2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.gui.OptsAndParamsPage.OptionBox;
21 import jalview.gui.OptsAndParamsPage.ParamBox;
22 import jalview.ws.jws2.JabaParamStore;
23 import jalview.ws.jws2.JabaPreset;
24 import jalview.ws.jws2.Jws2Discoverer;
25 import jalview.ws.jws2.jabaws2.Jws2Instance;
26 import jalview.ws.params.ArgumentI;
27 import jalview.ws.params.OptionI;
28 import jalview.ws.params.ParamDatastoreI;
29 import jalview.ws.params.ParameterI;
30 import jalview.ws.params.WsParamSetI;
32 import java.awt.BorderLayout;
33 import java.awt.Component;
34 import java.awt.Dimension;
35 import java.awt.FlowLayout;
37 import java.awt.GridBagConstraints;
38 import java.awt.GridBagLayout;
39 import java.awt.GridLayout;
40 import java.awt.Rectangle;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.HierarchyBoundsListener;
44 import java.awt.event.HierarchyEvent;
45 import java.awt.event.ItemEvent;
46 import java.awt.event.ItemListener;
47 import java.awt.event.WindowEvent;
48 import java.awt.event.WindowListener;
50 import java.util.Hashtable;
51 import java.util.Iterator;
52 import java.util.List;
53 import java.util.Vector;
55 import javax.swing.JButton;
56 import javax.swing.JComboBox;
57 import javax.swing.JDialog;
58 import javax.swing.JFrame;
59 import javax.swing.JLabel;
60 import javax.swing.JOptionPane;
61 import javax.swing.JPanel;
62 import javax.swing.JScrollPane;
63 import javax.swing.JSplitPane;
64 import javax.swing.JTextArea;
65 import javax.swing.border.TitledBorder;
66 import javax.swing.event.DocumentEvent;
67 import javax.swing.event.DocumentListener;
69 import net.miginfocom.swing.MigLayout;
71 import compbio.metadata.Argument;
72 import compbio.metadata.Option;
73 import compbio.metadata.Parameter;
74 import compbio.metadata.Preset;
75 import compbio.metadata.PresetManager;
76 import compbio.metadata.RunnerConfig;
79 * job parameter editing/browsing dialog box. User can browse existing settings
80 * (user + presets + Defaults), and any changes to parameters creates a modified
81 * user parameter set. LOGIC: If the parameter set is modified, and its name is
82 * a valid, non-existant user parameter set, then a save button is shown. If the
83 * parameter set is modified and its name is a valid, extant user parameter set,
84 * then an update button is shown. If user parameter set's name is edited, and
85 * old name exists as a writable user parameter set, then rename button is
86 * shown. If current parameter set is associated with a user defined parameter
87 * set, then : if set is modifed, a 'revert' button is shown. if set is not
88 * modified, a 'delete' button is shown.
93 public class WsJobParameters extends JPanel implements ItemListener,
94 ActionListener, DocumentListener, OptsParametersContainerI
96 URL linkImageURL = getClass().getResource("/images/link.gif");
98 private static final String SVC_DEF = "Defaults"; // this is the null
99 // parameter set as shown to
103 * manager for options and parameters.
105 OptsAndParamsPage opanp = new OptsAndParamsPage(this);
108 * panel containing job options
110 JPanel jobOptions = new JPanel();
113 * panel containing job parameters
115 JPanel paramList = new JPanel();
119 JPanel SetNamePanel = new JPanel();
121 JPanel setDetails = new JPanel();
123 JSplitPane settingsPanel = new JSplitPane();
125 JPanel jobPanel = new JPanel();
128 JScrollPane jobOptionsPane = new JScrollPane();
130 JButton createpref = new JButton();
132 JButton deletepref = new JButton();
134 JButton revertpref = new JButton();
136 JButton updatepref = new JButton();
138 JButton startjob = new JButton();
140 JButton canceljob = new JButton();
142 JComboBox setName = new JComboBox();
144 JTextArea setDescr = new JTextArea();
146 JScrollPane paramPane = new JScrollPane();
149 // ScrollablePanel optsAndparams = new ScrollablePanel();
150 JPanel optsAndparams = new JPanel();
151 RunnerConfig serviceOptions;
153 ParamDatastoreI paramStore;
155 private int MAX_OPTWIDTH = 200;
157 WsJobParameters(Jws2Instance service)
162 public WsJobParameters(Jws2Instance service, WsParamSetI preset)
164 this(null, service, preset, null);
170 * - if null, create new JFrame outside of desktop
174 public WsJobParameters(JFrame parent, Jws2Instance service,
175 WsParamSetI preset, List<Argument> jobArgset)
177 this(parent, null, service, preset, jobArgset);
188 public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
189 Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
193 this.paramStore = paramStorei;
194 if (paramStore == null)
196 paramStore = service.getParamStore();
198 this.service = service;
199 // argSetModified(false);
200 // populate parameter table
201 initForService(service, preset, jobArgset);
202 // display in new JFrame attached to parent.
208 JDialog frame = null;
211 * shows a modal dialog containing the parameters.
215 public boolean showRunDialog()
218 frame = new JDialog(Desktop.instance, true);
220 frame.setTitle("Edit parameters for " + service.getActionText());
221 Rectangle deskr = Desktop.instance.getBounds();
222 Dimension pref = this.getPreferredSize();
223 frame.setBounds(new Rectangle((int) (deskr.getCenterX() - pref.width/2),
224 (int) (deskr.getCenterY() - pref.height/2), pref.width, pref.height));
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("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(new BorderLayout());
385 bjo.add(jobOptions, BorderLayout.CENTER);
386 bjp.add(paramList, BorderLayout.CENTER);
389 //optsAndparams.setScrollableWidth(ScrollableSizeHint.FIT);
390 // optsAndparams.setScrollableHeight(ScrollableSizeHint.NONE);
391 // optsAndparams.setLayout(new BorderLayout());
392 optsAndparams.setLayout(new BorderLayout());
393 optsAndparams.add(jobOptions, BorderLayout.NORTH);
394 optsAndparams.add(paramList, BorderLayout.CENTER);
395 JPanel jp=new JPanel(new BorderLayout());
396 jp.add(optsAndparams, BorderLayout.CENTER);
397 paramPane.getViewport().setView(jp);
398 paramPane.setBorder(null);
399 setLayout(new BorderLayout());
400 jobPanel.setPreferredSize(null);
401 jobPanel.setLayout(new BorderLayout());
402 jobPanel.add(setDetails, BorderLayout.NORTH);
403 jobPanel.add(paramPane, BorderLayout.CENTER);
404 // jobPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
406 add(SetNamePanel, BorderLayout.NORTH);
407 add(jobPanel, BorderLayout.CENTER);
409 JPanel dialogpanel = new JPanel();
410 dialogpanel.add(startjob);
411 dialogpanel.add(canceljob);
412 add(dialogpanel, BorderLayout.SOUTH);
416 protected void revert_actionPerformed(ActionEvent e)
418 reInitDialog(lastParmSet);
422 protected void update_actionPerformed(ActionEvent e)
426 String curname = ((String) setName.getSelectedItem()).trim();
427 _updatePreset(lastParmSet, curname);
428 lastParmSet = curname;
430 initArgSetModified();
431 syncSetNamesWithStore();
435 private void _deleteUserPreset(String lastParmSet2)
437 paramStore.deletePreset(lastParmSet2);
440 protected void delete_actionPerformed(ActionEvent e)
444 // delete current preset's saved entry
445 _deleteUserPreset(lastParmSet);
447 reInitDialog(null); // service default
450 protected void create_actionPerformed(ActionEvent e)
452 String curname = ((String) setName.getSelectedItem()).trim();
453 if (curname.length() > 0)
455 _storeCurrentPreset(curname);
456 lastParmSet = curname;
458 initArgSetModified();
462 // TODO: show warning
463 System.err.println("Invalid name. Not saved.");
467 protected void canceljob_actionPerformed(ActionEvent e)
472 frame.setVisible(false);
476 protected void startjob_actionPerformed(ActionEvent e)
481 frame.setVisible(false);
485 Jws2Instance service;
488 * list of service presets in the gui
490 Hashtable servicePresets = null;
493 * set if dialog is being set - so handlers will avoid spurious events
495 boolean settingDialog = false;
497 void initForService(Jws2Instance service, WsParamSetI jabap,
498 List<Argument> jabajobArgset)
500 WsParamSetI p = null;
501 List<ArgumentI> jobArgset = null;
502 settingDialog = true;
503 { // instantiate the abstract proxy for Jaba objects
504 jobArgset = jabajobArgset == null ? null : JabaParamStore
505 .getJwsArgsfromJaba(jabajobArgset);
506 p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
510 Hashtable exnames = new Hashtable();
511 for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
513 exnames.put((String) setName.getItemAt(i), setName.getItemAt(i));
515 servicePresets = new Hashtable();
516 // Add the default entry - if not present already.
517 if (!exnames.contains(SVC_DEF))
519 setName.addItem(SVC_DEF);
520 exnames.put(SVC_DEF, SVC_DEF);
521 servicePresets.put(SVC_DEF, SVC_DEF);
523 String curname = (p == null ? "" : p.getName());
524 for (WsParamSetI pr : paramStore.getPresets())
526 if (!pr.isModifiable())
528 servicePresets.put(pr.getName(), "preset");
533 if (!exnames.contains(pr.getName()))
535 setName.addItem(pr.getName());
538 // TODO: if initial jobArgset matches a given user setting or preset then
539 // should recover setting accordingly
540 // updateTable(p, jobArgset);
543 reInitDialog(p.getName());
544 initArgSetModified();
548 if (jobArgset != null && jobArgset.size() > 0)
550 curSetName = "Supplied Settings";
551 updateTable(p, jobArgset);
559 settingDialog = false;
563 @SuppressWarnings("unchecked")
564 private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
566 // populate table from default parameter set.
567 List<ArgumentI> args = paramStore.getServiceParameters();
569 // split to params and required arguments
572 for (ArgumentI myarg : args)
574 // Ideally, Argument would implement isRequired !
575 if (myarg instanceof ParameterI)
577 ParameterI parm = (ParameterI) myarg;
578 opanp.addParameter(parm).validate();
582 if (myarg instanceof OptionI)
584 OptionI opt = (OptionI) myarg;
585 OptionBox ob = opanp.addOption(opt);
587 if (MAX_OPTWIDTH < ob.getPreferredSize().width)
589 MAX_OPTWIDTH = ob.getPreferredSize().width;
592 cw+=ob.getPreferredSize().width+5;
596 System.err.println("Ignoring unknown service argument type "
597 + myarg.getClass().getName());
601 args = null; // no more args to process.
605 isUserPreset = false;
606 // initialise setname
607 setName.setSelectedItem(lastSetName = p.getName());
608 setDescr.setText(lastDescrText = p.getDescription());
612 args = p.getArguments();
613 } catch (Exception e)
617 // TODO: check if args should be unselected prior to resetting using the
622 if (lastParmSet == null)
624 isUserPreset = false;
625 // first call - so create a dummy name
627 setName.setSelectedItem(lastSetName = SVC_DEF);
631 if (jobArgset != null)
633 argSetModified(jobArgset, true);
636 // get setargs from current object
639 for (ArgumentI arg : args)
641 if (arg instanceof ParameterI)
643 opanp.setParameter((ParameterI) arg);
647 if (arg instanceof OptionI)
649 // System.out.println("Setting option "
650 // + System.identityHashCode(arg) + ":" + arg.getName()
651 // + " with " + arg.getDefaultValue());
652 opanp.selectOption((OptionI) arg, arg.getValue());
659 refreshParamLayout();
663 private boolean isModified()
665 return modifiedElements.size() > 0;
668 private Hashtable modifiedElements = new Hashtable();
671 * reset gui and modification state settings
673 private void initArgSetModified()
676 modifiedElements.clear();
677 updateButtonDisplay();
680 private void updateButtonDisplay()
682 boolean _update = false, _create = false, _delete = false, _revert = false;
683 if (modifiedElements.size() > 0)
687 _update = isUserPreset; // can only update user presets
688 if (!isUserPreset || modifiedElements.containsKey(setName))
690 // name modified - can create new preset
698 // can still delete a user preset
699 _delete = isUserPreset;
701 createpref.setVisible(_create);
702 updatepref.setVisible(_update);
703 deletepref.setVisible(_delete);
704 revertpref.setVisible(_revert);
708 public void argSetModified(Object modifiedElement, boolean b)
716 modifiedElements.remove(modifiedElement);
720 if (b && modifiedElement == setName
721 && modifiedElements.contains(modifiedElement))
723 // HACK! prevents iteration on makeSetNameValid
726 modifiedElements.put(modifiedElement, modifiedElement);
728 // set mod status based on presence of elements in table
729 if (b && modifiedElements.size() > 0)
731 makeSetNameValid(!isUserPreset);
732 SetNamePanel.revalidate();
734 updateButtonDisplay();
737 private boolean isServicePreset(String selectedItem)
739 return selectedItem.equals(SVC_DEF)
740 || servicePresets.containsKey(selectedItem);
744 * check if the current set name is a valid set name for saving, if not, then
747 private void makeSetNameValid(boolean newuserset)
749 boolean stn = settingDialog;
750 boolean renamed = false;
751 settingDialog = true;
752 String nm = (curSetName != null ? curSetName : (String) setName
754 // check if the name is reserved - if it is, rename it.
755 if (isServicePreset(nm))
764 while (paramStore.getPreset(tnm) != null)
766 tnm = nm + " (" + (++i) + ")";
775 boolean makeupdate = false;
776 // sync the gui with the preset database
777 for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
779 String snm = (String) setName.getItemAt(i);
783 // setName.setSelectedIndex(i);
788 setName.addItem(curSetName = nm);
789 setName.setSelectedItem(curSetName);
793 settingDialog = false; // we need this name change to be registered.
794 argSetModified(setName, renamed);
800 public void refreshParamLayout()
802 // optsAndparams.setPreferredSize(null);
803 FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
804 int sep=fl.getVgap();
806 int os=0,s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom+jobOptions.getBorder().getBorderInsets(jobOptions).top+2 * sep;
808 * final height for viewport
811 int panewidth = paramPane.getViewport().getSize().width-120-jobOptions.getBorder().getBorderInsets(jobOptions).left+jobOptions.getBorder().getBorderInsets(jobOptions).right;
813 int w = 2 * fl.getHgap() + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH : OptsAndParamsPage.PARAM_WIDTH);
814 int hgap=fl.getHgap(),cw=hgap;
816 if (opanp.getOptSet().size() > 0)
819 jobOptions.setLayout(new MigLayout("","", ""));
820 jobOptions.removeAll();
822 for (OptionBox pbox : opanp.getOptSet().values())
825 cw+=pbox.getSize().width+hgap;
826 if (cw+120>panewidth)
828 jobOptions.add(pbox, "wrap");
829 // System.out.println("Wrap on "+pbox.option.getName());
830 cw=hgap+pbox.getSize().width;
833 jobOptions.add(pbox);
837 finalh+=pbox.getSize().height+fl.getVgap();
841 jobOptions.revalidate();
845 jobOptions.setVisible(false);
848 // Now layout the parameters assuming they occupy one column - to calculate total height of options+parameters
849 fl = new FlowLayout(FlowLayout.LEFT);
850 // helpful hint from http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
851 fl.setAlignOnBaseline(true);
852 if (opanp.getParamSet().size() > 0)
854 paramList.removeAll();
855 paramList.setLayout(new MigLayout("","",""));
857 for (ParamBox pbox:opanp.getParamSet().values())
860 cw+=pbox.getSize().width+hgap;
861 if (cw+160>panewidth) {
862 paramList.add(pbox, "wrap");
863 cw=pbox.getSize().width+hgap;
870 finalh+=pbox.getSize().height+fl.getVgap();
876 for (ParamBox pbox : opanp.getParamSet().values())
879 s += sep + pbox.getPreferredSize().height+pbox.getBorder().getBorderInsets(pbox).bottom;
882 // paramList.setPreferredSize(new Dimension(w, s));
883 os+=s+2*sep+paramList.getBorder().getBorderInsets(paramList).bottom+paramList.getBorder().getBorderInsets(paramList).top;
885 paramList.revalidate();
889 paramList.setVisible(false);
891 // TODO: waste some time trying to eliminate any unnecessary .validate calls here
892 // System.out.println("Size will be : "+w+","+os);
893 // optsAndparams.setPreferredSize(null);
894 // paramPane.getViewport().setView(optsAndparams);
895 paramPane.getViewport().setAutoscrolls(true);
896 paramPane.revalidate();
901 * testing method - grab a service and parameter set and show the window
905 public static void main(String[] args)
907 jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
912 Vector<String> services = new Vector<String>();
913 services.addElement(args[p++]);
914 Jws2Discoverer.setServiceUrls(services);
919 } catch (Exception e)
921 System.err.println("Aborting. Problem discovering services.");
925 Jws2Instance lastserv = null;
926 for (Jws2Instance service : disc.getServices())
929 if (p >= args.length || service.serviceType.equalsIgnoreCase(args[p]))
931 if (lastserv != null)
933 List<Preset> prl = null;
935 if (++p < args.length)
937 PresetManager prman = lastserv.getPresets();
940 pr = prman.getPresetByName(args[p]);
943 // just grab the last preset.
944 prl = prman.getPresets();
950 PresetManager prman = lastserv.getPresets();
953 prl = prman.getPresets();
956 Iterator<Preset> en = (prl == null) ? null : prl.iterator();
957 while (en != null && en.hasNext())
968 System.out.println("Testing opts dupes for "
969 + lastserv.getUri() + " : "
970 + lastserv.getActionText() + ":" + pr.getName());
971 List<Option> rg = lastserv.getRunnerConfig().getOptions();
976 Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
977 } catch (Exception e)
979 System.err.println("Failed to copy " + o.getName());
983 System.err.println("Failed to copy " + o.getName());
989 System.out.println("Testing param dupes:");
990 List<Parameter> rg = lastserv.getRunnerConfig()
992 for (Parameter o : rg)
996 Parameter cpy = jalview.ws.jws2.ParameterUtils
998 } catch (Exception e)
1000 System.err.println("Failed to copy " + o.getName());
1001 e.printStackTrace();
1004 System.err.println("Failed to copy " + o.getName());
1005 e.printStackTrace();
1010 System.out.println("Testing param write:");
1011 List<String> writeparam = null, readparam = null;
1014 writeparam = jalview.ws.jws2.ParameterUtils
1016 pr.getArguments(lastserv.getRunnerConfig()),
1018 System.out.println("Testing param read :");
1019 List<Option> pset = jalview.ws.jws2.ParameterUtils
1020 .processParameters(writeparam,
1021 lastserv.getRunnerConfig(), " ");
1022 readparam = jalview.ws.jws2.ParameterUtils
1023 .writeParameterSet(pset, " ");
1024 Iterator<String> o = pr.getOptions().iterator(), s = writeparam
1025 .iterator(), t = readparam.iterator();
1026 boolean failed = false;
1027 while (s.hasNext() && t.hasNext())
1029 String on = o.next(), sn = s.next(), st = t.next();
1032 System.out.println("Original was " + on
1033 + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
1040 System.out.println("Original parameters:\n"
1042 System.out.println("Wrote parameters in first set:\n"
1044 System.out.println("Wrote parameters in second set:\n"
1048 } catch (Exception e)
1050 e.printStackTrace();
1053 WsJobParameters pgui = new WsJobParameters(lastserv,
1054 new JabaPreset(lastserv, pr));
1055 JFrame jf = new JFrame("Parameters for "
1056 + lastserv.getActionText());
1057 JPanel cont = new JPanel(new BorderLayout());
1059 cont.setPreferredSize(pgui.getPreferredSize());
1060 cont.add(pgui, BorderLayout.CENTER);
1061 jf.setLayout(new BorderLayout());
1062 jf.add(cont, BorderLayout.CENTER);
1064 final Thread thr = Thread.currentThread();
1065 jf.addWindowListener(new WindowListener()
1068 public void windowActivated(WindowEvent e)
1070 // TODO Auto-generated method stub
1074 public void windowClosed(WindowEvent e)
1078 public void windowClosing(WindowEvent e)
1084 public void windowDeactivated(WindowEvent e)
1086 // TODO Auto-generated method stub
1090 public void windowDeiconified(WindowEvent e)
1092 // TODO Auto-generated method stub
1096 public void windowIconified(WindowEvent e)
1098 // TODO Auto-generated method stub
1102 public void windowOpened(WindowEvent e)
1104 // TODO Auto-generated method stub
1109 jf.setVisible(true);
1110 boolean inter = false;
1115 Thread.sleep(10000);
1116 } catch (Exception e)
1129 public boolean isServiceDefaults()
1131 return (!isModified() && (lastParmSet != null && lastParmSet.equals(SVC_DEF)));
1133 public List<ArgumentI> getJobParams()
1135 return opanp.getCurrentSettings();
1138 String lastParmSet = null;
1141 * Hashtable<String, Object[]> editedParams = new Hashtable<String,
1144 * store the given parameters in the user parameter set database.
1146 * @param storeSetName - lastParmSet
1148 * @param descr - setDescr.getText()
1150 * @param jobParams - getJobParams()
1152 * private void _storeUserPreset(String storeSetName, String descr,
1153 * List<ArgumentI> jobParams) { // this is a simple hash store. Object[] pset;
1154 * editedParams.put(storeSetName, pset = new Object[3]); pset[0] =
1155 * storeSetName; pset[1] = descr; pset[2] = jobParams; // writeParam("Saving "
1156 * + storeSetName + ": ", jobParams); }
1158 * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
1159 * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
1160 * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
1162 * private Object[] _getUserPreset(String setName) { Object[] pset =
1163 * editedParams.get(setName); // if (pset != null) // writeParam("Retrieving "
1164 * + setName + ": ", (List<Argument>) pset[2]); return pset; }
1166 * * remove the given user preset from the preset stash
1170 * private void _deleteUserPreset(String setName) {
1171 * editedParams.remove(setName); }
1174 private void syncSetNamesWithStore()
1177 // remove any set names in the drop down menu that aren't either a reserved
1178 // setting, or a user defined or service preset.
1179 Vector items = new Vector();
1180 while (n < setName.getItemCount())
1182 String item = (String) setName.getItemAt(n);
1183 if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
1185 setName.removeItemAt(n);
1189 items.addElement(item);
1193 if (!items.contains(SVC_DEF))
1195 setName.addItem(SVC_DEF);
1197 for (WsParamSetI upn : paramStore.getPresets())
1199 if (!items.contains(upn.getName()))
1201 setName.addItem(upn.getName());
1207 * true if lastParmSet is a user preset
1209 boolean isUserPreset = false;
1211 private void reInitDialog(String nextPreset)
1213 settingDialog = true;
1214 // updateTable(null,null); // first reset to defaults
1215 WsParamSetI pset = null;
1216 if (nextPreset != null && nextPreset.length() > 0)
1218 pset = paramStore.getPreset(nextPreset);
1222 if (pset.isModifiable())
1224 isUserPreset = true;
1225 setDescr.setText(pset.getDescription());
1226 updateTable(null, pset.getArguments());
1227 lastParmSet = nextPreset;
1231 isUserPreset = false;
1232 setDescr.setText("");
1233 // must be a default preset from service
1234 updateTable(pset, null);
1235 lastParmSet = nextPreset;
1240 isUserPreset = false;
1242 setDescr.setText("");
1243 updateTable(null, null);
1244 lastParmSet = SVC_DEF;
1247 initArgSetModified();
1248 syncSetNamesWithStore();
1249 setName.setSelectedItem(lastParmSet);
1250 SetNamePanel.validate();
1252 settingDialog = false;
1256 String curSetName = null;
1258 public void itemStateChanged(ItemEvent e)
1260 if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
1262 final String setname = (String) setName.getSelectedItem();
1263 System.out.println("Item state changed for " + setname
1264 + " (handling ? " + !settingDialog + ")");
1270 if (setname == null)
1274 javax.swing.SwingUtilities.invokeLater(new Runnable()
1278 doPreferenceComboStateChange(setname);
1284 private void doPreferenceComboStateChange(String setname)
1286 // user has selected a different item from combo-box
1289 String lsetname = (curSetName != null) ? curSetName : lastParmSet;
1290 if (lsetname.equals(setname))
1292 // setname was just edited - so ignore this event.
1295 settingDialog = true;
1296 System.out.println("Prompting to save " + lsetname);
1297 if (javax.swing.JOptionPane
1302 + "' is modifed, and your changes will be lost.\nReally change preset ?",
1303 "Warning: Unsaved Changes",
1304 javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
1306 // revert the combobox to the current item
1307 settingDialog = true;
1308 setName.setSelectedItem(lsetname);
1309 settingDialog = false;
1312 // System.out.println("Saving for " + lsetname);
1313 // _storeCurrentPreset(lsetname);
1317 settingDialog = true;
1318 reInitDialog(setname);
1319 settingDialog = false;
1323 private void _renameExistingPreset(String oldName, String curSetName2)
1325 paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
1330 * store current settings as given name. You should then reset gui.
1332 * @param curSetName2
1334 private void _storeCurrentPreset(String curSetName2)
1336 paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
1339 private void _updatePreset(String lastParmSet2, String curname)
1341 paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(),
1347 * last saved name for this user preset
1349 String lastSetName = null;
1352 * last saved value of the description text for this user preset
1354 String lastDescrText = null;
1356 public void actionPerformed(ActionEvent e)
1358 if (e.getSource() instanceof Component)
1360 Component src = (Component) e.getSource();
1361 if (src.getParent() == setName)
1363 // rename any existing records we know about for this set.
1364 String newname = (String) e.getActionCommand().trim();
1366 if (isServicePreset(newname))
1368 final String oldname = curSetName != null ? curSetName
1370 final Component ourframe = this;
1371 settingDialog = true;
1372 setName.getEditor().setItem(oldname);
1373 settingDialog = false;
1374 javax.swing.SwingUtilities.invokeLater(new Runnable()
1378 JOptionPane.showMessageDialog(ourframe,
1379 "Invalid name - preset already exists.",
1380 "Invalid name", JOptionPane.WARNING_MESSAGE);
1386 curSetName = newname;
1387 System.err.println("New name for user setting " + curSetName
1388 + " (was " + setName.getSelectedItem() + ")");
1389 if (curSetName.equals(setName.getSelectedItem()))
1393 if (curSetName != null)
1395 argSetModified(setName, true);
1403 private void checkDescrModified()
1410 (lastDescrText == null ? setDescr.getText().trim().length() > 0
1411 : !setDescr.getText().equals(lastDescrText)));
1416 public void insertUpdate(DocumentEvent e)
1418 checkDescrModified();
1421 public void removeUpdate(DocumentEvent e)
1423 checkDescrModified();
1426 public void changedUpdate(DocumentEvent e)
1428 checkDescrModified();
1433 * @return null or the service preset selected by the user
1435 public WsParamSetI getPreset()
1437 if (isUserPreset || isModified()
1438 || (lastParmSet != null && lastParmSet.equals(SVC_DEF)))
1444 return paramStore.getPreset(lastParmSet);