JAL-3187 basic first version for tooltips only (rendering yet to do)

[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 c58461e..1f69776 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -320,12 +320,12 @@ public abstract class FeatureRendererModel
             visibleTypes);
 
     /*
-     * include features unless their feature group is not displayed, or
-     * they are hidden (have no colour) based on a filter or colour threshold
+     * include features unless they are hidden (have no colour), based on 
+     * feature group visibility, or a filter or colour threshold
      */
     for (SequenceFeature sf : features)
     {
-      if (!featureGroupNotShown(sf) && getColour(sf) != null)
+      if (getColour(sf) != null)
       {
         result.add(sf);
       }
@@ -1032,16 +1032,24 @@ public abstract class FeatureRendererModel
    * Removes from the list of features any that duplicate the location of a
    * feature of the same type. Should be used only for features of the same,
    * simple, feature colour (which normally implies the same feature type). Does
-   * not check visibility settings for feature type or feature group.
+   * not check visibility settings for feature type or feature group. No
+   * filtering is done if transparency, or any feature filters, are in force.
    * 
    * @param features
    */
   public void filterFeaturesForDisplay(List<SequenceFeature> features)
   {
-    if (features.isEmpty())
+    /*
+     * 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)
+     */
+    if (features.isEmpty() || transparency != 1f
+            || !featureFilters.isEmpty())
     {
       return;
     }
+
     SequenceFeatures.sortFeatures(features, true);
     SequenceFeature lastFeature = null;
 
@@ -1070,7 +1078,7 @@ public abstract class FeatureRendererModel
   @Override
   public Map<String, FeatureMatcherSetI> getFeatureFilters()
   {
-    return new HashMap<>(featureFilters);
+    return featureFilters;
   }
 
   @Override
@@ -1100,8 +1108,8 @@ public abstract class FeatureRendererModel
 
   /**
    * Answers the colour for the feature, or null if the feature is excluded by
-   * feature type or group visibility, by filters, or by colour threshold
-   * settings
+   * feature group visibility, by filters, or by colour threshold settings. This
+   * method does not take feature visibility into account.
    * 
    * @param sf
    * @param fc
@@ -1110,14 +1118,6 @@ public abstract class FeatureRendererModel
   public Color getColor(SequenceFeature sf, FeatureColourI fc)
   {
     /*
-     * is the feature type displayed?
-     */
-    if (!showFeatureOfType(sf.getType()))
-    {
-      return null;
-    }
-
-    /*
      * is the feature group displayed?
      */
     if (featureGroupNotShown(sf))