From 2d6be9a94eb65474a7272d3766881521ed35a760 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 21 Oct 2011 12:54:18 +0100
Subject: [PATCH] (JAL-962) rejig parameter processing order so groups are
 hidden/shown before features are loaded on to alignment.

---
 src/jalview/bin/JalviewLite.java |   37 +++++++++++++++++++++----------------
 1 file changed, 21 insertions(+), 16 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 52e7408..562bc92 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1840,7 +1840,27 @@ public class JalviewLite extends Applet implements
           }
         }
 
-        String param = applet.getParameter("features");
+        // ///////////////////////////
+        // modify display of features
+        // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed
+        //
+        // hide specific groups
+        // 
+        String param = applet.getParameter("hidefeaturegroups");
+        if (param != null)
+        {
+          newAlignFrame.setFeatureGroupState(separatorListToArray(param), false);        
+//          applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+        }
+        // show specific groups
+        param = applet.getParameter("showfeaturegroups");
+        if (param != null)
+        {
+          newAlignFrame.setFeatureGroupState(separatorListToArray(param), true);        
+//          applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+        }
+        // and now load features
+        param = applet.getParameter("features");
         if (param != null)
         {
           param = setProtocolState(param);
@@ -2059,21 +2079,6 @@ public class JalviewLite extends Applet implements
                   protocols);
 
         }
-        // ///////////////////////////
-        // modify display of features
-        //
-        // hide specific groups
-        param = applet.getParameter("hidefeaturegroups");
-        if (param != null)
-        {
-          applet.setFeatureGroupStateOn(newAlignFrame, param, false);
-        }
-        // show specific groups
-        param = applet.getParameter("showfeaturegroups");
-        if (param != null)
-        {
-          applet.setFeatureGroupStateOn(newAlignFrame, param, true);
-        }
       }
       else
       {
-- 
1.7.10.2