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;
43 import java.util.Locale;
45 import javax.swing.JMenu;
46 import javax.swing.JMenuItem;
47 import javax.swing.ToolTipManager;
53 * Instantiates web service menu items for multiple alignment services, and
54 * holds logic for constructing a web service thread.
56 * TODO remove dependency on Jws2Client methods for creating AACon service UI
59 * @author Jim Procter et al
62 public class MsaWSClient extends Jws2Client implements WSMenuEntryProviderI
65 * server is a proxy class implementing the core methods for submitting,
66 * monitoring and retrieving results from a multiple sequence alignment
69 MultipleSequenceAlignmentI server;
71 public MsaWSClient(ServiceWithParameters sh, String altitle,
72 jalview.datamodel.AlignmentView msa, boolean submitGaps,
73 boolean preserveOrder, AlignmentI seqdataset,
74 AlignFrame _alignFrame)
76 this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
77 seqdataset, _alignFrame);
78 // TODO Auto-generated constructor stub
81 public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
83 jalview.datamodel.AlignmentView msa, boolean submitGaps,
84 boolean preserveOrder, AlignmentI seqdataset,
85 AlignFrame _alignFrame)
87 this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
88 seqdataset, _alignFrame);
89 // TODO Auto-generated constructor stub
93 * Creates a new MsaWSClient object that uses a service given by an externally
94 * retrieved ServiceHandle
97 * service handle of type AbstractName(MsaWS)
104 * @param preserveOrder
108 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)
114 super(_alignFrame, preset, arguments);
115 processParams(sh, editParams).thenAccept((startJob) -> {
119 if (!(sh instanceof JalviewServiceEndpointProviderI
120 && ((JalviewServiceEndpointProviderI) sh)
121 .getEndpoint() instanceof MultipleSequenceAlignmentI))
123 // redundant at mo - but may change
124 JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
125 MessageManager.formatMessage(
126 "label.service_called_is_not_msa_service",
129 MessageManager.getString("label.internal_jalview_error"),
130 JvOptionPane.WARNING_MESSAGE);
135 server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh)
137 if ((wsInfo = setWebService(sh, false)) == null)
139 JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager
140 .formatMessage("label.msa_service_is_unknown", new String[]
142 MessageManager.getString("label.internal_jalview_error"),
143 JvOptionPane.WARNING_MESSAGE);
148 startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
156 // add a class reference to the list
159 private void startMsaWSClient(String altitle, AlignmentView msa,
160 boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
162 // if (!locateWebService())
167 wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
168 + " of " + altitle + "\nJob details\n");
169 String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
170 if (jobtitle.endsWith("alignment"))
172 if (submitGaps && (!jobtitle.endsWith("realignment")
173 || jobtitle.indexOf("profile") == -1))
175 int pos = jobtitle.indexOf("alignment");
176 jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
181 jobtitle = WebServiceName + " of " + altitle;
186 jobtitle = WebServiceName + (submitGaps ? " re" : " ")
187 + "alignment of " + altitle;
190 MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL,
191 wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps,
192 preserveOrder, seqdataset);
193 if (msathread.hasValidInput())
195 wsInfo.setthisService(msathread);
196 wsInfo.setVisible(true);
201 wsInfo.setVisible(false);
202 JvOptionPane.showMessageDialog(alignFrame,
203 MessageManager.getString("info.invalid_msa_input_mininfo"),
204 MessageManager.getString("info.invalid_msa_notenough"),
205 JvOptionPane.INFORMATION_MESSAGE);
209 protected String getServiceActionKey()
214 protected String getServiceActionDescription()
216 return "Multiple Sequence Alignment";
220 * look at ourselves and work out if we are a service that can take a profile
223 * @return true if we can send gapped sequences to the alignment service
225 private boolean canSubmitGaps()
227 // TODO: query service or extract service handle props to check if we can
229 return (WebServiceName.indexOf("lustal") > -1); // cheat!
233 public void attachWSMenuEntry(JMenu rmsawsmenu,
234 final ServiceWithParameters service, final AlignFrame alignFrame)
236 if (Jws2ClientFactory.registerAAConWSInstance(rmsawsmenu,
237 service, alignFrame))
239 // Alignment dependent analysis calculation WS gui
242 serviceHandle = service;
243 setWebService(service, true); // headless
244 attachWSMenuEntry(rmsawsmenu, alignFrame);
248 public void attachWSMenuEntry(JMenu wsmenu, AlignFrame alignFrame)
250 boolean finished = true, submitGaps = false;
252 * temp variables holding msa service submenu or root service menu
254 JMenu msawsmenu = wsmenu;
255 JMenu rmsawsmenu = wsmenu;
256 String svcname = WebServiceName;
257 if (svcname.endsWith("WS"))
259 svcname = svcname.substring(0, svcname.length() - 2);
261 String calcName = svcname + " ";
264 msawsmenu = new JMenu(svcname);
265 rmsawsmenu.add(msawsmenu);
268 boolean hasparams = serviceHandle.hasParameters();
269 ServiceWithParameters service = (ServiceWithParameters) serviceHandle;
272 String action = "Align ";
273 if (submitGaps == true)
276 msawsmenu = new JMenu(MessageManager
277 .formatMessage("label.realign_with_params", new String[]
279 msawsmenu.setToolTipText(MessageManager
280 .getString("label.align_sequences_to_existing_alignment"));
281 rmsawsmenu.add(msawsmenu);
283 final boolean withGaps = submitGaps;
285 JMenuItem method = new JMenuItem(MessageManager.formatMessage(
286 "label.calcname_with_default_settings", new String[]
288 method.setToolTipText(MessageManager.formatMessage(
289 "label.action_with_default_settings", new String[]
292 method.addActionListener(new ActionListener()
295 public void actionPerformed(ActionEvent e)
297 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
301 new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
303 alignFrame.getViewport().getAlignment().getDataset(),
309 msawsmenu.add(method);
312 // only add these menu options if the service has user-modifiable
314 method = new JMenuItem(
315 MessageManager.getString("label.edit_settings_and_run"));
316 method.setToolTipText(MessageManager.getString(
317 "label.view_and_change_parameters_before_alignment"));
319 method.addActionListener(new ActionListener()
322 public void actionPerformed(ActionEvent e)
324 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
327 new MsaWSClient(service, null, null, true,
328 alignFrame.getTitle(), msa, withGaps, true,
329 alignFrame.getViewport().getAlignment().getDataset(),
335 msawsmenu.add(method);
336 List<WsParamSetI> presets = service.getParamStore().getPresets();
337 if (presets != null && presets.size() > 0)
339 JMenu presetlist = new JMenu(MessageManager.formatMessage(
340 "label.run_with_preset_params", new String[]
343 final int showToolTipFor = ToolTipManager.sharedInstance()
345 for (final WsParamSetI preset : presets)
347 final JMenuItem methodR = new JMenuItem(preset.getName());
348 final int QUICK_TOOLTIP = 1500;
349 // JAL-1582 shorten tooltip display time in these menu items as
350 // they can obscure other options
351 methodR.addMouseListener(new MouseAdapter()
354 public void mouseEntered(MouseEvent e)
356 ToolTipManager.sharedInstance()
357 .setDismissDelay(QUICK_TOOLTIP);
361 public void mouseExited(MouseEvent e)
363 ToolTipManager.sharedInstance()
364 .setDismissDelay(showToolTipFor);
368 String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
369 + (preset.isModifiable()
370 ? MessageManager.getString("label.user_preset")
372 .getString("label.service_preset"))
373 + "</strong><br/>" + preset.getDescription());
374 methodR.setToolTipText(tooltip);
375 methodR.addActionListener(new ActionListener()
378 public void actionPerformed(ActionEvent e)
380 AlignmentView msa = alignFrame
381 .gatherSequencesForAlignment();
385 MsaWSClient msac = new MsaWSClient(service, preset,
386 alignFrame.getTitle(), msa, false, true,
387 alignFrame.getViewport().getAlignment()
395 presetlist.add(methodR);
397 msawsmenu.add(presetlist);
400 if (!submitGaps && canSubmitGaps())