X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=46498adac06c2650b7768070c6723d40753281e3;hb=fbbd34a30d809bac64f708900ce8a53d2e79d866;hp=b0bb372e4d9f84356de3699a7794a70d2f68d8c3;hpb=691e7f3e04f4ddc3ae858257f063a0b01be265fc;p=jalview.git

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