From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 6 Nov 2006 17:12:05 +0000 (+0000)
Subject: Only calculate consenus from start to end
X-Git-Tag: Release_2_2~176
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5da6500eacd4ab3a0e5b156b2e47ae9467343555;p=jalview.git

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