2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
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.
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.
21 package jalview.ws.jws2;
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;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.ActionListener;
35 import java.util.List;
37 import javax.swing.JMenu;
38 import javax.swing.JMenuItem;
44 public class SequenceAnnotationWSClient extends Jws2Client
47 * initialise a client so its attachWSMenuEntry method can be called.
49 public SequenceAnnotationWSClient()
51 // TODO Auto-generated constructor stub
54 public SequenceAnnotationWSClient(final ServiceWithParameters sh,
55 AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
57 super(alignFrame, preset, null);
58 initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
61 // dan think. Do I need to change this method to run RNAalifold through the
64 private void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
65 AlignFrame alignFrame, final WsParamSetI preset, boolean editParams)
67 // dan changed! dan test. comment out if conditional
68 // if (alignFrame.getViewport().getAlignment().isNucleotide())
70 // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
71 // + " can only be used\nfor amino acid alignments.",
72 // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
76 AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
79 Class clientClass = aaui.getClient();
81 // Build an AACon style client - take alignment, return annotation for
84 List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
86 .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
88 SeqAnnotationServiceCalcWorker tmpworker = null;
91 for (AlignCalcWorkerI _worker : clnts)
93 tmpworker = (SeqAnnotationServiceCalcWorker) _worker;
94 if (tmpworker.hasService()
95 && tmpworker.getService().getClass().equals(clientClass))
102 final var worker = tmpworker;
105 processParams(sh, editParams).thenAccept((startJob) -> {
108 final SeqAnnotationServiceCalcWorker worker_;
111 worker_ = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
113 } catch (Exception x)
117 MessageManager.getString("error.implementation_error"),
120 alignFrame.getViewport().getCalcManager().registerWorker(worker_);
121 // also starts the worker
122 startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
131 paramset = worker.getArguments();
132 preset_ = worker.getPreset();
138 processParams(sh, editParams, true).thenAccept((startJob) -> {
141 // reinstate worker if it was blacklisted (might have happened due
143 // invalid parameters)
144 alignFrame.getViewport().getCalcManager().enableWorker(worker);
145 worker.updateParameters(this.preset, paramset);
146 startSeqAnnotationWorker(sh, alignFrame, preset_, editParams);
153 startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
157 private void startSeqAnnotationWorker(ServiceWithParameters sh,
158 AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
160 if (!sh.isInteractiveUpdate())
162 // build IUPred style client. take sequences, returns annotation per
164 processParams(sh, editParams).thenAccept((startJob) -> {
167 alignFrame.getViewport().getCalcManager().startWorker(
168 new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
174 public SequenceAnnotationWSClient(AutoCalcSetting fave,
175 AlignFrame alignFrame, boolean b)
177 super(alignFrame, fave.getPreset(), fave.getArgumentSet());
178 initSequenceAnnotationWSClient(fave.getService(), alignFrame,
179 fave.getPreset(), b);
185 * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
186 * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
189 public void attachWSMenuEntry(JMenu wsmenu,
190 final ServiceWithParameters service,
191 final AlignFrame alignFrame)
193 if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
194 service, alignFrame))
196 // Alignment dependent analysis calculation WS gui
199 boolean hasparams = service.hasParameters();
200 String calcName = service.getName();
201 if (calcName.endsWith("WS"))
203 // Remove "WS" suffix
204 calcName = calcName.substring(0, calcName.length() - 2);
207 JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
208 "label.calcname_with_default_settings", new String[]
210 annotservice.addActionListener(new ActionListener()
214 public void actionPerformed(ActionEvent e)
216 new SequenceAnnotationWSClient(service, alignFrame,
220 wsmenu.add(annotservice);
223 // only add these menu options if the service has user-modifiable
225 annotservice = new JMenuItem(
226 MessageManager.getString("label.edit_settings_and_run"));
227 annotservice.setToolTipText(MessageManager.getString(
228 "label.view_and_change_parameters_before_running_calculation"));
230 annotservice.addActionListener(new ActionListener()
233 public void actionPerformed(ActionEvent e)
235 new SequenceAnnotationWSClient(service, alignFrame,
239 wsmenu.add(annotservice);
240 List<WsParamSetI> presets = service.getParamStore().getPresets();
241 if (presets != null && presets.size() > 0)
243 JMenu presetlist = new JMenu(MessageManager
244 .formatMessage("label.run_with_preset", new String[]
247 for (final WsParamSetI preset : presets)
249 final JMenuItem methodR = new JMenuItem(preset.getName());
250 methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
251 + (preset.isModifiable()
252 ? MessageManager.getString("label.user_preset")
254 .getString("label.service_preset"))
255 + "</strong><br/>" + preset.getDescription()));
256 methodR.addActionListener(new ActionListener()
259 public void actionPerformed(ActionEvent e)
261 new SequenceAnnotationWSClient(service,
267 presetlist.add(methodR);
269 wsmenu.add(presetlist);
275 annotservice = new JMenuItem(
276 MessageManager.getString("label.view_documentation"));
277 if (service != null && service.hasDocumentationUrl())
279 annotservice.addActionListener(new ActionListener()
283 public void actionPerformed(ActionEvent arg0)
285 Desktop.getInstance().showUrl(service.getDocumentationUrl());
288 annotservice.setToolTipText(
289 JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
290 "label.view_service_doc_url", new String[]
291 { service.getDocumentationUrl(),
292 service.getDocumentationUrl() })));
293 wsmenu.add(annotservice);