From 92f934a3ed429a46227cf829f985d72cb7e86fb7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Sep 2005 15:52:52 +0000
Subject: [PATCH] Dont calculate conservation for nucleotides

---
 src/jalview/appletgui/AlignViewport.java |    3 +++
 src/jalview/gui/AlignViewport.java       |    4 ++++
 2 files changed, 7 insertions(+)

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 40d3dd4..30724a4 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -150,6 +150,9 @@ public class AlignViewport
 
   public void updateConservation()
   {
+    if(alignment.isNucleotide())
+          return;
+
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3420993..2922f09 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -138,6 +138,7 @@ public class AlignViewport
         // We must set conservation and consensus before setting colour,
         // as Blosum and Clustal require this to be done
         updateConservation();
+
         updateConsensus();
 
         if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@ -175,6 +176,9 @@ public class AlignViewport
      */
     public void updateConservation()
     {
+      if(alignment.isNucleotide())
+          return;
+
       try{
         Conservation cons = new jalview.analysis.Conservation("All",
             jalview.schemes.ResidueProperties.propHash, 3,
-- 
1.7.10.2