2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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;
53 import java.util.Hashtable;
54 import java.util.Iterator;
55 import java.util.List;
56 import java.util.Vector;
58 import javax.swing.JButton;
59 import javax.swing.JComboBox;
60 import javax.swing.JDialog;
61 import javax.swing.JFrame;
62 import javax.swing.JLabel;
63 import javax.swing.JPanel;
64 import javax.swing.JScrollPane;
65 import javax.swing.JTextArea;
66 import javax.swing.border.TitledBorder;
67 import javax.swing.event.DocumentEvent;
68 import javax.swing.event.DocumentListener;
70 import compbio.metadata.Argument;
71 import compbio.metadata.Option;
72 import compbio.metadata.Parameter;
73 import compbio.metadata.Preset;
74 import compbio.metadata.PresetManager;
75 import net.miginfocom.swing.MigLayout;
78 * job parameter editing/browsing dialog box. User can browse existing settings
79 * (user + presets + Defaults), and any changes to parameters creates a modified
80 * user parameter set. LOGIC: If the parameter set is modified, and its name is
81 * a valid, non-existant user parameter set, then a save button is shown. If the
82 * parameter set is modified and its name is a valid, extant user parameter set,
83 * then an update button is shown. If user parameter set's name is edited, and
84 * old name exists as a writable user parameter set, then rename button is
85 * shown. If current parameter set is associated with a user defined parameter
86 * set, then : if set is modifed, a 'revert' button is shown. if set is not
87 * modified, a 'delete' button is shown.
92 public class WsJobParameters extends JPanel implements ItemListener,
93 ActionListener, DocumentListener, OptsParametersContainerI
95 private static final int PREFERRED_WIDTH = 540;
97 private static final int DEFAULT_HEIGHT = 640;
99 // the default parameter set shown to the user
100 private static final String SVC_DEF = "Defaults";
102 private int maxOptWidth = 200;
104 // URL linkImageURL = getClass().getResource("/images/link.gif");
107 * controller for options and parameters layout
109 OptsAndParamsPage opanp;
112 * panel containing job options
114 JPanel optionsPanel = new JPanel();
117 * panel containing job parameters
119 JPanel paramsPanel = new JPanel();
121 JPanel setNamePanel = new JPanel();
123 JButton createpref = new JButton();
125 JButton deletepref = new JButton();
127 JButton revertpref = new JButton();
129 JButton updatepref = new JButton();
131 JComboBox<String> setName = new JComboBox<>();
133 JTextArea setDescr = new JTextArea();
135 JScrollPane paramPane = new JScrollPane();
137 ParamDatastoreI paramStore;
139 // set true when 'Start Job' is clicked
140 boolean startJob = false;
142 JDialog frame = null;
144 Jws2Instance service;
147 * list of service presets in the gui
149 Hashtable<String, String> servicePresets = null;
152 * set if dialog is being set - so handlers will avoid spurious events
154 boolean settingDialog = false;
156 private Hashtable<Object, Object> modifiedElements = new Hashtable<>();
158 String lastParmSet = null;
160 public WsJobParameters(ParamDatastoreI store, WsParamSetI preset,
161 List<ArgumentI> args)
165 // parameters dialog in 'compact' format (help as tooltips)
166 opanp = new OptsAndParamsPage(this, true);
168 this.paramStore = store;
175 * Constructor given a set of parameters and presets, a service to be invoked,
176 * and a list of (Jabaws client) arguments
183 public WsJobParameters(ParamDatastoreI paramStorei, Jws2Instance service,
184 WsParamSetI preset, List<Argument> jobArgset)
188 // parameters dialog in 'expanded' format (help text boxes)
189 opanp = new OptsAndParamsPage(this, false);
192 this.paramStore = paramStorei;
193 if (paramStore == null && service != null)
195 paramStore = service.getParamStore();
197 this.service = service;
198 initForService(preset, jobArgset);
203 * Shows a modal dialog containing the parameters and Start or Cancel options.
204 * Answers true if the job is started, false if cancelled.
208 public boolean showRunDialog()
211 frame = new JDialog(Desktop.instance, true);
214 frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
216 { service.getActionText() }));
219 Rectangle deskr = Desktop.instance.getBounds();
220 Dimension pref = this.getPreferredSize();
222 new Rectangle((int) (deskr.getCenterX() - pref.width / 2),
223 (int) (deskr.getCenterY() - pref.height / 2),
224 pref.width, pref.height));
225 frame.setContentPane(this);
227 // should perhaps recover defaults from user prefs.
230 javax.swing.SwingUtilities.invokeLater(new Runnable()
235 // jobPanel.setDividerLocation(0.25);
239 frame.setVisible(true);
244 private void jbInit()
246 this.addHierarchyBoundsListener(new HierarchyBoundsListener()
250 public void ancestorResized(HierarchyEvent arg0)
252 refreshParamLayout();
256 public void ancestorMoved(HierarchyEvent arg0)
258 // TODO Auto-generated method stub
262 updatepref = JvSwingUtils.makeButton(
263 MessageManager.getString("action.update"),
264 MessageManager.getString("label.update_user_parameter_set"),
269 public void actionPerformed(ActionEvent e)
271 update_actionPerformed();
274 deletepref = JvSwingUtils.makeButton(
275 MessageManager.getString("action.delete"),
276 MessageManager.getString("label.delete_user_parameter_set"),
281 public void actionPerformed(ActionEvent e)
283 delete_actionPerformed();
286 createpref = JvSwingUtils.makeButton(
287 MessageManager.getString("action.create"),
288 MessageManager.getString("label.create_user_parameter_set"),
293 public void actionPerformed(ActionEvent e)
295 create_actionPerformed();
298 revertpref = JvSwingUtils.makeButton(
299 MessageManager.getString("action.revert"),
301 .getString("label.revert_changes_user_parameter_set"),
306 public void actionPerformed(ActionEvent e)
308 revert_actionPerformed();
312 JButton startjob = JvSwingUtils.makeButton(
313 MessageManager.getString("action.start_job"),
314 MessageManager.getString("label.start_job_current_settings"),
318 public void actionPerformed(ActionEvent e)
320 startjob_actionPerformed();
323 JButton canceljob = JvSwingUtils.makeButton(
324 MessageManager.getString("action.cancel_job"),
325 MessageManager.getString("label.cancel_job_close_dialog"),
329 public void actionPerformed(ActionEvent e)
331 canceljob_actionPerformed();
335 JPanel setDetails = new JPanel();
336 setDetails.setBorder(
337 new TitledBorder(MessageManager.getString("label.details")));
338 setDetails.setLayout(new BorderLayout());
339 setDescr.setColumns(40);
340 setDescr.setWrapStyleWord(true);
341 setDescr.setLineWrap(true);
342 setDescr.setBackground(getBackground());
343 setDescr.setEditable(true);
344 setDescr.getDocument().addDocumentListener(this);
345 setDescr.setToolTipText(
346 MessageManager.getString("label.edit_notes_parameter_set"));
347 JScrollPane setDescrView = new JScrollPane();
348 setDescrView.getViewport().setView(setDescr);
349 setName.setEditable(true);
350 setName.addItemListener(this);
351 setName.getEditor().addActionListener(this);
352 JPanel setNameInfo = new JPanel(new FlowLayout(FlowLayout.LEFT));
353 GridBagLayout gbl = new GridBagLayout();
354 setNamePanel.setLayout(gbl);
356 JLabel setNameLabel = new JLabel(
357 MessageManager.getString("label.current_parameter_set_name"));
358 setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
360 setNameInfo.add(setNameLabel);
361 setNameInfo.add(setName);
363 // initial button visibility
364 updatepref.setVisible(false);
365 deletepref.setVisible(false);
366 revertpref.setVisible(false);
367 createpref.setVisible(false);
368 JPanel setsavebuts = new JPanel();
369 setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT, 10, 0)); // GridLayout(1,2));
370 JPanel spacer = new JPanel();
371 spacer.setPreferredSize(new Dimension(2, 30));
372 setsavebuts.add(spacer);
373 setsavebuts.add(deletepref);
374 setsavebuts.add(revertpref);
375 setsavebuts.add(createpref);
376 setsavebuts.add(updatepref);
377 // setsavebuts.setSize(new Dimension(150, 30));
378 JPanel buttonArea = new JPanel(new GridLayout(1, 1));
379 buttonArea.add(setsavebuts);
380 setNamePanel.add(setNameInfo);
381 GridBagConstraints gbc = new GridBagConstraints();
383 gbl.setConstraints(setNameInfo, gbc);
384 setNamePanel.add(buttonArea);
385 gbc = new GridBagConstraints();
389 gbl.setConstraints(buttonArea, gbc);
390 setDetails.add(setDescrView, BorderLayout.CENTER);
392 // paramPane.setPreferredSize(new Dimension(360, 400));
393 // paramPane.setPreferredSize(null);
394 optionsPanel.setBorder(
395 new TitledBorder(MessageManager.getString("label.options")));
396 optionsPanel.setOpaque(true);
397 paramsPanel.setBorder(
398 new TitledBorder(MessageManager.getString("label.parameters")));
399 paramsPanel.setOpaque(true);
400 // optsAndparams.setScrollableWidth(ScrollableSizeHint.FIT);
401 // optsAndparams.setScrollableHeight(ScrollableSizeHint.NONE);
402 // optsAndparams.setLayout(new BorderLayout());
403 JPanel optsAndparams = new JPanel();
404 optsAndparams.setLayout(new BorderLayout());
405 optsAndparams.add(optionsPanel, BorderLayout.NORTH);
406 optsAndparams.add(paramsPanel, BorderLayout.CENTER);
407 JPanel jp = new JPanel(new BorderLayout());
408 jp.add(optsAndparams, BorderLayout.CENTER);
409 paramPane.getViewport().setView(jp);
410 paramPane.setBorder(null);
411 setLayout(new BorderLayout());
413 JPanel jobPanel = new JPanel();
414 jobPanel.setPreferredSize(null);
415 jobPanel.setLayout(new BorderLayout());
416 jobPanel.add(setDetails, BorderLayout.NORTH);
417 jobPanel.add(paramPane, BorderLayout.CENTER);
418 // jobPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
420 add(setNamePanel, BorderLayout.NORTH);
421 add(jobPanel, BorderLayout.CENTER);
423 JPanel dialogpanel = new JPanel();
424 dialogpanel.add(startjob);
425 dialogpanel.add(canceljob);
426 // JAL-1580: setMaximumSize() doesn't work, so just size for the worst case:
427 // check for null is for JUnit usage
428 final int windowHeight = Desktop.instance == null ? DEFAULT_HEIGHT
429 : Desktop.instance.getHeight();
430 // setPreferredSize(new Dimension(PREFERRED_WIDTH, windowHeight));
431 add(dialogpanel, BorderLayout.SOUTH);
435 protected void revert_actionPerformed()
437 reInitDialog(lastParmSet);
438 updateWebServiceMenus();
441 protected void update_actionPerformed()
445 String curname = ((String) setName.getSelectedItem()).trim();
446 _updatePreset(lastParmSet, curname);
447 lastParmSet = curname;
449 initArgSetModified();
450 syncSetNamesWithStore();
454 private void _deleteUserPreset(String lastParmSet2)
456 paramStore.deletePreset(lastParmSet2);
459 protected void delete_actionPerformed()
463 // delete current preset's saved entry
464 _deleteUserPreset(lastParmSet);
466 reInitDialog(null); // service default
467 updateWebServiceMenus();
470 protected void create_actionPerformed()
472 String curname = ((String) setName.getSelectedItem()).trim();
473 if (curname.length() > 0)
475 _storeCurrentPreset(curname);
476 lastParmSet = curname;
478 reInitDialog(curname);
479 initArgSetModified();
480 updateWebServiceMenus();
484 // TODO: show warning
485 System.err.println("Invalid name. Not saved.");
489 protected void canceljob_actionPerformed()
494 frame.setVisible(false);
498 protected void startjob_actionPerformed()
503 frame.setVisible(false);
507 void initForService(WsParamSetI jabap, List<Argument> jabajobArgset)
509 WsParamSetI p = null;
510 List<ArgumentI> jobArgset = null;
511 settingDialog = true;
512 { // instantiate the abstract proxy for Jaba objects
513 jobArgset = jabajobArgset == null ? null
514 : JabaParamStore.getJwsArgsfromJaba(jabajobArgset);
515 p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
523 void init(WsParamSetI p, List<ArgumentI> jobArgset)
525 Hashtable<String, String> exnames = new Hashtable<>();
526 for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
528 exnames.put(setName.getItemAt(i), setName.getItemAt(i));
530 servicePresets = new Hashtable<>();
531 // Add the default entry - if not present already.
532 if (!exnames.contains(SVC_DEF))
534 setName.addItem(SVC_DEF);
535 exnames.put(SVC_DEF, SVC_DEF);
536 servicePresets.put(SVC_DEF, SVC_DEF);
539 // String curname = (p == null ? "" : p.getName());
540 for (WsParamSetI pr : paramStore.getPresets())
542 if (!pr.isModifiable())
544 servicePresets.put(pr.getName(), "preset");
549 if (!exnames.contains(pr.getName()))
551 setName.addItem(pr.getName());
554 // TODO: if initial jobArgset matches a given user setting or preset then
555 // should recover setting accordingly
556 // updateTable(p, jobArgset);
559 reInitDialog(p.getName());
560 initArgSetModified();
564 if (jobArgset != null && jobArgset.size() > 0)
566 curSetName = "Supplied Settings";
567 isUserPreset = false;
568 updateTable(p, jobArgset);
569 setName.setSelectedItem(curSetName);
570 updateButtonDisplay();
578 settingDialog = false;
581 private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
583 boolean setDefaultParams = false;
584 if (lastParmSet == null)
586 isUserPreset = false;
587 // First call - so provide Service default settings
588 setName.setSelectedItem(lastSetName = SVC_DEF);
590 if (p == null && SVC_DEF.equals("" + setName.getSelectedItem()))
592 // indicate that service defaults should be set if available
593 setDefaultParams = true;
595 // populate table from default parameter set.
596 List<ArgumentI> args = paramStore.getServiceParameters();
598 // split to params and required arguments
601 boolean optset = false;
602 for (ArgumentI myarg : args)
604 // Ideally, Argument would implement isRequired !
605 if (myarg instanceof ParameterI)
607 ParameterI parm = (ParameterI) myarg;
608 opanp.addParameter(parm).validate();
612 if (myarg instanceof OptionI)
614 OptionI opt = (OptionI) myarg;
615 OptionBox ob = opanp.addOption(opt);
616 ob.resetToDefault(setDefaultParams);
617 if (maxOptWidth < ob.getPreferredSize().width)
619 maxOptWidth = ob.getPreferredSize().width;
622 cw += ob.getPreferredSize().width + 5;
626 System.err.println("Ignoring unknown service argument type "
627 + myarg.getClass().getName());
631 args = null; // no more args to process.
635 isUserPreset = false;
636 // initialise setname
637 setName.setSelectedItem(lastSetName = p.getName());
638 setDescr.setText(lastDescrText = p.getDescription());
642 args = p.getArguments();
643 } catch (Exception e)
647 // TODO: check if args should be unselected prior to resetting using the
651 if (jobArgset != null)
653 argSetModified(jobArgset, true);
656 // get setargs from current object
659 for (ArgumentI arg : args)
661 if (arg instanceof ParameterI)
663 opanp.setParameter((ParameterI) arg);
667 if (arg instanceof OptionI)
669 // System.out.println("Setting option "
670 // + System.identityHashCode(arg) + ":" + arg.getName()
671 // + " with " + arg.getDefaultValue());
672 opanp.selectOption((OptionI) arg, arg.getValue());
679 refreshParamLayout();
683 private boolean isModified()
685 return modifiedElements.size() > 0;
689 * reset gui and modification state settings
691 private void initArgSetModified()
694 modifiedElements.clear();
695 updateButtonDisplay();
698 private void updateButtonDisplay()
700 boolean _update = false, _create = false, _delete = false,
702 if (modifiedElements.size() > 0)
706 _update = isUserPreset; // can only update user presets
707 if (!isUserPreset || modifiedElements.containsKey(setName))
709 // name modified - can create new preset
717 // can still delete a user preset
718 _delete = isUserPreset;
720 createpref.setVisible(_create);
721 updatepref.setVisible(_update);
722 deletepref.setVisible(_delete);
723 revertpref.setVisible(_revert);
728 public void argSetModified(Object modifiedElement, boolean b)
736 modifiedElements.remove(modifiedElement);
740 if (b && modifiedElement == setName
741 && modifiedElements.contains(modifiedElement))
743 // HACK! prevents iteration on makeSetNameValid
746 modifiedElements.put(modifiedElement, modifiedElement);
748 // set mod status based on presence of elements in table
749 if (b && modifiedElements.size() > 0)
751 makeSetNameValid(!isUserPreset);
752 setNamePanel.revalidate();
754 updateButtonDisplay();
757 private boolean isServicePreset(String selectedItem)
759 return selectedItem.equals(SVC_DEF)
760 || servicePresets.containsKey(selectedItem);
764 * check if the current set name is a valid set name for saving, if not, then
767 private void makeSetNameValid(boolean newuserset)
769 boolean stn = settingDialog;
770 boolean renamed = false;
771 settingDialog = true;
772 String nm = (curSetName != null ? curSetName
773 : (String) setName.getSelectedItem());
774 // check if the name is reserved - if it is, rename it.
775 if (isServicePreset(nm))
784 while (paramStore.getPreset(tnm) != null)
786 tnm = nm + " (" + (++i) + ")";
795 boolean makeupdate = false;
796 // sync the gui with the preset database
797 for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
799 String snm = setName.getItemAt(i);
803 // setName.setSelectedIndex(i);
808 setName.addItem(curSetName = nm);
809 setName.setSelectedItem(curSetName);
813 settingDialog = false; // we need this name change to be registered.
814 argSetModified(setName, renamed);
820 * Rebuilds the Options and Parameters panels
823 public void refreshParamLayout()
825 final int rightMargin = 40;
826 final int availableWidth = paramPane.getViewport().getSize().width
828 - optionsPanel.getBorder().getBorderInsets(optionsPanel).left
829 + optionsPanel.getBorder().getBorderInsets(optionsPanel).right;
831 if (opanp.getOptSet().size() > 0)
834 int currentWidth = hgap;
837 * layout constraint 'nogrid' prevents vertical column alignment,
838 * allowing controls to flow without extra space inserted to align
840 optionsPanel.setLayout(new MigLayout("nogrid", "", ""));
841 optionsPanel.removeAll();
842 JPanel lastAdded = null;
845 * add each control in turn; if adding would overflow the right margin,
846 * remove and re-add the previous parameter with "wrap" (after)
847 * in order to start a new row
849 for (OptionBox pbox : opanp.getOptSet().values())
852 int boxWidth = pbox.getSize().width;
853 currentWidth += boxWidth + hgap;
854 boolean wrapAfterLast = currentWidth > availableWidth
855 && lastAdded != null;
856 // System.out.println(String.format(
857 // "%s width=%d, paneWidth=%d, currentWidth=%d, wrapAfterLast=%s",
858 // pbox.toString(), boxWidth, panewidth, currentWidth,
862 optionsPanel.remove(lastAdded);
863 optionsPanel.add(lastAdded, "wrap");
864 currentWidth = hgap + boxWidth;
866 optionsPanel.add(pbox);
869 optionsPanel.revalidate();
873 optionsPanel.setVisible(false);
876 if (opanp.getParamSet().size() > 0)
878 paramsPanel.removeAll();
879 paramsPanel.setLayout(new MigLayout("", "", ""));
881 int currentWidth = hgap;
883 JPanel lastAdded = null;
884 for (ParamBox pbox : opanp.getParamSet().values())
887 int boxWidth = pbox.getSize().width;
888 currentWidth += boxWidth + hgap;
889 boolean wrapAfterLast = currentWidth > availableWidth
890 && lastAdded != null;
893 paramsPanel.remove(lastAdded);
894 paramsPanel.add(lastAdded, "wrap");
895 currentWidth = pbox.getSize().width + hgap;
897 paramsPanel.add(pbox);
902 * s = 2 * sep; for (ParamBox pbox : opanp.getParamSet().values()) {
903 * pbox.validate(); s += sep +
904 * pbox.getPreferredSize().height+pbox.getBorder
905 * ().getBorderInsets(pbox).bottom; }
907 * // paramList.setPreferredSize(new Dimension(w, s));
908 * os+=s+2*sep+paramList
909 * .getBorder().getBorderInsets(paramList).bottom+paramList
910 * .getBorder().getBorderInsets(paramList).top;
912 paramsPanel.revalidate();
916 paramsPanel.setVisible(false);
918 // TODO: waste some time trying to eliminate any unnecessary .validate calls
920 // System.out.println("Size will be : "+w+","+os);
921 // optsAndparams.setPreferredSize(null);
922 // paramPane.getViewport().setView(optsAndparams);
923 paramPane.getViewport().setAutoscrolls(true);
924 paramPane.revalidate();
929 * testing method - grab a service and parameter set and show the window
933 public static void main(String[] args)
935 jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
940 Vector<String> services = new Vector<>();
941 services.addElement(args[p++]);
942 Jws2Discoverer.getDiscoverer().setServiceUrls(services);
947 } catch (Exception e)
949 System.err.println("Aborting. Problem discovering services.");
953 Jws2Instance lastserv = null;
954 for (Jws2Instance service : disc.getServices())
957 if (p >= args.length || service.getName().equalsIgnoreCase(args[p]))
959 if (lastserv != null)
961 List<Preset> prl = null;
963 if (++p < args.length)
965 PresetManager prman = lastserv.getPresets();
968 pr = prman.getPresetByName(args[p]);
971 // just grab the last preset.
972 prl = prman.getPresets();
978 PresetManager prman = lastserv.getPresets();
981 prl = prman.getPresets();
984 Iterator<Preset> en = (prl == null) ? null : prl.iterator();
985 while (en != null && en.hasNext())
996 System.out.println("Testing opts dupes for "
997 + lastserv.getUri() + " : " + lastserv.getActionText()
998 + ":" + pr.getName());
999 List<Option> rg = lastserv.getRunnerConfig().getOptions();
1004 Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
1005 } catch (Exception e)
1007 System.err.println("Failed to copy " + o.getName());
1008 e.printStackTrace();
1011 System.err.println("Failed to copy " + o.getName());
1012 e.printStackTrace();
1017 System.out.println("Testing param dupes:");
1018 List<Parameter> rg = lastserv.getRunnerConfig()
1020 for (Parameter o : rg)
1024 Parameter cpy = jalview.ws.jws2.ParameterUtils
1026 } catch (Exception e)
1028 System.err.println("Failed to copy " + o.getName());
1029 e.printStackTrace();
1032 System.err.println("Failed to copy " + o.getName());
1033 e.printStackTrace();
1038 System.out.println("Testing param write:");
1039 List<String> writeparam = null, readparam = null;
1042 writeparam = jalview.ws.jws2.ParameterUtils
1044 pr.getArguments(lastserv.getRunnerConfig()),
1046 System.out.println("Testing param read :");
1047 List<Option> pset = jalview.ws.jws2.ParameterUtils
1048 .processParameters(writeparam,
1049 lastserv.getRunnerConfig(), " ");
1050 readparam = jalview.ws.jws2.ParameterUtils
1051 .writeParameterSet(pset, " ");
1052 Iterator<String> o = pr.getOptions().iterator(),
1053 s = writeparam.iterator(), t = readparam.iterator();
1054 boolean failed = false;
1055 while (s.hasNext() && t.hasNext())
1057 String on = o.next(), sn = s.next(), st = t.next();
1061 "Original was " + on + " Phase 1 wrote " + sn
1062 + "\tPhase 2 wrote " + st);
1069 "Original parameters:\n" + pr.getOptions());
1071 "Wrote parameters in first set:\n" + writeparam);
1073 "Wrote parameters in second set:\n" + readparam);
1076 } catch (Exception e)
1078 e.printStackTrace();
1081 WsJobParameters pgui = new WsJobParameters(null, lastserv,
1082 new JabaPreset(lastserv, pr), null);
1083 JFrame jf = new JFrame(MessageManager
1084 .formatMessage("label.ws_parameters_for", new String[]
1085 { lastserv.getActionText() }));
1086 JPanel cont = new JPanel(new BorderLayout());
1088 cont.setPreferredSize(pgui.getPreferredSize());
1089 cont.add(pgui, BorderLayout.CENTER);
1090 jf.setLayout(new BorderLayout());
1091 jf.add(cont, BorderLayout.CENTER);
1093 final Thread thr = Thread.currentThread();
1094 jf.addWindowListener(new WindowListener()
1098 public void windowActivated(WindowEvent e)
1100 // TODO Auto-generated method stub
1105 public void windowClosed(WindowEvent e)
1110 public void windowClosing(WindowEvent e)
1117 public void windowDeactivated(WindowEvent e)
1119 // TODO Auto-generated method stub
1124 public void windowDeiconified(WindowEvent e)
1126 // TODO Auto-generated method stub
1131 public void windowIconified(WindowEvent e)
1133 // TODO Auto-generated method stub
1138 public void windowOpened(WindowEvent e)
1140 // TODO Auto-generated method stub
1145 jf.setVisible(true);
1146 boolean inter = false;
1151 Thread.sleep(10000);
1152 } catch (Exception e)
1165 public boolean isServiceDefaults()
1167 return (!isModified()
1168 && (lastParmSet != null && lastParmSet.equals(SVC_DEF)));
1171 public List<ArgumentI> getJobParams()
1173 return opanp.getCurrentSettings();
1177 * Hashtable<String, Object[]> editedParams = new Hashtable<String,
1180 * store the given parameters in the user parameter set database.
1182 * @param storeSetName - lastParmSet
1184 * @param descr - setDescr.getText()
1186 * @param jobParams - getJobParams()
1188 * private void _storeUserPreset(String storeSetName, String descr,
1189 * List<ArgumentI> jobParams) { // this is a simple hash store. Object[] pset;
1190 * editedParams.put(storeSetName, pset = new Object[3]); pset[0] =
1191 * storeSetName; pset[1] = descr; pset[2] = jobParams; // writeParam("Saving "
1192 * + storeSetName + ": ", jobParams); }
1194 * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
1195 * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
1196 * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
1198 * private Object[] _getUserPreset(String setName) { Object[] pset =
1199 * editedParams.get(setName); // if (pset != null) // writeParam("Retrieving "
1200 * + setName + ": ", (List<Argument>) pset[2]); return pset; }
1202 * * remove the given user preset from the preset stash
1206 * private void _deleteUserPreset(String setName) {
1207 * editedParams.remove(setName); }
1210 private void syncSetNamesWithStore()
1213 // remove any set names in the drop down menu that aren't either a reserved
1214 // setting, or a user defined or service preset.
1215 Vector<String> items = new Vector<>();
1216 while (n < setName.getItemCount())
1218 String item = setName.getItemAt(n);
1219 if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
1221 setName.removeItemAt(n);
1225 items.addElement(item);
1229 if (!items.contains(SVC_DEF))
1231 setName.addItem(SVC_DEF);
1233 for (WsParamSetI upn : paramStore.getPresets())
1235 if (!items.contains(upn.getName()))
1237 setName.addItem(upn.getName());
1243 * true if lastParmSet is a user preset
1245 boolean isUserPreset = false;
1247 private void reInitDialog(String nextPreset)
1249 settingDialog = true;
1250 // updateTable(null,null); // first reset to defaults
1251 WsParamSetI pset = null;
1252 if (nextPreset != null && nextPreset.length() > 0)
1254 pset = paramStore.getPreset(nextPreset);
1258 if (pset.isModifiable())
1260 isUserPreset = true;
1261 setDescr.setText(pset.getDescription());
1262 updateTable(null, pset.getArguments());
1263 lastParmSet = nextPreset;
1267 isUserPreset = false;
1268 setDescr.setText("");
1269 // must be a default preset from service
1270 updateTable(pset, null);
1271 lastParmSet = nextPreset;
1276 isUserPreset = false;
1278 setDescr.setText("");
1279 updateTable(null, null);
1280 lastParmSet = SVC_DEF;
1283 initArgSetModified();
1284 syncSetNamesWithStore();
1285 setName.setSelectedItem(lastParmSet);
1286 setNamePanel.validate();
1288 settingDialog = false;
1292 * Rebuild the AlignFrame web service menus (after add/delete of a preset
1295 protected void updateWebServiceMenus()
1297 for (AlignFrame alignFrame : Desktop.getAlignFrames())
1299 alignFrame.BuildWebServiceMenu();
1303 String curSetName = null;
1306 public void itemStateChanged(ItemEvent e)
1308 if (e.getSource() == setName
1309 && e.getStateChange() == ItemEvent.SELECTED)
1311 final String setname = (String) setName.getSelectedItem();
1312 // System.out.println("Item state changed for " + setname
1313 // + " (handling ? " + !settingDialog + ")");
1319 if (setname == null)
1323 javax.swing.SwingUtilities.invokeLater(new Runnable()
1328 doPreferenceComboStateChange(setname);
1334 private void doPreferenceComboStateChange(String setname)
1336 // user has selected a different item from combo-box
1339 String lsetname = (curSetName != null) ? curSetName : lastParmSet;
1340 if (lsetname.equals(setname))
1342 // setname was just edited - so ignore this event.
1345 settingDialog = true;
1346 System.out.println("Prompting to save " + lsetname);
1347 if (JvOptionPane.showConfirmDialog(this, "Parameter set '" + lsetname
1348 + "' is modifed, and your changes will be lost.\nReally change preset ?",
1349 "Warning: Unsaved Changes",
1350 JvOptionPane.OK_CANCEL_OPTION) != JvOptionPane.OK_OPTION)
1352 // revert the combobox to the current item
1353 settingDialog = true;
1354 setName.setSelectedItem(lsetname);
1355 settingDialog = false;
1358 // System.out.println("Saving for " + lsetname);
1359 // _storeCurrentPreset(lsetname);
1363 settingDialog = true;
1364 reInitDialog(setname);
1365 settingDialog = false;
1369 private void _renameExistingPreset(String oldName, String curSetName2)
1371 paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
1376 * store current settings as given name. You should then reset gui.
1378 * @param curSetName2
1380 private void _storeCurrentPreset(String curSetName2)
1382 paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
1385 private void _updatePreset(String lastParmSet2, String curname)
1387 paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(),
1393 * last saved name for this user preset
1395 String lastSetName = null;
1398 * last saved value of the description text for this user preset
1400 String lastDescrText = null;
1403 public void actionPerformed(ActionEvent e)
1405 if (e.getSource() instanceof Component)
1407 Component src = (Component) e.getSource();
1408 if (src.getParent() == setName)
1410 // rename any existing records we know about for this set.
1411 String newname = e.getActionCommand().trim();
1413 if (isServicePreset(newname))
1415 final String oldname = curSetName != null ? curSetName
1417 final Component ourframe = this;
1418 settingDialog = true;
1419 setName.getEditor().setItem(oldname);
1420 settingDialog = false;
1421 javax.swing.SwingUtilities.invokeLater(new Runnable()
1426 JvOptionPane.showMessageDialog(ourframe,
1427 MessageManager.getString(
1428 "label.invalid_name_preset_exists"),
1429 MessageManager.getString("label.invalid_name"),
1430 JvOptionPane.WARNING_MESSAGE);
1436 curSetName = newname;
1437 System.err.println("New name for user setting " + curSetName
1438 + " (was " + setName.getSelectedItem() + ")");
1439 if (curSetName.equals(setName.getSelectedItem()))
1443 if (curSetName != null)
1445 argSetModified(setName, true);
1453 private void checkDescrModified()
1458 argSetModified(setDescr,
1459 (lastDescrText == null
1460 ? setDescr.getText().trim().length() > 0
1461 : !setDescr.getText().equals(lastDescrText)));
1467 public void insertUpdate(DocumentEvent e)
1469 checkDescrModified();
1473 public void removeUpdate(DocumentEvent e)
1475 checkDescrModified();
1479 public void changedUpdate(DocumentEvent e)
1481 checkDescrModified();
1486 * @return null or the service preset selected by the user
1488 public WsParamSetI getPreset()
1490 if (isUserPreset || isModified()
1491 || (lastParmSet != null && lastParmSet.equals(SVC_DEF)))
1497 return paramStore.getPreset(lastParmSet);