temp push

[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 f9c9782..5ca3ac5 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;
@@ -37,20 +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.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
@@ -326,12 +328,14 @@ public abstract class FeatureRendererModel
             visibleTypes);
 
     /*
-     * include features unless they are hidden (have no colour), based on 
-     * feature group visibility, or a filter or colour threshold
+     * include features unless their feature group is not displayed, or
+     * they are hidden (have no colour) based on a filter or colour threshold
      */
+    
+    // BH! check -- !featureGroupNotShown(sf) is from applet branch. 
     for (SequenceFeature sf : features)
     {
-      if (getColour(sf) != null)
+      if (!featureGroupNotShown(sf) && getColour(sf) != null)
       {
         result.add(sf);
       }
@@ -618,7 +622,7 @@ public abstract class FeatureRendererModel
    * @param type
    * @return
    */
-  protected boolean showFeatureOfType(String type)
+  public boolean showFeatureOfType(String type)
   {
     return type == null ? false : (av.getFeaturesDisplayed() == null ? true
             : av.getFeaturesDisplayed().isVisible(type));
@@ -1044,6 +1048,16 @@ public abstract class FeatureRendererModel
    */
   public void filterFeaturesForDisplay(List<SequenceFeature> features)
   {
+// BH! check -- what was the problem here? How is JalviewJS's IntervalStore different from 
+    // other IntervalStore?
+    /*
+     * 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)
@@ -1161,6 +1175,33 @@ public abstract class FeatureRendererModel
     return filter == null ? true : filter.matches(sf);
   }
 
+  /**
+   * Answers true unless the specified group is set to hidden. Defaults to true
+   * if group visibility is not set.
+   * 
+   * @param group
+   * @return
+   */
+  public boolean isGroupVisible(String group)
+  {
+    if (!featureGroups.containsKey(group))
+    {
+      return true;
+    }
+    return featureGroups.get(group);
+  }
+
+  /**
+   * Orders features in render precedence (last in order is last to render, so
+   * displayed on top of other features)
+   * 
+   * @param order
+   */
+  public void orderFeatures(Comparator<String> order)
+  {
+    Arrays.sort(renderOrder, order);
+  }
+
   @Override
   public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
           int pos)
@@ -1177,6 +1218,16 @@ 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
      */
@@ -1198,7 +1249,7 @@ 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))
@@ -1271,5 +1322,4 @@ public abstract class FeatureRendererModel
     }
     return true;
   }
-
 }