X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=9a8a0861fb5e21c084c4ee46f6dd3a389b967ac8;hb=705635fb3c936cfc7c61f4d4e697ddb1d2b589b7;hp=f9c9782df4e1e9100c7f1dba16949623dce445e6;hpb=0d1529f5a1f02b9cb959f0fe0d3e7f468723b83a;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index f9c9782..9a8a086 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -1177,6 +1177,16 @@ public abstract class FeatureRendererModel
             .getCodonFrame(sequence);
 
     /*
+     * fudge: if no mapping found, check the complementary alignment
+     * todo: only store in one place? StructureSelectionManager?
+     */
+    if (mappings.isEmpty())
+    {
+      mappings = this.av.getCodingComplement().getAlignment()
+              .getCodonFrame(sequence);
+    }
+
+    /*
      * todo: direct lookup of CDS for peptide and vice-versa; for now,
      * have to search through an unordered list of mappings for a candidate
      */
@@ -1198,7 +1208,7 @@ public abstract class FeatureRendererModel
         int toRes = match.getEnd();
         mapFrom = match.getSequence();
         List<SequenceFeature> fs = findFeaturesAtResidue(
-                match.getSequence(), fromRes, toRes);
+                mapFrom, fromRes, toRes);
         for (SequenceFeature sf : fs)
         {
           if (!found.contains(sf))