X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainSimilarity.java;h=bf9cef44cd3f65e57e9509e40d7a6ee96168bb7e;hb=f47b5de663d2ca59a4d53587ea8d5cd20c594db2;hp=b6ae5767f51f0d80d1e12e5f5c453194bcc8e6fb;hpb=6ec28d1a3a137c14c9647aec7b9e40b77fe968bf;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
index b6ae576..bf9cef4 100644
--- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
@@ -30,7 +30,6 @@ import java.util.Map;
 import java.util.SortedMap;
 import java.util.SortedSet;
 
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
 
@@ -48,9 +47,9 @@ public interface DomainSimilarity extends Comparable<DomainSimilarity> {
         MIN, MAX, SD, MEAN, ABS_MAX_COUNTS_DIFFERENCE, MAX_COUNTS_DIFFERENCE, MAX_DIFFERENCE, SPECIES_COUNT, DOMAIN_ID,
     }
 
-    public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain );;
+    public SortedSet<String> getCombinableDomainIds( final Species species_of_combinable_domain );
 
-    public DomainId getDomainId();
+    public String getDomainId();
 
     /**
      * For pairwise similarities, this should return the "difference"; for example the difference in counts
@@ -98,7 +97,7 @@ public interface DomainSimilarity extends Comparable<DomainSimilarity> {
      * 
      * @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
      */
-    public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData();
+    public SortedMap<Species, SpeciesSpecificDcData> getSpeciesData();
 
     public double getStandardDeviationOfSimilarityScore();