JAL-1027 fix errors in alternative codon table

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index bc1e5ab..0ae49b9 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -585,10 +585,9 @@ public class EmblEntry
     {
       // extract proteins.
       product = new Sequence(prid, prseq, 1, prseq.length());
-      product
-              .setDescription(((prname.length() == 0) ? "Protein Product from "
-                      + sourceDb
-                      : prname));
+      product.setDescription(((prname.length() == 0) ? "Protein Product from "
+              + sourceDb
+              : prname));
       if (!noPeptide)
       {
         // Protein is also added to vector of sequences returned
@@ -713,16 +712,16 @@ public class EmblEntry
         }
         if (product != null)
         {
-          DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
-                  .getVersion(), ref.getAccessionId());
+          DBRefEntry pref = new DBRefEntry(ref.getSource(),
+                  ref.getVersion(), ref.getAccessionId());
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference
           if (map != null)
           {
             Mapping pmap = new Mapping(dna, map.getMap().getInverse());
-            pref = new DBRefEntry(sourceDb, getVersion(), this
-                    .getAccession());
+            pref = new DBRefEntry(sourceDb, getVersion(),
+                    this.getAccession());
             pref.setMap(pmap);
             if (map.getTo() != null)
             {