X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=60fa85b3fc7817595bb2db9487ac0eb27cd83a7b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2528308683faf7ad3ed29a98e91996c28ee47ecf;hpb=439d5ad378494d0afa9668e2308ad605c51afcc0;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 2528308..60fa85b 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,33 +1,56 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.jws2;
 
+import jalview.bin.Cache;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ParamDatastoreI;
+
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
-import java.io.Closeable;
-import java.net.ConnectException;
+import java.beans.PropertyChangeSupport;
+import java.net.MalformedURLException;
 import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 
-import org.apache.log4j.Level;
-
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.ws.WSMenuEntryProviderI;
-import compbio.data.msa.MsaWS;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.RunnerConfig;
-import compbio.ws.client.Jws2Client;
 import compbio.ws.client.Services;
 
 /**
@@ -39,9 +62,48 @@ import compbio.ws.client.Services;
  */
 public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 {
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+  public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
+
+  /*
+   * the .jalview_properties entry for JWS2 URLS
+   */
+  final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+
+  /*
+   * Singleton instance
+   */
+  private static Jws2Discoverer discoverer;
+
+  /*
+   * Override for testing only
+   */
+  private static List<String> testUrls = null;
+
+  // preferred url has precedence over others
+  private String preferredUrl;
+
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
           this);
 
+  Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
+          validServiceUrls = null;
+
+  boolean running = false, aborted = false;
+
+  Thread oldthread = null;
+
+  /**
+   * holds list of services.
+   */
+  protected Vector<Jws2Instance> services;
+
+  /**
+   * Private constructor enforces use of singleton via getDiscoverer()
+   */
+  private Jws2Discoverer()
+  {
+  }
+
   /**
    * change listeners are notified of "services" property changes
    * 
@@ -66,17 +128,58 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     changeSupport.removePropertyChangeListener(listener);
   }
 
-  boolean running = false;
+  /**
+   * @return the aborted
+   */
+  public boolean isAborted()
+  {
+    return aborted;
+  }
 
-  Thread oldthread = null;
+  /**
+   * @param aborted
+   *          the aborted to set
+   */
+  public void setAborted(boolean aborted)
+  {
+    this.aborted = aborted;
+
+  }
 
   public void run()
   {
+
     if (running && oldthread != null && oldthread.isAlive())
     {
-      return;
+      if (!aborted)
+      {
+        return;
+      }
+      while (running)
+      {
+        try
+        {
+          Cache.log
+                  .debug("Waiting around for old discovery thread to finish.");
+          // wait around until old discoverer dies
+          Thread.sleep(100);
+        } catch (Exception e)
+        {
+        }
+      }
+      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("\\|"))
+    {
+      ignoredServices.add(ignored);
+    }
+
+    changeSupport.firePropertyChange("services", services, new Vector());
     oldthread = Thread.currentThread();
     try
     {
@@ -85,57 +188,104 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     } catch (ClassNotFoundException e)
     {
       System.err
-              .println("Not enabling Jalview Webservices version 2: client jar is not available."
+              .println("Not enabling JABA Webservices : client jar is not available."
                       + "\nPlease check that your webstart JNLP file is up to date!");
       running = false;
       return;
     }
+    // reinitialise records of good and bad service URLs
     if (services != null)
     {
       services.removeAllElements();
     }
-    for (String jwsservers : getServiceUrls())
+    if (urlsWithoutServices != null)
     {
-      try
+      urlsWithoutServices.removeAllElements();
+    }
+    if (invalidServiceUrls != null)
+    {
+      invalidServiceUrls.removeAllElements();
+    }
+    if (validServiceUrls != null)
+    {
+      validServiceUrls.removeAllElements();
+    }
+    ArrayList<String> svctypes = new ArrayList<String>();
+
+    List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+    for (final String jwsserver : getServiceUrls())
+    {
+      JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
+      if (svctypes.size() == 0)
       {
-        if (Jws2Client.validURL(jwsservers))
+        // TODO: remove this ugly hack to get Canonical JABA service ordering
+        // for all possible services
+        for (Services sv : squery.JABAWS2SERVERS)
         {
-          // look for services
-          for (Services srv : Services.values())
+          if (!ignoredServices.contains(sv.toString()))
           {
-            MsaWS service = null;
-            try
-            {
-              service = Jws2Client.connect(jwsservers, srv);
-            } catch (Exception e)
-            {
-              System.err.println("Jws2 Discoverer: Problem on "
-                      + jwsservers + " with service " + srv + ":\n"
-                      + e.getMessage());
-              if (!(e instanceof javax.xml.ws.WebServiceException))
-              {
-                e.printStackTrace();
-              }
-            }
-            ;
-            if (service != null)
-            {
-              addService(jwsservers, srv, service);
-            }
+            svctypes.add(sv.toString());
           }
-
         }
-        else
+
+      }
+      qrys.add(squery);
+      new Thread(squery).start();
+    }
+    boolean finished = true;
+    do
+    {
+      finished = true;
+      try
+      {
+        Thread.sleep(100);
+      } catch (Exception e)
+      {
+      }
+      ;
+      for (JabaWsServerQuery squery : qrys)
+      {
+        if (squery.isRunning())
         {
-          Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+          finished = false;
         }
-      } catch (Exception e)
+      }
+      if (aborted)
       {
-        e.printStackTrace();
-        Cache.log.warn("Exception when discovering Jws2 services.", e);
-      } catch (Error e)
+        Cache.log.debug("Aborting " + qrys.size()
+                + " JABAWS discovery threads.");
+        for (JabaWsServerQuery squery : qrys)
+        {
+          squery.setQuit(true);
+        }
+      }
+    } while (!aborted && !finished);
+    if (!aborted)
+    {
+      // resort services according to order found in jabaws service list
+      // also ensure servics for each host are ordered in same way.
+
+      if (services != null && services.size() > 0)
       {
-        Cache.log.error("Exception when discovering Jws2 services.", e);
+        Jws2Instance[] svcs = new Jws2Instance[services.size()];
+        int[] spos = new int[services.size()];
+        int ipos = 0;
+        List<String> svcUrls = getServiceUrls();
+        for (Jws2Instance svc : services)
+        {
+          svcs[ipos] = svc;
+          spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1
+                  + svctypes.indexOf(svc.serviceType);
+        }
+        jalview.util.QuickSort.sort(spos, svcs);
+        services = new Vector<Jws2Instance>();
+        for (Jws2Instance svc : svcs)
+        {
+          if (!ignoredServices.contains(svc.serviceType))
+          {
+            services.add(svc);
+          }
+        }
       }
     }
     oldthread = null;
@@ -150,221 +300,314 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    * @param srv
    * @param service2
    */
-  private void addService(String jwsservers, Services srv, MsaWS service2)
+  synchronized void addService(String jwsservers, Jws2Instance service)
   {
     if (services == null)
     {
       services = new Vector<Jws2Instance>();
     }
     System.out.println("Discovered service: " + jwsservers + " "
-            + srv.toString());
-    services.add(new Jws2Instance(jwsservers, srv.toString(), service2));
+            + service.toString());
+    // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+    // service2);
+
+    services.add(service);
+    // retrieve the presets and parameter set and cache now
+    ParamDatastoreI pds = service.getParamStore();
+    if (pds != null)
+    {
+      pds.getPresets();
+    }
+    service.hasParameters();
+    if (validServiceUrls == null)
+    {
+      validServiceUrls = new Vector();
+    }
+    validServiceUrls.add(jwsservers);
   }
 
-  public class Jws2Instance
+  /**
+   * attach all available web services to the appropriate submenu in the given
+   * JMenu
+   */
+  public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
-    public String hosturl;
-
-    public String serviceType;
+    // dynamically regenerate service list.
+    populateWSMenuEntry(wsmenu, alignFrame, null);
+  }
 
-    public MsaWS service;
+  private boolean isRecalculable(String action)
+  {
+    return (action != null && action.equalsIgnoreCase("conservation"));
+  }
 
-    public Jws2Instance(String hosturl, String serviceType, MsaWS service)
+  private void populateWSMenuEntry(JMenu jws2al,
+          final AlignFrame alignFrame, String typeFilter)
+  {
+    if (running || services == null || services.size() == 0)
     {
-      super();
-      this.hosturl = hosturl;
-      this.serviceType = serviceType;
-      this.service = service;
+      return;
     }
-
-    PresetManager presets = null;
-
+    boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
+            .getDefault("WSMENU_BYTYPE", false);
     /**
-     * non thread safe - gets the presets for this service (blocks whilst it
-     * calls the service to get the preset set)
-     * 
-     * @return service presets or null if exceptions were raised.
+     * eventually, JWS2 services will appear under the same align/etc submenus.
+     * for moment we keep them separate.
      */
-    public PresetManager getPresets()
+    JMenu atpoint;
+    List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+    // 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]))
     {
-      if (presets == null)
+      if (!isRecalculable(service.action))
       {
-        try
+        // add 'one shot' services to be displayed using the classic menu
+        // structure
+        enumerableServices.add(service);
+      }
+      else
+      {
+        if (!preferredHosts.containsKey(service.serviceType))
         {
-          presets = service.getPresets();
-        } catch (Exception ex)
+          Jws2Instance preferredInstance = getPreferredServiceFor(
+                  alignFrame, service.serviceType);
+          if (preferredInstance != null)
+          {
+            preferredHosts.put(service.serviceType, preferredInstance);
+          }
+          else
+          {
+            preferredHosts.put(service.serviceType, service);
+          }
+        }
+        List<Jws2Instance> ph = alternates.get(service.serviceType);
+        if (preferredHosts.get(service.serviceType) != service)
         {
-          System.err
-                  .println("Exception when retrieving presets for service "
-                          + serviceType + " at " + hosturl);
+          if (ph == null)
+          {
+            ph = new ArrayList<Jws2Instance>();
+          }
+          ph.add(service);
+          alternates.put(service.serviceType, ph);
         }
       }
-      return presets;
-    }
 
-    public String getHost()
-    {
-      return hosturl;
-      /*
-       * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80)
-       * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return
-       * serviceurl.getHost(); } catch (Exception e) {
-       * System.err.println("Failed to parse service URL '" + hosturl +
-       * "' as a valid URL!"); } return null;
-       */
     }
 
-    /**
-     * @return short description of what the service will do
-     */
-    public String getActionText()
+    // create GUI element for classic services
+    addEnumeratedServices(jws2al, alignFrame, enumerableServices);
+    // and the instantaneous services
+    for (final Jws2Instance service : preferredHosts.values())
     {
-      return "Align with " + serviceType;
-    }
+      atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
+      JMenuItem hitm;
+      if (atpoint.getItemCount() > 1)
+      {
+        // previous service of this type already present
+        atpoint.addSeparator();
+      }
+      atpoint.add(hitm = new JMenuItem(service.getHost()));
+      hitm.setForeground(Color.blue);
+      hitm.addActionListener(new ActionListener()
+      {
 
-    /**
-     * non-thread safe - blocks whilst accessing service to get complete set of
-     * available options and parameters
-     * 
-     * @return
-     */
-    public RunnerConfig getRunnerConfig()
-    {
-      return service.getRunnerOptions();
-    }
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          Desktop.showUrl(service.getHost());
+        }
+      });
+      hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
+              MessageManager.getString("label.open_jabaws_web_page")));
 
-    @Override
-    protected void finalize() throws Throwable
-    {
-      if (service != null)
+      service.attachWSMenuEntry(atpoint, alignFrame);
+      if (alternates.containsKey(service.serviceType))
       {
-        try
-        {
-          Closeable svc = (Closeable) service;
-          service = null;
-          svc.close();
-        } catch (Exception e)
+        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))
         {
-        }
-        ;
-      }
-      super.finalize();
-    }
-  };
+          JMenuItem itm;
+          hitm.add(itm = new JMenuItem(sv.getHost()));
+          itm.setForeground(Color.blue);
+          itm.addActionListener(new ActionListener()
+          {
 
-  /**
-   * holds list of services.
-   */
-  protected Vector<Jws2Instance> services;
+            @Override
+            public void actionPerformed(ActionEvent arg0)
+            {
+              new Thread(new Runnable()
+              {
+                public void run()
+                {
+                  setPreferredServiceFor(alignFrame, sv.serviceType,
+                          sv.action, sv);
+                  changeSupport.firePropertyChange("services",
+                          new Vector(), services);
+                };
+              }).start();
 
-  /**
-   * find or add a submenu with the given title in the given menu
-   * 
-   * @param menu
-   * @param submenu
-   * @return the new or existing submenu
-   */
-  private JMenu findOrCreateMenu(JMenu menu, String submenu)
-  {
-    JMenu submenuinstance = null;
-    for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++)
-    {
-      if (menu.getMenuComponent(i) instanceof JMenu
-              && ((JMenu) menu.getMenuComponent(i)).getText().equals(
-                      submenu))
-      {
-        submenuinstance = (JMenu) menu.getMenuComponent(i);
+            }
+          });
+        }
+        /*
+         * 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(); } });
+         */
       }
     }
-    if (submenuinstance == null)
-    {
-      submenuinstance = new JMenu(submenu);
-      menu.add(submenuinstance);
-    }
-    return submenuinstance;
-
   }
 
-  public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+  /**
+   * add services using the Java 2.5/2.6/2.7 system which optionally creates
+   * submenus to index by host and service program type
+   */
+  private void addEnumeratedServices(final JMenu jws2al,
+          final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
   {
-    if (running || services == null || services.size() == 0)
-    {
-      return;
-    }
-    boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache
-            .getDefault("WSMENU_BYTYPE", true);
+    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, jws2al = new JMenu("JABA Alignment");
+    JMenu atpoint;
     MsaWSClient msacl = new MsaWSClient();
-    Vector hostLabels = new Vector();
-    for (final Jws2Instance service : services)
+    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)
     {
-      atpoint = jws2al;
-      String host = service.getHost();
-      String type = service.serviceType;
-      if (byhost)
+      ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
+      if (hostservices == null)
       {
-        atpoint = findOrCreateMenu(atpoint, host);
-        if (atpoint.getToolTipText() == null)
-        {
-          atpoint.setToolTipText("Services at " + host);
-        }
+        hosts.put(service.getHost(),
+                hostservices = new ArrayList<Jws2Instance>());
+        hostlist.add(service.getHost());
       }
-      if (bytype)
+      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]);
+      String sortbytype[] = new String[orderedsvcs.length];
+      for (int i = 0; i < sortbytype.length; i++)
       {
-        atpoint = findOrCreateMenu(atpoint, type);
-        if (atpoint.getToolTipText() == null)
-        {
-          atpoint.setToolTipText(service.getActionText());
-        }
+        sortbytype[i] = orderedsvcs[i].serviceType;
       }
-      if (!byhost && !hostLabels.contains(host + service.getActionText()))
+      jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
+      for (final Jws2Instance service : orderedsvcs)
       {
-        // add a marker indicating where this service is hosted
-        // relies on services from the same host being listed in a contiguous
-        // group
-        JMenuItem hitm;
-        atpoint.addSeparator();
-        atpoint.add(hitm = new JMenuItem(host));
-        hitm.setForeground(Color.blue);
-        hostLabels.addElement(host);
+        atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
+        String type = service.serviceType;
+        if (byhost)
+        {
+          atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
+          if (atpoint.getToolTipText() == null)
+          {
+            atpoint.setToolTipText(MessageManager.formatMessage(
+                    "label.services_at", new String[] { host }));
+          }
+        }
+        if (bytype)
+        {
+          atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type);
+          if (atpoint.getToolTipText() == null)
+          {
+            atpoint.setToolTipText(service.getActionText());
+          }
+        }
+        if (!byhost
+                && !hostLabels.contains(host + service.serviceType
+                        + service.getActionText()))
+        // !hostLabels.contains(host + (bytype ?
+        // service.serviceType+service.getActionText() : "")))
+        {
+          // add a marker indicating where this service is hosted
+          // relies on services from the same host being listed in a
+          // contiguous
+          // group
+          JMenuItem hitm;
+          if (hostLabels.contains(host))
+          {
+            atpoint.addSeparator();
+          }
+          else
+          {
+            hostLabels.add(host);
+          }
+          if (lasthostFor.get(service.action) == null
+                  || !lasthostFor.get(service.action).equals(host))
+          {
+            atpoint.add(hitm = new JMenuItem(host));
+            hitm.setForeground(Color.blue);
+            hitm.addActionListener(new ActionListener()
+            {
+
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                Desktop.showUrl(service.getHost());
+              }
+            });
+            hitm.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                    MessageManager.getString("label.open_jabaws_web_page")));
+            lasthostFor.put(service.action, host);
+          }
+          hostLabels.add(host + service.serviceType
+                  + service.getActionText());
+        }
+
+        service.attachWSMenuEntry(atpoint, alignFrame);
       }
-      msacl.attachWSMenuEntry(atpoint, service, alignFrame);
-      /*
-       * JMenuItem sitem = new JMenuItem(service.serviceType);
-       * sitem.setToolTipText("Hosted at " + service.hosturl);
-       * sitem.addActionListener(new ActionListener() {
-       * 
-       * @Override public void actionPerformed(ActionEvent e) { AlignmentView
-       * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client =
-       * new MsaWSClient(service, "JWS2 Alignment of " + alignFrame.getTitle(),
-       * msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
-       * alignFrame); } });
-       */
-    }
-    if (services.size() > 0)
-    {
-      wsmenu.add(jws2al);
     }
-
   }
 
   public static void main(String[] args)
   {
-    Thread runner = new Thread(getDiscoverer());
-    getDiscoverer().addPropertyChangeListener(new PropertyChangeListener()
+    if (args.length > 0)
     {
-
-      public void propertyChange(PropertyChangeEvent evt)
+      testUrls = new ArrayList<String>();
+      for (String url : args)
       {
-        System.out.println("Changesupport: There are now "
-                + getDiscoverer().services.size() + " services");
+        testUrls.add(url);
       }
-    });
-    runner.start();
+      ;
+    }
+    Thread runner = getDiscoverer().startDiscoverer(
+            new PropertyChangeListener()
+            {
+
+              public void propertyChange(PropertyChangeEvent evt)
+              {
+                if (getDiscoverer().services != null)
+                {
+                  System.out.println("Changesupport: There are now "
+                          + getDiscoverer().services.size() + " services");
+                  int i = 1;
+                  for (Jws2Instance instance : getDiscoverer().services)
+                  {
+                    System.out.println("Service " + i++ + " "
+                            + instance.getClass() + "@"
+                            + instance.getHost() + ": "
+                            + instance.getActionText());
+                  }
+
+                }
+              }
+            });
     while (runner.isAlive())
     {
       try
@@ -375,10 +618,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
       ;
     }
+    try
+    {
+      Thread.sleep(50);
+    } catch (InterruptedException x)
+    {
+    }
   }
 
-  private static Jws2Discoverer discoverer;
-
+  /**
+   * Returns the singleton instance of this class.
+   * 
+   * @return
+   */
   public static Jws2Discoverer getDiscoverer()
   {
     if (discoverer == null)
@@ -390,7 +642,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public boolean hasServices()
   {
-    // TODO Auto-generated method stub
     return !running && services != null && services.size() > 0;
   }
 
@@ -399,24 +650,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return running;
   }
 
-  /**
-   * the jalview .properties entry for JWS2 URLS
-   */
-  final static String JWS2HOSTURLS = "JWS2HOSTURLS";
-
-  public static void setServiceUrls(Vector<String> urls)
+  public void setServiceUrls(List<String> wsUrls)
   {
-    if (urls != null)
+    if (wsUrls != null && !wsUrls.isEmpty())
     {
-      StringBuffer urlbuffer = new StringBuffer();
+      StringBuilder urls = new StringBuilder(128);
       String sep = "";
-      for (String url : urls)
+      for (String url : wsUrls)
       {
-        urlbuffer.append(sep);
-        urlbuffer.append(url);
+        urls.append(sep);
+        urls.append(url);
         sep = ",";
       }
-      Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
+      Cache.setProperty(JWS2HOSTURLS, urls.toString());
     }
     else
     {
@@ -424,11 +670,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
-  public static Vector<String> getServiceUrls()
+  /**
+   * Returns web service URLs, in the order in which they should be tried (or an
+   * empty list).
+   * 
+   * @return
+   */
+  public List<String> getServiceUrls()
   {
-    String surls = Cache.getDefault(JWS2HOSTURLS,
-            "http://www.compbio.dundee.ac.uk/jabaws");
-    Vector<String> urls = new Vector<String>();
+    if (testUrls != null)
+    {
+      // return test urls, if there are any, instead of touching cache
+      return testUrls;
+    }
+    List<String> urls = new ArrayList<String>();
+
+    if (this.preferredUrl != null)
+    {
+      urls.add(preferredUrl);
+    }
+
+    String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
     try
     {
       StringTokenizer st = new StringTokenizer(surls, ",");
@@ -437,40 +699,35 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         String url = null;
         try
         {
-          java.net.URL u = new java.net.URL(url = st.nextToken());
+          url = st.nextToken();
+          new URL(url);
           if (!urls.contains(url))
           {
             urls.add(url);
           }
           else
           {
-            jalview.bin.Cache.log.info("Ignoring duplicate url in "
+            Cache.log.warn("Ignoring duplicate url " + url + " in "
                     + JWS2HOSTURLS + " list");
           }
-        } catch (Exception ex)
+        } catch (MalformedURLException ex)
         {
-          jalview.bin.Cache.log
-                  .warn("Problem whilst trying to make a URL from '"
-                          + ((url != null) ? url : "<null>") + "'");
-          jalview.bin.Cache.log
+          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
                           + " entry of $(HOME)/.jalview_properties)");
-          jalview.bin.Cache.log.debug("Exception was ", ex);
+          Cache.log.debug("Exception was ", ex);
         }
       }
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.warn(
-              "Error parsing comma separated list of urls in "
-                      + JWS2HOSTURLS + " preference.", ex);
-    }
-    if (urls.size() >= 0)
-    {
-      return urls;
+      Cache.log.warn("Error parsing comma separated list of urls in "
+              + JWS2HOSTURLS + " preference.", ex);
     }
-    return null;
+    return urls;
   }
 
   public Vector<Jws2Instance> getServices()
@@ -481,26 +738,297 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   /**
    * test the given URL with the JabaWS test code
+   * 
    * @param foo
    * @return
    */
   public static boolean testServiceUrl(URL foo)
   {
-    try {
-      compbio.ws.client.WSTester.main(new String[] { "-h="+foo.toString()});
+    try
+    {
+      compbio.ws.client.WSTester
+              .main(new String[] { "-h=" + foo.toString() });
     } catch (Exception e)
     {
+      e.printStackTrace();
       return false;
-    }
-    catch (OutOfMemoryError e)
+    } catch (OutOfMemoryError e)
     {
+      e.printStackTrace();
       return false;
-    }
-    catch (Error e)
+    } catch (Error e)
     {
+      e.printStackTrace();
       return false;
     }
+
     return true;
   }
 
+  /**
+   * 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
+   * started.
+   * 
+   * @param changeSupport2
+   * @return new thread
+   */
+  public Thread startDiscoverer(PropertyChangeListener changeSupport2)
+  {
+    if (isRunning())
+    {
+      setAborted(true);
+    }
+    addPropertyChangeListener(changeSupport2);
+    Thread thr = new Thread(this);
+    thr.start();
+    return thr;
+  }
+
+  /**
+   * @return the invalidServiceUrls
+   */
+  public Vector<String> getInvalidServiceUrls()
+  {
+    return invalidServiceUrls;
+  }
+
+  /**
+   * @return the urlsWithoutServices
+   */
+  public Vector<String> getUrlsWithoutServices()
+  {
+    return urlsWithoutServices;
+  }
+
+  /**
+   * add an 'empty' JABA server to the list. Only servers not already in the
+   * 'bad URL' list will be added to this list.
+   * 
+   * @param jwsservers
+   */
+  public synchronized void addUrlwithnoservices(String jwsservers)
+  {
+    if (urlsWithoutServices == null)
+    {
+      urlsWithoutServices = new Vector<String>();
+    }
+
+    if ((invalidServiceUrls == null || !invalidServiceUrls
+            .contains(jwsservers))
+            && !urlsWithoutServices.contains(jwsservers))
+    {
+      urlsWithoutServices.add(jwsservers);
+    }
+  }
+
+  /**
+   * add a bad URL to the list
+   * 
+   * @param jwsservers
+   */
+  public synchronized void addInvalidServiceUrl(String jwsservers)
+  {
+    if (invalidServiceUrls == null)
+    {
+      invalidServiceUrls = new Vector<String>();
+    }
+    if (!invalidServiceUrls.contains(jwsservers))
+    {
+      invalidServiceUrls.add(jwsservers);
+    }
+  }
+
+  /**
+   * 
+   * @return a human readable report of any problems with the service URLs used
+   *         for discovery
+   */
+  public String getErrorMessages()
+  {
+    if (!isRunning() && !isAborted())
+    {
+      StringBuffer ermsg = new StringBuffer();
+      boolean list = false;
+      if (getInvalidServiceUrls() != null
+              && getInvalidServiceUrls().size() > 0)
+      {
+        ermsg.append(MessageManager.getString("warn.urls_not_contacted")
+                + ": \n");
+        for (String svcurl : getInvalidServiceUrls())
+        {
+          if (list)
+          {
+            ermsg.append(", ");
+          }
+          list = true;
+          ermsg.append(svcurl);
+        }
+        ermsg.append("\n\n");
+      }
+      list = false;
+      if (getUrlsWithoutServices() != null
+              && getUrlsWithoutServices().size() > 0)
+      {
+        ermsg.append(MessageManager.getString("warn.urls_no_jaba") + ": \n");
+        for (String svcurl : getUrlsWithoutServices())
+        {
+          if (list)
+          {
+            ermsg.append(", ");
+          }
+          list = true;
+          ermsg.append(svcurl);
+        }
+        ermsg.append("\n");
+      }
+      if (ermsg.length() > 1)
+      {
+        return ermsg.toString();
+      }
+
+    }
+    return null;
+  }
+
+  public int getServerStatusFor(String url)
+  {
+    if (validServiceUrls != null && validServiceUrls.contains(url))
+    {
+      return 1;
+    }
+    if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
+    {
+      return 0;
+    }
+    if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
+    {
+      return -1;
+    }
+    return -2;
+  }
+
+  /**
+   * 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.
+   * 
+   * @param value
+   * @throws MalformedURLException
+   */
+  public void setPreferredUrl(String value) throws MalformedURLException
+  {
+    if (value != null && value.trim().length() > 0)
+    {
+      new URL(value);
+      preferredUrl = value;
+    }
+  }
 }