X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=d3b93bfe77faa62eb8da85463b0ee1fd8219a883;hb=3d941a02a998676a12f8ff43fa98d9e1f4c27142;hp=ec5d4f1517aa4f3e120097d4a268f8ddc7761c92;hpb=0fc704a18faa7d11b6d02876bb6c1e8bc19f343c;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index ec5d4f1..d3b93bf 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -32,6 +32,7 @@ public class Blosum62ColourScheme
 
   public Color findColour(String s, int j)
   {
+
     char res = s.charAt(0);
     if ('a' <= res && res <= 'z' )
     {
@@ -47,6 +48,8 @@ public class Blosum62ColourScheme
       return Color.white;
     }
 
+    Color currentColour;
+
     if (!jalview.util.Comparison.isGap( res ))
     {
       String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
@@ -79,7 +82,7 @@ public class Blosum62ColourScheme
       }
 
       if(conservationColouring)
-         applyConservation(j);
+         applyConservation(currentColour, j);
     }
     else
     {