X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=a33e118625585a423e6f9f4a15d0ebb365906be4;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=4c07ac934f44918417a49dd354bf96e73137bd40;hpb=04011072920c5e2587a8d549869ee47e28ad7d81;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 4c07ac9..a33e118 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -83,12 +83,6 @@ public class PIRFile
         {
           sequence.setLength(sequence.length() - 1);
           newSeq.setSequence(sequence.toString());
-          if (!isValidProteinSequence(newSeq.getSequence()))
-          {
-            throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
-                                  +" : "+ newSeq.getName()
-                                  +" : "+invalidCharacter);
-          }
 
           seqs.addElement(newSeq);
 
@@ -114,7 +108,7 @@ public class PIRFile
 
     while ( (i < s.length) && (s[i] != null))
     {
-      String seq = s[i].getSequence();
+      String seq = s[i].getSequenceAsString();
       seq = seq + "*";