JAL-715 - better validation logic
[jalview.git] / src / jalview / gui / WsJobParameters.java
index 58c9646..6017765 100644 (file)
@@ -1,32 +1,52 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 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.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.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;
@@ -40,7 +60,6 @@ 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;
@@ -48,19 +67,14 @@ import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
 import javax.swing.JSlider;
 import javax.swing.JSplitPane;
-import javax.swing.JTable;
+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.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
-import javax.swing.table.*;
 
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
@@ -68,25 +82,8 @@ 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.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
  * (user + presets + Defaults), and any changes to parameters creates a modified
@@ -105,6 +102,8 @@ import jalview.ws.params.WsParamSetI;
 public class WsJobParameters extends JPanel implements ItemListener,
         ActionListener, DocumentListener
 {
+  URL linkImageURL = getClass().getResource("/images/link.gif");
+
   private static final String SVC_DEF = "Defaults"; // this is the null
                                                     // parameter set as shown to
                                                     // user
@@ -112,8 +111,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
   private static final int PARAM_WIDTH = 340, PARAM_HEIGHT = 150,
           PARAM_CLOSEDHEIGHT = 80;
 
-  private static final int OPTSET_HEIGHT = 30;
-
   JPanel SetNamePanel = new JPanel();
 
   JPanel setDetails = new JPanel();
@@ -148,10 +145,14 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   JPanel paramList = new JPanel();
 
+  JPanel optsAndparams = new JPanel();
+
   RunnerConfig serviceOptions;
 
   ParamDatastoreI paramStore;
 
+  private int MAX_OPTWIDTH = 200;
+
   WsJobParameters(Jws2Instance service)
   {
     this(service, null);
@@ -169,8 +170,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * @param service
    * @param preset
    */
-  public WsJobParameters(JFrame parent, Jws2Instance service, WsParamSetI preset,
-          List<Argument> jobArgset)
+  public WsJobParameters(JFrame parent, Jws2Instance service,
+          WsParamSetI preset, List<Argument> jobArgset)
   {
     this(parent, null, service, preset, jobArgset);
   }
@@ -217,14 +218,23 @@ 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() - 250), 480, 500));
+    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 recover defaults from user prefs.
+    
+    // should perhaps recover defaults from user prefs.
+
     frame.validate();
-    settingsPanel.setDividerLocation(0.4);
-    jobPanel.setDividerLocation(0.3);
-    frame.setVisible(true);
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+        public void run()
+        {
+          jobPanel.setDividerLocation(0.25); 
+
+        }
+      });
+  frame.setVisible(true);
 
     if (response > 0)
     {
@@ -233,22 +243,10 @@ public class WsJobParameters extends JPanel implements ItemListener,
     return false;
   }
 
-  protected JButton makeButton(String label, String tooltip,
-          ActionListener action)
-  {
-    JButton button = new JButton();
-    button.setText(label);
-    button.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    button.setForeground(Color.black);
-    button.setHorizontalAlignment(SwingConstants.CENTER);
-    button.setToolTipText(tooltip);
-    button.addActionListener(action);
-    return button;
-  }
-
   private void jbInit()
   {
-    updatepref = makeButton("Update", "Update the stored user preference",
+    updatepref = JvSwingUtils.makeButton("Update",
+            "Update this existing user parameter set.",
             new ActionListener()
             {
 
@@ -257,7 +255,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
                 update_actionPerformed(e);
               }
             });
-    deletepref = makeButton("Delete", "Delete the user preference",
+    deletepref = JvSwingUtils.makeButton("Delete",
+            "Delete the currently selected user parameter set.",
             new ActionListener()
             {
 
@@ -266,7 +265,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
                 delete_actionPerformed(e);
               }
             });
-    createpref = makeButton("Create", "Create a new preference",
+    createpref = JvSwingUtils.makeButton("Create",
+            "Create a new parameter set with the current settings.",
             new ActionListener()
             {
 
@@ -275,8 +275,9 @@ public class WsJobParameters extends JPanel implements ItemListener,
                 create_actionPerformed(e);
               }
             });
-    revertpref = makeButton("Revert",
-            "Undo all changes to the current set", new ActionListener()
+    revertpref = JvSwingUtils.makeButton("Revert",
+            "Undo all changes to the current parameter set",
+            new ActionListener()
             {
 
               public void actionPerformed(ActionEvent e)
@@ -284,26 +285,22 @@ public class WsJobParameters extends JPanel implements ItemListener,
                 revert_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);
-      }
-    });
+    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());
@@ -313,6 +310,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     setDescr.setBackground(getBackground());
     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);
@@ -320,13 +318,15 @@ public class WsJobParameters extends JPanel implements ItemListener,
     setName.addItemListener(this);
     setName.getEditor().addActionListener(this);
     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: ");
+    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));
-    // setNameLabel.setHorizontalAlignment(FlowLayout.LEFT);
+    
     setNameInfo.add(setNameLabel);
     setNameInfo.add(setName);
+    
     // initial button visibility
     updatepref.setVisible(false);
     deletepref.setVisible(false);
@@ -336,42 +336,51 @@ public class WsJobParameters extends JPanel implements ItemListener,
     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, 20));
+//    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(new BorderLayout());
-    paramPane.setPreferredSize(new Dimension(360, 300));
-    paramPane.getVerticalScrollBar().setUnitIncrement(20);
-    // paramPanel.setPreferredSize(new Dimension(360, 300));
-    // TODO: relayout buttons nicely
-    paramPane.getViewport().setView(paramList);
-    jobParameters.add(paramPane, BorderLayout.CENTER);
-    JPanel jobOptionsPanel = new JPanel();
-    jobOptionsPanel.setLayout(new BorderLayout());
-    jobOptionsPanel.setBorder(new TitledBorder("Options"));
-    jobOptionsPane.getViewport().setView(jobOptions);
-    jobOptionsPanel.add(jobOptionsPane, BorderLayout.CENTER);
-    settingsPanel.setLeftComponent(jobOptionsPanel);
-    settingsPanel.setRightComponent(jobParameters);
-    settingsPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
 
+    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));
     jobPanel.setLeftComponent(setDetails);
-    jobPanel.setRightComponent(settingsPanel);
+    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);
@@ -389,11 +398,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     if (isUserPreset)
     {
       String curname = ((String) setName.getSelectedItem()).trim();
-      if (curname.length() > 0 && !curname.equals(lastParmSet))
-      {
-        _deleteUserPreset(lastParmSet);
-      }
-      _storeCurrentPreset(curname);
+      _updatePreset(lastParmSet, curname);
       lastParmSet = curname;
       isUserPreset = true;
       initArgSetModified();
@@ -472,11 +477,10 @@ public class WsJobParameters extends JPanel implements ItemListener,
     { // instantiate the abstract proxy for Jaba objects
       jobArgset = jabajobArgset == null ? null : JabaParamStore
               .getJwsArgsfromJaba(jabajobArgset);
-      p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) : null;
+      p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
+                 // null;
     }
-    // TODO: Recover window geometry prefs for this service
-    // jobPanel.setDividerLocation(proportionalLocation)
-    // settingsPanel.setDividerLocation(proportionalLocation)
+
     Hashtable exnames = new Hashtable();
     for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
     {
@@ -551,7 +555,13 @@ public class WsJobParameters extends JPanel implements ItemListener,
           if (myarg instanceof OptionI)
           {
             OptionI opt = (OptionI) myarg;
-            addOption(opt).resetToDefault();
+            OptionBox ob = addOption(opt);
+            ob.resetToDefault();
+            if (MAX_OPTWIDTH < ob.getPreferredSize().width)
+            {
+              MAX_OPTWIDTH = ob.getPreferredSize().width;
+            }
+
           }
           else
           {
@@ -618,11 +628,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
       }
     }
 
-    jobOptions.setPreferredSize(new Dimension(PARAM_WIDTH, optSet.size()
-            * OPTSET_HEIGHT));
-    jobOptions.setLayout(new GridLayout(optSet.size(), 1));
     refreshParamLayout();
-    paramPane.validate();
     revalidate();
   }
 
@@ -715,7 +721,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
     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))
     {
@@ -857,23 +864,30 @@ public class WsJobParameters extends JPanel implements ItemListener,
       showDesc.setText("+");
       string.setFont(new Font("Verdana", Font.PLAIN, 11));
       string.setBackground(getBackground());
-      // string.setSize(new Dimension(PARAM_WIDTH, 80));
+
       string.setEditable(false);
       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;
       finfo = parm.getFurtherDetails();
       if (finfo != null)
       {
-        showDesc.setToolTipText("<html><p>Click to show brief description, and right click to open link for further information.</p></html>");
+        showDesc.setToolTipText("<html>"
+                + JvSwingUtils
+                        .wrapTooltip("Click to show brief description<br><img src=\""
+                                + linkImageURL
+                                + "\"/> Right click for further information.")
+                + "</html>");
         showDesc.addMouseListener(this);
       }
       else
       {
-        showDesc.setToolTipText("<html><p>Click to show brief description.</p></html>");
+        showDesc.setToolTipText("<html>"
+                + JvSwingUtils
+                        .wrapTooltip("Click to show brief description.")
+                + "</html>");
       }
       showDesc.addActionListener(new ActionListener()
       {
@@ -882,6 +896,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         {
           descisvisible = !descisvisible;
           descPanel.setVisible(descisvisible);
+          descPanel.getVerticalScrollBar().setValue(0);
           me.setPreferredSize(new Dimension(PARAM_WIDTH,
                   (descisvisible) ? PARAM_HEIGHT : PARAM_CLOSEDHEIGHT));
           me.validate();
@@ -944,8 +959,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
     {
       adjusting = true;
       boolean init = (choicebox == null && valueField == null);
-      float fVal = 0f;
-      int iVal = 0;
       if (init)
       {
         if (choice)
@@ -1023,15 +1036,19 @@ 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)
+            if (validator.getMin() != null
+                    && validator.getMin().intValue() > iVal)
             {
               iVal = validator.getMin().intValue();
-              // TODO: provide visual indication that hard limit was reached for this parameter
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
             }
-            if (validator.getMax()!=null && validator.getMax().intValue()<iVal)
+            if (validator.getMax() != null
+                    && validator.getMax().intValue() < iVal)
             {
               iVal = validator.getMax().intValue();
-              // TODO: provide visual indication that hard limit was reached for this parameter
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
             }
           } catch (Exception e)
           {
@@ -1056,15 +1073,19 @@ public class WsJobParameters extends JPanel implements ItemListener,
           try
           {
             fVal = Float.valueOf(valueField.getText());
-            if (validator.getMin()!=null && validator.getMin().floatValue()>fVal)
+            if (validator.getMin() != null
+                    && validator.getMin().floatValue() > fVal)
             {
               fVal = validator.getMin().floatValue();
-              // TODO: provide visual indication that hard limit was reached for this parameter
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
             }
-            if (validator.getMax()!=null && validator.getMax().floatValue()<fVal)
+            if (validator.getMax() != null
+                    && validator.getMax().floatValue() < fVal)
             {
               fVal = validator.getMax().floatValue();
-              // TODO: provide visual indication that hard limit was reached for this parameter
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
             }
           } catch (Exception e)
           {
@@ -1152,7 +1173,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     {
       if (javax.swing.SwingUtilities.isRightMouseButton(e))
       {
-        Desktop.showUrl(finfo.toString());
+        showUrlPopUp(this, finfo.toString(), e.getX(), e.getY());
       }
     }
 
@@ -1179,7 +1200,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
       // TODO Auto-generated method stub
 
     }
+    // from http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
+    // helpful hint of using the Java 1.6 alignBaseLine property of FlowLayout
+    @Override
+    public Component.BaselineResizeBehavior getBaselineResizeBehavior() {
+        return Component.BaselineResizeBehavior.CONSTANT_ASCENT;
+    }
 
+    @Override
+    public int getBaseline(int width, int height) {
+        return 0;
+    }
   }
 
   Map<String, OptionBox> optSet = new Hashtable<String, OptionBox>();
@@ -1193,8 +1224,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     JLabel optlabel = new JLabel();
 
-    URL linkImageURL = getClass().getResource("/images/link.gif");
-
     final URL finfo;
 
     boolean hasLink = false;
@@ -1214,16 +1243,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
       if (finfo != null)
       {
         hasLink = true;
-        // optlabel.setToolTipText("<html><p>"+opt.getDescription()+"</p><img src=\""+linkImageURL+"\"/></html>");
-        enabled.setToolTipText("<html><p>" + opt.getDescription()
-                + "</p><img src=\"" + linkImageURL + "\"/></html>");
-        // optlabel.addMouseListener(this);
+        enabled.setToolTipText("<html>"
+                + JvSwingUtils.wrapTooltip(opt.getDescription()
+                        + "<br><img src=\"" + linkImageURL + "\"/>")
+                + "</html>");
         enabled.addMouseListener(this);
       }
       else
       {
-        // optlabel.setToolTipText(opt.getDescription());
-        enabled.setToolTipText(opt.getDescription());
+        enabled.setToolTipText("<html>"
+                + JvSwingUtils.wrapTooltip(opt.getDescription())
+                + "</html>");
       }
       add(enabled, BorderLayout.NORTH);
       if (opt.getPossibleValues().size() > 1)
@@ -1239,7 +1269,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
       }
       // TODO: add actionListeners for popup (to open further info),
       // and to update list of parameters if an option is enabled
-      // that takes a value.
+      // that takes a value. JBPNote: is this TODO still valid ?
       setInitialValue();
     }
 
@@ -1359,7 +1389,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     {
       cb = new OptionBox(opt);
       optSet.put(opt.getName(), cb);
-      jobOptions.add(cb);
+      jobOptions.add(cb, FlowLayout.LEFT);
     }
     return cb;
   }
@@ -1386,14 +1416,58 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   protected void refreshParamLayout()
   {
-    FlowLayout fl = new FlowLayout();
-    paramList.setLayout(fl);
-    int s = 2 * fl.getVgap();
-    for (ParamBox pbox : paramSet.values())
+    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 > PARAM_WIDTH ? MAX_OPTWIDTH : PARAM_WIDTH);
+    jobOptions.setLayout(fl);
+    if (optSet.size() > 0)
+    {
+      
+      for (OptionBox pbox : optSet.values())
+      {
+         pbox.revalidate();
+        s += sep + pbox.getPreferredSize().height; 
+      }
+      jobOptions.setPreferredSize(new Dimension(w, s));
+      jobOptions.setLayout(new GridLayout(optSet.size(),1));
+      os=s;
+    }
+    else
+    {
+      jobOptions.setVisible(false);
+    }
+
+    // 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 (paramSet.size() > 0)
+    {
+      paramList.setLayout(fl);
+
+      s = 2 * sep;
+      for (ParamBox pbox : paramSet.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;
+    }
+    else
     {
-      s += fl.getVgap() + pbox.getBoxHeight(); // getBoxHeight();
+      paramList.setVisible(false);
     }
-    paramList.setPreferredSize(new Dimension(PARAM_WIDTH, s));
+    // 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(PARAM_CLOSEDHEIGHT*2);
+    paramPane.validate();
     validate();
   }
 
@@ -1407,7 +1481,7 @@ 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++]);
@@ -1466,7 +1540,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
             }
             {
               System.out.println("Testing opts dupes for "
-                      + lastserv.getHost() + " : "
+                      + lastserv.getUri() + " : "
                       + lastserv.getActionText() + ":" + pr.getName());
               List<Option> rg = lastserv.getRunnerConfig().getOptions();
               for (Option o : rg)
@@ -1550,13 +1624,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
                 e.printStackTrace();
               }
             }
-            WsJobParameters pgui = new WsJobParameters(lastserv, new JabaPreset(lastserv, pr));
+            WsJobParameters pgui = new WsJobParameters(lastserv,
+                    new JabaPreset(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);
+            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()
             {
@@ -1750,6 +1828,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     {
       isUserPreset = false;
       // Service defaults
+      setDescr.setText("");
       updateTable(null, null);
       lastParmSet = SVC_DEF;
     }
@@ -1757,6 +1836,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     initArgSetModified();
     syncSetNamesWithStore();
     setName.setSelectedItem(lastParmSet);
+    SetNamePanel.validate();
     validate();
     settingDialog = false;
 
@@ -1768,7 +1848,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
   {
     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)
@@ -1780,31 +1860,59 @@ public class WsJobParameters extends JPanel implements ItemListener,
       {
         return;
       }
-      // user has selected a different item from combo-box
-      if (isModified())
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
-        String lsetname = (curSetName != null) ? curSetName : lastParmSet;
-        if (lsetname.equals(setname))
+        public void run()
         {
-          // setname was just edited - so ignore this event.
-          return;
+          doPreferenceComboStateChange(setname);
         }
-        settingDialog = true;
-        System.out.println("Prompting to save " + lsetname);
-        if (javax.swing.JOptionPane.showConfirmDialog(this,
-                "Parameter set '" + lsetname + "' is modifed\nsave ?",
-                "Save changes ?", javax.swing.JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION)
-        {
-          System.out.println("Saving for " + lsetname);
-          _storeCurrentPreset(lsetname);
+      });
+    }
+  }
 
-        }
+  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;
-      reInitDialog(setname);
-      settingDialog = false;
+      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());
   }
 
   /**
@@ -1817,6 +1925,13 @@ public class WsJobParameters extends JPanel implements ItemListener,
     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
    */
@@ -1839,11 +1954,22 @@ public class WsJobParameters extends JPanel implements ItemListener,
         String msg = null;
         if (isServicePreset(newname))
         {
-          JOptionPane.showConfirmDialog(this,
-                  "Invalid name - preset already exists.", "Invalid name",
-                  JOptionPane.OK_OPTION);
-          // reset name
-          setName.setSelectedItem(curSetName);
+          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;
@@ -1907,4 +2033,4 @@ public class WsJobParameters extends JPanel implements ItemListener,
       return paramStore.getPreset(lastParmSet);
     }
   }
-}
\ No newline at end of file
+}