From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 23 Apr 2015 08:23:17 +0000 (+0100)
Subject: JAL-845 only 'follow' sort command in coding complement alignment
X-Git-Tag: Jalview_2_9~54
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=30430dc0a4b26c410928adb24c296e6c654b5847;p=jalview.git

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
--- 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())