JAL-845 only 'follow' sort command in coding complement alignment

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 4aed258..df21355 100644 (file)
--- 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())