Changed more concrete DistanceMatrix references to reference interface

[jalview.git] / forester / java / src / org / forester / surfacing / PairwiseGenomeComparator.java

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index c020d82..ed4eae7 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -43,6 +43,7 @@ import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.go.GoId;
 import org.forester.go.GoNameSpace;
 import org.forester.go.GoTerm;
+import org.forester.phylogeny.Phylogeny;
 import org.forester.species.Species;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
 import org.forester.util.DescriptiveStatistics;
@@ -51,8 +52,8 @@ import org.forester.util.ForesterUtil;
 public class PairwiseGenomeComparator {
 
     private List<DistanceMatrix> _domain_distance_scores_means;
-    private List<DistanceMatrix> _shared_domains_based_distances;
     private List<DistanceMatrix> _shared_binary_combinations_based_distances;
+    private List<DistanceMatrix> _shared_domains_based_distances;
 
     public PairwiseGenomeComparator() {
         init();
@@ -70,19 +71,13 @@ public class PairwiseGenomeComparator {
         return _shared_domains_based_distances;
     }
 
-    private void init() {
-        _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
-        _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
-        _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
-    }
-
     public void performPairwiseComparisons( final StringBuilder html_desc,
                                             final boolean sort_by_species_count_first,
                                             final Detailedness detailedness,
                                             final boolean ignore_domains_without_combs_in_all_spec,
                                             final boolean ignore_domains_specific_to_one_species,
                                             final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
-                                            final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+                                            final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
                                             final DomainSimilarity.DomainSimilarityScoring scoring,
                                             final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                             final Map<GoId, GoTerm> go_id_to_term_map,
@@ -98,11 +93,12 @@ public class PairwiseGenomeComparator {
                                             final File out_dir,
                                             final boolean write_pairwise_comparisons,
                                             final Map<String, Integer> tax_code_to_id_map,
-                                            final boolean calc_similarity_scores ) {
+                                            final boolean calc_similarity_scores,
+                                            final Phylogeny phy ) {
         init();
-        final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
-        final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
-        final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
         if ( verbose ) {
             System.out.println();
             System.out.println( "Pairwise genome distances:" );
@@ -126,11 +122,11 @@ public class PairwiseGenomeComparator {
                 if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
                         || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
                     domain_distance_scores_means
-                            .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
+                    .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
                     shared_domains_based_distances
-                            .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
+                    .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
                     shared_binary_combinations_based_distances
-                            .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
+                    .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
                     continue;
                 }
                 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
@@ -143,7 +139,8 @@ public class PairwiseGenomeComparator {
                 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
                                                                                              sort_by_species_count_first,
                                                                                              true,
-                                                                                             calc_similarity_scores );
+                                                                                             calc_similarity_scores,
+                                                                                             true );
                 final SortedSet<DomainSimilarity> similarities = calc
                         .calculateSimilarities( pw_calc,
                                                 genome_pair,
@@ -154,9 +151,9 @@ public class PairwiseGenomeComparator {
                         .calculateDescriptiveStatisticsForMeanValues( similarities );
                 final String species_j = species[ j ].getSpeciesId();
                 final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
-                                                                                                                                                                      .get( i ),
+                                                                                                                                                              .get( i ),
                                                                                                                                                               list_of_genome_wide_combinable_domains
-                                                                                                                                                                      .get( j ) );
+                                                                                                                                                              .get( j ) );
                 genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
                 double dissimilarity_score_mean;
                 if ( stats.getN() < 1 ) {
@@ -206,6 +203,7 @@ public class PairwiseGenomeComparator {
                                 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
                         SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
                                                                      new StringBuilder( species_i + "-" + species_j ),
+                                                                     null,
                                                                      writer,
                                                                      null,
                                                                      similarities,
@@ -214,7 +212,9 @@ public class PairwiseGenomeComparator {
                                                                      domain_similarity_print_option,
                                                                      scoring,
                                                                      false,
-                                                                     tax_code_to_id_map );
+                                                                     tax_code_to_id_map,
+                                                                     phy,
+                                                                     null );
                     }
                     catch ( final IOException e ) {
                         ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
@@ -264,8 +264,8 @@ public class PairwiseGenomeComparator {
             final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
                                                                                   jacknife_ratio,
                                                                                   generator );
-            final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
-            final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+            final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+            final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
             for( int i = 0; i < number_of_genomes; ++i ) {
                 final String species_i = species[ i ].getSpeciesId();
                 shared_domains_based_distances.setIdentifier( i, species_i );
@@ -275,15 +275,15 @@ public class PairwiseGenomeComparator {
                     genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
                     genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
                     final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
-                                                                                                                                                                         .get( i ),
+                                                                                                                                                                 .get( i ),
                                                                                                                                                                  list_of_genome_wide_combinable_domains
-                                                                                                                                                                         .get( j ) );
+                                                                                                                                                                 .get( j ) );
                     genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
                     genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
                     shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
-                            .calculateSharedDomainsBasedGenomeSimilarityScore() );
+                                                             .calculateSharedDomainsBasedGenomeSimilarityScore() );
                     shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
-                            .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
+                                                                         .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
                 }
             }
             getSharedDomainsBasedDistances().add( shared_domains_based_distances );
@@ -294,6 +294,12 @@ public class PairwiseGenomeComparator {
         }
     }
 
+    private void init() {
+        _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
+        _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
+        _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
+    }
+
     static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
         String[] all_domain_ids_array;
         final SortedSet<String> all_domain_ids = new TreeSet<String>();