JAL-2816 exclude filtered / thresholded out features when finding

[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 28fceec..6afec67 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -297,9 +297,13 @@ public abstract class FeatureRendererModel
     List<SequenceFeature> features = sequence.findFeatures(column, column,
             visibleTypes);
 
+    /*
+     * include features unless their feature group is not displayed, or
+     * they are hidden (have no colour) based on a filter or colour threshold
+     */
     for (SequenceFeature sf : features)
     {
-      if (!featureGroupNotShown(sf))
+      if (!featureGroupNotShown(sf) && getColour(sf) != null)
       {
         result.add(sf);
       }
@@ -993,7 +997,7 @@ public abstract class FeatureRendererModel
   
     for (SequenceFeature sf : features)
     {
-      if (!featureGroupNotShown(sf))
+      if (!featureGroupNotShown(sf) && getColour(sf) != null)
       {
         result.add(sf);
       }