X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainSimilarityCalculator.java;h=3983dd65cd9b97f03139c2fec11705bd0717dae5;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;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..3983dd6 100644
--- a/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java
@@ -32,16 +32,16 @@ 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
-    }
+                                                              public static enum Detailedness {
+                                                                  BASIC, LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, PUNCTILIOUS
+                                                              }
 
-    public static enum GoAnnotationOutput {
-        ALL, NONE
-    }
+                                                              public static enum GoAnnotationOutput {
+                                                                  ALL, NONE
+                                                              }
 }