X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=6d218f434515fa862b5ec3356704d2ae9f97e301;hb=2bb1ec443f93d558beeca5174023e2b9833243fc;hp=37c96f600a5c9b1f34282255b7ad085088b10fd7;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 37c96f6..6d218f4 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -76,12 +76,20 @@ 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 +108,11 @@ 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());