From d68c7e07403bd581700e4a79a269b221e0018d36 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 24 Aug 2007 15:20:33 +0000
Subject: [PATCH] todo comments

---
 src/jalview/datamodel/xdb/embl/EmblEntry.java |    7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index a1c4c3c..350c44e 100644
--- 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
     {
-- 
1.7.10.2