From 5da6500eacd4ab3a0e5b156b2e47ae9467343555 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 6 Nov 2006 17:12:05 +0000
Subject: [PATCH] Only calculate consenus from start to end

---
 src/jalview/datamodel/SequenceGroup.java |    4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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);
 
-- 
1.7.10.2