JAL-3690 restore jws1 JPred

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d7a95a4..71f8c7d 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -160,6 +160,7 @@ import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.ServiceChangeListener;
 import jalview.ws.WSDiscovererI;
 import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.PreferredServiceRegistry;
 import jalview.ws.params.ArgumentI;
@@ -4421,12 +4422,31 @@ public class AlignFrame extends GAlignFrame
       {
         WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer();
         JMenu submenu = new JMenu("JABAWS");
+        buildLegacyWebServicesMenu(submenu);
         buildWebServicesMenu(jws2servs, submenu);
         webService.add(submenu);
       }
     });
   }
 
+  private void buildLegacyWebServicesMenu(JMenu menu)
+  {
+    JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
+    if (Discoverer.services != null && Discoverer.services.size() > 0) 
+    {
+      var secstrpred = Discoverer.services.get("SecStrPred");
+      if (secstrpred != null) 
+      {
+        for (ext.vamsas.ServiceHandle sh : secstrpred) 
+        {
+          var menuProvider = Discoverer.getServiceClient(sh);
+          menuProvider.attachWSMenuEntry(secstrmenu, this);
+        }
+      }
+    }
+    menu.add(secstrmenu);
+  }
+
   /**
    * Constructs the web services menu for the given discoverer under the
    * specified menu. This method must be called on the EDT
@@ -4457,206 +4477,6 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
-//  private boolean buildingMenu = false;
-
-  /**
-   * Generates menu items and listener event actions for web service clients
-   * 
-   */
-//  public void BuildWebServiceMenu()
-//  {
-//    while (buildingMenu)
-//    {
-//      try
-//      {
-//        System.err.println("Waiting for building menu to finish.");
-//        Thread.sleep(10);
-//      } catch (Exception e)
-//      {
-//      }
-//    }
-//    final AlignFrame me = this;
-//    buildingMenu = true;
-//    new Thread(new Runnable()
-//    {
-//      @Override
-//      public void run()
-//      {
-//        final List<JMenuItem> legacyItems = new ArrayList<>();
-//        try
-//        {
-//          // System.err.println("Building ws menu again "
-//          // + Thread.currentThread());
-//          // TODO: add support for context dependent disabling of services based
-//          // on
-//          // alignment and current selection
-//          // TODO: add additional serviceHandle parameter to specify abstract
-//          // handler
-//          // class independently of AbstractName
-//          // TODO: add in rediscovery GUI function to restart discoverer
-//          // TODO: group services by location as well as function and/or
-//          // introduce
-//          // object broker mechanism.
-//          final Vector<JMenu> wsmenu = new Vector<>();
-//          final IProgressIndicator af = me;
-//
-//          /*
-//           * do not i18n these strings - they are hard-coded in class
-//           * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
-//           * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
-//           */
-//          final JMenu msawsmenu = new JMenu("Alignment");
-//          final JMenu secstrmenu = new JMenu(
-//                  "Secondary Structure Prediction");
-//          final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
-//          final JMenu analymenu = new JMenu("Analysis");
-//          final JMenu dismenu = new JMenu("Protein Disorder");
-//          // 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
-//            // No MSAWS used any more:
-//            // Vector msaws = null; // (Vector)
-//            // Discoverer.services.get("MsaWS");
-//            Vector<ServiceHandle> secstrpr = Discoverer.services
-//                    .get("SecStrPred");
-//            if (secstrpr != null)
-//            {
-//              // Add any secondary structure prediction services
-//              for (int i = 0, j = secstrpr.size(); i < j; i++)
-//              {
-//                final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
-//                jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
-//                        .getServiceClient(sh);
-//                int p = secstrmenu.getItemCount();
-//                impl.attachWSMenuEntry(secstrmenu, me);
-//                int q = secstrmenu.getItemCount();
-//                for (int litm = p; litm < q; litm++)
-//                {
-//                  legacyItems.add(secstrmenu.getItem(litm));
-//                }
-//              }
-//            }
-//          }
-//
-//          // Add all submenus in the order they should appear on the web
-//          // services menu
-//          wsmenu.add(msawsmenu);
-//          wsmenu.add(secstrmenu);
-//          wsmenu.add(dismenu);
-//          wsmenu.add(analymenu);
-//          // No search services yet
-//          // wsmenu.add(seqsrchmenu);
-//
-//          javax.swing.SwingUtilities.invokeLater(new Runnable()
-//          {
-//            @Override
-//            public void run()
-//            {
-//              try
-//              {
-//                webService.removeAll();
-//                // first, add discovered services onto the webservices menu
-//                if (wsmenu.size() > 0)
-//                {
-//                  for (int i = 0, j = wsmenu.size(); i < j; i++)
-//                  {
-//                    webService.add(wsmenu.get(i));
-//                  }
-//                }
-//                else
-//                {
-//                  webService.add(me.webServiceNoServices);
-//                }
-//                // TODO: move into separate menu builder class.
-//                boolean new_sspred = false;
-//
-//                if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
-//                {
-//                  WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer();
-//                  if (jws2servs != null)
-//                  {
-//                    if (jws2servs.hasServices())
-//                    {
-//                      jws2servs.attachWSMenuEntry(webService, me);
-//                      for (ServiceWithParameters sv : jws2servs
-//                              .getServices())
-//                      {
-//                        if (sv.getName().toLowerCase().contains("jpred"))
-//                        {
-//                          for (JMenuItem jmi : legacyItems)
-//                          {
-//                            jmi.setVisible(false);
-//                          }
-//                        }
-//                      }
-//
-//                    }
-//                    if (jws2servs.isRunning())
-//                    {
-//                      JMenuItem tm = new JMenuItem(
-//                              "Still discovering JABA Services");
-//                      tm.setEnabled(false);
-//                      webService.add(tm);
-//                    }
-//                  }
-//                }
-//
-//                if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
-//                {
-//                  WSDiscovererI discoverer = SlivkaWSDiscoverer
-//                          .getInstance();
-//                  if (discoverer != null)
-//                  {
-//                    if (discoverer.hasServices())
-//                    {
-//                      discoverer.attachWSMenuEntry(webService, me);
-//                    }
-//                    if (discoverer.isRunning())
-//                    {
-//                      JMenuItem tm = new JMenuItem(
-//                              "Still discovering Slivka Services");
-//                      tm.setEnabled(false);
-//                      webService.add(tm);
-//                    }
-//                  }
-//                }
-//
-//                build_urlServiceMenu(me.webService);
-//                build_fetchdbmenu(webService);
-//                for (JMenu item : wsmenu)
-//                {
-//                  if (item.getItemCount() == 0)
-//                  {
-//                    item.setEnabled(false);
-//                  }
-//                  else
-//                  {
-//                    item.setEnabled(true);
-//                  }
-//                }
-//              } catch (Exception e)
-//              {
-//                Cache.log.debug(
-//                        "Exception during web service menu building process.",
-//                        e);
-//              }
-//            }
-//          });
-//        } catch (Exception e)
-//        {
-//        }
-//        buildingMenu = false;
-//      }
-//    }).start();
-//
-//  }
-
   /**
    * construct any groupURL type service menu entries.
    * 

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 7ab8117..65d01b4 100644 (file)
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.jws1;
 
+import jalview.bin.Cache;
 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 
@@ -379,6 +380,7 @@ public class Discoverer implements Runnable
   @Override
   public void run()
   {
+    Cache.log.info("Discovering jws1 services");
     Discoverer.doDiscovery();
     discoverServices();
   }