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.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;
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;
44 import javax.swing.JMenu;
45 import javax.swing.JMenuItem;
46 import javax.swing.ToolTipManager;
51 * Instantiates web service menu items for multiple alignment services, and
52 * holds logic for constructing a web service thread.
54 * TODO remove dependency on Jws2Client methods for creating AACon service UI
57 * @author Jim Procter et al
60 public class MsaWSClient extends Jws2Client implements WSMenuEntryProviderI
63 * server is a proxy class implementing the core methods for submitting,
64 * monitoring and retrieving results from a multiple sequence alignment
67 MultipleSequenceAlignmentI server;
69 public MsaWSClient(ServiceWithParameters sh, String altitle,
70 jalview.datamodel.AlignmentView msa, boolean submitGaps,
71 boolean preserveOrder, AlignmentI seqdataset,
72 AlignFrame _alignFrame)
74 this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
75 seqdataset, _alignFrame);
76 // TODO Auto-generated constructor stub
79 public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
81 jalview.datamodel.AlignmentView msa, boolean submitGaps,
82 boolean preserveOrder, AlignmentI seqdataset,
83 AlignFrame _alignFrame)
85 this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
86 seqdataset, _alignFrame);
87 // TODO Auto-generated constructor stub
91 * Creates a new MsaWSClient object that uses a service given by an externally
92 * retrieved ServiceHandle
95 * service handle of type AbstractName(MsaWS)
102 * @param preserveOrder
106 public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
107 List<ArgumentI> arguments, boolean editParams, String altitle,
108 jalview.datamodel.AlignmentView msa, boolean submitGaps,
109 boolean preserveOrder, AlignmentI seqdataset,
110 AlignFrame _alignFrame)
112 super(_alignFrame, preset, arguments);
113 processParams(sh, editParams).thenAccept((startJob) -> {
117 if (!(sh instanceof JalviewServiceEndpointProviderI
118 && ((JalviewServiceEndpointProviderI) sh)
119 .getEndpoint() instanceof MultipleSequenceAlignmentI))
121 // redundant at mo - but may change
122 JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
123 MessageManager.formatMessage(
124 "label.service_called_is_not_msa_service",
127 MessageManager.getString("label.internal_jalview_error"),
128 JvOptionPane.WARNING_MESSAGE);
133 server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh)
135 if ((wsInfo = setWebService(sh, false)) == null)
137 JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager
138 .formatMessage("label.msa_service_is_unknown", new String[]
140 MessageManager.getString("label.internal_jalview_error"),
141 JvOptionPane.WARNING_MESSAGE);
146 startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
153 // add a class reference to the list
156 private void startMsaWSClient(String altitle, AlignmentView msa,
157 boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
159 // if (!locateWebService())
164 wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
165 + " of " + altitle + "\nJob details\n");
166 String jobtitle = WebServiceName.toLowerCase();
167 if (jobtitle.endsWith("alignment"))
169 if (submitGaps && (!jobtitle.endsWith("realignment")
170 || jobtitle.indexOf("profile") == -1))
172 int pos = jobtitle.indexOf("alignment");
173 jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
178 jobtitle = WebServiceName + " of " + altitle;
183 jobtitle = WebServiceName + (submitGaps ? " re" : " ")
184 + "alignment of " + altitle;
187 MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL,
188 wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps,
189 preserveOrder, seqdataset);
190 if (msathread.hasValidInput())
192 wsInfo.setthisService(msathread);
193 wsInfo.setVisible(true);
198 wsInfo.setVisible(false);
199 JvOptionPane.showMessageDialog(alignFrame,
200 MessageManager.getString("info.invalid_msa_input_mininfo"),
201 MessageManager.getString("info.invalid_msa_notenough"),
202 JvOptionPane.INFORMATION_MESSAGE);
206 protected String getServiceActionKey()
211 protected String getServiceActionDescription()
213 return "Multiple Sequence Alignment";
217 * look at ourselves and work out if we are a service that can take a profile
220 * @return true if we can send gapped sequences to the alignment service
222 private boolean canSubmitGaps()
224 // TODO: query service or extract service handle props to check if we can
226 return (WebServiceName.indexOf("lustal") > -1); // cheat!
230 public void attachWSMenuEntry(JMenu rmsawsmenu,
231 final ServiceWithParameters service, final AlignFrame alignFrame)
233 if (Jws2ClientFactory.registerAAConWSInstance(rmsawsmenu,
234 service, alignFrame))
236 // Alignment dependent analysis calculation WS gui
239 serviceHandle = service;
240 setWebService(service, true); // headless
241 attachWSMenuEntry(rmsawsmenu, alignFrame);
245 public void attachWSMenuEntry(JMenu wsmenu, AlignFrame alignFrame)
247 boolean finished = true, submitGaps = false;
249 * temp variables holding msa service submenu or root service menu
251 JMenu msawsmenu = wsmenu;
252 JMenu rmsawsmenu = wsmenu;
253 String svcname = WebServiceName;
254 if (svcname.endsWith("WS"))
256 svcname = svcname.substring(0, svcname.length() - 2);
258 String calcName = svcname + " ";
261 msawsmenu = new JMenu(svcname);
262 rmsawsmenu.add(msawsmenu);
265 boolean hasparams = serviceHandle.hasParameters();
266 ServiceWithParameters service = (ServiceWithParameters) serviceHandle;
269 String action = "Align ";
270 if (submitGaps == true)
273 msawsmenu = new JMenu(MessageManager
274 .formatMessage("label.realign_with_params", new String[]
276 msawsmenu.setToolTipText(MessageManager
277 .getString("label.align_sequences_to_existing_alignment"));
278 rmsawsmenu.add(msawsmenu);
280 final boolean withGaps = submitGaps;
282 JMenuItem method = new JMenuItem(MessageManager.formatMessage(
283 "label.calcname_with_default_settings", new String[]
285 method.setToolTipText(MessageManager.formatMessage(
286 "label.action_with_default_settings", new String[]
289 method.addActionListener(new ActionListener()
292 public void actionPerformed(ActionEvent e)
294 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
298 new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
300 alignFrame.getViewport().getAlignment().getDataset(),
306 msawsmenu.add(method);
309 // only add these menu options if the service has user-modifiable
311 method = new JMenuItem(
312 MessageManager.getString("label.edit_settings_and_run"));
313 method.setToolTipText(MessageManager.getString(
314 "label.view_and_change_parameters_before_alignment"));
316 method.addActionListener(new ActionListener()
319 public void actionPerformed(ActionEvent e)
321 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
324 new MsaWSClient(service, null, null, true,
325 alignFrame.getTitle(), msa, withGaps, true,
326 alignFrame.getViewport().getAlignment().getDataset(),
332 msawsmenu.add(method);
333 List<WsParamSetI> presets = service.getParamStore().getPresets();
334 if (presets != null && presets.size() > 0)
336 JMenu presetlist = new JMenu(MessageManager.formatMessage(
337 "label.run_with_preset_params", new String[]
340 final int showToolTipFor = ToolTipManager.sharedInstance()
342 for (final WsParamSetI preset : presets)
344 final JMenuItem methodR = new JMenuItem(preset.getName());
345 final int QUICK_TOOLTIP = 1500;
346 // JAL-1582 shorten tooltip display time in these menu items as
347 // they can obscure other options
348 methodR.addMouseListener(new MouseAdapter()
351 public void mouseEntered(MouseEvent e)
353 ToolTipManager.sharedInstance()
354 .setDismissDelay(QUICK_TOOLTIP);
358 public void mouseExited(MouseEvent e)
360 ToolTipManager.sharedInstance()
361 .setDismissDelay(showToolTipFor);
365 String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
366 + (preset.isModifiable()
367 ? MessageManager.getString("label.user_preset")
369 .getString("label.service_preset"))
370 + "</strong><br/>" + preset.getDescription());
371 methodR.setToolTipText(tooltip);
372 methodR.addActionListener(new ActionListener()
375 public void actionPerformed(ActionEvent e)
377 AlignmentView msa = alignFrame
378 .gatherSequencesForAlignment();
382 MsaWSClient msac = new MsaWSClient(service, preset,
383 alignFrame.getTitle(), msa, false, true,
384 alignFrame.getViewport().getAlignment()
392 presetlist.add(methodR);
394 msawsmenu.add(presetlist);
397 if (!submitGaps && canSubmitGaps())