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 if (!processParams(sh, editParams))
118 if (!(sh instanceof JalviewServiceEndpointProviderI
119 && ((JalviewServiceEndpointProviderI) sh)
120 .getEndpoint() instanceof MultipleSequenceAlignmentI))
122 // redundant at mo - but may change
123 JvOptionPane.showMessageDialog(Desktop.desktop,
124 MessageManager.formatMessage(
125 "label.service_called_is_not_msa_service",
128 MessageManager.getString("label.internal_jalview_error"),
129 JvOptionPane.WARNING_MESSAGE);
134 server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh)
136 if ((wsInfo = setWebService(sh, false)) == null)
138 JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
139 .formatMessage("label.msa_service_is_unknown", new String[]
141 MessageManager.getString("label.internal_jalview_error"),
142 JvOptionPane.WARNING_MESSAGE);
147 startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
154 // add a class reference to the list
157 private void startMsaWSClient(String altitle, AlignmentView msa,
158 boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
160 // if (!locateWebService())
165 wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
166 + " of " + altitle + "\nJob details\n");
167 String jobtitle = WebServiceName.toLowerCase();
168 if (jobtitle.endsWith("alignment"))
170 if (submitGaps && (!jobtitle.endsWith("realignment")
171 || jobtitle.indexOf("profile") == -1))
173 int pos = jobtitle.indexOf("alignment");
174 jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
179 jobtitle = WebServiceName + " of " + altitle;
184 jobtitle = WebServiceName + (submitGaps ? " re" : " ")
185 + "alignment of " + altitle;
188 MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL,
189 wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps,
190 preserveOrder, seqdataset);
191 if (msathread.hasValidInput())
193 wsInfo.setthisService(msathread);
194 wsInfo.setVisible(true);
199 JvOptionPane.showMessageDialog(alignFrame,
200 MessageManager.getString("info.invalid_msa_input_mininfo"),
201 MessageManager.getString("info.invalid_msa_notenough"),
202 JvOptionPane.INFORMATION_MESSAGE);
203 wsInfo.setVisible(false);
207 public static void main(String[] args)
209 System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
212 protected String getServiceActionKey()
217 protected String getServiceActionDescription()
219 return "Multiple Sequence Alignment";
223 * look at ourselves and work out if we are a service that can take a profile
226 * @return true if we can send gapped sequences to the alignment service
228 private boolean canSubmitGaps()
230 // TODO: query service or extract service handle props to check if we can
232 return (WebServiceName.indexOf("lustal") > -1); // cheat!
236 public void attachWSMenuEntry(JMenu rmsawsmenu,
237 final ServiceWithParameters service, final AlignFrame alignFrame)
239 if (Jws2ClientFactory.registerAAConWSInstance(rmsawsmenu,
240 service, alignFrame))
242 // Alignment dependent analysis calculation WS gui
245 serviceHandle = service;
246 setWebService(service, true); // headless
247 attachWSMenuEntry(rmsawsmenu, alignFrame);
251 public void attachWSMenuEntry(JMenu wsmenu, AlignFrame alignFrame)
253 boolean finished = true, submitGaps = false;
255 * temp variables holding msa service submenu or root service menu
257 JMenu msawsmenu = wsmenu;
258 JMenu rmsawsmenu = wsmenu;
259 String svcname = WebServiceName;
260 if (svcname.endsWith("WS"))
262 svcname = svcname.substring(0, svcname.length() - 2);
264 String calcName = svcname + " ";
267 msawsmenu = new JMenu(svcname);
268 rmsawsmenu.add(msawsmenu);
271 boolean hasparams = serviceHandle.hasParameters();
272 ServiceWithParameters service = (ServiceWithParameters) serviceHandle;
275 String action = "Align ";
276 if (submitGaps == true)
279 msawsmenu = new JMenu(MessageManager
280 .formatMessage("label.realign_with_params", new String[]
282 msawsmenu.setToolTipText(MessageManager
283 .getString("label.align_sequences_to_existing_alignment"));
284 rmsawsmenu.add(msawsmenu);
286 final boolean withGaps = submitGaps;
288 JMenuItem method = new JMenuItem(MessageManager.formatMessage(
289 "label.calcname_with_default_settings", new String[]
291 method.setToolTipText(MessageManager.formatMessage(
292 "label.action_with_default_settings", new String[]
295 method.addActionListener(new ActionListener()
298 public void actionPerformed(ActionEvent e)
300 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
304 new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
306 alignFrame.getViewport().getAlignment().getDataset(),
312 msawsmenu.add(method);
315 // only add these menu options if the service has user-modifiable
317 method = new JMenuItem(
318 MessageManager.getString("label.edit_settings_and_run"));
319 method.setToolTipText(MessageManager.getString(
320 "label.view_and_change_parameters_before_alignment"));
322 method.addActionListener(new ActionListener()
325 public void actionPerformed(ActionEvent e)
327 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
330 new MsaWSClient(service, null, null, true,
331 alignFrame.getTitle(), msa, withGaps, true,
332 alignFrame.getViewport().getAlignment().getDataset(),
338 msawsmenu.add(method);
339 List<WsParamSetI> presets = service.getParamStore().getPresets();
340 if (presets != null && presets.size() > 0)
342 JMenu presetlist = new JMenu(MessageManager.formatMessage(
343 "label.run_with_preset_params", new String[]
346 final int showToolTipFor = ToolTipManager.sharedInstance()
348 for (final WsParamSetI preset : presets)
350 final JMenuItem methodR = new JMenuItem(preset.getName());
351 final int QUICK_TOOLTIP = 1500;
352 // JAL-1582 shorten tooltip display time in these menu items as
353 // they can obscure other options
354 methodR.addMouseListener(new MouseAdapter()
357 public void mouseEntered(MouseEvent e)
359 ToolTipManager.sharedInstance()
360 .setDismissDelay(QUICK_TOOLTIP);
364 public void mouseExited(MouseEvent e)
366 ToolTipManager.sharedInstance()
367 .setDismissDelay(showToolTipFor);
371 String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
372 + (preset.isModifiable()
373 ? MessageManager.getString("label.user_preset")
375 .getString("label.service_preset"))
376 + "</strong><br/>" + preset.getDescription());
377 methodR.setToolTipText(tooltip);
378 methodR.addActionListener(new ActionListener()
381 public void actionPerformed(ActionEvent e)
383 AlignmentView msa = alignFrame
384 .gatherSequencesForAlignment();
388 MsaWSClient msac = new MsaWSClient(service, preset,
389 alignFrame.getTitle(), msa, false, true,
390 alignFrame.getViewport().getAlignment()
398 presetlist.add(methodR);
400 msawsmenu.add(presetlist);
403 if (!submitGaps && canSubmitGaps())