X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FPairwiseGenomeComparator.java;h=b23f82b9ec058b0bfc94a74210acb274fda9e4ab;hb=63685dd0262a506f0bf17cba6be1aa1ada5330f3;hp=a3b0e668cf8f42f86431e5f9dccf93db19c31452;hpb=bd7bf76e7b7d9f4f643f05f6aadc4f517f875254;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index a3b0e66..b23f82b 100644
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -122,11 +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 );
@@ -139,7 +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,
@@ -150,9 +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 ) {
@@ -274,15 +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 );