X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=4afb3219a95fa2a62c291434900790ef2f7952de;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=6aaef7dfc707b71eadb992cbfce7cba96a7384fe;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 6aaef7d..4afb321 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -60,6 +60,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
      */
     public Color findColour(String n, int j)
     {
+        Color currentColour;
         if ((threshold == 0) || aboveThreshold(n, j))
         {
             try
@@ -77,7 +78,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
         }
 
         if(conservationColouring)
-         applyConservation(j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }