JAL-367 code tidy

[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 2a17bf2..426ec1f 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -20,6 +20,20 @@
  */
 package jalview.viewmodel.seqfeatures;
 
+import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
+
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.api.FeaturesDisplayedI;
@@ -38,20 +52,6 @@ import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
 import jalview.util.ColorUtils;
 
-import java.awt.Color;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.concurrent.ConcurrentHashMap;
-
 public abstract class FeatureRendererModel
         implements jalview.api.FeatureRenderer
 {
@@ -1161,19 +1161,9 @@ public abstract class FeatureRendererModel
     return filter == null ? true : filter.matches(sf);
   }
 
-  /**
-   * Answers a bean containing a mapping, and a list of features in this
-   * alignment at a position (or range) which is mappable from the given
-   * sequence residue position in a mapped alignment. Features are returned in
-   * render order of feature type (on top last), with order within feature type
-   * undefined. If no features or mapping are found, answers null.
-   * 
-   * @param sequence
-   * @param pos
-   * @return
-   */
-  public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
-          int pos)
+  @Override
+  public MappedFeatures findComplementFeaturesAtResidue(
+          final SequenceI sequence, final int pos)
   {
     SequenceI ds = sequence.getDatasetSequence();
     if (ds == null)
@@ -1187,6 +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
      */
@@ -1195,9 +1195,8 @@ public abstract class FeatureRendererModel
 
     for (AlignedCodonFrame acf : mappings)
     {
-      mapping = acf.getMappingForSequence(sequence, true);
-      if (mapping == null || mapping.getMap().getFromRatio() == mapping
-              .getMap().getToRatio())
+      mapping = acf.getMappingForSequence(sequence);
+      if (mapping == null || !mapping.getMap().isTripletMap())
       {
         continue; // we are only looking for 3:1 or 1:3 mappings
       }
@@ -1209,7 +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))
@@ -1233,9 +1232,12 @@ public abstract class FeatureRendererModel
     }
 
     /*
-     * sort by renderorder, inefficiently
+     * sort by renderorder (inefficiently but ok for small scale);
+     * NB this sorts 'on top' feature to end, for rendering
      */
     List<SequenceFeature> result = new ArrayList<>();
+    final int toAdd = found.size();
+    int added = 0;
     for (String type : renderOrder)
     {
       for (SequenceFeature sf : found)
@@ -1243,11 +1245,11 @@ public abstract class FeatureRendererModel
         if (type.equals(sf.getType()))
         {
           result.add(sf);
-          if (result.size() == found.size())
-          {
-            return new MappedFeatures(mapping, mapFrom, pos, residue,
-                    result);
-          }
+          added++;
+        }
+        if (added == toAdd)
+        {
+          break;
         }
       }
     }