X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=942e55b9854c8089b886db22db4d9d147173e500;hb=95789943eb181b1768a081e779a044bf595b6bf6;hp=8785954c60a271a2e3bdcd0a868e8fd2b2923024;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 8785954..942e55b 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -64,7 +64,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
         {
             try
             {
-                return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+                currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
             }
             catch (Exception ex)
             {
@@ -75,5 +75,10 @@ public class NucleotideColourScheme extends ResidueColourScheme
         {
             return Color.white;
         }
+
+        if(conservationColouring)
+         applyConservation(j);
+
+       return currentColour;
     }
 }