From fbbd34a30d809bac64f708900ce8a53d2e79d866 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 30 Jun 2017 16:16:13 +0100
Subject: [PATCH] JAL-2483 corrected finding feature groups

---
 src/jalview/appletgui/FeatureSettings.java |    4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index b0bb372..46498ad 100755
--- 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
-- 
1.7.10.2