X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=49f31952553309e7e7676278dee62ca9f4097283;hb=95e91262358d5232185ad1140505f289a270a8cd;hp=60fa85b3fc7817595bb2db9487ac0eb27cd83a7b;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 60fa85b..49f3195 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,6 +26,7 @@ import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ParamDatastoreI;
 
@@ -67,7 +68,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   /*
    * the .jalview_properties entry for JWS2 URLS
    */
-  final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+  private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
 
   /*
    * Singleton instance
@@ -85,12 +86,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
           this);
 
-  Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
-          validServiceUrls = null;
+  private Vector<String> invalidServiceUrls = null;
 
-  boolean running = false, aborted = false;
+  private Vector<String> urlsWithoutServices = null;
 
-  Thread oldthread = null;
+  private Vector<String> validServiceUrls = null;
+
+  private volatile boolean running = false;
+
+  private volatile boolean aborted = false;
+
+  private Thread oldthread = null;
 
   /**
    * holds list of services.
@@ -143,9 +149,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   public void setAborted(boolean aborted)
   {
     this.aborted = aborted;
-
   }
 
+  @Override
   public void run()
   {
 
@@ -159,36 +165,38 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       {
         try
         {
-          Cache.log
-                  .debug("Waiting around for old discovery thread to finish.");
+          Cache.log.debug(
+                  "Waiting around for old discovery thread to finish.");
           // wait around until old discoverer dies
           Thread.sleep(100);
         } catch (Exception e)
         {
         }
       }
+      aborted = false;
       Cache.log.debug("Old discovery thread has finished.");
     }
     running = true;
 
     // first set up exclusion list if needed
-    final Set<String> ignoredServices = new HashSet<String>();
-    for (String ignored : Cache.getDefault("IGNORED_JABAWS_SERVICETYPES",
-            "").split("\\|"))
+    final Set<String> ignoredServices = new HashSet<>();
+    for (String ignored : Cache
+            .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
     {
       ignoredServices.add(ignored);
     }
 
-    changeSupport.firePropertyChange("services", services, new Vector());
+    changeSupport.firePropertyChange("services", services,
+            new Vector<Jws2Instance>());
     oldthread = Thread.currentThread();
     try
     {
-      Class foo = getClass().getClassLoader().loadClass(
-              "compbio.ws.client.Jws2Client");
+      Class foo = getClass().getClassLoader()
+              .loadClass("compbio.ws.client.Jws2Client");
     } catch (ClassNotFoundException e)
     {
-      System.err
-              .println("Not enabling JABA Webservices : client jar is not available."
+      System.err.println(
+              "Not enabling JABA Webservices : client jar is not available."
                       + "\nPlease check that your webstart JNLP file is up to date!");
       running = false;
       return;
@@ -210,9 +218,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       validServiceUrls.removeAllElements();
     }
-    ArrayList<String> svctypes = new ArrayList<String>();
+    ArrayList<String> svctypes = new ArrayList<>();
 
-    List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+    List<JabaWsServerQuery> qrys = new ArrayList<>();
     for (final String jwsserver : getServiceUrls())
     {
       JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
@@ -252,8 +260,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
       if (aborted)
       {
-        Cache.log.debug("Aborting " + qrys.size()
-                + " JABAWS discovery threads.");
+        Cache.log.debug(
+                "Aborting " + qrys.size() + " JABAWS discovery threads.");
         for (JabaWsServerQuery squery : qrys)
         {
           squery.setQuit(true);
@@ -263,7 +271,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     if (!aborted)
     {
       // resort services according to order found in jabaws service list
-      // also ensure servics for each host are ordered in same way.
+      // also ensure services for each host are ordered in same way.
 
       if (services != null && services.size() > 0)
       {
@@ -274,14 +282,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         for (Jws2Instance svc : services)
         {
           svcs[ipos] = svc;
-          spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1
-                  + svctypes.indexOf(svc.serviceType);
+          spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHostURL()) + 1
+                  + svctypes.indexOf(svc.getName());
         }
         jalview.util.QuickSort.sort(spos, svcs);
-        services = new Vector<Jws2Instance>();
+        services = new Vector<>();
         for (Jws2Instance svc : svcs)
         {
-          if (!ignoredServices.contains(svc.serviceType))
+          if (!ignoredServices.contains(svc.getName()))
           {
             services.add(svc);
           }
@@ -290,7 +298,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
     oldthread = null;
     running = false;
-    changeSupport.firePropertyChange("services", new Vector(), services);
+    changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(),
+            services);
   }
 
   /**
@@ -304,10 +313,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (services == null)
     {
-      services = new Vector<Jws2Instance>();
+      services = new Vector<>();
     }
-    System.out.println("Discovered service: " + jwsservers + " "
-            + service.toString());
+    System.out.println(
+            "Discovered service: " + jwsservers + " " + service.toString());
     // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
     // service2);
 
@@ -321,7 +330,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     service.hasParameters();
     if (validServiceUrls == null)
     {
-      validServiceUrls = new Vector();
+      validServiceUrls = new Vector<>();
     }
     validServiceUrls.add(jwsservers);
   }
@@ -330,6 +339,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    * attach all available web services to the appropriate submenu in the given
    * JMenu
    */
+  @Override
   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
     // dynamically regenerate service list.
@@ -348,20 +358,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       return;
     }
-    boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
-            .getDefault("WSMENU_BYTYPE", false);
+
     /**
      * eventually, JWS2 services will appear under the same align/etc submenus.
      * for moment we keep them separate.
      */
     JMenu atpoint;
-    List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+    List<ServiceWithParameters> enumerableServices = new ArrayList<>();
     // jws2al.removeAll();
-    Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
-    Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
-    for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
+    Map<String, ServiceWithParameters> preferredHosts = new HashMap<>();
+    Map<String, List<ServiceWithParameters>> alternates = new HashMap<>();
+    for (ServiceWithParameters service : getServices())
     {
-      if (!isRecalculable(service.action))
+      // TODO: check this behaves with refactored serviceType to getName
+      if (!isRecalculable(service.getName()))
       {
         // add 'one shot' services to be displayed using the classic menu
         // structure
@@ -369,28 +379,28 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
       else
       {
-        if (!preferredHosts.containsKey(service.serviceType))
+        if (!preferredHosts.containsKey(service.getName()))
         {
-          Jws2Instance preferredInstance = getPreferredServiceFor(
-                  alignFrame, service.serviceType);
+          ServiceWithParameters preferredInstance = getPreferredServiceFor(
+                  alignFrame, service.getName());
           if (preferredInstance != null)
           {
-            preferredHosts.put(service.serviceType, preferredInstance);
+            preferredHosts.put(service.getName(), preferredInstance);
           }
           else
           {
-            preferredHosts.put(service.serviceType, service);
+            preferredHosts.put(service.getName(), service);
           }
         }
-        List<Jws2Instance> ph = alternates.get(service.serviceType);
-        if (preferredHosts.get(service.serviceType) != service)
+        List<ServiceWithParameters> ph = alternates.get(service.getName());
+        if (preferredHosts.get(service.getName()) != service)
         {
           if (ph == null)
           {
-            ph = new ArrayList<Jws2Instance>();
+            ph = new ArrayList<>();
           }
           ph.add(service);
-          alternates.put(service.serviceType, ph);
+          alternates.put(service.getName(), ph);
         }
       }
 
@@ -399,16 +409,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     // create GUI element for classic services
     addEnumeratedServices(jws2al, alignFrame, enumerableServices);
     // and the instantaneous services
-    for (final Jws2Instance service : preferredHosts.values())
+    for (final ServiceWithParameters service : preferredHosts.values())
     {
-      atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
+      atpoint = JvSwingUtils.findOrCreateMenu(jws2al,
+              service.getServiceType());
       JMenuItem hitm;
       if (atpoint.getItemCount() > 1)
       {
         // previous service of this type already present
         atpoint.addSeparator();
       }
-      atpoint.add(hitm = new JMenuItem(service.getHost()));
+      atpoint.add(hitm = new JMenuItem(service.getHostURL()));
       hitm.setForeground(Color.blue);
       hitm.addActionListener(new ActionListener()
       {
@@ -416,23 +427,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          Desktop.showUrl(service.getHost());
+          Desktop.showUrl(service.getHostURL());
         }
       });
       hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
               MessageManager.getString("label.open_jabaws_web_page")));
 
       service.attachWSMenuEntry(atpoint, alignFrame);
-      if (alternates.containsKey(service.serviceType))
+      if (alternates.containsKey(service.getName()))
       {
-        atpoint.add(hitm = new JMenu(MessageManager
-                .getString("label.switch_server")));
+        atpoint.add(hitm = new JMenu(
+                MessageManager.getString("label.switch_server")));
         hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
                 MessageManager.getString("label.choose_jabaws_server")));
-        for (final Jws2Instance sv : alternates.get(service.serviceType))
+        for (final ServiceWithParameters sv : alternates.get(service.getName()))
         {
           JMenuItem itm;
-          hitm.add(itm = new JMenuItem(sv.getHost()));
+          hitm.add(itm = new JMenuItem(sv.getHostURL()));
           itm.setForeground(Color.blue);
           itm.addActionListener(new ActionListener()
           {
@@ -442,27 +453,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
             {
               new Thread(new Runnable()
               {
+                @Override
                 public void run()
                 {
-                  setPreferredServiceFor(alignFrame, sv.serviceType,
-                          sv.action, sv);
+                  setPreferredServiceFor(alignFrame, sv.getName(),
+                          sv.getServiceType(), sv);
                   changeSupport.firePropertyChange("services",
-                          new Vector(), services);
+                          new Vector<Jws2Instance>(), services);
                 };
               }).start();
 
             }
           });
         }
-        /*
-         * hitm.addActionListener(new ActionListener() {
-         * 
-         * @Override public void actionPerformed(ActionEvent arg0) { new
-         * Thread(new Runnable() {
-         * 
-         * @Override public void run() { new SetPreferredServer(alignFrame,
-         * service.serviceType, service.action); } }).start(); } });
-         */
       }
     }
   }
@@ -472,53 +475,57 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    * submenus to index by host and service program type
    */
   private void addEnumeratedServices(final JMenu jws2al,
-          final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
+          final AlignFrame alignFrame,
+          List<ServiceWithParameters> enumerableServices)
   {
-    boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
-            .getDefault("WSMENU_BYTYPE", false);
+    boolean byhost = Cache.getDefault("WSMENU_BYHOST", false),
+            bytype = Cache.getDefault("WSMENU_BYTYPE", false);
     /**
      * eventually, JWS2 services will appear under the same align/etc submenus.
      * for moment we keep them separate.
      */
     JMenu atpoint;
-    MsaWSClient msacl = new MsaWSClient();
-    List<String> hostLabels = new ArrayList<String>();
-    Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
-    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
-    ArrayList<String> hostlist = new ArrayList<String>();
-    for (Jws2Instance service : enumerableServices)
+
+    List<String> hostLabels = new ArrayList<>();
+    Hashtable<String, String> lasthostFor = new Hashtable<>();
+    Hashtable<String, ArrayList<ServiceWithParameters>> hosts = new Hashtable<>();
+    ArrayList<String> hostlist = new ArrayList<>();
+    for (ServiceWithParameters service : enumerableServices)
     {
-      ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
+      ArrayList<ServiceWithParameters> hostservices = hosts
+              .get(service.getHostURL());
       if (hostservices == null)
       {
-        hosts.put(service.getHost(),
-                hostservices = new ArrayList<Jws2Instance>());
-        hostlist.add(service.getHost());
+        hosts.put(service.getHostURL(),
+                hostservices = new ArrayList<>());
+        hostlist.add(service.getHostURL());
       }
       hostservices.add(service);
     }
     // now add hosts in order of the given array
     for (String host : hostlist)
     {
-      Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
-              new Jws2Instance[1]);
+      Jws2Instance orderedsvcs[] = hosts.get(host)
+              .toArray(new Jws2Instance[1]);
       String sortbytype[] = new String[orderedsvcs.length];
       for (int i = 0; i < sortbytype.length; i++)
       {
-        sortbytype[i] = orderedsvcs[i].serviceType;
+        sortbytype[i] = orderedsvcs[i].getName();
       }
       jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
       for (final Jws2Instance service : orderedsvcs)
       {
-        atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
-        String type = service.serviceType;
+        atpoint = JvSwingUtils.findOrCreateMenu(jws2al,
+                service.getAction());
+        String type = service.getName();
         if (byhost)
         {
           atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
           if (atpoint.getToolTipText() == null)
           {
-            atpoint.setToolTipText(MessageManager.formatMessage(
-                    "label.services_at", new String[] { host }));
+            atpoint.setToolTipText(MessageManager
+                    .formatMessage("label.services_at", new String[]
+                    { host }));
           }
         }
         if (bytype)
@@ -529,9 +536,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
             atpoint.setToolTipText(service.getActionText());
           }
         }
-        if (!byhost
-                && !hostLabels.contains(host + service.serviceType
-                        + service.getActionText()))
+        if (!byhost && !hostLabels.contains(
+                host + service.getName() + service.getActionText()))
         // !hostLabels.contains(host + (bytype ?
         // service.serviceType+service.getActionText() : "")))
         {
@@ -548,8 +554,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           {
             hostLabels.add(host);
           }
-          if (lasthostFor.get(service.action) == null
-                  || !lasthostFor.get(service.action).equals(host))
+          if (lasthostFor.get(service.getAction()) == null
+                  || !lasthostFor.get(service.getAction()).equals(host))
           {
             atpoint.add(hitm = new JMenuItem(host));
             hitm.setForeground(Color.blue);
@@ -559,15 +565,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
               @Override
               public void actionPerformed(ActionEvent e)
               {
-                Desktop.showUrl(service.getHost());
+                Desktop.showUrl(service.getHostURL());
               }
             });
-            hitm.setToolTipText(JvSwingUtils.wrapTooltip(true,
-                    MessageManager.getString("label.open_jabaws_web_page")));
-            lasthostFor.put(service.action, host);
+            hitm.setToolTipText(
+                    JvSwingUtils.wrapTooltip(true, MessageManager
+                            .getString("label.open_jabaws_web_page")));
+            lasthostFor.put(service.getAction(), host);
           }
-          hostLabels.add(host + service.serviceType
-                  + service.getActionText());
+          hostLabels.add(
+                  host + service.getName() + service.getActionText());
         }
 
         service.attachWSMenuEntry(atpoint, alignFrame);
@@ -575,21 +582,136 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
+  /**
+   * pick the user's preferred service based on a set of URLs (jaba server
+   * locations) and service URIs (specifying version and service interface
+   * class)
+   * 
+   * @param serviceURL
+   * @return null or best match for given uri/ls.
+   */
+  public ServiceWithParameters getPreferredServiceFor(String[] serviceURLs)
+  {
+    HashSet<String> urls = new HashSet<>();
+    urls.addAll(Arrays.asList(serviceURLs));
+    ServiceWithParameters match = null;
+    List<ServiceWithParameters> ourServices = getServices();
+
+    if (ourServices != null)
+    {
+      for (ServiceWithParameters svc : ourServices)
+      {
+        // TODO getNameURI Should return a versioned URI for the service, but
+        // doesn't as of 2.11
+        if (urls.contains(svc.getNameURI()))
+        {
+          if (match == null)
+          {
+            // for moment we always pick service from server ordered first in
+            // user's preferences
+            match = svc;
+          }
+          if (urls.contains(svc.getUri()))
+          {
+            // stop and return - we've matched type URI and URI for service
+            // endpoint
+            return svc;
+          }
+        }
+      }
+    }
+    return match;
+  }
+
+  Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();
+
+  /**
+   * get current preferred endpoint of the given Jabaws service, or global
+   * default
+   * 
+   * @param af
+   *          null or a specific alignFrame
+   * @param serviceName
+   *          Jws2Instance.getName() for service
+   * @return null if no service of this type is available, the preferred service
+   *         for the serviceType and af if specified and if defined.
+   */
+  public ServiceWithParameters getPreferredServiceFor(AlignFrame af,
+          String serviceName)
+  {
+    String serviceurl = null;
+    synchronized (preferredServiceMap)
+    {
+      String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+      Map<String, String> prefmap = preferredServiceMap.get(afid);
+      if (afid.length() > 0 && prefmap == null)
+      {
+        // recover global setting, if any
+        prefmap = preferredServiceMap.get("");
+      }
+      if (prefmap != null)
+      {
+        serviceurl = prefmap.get(serviceName);
+      }
+
+    }
+    ServiceWithParameters response = null;
+    for (ServiceWithParameters svc : getServices())
+    {
+      if (svc.getName().equals(serviceName))
+      {
+        if (serviceurl == null || serviceurl.equals(svc.getHostURL()))
+        {
+          response = svc;
+          break;
+        }
+      }
+    }
+    return response;
+  }
+
+  public void setPreferredServiceFor(AlignFrame af, String serviceName,
+          String serviceAction, ServiceWithParameters selectedServer)
+  {
+    // TODO: pull out and generalise for the selectedServer's attributes
+    String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+    if (preferredServiceMap == null)
+    {
+      preferredServiceMap = new HashMap<>();
+    }
+    Map<String, String> prefmap = preferredServiceMap.get(afid);
+    if (prefmap == null)
+    {
+      prefmap = new HashMap<>();
+      preferredServiceMap.put(afid, prefmap);
+    }
+    prefmap.put(serviceName, selectedServer.getHostURL());
+    prefmap.put(serviceAction, selectedServer.getHostURL());
+  }
+
+  public void setPreferredServiceFor(String serviceType,
+          String serviceAction, ServiceWithParameters selectedServer)
+  {
+    setPreferredServiceFor(null, serviceType, serviceAction,
+            selectedServer);
+  }
+
   public static void main(String[] args)
   {
     if (args.length > 0)
     {
-      testUrls = new ArrayList<String>();
+      testUrls = new ArrayList<>();
       for (String url : args)
       {
         testUrls.add(url);
       }
       ;
     }
-    Thread runner = getDiscoverer().startDiscoverer(
-            new PropertyChangeListener()
+    Thread runner = getDiscoverer()
+            .startDiscoverer(new PropertyChangeListener()
             {
 
+              @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
                 if (getDiscoverer().services != null)
@@ -597,12 +719,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                   System.out.println("Changesupport: There are now "
                           + getDiscoverer().services.size() + " services");
                   int i = 1;
-                  for (Jws2Instance instance : getDiscoverer().services)
+                  for (ServiceWithParameters instance : getDiscoverer().services)
                   {
                     System.out.println("Service " + i++ + " "
                             + instance.getClass() + "@"
-                            + instance.getHost() + ": "
-                            + instance.getActionText());
+                            + instance.getHostURL()
+                            + ": " + instance.getActionText());
                   }
 
                 }
@@ -683,7 +805,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       // return test urls, if there are any, instead of touching cache
       return testUrls;
     }
-    List<String> urls = new ArrayList<String>();
+    List<String> urls = new ArrayList<>();
 
     if (this.preferredUrl != null)
     {
@@ -714,10 +836,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         {
           Cache.log.warn("Problem whilst trying to make a URL from '"
                   + ((url != null) ? url : "<null>") + "'");
-          Cache.log
-                  .warn("This was probably due to a malformed comma separated list"
-                          + " in the "
-                          + JWS2HOSTURLS
+          Cache.log.warn(
+                  "This was probably due to a malformed comma separated list"
+                          + " in the " + JWS2HOSTURLS
                           + " entry of $(HOME)/.jalview_properties)");
           Cache.log.debug("Exception was ", ex);
         }
@@ -730,10 +851,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return urls;
   }
 
-  public Vector<Jws2Instance> getServices()
+  public Vector<ServiceWithParameters> getServices()
   {
-    return (services == null) ? new Vector<Jws2Instance>()
-            : new Vector<Jws2Instance>(services);
+    return (services == null) ? new Vector<>()
+            : new Vector<>(services);
   }
 
   /**
@@ -747,7 +868,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     try
     {
       compbio.ws.client.WSTester
-              .main(new String[] { "-h=" + foo.toString() });
+              .main(new String[]
+              { "-h=" + foo.toString() });
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -765,6 +887,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return true;
   }
 
+  public boolean restart()
+  {
+    synchronized (this)
+    {
+      if (running)
+      {
+        aborted = true;
+      }
+      else
+      {
+        running = true;
+      }
+      return aborted;
+    }
+  }
+
   /**
    * Start a fresh discovery thread and notify the given object when we're
    * finished. Any known existing threads will be killed before this one is
@@ -775,6 +913,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public Thread startDiscoverer(PropertyChangeListener changeSupport2)
   {
+    /*    if (restart())
+        {
+          return;
+        }
+        else
+        {
+          Thread thr = new Thread(this);
+          thr.start();
+        }
+       */
     if (isRunning())
     {
       setAborted(true);
@@ -811,11 +959,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (urlsWithoutServices == null)
     {
-      urlsWithoutServices = new Vector<String>();
+      urlsWithoutServices = new Vector<>();
     }
 
-    if ((invalidServiceUrls == null || !invalidServiceUrls
-            .contains(jwsservers))
+    if ((invalidServiceUrls == null
+            || !invalidServiceUrls.contains(jwsservers))
             && !urlsWithoutServices.contains(jwsservers))
     {
       urlsWithoutServices.add(jwsservers);
@@ -831,7 +979,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (invalidServiceUrls == null)
     {
-      invalidServiceUrls = new Vector<String>();
+      invalidServiceUrls = new Vector<>();
     }
     if (!invalidServiceUrls.contains(jwsservers))
     {
@@ -870,7 +1018,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       if (getUrlsWithoutServices() != null
               && getUrlsWithoutServices().size() > 0)
       {
-        ermsg.append(MessageManager.getString("warn.urls_no_jaba") + ": \n");
+        ermsg.append(
+                MessageManager.getString("warn.urls_no_jaba") + ": \n");
         for (String svcurl : getUrlsWithoutServices())
         {
           if (list)
@@ -909,113 +1058,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   }
 
   /**
-   * pick the user's preferred service based on a set of URLs (jaba server
-   * locations) and service URIs (specifying version and service interface
-   * class)
-   * 
-   * @param serviceURL
-   * @return null or best match for given uri/ls.
-   */
-  public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
-  {
-    HashSet<String> urls = new HashSet<String>();
-    urls.addAll(Arrays.asList(serviceURLs));
-    Jws2Instance match = null;
-    if (services != null)
-    {
-      for (Jws2Instance svc : services)
-      {
-        if (urls.contains(svc.getServiceTypeURI()))
-        {
-          if (match == null)
-          {
-            // for moment we always pick service from server ordered first in
-            // user's preferences
-            match = svc;
-          }
-          if (urls.contains(svc.getUri()))
-          {
-            // stop and return - we've matched type URI and URI for service
-            // endpoint
-            return svc;
-          }
-        }
-      }
-    }
-    return match;
-  }
-
-  Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
-
-  /**
-   * get current preferred service of the given type, or global default
-   * 
-   * @param af
-   *          null or a specific alignFrame
-   * @param serviceType
-   *          Jws2Instance.serviceType for service
-   * @return null if no service of this type is available, the preferred service
-   *         for the serviceType and af if specified and if defined.
-   */
-  public Jws2Instance getPreferredServiceFor(AlignFrame af,
-          String serviceType)
-  {
-    String serviceurl = null;
-    synchronized (preferredServiceMap)
-    {
-      String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
-      Map<String, String> prefmap = preferredServiceMap.get(afid);
-      if (afid.length() > 0 && prefmap == null)
-      {
-        // recover global setting, if any
-        prefmap = preferredServiceMap.get("");
-      }
-      if (prefmap != null)
-      {
-        serviceurl = prefmap.get(serviceType);
-      }
-
-    }
-    Jws2Instance response = null;
-    for (Jws2Instance svc : services)
-    {
-      if (svc.serviceType.equals(serviceType))
-      {
-        if (serviceurl == null || serviceurl.equals(svc.getHost()))
-        {
-          response = svc;
-          break;
-        }
-      }
-    }
-    return response;
-  }
-
-  public void setPreferredServiceFor(AlignFrame af, String serviceType,
-          String serviceAction, Jws2Instance selectedServer)
-  {
-    String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
-    if (preferredServiceMap == null)
-    {
-      preferredServiceMap = new HashMap<String, Map<String, String>>();
-    }
-    Map<String, String> prefmap = preferredServiceMap.get(afid);
-    if (prefmap == null)
-    {
-      prefmap = new HashMap<String, String>();
-      preferredServiceMap.put(afid, prefmap);
-    }
-    prefmap.put(serviceType, selectedServer.getHost());
-    prefmap.put(serviceAction, selectedServer.getHost());
-  }
-
-  public void setPreferredServiceFor(String serviceType,
-          String serviceAction, Jws2Instance selectedServer)
-  {
-    setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
-  }
-
-  /**
    * Set a URL to try before any others. For use with command-line parameter to
    * configure a local Jabaws installation without the need to add to property
    * files.