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=9c6e1b5cf2c3dbc40898cc677779bcdd91768dde;hpb=3d68fcd1fc4272b56546f78f3cbd437237af5cfa;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index 9c6e1b5..b23f82b 100644
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -76,9 +76,9 @@ public class PairwiseGenomeComparator {
                                             final Detailedness detailedness,
                                             final boolean ignore_domains_without_combs_in_all_spec,
                                             final boolean ignore_domains_specific_to_one_species,
-                                            final PrintableDomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
-                                            final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
-                                            final PrintableDomainSimilarity.DomainSimilarityScoring scoring,
+                                            final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
+                                            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,
                                             final GoNameSpace go_namespace_limit,
@@ -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 );
@@ -139,8 +139,9 @@ public class PairwiseGenomeComparator {
                 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
                                                                                              sort_by_species_count_first,
                                                                                              true,
-                                                                                             calc_similarity_scores );
-                final SortedSet<PrintableDomainSimilarity> similarities = calc
+                                                                                             calc_similarity_scores,
+                                                                                             true );
+                final SortedSet<DomainSimilarity> similarities = calc
                         .calculateSimilarities( pw_calc,
                                                 genome_pair,
                                                 ignore_domains_without_combs_in_all_spec,
@@ -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 );