/*\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
\r
// Checks whether sequence is valid aa characters\r
- protected boolean isValidProteinSequence(String sequence)\r
+ protected boolean isValidProteinSequence(char [] sequence)\r
{\r
- for (int i = 0; i < sequence.length(); i++)\r
- if (!jalview.schemes.ResidueProperties.aaHash.containsKey(\r
- String.valueOf(sequence.charAt(i))))\r
+ for (int i = 0; i < sequence.length; i++)\r
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[i]]==-1)\r
{\r
- invalidCharacter = sequence.charAt(i);\r
+ invalidCharacter = sequence[i];\r
return false;\r
}\r
\r