2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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 java.awt.event.ActionEvent;
24 import java.awt.event.ActionListener;
25 import java.util.List;
29 import jalview.datamodel.*;
31 import compbio.data.msa.MsaWS;
32 import compbio.metadata.Argument;
33 import jalview.util.MessageManager;
34 import jalview.ws.jws2.jabaws2.Jws2Instance;
35 import jalview.ws.params.WsParamSetI;
43 public class MsaWSClient extends Jws2Client
46 * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
50 public MsaWSClient(Jws2Instance sh, String altitle,
51 jalview.datamodel.AlignmentView msa, boolean submitGaps,
52 boolean preserveOrder, Alignment seqdataset,
53 AlignFrame _alignFrame)
55 this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
56 seqdataset, _alignFrame);
57 // TODO Auto-generated constructor stub
60 public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
61 jalview.datamodel.AlignmentView msa, boolean submitGaps,
62 boolean preserveOrder, Alignment seqdataset,
63 AlignFrame _alignFrame)
65 this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
66 seqdataset, _alignFrame);
67 // TODO Auto-generated constructor stub
71 * Creates a new MsaWSClient object that uses a service given by an externally
72 * retrieved ServiceHandle
75 * service handle of type AbstractName(MsaWS)
82 * @param preserveOrder
86 public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
87 List<Argument> arguments, boolean editParams, String altitle,
88 jalview.datamodel.AlignmentView msa, boolean submitGaps,
89 boolean preserveOrder, Alignment seqdataset,
90 AlignFrame _alignFrame)
92 super(_alignFrame, preset, arguments);
93 if (!processParams(sh, editParams))
98 if (!(sh.service instanceof MsaWS))
100 // redundant at mo - but may change
104 MessageManager.formatMessage("label.service_called_is_not_msa_service", new String[]{sh.serviceType}),
105 MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
109 server = (MsaWS) sh.service;
110 if ((wsInfo = setWebService(sh, false)) == null)
112 JOptionPane.showMessageDialog(Desktop.desktop,
113 MessageManager.formatMessage("label.msa_service_is_unknown", new String[]{sh.serviceType}),
114 MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
118 startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
125 // add a class reference to the list
128 private void startMsaWSClient(String altitle, AlignmentView msa,
129 boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
131 // if (!locateWebService())
136 wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
137 + " of " + altitle + "\nJob details\n");
138 String jobtitle = WebServiceName.toLowerCase();
139 if (jobtitle.endsWith("alignment"))
142 && (!jobtitle.endsWith("realignment") || jobtitle
143 .indexOf("profile") == -1))
145 int pos = jobtitle.indexOf("alignment");
146 jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
151 jobtitle = WebServiceName + " of " + altitle;
156 jobtitle = WebServiceName + (submitGaps ? " re" : " ")
157 + "alignment of " + altitle;
160 MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
161 WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
162 submitGaps, preserveOrder, seqdataset);
163 wsInfo.setthisService(msathread);
167 protected String getServiceActionKey()
172 protected String getServiceActionDescription()
174 return "Multiple Sequence Alignment";
178 * look at ourselves and work out if we are a service that can take a profile
181 * @return true if we can send gapped sequences to the alignment service
183 private boolean canSubmitGaps()
185 // TODO: query service or extract service handle props to check if we can
187 return (WebServiceName.indexOf("lustal") > -1); // cheat!
190 public void attachWSMenuEntry(JMenu rmsawsmenu,
191 final Jws2Instance service, final AlignFrame alignFrame)
193 if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
195 // Alignment dependent analysis calculation WS gui
198 setWebService(service, true); // headless
199 boolean finished = true, submitGaps = false;
200 JMenu msawsmenu = rmsawsmenu;
201 String svcname = WebServiceName;
202 if (svcname.endsWith("WS"))
204 svcname = svcname.substring(0, svcname.length() - 2);
206 String calcName = svcname + " ";
209 msawsmenu = new JMenu(svcname);
210 rmsawsmenu.add(msawsmenu);
213 boolean hasparams = service.hasParameters();
216 String action = "Align ";
217 if (submitGaps == true)
220 msawsmenu = new JMenu(MessageManager.formatMessage(
221 "label.realign_with_params", new String[]
223 msawsmenu.setToolTipText(MessageManager
224 .getString("label.align_sequences_to_existing_alignment"));
225 rmsawsmenu.add(msawsmenu);
227 final boolean withGaps = submitGaps;
229 JMenuItem method = new JMenuItem(MessageManager.formatMessage(
230 "label.calcname_with_default_settings", new String[]
232 method.setToolTipText(MessageManager.formatMessage(
233 "label.action_with_default_settings", new String[]
236 method.addActionListener(new ActionListener()
238 public void actionPerformed(ActionEvent e)
240 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
241 new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
242 true, alignFrame.getViewport().getAlignment()
243 .getDataset(), alignFrame);
247 msawsmenu.add(method);
250 // only add these menu options if the service has user-modifiable
252 method = new JMenuItem(
253 MessageManager.getString("label.edit_settings_and_run"));
254 method.setToolTipText(MessageManager
255 .getString("label.view_and_change_parameters_before_alignment"));
257 method.addActionListener(new ActionListener()
259 public void actionPerformed(ActionEvent e)
261 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
262 new MsaWSClient(service, null, null, true, alignFrame
263 .getTitle(), msa, withGaps, true, alignFrame
264 .getViewport().getAlignment().getDataset(), alignFrame);
268 msawsmenu.add(method);
269 List<WsParamSetI> presets = service.getParamStore().getPresets();
270 if (presets != null && presets.size() > 0)
272 JMenu presetlist = new JMenu(MessageManager.formatMessage(
273 "label.run_with_preset_params", new String[]
276 for (final WsParamSetI preset : presets)
278 final JMenuItem methodR = new JMenuItem(preset.getName());
279 methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<p><strong>"
280 + (preset.isModifiable() ? MessageManager.getString("label.user_preset")
281 : MessageManager.getString("label.service_preset")) + "</strong><br/>"
282 + preset.getDescription() + "</p>"));
283 methodR.addActionListener(new ActionListener()
285 public void actionPerformed(ActionEvent e)
287 AlignmentView msa = alignFrame
288 .gatherSequencesForAlignment();
289 new MsaWSClient(service, preset, alignFrame.getTitle(),
290 msa, false, true, alignFrame.getViewport()
291 .getAlignment().getDataset(), alignFrame);
296 presetlist.add(methodR);
298 msawsmenu.add(presetlist);
301 if (!submitGaps && canSubmitGaps())