X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FWsJobParameters.java;h=d8259f9f2022d92c7990a0c2b7e31cc6913ed800;hb=cd669a0e8c7b91b379bca8fe6e702cf0fcbd1ce0;hp=b905b639fbaeb270e0fa7ea414140f48409e24b6;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index b905b63..d8259f9 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -1,36 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.gui;
 
-import jalview.gui.OptsAndParamsPage.OptionBox;
-import jalview.gui.OptsAndParamsPage.ParamBox;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.params.WsParamSetI;
-
 import java.awt.BorderLayout;
 import java.awt.Component;
 import java.awt.Dimension;
@@ -59,7 +48,6 @@ import javax.swing.JComboBox;
 import javax.swing.JDialog;
 import javax.swing.JFrame;
 import javax.swing.JLabel;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JSplitPane;
@@ -68,14 +56,26 @@ import javax.swing.border.TitledBorder;
 import javax.swing.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
 
-import net.miginfocom.swing.MigLayout;
-
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
 import compbio.metadata.Parameter;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
+import jalview.bin.Console;
+import jalview.gui.OptsAndParamsPage.OptionBox;
+import jalview.gui.OptsAndParamsPage.ParamBox;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.WsParamSetI;
+import net.miginfocom.swing.MigLayout;
 
 /**
  * job parameter editing/browsing dialog box. User can browse existing settings
@@ -185,7 +185,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * @param jobArgset
    */
   public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
-          Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
+          Jws2Instance service, WsParamSetI preset,
+          List<Argument> jobArgset)
   {
     super();
     jbInit();
@@ -216,13 +217,15 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     frame = new JDialog(Desktop.instance, true);
 
-    frame.setTitle("Edit parameters for " + service.getActionText());
+    frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
+            new String[]
+            { service.getActionText() }));
     Rectangle deskr = Desktop.instance.getBounds();
     Dimension pref = this.getPreferredSize();
-    frame.setBounds(new Rectangle(
-            (int) (deskr.getCenterX() - pref.width / 2), (int) (deskr
-                    .getCenterY() - pref.height / 2), pref.width,
-            pref.height));
+    frame.setBounds(
+            new Rectangle((int) (deskr.getCenterX() - pref.width / 2),
+                    (int) (deskr.getCenterY() - pref.height / 2),
+                    pref.width, pref.height));
     frame.setContentPane(this);
 
     // should perhaps recover defaults from user prefs.
@@ -230,6 +233,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     frame.validate();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         // jobPanel.setDividerLocation(0.25);
@@ -263,64 +267,80 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
       }
     });
-    updatepref = JvSwingUtils.makeButton(MessageManager.getString("action.update"),
+    updatepref = JvSwingUtils.makeButton(
+            MessageManager.getString("action.update"),
             MessageManager.getString("label.update_user_parameter_set"),
             new ActionListener()
             {
 
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 update_actionPerformed(e);
               }
             });
-    deletepref = JvSwingUtils.makeButton(MessageManager.getString("action.delete"),
+    deletepref = JvSwingUtils.makeButton(
+            MessageManager.getString("action.delete"),
             MessageManager.getString("label.delete_user_parameter_set"),
             new ActionListener()
             {
 
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 delete_actionPerformed(e);
               }
             });
-    createpref = JvSwingUtils.makeButton(MessageManager.getString("action.create"),
+    createpref = JvSwingUtils.makeButton(
+            MessageManager.getString("action.create"),
             MessageManager.getString("label.create_user_parameter_set"),
             new ActionListener()
             {
 
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 create_actionPerformed(e);
               }
             });
-    revertpref = JvSwingUtils.makeButton(MessageManager.getString("action.revert"),
-            MessageManager.getString("label.revert_changes_user_parameter_set"),
+    revertpref = JvSwingUtils.makeButton(
+            MessageManager.getString("action.revert"),
+            MessageManager
+                    .getString("label.revert_changes_user_parameter_set"),
             new ActionListener()
             {
 
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 revert_actionPerformed(e);
               }
             });
-    startjob = JvSwingUtils.makeButton(MessageManager.getString("action.start_job"),
-            MessageManager.getString("label.start_job_current_settings"), new ActionListener()
+    startjob = JvSwingUtils.makeButton(
+            MessageManager.getString("action.start_job"),
+            MessageManager.getString("label.start_job_current_settings"),
+            new ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 startjob_actionPerformed(e);
               }
             });
-    canceljob = JvSwingUtils.makeButton(MessageManager.getString("action.cancel_job"),
-            MessageManager.getString("label.cancel_job_close_dialog"), new ActionListener()
+    canceljob = JvSwingUtils.makeButton(
+            MessageManager.getString("action.cancel_job"),
+            MessageManager.getString("label.cancel_job_close_dialog"),
+            new ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 canceljob_actionPerformed(e);
               }
             });
 
-    setDetails.setBorder(new TitledBorder(MessageManager.getString("label.details")));
+    setDetails.setBorder(
+            new TitledBorder(MessageManager.getString("label.details")));
     setDetails.setLayout(new BorderLayout());
     setDescr.setColumns(40);
     setDescr.setWrapStyleWord(true);
@@ -328,9 +348,9 @@ public class WsJobParameters extends JPanel implements ItemListener,
     setDescr.setBackground(getBackground());
     setDescr.setEditable(true);
     setDescr.getDocument().addDocumentListener(this);
-    setDescr.setToolTipText(MessageManager.getString("label.edit_notes_parameter_set"));
+    setDescr.setToolTipText(
+            MessageManager.getString("label.edit_notes_parameter_set"));
     JScrollPane setDescrView = new JScrollPane();
-    // setDescrView.setPreferredSize(new Dimension(350, 200));
     setDescrView.getViewport().setView(setDescr);
     setName.setEditable(true);
     setName.addItemListener(this);
@@ -339,7 +359,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
     GridBagLayout gbl = new GridBagLayout();
     SetNamePanel.setLayout(gbl);
 
-    JLabel setNameLabel = new JLabel(MessageManager.getString("label.current_parameter_set_name"));
+    JLabel setNameLabel = new JLabel(
+            MessageManager.getString("label.current_parameter_set_name"));
     setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
 
     setNameInfo.add(setNameLabel);
@@ -378,12 +399,14 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     // paramPane.setPreferredSize(new Dimension(360, 400));
     // paramPane.setPreferredSize(null);
-    jobOptions.setBorder(new TitledBorder(MessageManager.getString("label.options")));
+    jobOptions.setBorder(
+            new TitledBorder(MessageManager.getString("label.options")));
     jobOptions.setOpaque(true);
-    paramList.setBorder(new TitledBorder(MessageManager.getString("label.parameters")));
+    paramList.setBorder(
+            new TitledBorder(MessageManager.getString("label.parameters")));
     paramList.setOpaque(true);
-    JPanel bjo = new JPanel(new BorderLayout()), bjp = new JPanel(
-            new BorderLayout());
+    JPanel bjo = new JPanel(new BorderLayout()),
+            bjp = new JPanel(new BorderLayout());
     bjo.add(jobOptions, BorderLayout.CENTER);
     bjp.add(paramList, BorderLayout.CENTER);
     bjp.setOpaque(true);
@@ -411,6 +434,11 @@ public class WsJobParameters extends JPanel implements ItemListener,
     JPanel dialogpanel = new JPanel();
     dialogpanel.add(startjob);
     dialogpanel.add(canceljob);
+    // JAL-1580: setMaximumSize() doesn't work, so just size for the worst case:
+    // check for null is for JUnit usage
+    final int windowHeight = Desktop.instance == null ? 540
+            : Desktop.instance.getHeight();
+    setPreferredSize(new Dimension(540, windowHeight));
     add(dialogpanel, BorderLayout.SOUTH);
     validate();
   }
@@ -418,7 +446,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
   protected void revert_actionPerformed(ActionEvent e)
   {
     reInitDialog(lastParmSet);
-
+    updateWebServiceMenus();
   }
 
   protected void update_actionPerformed(ActionEvent e)
@@ -447,6 +475,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
       _deleteUserPreset(lastParmSet);
     }
     reInitDialog(null); // service default
+    updateWebServiceMenus();
   }
 
   protected void create_actionPerformed(ActionEvent e)
@@ -457,12 +486,14 @@ public class WsJobParameters extends JPanel implements ItemListener,
       _storeCurrentPreset(curname);
       lastParmSet = curname;
       isUserPreset = true;
+      reInitDialog(curname);
       initArgSetModified();
+      updateWebServiceMenus();
     }
     else
     {
       // TODO: show warning
-      System.err.println("Invalid name. Not saved.");
+      jalview.bin.Console.errPrintln("Invalid name. Not saved.");
     }
   }
 
@@ -503,8 +534,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
     List<ArgumentI> jobArgset = null;
     settingDialog = true;
     { // instantiate the abstract proxy for Jaba objects
-      jobArgset = jabajobArgset == null ? null : JabaParamStore
-              .getJwsArgsfromJaba(jabajobArgset);
+      jobArgset = jabajobArgset == null ? null
+              : JabaParamStore.getJwsArgsfromJaba(jabajobArgset);
       p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
                  // null;
     }
@@ -512,7 +543,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     Hashtable exnames = new Hashtable();
     for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
     {
-      exnames.put((String) setName.getItemAt(i), setName.getItemAt(i));
+      exnames.put(setName.getItemAt(i), setName.getItemAt(i));
     }
     servicePresets = new Hashtable();
     // Add the default entry - if not present already.
@@ -568,17 +599,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
   @SuppressWarnings("unchecked")
   private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
   {
-    boolean setDefaultParams=false;
+    boolean setDefaultParams = false;
     if (lastParmSet == null)
     {
       isUserPreset = false;
       // First call - so provide Service default settings
       setName.setSelectedItem(lastSetName = SVC_DEF);
     }
-    if (p==null && SVC_DEF.equals(""+setName.getSelectedItem()))
+    if (p == null && SVC_DEF.equals("" + setName.getSelectedItem()))
     {
       // indicate that service defaults should be set if available
-      setDefaultParams=true;
+      setDefaultParams = true;
     }
     // populate table from default parameter set.
     List<ArgumentI> args = paramStore.getServiceParameters();
@@ -586,9 +617,9 @@ public class WsJobParameters extends JPanel implements ItemListener,
     // split to params and required arguments
     {
       int cw = 0;
-      boolean optset=false;
+      boolean optset = false;
       for (ArgumentI myarg : args)
-      { 
+      {
         // Ideally, Argument would implement isRequired !
         if (myarg instanceof ParameterI)
         {
@@ -611,7 +642,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
           }
           else
           {
-            System.err.println("Ignoring unknown service argument type "
+            jalview.bin.Console.errPrintln("Ignoring unknown service argument type "
                     + myarg.getClass().getName());
           }
         }
@@ -654,7 +685,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         {
           if (arg instanceof OptionI)
           {
-            // System.out.println("Setting option "
+            // jalview.bin.Console.outPrintln("Setting option "
             // + System.identityHashCode(arg) + ":" + arg.getName()
             // + " with " + arg.getDefaultValue());
             opanp.selectOption((OptionI) arg, arg.getValue());
@@ -687,7 +718,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   private void updateButtonDisplay()
   {
-    boolean _update = false, _create = false, _delete = false, _revert = false;
+    boolean _update = false, _create = false, _delete = false,
+            _revert = false;
     if (modifiedElements.size() > 0)
     {
       // set modified
@@ -713,6 +745,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     validate();
   }
 
+  @Override
   public void argSetModified(Object modifiedElement, boolean b)
   {
     if (settingDialog)
@@ -757,8 +790,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
     boolean stn = settingDialog;
     boolean renamed = false;
     settingDialog = true;
-    String nm = (curSetName != null ? curSetName : (String) setName
-            .getSelectedItem());
+    String nm = (curSetName != null ? curSetName
+            : (String) setName.getSelectedItem());
     // check if the name is reserved - if it is, rename it.
     if (isServicePreset(nm))
     {
@@ -804,16 +837,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
     settingDialog = stn;
   }
 
+  @Override
   public void refreshParamLayout()
   {
     // optsAndparams.setPreferredSize(null);
     FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
     int sep = fl.getVgap();
     boolean fh = true;
-    int os = 0, s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
-            + jobOptions.getBorder().getBorderInsets(jobOptions).top
-            + 2
-            * sep;
+    int os = 0,
+            s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
+                    + jobOptions.getBorder().getBorderInsets(jobOptions).top
+                    + 2 * sep;
     /**
      * final height for viewport
      */
@@ -822,8 +856,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
             - jobOptions.getBorder().getBorderInsets(jobOptions).left
             + jobOptions.getBorder().getBorderInsets(jobOptions).right;
 
-    int w = 2
-            * fl.getHgap()
+    int w = 2 * fl.getHgap()
             + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH
                     : OptsAndParamsPage.PARAM_WIDTH);
     int hgap = fl.getHgap(), cw = hgap;
@@ -841,7 +874,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         if (cw + 120 > panewidth)
         {
           jobOptions.add(pbox, "wrap");
-          // System.out.println("Wrap on "+pbox.option.getName());
+          // jalview.bin.Console.outPrintln("Wrap on "+pbox.option.getName());
           cw = hgap + pbox.getSize().width;
           fh = true;
         }
@@ -913,7 +946,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
     // TODO: waste some time trying to eliminate any unnecessary .validate calls
     // here
-    // System.out.println("Size will be : "+w+","+os);
+    // jalview.bin.Console.outPrintln("Size will be : "+w+","+os);
     // optsAndparams.setPreferredSize(null);
     // paramPane.getViewport().setView(optsAndparams);
     paramPane.getViewport().setAutoscrolls(true);
@@ -925,6 +958,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * testing method - grab a service and parameter set and show the window
    * 
    * @param args
+   * @j2sIgnore
    */
   public static void main(String[] args)
   {
@@ -933,16 +967,16 @@ public class WsJobParameters extends JPanel implements ItemListener,
     int p = 0;
     if (args.length > 0)
     {
-      Vector<String> services = new Vector<String>();
+      Vector<String> services = new Vector<>();
       services.addElement(args[p++]);
-      Jws2Discoverer.setServiceUrls(services);
+      Jws2Discoverer.getDiscoverer().setServiceUrls(services);
     }
     try
     {
       disc.run();
     } catch (Exception e)
     {
-      System.err.println("Aborting. Problem discovering services.");
+      jalview.bin.Console.errPrintln("Aborting. Problem discovering services.");
       e.printStackTrace();
       return;
     }
@@ -989,9 +1023,9 @@ public class WsJobParameters extends JPanel implements ItemListener,
               pr = en.next();
             }
             {
-              System.out.println("Testing opts dupes for "
-                      + lastserv.getUri() + " : "
-                      + lastserv.getActionText() + ":" + pr.getName());
+              jalview.bin.Console.outPrintln("Testing opts dupes for "
+                      + lastserv.getUri() + " : " + lastserv.getActionText()
+                      + ":" + pr.getName());
               List<Option> rg = lastserv.getRunnerConfig().getOptions();
               for (Option o : rg)
               {
@@ -1000,17 +1034,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
                   Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
                 } catch (Exception e)
                 {
-                  System.err.println("Failed to copy " + o.getName());
+                  jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
                   e.printStackTrace();
                 } catch (Error e)
                 {
-                  System.err.println("Failed to copy " + o.getName());
+                  jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
                   e.printStackTrace();
                 }
               }
             }
             {
-              System.out.println("Testing param dupes:");
+              jalview.bin.Console.outPrintln("Testing param dupes:");
               List<Parameter> rg = lastserv.getRunnerConfig()
                       .getParameters();
               for (Parameter o : rg)
@@ -1021,17 +1055,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
                           .copyParameter(o);
                 } catch (Exception e)
                 {
-                  System.err.println("Failed to copy " + o.getName());
+                  jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
                   e.printStackTrace();
                 } catch (Error e)
                 {
-                  System.err.println("Failed to copy " + o.getName());
+                  jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
                   e.printStackTrace();
                 }
               }
             }
             {
-              System.out.println("Testing param write:");
+              jalview.bin.Console.outPrintln("Testing param write:");
               List<String> writeparam = null, readparam = null;
               try
               {
@@ -1039,34 +1073,34 @@ public class WsJobParameters extends JPanel implements ItemListener,
                         .writeParameterSet(
                                 pr.getArguments(lastserv.getRunnerConfig()),
                                 " ");
-                System.out.println("Testing param read :");
+                jalview.bin.Console.outPrintln("Testing param read :");
                 List<Option> pset = jalview.ws.jws2.ParameterUtils
                         .processParameters(writeparam,
                                 lastserv.getRunnerConfig(), " ");
                 readparam = jalview.ws.jws2.ParameterUtils
                         .writeParameterSet(pset, " ");
-                Iterator<String> o = pr.getOptions().iterator(), s = writeparam
-                        .iterator(), t = readparam.iterator();
+                Iterator<String> o = pr.getOptions().iterator(),
+                        s = writeparam.iterator(), t = readparam.iterator();
                 boolean failed = false;
                 while (s.hasNext() && t.hasNext())
                 {
                   String on = o.next(), sn = s.next(), st = t.next();
                   if (!sn.equals(st))
                   {
-                    System.out.println("Original was " + on
-                            + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
-                            + st);
+                    jalview.bin.Console.outPrintln(
+                            "Original was " + on + " Phase 1 wrote " + sn
+                                    + "\tPhase 2 wrote " + st);
                     failed = true;
                   }
                 }
                 if (failed)
                 {
-                  System.out.println("Original parameters:\n"
-                          + pr.getOptions());
-                  System.out.println("Wrote parameters in first set:\n"
-                          + writeparam);
-                  System.out.println("Wrote parameters in second set:\n"
-                          + readparam);
+                  jalview.bin.Console.outPrintln(
+                          "Original parameters:\n" + pr.getOptions());
+                  jalview.bin.Console.outPrintln(
+                          "Wrote parameters in first set:\n" + writeparam);
+                  jalview.bin.Console.outPrintln(
+                          "Wrote parameters in second set:\n" + readparam);
 
                 }
               } catch (Exception e)
@@ -1076,8 +1110,9 @@ public class WsJobParameters extends JPanel implements ItemListener,
             }
             WsJobParameters pgui = new WsJobParameters(lastserv,
                     new JabaPreset(lastserv, pr));
-            JFrame jf = new JFrame("Parameters for "
-                    + lastserv.getActionText());
+            JFrame jf = new JFrame(MessageManager
+                    .formatMessage("label.ws_parameters_for", new String[]
+                    { lastserv.getActionText() }));
             JPanel cont = new JPanel(new BorderLayout());
             pgui.validate();
             cont.setPreferredSize(pgui.getPreferredSize());
@@ -1089,40 +1124,47 @@ public class WsJobParameters extends JPanel implements ItemListener,
             jf.addWindowListener(new WindowListener()
             {
 
+              @Override
               public void windowActivated(WindowEvent e)
               {
                 // TODO Auto-generated method stub
 
               }
 
+              @Override
               public void windowClosed(WindowEvent e)
               {
               }
 
+              @Override
               public void windowClosing(WindowEvent e)
               {
                 thr.interrupt();
 
               }
 
+              @Override
               public void windowDeactivated(WindowEvent e)
               {
                 // TODO Auto-generated method stub
 
               }
 
+              @Override
               public void windowDeiconified(WindowEvent e)
               {
                 // TODO Auto-generated method stub
 
               }
 
+              @Override
               public void windowIconified(WindowEvent e)
               {
                 // TODO Auto-generated method stub
 
               }
 
+              @Override
               public void windowOpened(WindowEvent e)
               {
                 // TODO Auto-generated method stub
@@ -1141,7 +1183,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
               {
                 inter = true;
               }
-              ;
             }
             jf.dispose();
           }
@@ -1152,8 +1193,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   public boolean isServiceDefaults()
   {
-    return (!isModified() && (lastParmSet != null && lastParmSet
-            .equals(SVC_DEF)));
+    return (!isModified()
+            && (lastParmSet != null && lastParmSet.equals(SVC_DEF)));
   }
 
   public List<ArgumentI> getJobParams()
@@ -1182,7 +1223,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * + storeSetName + ": ", jobParams); }
    * 
    * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
-   * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
+   * p : params) { jalview.bin.Console.outPrintln(nm + ":" + System.identityHashCode(p) +
    * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
    * 
    * private Object[] _getUserPreset(String setName) { Object[] pset =
@@ -1276,18 +1317,33 @@ public class WsJobParameters extends JPanel implements ItemListener,
     SetNamePanel.validate();
     validate();
     settingDialog = false;
+  }
 
+  /**
+   * Rebuild the AlignFrame web service menus (after add/delete of a preset
+   * option).
+   */
+  protected void updateWebServiceMenus()
+  {
+    for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames())
+    {
+      alignFrame.BuildWebServiceMenu();
+    }
   }
 
   String curSetName = null;
 
+  @Override
   public void itemStateChanged(ItemEvent e)
   {
     if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
     {
       final String setname = (String) setName.getSelectedItem();
-      System.out.println("Item state changed for " + setname
-              + " (handling ? " + !settingDialog + ")");
+      if (Console.isDebugEnabled())
+      {
+        Console.debug("Item state changed for " + setname + " (handling ? "
+                + !settingDialog + ")");
+      }
       if (settingDialog)
       {
         // ignore event
@@ -1299,6 +1355,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
       }
       javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
+        @Override
         public void run()
         {
           doPreferenceComboStateChange(setname);
@@ -1319,15 +1376,11 @@ public class WsJobParameters extends JPanel implements ItemListener,
         return;
       }
       settingDialog = true;
-      System.out.println("Prompting to save " + lsetname);
-      if (javax.swing.JOptionPane
-              .showConfirmDialog(
-                      this,
-                      "Parameter set '"
-                              + lsetname
-                              + "' is modifed, and your changes will be lost.\nReally change preset ?",
-                      "Warning: Unsaved Changes",
-                      javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
+      jalview.bin.Console.outPrintln("Prompting to save " + lsetname);
+      if (JvOptionPane.showConfirmDialog(this, "Parameter set '" + lsetname
+              + "' is modifed, and your changes will be lost.\nReally change preset ?",
+              "Warning: Unsaved Changes",
+              JvOptionPane.OK_CANCEL_OPTION) != JvOptionPane.OK_OPTION)
       {
         // revert the combobox to the current item
         settingDialog = true;
@@ -1335,7 +1388,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         settingDialog = false;
         // and leave.
         return;
-        // System.out.println("Saving for " + lsetname);
+        // jalview.bin.Console.outPrintln("Saving for " + lsetname);
         // _storeCurrentPreset(lsetname);
 
       }
@@ -1379,6 +1432,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
    */
   String lastDescrText = null;
 
+  @Override
   public void actionPerformed(ActionEvent e)
   {
     if (e.getSource() instanceof Component)
@@ -1387,7 +1441,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
       if (src.getParent() == setName)
       {
         // rename any existing records we know about for this set.
-        String newname = (String) e.getActionCommand().trim();
+        String newname = e.getActionCommand().trim();
         String msg = null;
         if (isServicePreset(newname))
         {
@@ -1399,18 +1453,21 @@ public class WsJobParameters extends JPanel implements ItemListener,
           settingDialog = false;
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
+            @Override
             public void run()
             {
-              JOptionPane.showMessageDialog(ourframe,
-                      "Invalid name - preset already exists.",
-                      "Invalid name", JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.showMessageDialog(ourframe,
+                      MessageManager.getString(
+                              "label.invalid_name_preset_exists"),
+                      MessageManager.getString("label.invalid_name"),
+                      JvOptionPane.WARNING_MESSAGE);
             }
           });
 
           return;
         }
         curSetName = newname;
-        System.err.println("New name for user setting " + curSetName
+        jalview.bin.Console.errPrintln("New name for user setting " + curSetName
                 + " (was " + setName.getSelectedItem() + ")");
         if (curSetName.equals(setName.getSelectedItem()))
         {
@@ -1431,24 +1488,27 @@ public class WsJobParameters extends JPanel implements ItemListener,
     if (!settingDialog)
     {
 
-      argSetModified(
-              setDescr,
-              (lastDescrText == null ? setDescr.getText().trim().length() > 0
+      argSetModified(setDescr,
+              (lastDescrText == null
+                      ? setDescr.getText().trim().length() > 0
                       : !setDescr.getText().equals(lastDescrText)));
 
     }
   }
 
+  @Override
   public void insertUpdate(DocumentEvent e)
   {
     checkDescrModified();
   }
 
+  @Override
   public void removeUpdate(DocumentEvent e)
   {
     checkDescrModified();
   }
 
+  @Override
   public void changedUpdate(DocumentEvent e)
   {
     checkDescrModified();