X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FPairwiseGenomeComparator.java;h=a3b0e668cf8f42f86431e5f9dccf93db19c31452;hb=1d144f35479f96cb36c5247d9711e22ed234651a;hp=4a78a138713d45ed82595eb97f95904922174b84;hpb=3b5c2fab212d221196ed1734ee9c623f45310bb7;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index 4a78a13..a3b0e66 100644
--- 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,
@@ -299,6 +293,12 @@ 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>();