use 3 as the threshold

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