From 30430dc0a4b26c410928adb24c296e6c654b5847 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 23 Apr 2015 09:23:17 +0100 Subject: [PATCH] JAL-845 only 'follow' sort command in coding complement alignment --- src/jalview/util/MappingUtils.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) 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 mappedOrder = new ArrayList(); 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()) -- 1.7.10.2