Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_...

[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 0a667aa..8f513c9 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -38,9 +38,9 @@ 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;
@@ -102,11 +102,11 @@ public abstract class FeatureRendererModel
 
   Map<String, Float> featureOrder = null;
 
-  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
-          this);
-
   protected AlignViewportI av;
 
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
   @Override
   public AlignViewportI getViewport()
   {
@@ -299,13 +299,19 @@ public abstract class FeatureRendererModel
       {
         firing = Boolean.TRUE;
         findAllFeatures(true); // add all new features as visible
-        changeSupport.firePropertyChange("changeSupport", null, null);
+        notifyFeaturesChanged();
         firing = Boolean.FALSE;
       }
     }
   }
 
   @Override
+  public void notifyFeaturesChanged()
+  {
+    changeSupport.firePropertyChange("changeSupport", null, null);
+  }
+
+  @Override
   public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
   {
     /*
@@ -1190,18 +1196,18 @@ 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();
@@ -1251,14 +1257,10 @@ public abstract class FeatureRendererModel
         {
           break;
         }
-        if (added == toAdd)
-        {
-          break;
-        }
       }
     }
     
-    return new MappedFeatures(mapping, mapFrom, pos, residue, result);
+    return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
   }
 
   @Override