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 // populate table from default parameter set.
570 List<ArgumentI> args = paramStore.getServiceParameters();
572 // split to params and required arguments
575 for (ArgumentI myarg : args)
577 // Ideally, Argument would implement isRequired !
578 if (myarg instanceof ParameterI)
580 ParameterI parm = (ParameterI) myarg;
581 opanp.addParameter(parm).validate();
585 if (myarg instanceof OptionI)
587 OptionI opt = (OptionI) myarg;
588 OptionBox ob = opanp.addOption(opt);
590 if (MAX_OPTWIDTH < ob.getPreferredSize().width)
592 MAX_OPTWIDTH = ob.getPreferredSize().width;
595 cw += ob.getPreferredSize().width + 5;
599 System.err.println("Ignoring unknown service argument type "
600 + myarg.getClass().getName());
604 args = null; // no more args to process.
608 isUserPreset = false;
609 // initialise setname
610 setName.setSelectedItem(lastSetName = p.getName());
611 setDescr.setText(lastDescrText = p.getDescription());
615 args = p.getArguments();
616 } catch (Exception e)
620 // TODO: check if args should be unselected prior to resetting using the
625 if (lastParmSet == null)
627 isUserPreset = false;
628 // first call - so create a dummy name
630 setName.setSelectedItem(lastSetName = SVC_DEF);
634 if (jobArgset != null)
636 argSetModified(jobArgset, true);
639 // get setargs from current object
642 for (ArgumentI arg : args)
644 if (arg instanceof ParameterI)
646 opanp.setParameter((ParameterI) arg);
650 if (arg instanceof OptionI)
652 // System.out.println("Setting option "
653 // + System.identityHashCode(arg) + ":" + arg.getName()
654 // + " with " + arg.getDefaultValue());
655 opanp.selectOption((OptionI) arg, arg.getValue());
662 refreshParamLayout();
666 private boolean isModified()
668 return modifiedElements.size() > 0;
671 private Hashtable modifiedElements = new Hashtable();
674 * reset gui and modification state settings
676 private void initArgSetModified()
679 modifiedElements.clear();
680 updateButtonDisplay();
683 private void updateButtonDisplay()
685 boolean _update = false, _create = false, _delete = false, _revert = false;
686 if (modifiedElements.size() > 0)
690 _update = isUserPreset; // can only update user presets
691 if (!isUserPreset || modifiedElements.containsKey(setName))
693 // name modified - can create new preset
701 // can still delete a user preset
702 _delete = isUserPreset;
704 createpref.setVisible(_create);
705 updatepref.setVisible(_update);
706 deletepref.setVisible(_delete);
707 revertpref.setVisible(_revert);
711 public void argSetModified(Object modifiedElement, boolean b)
719 modifiedElements.remove(modifiedElement);
723 if (b && modifiedElement == setName
724 && modifiedElements.contains(modifiedElement))
726 // HACK! prevents iteration on makeSetNameValid
729 modifiedElements.put(modifiedElement, modifiedElement);
731 // set mod status based on presence of elements in table
732 if (b && modifiedElements.size() > 0)
734 makeSetNameValid(!isUserPreset);
735 SetNamePanel.revalidate();
737 updateButtonDisplay();
740 private boolean isServicePreset(String selectedItem)
742 return selectedItem.equals(SVC_DEF)
743 || servicePresets.containsKey(selectedItem);
747 * check if the current set name is a valid set name for saving, if not, then
750 private void makeSetNameValid(boolean newuserset)
752 boolean stn = settingDialog;
753 boolean renamed = false;
754 settingDialog = true;
755 String nm = (curSetName != null ? curSetName : (String) setName
757 // check if the name is reserved - if it is, rename it.
758 if (isServicePreset(nm))
767 while (paramStore.getPreset(tnm) != null)
769 tnm = nm + " (" + (++i) + ")";
778 boolean makeupdate = false;
779 // sync the gui with the preset database
780 for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
782 String snm = (String) setName.getItemAt(i);
786 // setName.setSelectedIndex(i);
791 setName.addItem(curSetName = nm);
792 setName.setSelectedItem(curSetName);
796 settingDialog = false; // we need this name change to be registered.
797 argSetModified(setName, renamed);
802 public void refreshParamLayout()
804 // optsAndparams.setPreferredSize(null);
805 FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
806 int sep = fl.getVgap();
808 int os = 0, s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
809 + jobOptions.getBorder().getBorderInsets(jobOptions).top
813 * final height for viewport
816 int panewidth = paramPane.getViewport().getSize().width - 120
817 - jobOptions.getBorder().getBorderInsets(jobOptions).left
818 + jobOptions.getBorder().getBorderInsets(jobOptions).right;
822 + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH
823 : OptsAndParamsPage.PARAM_WIDTH);
824 int hgap = fl.getHgap(), cw = hgap;
826 if (opanp.getOptSet().size() > 0)
829 jobOptions.setLayout(new MigLayout("", "", ""));
830 jobOptions.removeAll();
832 for (OptionBox pbox : opanp.getOptSet().values())
835 cw += pbox.getSize().width + hgap;
836 if (cw + 120 > panewidth)
838 jobOptions.add(pbox, "wrap");
839 // System.out.println("Wrap on "+pbox.option.getName());
840 cw = hgap + pbox.getSize().width;
845 jobOptions.add(pbox);
849 finalh += pbox.getSize().height + fl.getVgap();
853 jobOptions.revalidate();
857 jobOptions.setVisible(false);
860 // Now layout the parameters assuming they occupy one column - to calculate
861 // total height of options+parameters
862 fl = new FlowLayout(FlowLayout.LEFT);
864 // http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
865 fl.setAlignOnBaseline(true);
866 if (opanp.getParamSet().size() > 0)
868 paramList.removeAll();
869 paramList.setLayout(new MigLayout("", "", ""));
871 for (ParamBox pbox : opanp.getParamSet().values())
874 cw += pbox.getSize().width + hgap;
875 if (cw + 160 > panewidth)
877 paramList.add(pbox, "wrap");
878 cw = pbox.getSize().width + hgap;
887 finalh += pbox.getSize().height + fl.getVgap();
893 * s = 2 * sep; for (ParamBox pbox : opanp.getParamSet().values()) {
894 * pbox.validate(); s += sep +
895 * pbox.getPreferredSize().height+pbox.getBorder
896 * ().getBorderInsets(pbox).bottom; }
898 * // paramList.setPreferredSize(new Dimension(w, s));
899 * os+=s+2*sep+paramList
900 * .getBorder().getBorderInsets(paramList).bottom+paramList
901 * .getBorder().getBorderInsets(paramList).top;
903 paramList.revalidate();
907 paramList.setVisible(false);
909 // TODO: waste some time trying to eliminate any unnecessary .validate calls
911 // System.out.println("Size will be : "+w+","+os);
912 // optsAndparams.setPreferredSize(null);
913 // paramPane.getViewport().setView(optsAndparams);
914 paramPane.getViewport().setAutoscrolls(true);
915 paramPane.revalidate();
920 * testing method - grab a service and parameter set and show the window
924 public static void main(String[] args)
926 jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
931 Vector<String> services = new Vector<String>();
932 services.addElement(args[p++]);
933 Jws2Discoverer.setServiceUrls(services);
938 } catch (Exception e)
940 System.err.println("Aborting. Problem discovering services.");
944 Jws2Instance lastserv = null;
945 for (Jws2Instance service : disc.getServices())
948 if (p >= args.length || service.serviceType.equalsIgnoreCase(args[p]))
950 if (lastserv != null)
952 List<Preset> prl = null;
954 if (++p < args.length)
956 PresetManager prman = lastserv.getPresets();
959 pr = prman.getPresetByName(args[p]);
962 // just grab the last preset.
963 prl = prman.getPresets();
969 PresetManager prman = lastserv.getPresets();
972 prl = prman.getPresets();
975 Iterator<Preset> en = (prl == null) ? null : prl.iterator();
976 while (en != null && en.hasNext())
987 System.out.println("Testing opts dupes for "
988 + lastserv.getUri() + " : "
989 + lastserv.getActionText() + ":" + pr.getName());
990 List<Option> rg = lastserv.getRunnerConfig().getOptions();
995 Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
996 } catch (Exception e)
998 System.err.println("Failed to copy " + o.getName());
1002 System.err.println("Failed to copy " + o.getName());
1003 e.printStackTrace();
1008 System.out.println("Testing param dupes:");
1009 List<Parameter> rg = lastserv.getRunnerConfig()
1011 for (Parameter o : rg)
1015 Parameter cpy = jalview.ws.jws2.ParameterUtils
1017 } catch (Exception e)
1019 System.err.println("Failed to copy " + o.getName());
1020 e.printStackTrace();
1023 System.err.println("Failed to copy " + o.getName());
1024 e.printStackTrace();
1029 System.out.println("Testing param write:");
1030 List<String> writeparam = null, readparam = null;
1033 writeparam = jalview.ws.jws2.ParameterUtils
1035 pr.getArguments(lastserv.getRunnerConfig()),
1037 System.out.println("Testing param read :");
1038 List<Option> pset = jalview.ws.jws2.ParameterUtils
1039 .processParameters(writeparam,
1040 lastserv.getRunnerConfig(), " ");
1041 readparam = jalview.ws.jws2.ParameterUtils
1042 .writeParameterSet(pset, " ");
1043 Iterator<String> o = pr.getOptions().iterator(), s = writeparam
1044 .iterator(), t = readparam.iterator();
1045 boolean failed = false;
1046 while (s.hasNext() && t.hasNext())
1048 String on = o.next(), sn = s.next(), st = t.next();
1051 System.out.println("Original was " + on
1052 + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
1059 System.out.println("Original parameters:\n"
1061 System.out.println("Wrote parameters in first set:\n"
1063 System.out.println("Wrote parameters in second set:\n"
1067 } catch (Exception e)
1069 e.printStackTrace();
1072 WsJobParameters pgui = new WsJobParameters(lastserv,
1073 new JabaPreset(lastserv, pr));
1074 JFrame jf = new JFrame("Parameters for "
1075 + lastserv.getActionText());
1076 JPanel cont = new JPanel(new BorderLayout());
1078 cont.setPreferredSize(pgui.getPreferredSize());
1079 cont.add(pgui, BorderLayout.CENTER);
1080 jf.setLayout(new BorderLayout());
1081 jf.add(cont, BorderLayout.CENTER);
1083 final Thread thr = Thread.currentThread();
1084 jf.addWindowListener(new WindowListener()
1087 public void windowActivated(WindowEvent e)
1089 // TODO Auto-generated method stub
1093 public void windowClosed(WindowEvent e)
1097 public void windowClosing(WindowEvent e)
1103 public void windowDeactivated(WindowEvent e)
1105 // TODO Auto-generated method stub
1109 public void windowDeiconified(WindowEvent e)
1111 // TODO Auto-generated method stub
1115 public void windowIconified(WindowEvent e)
1117 // TODO Auto-generated method stub
1121 public void windowOpened(WindowEvent e)
1123 // TODO Auto-generated method stub
1128 jf.setVisible(true);
1129 boolean inter = false;
1134 Thread.sleep(10000);
1135 } catch (Exception e)
1148 public boolean isServiceDefaults()
1150 return (!isModified() && (lastParmSet != null && lastParmSet
1154 public List<ArgumentI> getJobParams()
1156 return opanp.getCurrentSettings();
1159 String lastParmSet = null;
1162 * Hashtable<String, Object[]> editedParams = new Hashtable<String,
1165 * store the given parameters in the user parameter set database.
1167 * @param storeSetName - lastParmSet
1169 * @param descr - setDescr.getText()
1171 * @param jobParams - getJobParams()
1173 * private void _storeUserPreset(String storeSetName, String descr,
1174 * List<ArgumentI> jobParams) { // this is a simple hash store. Object[] pset;
1175 * editedParams.put(storeSetName, pset = new Object[3]); pset[0] =
1176 * storeSetName; pset[1] = descr; pset[2] = jobParams; // writeParam("Saving "
1177 * + storeSetName + ": ", jobParams); }
1179 * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
1180 * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
1181 * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
1183 * private Object[] _getUserPreset(String setName) { Object[] pset =
1184 * editedParams.get(setName); // if (pset != null) // writeParam("Retrieving "
1185 * + setName + ": ", (List<Argument>) pset[2]); return pset; }
1187 * * remove the given user preset from the preset stash
1191 * private void _deleteUserPreset(String setName) {
1192 * editedParams.remove(setName); }
1195 private void syncSetNamesWithStore()
1198 // remove any set names in the drop down menu that aren't either a reserved
1199 // setting, or a user defined or service preset.
1200 Vector items = new Vector();
1201 while (n < setName.getItemCount())
1203 String item = (String) setName.getItemAt(n);
1204 if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
1206 setName.removeItemAt(n);
1210 items.addElement(item);
1214 if (!items.contains(SVC_DEF))
1216 setName.addItem(SVC_DEF);
1218 for (WsParamSetI upn : paramStore.getPresets())
1220 if (!items.contains(upn.getName()))
1222 setName.addItem(upn.getName());
1228 * true if lastParmSet is a user preset
1230 boolean isUserPreset = false;
1232 private void reInitDialog(String nextPreset)
1234 settingDialog = true;
1235 // updateTable(null,null); // first reset to defaults
1236 WsParamSetI pset = null;
1237 if (nextPreset != null && nextPreset.length() > 0)
1239 pset = paramStore.getPreset(nextPreset);
1243 if (pset.isModifiable())
1245 isUserPreset = true;
1246 setDescr.setText(pset.getDescription());
1247 updateTable(null, pset.getArguments());
1248 lastParmSet = nextPreset;
1252 isUserPreset = false;
1253 setDescr.setText("");
1254 // must be a default preset from service
1255 updateTable(pset, null);
1256 lastParmSet = nextPreset;
1261 isUserPreset = false;
1263 setDescr.setText("");
1264 updateTable(null, null);
1265 lastParmSet = SVC_DEF;
1268 initArgSetModified();
1269 syncSetNamesWithStore();
1270 setName.setSelectedItem(lastParmSet);
1271 SetNamePanel.validate();
1273 settingDialog = false;
1277 String curSetName = null;
1279 public void itemStateChanged(ItemEvent e)
1281 if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
1283 final String setname = (String) setName.getSelectedItem();
1284 System.out.println("Item state changed for " + setname
1285 + " (handling ? " + !settingDialog + ")");
1291 if (setname == null)
1295 javax.swing.SwingUtilities.invokeLater(new Runnable()
1299 doPreferenceComboStateChange(setname);
1305 private void doPreferenceComboStateChange(String setname)
1307 // user has selected a different item from combo-box
1310 String lsetname = (curSetName != null) ? curSetName : lastParmSet;
1311 if (lsetname.equals(setname))
1313 // setname was just edited - so ignore this event.
1316 settingDialog = true;
1317 System.out.println("Prompting to save " + lsetname);
1318 if (javax.swing.JOptionPane
1323 + "' is modifed, and your changes will be lost.\nReally change preset ?",
1324 "Warning: Unsaved Changes",
1325 javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
1327 // revert the combobox to the current item
1328 settingDialog = true;
1329 setName.setSelectedItem(lsetname);
1330 settingDialog = false;
1333 // System.out.println("Saving for " + lsetname);
1334 // _storeCurrentPreset(lsetname);
1338 settingDialog = true;
1339 reInitDialog(setname);
1340 settingDialog = false;
1344 private void _renameExistingPreset(String oldName, String curSetName2)
1346 paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
1351 * store current settings as given name. You should then reset gui.
1353 * @param curSetName2
1355 private void _storeCurrentPreset(String curSetName2)
1357 paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
1360 private void _updatePreset(String lastParmSet2, String curname)
1362 paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(),
1368 * last saved name for this user preset
1370 String lastSetName = null;
1373 * last saved value of the description text for this user preset
1375 String lastDescrText = null;
1377 public void actionPerformed(ActionEvent e)
1379 if (e.getSource() instanceof Component)
1381 Component src = (Component) e.getSource();
1382 if (src.getParent() == setName)
1384 // rename any existing records we know about for this set.
1385 String newname = (String) e.getActionCommand().trim();
1387 if (isServicePreset(newname))
1389 final String oldname = curSetName != null ? curSetName
1391 final Component ourframe = this;
1392 settingDialog = true;
1393 setName.getEditor().setItem(oldname);
1394 settingDialog = false;
1395 javax.swing.SwingUtilities.invokeLater(new Runnable()
1399 JOptionPane.showMessageDialog(ourframe,
1400 "Invalid name - preset already exists.",
1401 "Invalid name", JOptionPane.WARNING_MESSAGE);
1407 curSetName = newname;
1408 System.err.println("New name for user setting " + curSetName
1409 + " (was " + setName.getSelectedItem() + ")");
1410 if (curSetName.equals(setName.getSelectedItem()))
1414 if (curSetName != null)
1416 argSetModified(setName, true);
1424 private void checkDescrModified()
1431 (lastDescrText == null ? setDescr.getText().trim().length() > 0
1432 : !setDescr.getText().equals(lastDescrText)));
1437 public void insertUpdate(DocumentEvent e)
1439 checkDescrModified();
1442 public void removeUpdate(DocumentEvent e)
1444 checkDescrModified();
1447 public void changedUpdate(DocumentEvent e)
1449 checkDescrModified();
1454 * @return null or the service preset selected by the user
1456 public WsParamSetI getPreset()
1458 if (isUserPreset || isModified()
1459 || (lastParmSet != null && lastParmSet.equals(SVC_DEF)))
1465 return paramStore.getPreset(lastParmSet);