Sequence is char []

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 1dafb91..85f23a4 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.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
@@ -111,13 +111,12 @@ public abstract class AlignFile extends FileParse
     }\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