Merge branch 'releases/Release_2_10_4_Branch' into develop

[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 e4d9d88..553f813 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -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;