X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=6e91e0b2256677455e368362efb51ae48ca60cb3;hb=2bab2ead5067d824be9a7716b0fb468b38787cac;hp=5e862635662f22345363260e016a8e049faae6c4;hpb=83b55697263efc7b0c660eba6ea7091f6904257d;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 5e86263..6e91e0b 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -34,6 +34,7 @@ public class Blosum62ColourScheme
     char res = s.charAt(0);
     if ('a' <= res && res <= 'z' )
     {
+       // TO UPPERCASE !!!
        s = String.valueOf( res -= ('a' - 'A') );
     }
 
@@ -49,7 +50,7 @@ public class Blosum62ColourScheme
 
       if (max.indexOf(s) > -1)
       {
-        return new Color(154, 154, 255);
+        currentColour = new Color(154, 154, 255);
       }
       else
       {
@@ -66,17 +67,22 @@ public class Blosum62ColourScheme
 
         if (c > 0)
         {
-          return new Color(204, 204, 255);
+          currentColour = new Color(204, 204, 255);
         }
         else
         {
-          return Color.white;
+          currentColour = Color.white;
         }
       }
+
+      if(conservationColouring)
+         applyConservation(j);
     }
     else
     {
       return Color.white;
     }
+
+    return currentColour;
   }
 }