inprogress

[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 a3b0e66..d0d2590 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -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,