Only calculate consenus from start to end

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index dc22704..df8c6ea 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -338,7 +338,7 @@ public class SequenceGroup
 \r
         try\r
         {\r
-          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+          cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));\r
 \r
           if (cs instanceof ClustalxColourScheme)\r
           {\r
@@ -349,7 +349,7 @@ public class SequenceGroup
           {\r
             Conservation c = new Conservation(groupName,\r
                                               ResidueProperties.propHash, 3, sequences,\r
-                                              0, getWidth());\r
+                                              startRes, endRes+1);\r
             c.calculate();\r
             c.verdict(false, 25);\r
 \r