From f885578ef3972d4a8b26af65e5a6d5e4e87cfa09 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 14 Apr 2005 16:53:51 +0000
Subject: [PATCH] use 3 as the threshold

---
 src/jalview/gui/AlignViewport.java |    6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 89aac5c..b661b87 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -84,9 +84,9 @@ public class AlignViewport
   public void updateConservation()
   {
     Conservation cons = new jalview.analysis.Conservation("All",
-        jalview.schemes.ResidueProperties.propHash, 1,
+        jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
-        alignment.getWidth());
+        alignment.getWidth()-1);
     cons.calculate();
     cons.verdict(false, ConsPercGaps);
     cons.findQuality();
@@ -159,7 +159,7 @@ public class AlignViewport
 
     Vector cons = alignment.getAAFrequency();
     Hashtable hash = null;
-    for (int i = 0, alWidth=alignment.getWidth(); i<alWidth; i++)
+    for (int i = 0; i<alignment.getWidth(); i++)
     {
         hash = (Hashtable) cons.elementAt(i);
         float value = Float.parseFloat(hash.get("maxCount").toString());
-- 
1.7.10.2