janiela -> xfam

[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 4699869..d0d2590 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -52,8 +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();
@@ -71,19 +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,
@@ -100,7 +94,7 @@ public class PairwiseGenomeComparator {
                                             final boolean write_pairwise_comparisons,
                                             final Map<String, Integer> tax_code_to_id_map,
                                             final boolean calc_similarity_scores,
-                                            Phylogeny phy ) {
+                                            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 );
@@ -145,7 +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,
@@ -218,7 +213,8 @@ public class PairwiseGenomeComparator {
                                                                      scoring,
                                                                      false,
                                                                      tax_code_to_id_map,
-                                                                     phy );
+                                                                     phy,
+                                                                     null );
                     }
                     catch ( final IOException e ) {
                         ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
@@ -298,6 +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>();