JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalvi...

[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 9e707f3..3608626 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -20,6 +20,21 @@
  */
 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.Comparator;
+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;
@@ -37,21 +52,7 @@ import jalview.datamodel.features.SequenceFeatures;
 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.Comparator;
-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.util.Platform;
 
 public abstract class FeatureRendererModel
         implements jalview.api.FeatureRenderer
@@ -1046,6 +1047,14 @@ public abstract class FeatureRendererModel
   public void filterFeaturesForDisplay(List<SequenceFeature> features)
   {
     /*
+     * fudge: JalviewJS's IntervalStore lacks the sort method called :-(
+     */
+    if (Platform.isJS())
+    {
+      return;
+    }
+
+    /*
      * don't remove 'redundant' features if 
      * - transparency is applied (feature count affects depth of feature colour)
      * - filters are applied (not all features may be displayable)
@@ -1121,7 +1130,7 @@ public abstract class FeatureRendererModel
   /**
    * Answers the colour for the feature, or null if the feature is excluded by
    * feature group visibility, by filters, or by colour threshold settings. This
-   * method does not take feature visibility into account.
+   * method does not take feature type visibility into account.
    * 
    * @param sf
    * @param fc
@@ -1190,8 +1199,8 @@ public abstract class FeatureRendererModel
   }
 
   @Override
-  public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
-          int pos)
+  public MappedFeatures findComplementFeaturesAtResidue(
+          final SequenceI sequence, final int pos)
   {
     SequenceI ds = sequence.getDatasetSequence();
     if (ds == null)
@@ -1260,9 +1269,12 @@ 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)
@@ -1270,11 +1282,11 @@ 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;
         }
       }
     }