X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=eb1030c3640b7d400586d6fa6600d76984aca7a4;hp=853bc3be23ce6c202c41676478a9717a9e1c23d8;hb=27aed96d1aeae689818bd0a0028553186e3c3839;hpb=7312fed439c2a32de989c6f5155203ebc0a7f854

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 853bc3b..eb1030c 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -39,9 +39,9 @@ import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.MappedFeatures;
-import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -1233,18 +1233,18 @@ public abstract class FeatureRendererModel
      * todo: direct lookup of CDS for peptide and vice-versa; for now,
      * have to search through an unordered list of mappings for a candidate
      */
-    Mapping mapping = null;
+    SequenceToSequenceMapping mapping = null;
     SequenceI mapFrom = null;
 
     for (AlignedCodonFrame acf : mappings)
     {
-      mapping = acf.getMappingForSequence(sequence);
-      if (mapping == null || !mapping.getMap().isTripletMap())
+      mapping = acf.getCoveringCodonMapping(ds);
+      if (mapping == null)
       {
-        continue; // we are only looking for 3:1 or 1:3 mappings
+        continue;
       }
       SearchResultsI sr = new SearchResults();
-      acf.markMappedRegion(ds, pos, sr);
+      mapping.markMappedRegion(ds, pos, sr);
       for (SearchResultMatchI match : sr.getResults())
       {
         int fromRes = match.getStart();
@@ -1297,7 +1297,7 @@ public abstract class FeatureRendererModel
       }
     }
     
-    return new MappedFeatures(mapping, mapFrom, pos, residue, result);
+    return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
   }
 
   @Override