X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=f2213adcdcffa65363e887cf4b6cad441f17a4ec;hb=2fc1013d3c126983a8d7d932671168e11cfab63d;hp=4aed258bf50b20b178be47d12c0c13e1e784109e;hpb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 4aed258..f2213ad 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -413,18 +413,18 @@ public final class MappingUtils
     SequenceI[] sortOrder = command.getSequenceOrder(undo);
     List<SequenceI> mappedOrder = new ArrayList<SequenceI>();
     int j = 0;
+
+    /*
+     * Assumption: we are only interested in a cDNA/protein mapping; refactor in
+     * future if we want to support sorting (c)dna as (c)dna or protein as
+     * protein
+     */
+    boolean mappingToNucleotide = mapTo.isNucleotide();
     for (SequenceI seq : sortOrder)
     {
       for (AlignedCodonFrame acf : mappings)
       {
-        /*
-         * Try protein-to-Dna, failing that try dna-to-protein
-         */
-        SequenceI mappedSeq = acf.getDnaForAaSeq(seq);
-        if (mappedSeq == null)
-        {
-          mappedSeq = acf.getAaForDnaSeq(seq);
-        }
+        SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq) : acf.getAaForDnaSeq(seq);
         if (mappedSeq != null)
         {
           for (SequenceI seq2 : mapTo.getSequences())
@@ -494,6 +494,12 @@ public final class MappingUtils
     Set<AlignedCodonFrame> codonFrames = protein.getAlignment()
             .getCodonFrames();
     ColumnSelection mappedColumns = new ColumnSelection();
+
+    if (colsel == null)
+    {
+      return mappedColumns;
+    }
+
     char fromGapChar = mapFrom.getAlignment().getGapCharacter();
 
     // FIXME allow for hidden columns