JAL-940 - removed legacy service options from preferences and noted deprecation in...

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b9ba4e0..30026ef 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -699,6 +699,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     applyToAllGroups.setState(av.colourAppliesToAllGroups);
     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
+    autoCalculate.setSelected(av.autoCalculateConsensus);
+    sortByTree.setSelected(av.sortByTree);
 
     setShowProductsEnabled();
 
@@ -3420,6 +3422,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .getAlignment().getSequences());
     }
   }
+  public void sortByTreeOption_actionPerformed(ActionEvent e)
+  {
+    viewport.sortByTree = sortByTree.isSelected();
+  }
 
   /**
    * DOCUMENT ME!
@@ -3703,21 +3709,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     for (i = 0; i < treePanels.size(); i++)
     {
-      TreePanel tp = (TreePanel) treePanels.elementAt(i);
+      final TreePanel tp = (TreePanel) treePanels.elementAt(i);
       final JMenuItem item = new JMenuItem(tp.getTitle());
       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
       item.addActionListener(new java.awt.event.ActionListener()
       {
         public void actionPerformed(ActionEvent e)
         {
-          SequenceI[] oldOrder = viewport.getAlignment()
-                  .getSequencesArray();
-          AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
-
-          addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
-                  viewport.alignment));
-
-          alignPanel.paintAlignment(true);
+          tp.sortByTree_actionPerformed(null);
+          addHistoryItem(tp.sortAlignmentIn(alignPanel));
+          
         }
       });
 
@@ -3968,18 +3969,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   "Sequence Database Search");
           final JMenu analymenu = new JMenu(
                   "Analysis");
-          
-          if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
-                  && Discoverer.services != null
+          // JAL-940 - only show secondary structure prediction services from the legacy server
+          if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
+                  // && 
+                  Discoverer.services != null
                   && (Discoverer.services.size() > 0))
           {
             // TODO: refactor to allow list of AbstractName/Handler bindings to
             // be
             // stored or retrieved from elsewhere
-            Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+            Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
             Vector secstrpr = (Vector) Discoverer.services
                     .get("SecStrPred");
-            Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
+            Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch");
             // TODO: move GUI generation code onto service implementation - so a
             // client instance attaches itself to the GUI with method call like
             // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,