header updated

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

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