JAL-3187 hacks to get peptide variant in to Jmol hover tooltip

[jalview.git] / src / jalview / viewmodel / seqfeatures / FeatureRendererModel.java

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 2324a64..4fc143e 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -25,6 +25,7 @@ import jalview.api.FeatureColourI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
@@ -1164,9 +1165,16 @@ public abstract class FeatureRendererModel
    * @param pos
    * @return
    */
-  public List<SequenceFeature> findComplementFeaturesAtResidue(SequenceI sequence, int pos)
+  public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
+          int pos)
   {
     SequenceI ds = sequence.getDatasetSequence();
+    if (ds == null)
+    {
+      ds = sequence;
+    }
+    final char residue = ds.getCharAt(pos - ds.getStart());
+
     List<SequenceFeature> found = new ArrayList<>();
     List<AlignedCodonFrame> mappings = this.av.getAlignment()
             .getCodonFrame(sequence);
@@ -1175,9 +1183,12 @@ 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;
+    SequenceI mapFrom = null;
+
     for (AlignedCodonFrame acf : mappings)
     {
-      Mapping mapping = acf.getMappingForSequence(sequence, true);
+      mapping = acf.getMappingForSequence(sequence, true);
       if (mapping == null || mapping.getMap().getFromRatio() == mapping
               .getMap().getToRatio())
       {
@@ -1189,6 +1200,7 @@ public abstract class FeatureRendererModel
       {
         int fromRes = match.getStart();
         int toRes = match.getEnd();
+        mapFrom = match.getSequence();
         List<SequenceFeature> fs = findFeaturesAtResidue(
                 match.getSequence(), fromRes, toRes);
         for (SequenceFeature sf : fs)
@@ -1199,7 +1211,16 @@ public abstract class FeatureRendererModel
           }
         }
       }
+
+      /*
+       * just take the first mapped features we find
+       */
+      if (!found.isEmpty())
+      {
+        break;
+      }
     }
+
     /*
      * sort by renderorder, inefficiently
      */
@@ -1213,13 +1234,14 @@ public abstract class FeatureRendererModel
           result.add(sf);
           if (result.size() == found.size())
           {
-            return result;
+            return new MappedFeatures(mapping, mapFrom, pos, residue,
+                    result);
           }
         }
       }
     }
     
-    return result;
+    return new MappedFeatures(mapping, mapFrom, pos, residue, result);
   }
 
 }