X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FWsPreferences.java;h=165e8f2b20f2bd018439c565d8ee8f1855de0e71;hb=fee1b781ca14aadea5d112fc554fe14879c787c5;hp=45654f2ba297013859971533c8f6cbcf84a31335;hpb=8a91e5ca60b3e9b96854cc753544d60f63a02810;p=jalview.git

diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 45654f2..165e8f2 100644
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -1,18 +1,48 @@
+/*
+ * 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.
+ *  
+ * 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.gui;
 
+import jalview.bin.Cache;
+import jalview.jbgui.GWsPreferences;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.rest.RestServiceDescription;
+
 import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
 import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.net.URL;
+import java.util.List;
 import java.util.Vector;
 
-import javax.swing.JCheckBox;
 import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
+import javax.swing.JTable;
 import javax.swing.JTextField;
-
-import jalview.bin.Cache;
-import jalview.jbgui.GWsPreferences;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableCellRenderer;
 
 public class WsPreferences extends GWsPreferences
 {
@@ -23,244 +53,640 @@ public class WsPreferences extends GWsPreferences
     initFromPreferences();
   }
 
-  Vector<String> wsUrls,oldUrls;
+  List<String> wsUrls;
+
+  Vector<String> oldUrls, rsbsUrls, oldRsbsUrls;
+
   private boolean needWsMenuUpdate;
-  private boolean oldJws1,oldJws2,oldIndexByHost,oldIndexByType,oldEnfin;
+
+  private boolean oldJws1, oldJws2, oldIndexByHost, oldIndexByType,
+          oldEnfin, oldWsWarning;
+
   private void initFromPreferences()
   {
 
-    wsUrls = jalview.ws.jws2.Jws2Discoverer.getServiceUrls();
-    if (wsUrls!=null) {
+    wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+    if (!wsUrls.isEmpty())
+    {
       oldUrls = new Vector<String>(wsUrls);
-    } else {
-      oldUrls=null;
-      wsUrls=new Vector<String>();
     }
+    else
+    {
+      oldUrls = null;
+      wsUrls = new Vector<String>();
+    }
+    wsList.setDefaultRenderer(Integer.class, new JabaWSStatusRenderer());
+    wsList.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
     updateList();
-    enableEnfinServices.setSelected(oldEnfin=Cache.getDefault(
+    rsbsUrls = jalview.ws.rest.RestClient.getRsbsDescriptions();
+    if (rsbsUrls != null)
+    {
+      oldRsbsUrls = new Vector<String>(rsbsUrls);
+    }
+    else
+    {
+      oldRsbsUrls = null;
+      rsbsUrls = new Vector<String>();
+    }
+    updateRsbsList();
+    enableEnfinServices.setSelected(oldEnfin = Cache.getDefault(
             "SHOW_ENFIN_SERVICES", true));
-    enableJws1Services.setSelected(oldJws1=Cache.getDefault("SHOW_JWS1_SERVICES",
-            true));
-    enableJws2Services.setSelected(oldJws2=Cache.getDefault("SHOW_JWS2_SERVICES",
-            true));
-    indexByHost.setSelected(oldIndexByHost=Cache.getDefault("WSMENU_BYHOST", true));
-    indexByType.setSelected(oldIndexByType=Cache.getDefault("WSMENU_BYTYPE", true));
+    enableEnfinServices.addActionListener(updateAction);
+    enableJws2Services.setSelected(oldJws2 = Cache.getDefault(
+            "SHOW_JWS2_SERVICES", true));
+    enableJws2Services.addActionListener(updateAction);
+    indexByHost.setSelected(oldIndexByHost = Cache.getDefault(
+            "WSMENU_BYHOST", false));
+    indexByHost.addActionListener(updateAction);
+    indexByType.setSelected(oldIndexByType = Cache.getDefault(
+            "WSMENU_BYTYPE", false));
+    indexByType.addActionListener(updateAction);
+    displayWsWarning.setSelected(oldWsWarning = Cache.getDefault(
+            "SHOW_WSDISCOVERY_ERRORS", true));
+  }
+
+  ActionListener updateAction = new ActionListener()
+  {
+
+    @Override
+    public void actionPerformed(ActionEvent e)
+    {
+      update++;
+    }
+
+  };
+
+  private void updateList()
+  {
+    Object tdat[][] = new Object[wsUrls.size()][2];
+    int r = 0;
+    for (String url : wsUrls)
+    {
+      int status = Jws2Discoverer.getDiscoverer().getServerStatusFor(url);
+      tdat[r][1] = new Integer(status);
+      tdat[r++][0] = url;
+    }
+
+    wsList.setModel(new WsUrlTableModel(tdat));
+    wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(
+            10);
+  }
+
+  private class JabaWSStatusRenderer extends JPanel implements
+          TableCellRenderer
+  {
+    public JabaWSStatusRenderer()
+    {
+      setOpaque(true);
+      setMinimumSize(new Dimension(10, 10));
+      // setText(" ");
+
+    }
+
+    /**
+     * render an Integer reflecting service status as a colour and symbol
+     */
+
+    @Override
+    public Component getTableCellRendererComponent(JTable arg0,
+            Object status, boolean isSelected, boolean hasFocus, int row,
+            int column)
+    {
+      Color c;
+      String t = new String("");
+      switch (((Integer) status).intValue())
+      {
+      case 1:
+        // cb.setSelected(true);
+        // cb.setBackground(
+        c = Color.green;
+        break;
+      case 0:
+        // cb.setSelected(true);
+        // cb.setBackground(
+        c = Color.lightGray;
+        break;
+      case -1:
+        // cb.setSelected(false);
+        // cb.setBackground(
+        c = Color.red;
+        break;
+      default:
+        // cb.setSelected(false);
+        // cb.setBackground(
+        c = Color.orange;
+      }
+      setBackground(c);
+      // setText(t);
+      return this;
+
+    }
+
+  }
+
+  private class WsUrlTableModel extends AbstractTableModel
+  {
+
+    private Object[][] data;
+
+    private String[] columnNames = new String[] {
+        MessageManager.getString("label.service_url"),
+        MessageManager.getString("label.status") };
+
+    public WsUrlTableModel(Object[][] tdat)
+    {
+      this.data = tdat;
+    }
+
+    @Override
+    public int getColumnCount()
+    {
+      return 2;
+    }
+
+    @Override
+    public String getColumnName(int column)
+    {
+      return columnNames[column];
+    }
+
+    @Override
+    public int getRowCount()
+    {
+      if (data == null)
+      {
+        return 0;
+      }
+      return data.length;
+    }
+
+    @Override
+    public java.lang.Class<?> getColumnClass(int columnIndex)
+    {
+      return getValueAt(0, columnIndex).getClass();
+    };
+
+    @Override
+    public Object getValueAt(int rowIndex, int columnIndex)
+    {
+      return data[rowIndex][columnIndex];
+    }
+
   }
-  private void updateList() {
-    wsList.setListData(wsUrls);
+
+  private void updateRsbsList()
+  {
+    sbrsList.setListData(rsbsUrls);
   }
-  private void updateServiceList() {
-    jalview.ws.jws2.Jws2Discoverer.setServiceUrls(wsUrls);
+
+  private void updateServiceList()
+  {
+    Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
   }
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GWsPreferences#deleteWsUrl_actionPerformed(java.awt.event.ActionEvent)
+
+  private void updateRsbsServiceList()
+  {
+    jalview.ws.rest.RestClient.setRsbsServices(rsbsUrls);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GWsPreferences#deleteWsUrl_actionPerformed(java.awt.event
+   * .ActionEvent)
    */
   @Override
   protected void deleteWsUrl_actionPerformed(ActionEvent e)
   {
-    int sel = wsList.getSelectedIndex();
-    if (sel>-1)
+    int sel = wsList.getSelectedRow();
+    if (sel > -1)
     {
-      wsUrls.removeElementAt(sel);
+      wsUrls.remove(sel);
+      update++;
       updateList();
     }
   }
 
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GWsPreferences#editWsUrl_actionPerformed(java.awt.event.ActionEvent)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.jbgui.GWsPreferences#editWsUrl_actionPerformed(java.awt.event.
+   * ActionEvent)
    */
   @Override
   protected void editWsUrl_actionPerformed(ActionEvent e)
   {
-    int sel = wsList.getSelectedIndex();
-    if (sel>-1)
+    int sel = wsList.getSelectedRow();
+    if (sel > -1)
     {
-      String url=editUrl(wsUrls.elementAt(sel),"Edit JWS2 URL");
-      if (url!=null)
+      String url = editUrl(wsUrls.get(sel),
+              MessageManager.getString("label.edit_jabaws_url"));
+      if (url != null)
       {
         int present = wsUrls.indexOf(url);
-        if (present==-1)
+        if (present == -1)
         {
-          wsUrls.setElementAt(url,sel);
+          update++;
+          wsUrls.set(sel, url);
           updateList();
-        } else {
-          if (present!=sel)
+        }
+        else
+        {
+          if (present != sel)
           {
-            wsUrls.removeElementAt(sel);
+            wsUrls.remove(sel);
             updateList();
           }
         }
       }
     }
   }
-  
-  void updateWsMenuConfig(boolean old) {
-    if (old) {
-      wsUrls = (oldUrls==null) ? null : new Vector(oldUrls);
+
+  @Override
+  protected void newSbrsUrl_actionPerformed(ActionEvent e)
+  {
+    RestServiceEditorPane rse = new RestServiceEditorPane();
+    rse.showDialog(MessageManager.getString("label.add_new_sbrs_service"));
+    String rservice = rse.getEditedRestService();
+    if (rservice != null && !rsbsUrls.contains(rservice))
+    {
+      rsbsUrls.add(rservice);
+      update++;
+      updateRsbsList();
     }
-    Cache.setProperty("SHOW_ENFIN_SERVICES", Boolean.valueOf(old ? oldEnfin : enableEnfinServices.isSelected()).toString());
-    Cache.setProperty("SHOW_JWS1_SERVICES", Boolean.valueOf(old ? oldJws1 : enableJws1Services.isSelected()).toString());
-    Cache.setProperty("SHOW_JWS2_SERVICES", Boolean.valueOf(old ? oldJws2 : enableJws2Services.isSelected()).toString());
-    Cache.setProperty("WSMENU_BYHOST", Boolean.valueOf(old ? oldIndexByHost : indexByHost.isSelected()).toString());
-    Cache.setProperty("WSMENU_BYTYPE", Boolean.valueOf(old ? oldIndexByType : indexByType.isSelected()).toString());
+  }
+
+  @Override
+  protected void editSbrsUrl_actionPerformed(ActionEvent e)
+  {
+    int sel = sbrsList.getSelectedIndex();
+    if (sel > -1)
+    {
+      RestServiceEditorPane rse = new RestServiceEditorPane(
+              new RestServiceDescription(rsbsUrls.elementAt(sel)));
+      rse.showDialog(MessageManager.getString("label.edit_sbrs_entry"));
+      String rservice = rse.getEditedRestService();
+      if (rservice != null)
+      {
+        int present = rsbsUrls.indexOf(rservice);
+        if (present == -1)
+        {
+          update++;
+          rsbsUrls.setElementAt(rservice, sel);
+          updateRsbsList();
+        }
+        else
+        {
+          if (present != sel)
+          {
+            rsbsUrls.removeElementAt(sel);
+            update++;
+            updateRsbsList();
+          }
+        }
+      }
+    }
+  }
+
+  void updateWsMenuConfig(boolean old)
+  {
+    if (old)
+    {
+      if (oldUrls != wsUrls
+              || (wsUrls != null && oldUrls != null && !wsUrls
+                      .equals(oldUrls)))
+      {
+        update++;
+      }
+      wsUrls = (oldUrls == null) ? null : new Vector(oldUrls);
+      if (oldRsbsUrls != rsbsUrls
+              || (rsbsUrls != null && oldRsbsUrls != null && !oldRsbsUrls
+                      .equals(rsbsUrls)))
+      {
+        update++;
+      }
+      oldRsbsUrls = (oldRsbsUrls == null) ? null : new Vector(oldRsbsUrls);
+    }
+    else
+    {
+
+    }
+    Cache.setProperty(
+            "SHOW_ENFIN_SERVICES",
+            Boolean.valueOf(
+                    old ? oldEnfin : enableEnfinServices.isSelected())
+                    .toString());
+    Cache.setProperty(
+            "SHOW_JWS2_SERVICES",
+            Boolean.valueOf(old ? oldJws2 : enableJws2Services.isSelected())
+                    .toString());
+    Cache.setProperty(
+            "WSMENU_BYHOST",
+            Boolean.valueOf(old ? oldIndexByHost : indexByHost.isSelected())
+                    .toString());
+    Cache.setProperty(
+            "WSMENU_BYTYPE",
+            Boolean.valueOf(old ? oldIndexByType : indexByType.isSelected())
+                    .toString());
+
+    Cache.setProperty(
+            "SHOW_WSDISCOVERY_ERRORS",
+            Boolean.valueOf(
+                    old ? oldWsWarning : displayWsWarning.isSelected())
+                    .toString());
     updateServiceList();
+    updateRsbsServiceList();
   }
-  
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GWsPreferences#moveWsUrlDown_actionPerformed(java.awt.event.ActionEvent)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GWsPreferences#moveWsUrlDown_actionPerformed(java.awt.event
+   * .ActionEvent)
    */
   @Override
   protected void moveWsUrlDown_actionPerformed(ActionEvent e)
   {
-    int p=wsList.getSelectedIndex();
-    if (p>-1 && p<wsUrls.size()-1)
+    int p = wsList.getSelectedRow();
+    if (p > -1 && p < wsUrls.size() - 1)
     {
-      String t = wsUrls.get(p+1);
-      wsUrls.setElementAt(wsUrls.elementAt(p), p+1);
-      wsUrls.setElementAt(t, p);
+      String t = wsUrls.get(p + 1);
+      wsUrls.set(p + 1, wsUrls.get(p));
+      wsUrls.set(p, t);
       updateList();
-      wsList.setSelectedIndex(p+1);
+      wsList.getSelectionModel().setSelectionInterval(p + 1, p + 1);
+      update++;
     }
   }
 
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GWsPreferences#moveWsUrlUp_actionPerformed(java.awt.event.ActionEvent)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GWsPreferences#moveWsUrlUp_actionPerformed(java.awt.event
+   * .ActionEvent)
    */
   @Override
   protected void moveWsUrlUp_actionPerformed(ActionEvent e)
   {
-    int p=wsList.getSelectedIndex();
-    if (p>0)
+    int p = wsList.getSelectedRow();
+    if (p > 0)
     {
-      String t = wsUrls.get(p-1);
-      wsUrls.setElementAt(wsUrls.elementAt(p), p-1);
-      wsUrls.setElementAt(t, p);
+      String t = wsUrls.get(p - 1);
+      wsUrls.set(p - 1, wsUrls.get(p));
+      wsUrls.set(p, t);
       updateList();
-      wsList.setSelectedIndex(p-1);
+      wsList.getSelectionModel().setSelectionInterval(p - 1, p - 1);
+      update++;
     }
   }
 
   private String editUrl(String initUrl, String title)
   {
-    String url=initUrl;
-    URL foo;
-    if (url==null)
+    String url = initUrl;
+    URL foo = null;
+    if (url == null)
     {
       url = "";
     }
     JTextField urltf = new JTextField(url, 40);
     JPanel panel = new JPanel(new BorderLayout());
     JPanel pane12 = new JPanel(new BorderLayout());
-    pane12.add(new JLabel("URL: "), BorderLayout.CENTER);
+    pane12.add(new JLabel(MessageManager.getString("label.url")),
+            BorderLayout.CENTER);
     pane12.add(urltf, BorderLayout.EAST);
     panel.add(pane12, BorderLayout.NORTH);
-    boolean valid=false;
-    int resp=JOptionPane.CANCEL_OPTION;
-    while (!valid && (resp=JOptionPane.showInternalConfirmDialog(Desktop.desktop, panel, title, JOptionPane.OK_CANCEL_OPTION))==JOptionPane.OK_OPTION)
+    boolean valid = false;
+    int resp = JvOptionPane.CANCEL_OPTION;
+    while (!valid
+            && (resp = JvOptionPane.showInternalConfirmDialog(
+                    Desktop.desktop, panel, title,
+                    JvOptionPane.OK_CANCEL_OPTION)) == JvOptionPane.OK_OPTION)
     {
-      try {
-        // TODO: do a better job of checking that the url is a valid discovery URL for web services.
-        foo = new URL(urltf.getText().trim());
+      try
+      {
+        // TODO: do a better job of checking that the url is a valid discovery
+        // URL for web services.
+        String tx = urltf.getText().trim();
+        while (tx.length() > 0 && tx.lastIndexOf('/') == tx.length() - 1)
+        {
+          tx = tx.substring(0, tx.length() - 1);
+        }
+        foo = new URL(tx);
         valid = true;
+        urltf.setText(tx);
       } catch (Exception e)
       {
         valid = false;
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "Invalid URL !");
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                MessageManager.getString("label.invalid_url"));
       }
     }
-    if (valid && resp==JOptionPane.OK_OPTION)
+    if (valid && resp == JvOptionPane.OK_OPTION)
     {
-      return urltf.getText().trim();
+      int validate = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+              MessageManager.getString("info.validate_jabaws_server"),
+              MessageManager.getString("label.test_server"),
+              JvOptionPane.YES_NO_OPTION);
+
+      if (validate == JvOptionPane.OK_OPTION)
+      {
+        if (Jws2Discoverer.testServiceUrl(foo))
+        {
+          return foo.toString();
+        }
+        else
+        {
+          int opt = JvOptionPane
+                  .showInternalOptionDialog(
+                          Desktop.desktop,
+                          "The Server  '"
+                                  + foo.toString()
+                                  + "' failed validation,\ndo you want to add it anyway? ",
+                          "Server Validation Failed",
+                          JvOptionPane.YES_NO_OPTION,
+                          JvOptionPane.INFORMATION_MESSAGE, null, null, null);
+          if (opt == JvOptionPane.YES_OPTION)
+          {
+            return foo.toString();
+          }
+          else
+          {
+            JvOptionPane
+                    .showInternalMessageDialog(
+                            Desktop.desktop,
+                            MessageManager
+                                    .getString("warn.server_didnt_pass_validation"));
+          }
+
+        }
+      }
+      else
+      {
+        // just return the URL anyway
+        return foo.toString();
+      }
     }
-    return initUrl; 
+    return initUrl;
   }
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GWsPreferences#newWsUrl_actionPerformed(java.awt.event.ActionEvent)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.jbgui.GWsPreferences#newWsUrl_actionPerformed(java.awt.event.
+   * ActionEvent)
    */
   @Override
   protected void newWsUrl_actionPerformed(ActionEvent e)
   {
-    String url=editUrl(null,"Add new JWS2 URL");
-    if (url!=null)
+    String url = editUrl(null,
+            MessageManager.getString("label.add_jabaws_url"));
+    if (url != null)
     {
       if (!wsUrls.contains(url))
       {
-        int selind = wsList.getSelectedIndex();
-        if (selind>-1)
+        int selind = wsList.getSelectedRow();
+        if (selind > -1)
+        {
+          wsUrls.add(selind, url);
+        }
+        else
         {
-          wsUrls.insertElementAt(url, selind);
-        } else {
-          wsUrls.addElement(url);
+          wsUrls.add(url);
         }
+        update++;
         updateList();
       }
     }
   }
 
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GWsPreferences#refreshWs_actionPerformed(java.awt.event.ActionEvent)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.jbgui.GWsPreferences#refreshWs_actionPerformed(java.awt.event.
+   * ActionEvent)
    */
   @Override
   protected void refreshWs_actionPerformed(ActionEvent e)
   {
-    new Thread(new Runnable() {
+    new Thread(new Runnable()
+    {
 
-      @Override
       public void run()
       {
+        // force a refresh.
+        lastrefresh = update - 1;
         updateWsMenuConfig(false);
         refreshWsMenu(true);
-      }      
+      }
     }).start();
-    
+
   }
 
+  /**
+   * Refresh the web services menus - but only if there has been a change in the
+   * configuration (indicated by update!=lastrefresh)
+   * 
+   * @param showProgress
+   *          show progress in dialog or on desktop
+   */
   protected void refreshWsMenu(boolean showProgress)
   {
     if (showProgress)
     {
-      new Thread(new Runnable() {
+      new Thread(new Runnable()
+      {
 
-        @Override
         public void run()
         {
           progressBar.setVisible(true);
           validate();
           progressBar.setIndeterminate(true);
-          Desktop.instance.startServiceDiscovery(true); // wait around for all threads to complete
+          if (lastrefresh != update)
+          {
+            lastrefresh = update;
+            Desktop.instance.startServiceDiscovery(true); // wait around for all
+                                                          // threads to complete
+            updateList();
+
+          }
           progressBar.setIndeterminate(false);
           progressBar.setVisible(false);
           validate();
-        }      
+        }
       }).start();
-      
-    } else {
-      new Thread(new Runnable() {
 
-        @Override
+    }
+    else
+    {
+      new Thread(new Runnable()
+      {
+
         public void run()
         {
-          Desktop.instance.startServiceDiscovery(false);
+          long ct = System.currentTimeMillis();
+          Desktop.instance.setProgressBar(MessageManager
+                  .getString("status.refreshing_web_service_menus"), ct);
+          if (lastrefresh != update)
+          {
+            lastrefresh = update;
+            Desktop.instance.startServiceDiscovery(true);
+            updateList();
+          }
+          Desktop.instance.setProgressBar(null, ct);
         }
-        
+
       }).start();
     }
   }
 
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GWsPreferences#resetWs_actionPerformed(java.awt.event.ActionEvent)
+  /**
+   * state counters for ensuring that updates only happen if config has changed.
+   */
+  private long update = 0, lastrefresh = 0;
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GWsPreferences#resetWs_actionPerformed(java.awt.event.ActionEvent
+   * )
    */
   @Override
   protected void resetWs_actionPerformed(ActionEvent e)
   {
-    jalview.ws.jws2.Jws2Discoverer.setServiceUrls(null);
-    wsUrls = jalview.ws.jws2.Jws2Discoverer.getServiceUrls(); 
+    Jws2Discoverer.getDiscoverer().setServiceUrls(null);
+    List<String> nwsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+    if (!wsUrls.equals(nwsUrls))
+    {
+      update++;
+    }
+    wsUrls = nwsUrls;
     updateList();
+
+    updateAndRefreshWsMenuConfig(true);
   }
-  protected void ok_ActionPerformed(ActionEvent e) {
-    updateWsMenuConfig(false);
-    // todo: work out if the ws list needs updating ?
-    updateServiceList();
-    refreshWsMenu(false);
+
+  protected void ok_ActionPerformed(ActionEvent e)
+  {
+    // update everything regardless.
+    updateAndRefreshWsMenuConfig(false);
+  }
+
+  public void updateAndRefreshWsMenuConfig(
+          final boolean showProgressInDialog)
+  {
+    new Thread(new Runnable()
+    {
+
+      public void run()
+      {
+        updateWsMenuConfig(false);
+        refreshWsMenu(showProgressInDialog);
+      }
+    }).start();
+
   }
 }