Dont calculate conservation for nucleotides

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 40d3dd4..30724a4 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -150,6 +150,9 @@ public class AlignViewport
 \r
   public void updateConservation()\r
   {\r
+    if(alignment.isNucleotide())\r
+          return;\r
+\r
     Conservation cons = new jalview.analysis.Conservation("All",\r
         jalview.schemes.ResidueProperties.propHash, 3,\r
         alignment.getSequences(), 0,\r

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3420993..2922f09 100755 (executable)
--- 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,\r
         // as Blosum and Clustal require this to be done\r
         updateConservation();\r
+\r
         updateConsensus();\r
 \r
         if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
@@ -175,6 +176,9 @@ public class AlignViewport
      */\r
     public void updateConservation()\r
     {\r
+      if(alignment.isNucleotide())\r
+          return;\r
+\r
       try{\r
         Conservation cons = new jalview.analysis.Conservation("All",\r
             jalview.schemes.ResidueProperties.propHash, 3,\r