formatting

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

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 4c07ac9..a33e118 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.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
@@ -83,12 +83,6 @@ public class PIRFile
         {\r
           sequence.setLength(sequence.length() - 1);\r
           newSeq.setSequence(sequence.toString());\r
-          if (!isValidProteinSequence(newSeq.getSequence()))\r
-          {\r
-            throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
-                                  +" : "+ newSeq.getName()\r
-                                  +" : "+invalidCharacter);\r
-          }\r
 \r
           seqs.addElement(newSeq);\r
 \r
@@ -114,7 +108,7 @@ public class PIRFile
 \r
     while ( (i < s.length) && (s[i] != null))\r
     {\r
-      String seq = s[i].getSequence();\r
+      String seq = s[i].getSequenceAsString();\r
       seq = seq + "*";\r
 \r
 \r