X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FWsJobParameters.java;h=b19948999b9f6004f156629c357618938d17acd3;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=89028ef14d191b314b88ef34536452605da96348;hpb=6bfff068aa9c55e54222855df1b1039722660037;p=jalview.git

diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 89028ef..b199489 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -1,31 +1,55 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
 package jalview.gui;
 
+import jalview.gui.OptsAndParamsPage.OptionBox;
+import jalview.gui.OptsAndParamsPage.ParamBox;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.Jws2Discoverer.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.ValueConstrainI;
+import jalview.ws.params.WsParamSetI;
+
 import java.awt.BorderLayout;
-import java.awt.Color;
 import java.awt.Component;
+import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.FlowLayout;
 import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
 import java.awt.GridLayout;
 import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.ContainerEvent;
-import java.awt.event.ContainerListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.WindowEvent;
 import java.awt.event.WindowListener;
-import java.awt.event.WindowStateListener;
+import java.net.URL;
 import java.util.ArrayList;
-import java.util.EventObject;
-import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -35,25 +59,25 @@ import java.util.Vector;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
+import javax.swing.JComponent;
 import javax.swing.JDialog;
 import javax.swing.JFrame;
 import javax.swing.JLabel;
-import javax.swing.JList;
+import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
 import javax.swing.JSlider;
-import javax.swing.JTable;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
 import javax.swing.JTextArea;
 import javax.swing.JTextField;
-import javax.swing.ListSelectionModel;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
 import javax.swing.border.TitledBorder;
-import javax.swing.event.CellEditorListener;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
-import javax.swing.table.*;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
 
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
@@ -61,51 +85,73 @@ import compbio.metadata.Parameter;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
-import compbio.metadata.ValueConstrain;
-import compbio.metadata.WrongParameterException;
 import compbio.metadata.ValueConstrain.Type;
 
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
-
+/**
+ * job parameter editing/browsing dialog box. User can browse existing settings
+ * (user + presets + Defaults), and any changes to parameters creates a modified
+ * user parameter set. LOGIC: If the parameter set is modified, and its name is
+ * a valid, non-existant user parameter set, then a save button is shown. If the
+ * parameter set is modified and its name is a valid, extant user parameter set,
+ * then an update button is shown. If user parameter set's name is edited, and
+ * old name exists as a writable user parameter set, then rename button is
+ * shown. If current parameter set is associated with a user defined parameter
+ * set, then : if set is modifed, a 'revert' button is shown. if set is not
+ * modified, a 'delete' button is shown.
+ * 
+ * @author JimP
+ * 
+ */
 public class WsJobParameters extends JPanel implements ItemListener,
-        ActionListener
+        ActionListener, DocumentListener, OptsParametersContainerI
 {
-  private static final int PARAM_WIDTH = 340, PARAM_HEIGHT = 150,PARAM_CLOSEDHEIGHT=80;
+  URL linkImageURL = getClass().getResource("/images/link.gif");
 
-  private static final int OPTSET_HEIGHT = 30;
-
-  JPanel setDetails = new JPanel();
+  private static final String SVC_DEF = "Defaults"; // this is the null
+                                                    // parameter set as shown to
+                                                    // user
 
-  JPanel settingsPanel = new JPanel();
+  /**
+   * manager for options and parameters.
+   */
+  OptsAndParamsPage opanp = new OptsAndParamsPage(this);
 
+  /**
+   * panel containing job options
+   */
   JPanel jobOptions = new JPanel();
 
-  JScrollPane jobOptionsPane = new JScrollPane();
+  /**
+   * panel containing job parameters
+   */
+  JPanel paramList = new JPanel();
 
-  JPanel jobParameters = new JPanel();
+  
+  
+  JPanel SetNamePanel = new JPanel();
 
-  JPanel paramButtons = new JPanel();
+  JPanel setDetails = new JPanel();
 
-  JPanel paramPanel = new JPanel();
+  JSplitPane settingsPanel = new JSplitPane();
 
-  JLabel modified = new JLabel();
+  JSplitPane jobPanel = new JSplitPane();
 
-  JButton startjob = new JButton();
 
-  JButton canceljob = new JButton();
+  JScrollPane jobOptionsPane = new JScrollPane();
 
-  JButton exportParams = new JButton();
+  JPanel jobParameters = new JPanel();
 
-  JButton importParams = new JButton();
+  JButton createpref = new JButton();
 
-  JButton resetParams = new JButton();
+  JButton deletepref = new JButton();
 
-  JButton addParam = new JButton();
+  JButton revertpref = new JButton();
 
-  JButton removeParam = new JButton();
+  JButton updatepref = new JButton();
 
-  JButton editParam = new JButton();
+  JButton startjob = new JButton();
+
+  JButton canceljob = new JButton();
 
   JComboBox setName = new JComboBox();
 
@@ -113,23 +159,23 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   JScrollPane paramPane = new JScrollPane();
 
-  // JList paramList = new JList();
-  JPanel paramList = new JPanel();
+
+  JPanel optsAndparams = new JPanel();
 
   RunnerConfig serviceOptions;
 
-  List<Parameter> availableParameters;
+  ParamDatastoreI paramStore;
 
-  private BorderLayout jparamLayout;
+  private int MAX_OPTWIDTH = 200;
 
   WsJobParameters(Jws2Instance service)
   {
     this(service, null);
   }
 
-  public WsJobParameters(Jws2Instance service, Preset p)
+  public WsJobParameters(Jws2Instance service, WsParamSetI preset)
   {
-    this(null, service, p, null);
+    this(null, service, preset, null);
   }
 
   /**
@@ -137,16 +183,36 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * @param desktop
    *          - if null, create new JFrame outside of desktop
    * @param service
-   * @param p
+   * @param preset
+   */
+  public WsJobParameters(JFrame parent, Jws2Instance service,
+          WsParamSetI preset, List<Argument> jobArgset)
+  {
+    this(parent, null, service, preset, jobArgset);
+  }
+
+  /**
+   * 
+   * @param parent
+   * @param paramStorei
+   * @param service
+   * @param preset
+   * @param jobArgset
    */
-  public WsJobParameters(JFrame parent, Jws2Instance service, Preset p,
-          List<Argument> jobArgset)
+  public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
+          Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
   {
     super();
     jbInit();
-    argSetModified(false);
+    this.paramStore = paramStorei;
+    if (paramStore == null)
+    {
+      paramStore = service.getParamStore();
+    }
+    this.service = service;
+    // argSetModified(false);
     // populate parameter table
-    initForService(service, p, jobArgset);
+    initForService(service, preset, jobArgset);
     // display in new JFrame attached to parent.
     validate();
   }
@@ -155,6 +221,11 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   JDialog frame = null;
 
+  /**
+   * shows a modal dialog containing the parameters.
+   * 
+   * @return
+   */
   public boolean showRunDialog()
   {
 
@@ -162,11 +233,23 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     frame.setTitle("Edit parameters for " + service.getActionText());
     Rectangle deskr = Desktop.instance.getBounds();
-    frame.setBounds(new Rectangle((int) (deskr.getCenterX() - 240),
-            (int) (deskr.getCenterY() - 92), 380, 385));
+    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.setContentPane(this);
+    
+    // should perhaps recover defaults from user prefs.
 
-    frame.setVisible(true);
+    frame.validate();
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+        public void run()
+        {
+          jobPanel.setDividerLocation(0.25); 
+
+        }
+      });
+  frame.setVisible(true);
 
     if (response > 0)
     {
@@ -177,91 +260,62 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   private void jbInit()
   {
-    modified.setText("*");
-    modified.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    modified.setForeground(Color.red);
-    modified.setHorizontalAlignment(SwingConstants.RIGHT);
-
-    exportParams.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    exportParams.setText("Export");
-    exportParams.setToolTipText("Export parameters to a file");
-    exportParams.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        exportParams_actionPerformed(e);
-      }
-    });
-    importParams.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    importParams.setText("Import");
-    importParams.setToolTipText("Import parameters from a file");
-    importParams.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        importParams_actionPerformed(e);
-      }
-    });
-    resetParams.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    resetParams.setText("Defaults");
-    resetParams.setToolTipText("Reset to defaults");
-    resetParams.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        resetParams_actionPerformed(e);
-      }
-    });
-    addParam.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    addParam.setText("Add");
-    addParam.setToolTipText("Add new parameter");
-    addParam.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        addParam_actionPerformed(e);
-      }
-    });
-    removeParam.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    removeParam.setText("Remove");
-    removeParam.setToolTipText("Remove selected parameter");
-    removeParam.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeParam_actionPerformed(e);
-      }
-    });
-    editParam.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    editParam.setText("Edit");
-    editParam.setToolTipText("Edit selected parameter");
-    editParam.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        editParam_actionPerformed(e);
-      }
-    });
-    startjob.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    startjob.setText("Start");
-    startjob.setToolTipText("Start Job");
-    startjob.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        startjob_actionPerformed(e);
-      }
-    });
-    canceljob.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    canceljob.setText("Cancel");
-    canceljob.setToolTipText("Cancel Job");
-    canceljob.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        canceljob_actionPerformed(e);
-      }
-    });
+    updatepref = JvSwingUtils.makeButton("Update",
+            "Update this existing user parameter set.",
+            new ActionListener()
+            {
+
+              public void actionPerformed(ActionEvent e)
+              {
+                update_actionPerformed(e);
+              }
+            });
+    deletepref = JvSwingUtils.makeButton("Delete",
+            "Delete the currently selected user parameter set.",
+            new ActionListener()
+            {
+
+              public void actionPerformed(ActionEvent e)
+              {
+                delete_actionPerformed(e);
+              }
+            });
+    createpref = JvSwingUtils.makeButton("Create",
+            "Create a new parameter set with the current settings.",
+            new ActionListener()
+            {
+
+              public void actionPerformed(ActionEvent e)
+              {
+                create_actionPerformed(e);
+              }
+            });
+    revertpref = JvSwingUtils.makeButton("Revert",
+            "Undo all changes to the current parameter set",
+            new ActionListener()
+            {
+
+              public void actionPerformed(ActionEvent e)
+              {
+                revert_actionPerformed(e);
+              }
+            });
+    startjob = JvSwingUtils.makeButton("Start Job",
+            "Start Job with current settings.", new ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                startjob_actionPerformed(e);
+              }
+            });
+    canceljob = JvSwingUtils.makeButton("Cancel Job",
+            "Close this dialog and cancel job.", new ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                canceljob_actionPerformed(e);
+              }
+            });
 
     setDetails.setBorder(new TitledBorder("Details"));
     setDetails.setLayout(new BorderLayout());
@@ -269,179 +323,266 @@ public class WsJobParameters extends JPanel implements ItemListener,
     setDescr.setWrapStyleWord(true);
     setDescr.setLineWrap(true);
     setDescr.setBackground(getBackground());
-    setDescr.setEditable(false);
+    setDescr.setEditable(true);
+    setDescr.getDocument().addDocumentListener(this);
+    setDescr.setToolTipText("Click to edit the notes for this parameter set.");
     JScrollPane setDescrView = new JScrollPane();
     // setDescrView.setPreferredSize(new Dimension(350, 200));
     setDescrView.getViewport().setView(setDescr);
     setName.setEditable(true);
     setName.addItemListener(this);
     setName.getEditor().addActionListener(this);
-    modified.setPreferredSize(new Dimension(15, 15));
-    JPanel SetNamePanel = new JPanel();
-    SetNamePanel.setLayout(new BorderLayout());
-    SetNamePanel.add(setName, BorderLayout.WEST);
-    SetNamePanel.add(modified, BorderLayout.EAST);
-    setDetails.add(SetNamePanel, BorderLayout.NORTH);
+    JPanel setNameInfo = new JPanel(new FlowLayout(FlowLayout.LEFT));
+    GridBagLayout gbl = new GridBagLayout();
+    SetNamePanel.setLayout(gbl);
+
+    JLabel setNameLabel = new JLabel("Current parameter set name :");
+    setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    
+    setNameInfo.add(setNameLabel);
+    setNameInfo.add(setName);
+    
+    // initial button visibility
+    updatepref.setVisible(false);
+    deletepref.setVisible(false);
+    revertpref.setVisible(false);
+    createpref.setVisible(false);
+    JPanel setsavebuts = new JPanel();
+    setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT)); // GridLayout(1,2));
+    ((FlowLayout) setsavebuts.getLayout()).setHgap(10);
+    ((FlowLayout) setsavebuts.getLayout()).setVgap(0);
+    JPanel spacer = new JPanel();
+    spacer.setPreferredSize(new Dimension(2,30));
+    setsavebuts.add(spacer);
+    setsavebuts.add(deletepref);
+    setsavebuts.add(revertpref);
+    setsavebuts.add(createpref);
+    setsavebuts.add(updatepref);
+//    setsavebuts.setSize(new Dimension(150, 30));
+    JPanel buttonArea = new JPanel(new GridLayout(1, 1));
+    buttonArea.add(setsavebuts);
+    SetNamePanel.add(setNameInfo);
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.gridheight = 2;
+    gbl.setConstraints(setNameInfo, gbc);
+    SetNamePanel.add(buttonArea);
+    gbc = new GridBagConstraints();
+    gbc.gridx = 0;
+    gbc.gridy = 2;
+    gbc.gridheight = 1;
+    gbl.setConstraints(buttonArea, gbc);
     setDetails.add(setDescrView, BorderLayout.CENTER);
-    // setDetails.setPreferredSize(new Dimension(360, 100));
-    jobParameters.setBorder(new TitledBorder("Parameters"));
-    jobParameters.setLayout(jparamLayout = new BorderLayout());
-    paramPane.setPreferredSize(new Dimension(360, 300));
-    paramPane.getVerticalScrollBar().setUnitIncrement(20);
-    // paramPanel.setPreferredSize(new Dimension(360, 300));
-    paramButtons.setLayout(new GridLayout(2, 3));
-    paramButtons.add(addParam);
-    paramButtons.add(editParam);
-    paramButtons.add(removeParam);
-    // TODO: relayout buttons nicely
-    paramButtons.add(exportParams);
-    paramButtons.add(importParams);
-    paramButtons.add(resetParams);
-    paramPane.getViewport().setView(paramList);
-    jobParameters.add(paramPane, BorderLayout.NORTH);
-    // jobParameters.add(paramButtons, BorderLayout.SOUTH);
-    settingsPanel.setLayout(new BorderLayout());
-    // settingsPanel.add(modified, BorderLayout.NORTH);
-    JPanel jobOptionsPanel = new JPanel();
-    jobOptionsPanel.setBorder(new TitledBorder("Options"));
-    jobOptionsPane.getViewport().setView(jobOptions);
-    jobOptionsPanel.add(jobOptionsPane);
-    settingsPanel.add(jobOptionsPanel, BorderLayout.NORTH);
-    settingsPanel.add(jobParameters, BorderLayout.SOUTH);
 
+    jobParameters.setBorder(new TitledBorder("Parameters"));
+    paramPane.setPreferredSize(new Dimension(360, 400));
+    jobOptions.setBorder(new TitledBorder("Options"));
+    
+    paramList.setBorder(new TitledBorder("Parameters"));
+    
+    JPanel bjo=new JPanel(new BorderLayout()),bjp=new JPanel(new BorderLayout());
+    bjo.add(jobOptions, BorderLayout.CENTER);
+    bjp.add(paramList, BorderLayout.CENTER);
+    optsAndparams.setLayout(new BorderLayout()); 
+
+    optsAndparams.add(bjo, BorderLayout.CENTER);
+    optsAndparams.add(bjp, BorderLayout.SOUTH);
+    paramPane.setViewportView(optsAndparams);
+ 
     setLayout(new BorderLayout());
-    // setPreferredSize(new Dimension(400, 600));
-    // setSize(new Dimension(400, 600));
-    add(setDetails, BorderLayout.NORTH);
-    add(settingsPanel, BorderLayout.CENTER);
+    jobPanel.setLeftComponent(setDetails);
+    jobPanel.setRightComponent(paramPane);
+    jobPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
+
+    add(SetNamePanel, BorderLayout.NORTH);
+    add(jobPanel, BorderLayout.CENTER);
+
     JPanel dialogpanel = new JPanel();
     dialogpanel.add(startjob);
     dialogpanel.add(canceljob);
     add(dialogpanel, BorderLayout.SOUTH);
   }
 
-  protected void canceljob_actionPerformed(ActionEvent e)
+  protected void revert_actionPerformed(ActionEvent e)
   {
-    response = 0;
-    if (frame != null)
-    {
-      frame.setVisible(false);
-    }
+    reInitDialog(lastParmSet);
+
   }
 
-  protected void startjob_actionPerformed(ActionEvent e)
+  protected void update_actionPerformed(ActionEvent e)
   {
-    response = 1;
-    if (frame != null)
+    if (isUserPreset)
     {
-      frame.setVisible(false);
+      String curname = ((String) setName.getSelectedItem()).trim();
+      _updatePreset(lastParmSet, curname);
+      lastParmSet = curname;
+      isUserPreset = true;
+      initArgSetModified();
+      syncSetNamesWithStore();
     }
   }
 
-  protected void editParam_actionPerformed(ActionEvent e)
+  private void _deleteUserPreset(String lastParmSet2)
   {
-    // TODO Auto-generated method stub
-
+    paramStore.deletePreset(lastParmSet2);
   }
 
-  protected void removeParam_actionPerformed(ActionEvent e)
+  protected void delete_actionPerformed(ActionEvent e)
   {
-    // TODO Auto-generated method stub
-
+    if (isUserPreset)
+    {
+      // delete current preset's saved entry
+      _deleteUserPreset(lastParmSet);
+    }
+    reInitDialog(null); // service default
   }
 
-  protected void addParam_actionPerformed(ActionEvent e)
+  protected void create_actionPerformed(ActionEvent e)
   {
-    // TODO Auto-generated method stub
-
+    String curname = ((String) setName.getSelectedItem()).trim();
+    if (curname.length() > 0)
+    {
+      _storeCurrentPreset(curname);
+      lastParmSet = curname;
+      isUserPreset = true;
+      initArgSetModified();
+    }
+    else
+    {
+      // TODO: show warning
+      System.err.println("Invalid name. Not saved.");
+    }
   }
 
-  protected void resetParams_actionPerformed(ActionEvent e)
+  protected void canceljob_actionPerformed(ActionEvent e)
   {
-    // TODO Auto-generated method stub
-
+    response = 0;
+    if (frame != null)
+    {
+      frame.setVisible(false);
+    }
   }
 
-  protected void importParams_actionPerformed(ActionEvent e)
+  protected void startjob_actionPerformed(ActionEvent e)
   {
-    // TODO Auto-generated method stub
-
+    response = 1;
+    if (frame != null)
+    {
+      frame.setVisible(false);
+    }
   }
 
-  protected void exportParams_actionPerformed(ActionEvent e)
-  {
-    // TODO Auto-generated method stub
+  Jws2Instance service;
 
-  }
+  /**
+   * list of service presets in the gui
+   */
+  Hashtable servicePresets = null;
 
-  Jws2Instance service;
+  /**
+   * set if dialog is being set - so handlers will avoid spurious events
+   */
+  boolean settingDialog = false;
 
-  void initForService(Jws2Instance service, Preset p,
-          List<Argument> jobArgset)
+  void initForService(Jws2Instance service, WsParamSetI jabap,
+          List<Argument> jabajobArgset)
   {
-    this.service = service;
-    serviceOptions = service.getRunnerConfig();
-    // add any presets not already added.
+    WsParamSetI p = null;
+    List<ArgumentI> jobArgset = null;
+    settingDialog = true;
+    { // instantiate the abstract proxy for Jaba objects
+      jobArgset = jabajobArgset == null ? null : JabaParamStore
+              .getJwsArgsfromJaba(jabajobArgset);
+      p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
+                 // null;
+    }
+
+    Hashtable exnames = new Hashtable();
+    for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
+    {
+      exnames.put((String) setName.getItemAt(i), setName.getItemAt(i));
+    }
+    servicePresets = new Hashtable();
+    // Add the default entry - if not present already.
+    if (!exnames.contains(SVC_DEF))
+    {
+      setName.addItem(SVC_DEF);
+      exnames.put(SVC_DEF, SVC_DEF);
+      servicePresets.put(SVC_DEF, SVC_DEF);
+    }
     String curname = (p == null ? "" : p.getName());
-    PresetManager prman = service.getPresets();
-    if (prman != null)
+    for (WsParamSetI pr : paramStore.getPresets())
     {
-      List prList = service.getPresets().getPresets();
-      if (prList != null)
+      if (!pr.isModifiable())
       {
-        for (Object pr : prList)
-        {
-          if (p == null || !curname.equals(((Preset) pr).getName()))
-          {
-            setName.addItem(((Preset) pr).getName());
-          }
-        }
+        servicePresets.put(pr.getName(), "preset");
+      }
+      else
+      {
+      }
+      if (!exnames.contains(pr.getName()))
+      {
+        setName.addItem(pr.getName());
       }
     }
-    updateTable(p, jobArgset);
+    // TODO: if initial jobArgset matches a given user setting or preset then
+    // should recover setting accordingly
+    // updateTable(p, jobArgset);
+    if (p != null)
+    {
+      reInitDialog(p.getName());
+      initArgSetModified();
+    }
+    else
+    {
+      if (jobArgset != null && jobArgset.size() > 0)
+      {
+        curSetName = "Supplied Settings";
+        updateTable(p, jobArgset);
+      }
+      else
+      {
+        curSetName = null;
+        reInitDialog(null);
+      }
+    }
+    settingDialog = false;
+
   }
 
   @SuppressWarnings("unchecked")
-  private void updateTable(Preset p, List<Argument> jobArgset)
+  private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
   {
-    availableParameters = new ArrayList<Parameter>();
-    List<Parameter> setargs = new ArrayList<Parameter>();
     // populate table from default parameter set.
-    List<Argument> args = serviceOptions.getArguments();
+    List<ArgumentI> args = paramStore.getServiceParameters();
 
     // split to params and required arguments
     {
-      for (Argument arg : args)
+      for (ArgumentI myarg : args)
       {
-        Argument myarg = (Argument) arg;
         // Ideally, Argument would implement isRequired !
-        if (myarg instanceof Parameter)
+        if (myarg instanceof ParameterI)
         {
-          Parameter parm = (Parameter) myarg;
-          if (true) // parm.isRequired())
-          {
-            addParameter(parm);
-          }
-          else
-          {
-            availableParameters.add(parm);
-          }
+          ParameterI parm = (ParameterI) myarg;
+          paramList.add(opanp.addParameter(parm));
         }
         else
         {
-          if (myarg instanceof Option)
+          if (myarg instanceof OptionI)
           {
-            Option opt = (Option) myarg;
-            addOption(opt);
-            if (opt.isRequired())
+            OptionI opt = (OptionI) myarg;
+            OptionBox ob = opanp.addOption(opt);
+            jobOptions.add(ob, FlowLayout.LEFT);
+            ob.resetToDefault();
+            if (MAX_OPTWIDTH < ob.getPreferredSize().width)
             {
-              selectOption(opt, opt.getDefaultValue());
+              MAX_OPTWIDTH = ob.getPreferredSize().width;
             }
+
           }
           else
           {
             System.err.println("Ignoring unknown service argument type "
-                    + arg.getClass().getName());
+                    + myarg.getClass().getName());
           }
         }
       }
@@ -449,480 +590,255 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
     if (p != null)
     {
-      if (lastParmSet == null)
-      {
-        // initialise setname
-        setName.addItem(p.getName());
-      }
-      setDescr.setText(p.getDescription());
+      isUserPreset = false;
+      // initialise setname
+      setName.setSelectedItem(lastSetName = p.getName());
+      setDescr.setText(lastDescrText = p.getDescription());
       // TODO - URL link
       try
       {
-        args = p.getArguments(serviceOptions);
+        args = p.getArguments();
       } catch (Exception e)
       {
         e.printStackTrace();
       }
       // TODO: check if args should be unselected prior to resetting using the
       // preset
-      setargs.clear();
     }
     else
     {
       if (lastParmSet == null)
       {
+        isUserPreset = false;
         // first call - so create a dummy name
-        setName.addItem("Defaults *");
+
+        setName.setSelectedItem(lastSetName = SVC_DEF);
       }
     }
+
     if (jobArgset != null)
     {
-      argSetModified(true);
+      argSetModified(jobArgset, true);
       args = jobArgset;
     }
     // get setargs from current object
     if (args != null)
     {
-      for (Argument arg : args)
+      for (ArgumentI arg : args)
       {
-        if (arg instanceof Parameter)
+        if (arg instanceof ParameterI)
         {
-          setargs.add((Parameter) arg);
+          opanp.setParameter((ParameterI) arg);
         }
         else
         {
-          if (arg instanceof Option)
+          if (arg instanceof OptionI)
           {
-            selectOption((Option) arg, arg.getDefaultValue());
+            // System.out.println("Setting option "
+            // + System.identityHashCode(arg) + ":" + arg.getName()
+            // + " with " + arg.getDefaultValue());
+            opanp.selectOption((OptionI) arg, arg.getValue());
           }
         }
 
       }
     }
 
-    // mdl.setData(setargs);
-    // jobOptions.setLayout(new GridLayout(optSet.size() / 2 + 1, 2));
-    jobOptions.setPreferredSize(new Dimension(PARAM_WIDTH, optSet.size()
-            * OPTSET_HEIGHT));
-    jobOptions.setLayout(new GridLayout(optSet.size(), 1));
     refreshParamLayout();
-    // paramPanel.setLayout(new GridLayout(paramSet.size(), 1));
-    // paramList.va
-    // paramPane.getViewport().validate();
-    paramPane.validate();
-    validate();
+    revalidate();
   }
 
   private boolean isModified()
   {
-    return modified.isVisible();
+    return modifiedElements.size() > 0;
   }
 
-  private void argSetModified(boolean b)
-  {
-    modified.setVisible(b);
-    /*
-     * String setn = (String)setName.getSelectedItem(); if (setn==null) return;
-     * int p = setName.getSelectedIndex(); if (b) { if (setn.length()<2 ||
-     * setn.lastIndexOf(" *")!=setn.length()-2) { setn = setn+" *"; } } else {
-     * if (setn.lastIndexOf(" *")==setn.length()-2) { setn =
-     * setn.substring(0,setn.length()-2); } } // edit the list
-     * 
-     * Object[] objects = new Object[setName.getItemCount()]; for (int
-     * i=0;i<objects.length; i++) { objects[i] = setName.getItemAt(i); }
-     * objects[p] = setn; setName.removeAllItems(); for (int
-     * i=0;i<objects.length; i++) { setName.addItem(objects[i]); }
-     * setName.setSelectedIndex(p);
-     */
-    validate();
-  }
+  private Hashtable modifiedElements = new Hashtable();
 
-  private void addParameter(Parameter parm)
+  /**
+   * reset gui and modification state settings
+   */
+  private void initArgSetModified()
   {
-    ParamBox pb = paramSet.get(parm.getName());
-    if (pb == null)
-    {
-      pb = new ParamBox(this, parm);
-      paramSet.put(parm.getName(), pb);
-      paramList.add(pb);
-    }
+    curSetName = null;
+    modifiedElements.clear();
+    updateButtonDisplay();
   }
 
-  private void selectOption(Option opt, String string)
+  private void updateButtonDisplay()
   {
-    OptionBox cb = optSet.get(opt.getName());
-    if (cb == null)
+    boolean _update = false, _create = false, _delete = false, _revert = false;
+    if (modifiedElements.size() > 0)
     {
-      cb = addOption(opt);
-    }
-    if (string == null)
-    {
-      // no value specified.
-      if (opt.isRequired())
-      {
-        // indicate option needs to be selected!
-      }
-      else
+      // set modified
+      _revert = true;
+      _update = isUserPreset; // can only update user presets
+      if (!isUserPreset || modifiedElements.containsKey(setName))
       {
-        cb.enabled.setSelected(false);
+        // name modified - can create new preset
+        _create = true;
       }
     }
     else
     {
-      cb.enabled.setSelected(true);
-
-      if (opt.getPossibleValues().contains(string))
-      {
-        cb.val.setSelectedItem(string);
-      }
-      else
-      {
-        throw new Error("Invalid value " + string + " for option " + opt);
-      }
-
+      // set unmodified
     }
-  }
+    // can still delete a user preset
+    _delete = isUserPreset;
 
-  Map<String, ParamBox> paramSet = new Hashtable<String, ParamBox>();
+    createpref.setVisible(_create);
+    updatepref.setVisible(_update);
+    deletepref.setVisible(_delete);
+    revertpref.setVisible(_revert);
+    validate();
+  }
 
-  public class ParamBox extends JPanel implements ChangeListener,
-          ActionListener
+  public void argSetModified(Object modifiedElement, boolean b)
   {
-    JCheckBox showDesc = new JCheckBox();
-
-    JTextArea string = new JTextArea();
-    JScrollPane descPanel = new JScrollPane();
-
-    JSlider slider = null;
-
-    JTextField valueField = null;
-
-    ValueConstrain validator = null;
-    JPanel settingPanel = new JPanel();
-    boolean integ = false;
-
-    boolean choice = false;
-
-    public ParamBox(final WsJobParameters pmlayout, Parameter parm)
+    if (settingDialog)
     {
-      setLayout(new FlowLayout(FlowLayout.LEFT));
-      setBorder(new TitledBorder(parm.getName()));
-      setPreferredSize(new Dimension(PARAM_WIDTH, PARAM_CLOSEDHEIGHT));
-      string.setFont(new Font("Verdana", Font.PLAIN, 11));
-      string.setBackground(getBackground());
-      // string.setSize(new Dimension(PARAM_WIDTH, 80));
-      string.setEditable(false);
-      showDesc.setText("Show Description");
-      showDesc.setSelected(false);
-      showDesc.setToolTipText(parm.getDescription());
-      //showDesc.setLocation(2,2);
-      descPanel.setPreferredSize(new Dimension(PARAM_WIDTH-20, 90));
-      descPanel.getViewport().setView(string);
-      //descPanel.setLocation(2,17);
-      descPanel.setVisible(false);
-      // string.setMinimumSize(new Dimension(140,80));
-      // string.setMaximumSize(new Dimension(280,80));
-      final ParamBox me=this;
-      showDesc.addActionListener(new ActionListener() {
-
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          boolean show = showDesc.isSelected();
-          descPanel.setVisible(show);
-          me.setPreferredSize(new Dimension(PARAM_WIDTH, (show) ? PARAM_HEIGHT : PARAM_CLOSEDHEIGHT));
-          me.validate();
-          pmlayout.refreshParamLayout();
-        }
-      });
-      string.setWrapStyleWord(true);
-      string.setLineWrap(true);
-      string.setColumns(32);
-      string.setText(parm.getDescription());
-      // name.setToolTipText(parm.getDescription());
-      add(showDesc);
-      validator = parm.getValidValue();
-      parameter = parm;
-      if (validator != null)
-      {
-        integ = validator.getType() == Type.Integer;
-      }
-      else
-      {
-        if (parameter.getPossibleValues() != null)
-        {
-          choice = true;
-        }
-      }
-      updateControls(parm);
-      add(descPanel); // , BorderLayout.NORTH);
-      validate();
+      return;
     }
-
-
-    boolean adjusting = false;
-
-    Parameter parameter;
-
-    JComboBox choicebox;
-    public int getBoxHeight()
+    if (!b)
     {
-      return (showDesc.isSelected() ? PARAM_HEIGHT : PARAM_CLOSEDHEIGHT);
+      modifiedElements.remove(modifiedElement);
     }
-    public void updateControls(Parameter parm)
+    else
     {
-      adjusting = true;
-      boolean init = valueField == null;
-      float fVal = 0f;
-      int iVal = 0;
-      if (init)
+      if (b && modifiedElement == setName
+              && modifiedElements.contains(modifiedElement))
       {
-        if (choice)
-        {
-          choicebox = new JComboBox();
-          choicebox.addActionListener(this);
-          add(choicebox);
-        }
-        else
-        {
-          slider = new JSlider();
-          slider.addChangeListener(this);
-          valueField = new JTextField();
-          valueField.addActionListener(this);
-          valueField.setPreferredSize(new Dimension(80, 25));
-          JPanel container = new JPanel();
-          // container.setLayout(new FlowLayout());
-          add(slider);// , BorderLayout.SOUTH);
-          add(valueField);// ,BorderLayout.CENTER);
-          // add(container, BorderLayout.EAST);
-          // container.validate();
-
-        }
+        // HACK! prevents iteration on makeSetNameValid
+        b = false;
       }
-
-      if (parm != null)
-      {
-        if (choice)
-        {
-          List vals = parm.getPossibleValues();
-          for (Object val : vals)
-          {
-            choicebox.addItem(val);
-          }
-          if (parm.getDefaultValue() != null)
-          {
-            choicebox.setSelectedItem(parm.getDefaultValue());
-          }
-        }
-        else
-        {
-          valueField.setText(parm.getDefaultValue());
-        }
-      }
-      updateSliderFromValueField();
-      adjusting = false;
+      modifiedElements.put(modifiedElement, modifiedElement);
     }
-
-    public Parameter getParameter()
+    // set mod status based on presence of elements in table
+    if (b && modifiedElements.size() > 0)
     {
-      try
-      {
-        if (choice)
-        {
-          parameter.setDefaultValue((String) choicebox.getSelectedItem());
-        }
-        else
-        {
-          parameter.setDefaultValue(valueField.getText());
-        }
-      } catch (WrongParameterException e)
-      {
-        e.printStackTrace();
-        return null;
-      }
-      return parameter;
+      makeSetNameValid(!isUserPreset);
+      SetNamePanel.revalidate();
     }
+    updateButtonDisplay();
+  }
 
-    public Object updateSliderFromValueField()
+  private boolean isServicePreset(String selectedItem)
+  {
+    return selectedItem.equals(SVC_DEF)
+            || servicePresets.containsKey(selectedItem);
+  }
+
+  /**
+   * check if the current set name is a valid set name for saving, if not, then
+   * fix it.
+   */
+  private void makeSetNameValid(boolean newuserset)
+  {
+    boolean stn = settingDialog;
+    boolean renamed = false;
+    settingDialog = true;
+    String nm = (curSetName != null ? curSetName : (String) setName
+            .getSelectedItem());
+    // check if the name is reserved - if it is, rename it.
+    if (isServicePreset(nm))
+    {
+      nm = "User " + nm;
+      renamed = true;
+    }
+    String tnm = nm;
+    if (newuserset)
     {
-      int iVal;
-      float fVal;
-      if (validator != null)
+      int i = 0;
+      while (paramStore.getPreset(tnm) != null)
       {
-        if (integ)
-        {
-          iVal = 0;
-          try
-          {
-            valueField.setText(valueField.getText().trim());
-            iVal = Integer.valueOf(valueField.getText());
-          } catch (Exception e)
-          {
-          }
-          ;
-          if (validator.getMin() != null && validator.getMax() != null)
-          {
-            slider.getModel().setRangeProperties(iVal, 1,
-                    validator.getMin().intValue(),
-                    validator.getMax().intValue(), true);
-          }
-          else
-          {
-            slider.setVisible(false);
-          }
-          return new int[]
-          { iVal };
-        }
-        else
-        {
-          fVal = 0f;
-          try
-          {
-            fVal = Float.valueOf(valueField.getText());
-          } catch (Exception e)
-          {
-          }
-          ;
-          if (validator.getMin() != null && validator.getMax() != null)
-          {
-            slider.getModel().setRangeProperties((int) fVal * 1000, 1,
-                    (int) validator.getMin().floatValue() * 1000,
-                    (int) validator.getMax().floatValue() * 1000, true);
-          }
-          else
-          {
-            slider.setVisible(false);
-          }
-          return new float[]
-          { fVal };
-        }
+        tnm = nm + " (" + (++i) + ")";
+        renamed = true;
       }
-      else
+      if (i > 0)
       {
-        if (!choice)
-        {
-          slider.setVisible(false);
-          return new String[]
-          { valueField.getText().trim() };
-        }
-        else
-        {
-          return new String[]
-          { (String) choicebox.getSelectedItem() };
-        }
+        nm = tnm;
       }
-
     }
 
-    @Override
-    public void stateChanged(ChangeEvent e)
+    boolean makeupdate = false;
+    // sync the gui with the preset database
+    for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
     {
-      if (!adjusting)
+      String snm = (String) setName.getItemAt(i);
+      if (snm.equals(nm))
       {
-        valueField.setText(""
-                + ((integ) ? ("" + (int) slider.getValue())
-                        : ("" + (float) (slider.getValue() / 1000f))));
+        makeupdate = true;
+        // setName.setSelectedIndex(i);
       }
     }
-
-    @Override
-    public void actionPerformed(ActionEvent e)
+    if (!makeupdate)
     {
-      if (choice)
-      {
-      }
-      else if (!adjusting)
-      {
-        updateSliderFromValueField();
-      }
-      argSetModified(true);
+      setName.addItem(curSetName = nm);
+      setName.setSelectedItem(curSetName);
     }
-
+    if (renamed)
+    {
+      settingDialog = false; // we need this name change to be registered.
+      argSetModified(setName, renamed);
+    }
+    settingDialog = stn;
   }
 
-  Map<String, OptionBox> optSet = new Hashtable<String, OptionBox>();
 
-  public class OptionBox extends JPanel implements ActionListener
+  public void refreshParamLayout()
   {
-    JComboBox val = new JComboBox();
-
-    JCheckBox enabled = new JCheckBox();
-
-    Option option;
-
-    public OptionBox(Option opt)
+    FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
+    int sep=fl.getVgap();
+    int os=0,s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom+jobOptions.getBorder().getBorderInsets(jobOptions).top+2 * sep;
+    int w = 2 * fl.getHgap() + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH : OptsAndParamsPage.PARAM_WIDTH);
+    jobOptions.setLayout(fl);
+    if (opanp.getOptSet().size() > 0)
     {
-      option = opt;
-      setLayout(new BorderLayout());
-      enabled.setSelected(opt.isRequired());
-      enabled.setFont(new Font("Verdana", Font.PLAIN, 11));
-      enabled.setText(opt.getName());
-      enabled.setToolTipText(opt.getDescription());
-      add(enabled, BorderLayout.NORTH);
-      if (opt.getPossibleValues().size() > 1)
+      
+      for (OptionBox pbox : opanp.getOptSet().values())
       {
-        setLayout(new GridLayout(1, 2));
-        for (Object str : opt.getPossibleValues())
-        {
-          val.addItem((String) str);
-        }
-        val.setSelectedItem((String) opt.getDefaultValue());
-        val.addActionListener(this);
-        add(val, BorderLayout.SOUTH);
+    	  pbox.revalidate();
+        s += sep + pbox.getPreferredSize().height; 
       }
-      // TODO: add actionListeners for popup (to open further info),
-      // and to update list of parameters if an option is enabled
-      // that takes a value.
+      jobOptions.setPreferredSize(new Dimension(w, s));
+      jobOptions.setLayout(new GridLayout(opanp.getOptSet().size(),1));
+      os=s;
     }
-
-    public Option getOptionIfEnabled()
+    else
     {
-      if (!enabled.isSelected())
-      {
-        return null;
-      }
-      try
-      {
-        if (val.getSelectedItem() != null)
-        {
-          option.setDefaultValue((String) val.getSelectedItem());
-        }
-      } catch (WrongParameterException e)
-      {
-        e.printStackTrace();
-        return null;
-      }
-      return option;
+      jobOptions.setVisible(false);
     }
 
-    @Override
-    public void actionPerformed(ActionEvent e)
+    // Now layout the parameters assuming they occupy one column - to calculate total height of options+parameters
+    fl = new FlowLayout(FlowLayout.CENTER);
+    // helpful hint from http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
+    fl.setAlignOnBaseline(true);
+    if (opanp.getParamSet().size() > 0)
     {
-      argSetModified(true);
-      enabled.setSelected(true);
-    }
-  }
+      paramList.setLayout(fl);
 
-  private OptionBox addOption(Option opt)
-  {
-    OptionBox cb = optSet.get(opt.getName());
-    if (cb == null)
-    {
-      cb = new OptionBox(opt);
-      optSet.put(opt.getName(), cb);
-      jobOptions.add(cb);
+      s = 2 * sep;
+      for (ParamBox pbox : opanp.getParamSet().values())
+      {
+        pbox.validate();
+        s += sep + pbox.getPreferredSize().height+pbox.getBorder().getBorderInsets(pbox).bottom; 
+      }
+      
+      paramList.setPreferredSize(new Dimension(w, s));
+      os+=s+2*sep+paramList.getBorder().getBorderInsets(paramList).bottom+paramList.getBorder().getBorderInsets(paramList).top;
     }
-    return cb;
-  }
-
-  protected void refreshParamLayout()
-  {
-    int s=100;
-    for (ParamBox pbox : paramSet.values()){
-      s+=pbox.getBoxHeight();
+    else
+    {
+      paramList.setVisible(false);
     }
-    paramList.setPreferredSize(new Dimension(PARAM_WIDTH, s));
-    paramList.setLayout(new FlowLayout());
+    // TODO: waste some time trying to eliminate any unnecessary .validate calls here
+    paramList.validate();
+    jobOptions.validate();
+    // System.out.println("Size will be : "+w+","+os);
+    optsAndparams.validate();
+    paramPane.getViewport().validate();
+    paramPane.getVerticalScrollBar().setBlockIncrement(OptsAndParamsPage.PARAM_CLOSEDHEIGHT*2);
+    paramPane.validate();
     validate();
   }
 
@@ -936,7 +852,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
             .getDiscoverer();
     int p = 0;
-    if (args.length > 3)
+    if (args.length > 0)
     {
       Vector<String> services = new Vector<String>();
       services.addElement(args[p++]);
@@ -955,202 +871,518 @@ public class WsJobParameters extends JPanel implements ItemListener,
     for (Jws2Discoverer.Jws2Instance service : disc.getServices())
     {
       lastserv = service;
-      if (p < args.length && service.serviceType.equalsIgnoreCase(args[p]))
-      {
-        break;
-      }
-    }
-    if (lastserv != null)
-    {
-      List<Preset> prl = null;
-      Preset pr = null;
-      if (++p < args.length)
+      if (p >= args.length || service.serviceType.equalsIgnoreCase(args[p]))
       {
-        PresetManager prman = lastserv.getPresets();
-        if (prman != null)
+        if (lastserv != null)
         {
-          pr = prman.getPresetByName(args[p]);
-          if (pr == null)
+          List<Preset> prl = null;
+          Preset pr = null;
+          if (++p < args.length)
           {
-            // just grab the last preset.
-            prl = prman.getPresets();
+            PresetManager prman = lastserv.getPresets();
+            if (prman != null)
+            {
+              pr = prman.getPresetByName(args[p]);
+              if (pr == null)
+              {
+                // just grab the last preset.
+                prl = prman.getPresets();
+              }
+            }
           }
-        }
-      }
-      Iterator<Preset> en = (prl == null) ? null : prl.iterator();
-      while (true)
-      {
-        if (en != null)
-        {
-          if (!en.hasNext())
+          else
           {
-            en = prl.iterator();
+            PresetManager prman = lastserv.getPresets();
+            if (prman != null)
+            {
+              prl = prman.getPresets();
+            }
           }
-          pr = en.next();
-        }
-        WsJobParameters pgui = new WsJobParameters(lastserv, pr);
-        JFrame jf = new JFrame("Parameters for " + lastserv.getActionText());
-        JPanel cont = new JPanel();
-        jf.setPreferredSize(new Dimension(600, 800));
-        cont.add(pgui);
-        jf.add(cont);
-        final Thread thr = Thread.currentThread();
-        jf.addWindowListener(new WindowListener()
-        {
-
-          @Override
-          public void windowActivated(WindowEvent e)
+          Iterator<Preset> en = (prl == null) ? null : prl.iterator();
+          while (en != null && en.hasNext())
           {
-            // TODO Auto-generated method stub
+            if (en != null)
+            {
+              if (!en.hasNext())
+              {
+                en = prl.iterator();
+              }
+              pr = en.next();
+            }
+            {
+              System.out.println("Testing opts dupes for "
+                      + lastserv.getUri() + " : "
+                      + lastserv.getActionText() + ":" + pr.getName());
+              List<Option> rg = lastserv.getRunnerConfig().getOptions();
+              for (Option o : rg)
+              {
+                try
+                {
+                  Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
+                } catch (Exception e)
+                {
+                  System.err.println("Failed to copy " + o.getName());
+                  e.printStackTrace();
+                } catch (Error e)
+                {
+                  System.err.println("Failed to copy " + o.getName());
+                  e.printStackTrace();
+                }
+              }
+            }
+            {
+              System.out.println("Testing param dupes:");
+              List<Parameter> rg = lastserv.getRunnerConfig()
+                      .getParameters();
+              for (Parameter o : rg)
+              {
+                try
+                {
+                  Parameter cpy = jalview.ws.jws2.ParameterUtils
+                          .copyParameter(o);
+                } catch (Exception e)
+                {
+                  System.err.println("Failed to copy " + o.getName());
+                  e.printStackTrace();
+                } catch (Error e)
+                {
+                  System.err.println("Failed to copy " + o.getName());
+                  e.printStackTrace();
+                }
+              }
+            }
+            {
+              System.out.println("Testing param write:");
+              List<String> writeparam = null, readparam = null;
+              try
+              {
+                writeparam = jalview.ws.jws2.ParameterUtils
+                        .writeParameterSet(
+                                pr.getArguments(lastserv.getRunnerConfig()),
+                                " ");
+                System.out.println("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();
+                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);
+                    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);
+
+                }
+              } catch (Exception e)
+              {
+                e.printStackTrace();
+              }
+            }
+            WsJobParameters pgui = new WsJobParameters(lastserv,
+                    new JabaPreset(lastserv, pr));
+            JFrame jf = new JFrame("Parameters for "
+                    + lastserv.getActionText());
+            JPanel cont = new JPanel(new BorderLayout());
+            pgui.validate();
+            cont.setPreferredSize(pgui.getPreferredSize());
+            cont.add(pgui, BorderLayout.CENTER);
+            jf.setLayout(new BorderLayout());
+            jf.add(cont, BorderLayout.CENTER);
+            jf.validate();
+            final Thread thr = Thread.currentThread();
+            jf.addWindowListener(new WindowListener()
+            {
 
-          }
+              public void windowActivated(WindowEvent e)
+              {
+                // TODO Auto-generated method stub
 
-          @Override
-          public void windowClosed(WindowEvent e)
-          {
-          }
+              }
 
-          @Override
-          public void windowClosing(WindowEvent e)
-          {
-            thr.interrupt();
+              public void windowClosed(WindowEvent e)
+              {
+              }
 
-          }
+              public void windowClosing(WindowEvent e)
+              {
+                thr.interrupt();
 
-          @Override
-          public void windowDeactivated(WindowEvent e)
-          {
-            // TODO Auto-generated method stub
+              }
 
-          }
+              public void windowDeactivated(WindowEvent e)
+              {
+                // TODO Auto-generated method stub
 
-          @Override
-          public void windowDeiconified(WindowEvent e)
-          {
-            // TODO Auto-generated method stub
+              }
 
-          }
+              public void windowDeiconified(WindowEvent e)
+              {
+                // TODO Auto-generated method stub
 
-          @Override
-          public void windowIconified(WindowEvent e)
-          {
-            // TODO Auto-generated method stub
+              }
 
-          }
+              public void windowIconified(WindowEvent e)
+              {
+                // TODO Auto-generated method stub
 
-          @Override
-          public void windowOpened(WindowEvent e)
-          {
-            // TODO Auto-generated method stub
+              }
 
-          }
+              public void windowOpened(WindowEvent e)
+              {
+                // TODO Auto-generated method stub
 
-        });
-        jf.setVisible(true);
-        boolean inter = false;
-        while (!inter)
-        {
-          try
-          {
-            Thread.sleep(10000);
-          } catch (Exception e)
-          {
-            inter = true;
+              }
+
+            });
+            jf.setVisible(true);
+            boolean inter = false;
+            while (!inter)
+            {
+              try
+              {
+                Thread.sleep(10000);
+              } catch (Exception e)
+              {
+                inter = true;
+              }
+              ;
+            }
+            jf.dispose();
           }
-          ;
         }
-        jf.dispose();
       }
     }
   }
 
-  public List<Argument> getJobParams()
+  public List<ArgumentI> getJobParams()
+  {
+    return opanp.getCurrentSettings();
+  }
+
+  String lastParmSet = null;
+
+  /*
+   * Hashtable<String, Object[]> editedParams = new Hashtable<String,
+   * Object[]>();
+   * 
+   * store the given parameters in the user parameter set database.
+   * 
+   * @param storeSetName - lastParmSet
+   * 
+   * @param descr - setDescr.getText()
+   * 
+   * @param jobParams - getJobParams()
+   * 
+   * private void _storeUserPreset(String storeSetName, String descr,
+   * List<ArgumentI> jobParams) { // this is a simple hash store. Object[] pset;
+   * editedParams.put(storeSetName, pset = new Object[3]); pset[0] =
+   * storeSetName; pset[1] = descr; pset[2] = jobParams; // writeParam("Saving "
+   * + storeSetName + ": ", jobParams); }
+   * 
+   * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
+   * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
+   * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
+   * 
+   * private Object[] _getUserPreset(String setName) { Object[] pset =
+   * editedParams.get(setName); // if (pset != null) // writeParam("Retrieving "
+   * + setName + ": ", (List<Argument>) pset[2]); return pset; }
+   * 
+   * * remove the given user preset from the preset stash
+   * 
+   * @param setName
+   * 
+   * private void _deleteUserPreset(String setName) {
+   * editedParams.remove(setName); }
+   */
+
+  private void syncSetNamesWithStore()
   {
-    List<Argument> argSet = new ArrayList<Argument>();
-    // recover options and parameters from GUI
-    for (OptionBox opts : optSet.values())
+    int n = 0;
+    // remove any set names in the drop down menu that aren't either a reserved
+    // setting, or a user defined or service preset.
+    Vector items = new Vector();
+    while (n < setName.getItemCount())
     {
-      Option opt = opts.getOptionIfEnabled();
-      if (opt != null)
+      String item = (String) setName.getItemAt(n);
+      if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
       {
-        argSet.add(opt);
+        setName.removeItemAt(n);
+      }
+      else
+      {
+        items.addElement(item);
+        n++;
       }
     }
-    for (ParamBox parambox : paramSet.values())
+    if (!items.contains(SVC_DEF))
     {
-      Parameter parm = parambox.getParameter();
-      if (parm != null)
+      setName.addItem(SVC_DEF);
+    }
+    for (WsParamSetI upn : paramStore.getPresets())
+    {
+      if (!items.contains(upn.getName()))
       {
-        argSet.add(parm);
+        setName.addItem(upn.getName());
       }
     }
-
-    return argSet;
   }
 
-  String lastParmSet = null;
+  /**
+   * true if lastParmSet is a user preset
+   */
+  boolean isUserPreset = false;
 
-  Hashtable<String, Object[]> editedParams = new Hashtable<String, Object[]>();
+  private void reInitDialog(String nextPreset)
+  {
+    settingDialog = true;
+    // updateTable(null,null); // first reset to defaults
+    WsParamSetI pset = null;
+    if (nextPreset != null && nextPreset.length() > 0)
+    {
+      pset = paramStore.getPreset(nextPreset);
+    }
+    if (pset != null)
+    {
+      if (pset.isModifiable())
+      {
+        isUserPreset = true;
+        setDescr.setText(pset.getDescription());
+        updateTable(null, pset.getArguments());
+        lastParmSet = nextPreset;
+      }
+      else
+      {
+        isUserPreset = false;
+        setDescr.setText("");
+        // must be a default preset from service
+        updateTable(pset, null);
+        lastParmSet = nextPreset;
+      }
+    }
+    else
+    {
+      isUserPreset = false;
+      // Service defaults
+      setDescr.setText("");
+      updateTable(null, null);
+      lastParmSet = SVC_DEF;
+    }
+
+    initArgSetModified();
+    syncSetNamesWithStore();
+    setName.setSelectedItem(lastParmSet);
+    SetNamePanel.validate();
+    validate();
+    settingDialog = false;
+
+  }
+
+  String curSetName = null;
 
-  @Override
   public void itemStateChanged(ItemEvent e)
   {
-    if (e.getSource() == setName)
+    if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
     {
-      String setname = (String) setName.getSelectedItem();
+      final String setname = (String) setName.getSelectedItem();
+      System.out.println("Item state changed for " + setname
+              + " (handling ? " + !settingDialog + ")");
+      if (settingDialog)
+      {
+        // ignore event
+        return;
+      }
       if (setname == null)
       {
         return;
       }
-      // if modified - warn user - or at least save current edited set.
-      if (lastParmSet != null)
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
+      {
+        public void run()
+        {
+          doPreferenceComboStateChange(setname);
+        }
+      });
+    }
+  }
+
+  private void doPreferenceComboStateChange(String setname)
+  {
+    // user has selected a different item from combo-box
+    if (isModified())
+    {
+      String lsetname = (curSetName != null) ? curSetName : lastParmSet;
+      if (lsetname.equals(setname))
       {
-        // save current state
-        Object[] pset;
-        editedParams.put(lastParmSet, pset = new Object[3]);
-        pset[0] = lastParmSet;
-        pset[1] = setDescr.getText();
-        pset[2] = getJobParams();
+        // setname was just edited - so ignore this event.
+        return;
       }
-      Object[] pset = editedParams.get(setname);
-      if (pset != null)
+      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)
       {
-        setDescr.setText((String) pset[1]);
-        updateTable(null, (List<Argument>) pset[2]);
-        lastParmSet = setname;
-        validate();
+        // revert the combobox to the current item
+        settingDialog = true;
+        setName.setSelectedItem(lsetname);
+        settingDialog = false;
+        // and leave.
+        return;
+        // System.out.println("Saving for " + lsetname);
+        // _storeCurrentPreset(lsetname);
+
       }
-      else
+    }
+    settingDialog = true;
+    reInitDialog(setname);
+    settingDialog = false;
+
+  }
+
+  private void _renameExistingPreset(String oldName, String curSetName2)
+  {
+    paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
+            getJobParams());
+  }
+
+  /**
+   * store current settings as given name. You should then reset gui.
+   * 
+   * @param curSetName2
+   */
+  private void _storeCurrentPreset(String curSetName2)
+  {
+    paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
+  }
+
+  private void _updatePreset(String lastParmSet2, String curname)
+  {
+    paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(),
+            getJobParams());
+
+  }
+
+  /**
+   * last saved name for this user preset
+   */
+  String lastSetName = null;
+
+  /**
+   * last saved value of the description text for this user preset
+   */
+  String lastDescrText = null;
+
+  public void actionPerformed(ActionEvent e)
+  {
+    if (e.getSource() instanceof Component)
+    {
+      Component src = (Component) e.getSource();
+      if (src.getParent() == setName)
       {
-        // must be a default preset from service
-        Preset p = null;
-        try
+        // rename any existing records we know about for this set.
+        String newname = (String) e.getActionCommand().trim();
+        String msg = null;
+        if (isServicePreset(newname))
         {
-          p = service.getPresets().getPresetByName(setname);
-        } catch (Exception ex)
+          final String oldname = curSetName != null ? curSetName
+                  : lastParmSet;
+          final Component ourframe = this;
+          settingDialog = true;
+          setName.getEditor().setItem(oldname);
+          settingDialog = false;
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+              JOptionPane.showMessageDialog(ourframe,
+                      "Invalid name - preset already exists.",
+                      "Invalid name", JOptionPane.WARNING_MESSAGE);
+            }
+          });
+
+          return;
+        }
+        curSetName = newname;
+        System.err.println("New name for user setting " + curSetName
+                + " (was " + setName.getSelectedItem() + ")");
+        if (curSetName.equals(setName.getSelectedItem()))
         {
-          ex.printStackTrace();
+          curSetName = null;
         }
-        if (p != null)
+        if (curSetName != null)
         {
-          updateTable(p, null);
-          validate();
-          lastParmSet = setname;
+          argSetModified(setName, true);
+          return;
         }
+
       }
+    }
+  }
+
+  private void checkDescrModified()
+  {
+    if (!settingDialog)
+    {
+
+      argSetModified(
+              setDescr,
+              (lastDescrText == null ? setDescr.getText().trim().length() > 0
+                      : !setDescr.getText().equals(lastDescrText)));
 
     }
   }
 
-  @Override
-  public void actionPerformed(ActionEvent e)
+  public void insertUpdate(DocumentEvent e)
   {
-    if (e.getSource() == setName)
+    checkDescrModified();
+  }
+
+  public void removeUpdate(DocumentEvent e)
+  {
+    checkDescrModified();
+  }
+
+  public void changedUpdate(DocumentEvent e)
+  {
+    checkDescrModified();
+  }
+
+  /**
+   * 
+   * @return null or the service preset selected by the user
+   */
+  public WsParamSetI getPreset()
+  {
+    if (isUserPreset || isModified()
+            || (lastParmSet != null && lastParmSet.equals(SVC_DEF)))
+    {
+      return null;
+    }
+    else
     {
-      // rename any existing records we know about for this set.
-      String newname = (String) setName.getSelectedItem();
-      System.err.println("Command " + newname + " : "
-              + e.getActionCommand());
+      return paramStore.getPreset(lastParmSet);
     }
   }
 }