2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.gui.OptsAndParamsPage.OptionBox;
21 import jalview.gui.OptsAndParamsPage.ParamBox;
22 import jalview.util.MessageManager;
23 import jalview.ws.jws2.JabaParamStore;
24 import jalview.ws.jws2.JabaPreset;
25 import jalview.ws.jws2.Jws2Discoverer;
26 import jalview.ws.jws2.jabaws2.Jws2Instance;
27 import jalview.ws.params.ArgumentI;
28 import jalview.ws.params.OptionI;
29 import jalview.ws.params.ParamDatastoreI;
30 import jalview.ws.params.ParameterI;
31 import jalview.ws.params.WsParamSetI;
33 import java.awt.BorderLayout;
34 import java.awt.Component;
35 import java.awt.Dimension;
36 import java.awt.FlowLayout;
38 import java.awt.GridBagConstraints;
39 import java.awt.GridBagLayout;
40 import java.awt.GridLayout;
41 import java.awt.Rectangle;
42 import java.awt.event.ActionEvent;
43 import java.awt.event.ActionListener;
44 import java.awt.event.HierarchyBoundsListener;
45 import java.awt.event.HierarchyEvent;
46 import java.awt.event.ItemEvent;
47 import java.awt.event.ItemListener;
48 import java.awt.event.WindowEvent;
49 import java.awt.event.WindowListener;
51 import java.util.Hashtable;
52 import java.util.Iterator;
53 import java.util.List;
54 import java.util.Vector;
56 import javax.swing.JButton;
57 import javax.swing.JComboBox;
58 import javax.swing.JDialog;
59 import javax.swing.JFrame;
60 import javax.swing.JLabel;
61 import javax.swing.JOptionPane;
62 import javax.swing.JPanel;
63 import javax.swing.JScrollPane;
64 import javax.swing.JSplitPane;
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 net.miginfocom.swing.MigLayout;
72 import compbio.metadata.Argument;
73 import compbio.metadata.Option;
74 import compbio.metadata.Parameter;
75 import compbio.metadata.Preset;
76 import compbio.metadata.PresetManager;
77 import compbio.metadata.RunnerConfig;
80 * job parameter editing/browsing dialog box. User can browse existing settings
81 * (user + presets + Defaults), and any changes to parameters creates a modified
82 * user parameter set. LOGIC: If the parameter set is modified, and its name is
83 * a valid, non-existant user parameter set, then a save button is shown. If the
84 * parameter set is modified and its name is a valid, extant user parameter set,
85 * then an update button is shown. If user parameter set's name is edited, and
86 * old name exists as a writable user parameter set, then rename button is
87 * shown. If current parameter set is associated with a user defined parameter
88 * set, then : if set is modifed, a 'revert' button is shown. if set is not
89 * modified, a 'delete' button is shown.
94 public class WsJobParameters extends JPanel implements ItemListener,
95 ActionListener, DocumentListener, OptsParametersContainerI
97 URL linkImageURL = getClass().getResource("/images/link.gif");
99 private static final String SVC_DEF = "Defaults"; // this is the null
100 // parameter set as shown to
104 * manager for options and parameters.
106 OptsAndParamsPage opanp = new OptsAndParamsPage(this);
109 * panel containing job options
111 JPanel jobOptions = new JPanel();
114 * panel containing job parameters
116 JPanel paramList = new JPanel();
118 JPanel SetNamePanel = new JPanel();
120 JPanel setDetails = new JPanel();
122 JSplitPane settingsPanel = new JSplitPane();
124 JPanel jobPanel = new JPanel();
126 JScrollPane jobOptionsPane = new JScrollPane();
128 JButton createpref = new JButton();
130 JButton deletepref = new JButton();
132 JButton revertpref = new JButton();
134 JButton updatepref = new JButton();
136 JButton startjob = new JButton();
138 JButton canceljob = new JButton();
140 JComboBox setName = new JComboBox();
142 JTextArea setDescr = new JTextArea();
144 JScrollPane paramPane = new JScrollPane();
146 // ScrollablePanel optsAndparams = new ScrollablePanel();
147 JPanel optsAndparams = new JPanel();
149 RunnerConfig serviceOptions;
151 ParamDatastoreI paramStore;
153 private int MAX_OPTWIDTH = 200;
155 WsJobParameters(Jws2Instance service)
160 public WsJobParameters(Jws2Instance service, WsParamSetI preset)
162 this(null, service, preset, null);
168 * - if null, create new JFrame outside of desktop
172 public WsJobParameters(JFrame parent, Jws2Instance service,
173 WsParamSetI preset, List<Argument> jobArgset)
175 this(parent, null, service, preset, jobArgset);
186 public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
187 Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
191 this.paramStore = paramStorei;
192 if (paramStore == null)
194 paramStore = service.getParamStore();
196 this.service = service;
197 // argSetModified(false);
198 // populate parameter table
199 initForService(service, preset, jobArgset);
200 // display in new JFrame attached to parent.
206 JDialog frame = null;
209 * shows a modal dialog containing the parameters.
213 public boolean showRunDialog()
216 frame = new JDialog(Desktop.instance, true);
218 frame.setTitle("Edit parameters for " + service.getActionText());
219 Rectangle deskr = Desktop.instance.getBounds();
220 Dimension pref = this.getPreferredSize();
221 frame.setBounds(new Rectangle(
222 (int) (deskr.getCenterX() - pref.width / 2), (int) (deskr
223 .getCenterY() - pref.height / 2), pref.width,
225 frame.setContentPane(this);
227 // should perhaps recover defaults from user prefs.
230 javax.swing.SwingUtilities.invokeLater(new Runnable()
234 // jobPanel.setDividerLocation(0.25);
238 frame.setVisible(true);
247 private void jbInit()
249 this.addHierarchyBoundsListener(new HierarchyBoundsListener()
253 public void ancestorResized(HierarchyEvent arg0)
255 refreshParamLayout();
259 public void ancestorMoved(HierarchyEvent arg0)
261 // TODO Auto-generated method stub
265 updatepref = JvSwingUtils.makeButton("Update",
266 "Update this existing user parameter set.",
270 public void actionPerformed(ActionEvent e)
272 update_actionPerformed(e);
275 deletepref = JvSwingUtils.makeButton("Delete",
276 "Delete the currently selected user parameter set.",
280 public void actionPerformed(ActionEvent e)
282 delete_actionPerformed(e);
285 createpref = JvSwingUtils.makeButton("Create",
286 "Create a new parameter set with the current settings.",
290 public void actionPerformed(ActionEvent e)
292 create_actionPerformed(e);
295 revertpref = JvSwingUtils.makeButton("Revert",
296 "Undo all changes to the current parameter set",
300 public void actionPerformed(ActionEvent e)
302 revert_actionPerformed(e);
305 startjob = JvSwingUtils.makeButton("Start Job",
306 "Start Job with current settings.", new ActionListener()
308 public void actionPerformed(ActionEvent e)
310 startjob_actionPerformed(e);
313 canceljob = JvSwingUtils.makeButton("Cancel Job",
314 "Close this dialog and cancel job.", new ActionListener()
316 public void actionPerformed(ActionEvent e)
318 canceljob_actionPerformed(e);
322 setDetails.setBorder(new TitledBorder("Details"));
323 setDetails.setLayout(new BorderLayout());
324 setDescr.setColumns(40);
325 setDescr.setWrapStyleWord(true);
326 setDescr.setLineWrap(true);
327 setDescr.setBackground(getBackground());
328 setDescr.setEditable(true);
329 setDescr.getDocument().addDocumentListener(this);
330 setDescr.setToolTipText("Click to edit the notes for this parameter set.");
331 JScrollPane setDescrView = new JScrollPane();
332 // setDescrView.setPreferredSize(new Dimension(350, 200));
333 setDescrView.getViewport().setView(setDescr);
334 setName.setEditable(true);
335 setName.addItemListener(this);
336 setName.getEditor().addActionListener(this);
337 JPanel setNameInfo = new JPanel(new FlowLayout(FlowLayout.LEFT));
338 GridBagLayout gbl = new GridBagLayout();
339 SetNamePanel.setLayout(gbl);
341 JLabel setNameLabel = new JLabel(MessageManager.getString("label.current_parameter_set_name"));
342 setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
344 setNameInfo.add(setNameLabel);
345 setNameInfo.add(setName);
347 // initial button visibility
348 updatepref.setVisible(false);
349 deletepref.setVisible(false);
350 revertpref.setVisible(false);
351 createpref.setVisible(false);
352 JPanel setsavebuts = new JPanel();
353 setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT)); // GridLayout(1,2));
354 ((FlowLayout) setsavebuts.getLayout()).setHgap(10);
355 ((FlowLayout) setsavebuts.getLayout()).setVgap(0);
356 JPanel spacer = new JPanel();
357 spacer.setPreferredSize(new Dimension(2, 30));
358 setsavebuts.add(spacer);
359 setsavebuts.add(deletepref);
360 setsavebuts.add(revertpref);
361 setsavebuts.add(createpref);
362 setsavebuts.add(updatepref);
363 // setsavebuts.setSize(new Dimension(150, 30));
364 JPanel buttonArea = new JPanel(new GridLayout(1, 1));
365 buttonArea.add(setsavebuts);
366 SetNamePanel.add(setNameInfo);
367 GridBagConstraints gbc = new GridBagConstraints();
369 gbl.setConstraints(setNameInfo, gbc);
370 SetNamePanel.add(buttonArea);
371 gbc = new GridBagConstraints();
375 gbl.setConstraints(buttonArea, gbc);
376 setDetails.add(setDescrView, BorderLayout.CENTER);
378 // paramPane.setPreferredSize(new Dimension(360, 400));
379 // paramPane.setPreferredSize(null);
380 jobOptions.setBorder(new TitledBorder("Options"));
381 jobOptions.setOpaque(true);
382 paramList.setBorder(new TitledBorder("Parameters"));
383 paramList.setOpaque(true);
384 JPanel bjo = new JPanel(new BorderLayout()), bjp = new JPanel(
386 bjo.add(jobOptions, BorderLayout.CENTER);
387 bjp.add(paramList, BorderLayout.CENTER);
390 // optsAndparams.setScrollableWidth(ScrollableSizeHint.FIT);
391 // optsAndparams.setScrollableHeight(ScrollableSizeHint.NONE);
392 // optsAndparams.setLayout(new BorderLayout());
393 optsAndparams.setLayout(new BorderLayout());
394 optsAndparams.add(jobOptions, BorderLayout.NORTH);
395 optsAndparams.add(paramList, BorderLayout.CENTER);
396 JPanel jp = new JPanel(new BorderLayout());
397 jp.add(optsAndparams, BorderLayout.CENTER);
398 paramPane.getViewport().setView(jp);
399 paramPane.setBorder(null);
400 setLayout(new BorderLayout());
401 jobPanel.setPreferredSize(null);
402 jobPanel.setLayout(new BorderLayout());
403 jobPanel.add(setDetails, BorderLayout.NORTH);
404 jobPanel.add(paramPane, BorderLayout.CENTER);
405 // jobPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
407 add(SetNamePanel, BorderLayout.NORTH);
408 add(jobPanel, BorderLayout.CENTER);
410 JPanel dialogpanel = new JPanel();
411 dialogpanel.add(startjob);
412 dialogpanel.add(canceljob);
413 add(dialogpanel, BorderLayout.SOUTH);
417 protected void revert_actionPerformed(ActionEvent e)
419 reInitDialog(lastParmSet);
423 protected void update_actionPerformed(ActionEvent e)
427 String curname = ((String) setName.getSelectedItem()).trim();
428 _updatePreset(lastParmSet, curname);
429 lastParmSet = curname;
431 initArgSetModified();
432 syncSetNamesWithStore();
436 private void _deleteUserPreset(String lastParmSet2)
438 paramStore.deletePreset(lastParmSet2);
441 protected void delete_actionPerformed(ActionEvent e)
445 // delete current preset's saved entry
446 _deleteUserPreset(lastParmSet);
448 reInitDialog(null); // service default
451 protected void create_actionPerformed(ActionEvent e)
453 String curname = ((String) setName.getSelectedItem()).trim();
454 if (curname.length() > 0)
456 _storeCurrentPreset(curname);
457 lastParmSet = curname;
459 initArgSetModified();
463 // TODO: show warning
464 System.err.println("Invalid name. Not saved.");
468 protected void canceljob_actionPerformed(ActionEvent e)
473 frame.setVisible(false);
477 protected void startjob_actionPerformed(ActionEvent e)
482 frame.setVisible(false);
486 Jws2Instance service;
489 * list of service presets in the gui
491 Hashtable servicePresets = null;
494 * set if dialog is being set - so handlers will avoid spurious events
496 boolean settingDialog = false;
498 void initForService(Jws2Instance service, WsParamSetI jabap,
499 List<Argument> jabajobArgset)
501 WsParamSetI p = null;
502 List<ArgumentI> jobArgset = null;
503 settingDialog = true;
504 { // instantiate the abstract proxy for Jaba objects
505 jobArgset = jabajobArgset == null ? null : JabaParamStore
506 .getJwsArgsfromJaba(jabajobArgset);
507 p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
511 Hashtable exnames = new Hashtable();
512 for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
514 exnames.put((String) setName.getItemAt(i), setName.getItemAt(i));
516 servicePresets = new Hashtable();
517 // Add the default entry - if not present already.
518 if (!exnames.contains(SVC_DEF))
520 setName.addItem(SVC_DEF);
521 exnames.put(SVC_DEF, SVC_DEF);
522 servicePresets.put(SVC_DEF, SVC_DEF);
524 String curname = (p == null ? "" : p.getName());
525 for (WsParamSetI pr : paramStore.getPresets())
527 if (!pr.isModifiable())
529 servicePresets.put(pr.getName(), "preset");
534 if (!exnames.contains(pr.getName()))
536 setName.addItem(pr.getName());
539 // TODO: if initial jobArgset matches a given user setting or preset then
540 // should recover setting accordingly
541 // updateTable(p, jobArgset);
544 reInitDialog(p.getName());
545 initArgSetModified();
549 if (jobArgset != null && jobArgset.size() > 0)
551 curSetName = "Supplied Settings";
552 isUserPreset = false;
553 updateTable(p, jobArgset);
554 setName.setSelectedItem(curSetName);
555 updateButtonDisplay();
563 settingDialog = false;
567 @SuppressWarnings("unchecked")
568 private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
570 boolean setDefaultParams=false;
571 if (lastParmSet == null)
573 isUserPreset = false;
574 // First call - so provide Service default settings
575 setName.setSelectedItem(lastSetName = SVC_DEF);
577 if (p==null && SVC_DEF.equals(""+setName.getSelectedItem()))
579 // indicate that service defaults should be set if available
580 setDefaultParams=true;
582 // populate table from default parameter set.
583 List<ArgumentI> args = paramStore.getServiceParameters();
585 // split to params and required arguments
588 boolean optset=false;
589 for (ArgumentI myarg : args)
591 // Ideally, Argument would implement isRequired !
592 if (myarg instanceof ParameterI)
594 ParameterI parm = (ParameterI) myarg;
595 opanp.addParameter(parm).validate();
599 if (myarg instanceof OptionI)
601 OptionI opt = (OptionI) myarg;
602 OptionBox ob = opanp.addOption(opt);
603 ob.resetToDefault(setDefaultParams);
604 if (MAX_OPTWIDTH < ob.getPreferredSize().width)
606 MAX_OPTWIDTH = ob.getPreferredSize().width;
609 cw += ob.getPreferredSize().width + 5;
613 System.err.println("Ignoring unknown service argument type "
614 + myarg.getClass().getName());
618 args = null; // no more args to process.
622 isUserPreset = false;
623 // initialise setname
624 setName.setSelectedItem(lastSetName = p.getName());
625 setDescr.setText(lastDescrText = p.getDescription());
629 args = p.getArguments();
630 } catch (Exception e)
634 // TODO: check if args should be unselected prior to resetting using the
638 if (jobArgset != null)
640 argSetModified(jobArgset, true);
643 // get setargs from current object
646 for (ArgumentI arg : args)
648 if (arg instanceof ParameterI)
650 opanp.setParameter((ParameterI) arg);
654 if (arg instanceof OptionI)
656 // System.out.println("Setting option "
657 // + System.identityHashCode(arg) + ":" + arg.getName()
658 // + " with " + arg.getDefaultValue());
659 opanp.selectOption((OptionI) arg, arg.getValue());
666 refreshParamLayout();
670 private boolean isModified()
672 return modifiedElements.size() > 0;
675 private Hashtable modifiedElements = new Hashtable();
678 * reset gui and modification state settings
680 private void initArgSetModified()
683 modifiedElements.clear();
684 updateButtonDisplay();
687 private void updateButtonDisplay()
689 boolean _update = false, _create = false, _delete = false, _revert = false;
690 if (modifiedElements.size() > 0)
694 _update = isUserPreset; // can only update user presets
695 if (!isUserPreset || modifiedElements.containsKey(setName))
697 // name modified - can create new preset
705 // can still delete a user preset
706 _delete = isUserPreset;
708 createpref.setVisible(_create);
709 updatepref.setVisible(_update);
710 deletepref.setVisible(_delete);
711 revertpref.setVisible(_revert);
715 public void argSetModified(Object modifiedElement, boolean b)
723 modifiedElements.remove(modifiedElement);
727 if (b && modifiedElement == setName
728 && modifiedElements.contains(modifiedElement))
730 // HACK! prevents iteration on makeSetNameValid
733 modifiedElements.put(modifiedElement, modifiedElement);
735 // set mod status based on presence of elements in table
736 if (b && modifiedElements.size() > 0)
738 makeSetNameValid(!isUserPreset);
739 SetNamePanel.revalidate();
741 updateButtonDisplay();
744 private boolean isServicePreset(String selectedItem)
746 return selectedItem.equals(SVC_DEF)
747 || servicePresets.containsKey(selectedItem);
751 * check if the current set name is a valid set name for saving, if not, then
754 private void makeSetNameValid(boolean newuserset)
756 boolean stn = settingDialog;
757 boolean renamed = false;
758 settingDialog = true;
759 String nm = (curSetName != null ? curSetName : (String) setName
761 // check if the name is reserved - if it is, rename it.
762 if (isServicePreset(nm))
771 while (paramStore.getPreset(tnm) != null)
773 tnm = nm + " (" + (++i) + ")";
782 boolean makeupdate = false;
783 // sync the gui with the preset database
784 for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
786 String snm = (String) setName.getItemAt(i);
790 // setName.setSelectedIndex(i);
795 setName.addItem(curSetName = nm);
796 setName.setSelectedItem(curSetName);
800 settingDialog = false; // we need this name change to be registered.
801 argSetModified(setName, renamed);
806 public void refreshParamLayout()
808 // optsAndparams.setPreferredSize(null);
809 FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
810 int sep = fl.getVgap();
812 int os = 0, s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
813 + jobOptions.getBorder().getBorderInsets(jobOptions).top
817 * final height for viewport
820 int panewidth = paramPane.getViewport().getSize().width - 120
821 - jobOptions.getBorder().getBorderInsets(jobOptions).left
822 + jobOptions.getBorder().getBorderInsets(jobOptions).right;
826 + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH
827 : OptsAndParamsPage.PARAM_WIDTH);
828 int hgap = fl.getHgap(), cw = hgap;
830 if (opanp.getOptSet().size() > 0)
833 jobOptions.setLayout(new MigLayout("", "", ""));
834 jobOptions.removeAll();
836 for (OptionBox pbox : opanp.getOptSet().values())
839 cw += pbox.getSize().width + hgap;
840 if (cw + 120 > panewidth)
842 jobOptions.add(pbox, "wrap");
843 // System.out.println("Wrap on "+pbox.option.getName());
844 cw = hgap + pbox.getSize().width;
849 jobOptions.add(pbox);
853 finalh += pbox.getSize().height + fl.getVgap();
857 jobOptions.revalidate();
861 jobOptions.setVisible(false);
864 // Now layout the parameters assuming they occupy one column - to calculate
865 // total height of options+parameters
866 fl = new FlowLayout(FlowLayout.LEFT);
868 // http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
869 fl.setAlignOnBaseline(true);
870 if (opanp.getParamSet().size() > 0)
872 paramList.removeAll();
873 paramList.setLayout(new MigLayout("", "", ""));
875 for (ParamBox pbox : opanp.getParamSet().values())
878 cw += pbox.getSize().width + hgap;
879 if (cw + 160 > panewidth)
881 paramList.add(pbox, "wrap");
882 cw = pbox.getSize().width + hgap;
891 finalh += pbox.getSize().height + fl.getVgap();
897 * s = 2 * sep; for (ParamBox pbox : opanp.getParamSet().values()) {
898 * pbox.validate(); s += sep +
899 * pbox.getPreferredSize().height+pbox.getBorder
900 * ().getBorderInsets(pbox).bottom; }
902 * // paramList.setPreferredSize(new Dimension(w, s));
903 * os+=s+2*sep+paramList
904 * .getBorder().getBorderInsets(paramList).bottom+paramList
905 * .getBorder().getBorderInsets(paramList).top;
907 paramList.revalidate();
911 paramList.setVisible(false);
913 // TODO: waste some time trying to eliminate any unnecessary .validate calls
915 // System.out.println("Size will be : "+w+","+os);
916 // optsAndparams.setPreferredSize(null);
917 // paramPane.getViewport().setView(optsAndparams);
918 paramPane.getViewport().setAutoscrolls(true);
919 paramPane.revalidate();
924 * testing method - grab a service and parameter set and show the window
928 public static void main(String[] args)
930 jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
935 Vector<String> services = new Vector<String>();
936 services.addElement(args[p++]);
937 Jws2Discoverer.setServiceUrls(services);
942 } catch (Exception e)
944 System.err.println("Aborting. Problem discovering services.");
948 Jws2Instance lastserv = null;
949 for (Jws2Instance service : disc.getServices())
952 if (p >= args.length || service.serviceType.equalsIgnoreCase(args[p]))
954 if (lastserv != null)
956 List<Preset> prl = null;
958 if (++p < args.length)
960 PresetManager prman = lastserv.getPresets();
963 pr = prman.getPresetByName(args[p]);
966 // just grab the last preset.
967 prl = prman.getPresets();
973 PresetManager prman = lastserv.getPresets();
976 prl = prman.getPresets();
979 Iterator<Preset> en = (prl == null) ? null : prl.iterator();
980 while (en != null && en.hasNext())
991 System.out.println("Testing opts dupes for "
992 + lastserv.getUri() + " : "
993 + lastserv.getActionText() + ":" + pr.getName());
994 List<Option> rg = lastserv.getRunnerConfig().getOptions();
999 Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
1000 } catch (Exception e)
1002 System.err.println("Failed to copy " + o.getName());
1003 e.printStackTrace();
1006 System.err.println("Failed to copy " + o.getName());
1007 e.printStackTrace();
1012 System.out.println("Testing param dupes:");
1013 List<Parameter> rg = lastserv.getRunnerConfig()
1015 for (Parameter o : rg)
1019 Parameter cpy = jalview.ws.jws2.ParameterUtils
1021 } catch (Exception e)
1023 System.err.println("Failed to copy " + o.getName());
1024 e.printStackTrace();
1027 System.err.println("Failed to copy " + o.getName());
1028 e.printStackTrace();
1033 System.out.println("Testing param write:");
1034 List<String> writeparam = null, readparam = null;
1037 writeparam = jalview.ws.jws2.ParameterUtils
1039 pr.getArguments(lastserv.getRunnerConfig()),
1041 System.out.println("Testing param read :");
1042 List<Option> pset = jalview.ws.jws2.ParameterUtils
1043 .processParameters(writeparam,
1044 lastserv.getRunnerConfig(), " ");
1045 readparam = jalview.ws.jws2.ParameterUtils
1046 .writeParameterSet(pset, " ");
1047 Iterator<String> o = pr.getOptions().iterator(), s = writeparam
1048 .iterator(), t = readparam.iterator();
1049 boolean failed = false;
1050 while (s.hasNext() && t.hasNext())
1052 String on = o.next(), sn = s.next(), st = t.next();
1055 System.out.println("Original was " + on
1056 + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
1063 System.out.println("Original parameters:\n"
1065 System.out.println("Wrote parameters in first set:\n"
1067 System.out.println("Wrote parameters in second set:\n"
1071 } catch (Exception e)
1073 e.printStackTrace();
1076 WsJobParameters pgui = new WsJobParameters(lastserv,
1077 new JabaPreset(lastserv, pr));
1078 JFrame jf = new JFrame("Parameters for "
1079 + lastserv.getActionText());
1080 JPanel cont = new JPanel(new BorderLayout());
1082 cont.setPreferredSize(pgui.getPreferredSize());
1083 cont.add(pgui, BorderLayout.CENTER);
1084 jf.setLayout(new BorderLayout());
1085 jf.add(cont, BorderLayout.CENTER);
1087 final Thread thr = Thread.currentThread();
1088 jf.addWindowListener(new WindowListener()
1091 public void windowActivated(WindowEvent e)
1093 // TODO Auto-generated method stub
1097 public void windowClosed(WindowEvent e)
1101 public void windowClosing(WindowEvent e)
1107 public void windowDeactivated(WindowEvent e)
1109 // TODO Auto-generated method stub
1113 public void windowDeiconified(WindowEvent e)
1115 // TODO Auto-generated method stub
1119 public void windowIconified(WindowEvent e)
1121 // TODO Auto-generated method stub
1125 public void windowOpened(WindowEvent e)
1127 // TODO Auto-generated method stub
1132 jf.setVisible(true);
1133 boolean inter = false;
1138 Thread.sleep(10000);
1139 } catch (Exception e)
1152 public boolean isServiceDefaults()
1154 return (!isModified() && (lastParmSet != null && lastParmSet
1158 public List<ArgumentI> getJobParams()
1160 return opanp.getCurrentSettings();
1163 String lastParmSet = null;
1166 * Hashtable<String, Object[]> editedParams = new Hashtable<String,
1169 * store the given parameters in the user parameter set database.
1171 * @param storeSetName - lastParmSet
1173 * @param descr - setDescr.getText()
1175 * @param jobParams - getJobParams()
1177 * private void _storeUserPreset(String storeSetName, String descr,
1178 * List<ArgumentI> jobParams) { // this is a simple hash store. Object[] pset;
1179 * editedParams.put(storeSetName, pset = new Object[3]); pset[0] =
1180 * storeSetName; pset[1] = descr; pset[2] = jobParams; // writeParam("Saving "
1181 * + storeSetName + ": ", jobParams); }
1183 * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
1184 * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
1185 * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
1187 * private Object[] _getUserPreset(String setName) { Object[] pset =
1188 * editedParams.get(setName); // if (pset != null) // writeParam("Retrieving "
1189 * + setName + ": ", (List<Argument>) pset[2]); return pset; }
1191 * * remove the given user preset from the preset stash
1195 * private void _deleteUserPreset(String setName) {
1196 * editedParams.remove(setName); }
1199 private void syncSetNamesWithStore()
1202 // remove any set names in the drop down menu that aren't either a reserved
1203 // setting, or a user defined or service preset.
1204 Vector items = new Vector();
1205 while (n < setName.getItemCount())
1207 String item = (String) setName.getItemAt(n);
1208 if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
1210 setName.removeItemAt(n);
1214 items.addElement(item);
1218 if (!items.contains(SVC_DEF))
1220 setName.addItem(SVC_DEF);
1222 for (WsParamSetI upn : paramStore.getPresets())
1224 if (!items.contains(upn.getName()))
1226 setName.addItem(upn.getName());
1232 * true if lastParmSet is a user preset
1234 boolean isUserPreset = false;
1236 private void reInitDialog(String nextPreset)
1238 settingDialog = true;
1239 // updateTable(null,null); // first reset to defaults
1240 WsParamSetI pset = null;
1241 if (nextPreset != null && nextPreset.length() > 0)
1243 pset = paramStore.getPreset(nextPreset);
1247 if (pset.isModifiable())
1249 isUserPreset = true;
1250 setDescr.setText(pset.getDescription());
1251 updateTable(null, pset.getArguments());
1252 lastParmSet = nextPreset;
1256 isUserPreset = false;
1257 setDescr.setText("");
1258 // must be a default preset from service
1259 updateTable(pset, null);
1260 lastParmSet = nextPreset;
1265 isUserPreset = false;
1267 setDescr.setText("");
1268 updateTable(null, null);
1269 lastParmSet = SVC_DEF;
1272 initArgSetModified();
1273 syncSetNamesWithStore();
1274 setName.setSelectedItem(lastParmSet);
1275 SetNamePanel.validate();
1277 settingDialog = false;
1281 String curSetName = null;
1283 public void itemStateChanged(ItemEvent e)
1285 if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
1287 final String setname = (String) setName.getSelectedItem();
1288 System.out.println("Item state changed for " + setname
1289 + " (handling ? " + !settingDialog + ")");
1295 if (setname == null)
1299 javax.swing.SwingUtilities.invokeLater(new Runnable()
1303 doPreferenceComboStateChange(setname);
1309 private void doPreferenceComboStateChange(String setname)
1311 // user has selected a different item from combo-box
1314 String lsetname = (curSetName != null) ? curSetName : lastParmSet;
1315 if (lsetname.equals(setname))
1317 // setname was just edited - so ignore this event.
1320 settingDialog = true;
1321 System.out.println("Prompting to save " + lsetname);
1322 if (javax.swing.JOptionPane
1327 + "' is modifed, and your changes will be lost.\nReally change preset ?",
1328 "Warning: Unsaved Changes",
1329 javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
1331 // revert the combobox to the current item
1332 settingDialog = true;
1333 setName.setSelectedItem(lsetname);
1334 settingDialog = false;
1337 // System.out.println("Saving for " + lsetname);
1338 // _storeCurrentPreset(lsetname);
1342 settingDialog = true;
1343 reInitDialog(setname);
1344 settingDialog = false;
1348 private void _renameExistingPreset(String oldName, String curSetName2)
1350 paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
1355 * store current settings as given name. You should then reset gui.
1357 * @param curSetName2
1359 private void _storeCurrentPreset(String curSetName2)
1361 paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
1364 private void _updatePreset(String lastParmSet2, String curname)
1366 paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(),
1372 * last saved name for this user preset
1374 String lastSetName = null;
1377 * last saved value of the description text for this user preset
1379 String lastDescrText = null;
1381 public void actionPerformed(ActionEvent e)
1383 if (e.getSource() instanceof Component)
1385 Component src = (Component) e.getSource();
1386 if (src.getParent() == setName)
1388 // rename any existing records we know about for this set.
1389 String newname = (String) e.getActionCommand().trim();
1391 if (isServicePreset(newname))
1393 final String oldname = curSetName != null ? curSetName
1395 final Component ourframe = this;
1396 settingDialog = true;
1397 setName.getEditor().setItem(oldname);
1398 settingDialog = false;
1399 javax.swing.SwingUtilities.invokeLater(new Runnable()
1403 JOptionPane.showMessageDialog(ourframe,
1404 "Invalid name - preset already exists.",
1405 "Invalid name", JOptionPane.WARNING_MESSAGE);
1411 curSetName = newname;
1412 System.err.println("New name for user setting " + curSetName
1413 + " (was " + setName.getSelectedItem() + ")");
1414 if (curSetName.equals(setName.getSelectedItem()))
1418 if (curSetName != null)
1420 argSetModified(setName, true);
1428 private void checkDescrModified()
1435 (lastDescrText == null ? setDescr.getText().trim().length() > 0
1436 : !setDescr.getText().equals(lastDescrText)));
1441 public void insertUpdate(DocumentEvent e)
1443 checkDescrModified();
1446 public void removeUpdate(DocumentEvent e)
1448 checkDescrModified();
1451 public void changedUpdate(DocumentEvent e)
1453 checkDescrModified();
1458 * @return null or the service preset selected by the user
1460 public WsParamSetI getPreset()
1462 if (isUserPreset || isModified()
1463 || (lastParmSet != null && lastParmSet.equals(SVC_DEF)))
1469 return paramStore.getPreset(lastParmSet);