X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=6e3ced88635f906442f3107133741b70732f9214;hb=6a698ae1f2a42d84b287f3095a9244c711e0ce2e;hp=37c96f600a5c9b1f34282255b7ad085088b10fd7;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 37c96f6..6e3ced8 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.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
@@ -41,16 +41,6 @@ public class FastaFile extends AlignFile
     /**
      * Creates a new FastaFile object.
      *
-     * @param inStr DOCUMENT ME!
-     */
-    public FastaFile(String inStr)
-    {
-        super(inStr);
-    }
-
-    /**
-     * Creates a new FastaFile object.
-     *
      * @param inFile DOCUMENT ME!
      * @param type DOCUMENT ME!
      *
@@ -76,12 +66,20 @@ public class FastaFile extends AlignFile
 
         while ((line = nextLine()) != null)
         {
+            line = line.trim();
             if (line.length() > 0)
             {
                 if (line.charAt(0)=='>')
                 {
                     if (count != 0)
                     {
+                      if (!isValidProteinSequence(sb.toString()))
+                      {
+                        throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+                                              +" : "+seq.getName()
+                                              +" : "+invalidCharacter);
+                      }
+
                        seq.setSequence(sb.toString());
                        seqs.addElement(seq);
                     }
@@ -100,9 +98,11 @@ public class FastaFile extends AlignFile
 
         if (count > 0)
         {
-            if (!isValidProteinSequence(sb.toString().toUpperCase()))
+            if (!isValidProteinSequence(sb.toString()))
             {
-                throw new IOException("Invalid protein sequence");
+                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+                                      +" : "+seq.getName()
+                                      +" : "+invalidCharacter);
             }
 
             seq.setSequence(sb.toString());