2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.gui.OptsAndParamsPage.OptionBox;
24 import jalview.gui.OptsAndParamsPage.ParamBox;
25 import jalview.util.MessageManager;
26 import jalview.ws.jws2.JabaParamStore;
27 import jalview.ws.jws2.JabaPreset;
28 import jalview.ws.jws2.Jws2Discoverer;
29 import jalview.ws.jws2.jabaws2.Jws2Instance;
30 import jalview.ws.params.ArgumentI;
31 import jalview.ws.params.OptionI;
32 import jalview.ws.params.ParamDatastoreI;
33 import jalview.ws.params.ParameterI;
34 import jalview.ws.params.WsParamSetI;
36 import java.awt.BorderLayout;
37 import java.awt.Component;
38 import java.awt.Dimension;
39 import java.awt.FlowLayout;
41 import java.awt.GridBagConstraints;
42 import java.awt.GridBagLayout;
43 import java.awt.GridLayout;
44 import java.awt.Rectangle;
45 import java.awt.event.ActionEvent;
46 import java.awt.event.ActionListener;
47 import java.awt.event.HierarchyBoundsListener;
48 import java.awt.event.HierarchyEvent;
49 import java.awt.event.ItemEvent;
50 import java.awt.event.ItemListener;
51 import java.awt.event.WindowEvent;
52 import java.awt.event.WindowListener;
54 import java.util.Hashtable;
55 import java.util.Iterator;
56 import java.util.List;
57 import java.util.Vector;
59 import javax.swing.JButton;
60 import javax.swing.JComboBox;
61 import javax.swing.JDialog;
62 import javax.swing.JFrame;
63 import javax.swing.JLabel;
64 import javax.swing.JOptionPane;
65 import javax.swing.JPanel;
66 import javax.swing.JScrollPane;
67 import javax.swing.JSplitPane;
68 import javax.swing.JTextArea;
69 import javax.swing.border.TitledBorder;
70 import javax.swing.event.DocumentEvent;
71 import javax.swing.event.DocumentListener;
73 import net.miginfocom.swing.MigLayout;
75 import compbio.metadata.Argument;
76 import compbio.metadata.Option;
77 import compbio.metadata.Parameter;
78 import compbio.metadata.Preset;
79 import compbio.metadata.PresetManager;
80 import compbio.metadata.RunnerConfig;
83 * job parameter editing/browsing dialog box. User can browse existing settings
84 * (user + presets + Defaults), and any changes to parameters creates a modified
85 * user parameter set. LOGIC: If the parameter set is modified, and its name is
86 * a valid, non-existant user parameter set, then a save button is shown. If the
87 * parameter set is modified and its name is a valid, extant user parameter set,
88 * then an update button is shown. If user parameter set's name is edited, and
89 * old name exists as a writable user parameter set, then rename button is
90 * shown. If current parameter set is associated with a user defined parameter
91 * set, then : if set is modifed, a 'revert' button is shown. if set is not
92 * modified, a 'delete' button is shown.
97 public class WsJobParameters extends JPanel implements ItemListener,
98 ActionListener, DocumentListener, OptsParametersContainerI
100 URL linkImageURL = getClass().getResource("/images/link.gif");
102 private static final String SVC_DEF = "Defaults"; // this is the null
103 // parameter set as shown to
107 * manager for options and parameters.
109 OptsAndParamsPage opanp = new OptsAndParamsPage(this);
112 * panel containing job options
114 JPanel jobOptions = new JPanel();
117 * panel containing job parameters
119 JPanel paramList = new JPanel();
121 JPanel SetNamePanel = new JPanel();
123 JPanel setDetails = new JPanel();
125 JSplitPane settingsPanel = new JSplitPane();
127 JPanel jobPanel = new JPanel();
129 JScrollPane jobOptionsPane = new JScrollPane();
131 JButton createpref = new JButton();
133 JButton deletepref = new JButton();
135 JButton revertpref = new JButton();
137 JButton updatepref = new JButton();
139 JButton startjob = new JButton();
141 JButton canceljob = new JButton();
143 JComboBox setName = new JComboBox();
145 JTextArea setDescr = new JTextArea();
147 JScrollPane paramPane = new JScrollPane();
149 // ScrollablePanel optsAndparams = new ScrollablePanel();
150 JPanel optsAndparams = new JPanel();
152 RunnerConfig serviceOptions;
154 ParamDatastoreI paramStore;
156 private int MAX_OPTWIDTH = 200;
158 WsJobParameters(Jws2Instance service)
163 public WsJobParameters(Jws2Instance service, WsParamSetI preset)
165 this(null, service, preset, null);
171 * - if null, create new JFrame outside of desktop
175 public WsJobParameters(JFrame parent, Jws2Instance service,
176 WsParamSetI preset, List<Argument> jobArgset)
178 this(parent, null, service, preset, jobArgset);
189 public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
190 Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
194 this.paramStore = paramStorei;
195 if (paramStore == null)
197 paramStore = service.getParamStore();
199 this.service = service;
200 // argSetModified(false);
201 // populate parameter table
202 initForService(service, preset, jobArgset);
203 // display in new JFrame attached to parent.
209 JDialog frame = null;
212 * shows a modal dialog containing the parameters.
216 public boolean showRunDialog()
219 frame = new JDialog(Desktop.instance, true);
221 frame.setTitle("Edit parameters for " + service.getActionText());
222 Rectangle deskr = Desktop.instance.getBounds();
223 Dimension pref = this.getPreferredSize();
224 frame.setBounds(new Rectangle(
225 (int) (deskr.getCenterX() - pref.width / 2), (int) (deskr
226 .getCenterY() - pref.height / 2), pref.width,
228 frame.setContentPane(this);
230 // should perhaps recover defaults from user prefs.
233 javax.swing.SwingUtilities.invokeLater(new Runnable()
237 // jobPanel.setDividerLocation(0.25);
241 frame.setVisible(true);
250 private void jbInit()
252 this.addHierarchyBoundsListener(new HierarchyBoundsListener()
256 public void ancestorResized(HierarchyEvent arg0)
258 refreshParamLayout();
262 public void ancestorMoved(HierarchyEvent arg0)
264 // TODO Auto-generated method stub
268 updatepref = JvSwingUtils.makeButton(MessageManager.getString("action.update"),
269 MessageManager.getString("label.update_user_parameter_set"),
273 public void actionPerformed(ActionEvent e)
275 update_actionPerformed(e);
278 deletepref = JvSwingUtils.makeButton(MessageManager.getString("action.delete"),
279 MessageManager.getString("label.delete_user_parameter_set"),
283 public void actionPerformed(ActionEvent e)
285 delete_actionPerformed(e);
288 createpref = JvSwingUtils.makeButton(MessageManager.getString("action.create"),
289 MessageManager.getString("label.create_user_parameter_set"),
293 public void actionPerformed(ActionEvent e)
295 create_actionPerformed(e);
298 revertpref = JvSwingUtils.makeButton(MessageManager.getString("action.revert"),
299 MessageManager.getString("label.revert_changes_user_parameter_set"),
303 public void actionPerformed(ActionEvent e)
305 revert_actionPerformed(e);
308 startjob = JvSwingUtils.makeButton(MessageManager.getString("action.start_job"),
309 MessageManager.getString("label.start_job_current_settings"), new ActionListener()
311 public void actionPerformed(ActionEvent e)
313 startjob_actionPerformed(e);
316 canceljob = JvSwingUtils.makeButton(MessageManager.getString("action.cancel_job"),
317 MessageManager.getString("label.cancel_job_close_dialog"), new ActionListener()
319 public void actionPerformed(ActionEvent e)
321 canceljob_actionPerformed(e);
325 setDetails.setBorder(new TitledBorder(MessageManager.getString("label.details")));
326 setDetails.setLayout(new BorderLayout());
327 setDescr.setColumns(40);
328 setDescr.setWrapStyleWord(true);
329 setDescr.setLineWrap(true);
330 setDescr.setBackground(getBackground());
331 setDescr.setEditable(true);
332 setDescr.getDocument().addDocumentListener(this);
333 setDescr.setToolTipText(MessageManager.getString("label.edit_notes_parameter_set"));
334 JScrollPane setDescrView = new JScrollPane();
335 // setDescrView.setPreferredSize(new Dimension(350, 200));
336 setDescrView.getViewport().setView(setDescr);
337 setName.setEditable(true);
338 setName.addItemListener(this);
339 setName.getEditor().addActionListener(this);
340 JPanel setNameInfo = new JPanel(new FlowLayout(FlowLayout.LEFT));
341 GridBagLayout gbl = new GridBagLayout();
342 SetNamePanel.setLayout(gbl);
344 JLabel setNameLabel = new JLabel(MessageManager.getString("label.current_parameter_set_name"));
345 setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
347 setNameInfo.add(setNameLabel);
348 setNameInfo.add(setName);
350 // initial button visibility
351 updatepref.setVisible(false);
352 deletepref.setVisible(false);
353 revertpref.setVisible(false);
354 createpref.setVisible(false);
355 JPanel setsavebuts = new JPanel();
356 setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT)); // GridLayout(1,2));
357 ((FlowLayout) setsavebuts.getLayout()).setHgap(10);
358 ((FlowLayout) setsavebuts.getLayout()).setVgap(0);
359 JPanel spacer = new JPanel();
360 spacer.setPreferredSize(new Dimension(2, 30));
361 setsavebuts.add(spacer);
362 setsavebuts.add(deletepref);
363 setsavebuts.add(revertpref);
364 setsavebuts.add(createpref);
365 setsavebuts.add(updatepref);
366 // setsavebuts.setSize(new Dimension(150, 30));
367 JPanel buttonArea = new JPanel(new GridLayout(1, 1));
368 buttonArea.add(setsavebuts);
369 SetNamePanel.add(setNameInfo);
370 GridBagConstraints gbc = new GridBagConstraints();
372 gbl.setConstraints(setNameInfo, gbc);
373 SetNamePanel.add(buttonArea);
374 gbc = new GridBagConstraints();
378 gbl.setConstraints(buttonArea, gbc);
379 setDetails.add(setDescrView, BorderLayout.CENTER);
381 // paramPane.setPreferredSize(new Dimension(360, 400));
382 // paramPane.setPreferredSize(null);
383 jobOptions.setBorder(new TitledBorder(MessageManager.getString("label.options")));
384 jobOptions.setOpaque(true);
385 paramList.setBorder(new TitledBorder(MessageManager.getString("label.parameters")));
386 paramList.setOpaque(true);
387 JPanel bjo = new JPanel(new BorderLayout()), bjp = new JPanel(
389 bjo.add(jobOptions, BorderLayout.CENTER);
390 bjp.add(paramList, BorderLayout.CENTER);
393 // optsAndparams.setScrollableWidth(ScrollableSizeHint.FIT);
394 // optsAndparams.setScrollableHeight(ScrollableSizeHint.NONE);
395 // optsAndparams.setLayout(new BorderLayout());
396 optsAndparams.setLayout(new BorderLayout());
397 optsAndparams.add(jobOptions, BorderLayout.NORTH);
398 optsAndparams.add(paramList, BorderLayout.CENTER);
399 JPanel jp = new JPanel(new BorderLayout());
400 jp.add(optsAndparams, BorderLayout.CENTER);
401 paramPane.getViewport().setView(jp);
402 paramPane.setBorder(null);
403 setLayout(new BorderLayout());
404 jobPanel.setPreferredSize(null);
405 jobPanel.setLayout(new BorderLayout());
406 jobPanel.add(setDetails, BorderLayout.NORTH);
407 jobPanel.add(paramPane, BorderLayout.CENTER);
408 // jobPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
410 add(SetNamePanel, BorderLayout.NORTH);
411 add(jobPanel, BorderLayout.CENTER);
413 JPanel dialogpanel = new JPanel();
414 dialogpanel.add(startjob);
415 dialogpanel.add(canceljob);
416 add(dialogpanel, BorderLayout.SOUTH);
420 protected void revert_actionPerformed(ActionEvent e)
422 reInitDialog(lastParmSet);
426 protected void update_actionPerformed(ActionEvent e)
430 String curname = ((String) setName.getSelectedItem()).trim();
431 _updatePreset(lastParmSet, curname);
432 lastParmSet = curname;
434 initArgSetModified();
435 syncSetNamesWithStore();
439 private void _deleteUserPreset(String lastParmSet2)
441 paramStore.deletePreset(lastParmSet2);
444 protected void delete_actionPerformed(ActionEvent e)
448 // delete current preset's saved entry
449 _deleteUserPreset(lastParmSet);
451 reInitDialog(null); // service default
454 protected void create_actionPerformed(ActionEvent e)
456 String curname = ((String) setName.getSelectedItem()).trim();
457 if (curname.length() > 0)
459 _storeCurrentPreset(curname);
460 lastParmSet = curname;
462 initArgSetModified();
466 // TODO: show warning
467 System.err.println("Invalid name. Not saved.");
471 protected void canceljob_actionPerformed(ActionEvent e)
476 frame.setVisible(false);
480 protected void startjob_actionPerformed(ActionEvent e)
485 frame.setVisible(false);
489 Jws2Instance service;
492 * list of service presets in the gui
494 Hashtable servicePresets = null;
497 * set if dialog is being set - so handlers will avoid spurious events
499 boolean settingDialog = false;
501 void initForService(Jws2Instance service, WsParamSetI jabap,
502 List<Argument> jabajobArgset)
504 WsParamSetI p = null;
505 List<ArgumentI> jobArgset = null;
506 settingDialog = true;
507 { // instantiate the abstract proxy for Jaba objects
508 jobArgset = jabajobArgset == null ? null : JabaParamStore
509 .getJwsArgsfromJaba(jabajobArgset);
510 p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
514 Hashtable exnames = new Hashtable();
515 for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
517 exnames.put((String) setName.getItemAt(i), setName.getItemAt(i));
519 servicePresets = new Hashtable();
520 // Add the default entry - if not present already.
521 if (!exnames.contains(SVC_DEF))
523 setName.addItem(SVC_DEF);
524 exnames.put(SVC_DEF, SVC_DEF);
525 servicePresets.put(SVC_DEF, SVC_DEF);
527 String curname = (p == null ? "" : p.getName());
528 for (WsParamSetI pr : paramStore.getPresets())
530 if (!pr.isModifiable())
532 servicePresets.put(pr.getName(), "preset");
537 if (!exnames.contains(pr.getName()))
539 setName.addItem(pr.getName());
542 // TODO: if initial jobArgset matches a given user setting or preset then
543 // should recover setting accordingly
544 // updateTable(p, jobArgset);
547 reInitDialog(p.getName());
548 initArgSetModified();
552 if (jobArgset != null && jobArgset.size() > 0)
554 curSetName = "Supplied Settings";
555 isUserPreset = false;
556 updateTable(p, jobArgset);
557 setName.setSelectedItem(curSetName);
558 updateButtonDisplay();
566 settingDialog = false;
570 @SuppressWarnings("unchecked")
571 private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
573 boolean setDefaultParams=false;
574 if (lastParmSet == null)
576 isUserPreset = false;
577 // First call - so provide Service default settings
578 setName.setSelectedItem(lastSetName = SVC_DEF);
580 if (p==null && SVC_DEF.equals(""+setName.getSelectedItem()))
582 // indicate that service defaults should be set if available
583 setDefaultParams=true;
585 // populate table from default parameter set.
586 List<ArgumentI> args = paramStore.getServiceParameters();
588 // split to params and required arguments
591 boolean optset=false;
592 for (ArgumentI myarg : args)
594 // Ideally, Argument would implement isRequired !
595 if (myarg instanceof ParameterI)
597 ParameterI parm = (ParameterI) myarg;
598 opanp.addParameter(parm).validate();
602 if (myarg instanceof OptionI)
604 OptionI opt = (OptionI) myarg;
605 OptionBox ob = opanp.addOption(opt);
606 ob.resetToDefault(setDefaultParams);
607 if (MAX_OPTWIDTH < ob.getPreferredSize().width)
609 MAX_OPTWIDTH = ob.getPreferredSize().width;
612 cw += ob.getPreferredSize().width + 5;
616 System.err.println("Ignoring unknown service argument type "
617 + myarg.getClass().getName());
621 args = null; // no more args to process.
625 isUserPreset = false;
626 // initialise setname
627 setName.setSelectedItem(lastSetName = p.getName());
628 setDescr.setText(lastDescrText = p.getDescription());
632 args = p.getArguments();
633 } catch (Exception e)
637 // TODO: check if args should be unselected prior to resetting using the
641 if (jobArgset != null)
643 argSetModified(jobArgset, true);
646 // get setargs from current object
649 for (ArgumentI arg : args)
651 if (arg instanceof ParameterI)
653 opanp.setParameter((ParameterI) arg);
657 if (arg instanceof OptionI)
659 // System.out.println("Setting option "
660 // + System.identityHashCode(arg) + ":" + arg.getName()
661 // + " with " + arg.getDefaultValue());
662 opanp.selectOption((OptionI) arg, arg.getValue());
669 refreshParamLayout();
673 private boolean isModified()
675 return modifiedElements.size() > 0;
678 private Hashtable modifiedElements = new Hashtable();
681 * reset gui and modification state settings
683 private void initArgSetModified()
686 modifiedElements.clear();
687 updateButtonDisplay();
690 private void updateButtonDisplay()
692 boolean _update = false, _create = false, _delete = false, _revert = false;
693 if (modifiedElements.size() > 0)
697 _update = isUserPreset; // can only update user presets
698 if (!isUserPreset || modifiedElements.containsKey(setName))
700 // name modified - can create new preset
708 // can still delete a user preset
709 _delete = isUserPreset;
711 createpref.setVisible(_create);
712 updatepref.setVisible(_update);
713 deletepref.setVisible(_delete);
714 revertpref.setVisible(_revert);
718 public void argSetModified(Object modifiedElement, boolean b)
726 modifiedElements.remove(modifiedElement);
730 if (b && modifiedElement == setName
731 && modifiedElements.contains(modifiedElement))
733 // HACK! prevents iteration on makeSetNameValid
736 modifiedElements.put(modifiedElement, modifiedElement);
738 // set mod status based on presence of elements in table
739 if (b && modifiedElements.size() > 0)
741 makeSetNameValid(!isUserPreset);
742 SetNamePanel.revalidate();
744 updateButtonDisplay();
747 private boolean isServicePreset(String selectedItem)
749 return selectedItem.equals(SVC_DEF)
750 || servicePresets.containsKey(selectedItem);
754 * check if the current set name is a valid set name for saving, if not, then
757 private void makeSetNameValid(boolean newuserset)
759 boolean stn = settingDialog;
760 boolean renamed = false;
761 settingDialog = true;
762 String nm = (curSetName != null ? curSetName : (String) setName
764 // check if the name is reserved - if it is, rename it.
765 if (isServicePreset(nm))
774 while (paramStore.getPreset(tnm) != null)
776 tnm = nm + " (" + (++i) + ")";
785 boolean makeupdate = false;
786 // sync the gui with the preset database
787 for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
789 String snm = (String) setName.getItemAt(i);
793 // setName.setSelectedIndex(i);
798 setName.addItem(curSetName = nm);
799 setName.setSelectedItem(curSetName);
803 settingDialog = false; // we need this name change to be registered.
804 argSetModified(setName, renamed);
809 public void refreshParamLayout()
811 // optsAndparams.setPreferredSize(null);
812 FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
813 int sep = fl.getVgap();
815 int os = 0, s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
816 + jobOptions.getBorder().getBorderInsets(jobOptions).top
820 * final height for viewport
823 int panewidth = paramPane.getViewport().getSize().width - 120
824 - jobOptions.getBorder().getBorderInsets(jobOptions).left
825 + jobOptions.getBorder().getBorderInsets(jobOptions).right;
829 + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH
830 : OptsAndParamsPage.PARAM_WIDTH);
831 int hgap = fl.getHgap(), cw = hgap;
833 if (opanp.getOptSet().size() > 0)
836 jobOptions.setLayout(new MigLayout("", "", ""));
837 jobOptions.removeAll();
839 for (OptionBox pbox : opanp.getOptSet().values())
842 cw += pbox.getSize().width + hgap;
843 if (cw + 120 > panewidth)
845 jobOptions.add(pbox, "wrap");
846 // System.out.println("Wrap on "+pbox.option.getName());
847 cw = hgap + pbox.getSize().width;
852 jobOptions.add(pbox);
856 finalh += pbox.getSize().height + fl.getVgap();
860 jobOptions.revalidate();
864 jobOptions.setVisible(false);
867 // Now layout the parameters assuming they occupy one column - to calculate
868 // total height of options+parameters
869 fl = new FlowLayout(FlowLayout.LEFT);
871 // http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
872 fl.setAlignOnBaseline(true);
873 if (opanp.getParamSet().size() > 0)
875 paramList.removeAll();
876 paramList.setLayout(new MigLayout("", "", ""));
878 for (ParamBox pbox : opanp.getParamSet().values())
881 cw += pbox.getSize().width + hgap;
882 if (cw + 160 > panewidth)
884 paramList.add(pbox, "wrap");
885 cw = pbox.getSize().width + hgap;
894 finalh += pbox.getSize().height + fl.getVgap();
900 * s = 2 * sep; for (ParamBox pbox : opanp.getParamSet().values()) {
901 * pbox.validate(); s += sep +
902 * pbox.getPreferredSize().height+pbox.getBorder
903 * ().getBorderInsets(pbox).bottom; }
905 * // paramList.setPreferredSize(new Dimension(w, s));
906 * os+=s+2*sep+paramList
907 * .getBorder().getBorderInsets(paramList).bottom+paramList
908 * .getBorder().getBorderInsets(paramList).top;
910 paramList.revalidate();
914 paramList.setVisible(false);
916 // TODO: waste some time trying to eliminate any unnecessary .validate calls
918 // System.out.println("Size will be : "+w+","+os);
919 // optsAndparams.setPreferredSize(null);
920 // paramPane.getViewport().setView(optsAndparams);
921 paramPane.getViewport().setAutoscrolls(true);
922 paramPane.revalidate();
927 * testing method - grab a service and parameter set and show the window
931 public static void main(String[] args)
933 jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
938 Vector<String> services = new Vector<String>();
939 services.addElement(args[p++]);
940 Jws2Discoverer.setServiceUrls(services);
945 } catch (Exception e)
947 System.err.println("Aborting. Problem discovering services.");
951 Jws2Instance lastserv = null;
952 for (Jws2Instance service : disc.getServices())
955 if (p >= args.length || service.serviceType.equalsIgnoreCase(args[p]))
957 if (lastserv != null)
959 List<Preset> prl = null;
961 if (++p < args.length)
963 PresetManager prman = lastserv.getPresets();
966 pr = prman.getPresetByName(args[p]);
969 // just grab the last preset.
970 prl = prman.getPresets();
976 PresetManager prman = lastserv.getPresets();
979 prl = prman.getPresets();
982 Iterator<Preset> en = (prl == null) ? null : prl.iterator();
983 while (en != null && en.hasNext())
994 System.out.println("Testing opts dupes for "
995 + lastserv.getUri() + " : "
996 + lastserv.getActionText() + ":" + pr.getName());
997 List<Option> rg = lastserv.getRunnerConfig().getOptions();
1002 Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
1003 } catch (Exception e)
1005 System.err.println("Failed to copy " + o.getName());
1006 e.printStackTrace();
1009 System.err.println("Failed to copy " + o.getName());
1010 e.printStackTrace();
1015 System.out.println("Testing param dupes:");
1016 List<Parameter> rg = lastserv.getRunnerConfig()
1018 for (Parameter o : rg)
1022 Parameter cpy = jalview.ws.jws2.ParameterUtils
1024 } catch (Exception e)
1026 System.err.println("Failed to copy " + o.getName());
1027 e.printStackTrace();
1030 System.err.println("Failed to copy " + o.getName());
1031 e.printStackTrace();
1036 System.out.println("Testing param write:");
1037 List<String> writeparam = null, readparam = null;
1040 writeparam = jalview.ws.jws2.ParameterUtils
1042 pr.getArguments(lastserv.getRunnerConfig()),
1044 System.out.println("Testing param read :");
1045 List<Option> pset = jalview.ws.jws2.ParameterUtils
1046 .processParameters(writeparam,
1047 lastserv.getRunnerConfig(), " ");
1048 readparam = jalview.ws.jws2.ParameterUtils
1049 .writeParameterSet(pset, " ");
1050 Iterator<String> o = pr.getOptions().iterator(), s = writeparam
1051 .iterator(), t = readparam.iterator();
1052 boolean failed = false;
1053 while (s.hasNext() && t.hasNext())
1055 String on = o.next(), sn = s.next(), st = t.next();
1058 System.out.println("Original was " + on
1059 + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
1066 System.out.println("Original parameters:\n"
1068 System.out.println("Wrote parameters in first set:\n"
1070 System.out.println("Wrote parameters in second set:\n"
1074 } catch (Exception e)
1076 e.printStackTrace();
1079 WsJobParameters pgui = new WsJobParameters(lastserv,
1080 new JabaPreset(lastserv, pr));
1081 JFrame jf = new JFrame("Parameters for "
1082 + lastserv.getActionText());
1083 JPanel cont = new JPanel(new BorderLayout());
1085 cont.setPreferredSize(pgui.getPreferredSize());
1086 cont.add(pgui, BorderLayout.CENTER);
1087 jf.setLayout(new BorderLayout());
1088 jf.add(cont, BorderLayout.CENTER);
1090 final Thread thr = Thread.currentThread();
1091 jf.addWindowListener(new WindowListener()
1094 public void windowActivated(WindowEvent e)
1096 // TODO Auto-generated method stub
1100 public void windowClosed(WindowEvent e)
1104 public void windowClosing(WindowEvent e)
1110 public void windowDeactivated(WindowEvent e)
1112 // TODO Auto-generated method stub
1116 public void windowDeiconified(WindowEvent e)
1118 // TODO Auto-generated method stub
1122 public void windowIconified(WindowEvent e)
1124 // TODO Auto-generated method stub
1128 public void windowOpened(WindowEvent e)
1130 // TODO Auto-generated method stub
1135 jf.setVisible(true);
1136 boolean inter = false;
1141 Thread.sleep(10000);
1142 } catch (Exception e)
1155 public boolean isServiceDefaults()
1157 return (!isModified() && (lastParmSet != null && lastParmSet
1161 public List<ArgumentI> getJobParams()
1163 return opanp.getCurrentSettings();
1166 String lastParmSet = null;
1169 * Hashtable<String, Object[]> editedParams = new Hashtable<String,
1172 * store the given parameters in the user parameter set database.
1174 * @param storeSetName - lastParmSet
1176 * @param descr - setDescr.getText()
1178 * @param jobParams - getJobParams()
1180 * private void _storeUserPreset(String storeSetName, String descr,
1181 * List<ArgumentI> jobParams) { // this is a simple hash store. Object[] pset;
1182 * editedParams.put(storeSetName, pset = new Object[3]); pset[0] =
1183 * storeSetName; pset[1] = descr; pset[2] = jobParams; // writeParam("Saving "
1184 * + storeSetName + ": ", jobParams); }
1186 * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
1187 * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
1188 * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
1190 * private Object[] _getUserPreset(String setName) { Object[] pset =
1191 * editedParams.get(setName); // if (pset != null) // writeParam("Retrieving "
1192 * + setName + ": ", (List<Argument>) pset[2]); return pset; }
1194 * * remove the given user preset from the preset stash
1198 * private void _deleteUserPreset(String setName) {
1199 * editedParams.remove(setName); }
1202 private void syncSetNamesWithStore()
1205 // remove any set names in the drop down menu that aren't either a reserved
1206 // setting, or a user defined or service preset.
1207 Vector items = new Vector();
1208 while (n < setName.getItemCount())
1210 String item = (String) setName.getItemAt(n);
1211 if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
1213 setName.removeItemAt(n);
1217 items.addElement(item);
1221 if (!items.contains(SVC_DEF))
1223 setName.addItem(SVC_DEF);
1225 for (WsParamSetI upn : paramStore.getPresets())
1227 if (!items.contains(upn.getName()))
1229 setName.addItem(upn.getName());
1235 * true if lastParmSet is a user preset
1237 boolean isUserPreset = false;
1239 private void reInitDialog(String nextPreset)
1241 settingDialog = true;
1242 // updateTable(null,null); // first reset to defaults
1243 WsParamSetI pset = null;
1244 if (nextPreset != null && nextPreset.length() > 0)
1246 pset = paramStore.getPreset(nextPreset);
1250 if (pset.isModifiable())
1252 isUserPreset = true;
1253 setDescr.setText(pset.getDescription());
1254 updateTable(null, pset.getArguments());
1255 lastParmSet = nextPreset;
1259 isUserPreset = false;
1260 setDescr.setText("");
1261 // must be a default preset from service
1262 updateTable(pset, null);
1263 lastParmSet = nextPreset;
1268 isUserPreset = false;
1270 setDescr.setText("");
1271 updateTable(null, null);
1272 lastParmSet = SVC_DEF;
1275 initArgSetModified();
1276 syncSetNamesWithStore();
1277 setName.setSelectedItem(lastParmSet);
1278 SetNamePanel.validate();
1280 settingDialog = false;
1284 String curSetName = null;
1286 public void itemStateChanged(ItemEvent e)
1288 if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
1290 final String setname = (String) setName.getSelectedItem();
1291 System.out.println("Item state changed for " + setname
1292 + " (handling ? " + !settingDialog + ")");
1298 if (setname == null)
1302 javax.swing.SwingUtilities.invokeLater(new Runnable()
1306 doPreferenceComboStateChange(setname);
1312 private void doPreferenceComboStateChange(String setname)
1314 // user has selected a different item from combo-box
1317 String lsetname = (curSetName != null) ? curSetName : lastParmSet;
1318 if (lsetname.equals(setname))
1320 // setname was just edited - so ignore this event.
1323 settingDialog = true;
1324 System.out.println("Prompting to save " + lsetname);
1325 if (javax.swing.JOptionPane
1330 + "' is modifed, and your changes will be lost.\nReally change preset ?",
1331 "Warning: Unsaved Changes",
1332 javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
1334 // revert the combobox to the current item
1335 settingDialog = true;
1336 setName.setSelectedItem(lsetname);
1337 settingDialog = false;
1340 // System.out.println("Saving for " + lsetname);
1341 // _storeCurrentPreset(lsetname);
1345 settingDialog = true;
1346 reInitDialog(setname);
1347 settingDialog = false;
1351 private void _renameExistingPreset(String oldName, String curSetName2)
1353 paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
1358 * store current settings as given name. You should then reset gui.
1360 * @param curSetName2
1362 private void _storeCurrentPreset(String curSetName2)
1364 paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
1367 private void _updatePreset(String lastParmSet2, String curname)
1369 paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(),
1375 * last saved name for this user preset
1377 String lastSetName = null;
1380 * last saved value of the description text for this user preset
1382 String lastDescrText = null;
1384 public void actionPerformed(ActionEvent e)
1386 if (e.getSource() instanceof Component)
1388 Component src = (Component) e.getSource();
1389 if (src.getParent() == setName)
1391 // rename any existing records we know about for this set.
1392 String newname = (String) e.getActionCommand().trim();
1394 if (isServicePreset(newname))
1396 final String oldname = curSetName != null ? curSetName
1398 final Component ourframe = this;
1399 settingDialog = true;
1400 setName.getEditor().setItem(oldname);
1401 settingDialog = false;
1402 javax.swing.SwingUtilities.invokeLater(new Runnable()
1406 JOptionPane.showMessageDialog(ourframe,
1407 "Invalid name - preset already exists.",
1408 "Invalid name", JOptionPane.WARNING_MESSAGE);
1414 curSetName = newname;
1415 System.err.println("New name for user setting " + curSetName
1416 + " (was " + setName.getSelectedItem() + ")");
1417 if (curSetName.equals(setName.getSelectedItem()))
1421 if (curSetName != null)
1423 argSetModified(setName, true);
1431 private void checkDescrModified()
1438 (lastDescrText == null ? setDescr.getText().trim().length() > 0
1439 : !setDescr.getText().equals(lastDescrText)));
1444 public void insertUpdate(DocumentEvent e)
1446 checkDescrModified();
1449 public void removeUpdate(DocumentEvent e)
1451 checkDescrModified();
1454 public void changedUpdate(DocumentEvent e)
1456 checkDescrModified();
1461 * @return null or the service preset selected by the user
1463 public WsParamSetI getPreset()
1465 if (isUserPreset || isModified()
1466 || (lastParmSet != null && lastParmSet.equals(SVC_DEF)))
1472 return paramStore.getPreset(lastParmSet);