X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=e3f83ee652bda92538a9e0e627c197065af4765b;hb=63f7dffaa9b668ad5ab7d8092e5232908e4b0bcb;hp=e72e0df32df2db9c21a6f78fbb39d2d7e2f199a3;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index e72e0df..e3f83ee 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.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
@@ -32,11 +32,6 @@ public class ClustalFile
   {
   }
 
-  public ClustalFile(String inStr)
-  {
-    super(inStr);
-  }
-
   public ClustalFile(String inFile, String type)
       throws IOException
   {
@@ -48,7 +43,7 @@ public class ClustalFile
     super.initData();
   }
 
-  public void parse()
+  public void parse() throws IOException
   {
     int i = 0;
     boolean flag = false;
@@ -131,6 +126,14 @@ public class ClustalFile
           Sequence newSeq = parseId(headers.elementAt(i).toString());
           newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );
 
+          if (!isValidProteinSequence(newSeq.getSequence()))
+          {
+              throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+                                    + " : " + newSeq.getName()
+                                    + " : " + invalidCharacter);
+          }
+
+
           seqs.addElement(newSeq);
         }
         else