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Coverage Report

  1. Project Clover database Wed May 27 2026 17:16:46 BST
  2. Package jalview.ws.jws2

File MsaWSClient.java

 

Coverage histogram

../../../img/srcFileCovDistChart5.png
43% of files have more coverage

Code metrics

40
97
15
1
411
300
40
0.41
6.47
15
2.67

Classes

Class Line # Actions
MsaWSClient 62 97 40
0.4736842247.4%
 

Contributing tests

This file is covered by 290 tests. .

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.ws.jws2;
22   
23    import jalview.datamodel.AlignmentI;
24    import jalview.datamodel.AlignmentView;
25    import jalview.gui.AlignFrame;
26    import jalview.gui.Desktop;
27    import jalview.gui.JvOptionPane;
28    import jalview.gui.JvSwingUtils;
29    import jalview.util.MessageManager;
30    import jalview.ws.WSMenuEntryProviderI;
31    import jalview.ws.api.JalviewServiceEndpointProviderI;
32    import jalview.ws.api.MultipleSequenceAlignmentI;
33    import jalview.ws.api.ServiceWithParameters;
34    import jalview.ws.gui.MsaWSThread;
35    import jalview.ws.params.ArgumentI;
36    import jalview.ws.params.WsParamSetI;
37   
38    import java.awt.event.ActionEvent;
39    import java.awt.event.ActionListener;
40    import java.awt.event.MouseAdapter;
41    import java.awt.event.MouseEvent;
42    import java.util.List;
43    import java.util.Locale;
44   
45    import javax.swing.JMenu;
46    import javax.swing.JMenuItem;
47    import javax.swing.ToolTipManager;
48   
49   
50    /**
51    * MsaWSClient
52    *
53    * Instantiates web service menu items for multiple alignment services, and
54    * holds logic for constructing a web service thread.
55    *
56    * TODO remove dependency on Jws2Client methods for creating AACon service UI
57    * elements.
58    *
59    * @author Jim Procter et al
60    * @version $Revision$
61    */
 
62    public class MsaWSClient extends Jws2Client implements WSMenuEntryProviderI
63    {
64    /**
65    * server is a proxy class implementing the core methods for submitting,
66    * monitoring and retrieving results from a multiple sequence alignment
67    * service
68    */
69    MultipleSequenceAlignmentI server;
70   
 
71  0 toggle public MsaWSClient(ServiceWithParameters sh, String altitle,
72    jalview.datamodel.AlignmentView msa, boolean submitGaps,
73    boolean preserveOrder, AlignmentI seqdataset,
74    AlignFrame _alignFrame)
75    {
76  0 this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
77    seqdataset, _alignFrame);
78    // TODO Auto-generated constructor stub
79    }
80   
 
81  0 toggle public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
82    String altitle,
83    jalview.datamodel.AlignmentView msa, boolean submitGaps,
84    boolean preserveOrder, AlignmentI seqdataset,
85    AlignFrame _alignFrame)
86    {
87  0 this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
88    seqdataset, _alignFrame);
89    // TODO Auto-generated constructor stub
90    }
91   
92    /**
93    * Creates a new MsaWSClient object that uses a service given by an externally
94    * retrieved ServiceHandle
95    *
96    * @param sh
97    * service handle of type AbstractName(MsaWS)
98    * @param altitle
99    * DOCUMENT ME!
100    * @param msa
101    * DOCUMENT ME!
102    * @param submitGaps
103    * DOCUMENT ME!
104    * @param preserveOrder
105    * DOCUMENT ME!
106    */
107   
 
108  0 toggle public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
109    List<ArgumentI> arguments, boolean editParams, String altitle,
110    jalview.datamodel.AlignmentView msa, boolean submitGaps,
111    boolean preserveOrder, AlignmentI seqdataset,
112    AlignFrame _alignFrame)
113    {
114  0 super(_alignFrame, preset, arguments);
115  0 processParams(sh, editParams).thenAccept((startJob) -> {
116  0 if (!startJob)
117  0 return;
118   
119  0 if (!(sh instanceof JalviewServiceEndpointProviderI
120    && ((JalviewServiceEndpointProviderI) sh)
121    .getEndpoint() instanceof MultipleSequenceAlignmentI))
122    {
123    // redundant at mo - but may change
124  0 JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
125    MessageManager.formatMessage(
126    "label.service_called_is_not_msa_service",
127    new String[]
128    { sh.getName() }),
129    MessageManager.getString("label.internal_jalview_error"),
130    JvOptionPane.WARNING_MESSAGE);
131   
132  0 return;
133    }
134  0 serviceHandle = sh;
135  0 server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh)
136    .getEndpoint();
137  0 if ((wsInfo = setWebService(sh, false)) == null)
138    {
139  0 JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager
140    .formatMessage("label.msa_service_is_unknown", new String[]
141    { sh.getName() }),
142    MessageManager.getString("label.internal_jalview_error"),
143    JvOptionPane.WARNING_MESSAGE);
144   
145  0 return;
146    }
147   
148  0 startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
149    });
150   
151    }
152   
 
153  14090 toggle public MsaWSClient()
154    {
155  14090 super();
156    // add a class reference to the list
157    }
158   
 
159  0 toggle private void startMsaWSClient(String altitle, AlignmentView msa,
160    boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
161    {
162    // if (!locateWebService())
163    // {
164    // return;
165    // }
166   
167  0 wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
168    + " of " + altitle + "\nJob details\n");
169  0 String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
170  0 if (jobtitle.endsWith("alignment"))
171    {
172  0 if (submitGaps && (!jobtitle.endsWith("realignment")
173    || jobtitle.indexOf("profile") == -1))
174    {
175  0 int pos = jobtitle.indexOf("alignment");
176  0 jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
177    + altitle;
178    }
179    else
180    {
181  0 jobtitle = WebServiceName + " of " + altitle;
182    }
183    }
184    else
185    {
186  0 jobtitle = WebServiceName + (submitGaps ? " re" : " ")
187    + "alignment of " + altitle;
188    }
189   
190  0 MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL,
191    wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps,
192    preserveOrder, seqdataset);
193  0 if (msathread.hasValidInput())
194    {
195  0 wsInfo.setthisService(msathread);
196  0 wsInfo.setVisible(true);
197  0 msathread.start();
198    }
199    else
200    {
201  0 wsInfo.setVisible(false);
202  0 JvOptionPane.showMessageDialog(alignFrame,
203    MessageManager.getString("info.invalid_msa_input_mininfo"),
204    MessageManager.getString("info.invalid_msa_notenough"),
205    JvOptionPane.INFORMATION_MESSAGE);
206    }
207    }
208   
 
209  0 toggle protected String getServiceActionKey()
210    {
211  0 return "MsaWS";
212    }
213   
 
214  0 toggle protected String getServiceActionDescription()
215    {
216  0 return "Multiple Sequence Alignment";
217    }
218   
219    /**
220    * look at ourselves and work out if we are a service that can take a profile
221    * and align to it
222    *
223    * @return true if we can send gapped sequences to the alignment service
224    */
 
225  28180 toggle private boolean canSubmitGaps()
226    {
227    // TODO: query service or extract service handle props to check if we can
228    // realign
229  28180 return (WebServiceName.indexOf("lustal") > -1); // cheat!
230    }
231   
 
232  14090 toggle @Override
233    public void attachWSMenuEntry(JMenu rmsawsmenu,
234    final ServiceWithParameters service, final AlignFrame alignFrame)
235    {
236  14090 if (Jws2ClientFactory.registerAAConWSInstance(rmsawsmenu,
237    service, alignFrame))
238    {
239    // Alignment dependent analysis calculation WS gui
240  0 return;
241    }
242  14090 serviceHandle = service;
243  14090 setWebService(service, true); // headless
244  14090 attachWSMenuEntry(rmsawsmenu, alignFrame);
245    }
246   
 
247  14090 toggle @Override
248    public void attachWSMenuEntry(JMenu wsmenu, AlignFrame alignFrame)
249    {
250  14090 boolean finished = true, submitGaps = false;
251    /**
252    * temp variables holding msa service submenu or root service menu
253    */
254  14090 JMenu msawsmenu = wsmenu;
255  14090 JMenu rmsawsmenu = wsmenu;
256  14090 String svcname = WebServiceName;
257  14090 if (svcname.endsWith("WS"))
258    {
259  14090 svcname = svcname.substring(0, svcname.length() - 2);
260    }
261  14090 String calcName = svcname + " ";
262  14090 if (canSubmitGaps())
263    {
264  3022 msawsmenu = new JMenu(svcname);
265  3022 rmsawsmenu.add(msawsmenu);
266  3022 calcName = "";
267    }
268  14090 boolean hasparams = serviceHandle.hasParameters();
269  14090 ServiceWithParameters service = (ServiceWithParameters) serviceHandle;
270  14090 do
271    {
272  17112 String action = "Align ";
273  17112 if (submitGaps == true)
274    {
275  3022 action = "Realign ";
276  3022 msawsmenu = new JMenu(MessageManager
277    .formatMessage("label.realign_with_params", new String[]
278    { svcname }));
279  3022 msawsmenu.setToolTipText(MessageManager
280    .getString("label.align_sequences_to_existing_alignment"));
281  3022 rmsawsmenu.add(msawsmenu);
282    }
283  17112 final boolean withGaps = submitGaps;
284   
285  17112 JMenuItem method = new JMenuItem(MessageManager.formatMessage(
286    "label.calcname_with_default_settings", new String[]
287    { calcName }));
288  17112 method.setToolTipText(MessageManager.formatMessage(
289    "label.action_with_default_settings", new String[]
290    { action }));
291   
292  17112 method.addActionListener(new ActionListener()
293    {
 
294  0 toggle @Override
295    public void actionPerformed(ActionEvent e)
296    {
297  0 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
298   
299  0 if (msa != null)
300    {
301  0 new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
302    true,
303    alignFrame.getViewport().getAlignment().getDataset(),
304    alignFrame);
305    }
306   
307    }
308    });
309  17112 msawsmenu.add(method);
310  17112 if (hasparams)
311    {
312    // only add these menu options if the service has user-modifiable
313    // arguments
314  17106 method = new JMenuItem(
315    MessageManager.getString("label.edit_settings_and_run"));
316  17106 method.setToolTipText(MessageManager.getString(
317    "label.view_and_change_parameters_before_alignment"));
318   
319  17106 method.addActionListener(new ActionListener()
320    {
 
321  0 toggle @Override
322    public void actionPerformed(ActionEvent e)
323    {
324  0 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
325  0 if (msa != null)
326    {
327  0 new MsaWSClient(service, null, null, true,
328    alignFrame.getTitle(), msa, withGaps, true,
329    alignFrame.getViewport().getAlignment().getDataset(),
330    alignFrame);
331    }
332   
333    }
334    });
335  17106 msawsmenu.add(method);
336  17106 List<WsParamSetI> presets = service.getParamStore().getPresets();
337  17106 if (presets != null && presets.size() > 0)
338    {
339  12205 JMenu presetlist = new JMenu(MessageManager.formatMessage(
340    "label.run_with_preset_params", new String[]
341    { calcName }));
342   
343  12205 final int showToolTipFor = ToolTipManager.sharedInstance()
344    .getDismissDelay();
345  12205 for (final WsParamSetI preset : presets)
346    {
347  45666 final JMenuItem methodR = new JMenuItem(preset.getName());
348  45666 final int QUICK_TOOLTIP = 1500;
349    // JAL-1582 shorten tooltip display time in these menu items as
350    // they can obscure other options
351  45666 methodR.addMouseListener(new MouseAdapter()
352    {
 
353  0 toggle @Override
354    public void mouseEntered(MouseEvent e)
355    {
356  0 ToolTipManager.sharedInstance()
357    .setDismissDelay(QUICK_TOOLTIP);
358    }
359   
 
360  0 toggle @Override
361    public void mouseExited(MouseEvent e)
362    {
363  0 ToolTipManager.sharedInstance()
364    .setDismissDelay(showToolTipFor);
365    }
366   
367    });
368  45666 String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
369  45666 + (preset.isModifiable()
370    ? MessageManager.getString("label.user_preset")
371    : MessageManager
372    .getString("label.service_preset"))
373    + "</strong><br/>" + preset.getDescription());
374  45666 methodR.setToolTipText(tooltip);
375  45666 methodR.addActionListener(new ActionListener()
376    {
 
377  0 toggle @Override
378    public void actionPerformed(ActionEvent e)
379    {
380  0 AlignmentView msa = alignFrame
381    .gatherSequencesForAlignment();
382   
383  0 if (msa != null)
384    {
385  0 MsaWSClient msac = new MsaWSClient(service, preset,
386    alignFrame.getTitle(), msa, false, true,
387    alignFrame.getViewport().getAlignment()
388    .getDataset(),
389    alignFrame);
390    }
391   
392    }
393   
394    });
395  45666 presetlist.add(methodR);
396    }
397  12205 msawsmenu.add(presetlist);
398    }
399    }
400  17112 if (!submitGaps && canSubmitGaps())
401    {
402  3022 submitGaps = true;
403  3022 finished = false;
404    }
405    else
406    {
407  14090 finished = true;
408    }
409  17112 } while (!finished);
410    }
411    }
  • Report generated by OpenClover v 4.4.1 on Wed May 27 2026 17:25:30 BST using coverage data from Wed May 27 2026 17:25:18 BST.
  • OpenClover is free and open-source software.