2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import jalview.gui.OptsAndParamsPage.OptionBox;
22 import jalview.gui.OptsAndParamsPage.ParamBox;
23 import jalview.util.MessageManager;
24 import jalview.ws.jws2.JabaParamStore;
25 import jalview.ws.jws2.JabaPreset;
26 import jalview.ws.jws2.Jws2Discoverer;
27 import jalview.ws.jws2.jabaws2.Jws2Instance;
28 import jalview.ws.params.ArgumentI;
29 import jalview.ws.params.OptionI;
30 import jalview.ws.params.ParamDatastoreI;
31 import jalview.ws.params.ParameterI;
32 import jalview.ws.params.WsParamSetI;
34 import java.awt.BorderLayout;
35 import java.awt.Component;
36 import java.awt.Dimension;
37 import java.awt.FlowLayout;
39 import java.awt.GridBagConstraints;
40 import java.awt.GridBagLayout;
41 import java.awt.GridLayout;
42 import java.awt.Rectangle;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.HierarchyBoundsListener;
46 import java.awt.event.HierarchyEvent;
47 import java.awt.event.ItemEvent;
48 import java.awt.event.ItemListener;
49 import java.awt.event.WindowEvent;
50 import java.awt.event.WindowListener;
52 import java.util.Hashtable;
53 import java.util.Iterator;
54 import java.util.List;
55 import java.util.Vector;
57 import javax.swing.JButton;
58 import javax.swing.JComboBox;
59 import javax.swing.JDialog;
60 import javax.swing.JFrame;
61 import javax.swing.JLabel;
62 import javax.swing.JOptionPane;
63 import javax.swing.JPanel;
64 import javax.swing.JScrollPane;
65 import javax.swing.JSplitPane;
66 import javax.swing.JTextArea;
67 import javax.swing.border.TitledBorder;
68 import javax.swing.event.DocumentEvent;
69 import javax.swing.event.DocumentListener;
71 import net.miginfocom.swing.MigLayout;
73 import compbio.metadata.Argument;
74 import compbio.metadata.Option;
75 import compbio.metadata.Parameter;
76 import compbio.metadata.Preset;
77 import compbio.metadata.PresetManager;
78 import compbio.metadata.RunnerConfig;
81 * job parameter editing/browsing dialog box. User can browse existing settings
82 * (user + presets + Defaults), and any changes to parameters creates a modified
83 * user parameter set. LOGIC: If the parameter set is modified, and its name is
84 * a valid, non-existant user parameter set, then a save button is shown. If the
85 * parameter set is modified and its name is a valid, extant user parameter set,
86 * then an update button is shown. If user parameter set's name is edited, and
87 * old name exists as a writable user parameter set, then rename button is
88 * shown. If current parameter set is associated with a user defined parameter
89 * set, then : if set is modifed, a 'revert' button is shown. if set is not
90 * modified, a 'delete' button is shown.
95 public class WsJobParameters extends JPanel implements ItemListener,
96 ActionListener, DocumentListener, OptsParametersContainerI
98 URL linkImageURL = getClass().getResource("/images/link.gif");
100 private static final String SVC_DEF = "Defaults"; // this is the null
101 // parameter set as shown to
105 * manager for options and parameters.
107 OptsAndParamsPage opanp = new OptsAndParamsPage(this);
110 * panel containing job options
112 JPanel jobOptions = new JPanel();
115 * panel containing job parameters
117 JPanel paramList = new JPanel();
119 JPanel SetNamePanel = new JPanel();
121 JPanel setDetails = new JPanel();
123 JSplitPane settingsPanel = new JSplitPane();
125 JPanel jobPanel = new JPanel();
127 JScrollPane jobOptionsPane = new JScrollPane();
129 JButton createpref = new JButton();
131 JButton deletepref = new JButton();
133 JButton revertpref = new JButton();
135 JButton updatepref = new JButton();
137 JButton startjob = new JButton();
139 JButton canceljob = new JButton();
141 JComboBox setName = new JComboBox();
143 JTextArea setDescr = new JTextArea();
145 JScrollPane paramPane = new JScrollPane();
147 // ScrollablePanel optsAndparams = new ScrollablePanel();
148 JPanel optsAndparams = new JPanel();
150 RunnerConfig serviceOptions;
152 ParamDatastoreI paramStore;
154 private int MAX_OPTWIDTH = 200;
156 WsJobParameters(Jws2Instance service)
161 public WsJobParameters(Jws2Instance service, WsParamSetI preset)
163 this(null, service, preset, null);
169 * - if null, create new JFrame outside of desktop
173 public WsJobParameters(JFrame parent, Jws2Instance service,
174 WsParamSetI preset, List<Argument> jobArgset)
176 this(parent, null, service, preset, jobArgset);
187 public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
188 Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
192 this.paramStore = paramStorei;
193 if (paramStore == null)
195 paramStore = service.getParamStore();
197 this.service = service;
198 // argSetModified(false);
199 // populate parameter table
200 initForService(service, preset, jobArgset);
201 // display in new JFrame attached to parent.
207 JDialog frame = null;
210 * shows a modal dialog containing the parameters.
214 public boolean showRunDialog()
217 frame = new JDialog(Desktop.instance, true);
219 frame.setTitle("Edit parameters for " + service.getActionText());
220 Rectangle deskr = Desktop.instance.getBounds();
221 Dimension pref = this.getPreferredSize();
222 frame.setBounds(new Rectangle(
223 (int) (deskr.getCenterX() - pref.width / 2), (int) (deskr
224 .getCenterY() - pref.height / 2), pref.width,
226 frame.setContentPane(this);
228 // should perhaps recover defaults from user prefs.
231 javax.swing.SwingUtilities.invokeLater(new Runnable()
235 // jobPanel.setDividerLocation(0.25);
239 frame.setVisible(true);
248 private void jbInit()
250 this.addHierarchyBoundsListener(new HierarchyBoundsListener()
254 public void ancestorResized(HierarchyEvent arg0)
256 refreshParamLayout();
260 public void ancestorMoved(HierarchyEvent arg0)
262 // TODO Auto-generated method stub
266 updatepref = JvSwingUtils.makeButton(MessageManager.getString("action.update"),
267 MessageManager.getString("label.update_user_parameter_set"),
271 public void actionPerformed(ActionEvent e)
273 update_actionPerformed(e);
276 deletepref = JvSwingUtils.makeButton(MessageManager.getString("action.delete"),
277 MessageManager.getString("label.delete_user_parameter_set"),
281 public void actionPerformed(ActionEvent e)
283 delete_actionPerformed(e);
286 createpref = JvSwingUtils.makeButton(MessageManager.getString("action.create"),
287 MessageManager.getString("label.create_user_parameter_set"),
291 public void actionPerformed(ActionEvent e)
293 create_actionPerformed(e);
296 revertpref = JvSwingUtils.makeButton(MessageManager.getString("action.revert"),
297 MessageManager.getString("label.revert_changes_user_parameter_set"),
301 public void actionPerformed(ActionEvent e)
303 revert_actionPerformed(e);
306 startjob = JvSwingUtils.makeButton(MessageManager.getString("action.start_job"),
307 MessageManager.getString("label.start_job_current_settings"), new ActionListener()
309 public void actionPerformed(ActionEvent e)
311 startjob_actionPerformed(e);
314 canceljob = JvSwingUtils.makeButton(MessageManager.getString("action.cancel_job"),
315 MessageManager.getString("label.cancel_job_close_dialog"), new ActionListener()
317 public void actionPerformed(ActionEvent e)
319 canceljob_actionPerformed(e);
323 setDetails.setBorder(new TitledBorder(MessageManager.getString("label.details")));
324 setDetails.setLayout(new BorderLayout());
325 setDescr.setColumns(40);
326 setDescr.setWrapStyleWord(true);
327 setDescr.setLineWrap(true);
328 setDescr.setBackground(getBackground());
329 setDescr.setEditable(true);
330 setDescr.getDocument().addDocumentListener(this);
331 setDescr.setToolTipText(MessageManager.getString("label.edit_notes_parameter_set"));
332 JScrollPane setDescrView = new JScrollPane();
333 // setDescrView.setPreferredSize(new Dimension(350, 200));
334 setDescrView.getViewport().setView(setDescr);
335 setName.setEditable(true);
336 setName.addItemListener(this);
337 setName.getEditor().addActionListener(this);
338 JPanel setNameInfo = new JPanel(new FlowLayout(FlowLayout.LEFT));
339 GridBagLayout gbl = new GridBagLayout();
340 SetNamePanel.setLayout(gbl);
342 JLabel setNameLabel = new JLabel(MessageManager.getString("label.current_parameter_set_name"));
343 setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
345 setNameInfo.add(setNameLabel);
346 setNameInfo.add(setName);
348 // initial button visibility
349 updatepref.setVisible(false);
350 deletepref.setVisible(false);
351 revertpref.setVisible(false);
352 createpref.setVisible(false);
353 JPanel setsavebuts = new JPanel();
354 setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT)); // GridLayout(1,2));
355 ((FlowLayout) setsavebuts.getLayout()).setHgap(10);
356 ((FlowLayout) setsavebuts.getLayout()).setVgap(0);
357 JPanel spacer = new JPanel();
358 spacer.setPreferredSize(new Dimension(2, 30));
359 setsavebuts.add(spacer);
360 setsavebuts.add(deletepref);
361 setsavebuts.add(revertpref);
362 setsavebuts.add(createpref);
363 setsavebuts.add(updatepref);
364 // setsavebuts.setSize(new Dimension(150, 30));
365 JPanel buttonArea = new JPanel(new GridLayout(1, 1));
366 buttonArea.add(setsavebuts);
367 SetNamePanel.add(setNameInfo);
368 GridBagConstraints gbc = new GridBagConstraints();
370 gbl.setConstraints(setNameInfo, gbc);
371 SetNamePanel.add(buttonArea);
372 gbc = new GridBagConstraints();
376 gbl.setConstraints(buttonArea, gbc);
377 setDetails.add(setDescrView, BorderLayout.CENTER);
379 // paramPane.setPreferredSize(new Dimension(360, 400));
380 // paramPane.setPreferredSize(null);
381 jobOptions.setBorder(new TitledBorder(MessageManager.getString("label.options")));
382 jobOptions.setOpaque(true);
383 paramList.setBorder(new TitledBorder(MessageManager.getString("label.parameters")));
384 paramList.setOpaque(true);
385 JPanel bjo = new JPanel(new BorderLayout()), bjp = new JPanel(
387 bjo.add(jobOptions, BorderLayout.CENTER);
388 bjp.add(paramList, BorderLayout.CENTER);
391 // optsAndparams.setScrollableWidth(ScrollableSizeHint.FIT);
392 // optsAndparams.setScrollableHeight(ScrollableSizeHint.NONE);
393 // optsAndparams.setLayout(new BorderLayout());
394 optsAndparams.setLayout(new BorderLayout());
395 optsAndparams.add(jobOptions, BorderLayout.NORTH);
396 optsAndparams.add(paramList, BorderLayout.CENTER);
397 JPanel jp = new JPanel(new BorderLayout());
398 jp.add(optsAndparams, BorderLayout.CENTER);
399 paramPane.getViewport().setView(jp);
400 paramPane.setBorder(null);
401 setLayout(new BorderLayout());
402 jobPanel.setPreferredSize(null);
403 jobPanel.setLayout(new BorderLayout());
404 jobPanel.add(setDetails, BorderLayout.NORTH);
405 jobPanel.add(paramPane, BorderLayout.CENTER);
406 // jobPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
408 add(SetNamePanel, BorderLayout.NORTH);
409 add(jobPanel, BorderLayout.CENTER);
411 JPanel dialogpanel = new JPanel();
412 dialogpanel.add(startjob);
413 dialogpanel.add(canceljob);
414 add(dialogpanel, BorderLayout.SOUTH);
418 protected void revert_actionPerformed(ActionEvent e)
420 reInitDialog(lastParmSet);
424 protected void update_actionPerformed(ActionEvent e)
428 String curname = ((String) setName.getSelectedItem()).trim();
429 _updatePreset(lastParmSet, curname);
430 lastParmSet = curname;
432 initArgSetModified();
433 syncSetNamesWithStore();
437 private void _deleteUserPreset(String lastParmSet2)
439 paramStore.deletePreset(lastParmSet2);
442 protected void delete_actionPerformed(ActionEvent e)
446 // delete current preset's saved entry
447 _deleteUserPreset(lastParmSet);
449 reInitDialog(null); // service default
452 protected void create_actionPerformed(ActionEvent e)
454 String curname = ((String) setName.getSelectedItem()).trim();
455 if (curname.length() > 0)
457 _storeCurrentPreset(curname);
458 lastParmSet = curname;
460 initArgSetModified();
464 // TODO: show warning
465 System.err.println("Invalid name. Not saved.");
469 protected void canceljob_actionPerformed(ActionEvent e)
474 frame.setVisible(false);
478 protected void startjob_actionPerformed(ActionEvent e)
483 frame.setVisible(false);
487 Jws2Instance service;
490 * list of service presets in the gui
492 Hashtable servicePresets = null;
495 * set if dialog is being set - so handlers will avoid spurious events
497 boolean settingDialog = false;
499 void initForService(Jws2Instance service, WsParamSetI jabap,
500 List<Argument> jabajobArgset)
502 WsParamSetI p = null;
503 List<ArgumentI> jobArgset = null;
504 settingDialog = true;
505 { // instantiate the abstract proxy for Jaba objects
506 jobArgset = jabajobArgset == null ? null : JabaParamStore
507 .getJwsArgsfromJaba(jabajobArgset);
508 p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
512 Hashtable exnames = new Hashtable();
513 for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
515 exnames.put((String) setName.getItemAt(i), setName.getItemAt(i));
517 servicePresets = new Hashtable();
518 // Add the default entry - if not present already.
519 if (!exnames.contains(SVC_DEF))
521 setName.addItem(SVC_DEF);
522 exnames.put(SVC_DEF, SVC_DEF);
523 servicePresets.put(SVC_DEF, SVC_DEF);
525 String curname = (p == null ? "" : p.getName());
526 for (WsParamSetI pr : paramStore.getPresets())
528 if (!pr.isModifiable())
530 servicePresets.put(pr.getName(), "preset");
535 if (!exnames.contains(pr.getName()))
537 setName.addItem(pr.getName());
540 // TODO: if initial jobArgset matches a given user setting or preset then
541 // should recover setting accordingly
542 // updateTable(p, jobArgset);
545 reInitDialog(p.getName());
546 initArgSetModified();
550 if (jobArgset != null && jobArgset.size() > 0)
552 curSetName = "Supplied Settings";
553 isUserPreset = false;
554 updateTable(p, jobArgset);
555 setName.setSelectedItem(curSetName);
556 updateButtonDisplay();
564 settingDialog = false;
568 @SuppressWarnings("unchecked")
569 private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
571 boolean setDefaultParams=false;
572 if (lastParmSet == null)
574 isUserPreset = false;
575 // First call - so provide Service default settings
576 setName.setSelectedItem(lastSetName = SVC_DEF);
578 if (p==null && SVC_DEF.equals(""+setName.getSelectedItem()))
580 // indicate that service defaults should be set if available
581 setDefaultParams=true;
583 // populate table from default parameter set.
584 List<ArgumentI> args = paramStore.getServiceParameters();
586 // split to params and required arguments
589 boolean optset=false;
590 for (ArgumentI myarg : args)
592 // Ideally, Argument would implement isRequired !
593 if (myarg instanceof ParameterI)
595 ParameterI parm = (ParameterI) myarg;
596 opanp.addParameter(parm).validate();
600 if (myarg instanceof OptionI)
602 OptionI opt = (OptionI) myarg;
603 OptionBox ob = opanp.addOption(opt);
604 ob.resetToDefault(setDefaultParams);
605 if (MAX_OPTWIDTH < ob.getPreferredSize().width)
607 MAX_OPTWIDTH = ob.getPreferredSize().width;
610 cw += ob.getPreferredSize().width + 5;
614 System.err.println("Ignoring unknown service argument type "
615 + myarg.getClass().getName());
619 args = null; // no more args to process.
623 isUserPreset = false;
624 // initialise setname
625 setName.setSelectedItem(lastSetName = p.getName());
626 setDescr.setText(lastDescrText = p.getDescription());
630 args = p.getArguments();
631 } catch (Exception e)
635 // TODO: check if args should be unselected prior to resetting using the
639 if (jobArgset != null)
641 argSetModified(jobArgset, true);
644 // get setargs from current object
647 for (ArgumentI arg : args)
649 if (arg instanceof ParameterI)
651 opanp.setParameter((ParameterI) arg);
655 if (arg instanceof OptionI)
657 // System.out.println("Setting option "
658 // + System.identityHashCode(arg) + ":" + arg.getName()
659 // + " with " + arg.getDefaultValue());
660 opanp.selectOption((OptionI) arg, arg.getValue());
667 refreshParamLayout();
671 private boolean isModified()
673 return modifiedElements.size() > 0;
676 private Hashtable modifiedElements = new Hashtable();
679 * reset gui and modification state settings
681 private void initArgSetModified()
684 modifiedElements.clear();
685 updateButtonDisplay();
688 private void updateButtonDisplay()
690 boolean _update = false, _create = false, _delete = false, _revert = false;
691 if (modifiedElements.size() > 0)
695 _update = isUserPreset; // can only update user presets
696 if (!isUserPreset || modifiedElements.containsKey(setName))
698 // name modified - can create new preset
706 // can still delete a user preset
707 _delete = isUserPreset;
709 createpref.setVisible(_create);
710 updatepref.setVisible(_update);
711 deletepref.setVisible(_delete);
712 revertpref.setVisible(_revert);
716 public void argSetModified(Object modifiedElement, boolean b)
724 modifiedElements.remove(modifiedElement);
728 if (b && modifiedElement == setName
729 && modifiedElements.contains(modifiedElement))
731 // HACK! prevents iteration on makeSetNameValid
734 modifiedElements.put(modifiedElement, modifiedElement);
736 // set mod status based on presence of elements in table
737 if (b && modifiedElements.size() > 0)
739 makeSetNameValid(!isUserPreset);
740 SetNamePanel.revalidate();
742 updateButtonDisplay();
745 private boolean isServicePreset(String selectedItem)
747 return selectedItem.equals(SVC_DEF)
748 || servicePresets.containsKey(selectedItem);
752 * check if the current set name is a valid set name for saving, if not, then
755 private void makeSetNameValid(boolean newuserset)
757 boolean stn = settingDialog;
758 boolean renamed = false;
759 settingDialog = true;
760 String nm = (curSetName != null ? curSetName : (String) setName
762 // check if the name is reserved - if it is, rename it.
763 if (isServicePreset(nm))
772 while (paramStore.getPreset(tnm) != null)
774 tnm = nm + " (" + (++i) + ")";
783 boolean makeupdate = false;
784 // sync the gui with the preset database
785 for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
787 String snm = (String) setName.getItemAt(i);
791 // setName.setSelectedIndex(i);
796 setName.addItem(curSetName = nm);
797 setName.setSelectedItem(curSetName);
801 settingDialog = false; // we need this name change to be registered.
802 argSetModified(setName, renamed);
807 public void refreshParamLayout()
809 // optsAndparams.setPreferredSize(null);
810 FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
811 int sep = fl.getVgap();
813 int os = 0, s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
814 + jobOptions.getBorder().getBorderInsets(jobOptions).top
818 * final height for viewport
821 int panewidth = paramPane.getViewport().getSize().width - 120
822 - jobOptions.getBorder().getBorderInsets(jobOptions).left
823 + jobOptions.getBorder().getBorderInsets(jobOptions).right;
827 + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH
828 : OptsAndParamsPage.PARAM_WIDTH);
829 int hgap = fl.getHgap(), cw = hgap;
831 if (opanp.getOptSet().size() > 0)
834 jobOptions.setLayout(new MigLayout("", "", ""));
835 jobOptions.removeAll();
837 for (OptionBox pbox : opanp.getOptSet().values())
840 cw += pbox.getSize().width + hgap;
841 if (cw + 120 > panewidth)
843 jobOptions.add(pbox, "wrap");
844 // System.out.println("Wrap on "+pbox.option.getName());
845 cw = hgap + pbox.getSize().width;
850 jobOptions.add(pbox);
854 finalh += pbox.getSize().height + fl.getVgap();
858 jobOptions.revalidate();
862 jobOptions.setVisible(false);
865 // Now layout the parameters assuming they occupy one column - to calculate
866 // total height of options+parameters
867 fl = new FlowLayout(FlowLayout.LEFT);
869 // http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
870 fl.setAlignOnBaseline(true);
871 if (opanp.getParamSet().size() > 0)
873 paramList.removeAll();
874 paramList.setLayout(new MigLayout("", "", ""));
876 for (ParamBox pbox : opanp.getParamSet().values())
879 cw += pbox.getSize().width + hgap;
880 if (cw + 160 > panewidth)
882 paramList.add(pbox, "wrap");
883 cw = pbox.getSize().width + hgap;
892 finalh += pbox.getSize().height + fl.getVgap();
898 * s = 2 * sep; for (ParamBox pbox : opanp.getParamSet().values()) {
899 * pbox.validate(); s += sep +
900 * pbox.getPreferredSize().height+pbox.getBorder
901 * ().getBorderInsets(pbox).bottom; }
903 * // paramList.setPreferredSize(new Dimension(w, s));
904 * os+=s+2*sep+paramList
905 * .getBorder().getBorderInsets(paramList).bottom+paramList
906 * .getBorder().getBorderInsets(paramList).top;
908 paramList.revalidate();
912 paramList.setVisible(false);
914 // TODO: waste some time trying to eliminate any unnecessary .validate calls
916 // System.out.println("Size will be : "+w+","+os);
917 // optsAndparams.setPreferredSize(null);
918 // paramPane.getViewport().setView(optsAndparams);
919 paramPane.getViewport().setAutoscrolls(true);
920 paramPane.revalidate();
925 * testing method - grab a service and parameter set and show the window
929 public static void main(String[] args)
931 jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
936 Vector<String> services = new Vector<String>();
937 services.addElement(args[p++]);
938 Jws2Discoverer.setServiceUrls(services);
943 } catch (Exception e)
945 System.err.println("Aborting. Problem discovering services.");
949 Jws2Instance lastserv = null;
950 for (Jws2Instance service : disc.getServices())
953 if (p >= args.length || service.serviceType.equalsIgnoreCase(args[p]))
955 if (lastserv != null)
957 List<Preset> prl = null;
959 if (++p < args.length)
961 PresetManager prman = lastserv.getPresets();
964 pr = prman.getPresetByName(args[p]);
967 // just grab the last preset.
968 prl = prman.getPresets();
974 PresetManager prman = lastserv.getPresets();
977 prl = prman.getPresets();
980 Iterator<Preset> en = (prl == null) ? null : prl.iterator();
981 while (en != null && en.hasNext())
992 System.out.println("Testing opts dupes for "
993 + lastserv.getUri() + " : "
994 + lastserv.getActionText() + ":" + pr.getName());
995 List<Option> rg = lastserv.getRunnerConfig().getOptions();
1000 Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
1001 } catch (Exception e)
1003 System.err.println("Failed to copy " + o.getName());
1004 e.printStackTrace();
1007 System.err.println("Failed to copy " + o.getName());
1008 e.printStackTrace();
1013 System.out.println("Testing param dupes:");
1014 List<Parameter> rg = lastserv.getRunnerConfig()
1016 for (Parameter o : rg)
1020 Parameter cpy = jalview.ws.jws2.ParameterUtils
1022 } catch (Exception e)
1024 System.err.println("Failed to copy " + o.getName());
1025 e.printStackTrace();
1028 System.err.println("Failed to copy " + o.getName());
1029 e.printStackTrace();
1034 System.out.println("Testing param write:");
1035 List<String> writeparam = null, readparam = null;
1038 writeparam = jalview.ws.jws2.ParameterUtils
1040 pr.getArguments(lastserv.getRunnerConfig()),
1042 System.out.println("Testing param read :");
1043 List<Option> pset = jalview.ws.jws2.ParameterUtils
1044 .processParameters(writeparam,
1045 lastserv.getRunnerConfig(), " ");
1046 readparam = jalview.ws.jws2.ParameterUtils
1047 .writeParameterSet(pset, " ");
1048 Iterator<String> o = pr.getOptions().iterator(), s = writeparam
1049 .iterator(), t = readparam.iterator();
1050 boolean failed = false;
1051 while (s.hasNext() && t.hasNext())
1053 String on = o.next(), sn = s.next(), st = t.next();
1056 System.out.println("Original was " + on
1057 + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
1064 System.out.println("Original parameters:\n"
1066 System.out.println("Wrote parameters in first set:\n"
1068 System.out.println("Wrote parameters in second set:\n"
1072 } catch (Exception e)
1074 e.printStackTrace();
1077 WsJobParameters pgui = new WsJobParameters(lastserv,
1078 new JabaPreset(lastserv, pr));
1079 JFrame jf = new JFrame("Parameters for "
1080 + lastserv.getActionText());
1081 JPanel cont = new JPanel(new BorderLayout());
1083 cont.setPreferredSize(pgui.getPreferredSize());
1084 cont.add(pgui, BorderLayout.CENTER);
1085 jf.setLayout(new BorderLayout());
1086 jf.add(cont, BorderLayout.CENTER);
1088 final Thread thr = Thread.currentThread();
1089 jf.addWindowListener(new WindowListener()
1092 public void windowActivated(WindowEvent e)
1094 // TODO Auto-generated method stub
1098 public void windowClosed(WindowEvent e)
1102 public void windowClosing(WindowEvent e)
1108 public void windowDeactivated(WindowEvent e)
1110 // TODO Auto-generated method stub
1114 public void windowDeiconified(WindowEvent e)
1116 // TODO Auto-generated method stub
1120 public void windowIconified(WindowEvent e)
1122 // TODO Auto-generated method stub
1126 public void windowOpened(WindowEvent e)
1128 // TODO Auto-generated method stub
1133 jf.setVisible(true);
1134 boolean inter = false;
1139 Thread.sleep(10000);
1140 } catch (Exception e)
1153 public boolean isServiceDefaults()
1155 return (!isModified() && (lastParmSet != null && lastParmSet
1159 public List<ArgumentI> getJobParams()
1161 return opanp.getCurrentSettings();
1164 String lastParmSet = null;
1167 * Hashtable<String, Object[]> editedParams = new Hashtable<String,
1170 * store the given parameters in the user parameter set database.
1172 * @param storeSetName - lastParmSet
1174 * @param descr - setDescr.getText()
1176 * @param jobParams - getJobParams()
1178 * private void _storeUserPreset(String storeSetName, String descr,
1179 * List<ArgumentI> jobParams) { // this is a simple hash store. Object[] pset;
1180 * editedParams.put(storeSetName, pset = new Object[3]); pset[0] =
1181 * storeSetName; pset[1] = descr; pset[2] = jobParams; // writeParam("Saving "
1182 * + storeSetName + ": ", jobParams); }
1184 * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
1185 * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
1186 * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
1188 * private Object[] _getUserPreset(String setName) { Object[] pset =
1189 * editedParams.get(setName); // if (pset != null) // writeParam("Retrieving "
1190 * + setName + ": ", (List<Argument>) pset[2]); return pset; }
1192 * * remove the given user preset from the preset stash
1196 * private void _deleteUserPreset(String setName) {
1197 * editedParams.remove(setName); }
1200 private void syncSetNamesWithStore()
1203 // remove any set names in the drop down menu that aren't either a reserved
1204 // setting, or a user defined or service preset.
1205 Vector items = new Vector();
1206 while (n < setName.getItemCount())
1208 String item = (String) setName.getItemAt(n);
1209 if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
1211 setName.removeItemAt(n);
1215 items.addElement(item);
1219 if (!items.contains(SVC_DEF))
1221 setName.addItem(SVC_DEF);
1223 for (WsParamSetI upn : paramStore.getPresets())
1225 if (!items.contains(upn.getName()))
1227 setName.addItem(upn.getName());
1233 * true if lastParmSet is a user preset
1235 boolean isUserPreset = false;
1237 private void reInitDialog(String nextPreset)
1239 settingDialog = true;
1240 // updateTable(null,null); // first reset to defaults
1241 WsParamSetI pset = null;
1242 if (nextPreset != null && nextPreset.length() > 0)
1244 pset = paramStore.getPreset(nextPreset);
1248 if (pset.isModifiable())
1250 isUserPreset = true;
1251 setDescr.setText(pset.getDescription());
1252 updateTable(null, pset.getArguments());
1253 lastParmSet = nextPreset;
1257 isUserPreset = false;
1258 setDescr.setText("");
1259 // must be a default preset from service
1260 updateTable(pset, null);
1261 lastParmSet = nextPreset;
1266 isUserPreset = false;
1268 setDescr.setText("");
1269 updateTable(null, null);
1270 lastParmSet = SVC_DEF;
1273 initArgSetModified();
1274 syncSetNamesWithStore();
1275 setName.setSelectedItem(lastParmSet);
1276 SetNamePanel.validate();
1278 settingDialog = false;
1282 String curSetName = null;
1284 public void itemStateChanged(ItemEvent e)
1286 if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
1288 final String setname = (String) setName.getSelectedItem();
1289 System.out.println("Item state changed for " + setname
1290 + " (handling ? " + !settingDialog + ")");
1296 if (setname == null)
1300 javax.swing.SwingUtilities.invokeLater(new Runnable()
1304 doPreferenceComboStateChange(setname);
1310 private void doPreferenceComboStateChange(String setname)
1312 // user has selected a different item from combo-box
1315 String lsetname = (curSetName != null) ? curSetName : lastParmSet;
1316 if (lsetname.equals(setname))
1318 // setname was just edited - so ignore this event.
1321 settingDialog = true;
1322 System.out.println("Prompting to save " + lsetname);
1323 if (javax.swing.JOptionPane
1328 + "' is modifed, and your changes will be lost.\nReally change preset ?",
1329 "Warning: Unsaved Changes",
1330 javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
1332 // revert the combobox to the current item
1333 settingDialog = true;
1334 setName.setSelectedItem(lsetname);
1335 settingDialog = false;
1338 // System.out.println("Saving for " + lsetname);
1339 // _storeCurrentPreset(lsetname);
1343 settingDialog = true;
1344 reInitDialog(setname);
1345 settingDialog = false;
1349 private void _renameExistingPreset(String oldName, String curSetName2)
1351 paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
1356 * store current settings as given name. You should then reset gui.
1358 * @param curSetName2
1360 private void _storeCurrentPreset(String curSetName2)
1362 paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
1365 private void _updatePreset(String lastParmSet2, String curname)
1367 paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(),
1373 * last saved name for this user preset
1375 String lastSetName = null;
1378 * last saved value of the description text for this user preset
1380 String lastDescrText = null;
1382 public void actionPerformed(ActionEvent e)
1384 if (e.getSource() instanceof Component)
1386 Component src = (Component) e.getSource();
1387 if (src.getParent() == setName)
1389 // rename any existing records we know about for this set.
1390 String newname = (String) e.getActionCommand().trim();
1392 if (isServicePreset(newname))
1394 final String oldname = curSetName != null ? curSetName
1396 final Component ourframe = this;
1397 settingDialog = true;
1398 setName.getEditor().setItem(oldname);
1399 settingDialog = false;
1400 javax.swing.SwingUtilities.invokeLater(new Runnable()
1404 JOptionPane.showMessageDialog(ourframe,
1405 "Invalid name - preset already exists.",
1406 "Invalid name", JOptionPane.WARNING_MESSAGE);
1412 curSetName = newname;
1413 System.err.println("New name for user setting " + curSetName
1414 + " (was " + setName.getSelectedItem() + ")");
1415 if (curSetName.equals(setName.getSelectedItem()))
1419 if (curSetName != null)
1421 argSetModified(setName, true);
1429 private void checkDescrModified()
1436 (lastDescrText == null ? setDescr.getText().trim().length() > 0
1437 : !setDescr.getText().equals(lastDescrText)));
1442 public void insertUpdate(DocumentEvent e)
1444 checkDescrModified();
1447 public void removeUpdate(DocumentEvent e)
1449 checkDescrModified();
1452 public void changedUpdate(DocumentEvent e)
1454 checkDescrModified();
1459 * @return null or the service preset selected by the user
1461 public WsParamSetI getPreset()
1463 if (isUserPreset || isModified()
1464 || (lastParmSet != null && lastParmSet.equals(SVC_DEF)))
1470 return paramStore.getPreset(lastParmSet);