X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2ecd947aca0c1aa12630497f580dd7ef27139944;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=ba112b85781dbd6ac2791d92bb9869226131f36f;hpb=f149a335b5467a4802eded5da0ca2fc732d7caf7;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ba112b8..2ecd947 100755
--- 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.
  * 
@@ -699,7 +699,10 @@ 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);
+    listenToViewSelections.setSelected(av.followSelection);
+    
     setShowProductsEnabled();
 
     updateEditMenuBar();
@@ -3420,7 +3423,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .getAlignment().getSequences());
     }
   }
+  public void sortByTreeOption_actionPerformed(ActionEvent e)
+  {
+    viewport.sortByTree = sortByTree.isSelected();
+  }
 
+  @Override
+  protected void listenToViewSelections_actionPerformed(ActionEvent e)
+  {
+    viewport.followSelection = listenToViewSelections.isSelected();
+  }
   /**
    * DOCUMENT ME!
    * 
@@ -3703,21 +3715,16 @@ 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));
+          
         }
       });
 
@@ -3967,19 +3974,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           final JMenu seqsrchmenu = new JMenu(
                   "Sequence Database Search");
           final JMenu analymenu = new JMenu(
-                  "Analyse Alignment");
-          
-          if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
-                  && Discoverer.services != null
+                  "Analysis");
+          // 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,
@@ -4031,23 +4039,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               if (jws2servs.hasServices())
               {
-                JMenu jws2men = new JMenu("Jaba Web Services");
                 jws2servs.attachWSMenuEntry(msawsmenu, me);
-//                for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
-//                {
-//                  msawsmenu.add(jws2men.getMenuComponent(i));
-//                }
               }
             }
           }
-          if (msawsmenu.getMenuComponentCount()>0)
-            wsmenu.add(msawsmenu);
-          if (secstrmenu.getMenuComponentCount()>0)
-            wsmenu.add(secstrmenu);
-          if (analymenu.getMenuComponentCount()>0)
-            wsmenu.add(analymenu);
-          if (seqsrchmenu.getMenuComponentCount()>0)
-            wsmenu.add(seqsrchmenu);
+          // Add all submenus in the order they should appear on the web services menu
+          wsmenu.add(msawsmenu);
+          wsmenu.add(secstrmenu);
+          wsmenu.add(analymenu);
+          // No search services yet
+          // wsmenu.add(seqsrchmenu);
 
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
@@ -4055,9 +4056,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               try
               {
-
-                resetWebServiceMenu();
-                // finally, add the whole shebang onto the webservices menu
+                webService.removeAll();
+                // first, add discovered services onto the webservices menu
                 if (wsmenu.size() > 0)
                 {
                   for (int i = 0, j = wsmenu.size(); i < j; i++)
@@ -4067,8 +4067,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
                 else
                 {
-                  me.webService.add(me.webServiceNoServices);
+                  webService.add(me.webServiceNoServices);
                 }
+                build_urlServiceMenu(me.webService);
+                build_fetchdbmenu(webService);
               } catch (Exception e)
               {
               }
@@ -4086,17 +4088,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
-  /**
-   * empty the web service menu and add any ad-hoc functions not dynamically
-   * discovered.
-   * 
-   */
-  private void resetWebServiceMenu()
-  {
-    webService.removeAll();
-    build_fetchdbmenu(webService);
-    build_urlServiceMenu(webService);
-  }
 
   /**
    * construct any groupURL type service menu entries.
@@ -4105,11 +4096,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   private void build_urlServiceMenu(JMenu webService)
   {
-    if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
-    {
-      jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
-              webService, this);
-    }
     // TODO: remove this code when 2.7 is released
     // DEBUG - alignmentView
     /*
@@ -4125,11 +4111,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // TODO: refactor to RestClient discoverer and merge menu entries for
     // rest-style services with other types of analysis/calculation service
     // SHmmr test client - still being implemented.
+    // DEBUG - alignmentView
     
     for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
       client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
     }
-    // DEBUG - alignmentView
+
+    if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+    {
+      jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
+              webService, this);
+    }
   }
 
   /*