X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;fp=src%2Fjalview%2Fdatamodel%2FSequence.java;h=6f5c18a6ce06b4512bd6294f034000487fe81813;hb=b2eb64f196223039a95348a4026f0453693ee0e7;hp=80310c0e3da1bfb45717f4490d072eb6154c7b9f;hpb=e080913138aa3287c60ed79c84a0cd128362c06b;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 80310c0..6f5c18a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -670,8 +670,8 @@ public class Sequence extends ASequence implements SequenceI
   public void setGeneLoci(String speciesId, String assemblyId,
           String chromosomeId, MapList map)
   {
-    addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME
-            + ":" + chromosomeId, new Mapping(map)));
+    addDBRef(new GeneLocus(speciesId, assemblyId, chromosomeId,
+            new Mapping(map)));
   }
 
   /**
@@ -687,36 +687,9 @@ public class Sequence extends ASequence implements SequenceI
     {
       for (final DBRefEntry ref : refs)
       {
-        if (ref.isChromosome())
+        if (ref instanceof GeneLociI)
         {
-          return new GeneLociI()
-          {
-            @Override
-            public String getSpeciesId()
-            {
-              return ref.getSource();
-            }
-
-            @Override
-            public String getAssemblyId()
-            {
-              return ref.getVersion();
-            }
-
-            @Override
-            public String getChromosomeId()
-            {
-              // strip off "chromosome:" prefix to chrId
-              return ref.getAccessionId().substring(
-                      DBRefEntry.CHROMOSOME.length() + 1);
-            }
-
-            @Override
-            public MapList getMap()
-            {
-              return ref.getMap().getMap();
-            }
-          };
+          return (GeneLociI) ref;
         }
       }
     }