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Coverage Report

  1. Project Clover database Wed Jan 14 2026 14:33:33 GMT
  2. Package jalview.ws.jws2

File SequenceAnnotationWSClient.java

 

Coverage histogram

../../../img/srcFileCovDistChart3.png
52% of files have more coverage

Code metrics

30
73
10
1
300
221
29
0.4
7.3
10
2.9

Classes

Class Line # Actions
SequenceAnnotationWSClient 46 73 29
0.2654867226.5%
 

Contributing tests

This file is covered by 143 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.api.AlignCalcWorkerI;
24    import jalview.gui.AlignFrame;
25    import jalview.gui.Desktop;
26    import jalview.gui.JvSwingUtils;
27    import jalview.util.MessageManager;
28    import jalview.ws.api.ServiceWithParameters;
29    import jalview.ws.params.AutoCalcSetting;
30    import jalview.ws.params.WsParamSetI;
31    import jalview.ws.uimodel.AlignAnalysisUIText;
32   
33    import java.awt.event.ActionEvent;
34    import java.awt.event.ActionListener;
35    import java.util.List;
36    import java.util.Locale;
37   
38   
39    import javax.swing.JMenu;
40    import javax.swing.JMenuItem;
41   
42    /**
43    * @author jprocter
44    *
45    */
 
46    public class SequenceAnnotationWSClient extends Jws2Client
47    {
48    /**
49    * initialise a client so its attachWSMenuEntry method can be called.
50    */
 
51  10347 toggle public SequenceAnnotationWSClient()
52    {
53    // TODO Auto-generated constructor stub
54    }
55   
 
56  0 toggle public SequenceAnnotationWSClient(final ServiceWithParameters sh,
57    AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
58    {
59  0 super(alignFrame, preset, null);
60  0 initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
61    }
62   
63    // dan think. Do I need to change this method to run RNAalifold through the
64    // GUI
65   
 
66  0 toggle private void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
67    AlignFrame alignFrame, final WsParamSetI preset, boolean editParams)
68    {
69    // dan changed! dan test. comment out if conditional
70    // if (alignFrame.getViewport().getAlignment().isNucleotide())
71    // {
72    // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
73    // + " can only be used\nfor amino acid alignments.",
74    // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
75    // return;
76    //
77    // }
78  0 AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
79  0 if (aaui != null)
80    {
81  0 Class clientClass = aaui.getClient();
82   
83    // Build an AACon style client - take alignment, return annotation for
84    // columns
85   
86  0 List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
87    .getCalcManager()
88    .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
89   
90  0 SeqAnnotationServiceCalcWorker tmpworker = null;
91  0 if (clnts != null)
92    {
93  0 for (AlignCalcWorkerI _worker : clnts)
94    {
95  0 tmpworker = (SeqAnnotationServiceCalcWorker) _worker;
96  0 if (tmpworker.hasService()
97    && tmpworker.getService().getClass().equals(clientClass))
98    {
99  0 break;
100    }
101  0 tmpworker = null;
102    }
103    }
104  0 final var worker = tmpworker;
105  0 if (worker == null)
106    {
107  0 processParams(sh, editParams).thenAccept((startJob) -> {
108  0 if (startJob)
109    {
110  0 final SeqAnnotationServiceCalcWorker worker_;
111  0 try
112    {
113  0 worker_ = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
114    paramset);
115    } catch (Exception x)
116    {
117  0 x.printStackTrace();
118  0 throw new Error(
119    MessageManager.getString("error.implementation_error"),
120    x);
121    }
122  0 alignFrame.getViewport().getCalcManager().registerWorker(worker_);
123    // also starts the worker
124  0 startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
125    }
126    });
127   
128    }
129    else
130    {
131  0 WsParamSetI preset_;
132  0 if (editParams)
133    {
134  0 paramset = worker.getArguments();
135  0 preset_ = worker.getPreset();
136    }
137    else
138    {
139  0 preset_ = preset;
140    }
141  0 processParams(sh, editParams, true).thenAccept((startJob) -> {
142  0 if (startJob)
143    {
144    // reinstate worker if it was blacklisted (might have happened due
145    // to
146    // invalid parameters)
147  0 alignFrame.getViewport().getCalcManager().enableWorker(worker);
148  0 worker.updateParameters(this.preset, paramset);
149  0 startSeqAnnotationWorker(sh, alignFrame, preset_, editParams);
150    }
151    });
152    }
153    }
154    else
155    {
156  0 startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
157    }
158    }
159   
 
160  0 toggle private void startSeqAnnotationWorker(ServiceWithParameters sh,
161    AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
162    {
163  0 if (!sh.isInteractiveUpdate())
164    {
165    // build IUPred style client. take sequences, returns annotation per
166    // sequence.
167  0 processParams(sh, editParams).thenAccept((startJob) -> {
168  0 if (startJob)
169    {
170  0 alignFrame.getViewport().getCalcManager().startWorker(
171    new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
172    }
173    });
174    }
175    }
176   
 
177  0 toggle public SequenceAnnotationWSClient(AutoCalcSetting fave,
178    AlignFrame alignFrame, boolean b)
179    {
180  0 super(alignFrame, fave.getPreset(), fave.getArgumentSet());
181  0 initSequenceAnnotationWSClient(fave.getService(), alignFrame,
182    fave.getPreset(), b);
183    }
184   
185    /*
186    * (non-Javadoc)
187    *
188    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
189    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
190    */
 
191  10347 toggle @Override
192    public void attachWSMenuEntry(JMenu wsmenu,
193    final ServiceWithParameters service,
194    final AlignFrame alignFrame)
195    {
196  10347 if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
197    service, alignFrame))
198    {
199    // Alignment dependent analysis calculation WS gui
200  3457 return;
201    }
202  6890 boolean hasparams = service.hasParameters();
203  6890 String calcName = service.getName();
204  6890 if (calcName.endsWith("WS"))
205    {
206    // Remove "WS" suffix
207  6890 calcName = calcName.substring(0, calcName.length() - 2);
208    }
209   
210  6890 JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
211    "label.calcname_with_default_settings", new String[]
212    { calcName }));
213  6890 annotservice.addActionListener(new ActionListener()
214    {
215   
 
216  0 toggle @Override
217    public void actionPerformed(ActionEvent e)
218    {
219  0 new SequenceAnnotationWSClient(service, alignFrame,
220    null, false);
221    }
222    });
223  6890 wsmenu.add(annotservice);
224  6890 if (hasparams)
225    {
226    // only add these menu options if the service has user-modifiable
227    // arguments
228  1721 annotservice = new JMenuItem(
229    MessageManager.getString("label.edit_settings_and_run"));
230  1721 annotservice.setToolTipText(MessageManager.getString(
231    "label.view_and_change_parameters_before_running_calculation"));
232   
233  1721 annotservice.addActionListener(new ActionListener()
234    {
 
235  0 toggle @Override
236    public void actionPerformed(ActionEvent e)
237    {
238  0 new SequenceAnnotationWSClient(service, alignFrame,
239    null, true);
240    }
241    });
242  1721 wsmenu.add(annotservice);
243  1721 List<WsParamSetI> presets = service.getParamStore().getPresets();
244  1721 if (presets != null && presets.size() > 0)
245    {
246  0 JMenu presetlist = new JMenu(MessageManager
247    .formatMessage("label.run_with_preset", new String[]
248    { calcName }));
249   
250  0 for (final WsParamSetI preset : presets)
251    {
252  0 final JMenuItem methodR = new JMenuItem(preset.getName());
253  0 methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
254  0 + (preset.isModifiable()
255    ? MessageManager.getString("label.user_preset")
256    : MessageManager
257    .getString("label.service_preset"))
258    + "</strong><br/>" + preset.getDescription()));
259  0 methodR.addActionListener(new ActionListener()
260    {
 
261  0 toggle @Override
262    public void actionPerformed(ActionEvent e)
263    {
264  0 new SequenceAnnotationWSClient(service,
265    alignFrame, preset,
266    false);
267    }
268   
269    });
270  0 presetlist.add(methodR);
271    }
272  0 wsmenu.add(presetlist);
273    }
274   
275    }
276    else
277    {
278  5169 annotservice = new JMenuItem(
279    MessageManager.getString("label.view_documentation"));
280  5169 if (service != null && service.hasDocumentationUrl())
281    {
282  5169 annotservice.addActionListener(new ActionListener()
283    {
284   
 
285  0 toggle @Override
286    public void actionPerformed(ActionEvent arg0)
287    {
288  0 Desktop.getInstance().showUrl(service.getDocumentationUrl());
289    }
290    });
291  5169 annotservice.setToolTipText(
292    JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
293    "label.view_service_doc_url", new String[]
294    { service.getDocumentationUrl(),
295    service.getDocumentationUrl() })));
296  5169 wsmenu.add(annotservice);
297    }
298    }
299    }
300    }
  • Report generated by OpenClover v 4.4.1 on Wed Jan 14 2026 14:41:35 GMT using coverage data from Wed Jan 14 2026 14:41:24 GMT.
  • OpenClover is free and open-source software.