Conservation colour scheme is no more

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

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