X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainSimilarity.java;h=5a0735e3a162489a05c4b164eb368e6e1a260ca2;hb=eae9b4d545845ccc94c1465c1664086b22188ad1;hp=be7273e9035e9f6fce916d087c7054ac72f1a1d0;hpb=f47d5c382bc4e329ff6977ebcc46b75b57ffc901;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
index be7273e..5a0735e 100644
--- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
@@ -30,6 +30,7 @@ import java.util.Map;
 import java.util.SortedMap;
 import java.util.SortedSet;
 
+import org.forester.phylogeny.Phylogeny;
 import org.forester.species.Species;
 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
 
@@ -97,9 +98,11 @@ public interface DomainSimilarity extends Comparable<DomainSimilarity> {
      * 
      * @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
      */
-    public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData();
+    public SortedMap<Species, SpeciesSpecificDcData> getSpeciesData();
 
     public double getStandardDeviationOfSimilarityScore();
 
-    public StringBuffer toStringBuffer( PRINT_OPTION print_option, Map<String, Integer> tax_code_to_id_map );
+    public StringBuffer toStringBuffer( PRINT_OPTION print_option,
+                                        Map<String, Integer> tax_code_to_id_map,
+                                        Phylogeny phy );
 }