X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FWsJobParameters.java;h=cf76f750d1f97d834c5db60ecb216e14c9239bd6;hb=e9dd79fe9d061dc449ede4d0150298f6621aed04;hp=e7ecc03755589b32cf52210cc16c3f64a2901a20;hpb=842559f239380e94327db76808eef6c4b28fdd89;p=jalview.git

diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index e7ecc037..cf76f75 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -33,6 +33,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
+import javax.swing.InputVerifier;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
@@ -73,9 +74,19 @@ import compbio.metadata.WrongParameterException;
 import compbio.metadata.ValueConstrain.Type;
 
 import jalview.util.jarInputStreamProvider;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.ParameterUtils;
 import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
+import jalview.ws.jws2.dm.JabaOption;
+import jalview.ws.jws2.dm.JabaParameter;
+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;
 
 /**
  * job parameter editing/browsing dialog box. User can browse existing settings
@@ -118,13 +129,13 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   JPanel jobParameters = new JPanel();
 
-  JButton savmodified = new JButton();
+  JButton createpref = new JButton();
 
-  JButton renmodified = new JButton();
+  JButton deletepref = new JButton();
 
-  JButton deletesetting = new JButton();
+  JButton revertpref = new JButton();
 
-  JButton revertsetting = new JButton();
+  JButton updatepref = new JButton();
 
   JButton startjob = new JButton();
 
@@ -136,21 +147,20 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   JScrollPane paramPane = new JScrollPane();
 
-  // JList paramList = new JList();
   JPanel paramList = new JPanel();
 
   RunnerConfig serviceOptions;
 
-  private BorderLayout jparamLayout;
+  ParamDatastoreI paramStore;
 
   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);
   }
 
   /**
@@ -158,16 +168,36 @@ 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, Preset p,
-          List<Argument> jobArgset)
+  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, ParamDatastoreI paramStorei,
+          Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
   {
     super();
     jbInit();
+    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();
   }
@@ -219,43 +249,42 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   private void jbInit()
   {
-    savmodified = makeButton("Save", "Not implemented yet :) ",
+    updatepref = makeButton("Update", "Update the stored user preference",
             new ActionListener()
             {
 
               public void actionPerformed(ActionEvent e)
               {
-                savModified_actionPerformed(e);
+                update_actionPerformed(e);
               }
             });
-    renmodified = makeButton("Rename", "Not implemented yet :) ",
+    deletepref = makeButton("Delete", "Delete the user preference",
             new ActionListener()
             {
 
               public void actionPerformed(ActionEvent e)
               {
-                renModified_actionPerformed(e);
+                delete_actionPerformed(e);
               }
             });
-    deletesetting = makeButton("Delete", "Not implemented yet :) ",
+    createpref = makeButton("Create", "Create a new preference",
             new ActionListener()
             {
 
               public void actionPerformed(ActionEvent e)
               {
-                deleteSetting_actionPerformed(e);
+                create_actionPerformed(e);
               }
             });
-    revertsetting = makeButton("Revert", "Undo changes to parameters.",
-            new ActionListener()
+    revertpref = makeButton("Revert",
+            "Undo all changes to the current set", new ActionListener()
             {
 
               public void actionPerformed(ActionEvent e)
               {
-                revertSetting_actionPerformed(e);
+                revert_actionPerformed(e);
               }
             });
-
     startjob.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
     startjob.setText("Start");
     startjob.setToolTipText("Start Job");
@@ -291,24 +320,36 @@ public class WsJobParameters extends JPanel implements ItemListener,
     setName.setEditable(true);
     setName.addItemListener(this);
     setName.getEditor().addActionListener(this);
-    SetNamePanel.setLayout(new BorderLayout());
-    SetNamePanel.add(setName, BorderLayout.WEST);
+    JPanel setNameInfo = new JPanel(new FlowLayout(FlowLayout.LEFT));
+    SetNamePanel.setLayout(new GridLayout(2, 1));
+    SetNamePanel.setMinimumSize(new Dimension(300, 40));
+    JLabel setNameLabel = new JLabel("Parameter set: ");
+    setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    // setNameLabel.setHorizontalAlignment(FlowLayout.LEFT);
+    setNameInfo.add(setNameLabel);
+    setNameInfo.add(setName);
     // initial button visibility
-    deletesetting.setVisible(false);
-    revertsetting.setVisible(false);
-    renmodified.setVisible(false);
-    savmodified.setVisible(false);
+    updatepref.setVisible(false);
+    deletepref.setVisible(false);
+    revertpref.setVisible(false);
+    createpref.setVisible(false);
     JPanel setsavebuts = new JPanel();
-    setsavebuts.setLayout(new FlowLayout());
-    setsavebuts.add(revertsetting, BorderLayout.CENTER);
-    setsavebuts.add(renmodified, BorderLayout.CENTER);
-    setsavebuts.add(deletesetting, BorderLayout.CENTER);
-    setsavebuts.add(savmodified, BorderLayout.EAST);
-    SetNamePanel.add(setsavebuts, BorderLayout.EAST);
+    setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT)); // GridLayout(1,2));
+    ((FlowLayout) setsavebuts.getLayout()).setHgap(10);
+    ((FlowLayout) setsavebuts.getLayout()).setVgap(0);
+    setsavebuts.add(deletepref);
+    setsavebuts.add(revertpref);
+    setsavebuts.add(createpref);
+    setsavebuts.add(updatepref);
+    setsavebuts.setSize(new Dimension(150, 20));
+    JPanel buttonArea = new JPanel(new GridLayout(1, 1));
+    buttonArea.add(setsavebuts);
+    SetNamePanel.add(setNameInfo);
+    SetNamePanel.add(buttonArea);
     setDetails.add(setDescrView, BorderLayout.CENTER);
     // setDetails.setPreferredSize(new Dimension(360, 100));
     jobParameters.setBorder(new TitledBorder("Parameters"));
-    jobParameters.setLayout(jparamLayout = new BorderLayout());
+    jobParameters.setLayout(new BorderLayout());
     paramPane.setPreferredSize(new Dimension(360, 300));
     paramPane.getVerticalScrollBar().setUnitIncrement(20);
     // paramPanel.setPreferredSize(new Dimension(360, 300));
@@ -338,52 +379,55 @@ public class WsJobParameters extends JPanel implements ItemListener,
     add(dialogpanel, BorderLayout.SOUTH);
   }
 
-  protected void revertSetting_actionPerformed(ActionEvent e)
+  protected void revert_actionPerformed(ActionEvent e)
   {
-    // TODO Auto-generated method stub
+    reInitDialog(lastParmSet);
 
   }
 
-  protected void deleteSetting_actionPerformed(ActionEvent e)
+  protected void update_actionPerformed(ActionEvent e)
   {
-    String setname = (String) setName.getSelectedItem();
-    int p = setName.getSelectedIndex();
-    if (_getUserPreset(setname) != null)
+    if (isUserPreset)
     {
-      _deleteUserPreset(setname);
-
-    }
-    if (p > 0 && p + 1 == setName.getItemCount())
-    {
-      p--;
+      String curname = ((String) setName.getSelectedItem()).trim();
+      _updatePreset(lastParmSet, curname);
+      lastParmSet = curname;
+      isUserPreset = true;
+      initArgSetModified();
+      syncSetNamesWithStore();
     }
-    setName.setSelectedIndex(p);
+  }
 
+  private void _deleteUserPreset(String lastParmSet2)
+  {
+    paramStore.deletePreset(lastParmSet2);
   }
 
-  protected void renModified_actionPerformed(ActionEvent e)
+  protected void delete_actionPerformed(ActionEvent e)
   {
-    if (curSetName == null || _getUserPreset(lastSetName) == null)
+    if (isUserPreset)
     {
-      System.err
-              .println("can't rename - names unchanged or original name not a preset.");
-      return;
+      // delete current preset's saved entry
+      _deleteUserPreset(lastParmSet);
     }
-    _deleteUserPreset(lastSetName);
-    lastSetName = curSetName;
-    savModified_actionPerformed(e);
-    curSetName = null;
-    boolean setd = settingDialog;
-    settingDialog = true;
-    syncSetNamesWithStore();
-    settingDialog = setd;
+    reInitDialog(null); // service default
   }
 
-  protected void savModified_actionPerformed(ActionEvent e)
+  protected void create_actionPerformed(ActionEvent e)
   {
-    _storeUserPreset(lastSetName=(String) setName.getSelectedItem(), setDescr.getText(), getJobParams());
-    curSetName = null;
-    initArgSetModified(); // reset the modification state
+    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 canceljob_actionPerformed(ActionEvent e)
@@ -416,11 +460,18 @@ public class WsJobParameters extends JPanel implements ItemListener,
    */
   boolean settingDialog = false;
 
-  void initForService(Jws2Instance service, Preset p,
-          List<Argument> jobArgset)
+  void initForService(Jws2Instance service, WsParamSetI jabap,
+          List<Argument> jabajobArgset)
   {
+    WsParamSetI p = null;
+    List<ArgumentI> jobArgset = null;
     settingDialog = true;
-    this.service = service;
+    { // instantiate the abstract proxy for Jaba objects
+      jobArgset = jabajobArgset == null ? null : JabaParamStore
+              .getJwsArgsfromJaba(jabajobArgset);
+      p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
+                 // null;
+    }
     // TODO: Recover window geometry prefs for this service
     // jobPanel.setDividerLocation(proportionalLocation)
     // settingsPanel.setDividerLocation(proportionalLocation)
@@ -429,67 +480,81 @@ public class WsJobParameters extends JPanel implements ItemListener,
     {
       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);
     }
-    serviceOptions = service.getRunnerConfig();
-    // add any presets not already added.
     String curname = (p == null ? "" : p.getName());
-    PresetManager prman = service.getPresets();
-    servicePresets = new Hashtable();
-    if (prman != null)
+    for (WsParamSetI pr : paramStore.getPresets())
     {
-      List prList = service.getPresets().getPresets();
-      if (prList != null)
+      if (!pr.isModifiable())
       {
-        for (Object pr : prList)
-        {
-          servicePresets.put(((Preset) pr).getName(), "preset");
-          if (!exnames.contains(((Preset) pr).getName()))
-          {
-            setName.addItem(((Preset) pr).getName());
-          }
-        }
+        servicePresets.put(pr.getName(), "preset");
+      }
+      else
+      {
+      }
+      if (!exnames.contains(pr.getName()))
+      {
+        setName.addItem(pr.getName());
+      }
+    }
+    // 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);
       }
     }
-    updateTable(p, jobArgset);
-    initArgSetModified();
     settingDialog = false;
 
   }
 
   @SuppressWarnings("unchecked")
-  private void updateTable(Preset p, List<Argument> jobArgset)
+  private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
   {
-    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;
+          ParameterI parm = (ParameterI) myarg;
           addParameter(parm);
         }
         else
         {
-          if (myarg instanceof Option)
+          if (myarg instanceof OptionI)
           {
-            Option opt = (Option) myarg;
+            OptionI opt = (OptionI) myarg;
             addOption(opt).resetToDefault();
           }
           else
           {
             System.err.println("Ignoring unknown service argument type "
-                    + arg.getClass().getName());
+                    + myarg.getClass().getName());
           }
         }
       }
@@ -497,26 +562,28 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
     if (p != null)
     {
+      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.setSelectedItem(lastSetName = SVC_DEF);
       }
     }
@@ -529,20 +596,20 @@ public class WsJobParameters extends JPanel implements ItemListener,
     // get setargs from current object
     if (args != null)
     {
-      for (Argument arg : args)
+      for (ArgumentI arg : args)
       {
-        if (arg instanceof Parameter)
+        if (arg instanceof ParameterI)
         {
-          setParameter((Parameter) arg);
+          setParameter((ParameterI) arg);
         }
         else
         {
-          if (arg instanceof Option)
+          if (arg instanceof OptionI)
           {
-//            System.out.println("Setting option "
-//                    + System.identityHashCode(arg) + ":" + arg.getName()
-//                    + " with " + arg.getDefaultValue());
-            selectOption((Option) arg, arg.getDefaultValue());
+            // System.out.println("Setting option "
+            // + System.identityHashCode(arg) + ":" + arg.getName()
+            // + " with " + arg.getDefaultValue());
+            selectOption((OptionI) arg, arg.getDefaultValue());
           }
         }
 
@@ -554,7 +621,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     jobOptions.setLayout(new GridLayout(optSet.size(), 1));
     refreshParamLayout();
     paramPane.validate();
-    validate();
+    revalidate();
   }
 
   private boolean isModified()
@@ -571,9 +638,35 @@ public class WsJobParameters extends JPanel implements ItemListener,
   {
     curSetName = null;
     modifiedElements.clear();
-    renmodified.setVisible(false);
-    savmodified.setVisible(false);
+    updateButtonDisplay();
+  }
 
+  private void updateButtonDisplay()
+  {
+    boolean _update = false, _create = false, _delete = false, _revert = false;
+    if (modifiedElements.size() > 0)
+    {
+      // set modified
+      _revert = true;
+      _update = isUserPreset; // can only update user presets
+      if (!isUserPreset || modifiedElements.containsKey(setName))
+      {
+        // name modified - can create new preset
+        _create = true;
+      }
+    }
+    else
+    {
+      // set unmodified
+    }
+    // can still delete a user preset
+    _delete = isUserPreset;
+
+    createpref.setVisible(_create);
+    updatepref.setVisible(_update);
+    deletepref.setVisible(_delete);
+    revertpref.setVisible(_revert);
+    validate();
   }
 
   private void argSetModified(Object modifiedElement, boolean b)
@@ -582,46 +675,27 @@ public class WsJobParameters extends JPanel implements ItemListener,
     {
       return;
     }
-
     if (!b)
     {
       modifiedElements.remove(modifiedElement);
     }
     else
     {
-      modifiedElements.put(modifiedElement, modifiedElement);
-    }
-    // set mod status based on presence of elements in table
-    if (modifiedElements.size() > 0)
-    {
-      makeSetNameValid();
-      savmodified.setVisible(true);
-      revertsetting.setVisible(false);
-    }
-    else
-    {
-      revertsetting.setVisible(false);
-      deletesetting
-              .setVisible(!isServicePreset((String) setName
-                      .getSelectedItem())
-                      && _getUserPreset((String) setName.getSelectedItem()) != null);
-      savmodified.setVisible(false);
-    }
-    // special reveal if setName has been modified
-    if (modifiedElements.get(setName) != null)
-    {
-      if (curSetName != null && lastSetName != null
-              && !lastSetName.equals(curSetName))
+      if (b && modifiedElement == setName
+              && modifiedElements.contains(modifiedElement))
       {
-        renmodified.setVisible(!isServicePreset(lastSetName));
+        // HACK! prevents iteration on makeSetNameValid
+        b = false;
       }
+      modifiedElements.put(modifiedElement, modifiedElement);
     }
-    else
+    // set mod status based on presence of elements in table
+    if (b && modifiedElements.size() > 0)
     {
-      // setname isn't in modlist - so don't rename
-      renmodified.setVisible(false);
+      makeSetNameValid(!isUserPreset);
+      SetNamePanel.revalidate();
     }
-    validate();
+    updateButtonDisplay();
   }
 
   private boolean isServicePreset(String selectedItem)
@@ -634,32 +708,33 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * check if the current set name is a valid set name for saving, if not, then
    * fix it.
    */
-  private void makeSetNameValid()
+  private void makeSetNameValid(boolean newuserset)
   {
     boolean stn = settingDialog;
     boolean renamed = false;
     settingDialog = true;
-    String nm = (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))
     {
       nm = "User " + nm;
-      String tnm=nm;
       renamed = true;
-      int i=0;
-      while (_getUserPreset(tnm)!=null)
+    }
+    String tnm = nm;
+    if (newuserset)
+    {
+      int i = 0;
+      while (paramStore.getPreset(tnm) != null)
       {
-        tnm = nm+" ("+(++i)+")";
+        tnm = nm + " (" + (++i) + ")";
+        renamed = true;
       }
-      if (i>0)
+      if (i > 0)
       {
         nm = tnm;
       }
     }
-    // if ()
-    // if nm exists in user's preset store then savmodified will update an
-    // existing user defined preset
-    // if nm doesn't exist, then the button will create a new preset.
 
     boolean makeupdate = false;
     // sync the gui with the preset database
@@ -669,41 +744,37 @@ public class WsJobParameters extends JPanel implements ItemListener,
       if (snm.equals(nm))
       {
         makeupdate = true;
-        setName.setSelectedIndex(i);
+        // setName.setSelectedIndex(i);
       }
     }
-
-    if (_getUserPreset(nm) != null)
+    if (!makeupdate)
     {
-      savmodified.setText("Update");
+      setName.addItem(curSetName = nm);
+      setName.setSelectedItem(curSetName);
     }
-    else
+    if (renamed)
     {
-      if (renamed)
-      {
-        setName.addItem(nm);
-        setName.setSelectedIndex(setName.getItemCount() - 1);
-      }
-      savmodified.setText("Save");
+      settingDialog = false; // we need this name change to be registered.
+      argSetModified(setName, renamed);
     }
     settingDialog = stn;
   }
 
-  private void addParameter(Parameter parm)
+  private void addParameter(ParameterI arg)
   {
-    ParamBox pb = paramSet.get(parm.getName());
+    ParamBox pb = paramSet.get(arg.getName());
     if (pb == null)
     {
-      pb = new ParamBox(this, parm);
-      paramSet.put(parm.getName(), pb);
+      pb = new ParamBox(this, arg);
+      paramSet.put(arg.getName(), pb);
       paramList.add(pb);
     }
     pb.init();
     // take the defaults from the parameter
-    pb.updateControls(parm);
+    pb.updateControls(arg);
   }
 
-  private void setParameter(Parameter arg)
+  private void setParameter(ParameterI arg)
   {
     ParamBox pb = paramSet.get(arg.getName());
     if (pb == null)
@@ -717,27 +788,27 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   }
 
-  private void selectOption(Option opt, String string)
+  private void selectOption(OptionI option, String string)
   {
-    OptionBox cb = optSet.get(opt.getName());
+    OptionBox cb = optSet.get(option.getName());
     if (cb == null)
     {
-      cb = addOption(opt);
+      cb = addOption(option);
     }
-    cb.enabled.setSelected(true); // initial state for an option.
+    cb.enabled.setSelected(string != null); // initial state for an option.
     if (string != null)
     {
-      if (opt.getPossibleValues().contains(string))
+      if (option.getPossibleValues().contains(string))
       {
         cb.val.setSelectedItem(string);
       }
       else
       {
-        throw new Error("Invalid value " + string + " for option " + opt);
+        throw new Error("Invalid value " + string + " for option " + option);
       }
 
     }
-    if (opt.isRequired() && !cb.enabled.isSelected())
+    if (option.isRequired() && !cb.enabled.isSelected())
     {
       // TODO: indicate paramset is not valid.. option needs to be selected!
     }
@@ -759,7 +830,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     JTextField valueField = null;
 
-    ValueConstrain validator = null;
+    ValueConstrainI validator = null;
 
     JPanel settingPanel = new JPanel();
 
@@ -775,7 +846,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     final URL finfo;
 
-    public ParamBox(final WsJobParameters pmlayout, Parameter parm)
+    public ParamBox(final WsJobParameters pmlayout, ParameterI parm)
     {
       pmdialogbox = pmlayout;
       setPreferredSize(new Dimension(PARAM_WIDTH, PARAM_CLOSEDHEIGHT));
@@ -859,7 +930,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     boolean adjusting = false;
 
-    Parameter parameter;
+    ParameterI parameter;
 
     JComboBox choicebox;
 
@@ -868,7 +939,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
       return (descisvisible ? PARAM_HEIGHT : PARAM_CLOSEDHEIGHT);
     }
 
-    public void updateControls(Parameter parm)
+    public void updateControls(ParameterI parm)
     {
       adjusting = true;
       boolean init = (choicebox == null && valueField == null);
@@ -924,23 +995,16 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     Object lastVal;
 
-    public Parameter getParameter()
+    public ParameterI getParameter()
     {
-      Parameter prm = ParameterUtils.copyParameter(parameter);
-      try
+      ParameterI prm = parameter.copy();
+      if (choice)
       {
-        if (choice)
-        {
-          prm.setDefaultValue((String) choicebox.getSelectedItem());
-        }
-        else
-        {
-          prm.setDefaultValue(valueField.getText());
-        }
-      } catch (WrongParameterException e)
+        prm.setDefaultValue((String) choicebox.getSelectedItem());
+      }
+      else
       {
-        e.printStackTrace();
-        return null;
+        prm.setDefaultValue(valueField.getText());
       }
       return prm;
     }
@@ -958,6 +1022,20 @@ public class WsJobParameters extends JPanel implements ItemListener,
           {
             valueField.setText(valueField.getText().trim());
             iVal = Integer.valueOf(valueField.getText());
+            if (validator.getMin() != null
+                    && validator.getMin().intValue() > iVal)
+            {
+              iVal = validator.getMin().intValue();
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
+            }
+            if (validator.getMax() != null
+                    && validator.getMax().intValue() < iVal)
+            {
+              iVal = validator.getMax().intValue();
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
+            }
           } catch (Exception e)
           {
           }
@@ -981,6 +1059,20 @@ public class WsJobParameters extends JPanel implements ItemListener,
           try
           {
             fVal = Float.valueOf(valueField.getText());
+            if (validator.getMin() != null
+                    && validator.getMin().floatValue() > fVal)
+            {
+              fVal = validator.getMin().floatValue();
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
+            }
+            if (validator.getMax() != null
+                    && validator.getMax().floatValue() < fVal)
+            {
+              fVal = validator.getMax().floatValue();
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
+            }
           } catch (Exception e)
           {
           }
@@ -1114,9 +1206,9 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     boolean hasLink = false;
 
-    Option option;
+    OptionI option;
 
-    public OptionBox(Option opt)
+    public OptionBox(OptionI opt)
     {
       option = opt;
       setLayout(new BorderLayout());
@@ -1182,30 +1274,23 @@ public class WsJobParameters extends JPanel implements ItemListener,
       }
       else
       {
-        initVal = null;
+        initVal = (initEnabled) ? option.getDefaultValue() : null;
       }
     }
 
-    public Option getOptionIfEnabled()
+    public OptionI getOptionIfEnabled()
     {
       if (!enabled.isSelected())
       {
         return null;
       }
-      try
-      {
-        Option opt = jalview.ws.jws2.ParameterUtils.copyOption(option);
+      OptionI opt = option.copy();
 
-        if (val.getSelectedItem() != null)
-        {
-          opt.setDefaultValue((String) val.getSelectedItem());
-        }
-      } catch (WrongParameterException e)
+      if (val.getSelectedItem() != null)
       {
-        e.printStackTrace();
-        return null;
+        opt.setDefaultValue((String) val.getSelectedItem());
       }
-      return option;
+      return opt;
     }
 
     public void actionPerformed(ActionEvent e)
@@ -1220,9 +1305,22 @@ public class WsJobParameters extends JPanel implements ItemListener,
     private void checkIfModified()
     {
       boolean notmod = (initEnabled == enabled.isSelected());
-      if (enabled.isSelected() && initVal != null)
+      if (enabled.isSelected())
+      {
+        if (initVal != null)
+        {
+          notmod &= initVal.equals(val.getSelectedItem());
+        }
+        else
+        {
+          // compare against default service setting
+          notmod &= option.getDefaultValue() == null
+                  || option.getDefaultValue().equals(val.getSelectedItem());
+        }
+      }
+      else
       {
-        notmod |= initVal.equals(val.getSelectedItem());
+        notmod &= initVal == null;
       }
       argSetModified(this, !notmod);
     }
@@ -1261,7 +1359,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   }
 
-  private OptionBox addOption(Option opt)
+  private OptionBox addOption(OptionI opt)
   {
     OptionBox cb = optSet.get(opt.getName());
     if (cb == null)
@@ -1295,13 +1393,14 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   protected void refreshParamLayout()
   {
-    int s = 100;
+    FlowLayout fl = new FlowLayout();
+    paramList.setLayout(fl);
+    int s = 2 * fl.getVgap();
     for (ParamBox pbox : paramSet.values())
     {
-      s += pbox.getBoxHeight();
+      s += fl.getVgap() + pbox.getBoxHeight(); // getBoxHeight();
     }
     paramList.setPreferredSize(new Dimension(PARAM_WIDTH, s));
-    paramList.setLayout(new FlowLayout());
     validate();
   }
 
@@ -1352,14 +1451,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
                 prl = prman.getPresets();
               }
             }
-          } else {
+          }
+          else
+          {
             PresetManager prman = lastserv.getPresets();
-            if (prman!=null) {
+            if (prman != null)
+            {
               prl = prman.getPresets();
             }
           }
           Iterator<Preset> en = (prl == null) ? null : prl.iterator();
-          while (en!=null && en.hasNext())
+          while (en != null && en.hasNext())
           {
             if (en != null)
             {
@@ -1370,7 +1472,9 @@ public class WsJobParameters extends JPanel implements ItemListener,
               pr = en.next();
             }
             {
-              System.out.println("Testing opts dupes for "+lastserv.getHost()+" : "+lastserv.getActionText()+":"+pr.getName());
+              System.out.println("Testing opts dupes for "
+                      + lastserv.getUri() + " : "
+                      + lastserv.getActionText() + ":" + pr.getName());
               List<Option> rg = lastserv.getRunnerConfig().getOptions();
               for (Option o : rg)
               {
@@ -1409,7 +1513,52 @@ public class WsJobParameters extends JPanel implements ItemListener,
                 }
               }
             }
-            WsJobParameters pgui = new WsJobParameters(lastserv, pr);
+            {
+              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();
@@ -1481,13 +1630,13 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
   }
 
-  public List<Argument> getJobParams()
+  public List<ArgumentI> getJobParams()
   {
-    List<Argument> argSet = new ArrayList<Argument>();
+    List<ArgumentI> argSet = new ArrayList<ArgumentI>();
     // recover options and parameters from GUI
     for (OptionBox opts : optSet.values())
     {
-      Option opt = opts.getOptionIfEnabled();
+      OptionI opt = opts.getOptionIfEnabled();
       if (opt != null)
       {
         argSet.add(opt);
@@ -1495,7 +1644,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
     for (ParamBox parambox : paramSet.values())
     {
-      Parameter parm = parambox.getParameter();
+      ParameterI parm = parambox.getParameter();
       if (parm != null)
       {
         argSet.add(parm);
@@ -1507,118 +1656,115 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   String lastParmSet = null;
 
-  Hashtable<String, Object[]> editedParams = new Hashtable<String, Object[]>();
-
-  /**
+  /*
+   * 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<Argument> 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<Argument> params)
-  {
-    for (Argument 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 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 _deleteUserPreset(String setName)
-  {
-    editedParams.remove(setName);
-  }
 
   private void syncSetNamesWithStore()
   {
     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())
     {
       String item = (String) setName.getItemAt(n);
-      if (!isServicePreset(item) && _getUserPreset(item) == null)
+      if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
       {
         setName.removeItemAt(n);
       }
       else
       {
+        items.addElement(item);
         n++;
       }
-
+    }
+    if (!items.contains(SVC_DEF))
+    {
+      setName.addItem(SVC_DEF);
+    }
+    for (WsParamSetI upn : paramStore.getPresets())
+    {
+      if (!items.contains(upn.getName()))
+      {
+        setName.addItem(upn.getName());
+      }
     }
   }
 
+  /**
+   * true if lastParmSet is a user preset
+   */
+  boolean isUserPreset = false;
+
   private void reInitDialog(String nextPreset)
   {
     settingDialog = true;
-    syncSetNamesWithStore();
     // updateTable(null,null); // first reset to defaults
-
-    Object[] pset = _getUserPreset(nextPreset);
-    if (pset != null)
+    WsParamSetI pset = null;
+    if (nextPreset != null && nextPreset.length() > 0)
     {
-      setDescr.setText((String) pset[1]);
-      updateTable(null, (List<Argument>) pset[2]);
-      lastParmSet = nextPreset;
-      validate();
+      pset = paramStore.getPreset(nextPreset);
     }
-    else
+    if (pset != null)
     {
-      setDescr.setText("");
-      // must be a default preset from service
-      Preset p = null;
-      try
+      if (pset.isModifiable())
       {
-        PresetManager prman = service.getPresets();
-        if (prman != null)
-        {
-          p = prman.getPresetByName(nextPreset);
-        }
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
-      if (p != null)
-      {
-        updateTable(p, null);
+        isUserPreset = true;
+        setDescr.setText(pset.getDescription());
+        updateTable(null, pset.getArguments());
         lastParmSet = nextPreset;
       }
       else
       {
-        updateTable(null, null);
+        isUserPreset = false;
+        setDescr.setText("");
+        // must be a default preset from service
+        updateTable(pset, null);
+        lastParmSet = nextPreset;
       }
     }
+    else
+    {
+      isUserPreset = false;
+      // Service defaults
+      updateTable(null, null);
+      lastParmSet = SVC_DEF;
+    }
+
     initArgSetModified();
+    syncSetNamesWithStore();
+    setName.setSelectedItem(lastParmSet);
     validate();
     settingDialog = false;
 
@@ -1628,36 +1774,90 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   public void itemStateChanged(ItemEvent e)
   {
-    if (settingDialog)
-    {
-      // ignore event
-      return;
-    }
-    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 (curSetName == null || !setname.equals(curSetName))
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
-        settingDialog = true;
-        if (isModified())
+        public void run()
         {
-          System.out.println("Prompting for "+setname);
-          if (javax.swing.JOptionPane.showConfirmDialog(this,
-                  "Parameter set is modifed - save ?", "Save changes ?",
-                  javax.swing.JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION)
-          {
-            System.out.println("Saving for "+setname);
-            savModified_actionPerformed(null);
-          }
+          doPreferenceComboStateChange(setname);
         }
-        reInitDialog(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))
+      {
+        // setname was just edited - so ignore this event.
+        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)
+      {
+        // 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);
 
       }
     }
+    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());
+
   }
 
   /**
@@ -1678,28 +1878,33 @@ 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();
+        String newname = (String) e.getActionCommand().trim();
         String msg = null;
         if (isServicePreset(newname))
         {
-          JOptionPane.showConfirmDialog(this,
-                  "Invalid name - preset already exists.", "Invalid name",
-                  JOptionPane.OK_OPTION);
+          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("Command " + curSetName + " : "
-                + setName.getSelectedItem());
-        if (curSetName.trim().equals(setName.getSelectedItem()))
+        System.err.println("New name for user setting " + curSetName
+                + " (was " + setName.getSelectedItem() + ")");
+        if (curSetName.equals(setName.getSelectedItem()))
         {
           curSetName = null;
         }
         if (curSetName != null)
         {
-          setName.addItem(curSetName);
-          setName.setSelectedItem(curSetName);
-          argSetModified(setName,
-                  lastSetName != null && !curSetName.equals(lastSetName));
+          argSetModified(setName, true);
           return;
         }
 
@@ -1734,4 +1939,21 @@ public class WsJobParameters extends JPanel implements ItemListener,
   {
     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
+    {
+      return paramStore.getPreset(lastParmSet);
+    }
+  }
 }
\ No newline at end of file