From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 27 Sep 2016 08:23:55 +0000 (+0100)
Subject: JAL-2230 use correct mapping to transfer features to CDS!
X-Git-Tag: Release_2_10_0~37
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9e96b685cef70e6ed165ba8f643fefd2996d688d

JAL-2230 use correct mapping to transfer features to CDS!
---

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index ea330d8..c521d9b 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1731,8 +1731,7 @@ public class AlignmentUtils
            */
           AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame();
           MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
-                  cdsRange, 1,
-                  1);
+                  cdsRange, 1, 1);
           dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss,
                   dnaToCdsMap);
           if (!mappings.contains(dnaToCdsMapping))
@@ -1786,7 +1785,7 @@ public class AlignmentUtils
           /*
            * transfer any features on dna that overlap the CDS
            */
-          transferFeatures(dnaSeq, cdsSeq, cdsToProteinMap, null,
+          transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null,
                   SequenceOntologyI.CDS);
         }
       }