.print( species_j + ": " );
177 System.out.print( ForesterUtil.round( dissimilarity_score_mean, 2 ) );
178 if ( stats.getN() > 1 ) {
179 System.out.print( " (" + ForesterUtil.round( stats.sampleStandardDeviation(), 2 ) + ")" );
182 System.out.print( " (n/a)" );
184 System.out.print( " [" + stats.getN() + "]" );
185 System.out.print( " | " );
186 System.out.print( ForesterUtil.round( shared_domains_based_genome_distance, 2 ) );
187 System.out.print( " | " );
188 System.out.println( ForesterUtil.round( shared_binary_combinations_based_genome_distance, 2 ) );
190 String pairwise_similarities_output_file_str = automated_pairwise_comparison_prefix + species_i + "_"
191 + species_j + automated_pairwise_comparison_suffix;
192 switch ( domain_similarity_print_option ) {
194 if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
195 pairwise_similarities_output_file_str += ".html";
199 if ( write_pairwise_comparisons ) {
201 final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
202 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
203 SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
204 new StringBuilder( species_i + "-" + species_j ),
211 domain_similarity_print_option,
218 catch ( final IOException e ) {
219 ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
220 + pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
225 getDomainDistanceScoresMeans().add( domain_distance_scores_means );
226 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
227 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
229 System.out.println();
233 public void performPairwiseComparisonsJacknifed( final Species[] species,
234 final int number_of_genomes,
235 final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
236 final boolean verbose,
237 final int number_of_resamplings,
238 final double jacknife_ratio,
239 final long random_seed ) {
241 if ( number_of_resamplings < 2 ) {
242 throw new IllegalArgumentException( "attempt to perform jacknife resampling with less than 2 resamplings" );
244 if ( jacknife_ratio <= 0.0 ) {
245 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio of 0.0 or less" );
247 else if ( jacknife_ratio >= 1.0 ) {
248 throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio 1.0 or more" );
250 final String[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
252 System.out.println();
253 System.out.println( "Jacknife: total of domains: " + all_unique_domain_ids.length );
256 System.out.print( "resampling " );
258 final Random generator = new Random( random_seed );
259 for( int r = 0; r < number_of_resamplings; ++r ) {
261 System.out.print( " " + r );
263 final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
266 final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
267 final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
268 for( int i = 0; i < number_of_genomes; ++i ) {
269 final String species_i = species[ i ].getSpeciesId();
270 shared_domains_based_distances.setIdentifier( i, species_i );
271 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
272 for( int j = 0; j < i; ++j ) {
273 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
274 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
275 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
276 final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
278 list_of_genome_wide_combinable_domains
280 genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
281 genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
282 shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
283 .calculateSharedDomainsBasedGenomeSimilarityScore() );
284 shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
285 .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
288 getSharedDomainsBasedDistances().add( shared_domains_based_distances );
289 getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
292 System.out.println();
296 private void init() {
297 _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
298 _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
299 _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
302 static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
303 String[] all_domain_ids_array;
304 final SortedSet<String> all_domain_ids = new TreeSet<String>();
305 for( final GenomeWideCombinableDomains genome_wide_combinable_domains : list_of_genome_wide_combinable_domains ) {
306 final SortedSet<String> all_domains = genome_wide_combinable_domains.getAllDomainIds();
307 for( final String domain : all_domains ) {
308 all_domain_ids.add( domain );
311 all_domain_ids_array = new String[ all_domain_ids.size() ];
313 for( final String domain_id : all_domain_ids ) {
314 all_domain_ids_array[ n++ ] = domain_id;
316 return all_domain_ids_array;
319 static private SortedSet<String> randomlyPickDomainIds( final String[] all_domain_ids_array,
320 final double jacknife_ratio,
321 final Random generator ) {
322 final int size = all_domain_ids_array.length;
323 final SortedSet<String> random_domain_ids = new TreeSet<String>();
324 final int number_of_ids_pick = ForesterUtil.roundToInt( jacknife_ratio * size );
325 while ( random_domain_ids.size() < number_of_ids_pick ) {
326 final int r = generator.nextInt( size );
327 random_domain_ids.add( all_domain_ids_array[ r ] );
329 return random_domain_ids;