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 68345b9..5ca3ac5 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -328,12 +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);
       }
@@ -1046,6 +1048,8 @@ 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 :-(
      */
@@ -1130,7 +1134,7 @@ 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 type visibility into account.
+   * method does not take feature visibility into account.
    * 
    * @param sf
    * @param fc