X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=2fb8974a858ed299a84118ee0a98283b9de38449;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=b440de8f8909011b2fef16d31960c23bb68621d0;hpb=3f72d101fbeb83a7526a3c4f8f62cfe8e8a0189d;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index b440de8..2fb8974 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- * 
+ * 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/>.
+ * 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;
 
@@ -21,18 +24,27 @@ 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.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;
 
@@ -50,9 +62,53 @@ 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
+   */
+  private 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);
 
+  private Vector<String> invalidServiceUrls = null;
+
+  private Vector<String> urlsWithoutServices = null;
+
+  private Vector<String> validServiceUrls = null;
+
+  private volatile boolean running = false;
+
+  private volatile boolean aborted = false;
+
+  private 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
    * 
@@ -77,8 +133,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     changeSupport.removePropertyChangeListener(listener);
   }
 
-  boolean running = false, aborted = false;
-
   /**
    * @return the aborted
    */
@@ -96,10 +150,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     this.aborted = aborted;
   }
 
-  Thread oldthread = null;
-
+  @Override
   public void run()
   {
+
     if (running && oldthread != null && oldthread.isAlive())
     {
       if (!aborted)
@@ -110,27 +164,38 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       {
         try
         {
-          Cache.log
-                  .debug("Waiting around for old discovery thread to finish.");
+          Cache.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.");
+      aborted = false;
+      Cache.debug("Old discovery thread has finished.");
     }
     running = true;
-    changeSupport.firePropertyChange("services", services, new Vector());
+
+    // first set up exclusion list if needed
+    final Set<String> ignoredServices = new HashSet<>();
+    for (String ignored : Cache
+            .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
+    {
+      ignoredServices.add(ignored);
+    }
+
+    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;
@@ -152,18 +217,22 @@ 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>();
-    for (final String jwsservers : getServiceUrls())
+    List<JabaWsServerQuery> qrys = new ArrayList<>();
+    for (final String jwsserver : getServiceUrls())
     {
-      JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
-      if (svctypes.size()==0)
+      JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
+      if (svctypes.size() == 0)
       {
-        // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services 
-        for (Services sv:squery.JABAWS2SERVERS)
+        // TODO: remove this ugly hack to get Canonical JABA service ordering
+        // for all possible services
+        for (Services sv : squery.JABAWS2SERVERS)
         {
-          svctypes.add(sv.toString());
+          if (!ignoredServices.contains(sv.toString()))
+          {
+            svctypes.add(sv.toString());
+          }
         }
 
       }
@@ -173,22 +242,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     boolean finished = true;
     do
     {
-      finished=true;
+      finished = true;
       try
       {
         Thread.sleep(100);
       } catch (Exception e)
       {
       }
-      ;
       for (JabaWsServerQuery squery : qrys)
       {
-        finished = finished && !squery.isRunning();
+        if (squery.isRunning())
+        {
+          finished = false;
+        }
       }
       if (aborted)
       {
-        Cache.log.debug("Aborting " + qrys.size()
-                + " JABAWS discovery threads.");
+        Cache.debug(
+                "Aborting " + qrys.size() + " JABAWS discovery threads.");
         for (JabaWsServerQuery squery : qrys)
         {
           squery.setQuit(true);
@@ -198,29 +269,35 @@ 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.
-      
-      if (services!=null && services.size()>0)
+      // also ensure services for each host are ordered in same way.
+
+      if (services != null && services.size() > 0)
       {
-        Jws2Instance[] svcs=new Jws2Instance[services.size()];
-        int[] spos=new int[services.size()];
-        int ipos=0;
-        Vector svcUrls = getServiceUrls();
-        for (Jws2Instance svc:services)
+        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);
+          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) {
-          services.add(svc);
+        services = new Vector<>();
+        for (Jws2Instance svc : svcs)
+        {
+          if (!ignoredServices.contains(svc.serviceType))
+          {
+            services.add(svc);
+          }
         }
       }
     }
     oldthread = null;
     running = false;
-    changeSupport.firePropertyChange("services", new Vector(), services);
+    changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(),
+            services);
   }
 
   /**
@@ -234,63 +311,188 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (services == null)
     {
-      services = new Vector<Jws2Instance>();
+      services = new Vector<>();
     }
-    System.out.println("Discovered service: " + jwsservers + " "
-            + service.toString());
-//    Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
-//            service2);
+    System.out.println(
+            "Discovered service: " + jwsservers + " " + service.toString());
+    // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+    // service2);
 
     services.add(service);
     // retrieve the presets and parameter set and cache now
-    service.getParamStore().getPresets();
+    ParamDatastoreI pds = service.getParamStore();
+    if (pds != null)
+    {
+      pds.getPresets();
+    }
     service.hasParameters();
-    if (validServiceUrls==null)
+    if (validServiceUrls == null)
     {
-      validServiceUrls=new Vector();
+      validServiceUrls = new Vector<>();
     }
     validServiceUrls.add(jwsservers);
   }
 
   /**
-   * holds list of services.
-   */
-  protected Vector<Jws2Instance> services;
-  /**
-   * attach all available web services to the appropriate submenu in the given JMenu
+   * 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.
     populateWSMenuEntry(wsmenu, alignFrame, null);
   }
 
-  private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
+  private boolean isRecalculable(String action)
+  {
+    return (action != null && action.equalsIgnoreCase("conservation"));
+  }
+
+  private void populateWSMenuEntry(JMenu jws2al,
+          final AlignFrame alignFrame, String typeFilter)
   {
     if (running || services == null || services.size() == 0)
     {
       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<>();
+    // jws2al.removeAll();
+    Map<String, Jws2Instance> preferredHosts = new HashMap<>();
+    Map<String, List<Jws2Instance>> alternates = new HashMap<>();
+    for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
+    {
+      if (!isRecalculable(service.action))
+      {
+        // add 'one shot' services to be displayed using the classic menu
+        // structure
+        enumerableServices.add(service);
+      }
+      else
+      {
+        if (!preferredHosts.containsKey(service.serviceType))
+        {
+          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)
+        {
+          if (ph == null)
+          {
+            ph = new ArrayList<>();
+          }
+          ph.add(service);
+          alternates.put(service.serviceType, ph);
+        }
+      }
+
+    }
+
+    // create GUI element for classic services
+    addEnumeratedServices(jws2al, alignFrame, enumerableServices);
+    // and the instantaneous services
+    for (final Jws2Instance service : preferredHosts.values())
+    {
+      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()
+      {
+
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          Desktop.showUrl(service.getHost());
+        }
+      });
+      hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
+              MessageManager.getString("label.open_jabaws_web_page")));
+
+      service.attachWSMenuEntry(atpoint, alignFrame);
+      if (alternates.containsKey(service.serviceType))
+      {
+        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))
+        {
+          JMenuItem itm;
+          hitm.add(itm = new JMenuItem(sv.getHost()));
+          itm.setForeground(Color.blue);
+          itm.addActionListener(new ActionListener()
+          {
+
+            @Override
+            public void actionPerformed(ActionEvent arg0)
+            {
+              new Thread(new Runnable()
+              {
+                @Override
+                public void run()
+                {
+                  setPreferredServiceFor(alignFrame, sv.serviceType,
+                          sv.action, sv);
+                  changeSupport.firePropertyChange("services",
+                          new Vector<Jws2Instance>(), services);
+                }
+              }).start();
+
+            }
+          });
+        }
+      }
+    }
+  }
+
+  /**
+   * 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)
+  {
+    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();
-    Vector hostLabels = new Vector();
-    jws2al.removeAll();
-    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 : services)
+
+    List<String> hostLabels = new ArrayList<>();
+    Hashtable<String, String> lasthostFor = new Hashtable<>();
+    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
+    ArrayList<String> hostlist = new ArrayList<>();
+    for (Jws2Instance service : enumerableServices)
     {
       ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
       if (hostservices == null)
       {
         hosts.put(service.getHost(),
-                hostservices = new ArrayList<Jws2Instance>());
+                hostservices = new ArrayList<>());
         hostlist.add(service.getHost());
       }
       hostservices.add(service);
@@ -298,8 +500,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     // 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++)
       {
@@ -308,14 +510,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
       for (final Jws2Instance service : orderedsvcs)
       {
-        atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+        atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
         String type = service.serviceType;
         if (byhost)
         {
           atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
           if (atpoint.getToolTipText() == null)
           {
-            atpoint.setToolTipText("Services at " + host);
+            atpoint.setToolTipText(MessageManager
+                    .formatMessage("label.services_at", new String[]
+                    { host }));
           }
         }
         if (bytype)
@@ -326,9 +530,8 @@ 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.serviceType + service.getActionText()))
         // !hostLabels.contains(host + (bytype ?
         // service.serviceType+service.getActionText() : "")))
         {
@@ -337,8 +540,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           // contiguous
           // group
           JMenuItem hitm;
-          atpoint.addSeparator();
-          if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).equals(host))
+          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);
@@ -351,58 +562,52 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                 Desktop.showUrl(service.getHost());
               }
             });
-            hitm.setToolTipText(JvSwingUtils
-                    .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
-            lasthostFor.put(service.action,host);
+            hitm.setToolTipText(
+                    JvSwingUtils.wrapTooltip(true, MessageManager
+                            .getString("label.open_jabaws_web_page")));
+            lasthostFor.put(service.action, host);
           }
-          hostLabels.addElement(host + service.serviceType
-                  + service.getActionText());
-          // hostLabels.addElement(host + (bytype ?
-          // service.serviceType+service.getActionText() : ""));
+          hostLabels.add(
+                  host + service.serviceType + service.getActionText());
         }
-        
+
         service.attachWSMenuEntry(atpoint, 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); }
-         * });
-         */
       }
     }
-
   }
 
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
-    if (args.length>0)
+    if (args.length > 0)
     {
-      testUrls = new Vector<String>();
-      for (String url:args)
+      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)
                 {
                   System.out.println("Changesupport: There are now "
                           + getDiscoverer().services.size() + " services");
-                  int i=1;
-                  for (Jws2Instance instance:getDiscoverer().services)
+                  int i = 1;
+                  for (Jws2Instance instance : getDiscoverer().services)
                   {
-                    System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText());
+                    System.out.println("Service " + i++ + " "
+                            + instance.getClass() + "@" + instance.getHost()
+                            + ": " + instance.getActionText());
                   }
 
                 }
@@ -416,15 +621,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       } catch (InterruptedException e)
       {
       }
-      ;
     }
-    try {
+    try
+    {
       Thread.sleep(50);
-    } catch (InterruptedException x) {}
+    } catch (InterruptedException x)
+    {
+    }
   }
 
-  private static Jws2Discoverer discoverer;
-
+  /**
+   * Returns the singleton instance of this class.
+   * 
+   * @return
+   */
   public static Jws2Discoverer getDiscoverer()
   {
     if (discoverer == null)
@@ -436,7 +646,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public boolean hasServices()
   {
-    // TODO Auto-generated method stub
     return !running && services != null && services.size() > 0;
   }
 
@@ -445,24 +654,19 @@ 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
     {
@@ -470,17 +674,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
-  private static Vector<String> testUrls=null;
-  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()
   {
-    if (testUrls!=null)
+    if (testUrls != null)
     {
       // return test urls, if there are any, instead of touching cache
       return testUrls;
     }
-    String surls = Cache.getDefault(JWS2HOSTURLS,
-            "http://www.compbio.dundee.ac.uk/jabaws");
-    Vector<String> urls = new Vector<String>();
+    List<String> urls = new ArrayList<>();
+
+    if (this.preferredUrl != null)
+    {
+      urls.add(preferredUrl);
+    }
+
+    String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
     try
     {
       StringTokenizer st = new StringTokenizer(surls, ",");
@@ -489,46 +703,40 @@ 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.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
-                  .warn("This was probably due to a malformed comma separated list"
-                          + " in the "
-                          + JWS2HOSTURLS
+          Cache.warn("Problem whilst trying to make a URL from '"
+                  + ((url != null) ? url : "<null>") + "'");
+          Cache.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.debug("Exception was ", ex);
         }
       }
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.warn(
-              "Error parsing comma separated list of urls in "
-                      + JWS2HOSTURLS + " preference.", ex);
+      Cache.warn("Error parsing comma separated list of urls in "
+              + JWS2HOSTURLS + " preference.", ex);
     }
-    if (urls.size() >= 0)
-    {
-      return urls;
-    }
-    return null;
+    return urls;
   }
 
   public Vector<Jws2Instance> getServices()
   {
-    return (services == null) ? new Vector<Jws2Instance>()
-            : new Vector<Jws2Instance>(services);
+    return (services == null) ? new Vector<>()
+            : new Vector<>(services);
   }
 
   /**
@@ -541,8 +749,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     try
     {
-      compbio.ws.client.WSTester.main(new String[]
-      { "-h=" + foo.toString() });
+      compbio.ws.client.WSTester
+              .main(new String[]
+              { "-h=" + foo.toString() });
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -560,6 +769,22 @@ 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
@@ -570,6 +795,16 @@ 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);
@@ -580,8 +815,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return thr;
   }
 
-  Vector<String> invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null;
-
   /**
    * @return the invalidServiceUrls
    */
@@ -608,11 +841,11 @@ 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);
@@ -628,7 +861,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (invalidServiceUrls == null)
     {
-      invalidServiceUrls = new Vector<String>();
+      invalidServiceUrls = new Vector<>();
     }
     if (!invalidServiceUrls.contains(jwsservers))
     {
@@ -650,7 +883,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       if (getInvalidServiceUrls() != null
               && getInvalidServiceUrls().size() > 0)
       {
-        ermsg.append("URLs that could not be contacted: \n");
+        ermsg.append(MessageManager.getString("warn.urls_not_contacted")
+                + ": \n");
         for (String svcurl : getInvalidServiceUrls())
         {
           if (list)
@@ -666,7 +900,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       if (getUrlsWithoutServices() != null
               && getUrlsWithoutServices().size() > 0)
       {
-        ermsg.append("URLs without any JABA Services : \n");
+        ermsg.append(
+                MessageManager.getString("warn.urls_no_jaba") + ": \n");
         for (String svcurl : getUrlsWithoutServices())
         {
           if (list)
@@ -689,16 +924,143 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public int getServerStatusFor(String url)
   {
-    if (validServiceUrls!=null && validServiceUrls.contains(url))
+    if (validServiceUrls != null && validServiceUrls.contains(url))
     {
       return 1;
     }
-    if (urlsWithoutServices!=null && urlsWithoutServices.contains(url))
-    return 0;
-    if (invalidServiceUrls!=null && invalidServiceUrls.contains(url))
+    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<>();
+    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<>();
+
+  /**
+   * 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<>();
+    }
+    Map<String, String> prefmap = preferredServiceMap.get(afid);
+    if (prefmap == null)
+    {
+      prefmap = new HashMap<>();
+      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;
+    }
+  }
 }