From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 23 Aug 2016 17:40:19 +0000 (+0100)
Subject: JAL-2154 should only add mappings between dataset sequences
X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~18
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=23eee41c81cbe59155bdb71f82cf92c7c58e578b;p=jalview.git

JAL-2154 should only add mappings between dataset sequences
---

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index ba9821c..b57fbbf 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1697,7 +1697,8 @@ public class AlignmentUtils
           MapList cdsToProteinMap = new MapList(cdsRange, mapList.getToRanges(),
                   mapList.getFromRatio(), mapList.getToRatio());
           AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame();
-          cdsToProteinMapping.addMap(cdsSeq, proteinProduct, cdsToProteinMap);
+          cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct,
+                  cdsToProteinMap);
 
           /*
            * guard against duplicating the mapping if repeating this action
@@ -1714,7 +1715,7 @@ public class AlignmentUtils
           MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
                   cdsRange, 1,
                   1);
-          dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeq,
+          dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss,
                   dnaToCdsMap);
           if (!mappings.contains(dnaToCdsMapping))
           {