Add nucleotide names

[jalview.git] / src / jalview / schemes / Blosum62ColourScheme.java

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 4b1bf15..6e91e0b 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -34,7 +34,8 @@ public class Blosum62ColourScheme
     char res = s.charAt(0);\r
     if ('a' <= res && res <= 'z' )\r
     {\r
-       s = Character.toString( res -= ('a' - 'A') );\r
+       // TO UPPERCASE !!!\r
+       s = String.valueOf( res -= ('a' - 'A') );\r
     }\r
 \r
 \r
@@ -49,7 +50,7 @@ public class Blosum62ColourScheme
 \r
       if (max.indexOf(s) > -1)\r
       {\r
-        return new Color(154, 154, 255);\r
+        currentColour = new Color(154, 154, 255);\r
       }\r
       else\r
       {\r
@@ -66,17 +67,22 @@ public class Blosum62ColourScheme
 \r
         if (c > 0)\r
         {\r
-          return new Color(204, 204, 255);\r
+          currentColour = new Color(204, 204, 255);\r
         }\r
         else\r
         {\r
-          return Color.white;\r
+          currentColour = Color.white;\r
         }\r
       }\r
+\r
+      if(conservationColouring)\r
+         applyConservation(j);\r
     }\r
     else\r
     {\r
       return Color.white;\r
     }\r
+\r
+    return currentColour;\r
   }\r
 }\r