X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FMSFfile.java;h=bae4342276b8a701109efd851b0ca3593c14a3f7;hb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;hp=179204e44a677d305ca68830775fa87704c69d4f;hpb=0e601aad1c53321613b6fe6727849f37eab89f48;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 179204e..bae4342 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -70,7 +70,7 @@ public class MSFfile extends AlignFile
     /**
      * DOCUMENT ME!
      */
-    public void parse()
+    public void parse() throws IOException
     {
         int i = 0;
         boolean seqFlag = false;
@@ -147,9 +147,6 @@ public class MSFfile extends AlignFile
                 String head = headers.elementAt(i).toString();
                 String seq = seqhash.get(head).toString();
 
-                int start = -1;
-                int end =  -1;
-
                 if (maxLength < head.length())
                 {
                     maxLength = head.length();
@@ -157,8 +154,17 @@ public class MSFfile extends AlignFile
 
                 // Replace ~ with a sensible gap character
                 seq = seq.replace('~', '-');
+                if (!isValidProteinSequence(seq))
+                {
+                    throw new IOException(AppletFormatAdapter.
+                                          INVALID_CHARACTERS
+                                          + " : " + head
+                                          + " : " + invalidCharacter);
+                }
+
 
                 Sequence newSeq = parseId(head);
+
                 newSeq.setSequence(seq);
 
                 seqs.addElement(newSeq);