removed all dasobert code and begun to replace with Jdas calls.

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9df4931..2ecd947 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -701,7 +701,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
     autoCalculate.setSelected(av.autoCalculateConsensus);
     sortByTree.setSelected(av.sortByTree);
-
+    listenToViewSelections.setSelected(av.followSelection);
+    
     setShowProductsEnabled();
 
     updateEditMenuBar();
@@ -3427,6 +3428,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.sortByTree = sortByTree.isSelected();
   }
 
+  @Override
+  protected void listenToViewSelections_actionPerformed(ActionEvent e)
+  {
+    viewport.followSelection = listenToViewSelections.isSelected();
+  }
   /**
    * DOCUMENT ME!
    * 
@@ -3969,18 +3975,19 @@ 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,