temporary bugfix ?

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