X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=5d7be8c52a9ba25275a8559fec5799b099cb6b4b;hb=00ac6f06b80b4a9b2b35490a7cb4033115390227;hp=b43e3ead651d9237ab44f18627f9647db41ae572;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index b43e3ea..5d7be8c 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -43,7 +43,8 @@ public class ClustalFile
     super.initData();
   }
 
-  public void parse() throws IOException
+  public void parse()
+      throws IOException
   {
     int i = 0;
     boolean flag = false;
@@ -97,7 +98,9 @@ public class ClustalFile
             }
           }
           else
+          {
             flag = true;
+          }
         }
       }
     }
@@ -124,15 +127,8 @@ 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);
-          }
-
+          newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
+                             toString());
 
           seqs.addElement(newSeq);
         }
@@ -193,7 +189,7 @@ public class ClustalFile
 
       while ( (j < s.length) && (s[j] != null))
       {
-        out.append(new Format("%-" + maxid + "s").form( printId(s[j]) + " "));
+        out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
 
         int start = i * len;
         int end = start + len;