X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=2c0836de99c6d7dec867547d7579e9c3cd4c30e2;hb=d187567c926fed31f9cd9bda0dc112bc4d1b1261;hp=356e3fe64dc4b5cac7eb8295b24fef3c89e7c91b;hpb=45845d73e614baf0e568c8bb384c5680d46e0e2e;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 356e3fe..2c0836d 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -31,19 +31,26 @@ public class Blosum62ColourScheme
 
   public Color findColour(String s, int j)
   {
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z' )
     {
-      return Color.white;
+       // TO UPPERCASE !!!
+       s = String.valueOf( res -= ('a' - 'A') );
     }
 
 
-    if (!jalview.util.Comparison.isGap( (s.charAt(0))))
+    if ( j>=consensus.length || (threshold != 0 && !aboveThreshold(s, j) ))
+    {
+      return Color.white;
+    }
+
+    if (!jalview.util.Comparison.isGap( res ))
     {
       String max = (String) consensus[j].get("maxResidue");
 
       if (max.indexOf(s) > -1)
       {
-        return new Color(154, 154, 255);
+        currentColour = new Color(154, 154, 255);
       }
       else
       {
@@ -60,17 +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;
   }
 }