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[jalview.git] / forester / java / src / org / forester / surfacing / DomainSimilarityCalculator.java

diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java
index ad72c45..3983dd6 100644 (file)
--- 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
+                                                              }
 }