From 23eee41c81cbe59155bdb71f82cf92c7c58e578b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 23 Aug 2016 18:40:19 +0100 Subject: [PATCH] JAL-2154 should only add mappings between dataset sequences --- src/jalview/analysis/AlignmentUtils.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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)) { -- 1.7.10.2