X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=4a9e77768e6f8da4767a96913e928b8fc7713dc6;hb=a7bec763a3e4f17a549115f8f9f19ee4c742c26b;hp=a7cc1eadf490f4b5b4ae6bec70c23b5de664d71b;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index a7cc1ea..4a9e777 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.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
@@ -42,15 +42,6 @@ public class BLCFile extends AlignFile
     {
     }
 
-    /**
-     * Creates a new BLCFile object.
-     *
-     * @param inStr DOCUMENT ME!
-     */
-    public BLCFile(String inStr)
-    {
-        super(inStr);
-    }
 
     /**
      * Creates a new BLCFile object.
@@ -77,7 +68,7 @@ public class BLCFile extends AlignFile
     /**
      * DOCUMENT ME!
      */
-    public void parse()
+    public void parse() throws IOException
     {
         boolean idsFound = false;
         Vector ids = new Vector();
@@ -87,8 +78,6 @@ public class BLCFile extends AlignFile
 
         String line = null;
 
-        try
-        {
             do
             {
                 line = nextLine();
@@ -146,17 +135,23 @@ public class BLCFile extends AlignFile
 
             for (int i = 0; i < ids.size(); i++)
             {
-                Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-                        seqstrings[i].toString(),
-                        Integer.parseInt(starts.elementAt(i).toString()),
-                        Integer.parseInt(ends.elementAt(i).toString()));
+              Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
+                                             seqstrings[i].toString(),
+                                             Integer.parseInt(starts.elementAt(i).
+                                                              toString()),
+                                             Integer.parseInt(ends.elementAt(i).toString()));
+
+              if (!isValidProteinSequence(newSeq.getSequence()))
+              {
+                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+                               +" : "+ newSeq.getName()
+                               +" : "+invalidCharacter);
+
+              }
+
                 seqs.addElement(newSeq);
             }
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
+
     }
 
     /**
@@ -193,9 +188,9 @@ public class BLCFile extends AlignFile
         {
             out.append(">" + printId(s[i]) +"\n");
 
-            if (s[i].getSequence().length() > max)
+            if (s[i].getSequence().length > max)
             {
-                max = s[i].getSequence().length();
+                max = s[i].getSequence().length;
             }
 
             i++;
@@ -209,9 +204,9 @@ public class BLCFile extends AlignFile
 
             while ((i < s.length) && (s[i] != null))
             {
-                if (s[i].getSequence().length() > j)
+                if (s[i].getSequence().length > j)
                 {
-                    out.append(s[i].getSequence().substring(j, j + 1));
+                    out.append(s[i].getSequenceAsString(j, j + 1));
                 }
                 else
                 {