/*\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
*/\r
package jalview.analysis;\r
\r
-import jalview.analysis.*;\r
-\r
import jalview.datamodel.*;\r
\r
import java.util.*;\r
* the values being the count of each residue in that column.\r
* This class is used extensively in calculating alignment colourschemes\r
* that depend on the amount of conservation in each alignment column. */\r
- public static Vector calculate(Vector sequences, int start, int end)\r
+ public static final Vector calculate(Vector sequences, int start, int end)\r
{\r
Vector result = new Vector();\r
Hashtable residueHash;\r
\r
if (sequence.length() > i)\r
{\r
- res = sequence.substring(i,i+1);\r
+ res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));\r
\r
if (jalview.util.Comparison.isGap(res.charAt(0)))\r
{\r