set icon false if raising windows

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 1e38a6d..04610ef 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -86,8 +86,7 @@ public class ClustalxColourScheme
         }\r
         else\r
         {\r
-          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +\r
-              "")).intValue();\r
+          res =  ResidueProperties.aaIndex[seq.charAt(i)];\r
         }\r
 \r
         cons2[i][res]++;\r
@@ -258,7 +257,7 @@ public class ClustalxColourScheme
       return Color.white;\r
     }\r
 \r
-    int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();\r
+    int i = ResidueProperties.aaIndex[s.charAt(0)];\r
 \r
     currentColour = Color.white;\r
 \r