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Coverage Report

  1. Project Clover database Wed Sep 17 2025 10:52:37 BST
  2. Package jalview.gui

File WsPreferences.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

78
211
35
3
702
538
89
0.42
6.03
11.67
2.54

Classes

Class Line # Actions
WsPreferences 47 185 77
0.00%
WsPreferences.JabaWSStatusRenderer 135 18 5
0.00%
WsPreferences.WsUrlTableModel 187 8 7
0.00%
 

Contributing tests

No tests hitting this source file were found.

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.gui;
22   
23    import java.awt.BorderLayout;
24    import java.awt.Color;
25    import java.awt.Component;
26    import java.awt.Dimension;
27    import java.awt.event.ActionEvent;
28    import java.awt.event.ActionListener;
29    import java.net.URL;
30    import java.util.List;
31    import java.util.Vector;
32   
33    import javax.swing.JLabel;
34    import javax.swing.JPanel;
35    import javax.swing.JTable;
36    import javax.swing.JTextField;
37    import javax.swing.SwingUtilities;
38    import javax.swing.table.AbstractTableModel;
39    import javax.swing.table.TableCellRenderer;
40   
41    import jalview.bin.Cache;
42    import jalview.jbgui.GWsPreferences;
43    import jalview.util.MessageManager;
44    import jalview.ws.jws2.Jws2Discoverer;
45    import jalview.ws.rest.RestServiceDescription;
46   
 
47    public class WsPreferences extends GWsPreferences
48    {
49   
 
50  0 toggle public WsPreferences()
51    {
52  0 super();
53  0 initFromPreferences();
54    }
55   
56    List<String> wsUrls;
57   
58    Vector<String> oldUrls, rsbsUrls, oldRsbsUrls;
59   
60    private boolean needWsMenuUpdate;
61   
62    private boolean oldJws1, oldJws2, oldIndexByHost, oldIndexByType,
63    oldEnfin, oldWsWarning;
64   
 
65  0 toggle private void initFromPreferences()
66    {
67   
68  0 wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
69  0 if (!wsUrls.isEmpty())
70    {
71  0 oldUrls = new Vector<String>(wsUrls);
72    }
73    else
74    {
75  0 oldUrls = null;
76  0 wsUrls = new Vector<String>();
77    }
78  0 wsList.setDefaultRenderer(Integer.class, new JabaWSStatusRenderer());
79  0 wsList.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
80  0 updateList();
81  0 rsbsUrls = jalview.ws.rest.RestClient.getRsbsDescriptions();
82  0 if (rsbsUrls != null)
83    {
84  0 oldRsbsUrls = new Vector<String>(rsbsUrls);
85    }
86    else
87    {
88  0 oldRsbsUrls = null;
89  0 rsbsUrls = new Vector<String>();
90    }
91  0 updateRsbsList();
92  0 enableEnfinServices.setSelected(
93    oldEnfin = Cache.getDefault("SHOW_ENFIN_SERVICES", true));
94  0 enableEnfinServices.addActionListener(updateAction);
95  0 enableJws2Services.setSelected(
96    oldJws2 = Cache.getDefault("SHOW_JWS2_SERVICES", true));
97  0 enableJws2Services.addActionListener(updateAction);
98  0 indexByHost.setSelected(
99    oldIndexByHost = Cache.getDefault("WSMENU_BYHOST", false));
100  0 indexByHost.addActionListener(updateAction);
101  0 indexByType.setSelected(
102    oldIndexByType = Cache.getDefault("WSMENU_BYTYPE", false));
103  0 indexByType.addActionListener(updateAction);
104  0 displayWsWarning.setSelected(oldWsWarning = Cache
105    .getDefault("SHOW_WSDISCOVERY_ERRORS", true));
106    }
107   
108    ActionListener updateAction = new ActionListener()
109    {
110   
 
111  0 toggle @Override
112    public void actionPerformed(ActionEvent e)
113    {
114  0 update++;
115    }
116   
117    };
118   
 
119  0 toggle private void updateList()
120    {
121  0 Object tdat[][] = new Object[wsUrls.size()][2];
122  0 int r = 0;
123  0 for (String url : wsUrls)
124    {
125  0 int status = Jws2Discoverer.getDiscoverer().getServerStatusFor(url);
126  0 tdat[r][1] = Integer.valueOf(status);
127  0 tdat[r++][0] = url;
128    }
129   
130  0 wsList.setModel(new WsUrlTableModel(tdat));
131  0 wsList.getColumn(MessageManager.getString("label.status"))
132    .setMinWidth(10);
133    }
134   
 
135    private class JabaWSStatusRenderer extends JPanel
136    implements TableCellRenderer
137    {
 
138  0 toggle public JabaWSStatusRenderer()
139    {
140  0 setOpaque(true);
141  0 setMinimumSize(new Dimension(10, 10));
142    // setText(" ");
143   
144    }
145   
146    /**
147    * render an Integer reflecting service status as a colour and symbol
148    */
149   
 
150  0 toggle @Override
151    public Component getTableCellRendererComponent(JTable arg0,
152    Object status, boolean isSelected, boolean hasFocus, int row,
153    int column)
154    {
155  0 Color c;
156  0 String t = new String("");
157  0 switch (((Integer) status).intValue())
158    {
159  0 case 1:
160    // cb.setSelected(true);
161    // cb.setBackground(
162  0 c = Color.green;
163  0 break;
164  0 case 0:
165    // cb.setSelected(true);
166    // cb.setBackground(
167  0 c = Color.lightGray;
168  0 break;
169  0 case -1:
170    // cb.setSelected(false);
171    // cb.setBackground(
172  0 c = Color.red;
173  0 break;
174  0 default:
175    // cb.setSelected(false);
176    // cb.setBackground(
177  0 c = Color.orange;
178    }
179  0 setBackground(c);
180    // setText(t);
181  0 return this;
182   
183    }
184   
185    }
186   
 
187    private class WsUrlTableModel extends AbstractTableModel
188    {
189   
190    private Object[][] data;
191   
192    private String[] columnNames = new String[] {
193    MessageManager.getString("label.service_url"),
194    MessageManager.getString("label.status") };
195   
 
196  0 toggle public WsUrlTableModel(Object[][] tdat)
197    {
198  0 this.data = tdat;
199    }
200   
 
201  0 toggle @Override
202    public int getColumnCount()
203    {
204  0 return 2;
205    }
206   
 
207  0 toggle @Override
208    public String getColumnName(int column)
209    {
210  0 return columnNames[column];
211    }
212   
 
213  0 toggle @Override
214    public int getRowCount()
215    {
216  0 if (data == null)
217    {
218  0 return 0;
219    }
220  0 return data.length;
221    }
222   
 
223  0 toggle @Override
224    public java.lang.Class<?> getColumnClass(int columnIndex)
225    {
226  0 return getValueAt(0, columnIndex).getClass();
227    };
228   
 
229  0 toggle @Override
230    public Object getValueAt(int rowIndex, int columnIndex)
231    {
232  0 return data[rowIndex][columnIndex];
233    }
234   
235    }
236   
 
237  0 toggle private void updateRsbsList()
238    {
239  0 sbrsList.setListData(rsbsUrls);
240    }
241   
 
242  0 toggle private void updateServiceList()
243    {
244  0 Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
245    }
246   
 
247  0 toggle private void updateRsbsServiceList()
248    {
249  0 jalview.ws.rest.RestClient.setRsbsServices(rsbsUrls);
250    }
251   
252    /*
253    * (non-Javadoc)
254    *
255    * @see
256    * jalview.jbgui.GWsPreferences#deleteWsUrl_actionPerformed(java.awt.event
257    * .ActionEvent)
258    */
 
259  0 toggle @Override
260    protected void deleteWsUrl_actionPerformed(ActionEvent e)
261    {
262  0 int sel = wsList.getSelectedRow();
263  0 if (sel > -1)
264    {
265  0 wsUrls.remove(sel);
266  0 update++;
267  0 updateList();
268    }
269    }
270   
271    /*
272    * (non-Javadoc)
273    *
274    * @see jalview.jbgui.GWsPreferences#editWsUrl_actionPerformed(java.awt.event.
275    * ActionEvent)
276    */
 
277  0 toggle @Override
278    protected void editWsUrl_actionPerformed(ActionEvent e)
279    {
280  0 int sel = wsList.getSelectedRow();
281  0 if (sel > -1)
282    {
283  0 String url = editUrl(wsUrls.get(sel),
284    MessageManager.getString("label.edit_jabaws_url"));
285  0 if (url != null)
286    {
287  0 int present = wsUrls.indexOf(url);
288  0 if (present == -1)
289    {
290  0 update++;
291  0 wsUrls.set(sel, url);
292  0 updateList();
293    }
294    else
295    {
296  0 if (present != sel)
297    {
298  0 wsUrls.remove(sel);
299  0 updateList();
300    }
301    }
302    }
303    }
304    }
305   
 
306  0 toggle @Override
307    protected void newSbrsUrl_actionPerformed(ActionEvent e)
308    {
309  0 RestServiceEditorPane rse = new RestServiceEditorPane();
310  0 rse.showDialog(MessageManager.getString("label.add_new_sbrs_service"));
311  0 String rservice = rse.getEditedRestService();
312  0 if (rservice != null && !rsbsUrls.contains(rservice))
313    {
314  0 rsbsUrls.add(rservice);
315  0 update++;
316  0 updateRsbsList();
317    }
318    }
319   
 
320  0 toggle @Override
321    protected void editSbrsUrl_actionPerformed(ActionEvent e)
322    {
323  0 int sel = sbrsList.getSelectedIndex();
324  0 if (sel > -1)
325    {
326  0 RestServiceEditorPane rse = new RestServiceEditorPane(
327    new RestServiceDescription(rsbsUrls.elementAt(sel)));
328  0 rse.showDialog(MessageManager.getString("label.edit_sbrs_entry"));
329  0 String rservice = rse.getEditedRestService();
330  0 if (rservice != null)
331    {
332  0 int present = rsbsUrls.indexOf(rservice);
333  0 if (present == -1)
334    {
335  0 update++;
336  0 rsbsUrls.setElementAt(rservice, sel);
337  0 updateRsbsList();
338    }
339    else
340    {
341  0 if (present != sel)
342    {
343  0 rsbsUrls.removeElementAt(sel);
344  0 update++;
345  0 updateRsbsList();
346    }
347    }
348    }
349    }
350    }
351   
 
352  0 toggle void updateWsMenuConfig(boolean old)
353    {
354  0 if (old)
355    {
356  0 if (oldUrls != wsUrls || (wsUrls != null && oldUrls != null
357    && !wsUrls.equals(oldUrls)))
358    {
359  0 update++;
360    }
361  0 wsUrls = (oldUrls == null) ? null : new Vector(oldUrls);
362  0 if (oldRsbsUrls != rsbsUrls || (rsbsUrls != null
363    && oldRsbsUrls != null && !oldRsbsUrls.equals(rsbsUrls)))
364    {
365  0 update++;
366    }
367  0 oldRsbsUrls = (oldRsbsUrls == null) ? null : new Vector(oldRsbsUrls);
368    }
369    else
370    {
371   
372    }
373  0 Cache.setProperty("SHOW_ENFIN_SERVICES",
374    Boolean.valueOf(
375  0 old ? oldEnfin : enableEnfinServices.isSelected())
376    .toString());
377  0 Cache.setProperty("SHOW_JWS2_SERVICES",
378  0 Boolean.valueOf(old ? oldJws2 : enableJws2Services.isSelected())
379    .toString());
380  0 Cache.setProperty("WSMENU_BYHOST",
381  0 Boolean.valueOf(old ? oldIndexByHost : indexByHost.isSelected())
382    .toString());
383  0 Cache.setProperty("WSMENU_BYTYPE",
384  0 Boolean.valueOf(old ? oldIndexByType : indexByType.isSelected())
385    .toString());
386   
387  0 Cache.setProperty("SHOW_WSDISCOVERY_ERRORS",
388    Boolean.valueOf(
389  0 old ? oldWsWarning : displayWsWarning.isSelected())
390    .toString());
391  0 updateServiceList();
392  0 updateRsbsServiceList();
393    }
394   
395    /*
396    * (non-Javadoc)
397    *
398    * @see
399    * jalview.jbgui.GWsPreferences#moveWsUrlDown_actionPerformed(java.awt.event
400    * .ActionEvent)
401    */
 
402  0 toggle @Override
403    protected void moveWsUrlDown_actionPerformed(ActionEvent e)
404    {
405  0 int p = wsList.getSelectedRow();
406  0 if (p > -1 && p < wsUrls.size() - 1)
407    {
408  0 String t = wsUrls.get(p + 1);
409  0 wsUrls.set(p + 1, wsUrls.get(p));
410  0 wsUrls.set(p, t);
411  0 updateList();
412  0 wsList.getSelectionModel().setSelectionInterval(p + 1, p + 1);
413  0 update++;
414    }
415    }
416   
417    /*
418    * (non-Javadoc)
419    *
420    * @see
421    * jalview.jbgui.GWsPreferences#moveWsUrlUp_actionPerformed(java.awt.event
422    * .ActionEvent)
423    */
 
424  0 toggle @Override
425    protected void moveWsUrlUp_actionPerformed(ActionEvent e)
426    {
427  0 int p = wsList.getSelectedRow();
428  0 if (p > 0)
429    {
430  0 String t = wsUrls.get(p - 1);
431  0 wsUrls.set(p - 1, wsUrls.get(p));
432  0 wsUrls.set(p, t);
433  0 updateList();
434  0 wsList.getSelectionModel().setSelectionInterval(p - 1, p - 1);
435  0 update++;
436    }
437    }
438   
 
439  0 toggle private String editUrl(String initUrl, String title)
440    {
441  0 String url = initUrl;
442  0 URL foo = null;
443  0 if (url == null)
444    {
445  0 url = "";
446    }
447  0 JTextField urltf = new JTextField(url, 40);
448  0 JPanel panel = new JPanel(new BorderLayout());
449  0 JPanel pane12 = new JPanel(new BorderLayout());
450  0 pane12.add(new JLabel(MessageManager.getString("label.url:")),
451    BorderLayout.CENTER);
452  0 pane12.add(urltf, BorderLayout.EAST);
453  0 panel.add(pane12, BorderLayout.NORTH);
454  0 boolean valid = false;
455  0 int resp = JvOptionPane.CANCEL_OPTION;
456  0 while (!valid && (resp = JvOptionPane.showInternalConfirmDialog(
457    Desktop.desktop, panel, title,
458    JvOptionPane.OK_CANCEL_OPTION)) == JvOptionPane.OK_OPTION)
459    {
460  0 try
461    {
462    // TODO: do a better job of checking that the url is a valid discovery
463    // URL for web services.
464  0 String tx = urltf.getText().trim();
465  0 while (tx.length() > 0 && tx.lastIndexOf('/') == tx.length() - 1)
466    {
467  0 tx = tx.substring(0, tx.length() - 1);
468    }
469  0 foo = new URL(tx);
470  0 valid = true;
471  0 urltf.setText(tx);
472    } catch (Exception e)
473    {
474  0 valid = false;
475  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
476    MessageManager.getString("label.invalid_url"));
477    }
478    }
479  0 if (valid && resp == JvOptionPane.OK_OPTION)
480    {
481  0 int validate = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
482    MessageManager.getString("info.validate_jabaws_server"),
483    MessageManager.getString("label.test_server"),
484    JvOptionPane.YES_NO_OPTION);
485   
486  0 if (validate == JvOptionPane.OK_OPTION)
487    {
488  0 if (Jws2Discoverer.testServiceUrl(foo))
489    {
490  0 return foo.toString();
491    }
492    else
493    {
494  0 int opt = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
495    "The Server '" + foo.toString()
496    + "' failed validation,\ndo you want to add it anyway? ",
497    "Server Validation Failed", JvOptionPane.YES_NO_OPTION,
498    JvOptionPane.INFORMATION_MESSAGE, null, null, null);
499  0 if (opt == JvOptionPane.YES_OPTION)
500    {
501  0 return foo.toString();
502    }
503    else
504    {
505  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
506    MessageManager.getString(
507    "warn.server_didnt_pass_validation"));
508    }
509   
510    }
511    }
512    else
513    {
514    // just return the URL anyway
515  0 return foo.toString();
516    }
517    }
518  0 return initUrl;
519    }
520   
521    /*
522    * (non-Javadoc)
523    *
524    * @see jalview.jbgui.GWsPreferences#newWsUrl_actionPerformed(java.awt.event.
525    * ActionEvent)
526    */
 
527  0 toggle @Override
528    protected void newWsUrl_actionPerformed(ActionEvent e)
529    {
530  0 String url = editUrl(null,
531    MessageManager.getString("label.add_jabaws_url"));
532  0 if (url != null)
533    {
534  0 if (!wsUrls.contains(url))
535    {
536  0 int selind = wsList.getSelectedRow();
537  0 if (selind > -1)
538    {
539  0 wsUrls.add(selind, url);
540    }
541    else
542    {
543  0 wsUrls.add(url);
544    }
545  0 update++;
546  0 updateList();
547    }
548    }
549    }
550   
551    /*
552    * (non-Javadoc)
553    *
554    * @see jalview.jbgui.GWsPreferences#refreshWs_actionPerformed(java.awt.event.
555    * ActionEvent)
556    */
 
557  0 toggle @Override
558    protected void refreshWs_actionPerformed(ActionEvent e)
559    {
560  0 new Thread(new Runnable()
561    {
562   
 
563  0 toggle @Override
564    public void run()
565    {
566    // force a refresh.
567  0 lastrefresh = update - 1;
568  0 updateWsMenuConfig(false);
569  0 refreshWsMenu(true);
570    }
571    }).start();
572   
573    }
574   
575    /**
576    * Refresh the web services menus - but only if there has been a change in the
577    * configuration (indicated by update!=lastrefresh)
578    *
579    * @param showProgress
580    * show progress in dialog or on desktop
581    */
 
582  0 toggle protected void refreshWsMenu(boolean showProgress)
583    {
584  0 if (showProgress)
585    {
586  0 new Thread(new Runnable()
587    {
588   
 
589  0 toggle @Override
590    public void run()
591    {
592  0 SwingUtilities.invokeLater(new Runnable()
593    {
 
594  0 toggle @Override
595    public void run()
596    {
597   
598  0 progressBar.setVisible(true);
599  0 validate();
600  0 progressBar.setIndeterminate(true);
601   
602    }
603    });
604  0 if (lastrefresh != update)
605    {
606  0 lastrefresh = update;
607  0 Desktop.instance.startServiceDiscovery(true); // wait around for all
608    // threads to complete
609  0 updateList();
610   
611    }
612  0 SwingUtilities.invokeLater(new Runnable()
613    {
 
614  0 toggle @Override
615    public void run()
616    {
617   
618  0 progressBar.setIndeterminate(false);
619  0 progressBar.setVisible(false);
620  0 validate();
621   
622    }
623    });
624   
625    }
626    }).start();
627    }
628    else
629    {
630  0 new Thread(new Runnable()
631    {
632   
 
633  0 toggle @Override
634    public void run()
635    {
636  0 long ct = System.currentTimeMillis();
637  0 Desktop.instance.setProgressBar(MessageManager
638    .getString("status.refreshing_web_service_menus"), ct);
639  0 if (lastrefresh != update)
640    {
641  0 lastrefresh = update;
642  0 Desktop.instance.startServiceDiscovery(true);
643  0 updateList();
644    }
645  0 Desktop.instance.setProgressBar(null, ct);
646    }
647   
648    }).start();
649    }
650    }
651   
652    /**
653    * state counters for ensuring that updates only happen if config has changed.
654    */
655    protected long update = 0;
656   
657    private long lastrefresh = 0;
658   
659    /*
660    * (non-Javadoc)
661    *
662    * @see
663    * jalview.jbgui.GWsPreferences#resetWs_actionPerformed(java.awt.event.ActionEvent
664    * )
665    */
 
666  0 toggle @Override
667    protected void resetWs_actionPerformed(ActionEvent e)
668    {
669  0 Jws2Discoverer.getDiscoverer().setServiceUrls(null);
670  0 List<String> nwsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
671  0 if (!wsUrls.equals(nwsUrls))
672    {
673  0 update++;
674    }
675  0 wsUrls = nwsUrls;
676  0 updateList();
677   
678  0 updateAndRefreshWsMenuConfig(true);
679    }
680   
 
681  0 toggle protected void ok_ActionPerformed(ActionEvent e)
682    {
683    // update everything regardless.
684  0 updateAndRefreshWsMenuConfig(false);
685    }
686   
 
687  0 toggle public void updateAndRefreshWsMenuConfig(
688    final boolean showProgressInDialog)
689    {
690  0 new Thread(new Runnable()
691    {
692   
 
693  0 toggle @Override
694    public void run()
695    {
696  0 updateWsMenuConfig(false);
697  0 refreshWsMenu(showProgressInDialog);
698    }
699    }).start();
700   
701    }
702    }
  • Report generated by OpenClover v 4.4.1 on Wed Sep 17 2025 11:01:30 BST using coverage data from Wed Sep 17 2025 11:01:17 BST.
  • OpenClover is free and open-source software.