new features or newly shown group features are placed at top of feature stack

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index f2e44f5..6670d2f 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -318,7 +318,16 @@ public class FeatureSettings
       check.addMouseMotionListener(this);
       check.setBackground(fr.getColour(type));
       check.addItemListener(this);
-      featurePanel.add(check);
+      if (groupsChanged)
+      {
+        // add at beginning of stack.
+        featurePanel.add(check, 0);
+      }
+      else
+      {
+        // add at end of stack.
+        featurePanel.add(check);
+      }
     }
   }