todo comments

[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 906122d..350c44e 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -387,11 +387,12 @@ public class EmblEntry
    */
   public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
           boolean noPeptide, String sourceDb)
-  {
+  { //TODO: ensure emblEntry.getSequences behaves correctly for returning all cases of noNa and noPeptide
     Vector seqs = new Vector();
     Sequence dna = null;
     if (!noNa)
     {
+      // In theory we still need to create this if noNa is set to avoid a null pointer exception
       dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
       dna.setDescription(desc);
       dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
@@ -399,8 +400,8 @@ public class EmblEntry
       // TODO: transform EMBL Database refs to canonical form
       if (dbRefs != null)
         for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
-                .addDBRef((DBRefEntry) i.next()))
-          ;
+        .addDBRef((DBRefEntry) i.next()))
+        ;
     }
     try
     {
@@ -642,15 +643,15 @@ public class EmblEntry
                 jalview.datamodel.DBRefSource.UNIPROT))
         {
           ref.setMap(map);
-          /*if (map.getTo()!=null)
+          if (map!=null && map.getTo()!=null)
           {
-            map.getTo().setName(map.getTo().getName()+"|"+ref.getSource()+"|"+ref.getAccessionId());
-          }*/
+            map.getTo().addDBRef(new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId())); // don't copy map over.
+          }
         }
         if (product != null)
         {
           DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
-                  .getVersion(), ref.getAccessionId());
+                .getVersion(), ref.getAccessionId());
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference