X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=6de42b9d23e704384ecc0af78a279b1bab9765a7;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=054896b2eca8854988efd7ebb52e5f8aa5cf6582;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 054896b..6de42b9 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -235,29 +235,31 @@ public class SequenceGroup
      */
     public void recalcConservation()
     {
-        if (cs != null)
-        {
-            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
-        }
+        if(cs == null)
+          return;
+
+        cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+
 
         if (cs instanceof ClustalxColourScheme)
         {
             ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
         }
 
-        if (cs instanceof ConservationColourScheme)
+
+        if (cs.conservationApplied())
         {
             Conservation c = new Conservation(groupName,
                     ResidueProperties.propHash, 3, sequences, 0, getWidth());
             c.calculate();
             c.verdict(false, 25);
 
-            ConservationColourScheme ccs = (ConservationColourScheme) cs;
-            ccs.conserve = c;
 
-            if (ccs.cs instanceof ClustalxColourScheme)
+            cs.setConservation(c);
+
+            if (cs instanceof ClustalxColourScheme)
             {
-                ((ClustalxColourScheme) ccs.cs).resetClustalX(sequences,
+                ((ClustalxColourScheme) cs).resetClustalX(sequences,
                     getWidth());
             }
         }