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 (file)
--- 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))
           {