2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.gui.OptsAndParamsPage.OptionBox;
21 import jalview.gui.OptsAndParamsPage.ParamBox;
22 import jalview.ws.jws2.JabaParamStore;
23 import jalview.ws.jws2.JabaPreset;
24 import jalview.ws.jws2.Jws2Discoverer;
25 import jalview.ws.jws2.jabaws2.Jws2Instance;
26 import jalview.ws.params.ArgumentI;
27 import jalview.ws.params.OptionI;
28 import jalview.ws.params.ParamDatastoreI;
29 import jalview.ws.params.ParameterI;
30 import jalview.ws.params.WsParamSetI;
32 import java.awt.BorderLayout;
33 import java.awt.Component;
34 import java.awt.Dimension;
35 import java.awt.FlowLayout;
37 import java.awt.GridBagConstraints;
38 import java.awt.GridBagLayout;
39 import java.awt.GridLayout;
40 import java.awt.Rectangle;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.HierarchyBoundsListener;
44 import java.awt.event.HierarchyEvent;
45 import java.awt.event.ItemEvent;
46 import java.awt.event.ItemListener;
47 import java.awt.event.WindowEvent;
48 import java.awt.event.WindowListener;
50 import java.util.Hashtable;
51 import java.util.Iterator;
52 import java.util.List;
53 import java.util.Vector;
55 import javax.swing.JButton;
56 import javax.swing.JComboBox;
57 import javax.swing.JDialog;
58 import javax.swing.JFrame;
59 import javax.swing.JLabel;
60 import javax.swing.JOptionPane;
61 import javax.swing.JPanel;
62 import javax.swing.JScrollPane;
63 import javax.swing.JSplitPane;
64 import javax.swing.JTextArea;
65 import javax.swing.border.TitledBorder;
66 import javax.swing.event.DocumentEvent;
67 import javax.swing.event.DocumentListener;
69 import net.miginfocom.swing.MigLayout;
71 import compbio.metadata.Argument;
72 import compbio.metadata.Option;
73 import compbio.metadata.Parameter;
74 import compbio.metadata.Preset;
75 import compbio.metadata.PresetManager;
76 import compbio.metadata.RunnerConfig;
79 * job parameter editing/browsing dialog box. User can browse existing settings
80 * (user + presets + Defaults), and any changes to parameters creates a modified
81 * user parameter set. LOGIC: If the parameter set is modified, and its name is
82 * a valid, non-existant user parameter set, then a save button is shown. If the
83 * parameter set is modified and its name is a valid, extant user parameter set,
84 * then an update button is shown. If user parameter set's name is edited, and
85 * old name exists as a writable user parameter set, then rename button is
86 * shown. If current parameter set is associated with a user defined parameter
87 * set, then : if set is modifed, a 'revert' button is shown. if set is not
88 * modified, a 'delete' button is shown.
93 public class WsJobParameters extends JPanel implements ItemListener,
94 ActionListener, DocumentListener, OptsParametersContainerI
96 URL linkImageURL = getClass().getResource("/images/link.gif");
98 private static final String SVC_DEF = "Defaults"; // this is the null
99 // parameter set as shown to
103 * manager for options and parameters.
105 OptsAndParamsPage opanp = new OptsAndParamsPage(this);
108 * panel containing job options
110 JPanel jobOptions = new JPanel();
113 * panel containing job parameters
115 JPanel paramList = new JPanel();
117 JPanel SetNamePanel = new JPanel();
119 JPanel setDetails = new JPanel();
121 JSplitPane settingsPanel = new JSplitPane();
123 JPanel jobPanel = new JPanel();
125 JScrollPane jobOptionsPane = new JScrollPane();
127 JButton createpref = new JButton();
129 JButton deletepref = new JButton();
131 JButton revertpref = new JButton();
133 JButton updatepref = new JButton();
135 JButton startjob = new JButton();
137 JButton canceljob = new JButton();
139 JComboBox setName = new JComboBox();
141 JTextArea setDescr = new JTextArea();
143 JScrollPane paramPane = new JScrollPane();
145 // ScrollablePanel optsAndparams = new ScrollablePanel();
146 JPanel optsAndparams = new JPanel();
148 RunnerConfig serviceOptions;
150 ParamDatastoreI paramStore;
152 private int MAX_OPTWIDTH = 200;
154 WsJobParameters(Jws2Instance service)
159 public WsJobParameters(Jws2Instance service, WsParamSetI preset)
161 this(null, service, preset, null);
167 * - if null, create new JFrame outside of desktop
171 public WsJobParameters(JFrame parent, Jws2Instance service,
172 WsParamSetI preset, List<Argument> jobArgset)
174 this(parent, null, service, preset, jobArgset);
185 public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
186 Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
190 this.paramStore = paramStorei;
191 if (paramStore == null)
193 paramStore = service.getParamStore();
195 this.service = service;
196 // argSetModified(false);
197 // populate parameter table
198 initForService(service, preset, jobArgset);
199 // display in new JFrame attached to parent.
205 JDialog frame = null;
208 * shows a modal dialog containing the parameters.
212 public boolean showRunDialog()
215 frame = new JDialog(Desktop.instance, true);
217 frame.setTitle("Edit parameters for " + service.getActionText());
218 Rectangle deskr = Desktop.instance.getBounds();
219 Dimension pref = this.getPreferredSize();
220 frame.setBounds(new Rectangle(
221 (int) (deskr.getCenterX() - pref.width / 2), (int) (deskr
222 .getCenterY() - pref.height / 2), pref.width,
224 frame.setContentPane(this);
226 // should perhaps recover defaults from user prefs.
229 javax.swing.SwingUtilities.invokeLater(new Runnable()
233 // jobPanel.setDividerLocation(0.25);
237 frame.setVisible(true);
246 private void jbInit()
248 this.addHierarchyBoundsListener(new HierarchyBoundsListener()
252 public void ancestorResized(HierarchyEvent arg0)
254 refreshParamLayout();
258 public void ancestorMoved(HierarchyEvent arg0)
260 // TODO Auto-generated method stub
264 updatepref = JvSwingUtils.makeButton("Update",
265 "Update this existing user parameter set.",
269 public void actionPerformed(ActionEvent e)
271 update_actionPerformed(e);
274 deletepref = JvSwingUtils.makeButton("Delete",
275 "Delete the currently selected user parameter set.",
279 public void actionPerformed(ActionEvent e)
281 delete_actionPerformed(e);
284 createpref = JvSwingUtils.makeButton("Create",
285 "Create a new parameter set with the current settings.",
289 public void actionPerformed(ActionEvent e)
291 create_actionPerformed(e);
294 revertpref = JvSwingUtils.makeButton("Revert",
295 "Undo all changes to the current parameter set",
299 public void actionPerformed(ActionEvent e)
301 revert_actionPerformed(e);
304 startjob = JvSwingUtils.makeButton("Start Job",
305 "Start Job with current settings.", new ActionListener()
307 public void actionPerformed(ActionEvent e)
309 startjob_actionPerformed(e);
312 canceljob = JvSwingUtils.makeButton("Cancel Job",
313 "Close this dialog and cancel job.", new ActionListener()
315 public void actionPerformed(ActionEvent e)
317 canceljob_actionPerformed(e);
321 setDetails.setBorder(new TitledBorder("Details"));
322 setDetails.setLayout(new BorderLayout());
323 setDescr.setColumns(40);
324 setDescr.setWrapStyleWord(true);
325 setDescr.setLineWrap(true);
326 setDescr.setBackground(getBackground());
327 setDescr.setEditable(true);
328 setDescr.getDocument().addDocumentListener(this);
329 setDescr.setToolTipText("Click to edit the notes for this parameter set.");
330 JScrollPane setDescrView = new JScrollPane();
331 // setDescrView.setPreferredSize(new Dimension(350, 200));
332 setDescrView.getViewport().setView(setDescr);
333 setName.setEditable(true);
334 setName.addItemListener(this);
335 setName.getEditor().addActionListener(this);
336 JPanel setNameInfo = new JPanel(new FlowLayout(FlowLayout.LEFT));
337 GridBagLayout gbl = new GridBagLayout();
338 SetNamePanel.setLayout(gbl);
340 JLabel setNameLabel = new JLabel("Current parameter set name :");
341 setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
343 setNameInfo.add(setNameLabel);
344 setNameInfo.add(setName);
346 // initial button visibility
347 updatepref.setVisible(false);
348 deletepref.setVisible(false);
349 revertpref.setVisible(false);
350 createpref.setVisible(false);
351 JPanel setsavebuts = new JPanel();
352 setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT)); // GridLayout(1,2));
353 ((FlowLayout) setsavebuts.getLayout()).setHgap(10);
354 ((FlowLayout) setsavebuts.getLayout()).setVgap(0);
355 JPanel spacer = new JPanel();
356 spacer.setPreferredSize(new Dimension(2, 30));
357 setsavebuts.add(spacer);
358 setsavebuts.add(deletepref);
359 setsavebuts.add(revertpref);
360 setsavebuts.add(createpref);
361 setsavebuts.add(updatepref);
362 // setsavebuts.setSize(new Dimension(150, 30));
363 JPanel buttonArea = new JPanel(new GridLayout(1, 1));
364 buttonArea.add(setsavebuts);
365 SetNamePanel.add(setNameInfo);
366 GridBagConstraints gbc = new GridBagConstraints();
368 gbl.setConstraints(setNameInfo, gbc);
369 SetNamePanel.add(buttonArea);
370 gbc = new GridBagConstraints();
374 gbl.setConstraints(buttonArea, gbc);
375 setDetails.add(setDescrView, BorderLayout.CENTER);
377 // paramPane.setPreferredSize(new Dimension(360, 400));
378 // paramPane.setPreferredSize(null);
379 jobOptions.setBorder(new TitledBorder("Options"));
380 jobOptions.setOpaque(true);
381 paramList.setBorder(new TitledBorder("Parameters"));
382 paramList.setOpaque(true);
383 JPanel bjo = new JPanel(new BorderLayout()), bjp = new JPanel(
385 bjo.add(jobOptions, BorderLayout.CENTER);
386 bjp.add(paramList, BorderLayout.CENTER);
389 // optsAndparams.setScrollableWidth(ScrollableSizeHint.FIT);
390 // optsAndparams.setScrollableHeight(ScrollableSizeHint.NONE);
391 // optsAndparams.setLayout(new BorderLayout());
392 optsAndparams.setLayout(new BorderLayout());
393 optsAndparams.add(jobOptions, BorderLayout.NORTH);
394 optsAndparams.add(paramList, BorderLayout.CENTER);
395 JPanel jp = new JPanel(new BorderLayout());
396 jp.add(optsAndparams, BorderLayout.CENTER);
397 paramPane.getViewport().setView(jp);
398 paramPane.setBorder(null);
399 setLayout(new BorderLayout());
400 jobPanel.setPreferredSize(null);
401 jobPanel.setLayout(new BorderLayout());
402 jobPanel.add(setDetails, BorderLayout.NORTH);
403 jobPanel.add(paramPane, BorderLayout.CENTER);
404 // jobPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
406 add(SetNamePanel, BorderLayout.NORTH);
407 add(jobPanel, BorderLayout.CENTER);
409 JPanel dialogpanel = new JPanel();
410 dialogpanel.add(startjob);
411 dialogpanel.add(canceljob);
412 add(dialogpanel, BorderLayout.SOUTH);
416 protected void revert_actionPerformed(ActionEvent e)
418 reInitDialog(lastParmSet);
422 protected void update_actionPerformed(ActionEvent e)
426 String curname = ((String) setName.getSelectedItem()).trim();
427 _updatePreset(lastParmSet, curname);
428 lastParmSet = curname;
430 initArgSetModified();
431 syncSetNamesWithStore();
435 private void _deleteUserPreset(String lastParmSet2)
437 paramStore.deletePreset(lastParmSet2);
440 protected void delete_actionPerformed(ActionEvent e)
444 // delete current preset's saved entry
445 _deleteUserPreset(lastParmSet);
447 reInitDialog(null); // service default
450 protected void create_actionPerformed(ActionEvent e)
452 String curname = ((String) setName.getSelectedItem()).trim();
453 if (curname.length() > 0)
455 _storeCurrentPreset(curname);
456 lastParmSet = curname;
458 initArgSetModified();
462 // TODO: show warning
463 System.err.println("Invalid name. Not saved.");
467 protected void canceljob_actionPerformed(ActionEvent e)
472 frame.setVisible(false);
476 protected void startjob_actionPerformed(ActionEvent e)
481 frame.setVisible(false);
485 Jws2Instance service;
488 * list of service presets in the gui
490 Hashtable servicePresets = null;
493 * set if dialog is being set - so handlers will avoid spurious events
495 boolean settingDialog = false;
497 void initForService(Jws2Instance service, WsParamSetI jabap,
498 List<Argument> jabajobArgset)
500 WsParamSetI p = null;
501 List<ArgumentI> jobArgset = null;
502 settingDialog = true;
503 { // instantiate the abstract proxy for Jaba objects
504 jobArgset = jabajobArgset == null ? null : JabaParamStore
505 .getJwsArgsfromJaba(jabajobArgset);
506 p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
510 Hashtable exnames = new Hashtable();
511 for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
513 exnames.put((String) setName.getItemAt(i), setName.getItemAt(i));
515 servicePresets = new Hashtable();
516 // Add the default entry - if not present already.
517 if (!exnames.contains(SVC_DEF))
519 setName.addItem(SVC_DEF);
520 exnames.put(SVC_DEF, SVC_DEF);
521 servicePresets.put(SVC_DEF, SVC_DEF);
523 String curname = (p == null ? "" : p.getName());
524 for (WsParamSetI pr : paramStore.getPresets())
526 if (!pr.isModifiable())
528 servicePresets.put(pr.getName(), "preset");
533 if (!exnames.contains(pr.getName()))
535 setName.addItem(pr.getName());
538 // TODO: if initial jobArgset matches a given user setting or preset then
539 // should recover setting accordingly
540 // updateTable(p, jobArgset);
543 reInitDialog(p.getName());
544 initArgSetModified();
548 if (jobArgset != null && jobArgset.size() > 0)
550 curSetName = "Supplied Settings";
551 isUserPreset = false;
552 updateTable(p, jobArgset);
553 setName.setSelectedItem(curSetName);
554 updateButtonDisplay();
562 settingDialog = false;
566 @SuppressWarnings("unchecked")
567 private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
569 boolean setDefaultParams=false;
570 if (lastParmSet == null)
572 isUserPreset = false;
573 // First call - so provide Service default settings
574 setName.setSelectedItem(lastSetName = SVC_DEF);
576 if (p==null && SVC_DEF.equals(""+setName.getSelectedItem()))
578 // indicate that service defaults should be set if available
579 setDefaultParams=true;
581 // populate table from default parameter set.
582 List<ArgumentI> args = paramStore.getServiceParameters();
584 // split to params and required arguments
587 boolean optset=false;
588 for (ArgumentI myarg : args)
590 // Ideally, Argument would implement isRequired !
591 if (myarg instanceof ParameterI)
593 ParameterI parm = (ParameterI) myarg;
594 opanp.addParameter(parm).validate();
598 if (myarg instanceof OptionI)
600 OptionI opt = (OptionI) myarg;
601 OptionBox ob = opanp.addOption(opt);
602 ob.resetToDefault(setDefaultParams);
603 if (MAX_OPTWIDTH < ob.getPreferredSize().width)
605 MAX_OPTWIDTH = ob.getPreferredSize().width;
608 cw += ob.getPreferredSize().width + 5;
612 System.err.println("Ignoring unknown service argument type "
613 + myarg.getClass().getName());
617 args = null; // no more args to process.
621 isUserPreset = false;
622 // initialise setname
623 setName.setSelectedItem(lastSetName = p.getName());
624 setDescr.setText(lastDescrText = p.getDescription());
628 args = p.getArguments();
629 } catch (Exception e)
633 // TODO: check if args should be unselected prior to resetting using the
637 if (jobArgset != null)
639 argSetModified(jobArgset, true);
642 // get setargs from current object
645 for (ArgumentI arg : args)
647 if (arg instanceof ParameterI)
649 opanp.setParameter((ParameterI) arg);
653 if (arg instanceof OptionI)
655 // System.out.println("Setting option "
656 // + System.identityHashCode(arg) + ":" + arg.getName()
657 // + " with " + arg.getDefaultValue());
658 opanp.selectOption((OptionI) arg, arg.getValue());
665 refreshParamLayout();
669 private boolean isModified()
671 return modifiedElements.size() > 0;
674 private Hashtable modifiedElements = new Hashtable();
677 * reset gui and modification state settings
679 private void initArgSetModified()
682 modifiedElements.clear();
683 updateButtonDisplay();
686 private void updateButtonDisplay()
688 boolean _update = false, _create = false, _delete = false, _revert = false;
689 if (modifiedElements.size() > 0)
693 _update = isUserPreset; // can only update user presets
694 if (!isUserPreset || modifiedElements.containsKey(setName))
696 // name modified - can create new preset
704 // can still delete a user preset
705 _delete = isUserPreset;
707 createpref.setVisible(_create);
708 updatepref.setVisible(_update);
709 deletepref.setVisible(_delete);
710 revertpref.setVisible(_revert);
714 public void argSetModified(Object modifiedElement, boolean b)
722 modifiedElements.remove(modifiedElement);
726 if (b && modifiedElement == setName
727 && modifiedElements.contains(modifiedElement))
729 // HACK! prevents iteration on makeSetNameValid
732 modifiedElements.put(modifiedElement, modifiedElement);
734 // set mod status based on presence of elements in table
735 if (b && modifiedElements.size() > 0)
737 makeSetNameValid(!isUserPreset);
738 SetNamePanel.revalidate();
740 updateButtonDisplay();
743 private boolean isServicePreset(String selectedItem)
745 return selectedItem.equals(SVC_DEF)
746 || servicePresets.containsKey(selectedItem);
750 * check if the current set name is a valid set name for saving, if not, then
753 private void makeSetNameValid(boolean newuserset)
755 boolean stn = settingDialog;
756 boolean renamed = false;
757 settingDialog = true;
758 String nm = (curSetName != null ? curSetName : (String) setName
760 // check if the name is reserved - if it is, rename it.
761 if (isServicePreset(nm))
770 while (paramStore.getPreset(tnm) != null)
772 tnm = nm + " (" + (++i) + ")";
781 boolean makeupdate = false;
782 // sync the gui with the preset database
783 for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
785 String snm = (String) setName.getItemAt(i);
789 // setName.setSelectedIndex(i);
794 setName.addItem(curSetName = nm);
795 setName.setSelectedItem(curSetName);
799 settingDialog = false; // we need this name change to be registered.
800 argSetModified(setName, renamed);
805 public void refreshParamLayout()
807 // optsAndparams.setPreferredSize(null);
808 FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
809 int sep = fl.getVgap();
811 int os = 0, s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
812 + jobOptions.getBorder().getBorderInsets(jobOptions).top
816 * final height for viewport
819 int panewidth = paramPane.getViewport().getSize().width - 120
820 - jobOptions.getBorder().getBorderInsets(jobOptions).left
821 + jobOptions.getBorder().getBorderInsets(jobOptions).right;
825 + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH
826 : OptsAndParamsPage.PARAM_WIDTH);
827 int hgap = fl.getHgap(), cw = hgap;
829 if (opanp.getOptSet().size() > 0)
832 jobOptions.setLayout(new MigLayout("", "", ""));
833 jobOptions.removeAll();
835 for (OptionBox pbox : opanp.getOptSet().values())
838 cw += pbox.getSize().width + hgap;
839 if (cw + 120 > panewidth)
841 jobOptions.add(pbox, "wrap");
842 // System.out.println("Wrap on "+pbox.option.getName());
843 cw = hgap + pbox.getSize().width;
848 jobOptions.add(pbox);
852 finalh += pbox.getSize().height + fl.getVgap();
856 jobOptions.revalidate();
860 jobOptions.setVisible(false);
863 // Now layout the parameters assuming they occupy one column - to calculate
864 // total height of options+parameters
865 fl = new FlowLayout(FlowLayout.LEFT);
867 // http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
868 fl.setAlignOnBaseline(true);
869 if (opanp.getParamSet().size() > 0)
871 paramList.removeAll();
872 paramList.setLayout(new MigLayout("", "", ""));
874 for (ParamBox pbox : opanp.getParamSet().values())
877 cw += pbox.getSize().width + hgap;
878 if (cw + 160 > panewidth)
880 paramList.add(pbox, "wrap");
881 cw = pbox.getSize().width + hgap;
890 finalh += pbox.getSize().height + fl.getVgap();
896 * s = 2 * sep; for (ParamBox pbox : opanp.getParamSet().values()) {
897 * pbox.validate(); s += sep +
898 * pbox.getPreferredSize().height+pbox.getBorder
899 * ().getBorderInsets(pbox).bottom; }
901 * // paramList.setPreferredSize(new Dimension(w, s));
902 * os+=s+2*sep+paramList
903 * .getBorder().getBorderInsets(paramList).bottom+paramList
904 * .getBorder().getBorderInsets(paramList).top;
906 paramList.revalidate();
910 paramList.setVisible(false);
912 // TODO: waste some time trying to eliminate any unnecessary .validate calls
914 // System.out.println("Size will be : "+w+","+os);
915 // optsAndparams.setPreferredSize(null);
916 // paramPane.getViewport().setView(optsAndparams);
917 paramPane.getViewport().setAutoscrolls(true);
918 paramPane.revalidate();
923 * testing method - grab a service and parameter set and show the window
927 public static void main(String[] args)
929 jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
934 Vector<String> services = new Vector<String>();
935 services.addElement(args[p++]);
936 Jws2Discoverer.setServiceUrls(services);
941 } catch (Exception e)
943 System.err.println("Aborting. Problem discovering services.");
947 Jws2Instance lastserv = null;
948 for (Jws2Instance service : disc.getServices())
951 if (p >= args.length || service.serviceType.equalsIgnoreCase(args[p]))
953 if (lastserv != null)
955 List<Preset> prl = null;
957 if (++p < args.length)
959 PresetManager prman = lastserv.getPresets();
962 pr = prman.getPresetByName(args[p]);
965 // just grab the last preset.
966 prl = prman.getPresets();
972 PresetManager prman = lastserv.getPresets();
975 prl = prman.getPresets();
978 Iterator<Preset> en = (prl == null) ? null : prl.iterator();
979 while (en != null && en.hasNext())
990 System.out.println("Testing opts dupes for "
991 + lastserv.getUri() + " : "
992 + lastserv.getActionText() + ":" + pr.getName());
993 List<Option> rg = lastserv.getRunnerConfig().getOptions();
998 Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
999 } catch (Exception e)
1001 System.err.println("Failed to copy " + o.getName());
1002 e.printStackTrace();
1005 System.err.println("Failed to copy " + o.getName());
1006 e.printStackTrace();
1011 System.out.println("Testing param dupes:");
1012 List<Parameter> rg = lastserv.getRunnerConfig()
1014 for (Parameter o : rg)
1018 Parameter cpy = jalview.ws.jws2.ParameterUtils
1020 } catch (Exception e)
1022 System.err.println("Failed to copy " + o.getName());
1023 e.printStackTrace();
1026 System.err.println("Failed to copy " + o.getName());
1027 e.printStackTrace();
1032 System.out.println("Testing param write:");
1033 List<String> writeparam = null, readparam = null;
1036 writeparam = jalview.ws.jws2.ParameterUtils
1038 pr.getArguments(lastserv.getRunnerConfig()),
1040 System.out.println("Testing param read :");
1041 List<Option> pset = jalview.ws.jws2.ParameterUtils
1042 .processParameters(writeparam,
1043 lastserv.getRunnerConfig(), " ");
1044 readparam = jalview.ws.jws2.ParameterUtils
1045 .writeParameterSet(pset, " ");
1046 Iterator<String> o = pr.getOptions().iterator(), s = writeparam
1047 .iterator(), t = readparam.iterator();
1048 boolean failed = false;
1049 while (s.hasNext() && t.hasNext())
1051 String on = o.next(), sn = s.next(), st = t.next();
1054 System.out.println("Original was " + on
1055 + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
1062 System.out.println("Original parameters:\n"
1064 System.out.println("Wrote parameters in first set:\n"
1066 System.out.println("Wrote parameters in second set:\n"
1070 } catch (Exception e)
1072 e.printStackTrace();
1075 WsJobParameters pgui = new WsJobParameters(lastserv,
1076 new JabaPreset(lastserv, pr));
1077 JFrame jf = new JFrame("Parameters for "
1078 + lastserv.getActionText());
1079 JPanel cont = new JPanel(new BorderLayout());
1081 cont.setPreferredSize(pgui.getPreferredSize());
1082 cont.add(pgui, BorderLayout.CENTER);
1083 jf.setLayout(new BorderLayout());
1084 jf.add(cont, BorderLayout.CENTER);
1086 final Thread thr = Thread.currentThread();
1087 jf.addWindowListener(new WindowListener()
1090 public void windowActivated(WindowEvent e)
1092 // TODO Auto-generated method stub
1096 public void windowClosed(WindowEvent e)
1100 public void windowClosing(WindowEvent e)
1106 public void windowDeactivated(WindowEvent e)
1108 // TODO Auto-generated method stub
1112 public void windowDeiconified(WindowEvent e)
1114 // TODO Auto-generated method stub
1118 public void windowIconified(WindowEvent e)
1120 // TODO Auto-generated method stub
1124 public void windowOpened(WindowEvent e)
1126 // TODO Auto-generated method stub
1131 jf.setVisible(true);
1132 boolean inter = false;
1137 Thread.sleep(10000);
1138 } catch (Exception e)
1151 public boolean isServiceDefaults()
1153 return (!isModified() && (lastParmSet != null && lastParmSet
1157 public List<ArgumentI> getJobParams()
1159 return opanp.getCurrentSettings();
1162 String lastParmSet = null;
1165 * Hashtable<String, Object[]> editedParams = new Hashtable<String,
1168 * store the given parameters in the user parameter set database.
1170 * @param storeSetName - lastParmSet
1172 * @param descr - setDescr.getText()
1174 * @param jobParams - getJobParams()
1176 * private void _storeUserPreset(String storeSetName, String descr,
1177 * List<ArgumentI> jobParams) { // this is a simple hash store. Object[] pset;
1178 * editedParams.put(storeSetName, pset = new Object[3]); pset[0] =
1179 * storeSetName; pset[1] = descr; pset[2] = jobParams; // writeParam("Saving "
1180 * + storeSetName + ": ", jobParams); }
1182 * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
1183 * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
1184 * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
1186 * private Object[] _getUserPreset(String setName) { Object[] pset =
1187 * editedParams.get(setName); // if (pset != null) // writeParam("Retrieving "
1188 * + setName + ": ", (List<Argument>) pset[2]); return pset; }
1190 * * remove the given user preset from the preset stash
1194 * private void _deleteUserPreset(String setName) {
1195 * editedParams.remove(setName); }
1198 private void syncSetNamesWithStore()
1201 // remove any set names in the drop down menu that aren't either a reserved
1202 // setting, or a user defined or service preset.
1203 Vector items = new Vector();
1204 while (n < setName.getItemCount())
1206 String item = (String) setName.getItemAt(n);
1207 if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
1209 setName.removeItemAt(n);
1213 items.addElement(item);
1217 if (!items.contains(SVC_DEF))
1219 setName.addItem(SVC_DEF);
1221 for (WsParamSetI upn : paramStore.getPresets())
1223 if (!items.contains(upn.getName()))
1225 setName.addItem(upn.getName());
1231 * true if lastParmSet is a user preset
1233 boolean isUserPreset = false;
1235 private void reInitDialog(String nextPreset)
1237 settingDialog = true;
1238 // updateTable(null,null); // first reset to defaults
1239 WsParamSetI pset = null;
1240 if (nextPreset != null && nextPreset.length() > 0)
1242 pset = paramStore.getPreset(nextPreset);
1246 if (pset.isModifiable())
1248 isUserPreset = true;
1249 setDescr.setText(pset.getDescription());
1250 updateTable(null, pset.getArguments());
1251 lastParmSet = nextPreset;
1255 isUserPreset = false;
1256 setDescr.setText("");
1257 // must be a default preset from service
1258 updateTable(pset, null);
1259 lastParmSet = nextPreset;
1264 isUserPreset = false;
1266 setDescr.setText("");
1267 updateTable(null, null);
1268 lastParmSet = SVC_DEF;
1271 initArgSetModified();
1272 syncSetNamesWithStore();
1273 setName.setSelectedItem(lastParmSet);
1274 SetNamePanel.validate();
1276 settingDialog = false;
1280 String curSetName = null;
1282 public void itemStateChanged(ItemEvent e)
1284 if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
1286 final String setname = (String) setName.getSelectedItem();
1287 System.out.println("Item state changed for " + setname
1288 + " (handling ? " + !settingDialog + ")");
1294 if (setname == null)
1298 javax.swing.SwingUtilities.invokeLater(new Runnable()
1302 doPreferenceComboStateChange(setname);
1308 private void doPreferenceComboStateChange(String setname)
1310 // user has selected a different item from combo-box
1313 String lsetname = (curSetName != null) ? curSetName : lastParmSet;
1314 if (lsetname.equals(setname))
1316 // setname was just edited - so ignore this event.
1319 settingDialog = true;
1320 System.out.println("Prompting to save " + lsetname);
1321 if (javax.swing.JOptionPane
1326 + "' is modifed, and your changes will be lost.\nReally change preset ?",
1327 "Warning: Unsaved Changes",
1328 javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
1330 // revert the combobox to the current item
1331 settingDialog = true;
1332 setName.setSelectedItem(lsetname);
1333 settingDialog = false;
1336 // System.out.println("Saving for " + lsetname);
1337 // _storeCurrentPreset(lsetname);
1341 settingDialog = true;
1342 reInitDialog(setname);
1343 settingDialog = false;
1347 private void _renameExistingPreset(String oldName, String curSetName2)
1349 paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
1354 * store current settings as given name. You should then reset gui.
1356 * @param curSetName2
1358 private void _storeCurrentPreset(String curSetName2)
1360 paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
1363 private void _updatePreset(String lastParmSet2, String curname)
1365 paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(),
1371 * last saved name for this user preset
1373 String lastSetName = null;
1376 * last saved value of the description text for this user preset
1378 String lastDescrText = null;
1380 public void actionPerformed(ActionEvent e)
1382 if (e.getSource() instanceof Component)
1384 Component src = (Component) e.getSource();
1385 if (src.getParent() == setName)
1387 // rename any existing records we know about for this set.
1388 String newname = (String) e.getActionCommand().trim();
1390 if (isServicePreset(newname))
1392 final String oldname = curSetName != null ? curSetName
1394 final Component ourframe = this;
1395 settingDialog = true;
1396 setName.getEditor().setItem(oldname);
1397 settingDialog = false;
1398 javax.swing.SwingUtilities.invokeLater(new Runnable()
1402 JOptionPane.showMessageDialog(ourframe,
1403 "Invalid name - preset already exists.",
1404 "Invalid name", JOptionPane.WARNING_MESSAGE);
1410 curSetName = newname;
1411 System.err.println("New name for user setting " + curSetName
1412 + " (was " + setName.getSelectedItem() + ")");
1413 if (curSetName.equals(setName.getSelectedItem()))
1417 if (curSetName != null)
1419 argSetModified(setName, true);
1427 private void checkDescrModified()
1434 (lastDescrText == null ? setDescr.getText().trim().length() > 0
1435 : !setDescr.getText().equals(lastDescrText)));
1440 public void insertUpdate(DocumentEvent e)
1442 checkDescrModified();
1445 public void removeUpdate(DocumentEvent e)
1447 checkDescrModified();
1450 public void changedUpdate(DocumentEvent e)
1452 checkDescrModified();
1457 * @return null or the service preset selected by the user
1459 public WsParamSetI getPreset()
1461 if (isUserPreset || isModified()
1462 || (lastParmSet != null && lastParmSet.equals(SVC_DEF)))
1468 return paramStore.getPreset(lastParmSet);