JAL-2483 corrected finding feature groups

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index b0bb372..46498ad 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -386,11 +386,13 @@ public class FeatureSettings extends Panel implements ItemListener,
       Set<String> visibleGroups = new HashSet<String>();
       for (String group : groups)
       {
-        if (group == null || fr.checkGroupVisibility(group, true))
+        // if (group == null || fr.checkGroupVisibility(group, true))
+        if (group == null || checkGroupState(group))
         {
           visibleGroups.add(group);
         }
       }
+      foundGroups.addAll(groups);
 
       /*
        * get distinct feature types for visible groups