From 6bbd76f4f20e5a69aa4359837af78474144877fc Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 21 Dec 2007 15:00:13 +0000
Subject: [PATCH] temporary bugfix ?

---
 src/jalview/datamodel/AlignedCodonFrame.java |    7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index f4e2d97..6c6c26e 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -134,6 +134,9 @@ public class AlignedCodonFrame
     nlen--;
     dnaSeqs[nlen] = (dnaseq.getDatasetSequence()==null) ? dnaseq : dnaseq.getDatasetSequence();
     Mapping mp = new Mapping(map);
+    // JBPNote DEBUG! THIS !
+    //dnaseq.transferAnnotation(aaseq, mp);
+    //aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
     mp.to = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();
     a_aaSeqs.addElement(aaseq);
     dnaToProt[nlen] = mp;
@@ -225,6 +228,10 @@ public class AlignedCodonFrame
    */
   public void markMappedRegion(SequenceI seq, int index, SearchResults results)
   {
+    if (dnaToProt==null)
+    {
+      return;
+    }
     int[] codon;
     SequenceI ds = seq.getDatasetSequence();
     for (int mi = 0; mi<dnaToProt.length; mi++)
-- 
1.7.10.2