X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainSimilarityCalculator.java;h=a1c944ab90cfea557a9d584101f233059e47e0da;hb=bf4f34e0511813622f68e54ffb783e4e6d92bfa4;hp=ad72c4562d7790e3f69c6778336cb40b8e044906;hpb=3d68fcd1fc4272b56546f78f3cbd437237af5cfa;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java
index ad72c45..a1c944a 100644
--- a/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java
@@ -32,10 +32,10 @@ import java.util.SortedSet;
 
 public interface DomainSimilarityCalculator {
 
-    public SortedSet<PrintableDomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
-                                                                       final List<GenomeWideCombinableDomains> cdc_list,
-                                                                       final boolean ignore_domains_without_combinations_in_any_genome,
-                                                                       final boolean ignore_domains_specific_to_one_genome );;
+    public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
+                                                              final List<GenomeWideCombinableDomains> cdc_list,
+                                                              final boolean ignore_domains_without_combinations_in_any_genome,
+                                                              final boolean ignore_domains_specific_to_one_genome );;
 
     public static enum Detailedness {
         BASIC, LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, PUNCTILIOUS