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 jalview.datamodel.Alignment;
24 import jalview.datamodel.AlignmentView;
25 import jalview.gui.AlignFrame;
26 import jalview.gui.Desktop;
27 import jalview.gui.JvSwingUtils;
28 import jalview.util.MessageManager;
29 import jalview.ws.jws2.jabaws2.Jws2Instance;
30 import jalview.ws.params.WsParamSetI;
32 import java.awt.event.ActionEvent;
33 import java.awt.event.ActionListener;
34 import java.awt.event.MouseAdapter;
35 import java.awt.event.MouseEvent;
36 import java.util.List;
38 import javax.swing.JMenu;
39 import javax.swing.JMenuItem;
40 import javax.swing.JOptionPane;
41 import javax.swing.ToolTipManager;
43 import compbio.data.msa.MsaWS;
44 import compbio.metadata.Argument;
52 public class MsaWSClient extends Jws2Client
55 * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
59 public MsaWSClient(Jws2Instance sh, String altitle,
60 jalview.datamodel.AlignmentView msa, boolean submitGaps,
61 boolean preserveOrder, Alignment seqdataset,
62 AlignFrame _alignFrame)
64 this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
65 seqdataset, _alignFrame);
66 // TODO Auto-generated constructor stub
69 public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
70 jalview.datamodel.AlignmentView msa, boolean submitGaps,
71 boolean preserveOrder, Alignment seqdataset,
72 AlignFrame _alignFrame)
74 this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
75 seqdataset, _alignFrame);
76 // TODO Auto-generated constructor stub
80 * Creates a new MsaWSClient object that uses a service given by an externally
81 * retrieved ServiceHandle
84 * service handle of type AbstractName(MsaWS)
91 * @param preserveOrder
95 public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
96 List<Argument> arguments, boolean editParams, String altitle,
97 jalview.datamodel.AlignmentView msa, boolean submitGaps,
98 boolean preserveOrder, Alignment seqdataset,
99 AlignFrame _alignFrame)
101 super(_alignFrame, preset, arguments);
102 if (!processParams(sh, editParams))
107 if (!(sh.service instanceof MsaWS))
109 // redundant at mo - but may change
110 JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
111 .formatMessage("label.service_called_is_not_msa_service",
113 { sh.serviceType }), MessageManager
114 .getString("label.internal_jalview_error"),
115 JOptionPane.WARNING_MESSAGE);
119 server = (MsaWS) sh.service;
120 if ((wsInfo = setWebService(sh, false)) == null)
122 JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
123 .formatMessage("label.msa_service_is_unknown", new String[]
124 { sh.serviceType }), MessageManager
125 .getString("label.internal_jalview_error"),
126 JOptionPane.WARNING_MESSAGE);
130 startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
137 // add a class reference to the list
140 private void startMsaWSClient(String altitle, AlignmentView msa,
141 boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
143 // if (!locateWebService())
148 wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
149 + " of " + altitle + "\nJob details\n");
150 String jobtitle = WebServiceName.toLowerCase();
151 if (jobtitle.endsWith("alignment"))
154 && (!jobtitle.endsWith("realignment") || jobtitle
155 .indexOf("profile") == -1))
157 int pos = jobtitle.indexOf("alignment");
158 jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
163 jobtitle = WebServiceName + " of " + altitle;
168 jobtitle = WebServiceName + (submitGaps ? " re" : " ")
169 + "alignment of " + altitle;
172 MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
173 WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
174 submitGaps, preserveOrder, seqdataset);
175 wsInfo.setthisService(msathread);
179 protected String getServiceActionKey()
184 protected String getServiceActionDescription()
186 return "Multiple Sequence Alignment";
190 * look at ourselves and work out if we are a service that can take a profile
193 * @return true if we can send gapped sequences to the alignment service
195 private boolean canSubmitGaps()
197 // TODO: query service or extract service handle props to check if we can
199 return (WebServiceName.indexOf("lustal") > -1); // cheat!
202 public void attachWSMenuEntry(JMenu rmsawsmenu,
203 final Jws2Instance service, final AlignFrame alignFrame)
205 if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
207 // Alignment dependent analysis calculation WS gui
210 setWebService(service, true); // headless
211 boolean finished = true, submitGaps = false;
212 JMenu msawsmenu = rmsawsmenu;
213 String svcname = WebServiceName;
214 if (svcname.endsWith("WS"))
216 svcname = svcname.substring(0, svcname.length() - 2);
218 String calcName = svcname + " ";
221 msawsmenu = new JMenu(svcname);
222 rmsawsmenu.add(msawsmenu);
225 boolean hasparams = service.hasParameters();
228 String action = "Align ";
229 if (submitGaps == true)
232 msawsmenu = new JMenu(MessageManager.formatMessage(
233 "label.realign_with_params", new String[]
235 msawsmenu.setToolTipText(MessageManager
236 .getString("label.align_sequences_to_existing_alignment"));
237 rmsawsmenu.add(msawsmenu);
239 final boolean withGaps = submitGaps;
241 JMenuItem method = new JMenuItem(MessageManager.formatMessage(
242 "label.calcname_with_default_settings", new String[]
244 method.setToolTipText(MessageManager.formatMessage(
245 "label.action_with_default_settings", new String[]
248 method.addActionListener(new ActionListener()
250 public void actionPerformed(ActionEvent e)
252 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
253 new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
254 true, alignFrame.getViewport().getAlignment()
255 .getDataset(), alignFrame);
259 msawsmenu.add(method);
262 // only add these menu options if the service has user-modifiable
264 method = new JMenuItem(
265 MessageManager.getString("label.edit_settings_and_run"));
266 method.setToolTipText(MessageManager
267 .getString("label.view_and_change_parameters_before_alignment"));
269 method.addActionListener(new ActionListener()
271 public void actionPerformed(ActionEvent e)
273 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
274 new MsaWSClient(service, null, null, true, alignFrame
275 .getTitle(), msa, withGaps, true, alignFrame
276 .getViewport().getAlignment().getDataset(), alignFrame);
280 msawsmenu.add(method);
281 List<WsParamSetI> presets = service.getParamStore().getPresets();
282 if (presets != null && presets.size() > 0)
284 JMenu presetlist = new JMenu(MessageManager.formatMessage(
285 "label.run_with_preset_params", new String[]
288 final int showToolTipFor = ToolTipManager.sharedInstance()
290 for (final WsParamSetI preset : presets)
292 final JMenuItem methodR = new JMenuItem(preset.getName());
293 final int QUICK_TOOLTIP = 1500;
294 // JAL-1582 shorten tooltip display time in these menu items as
295 // they can obscure other options
296 methodR.addMouseListener(new MouseAdapter()
299 public void mouseEntered(MouseEvent e)
301 ToolTipManager.sharedInstance().setDismissDelay(
306 public void mouseExited(MouseEvent e)
308 ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
312 methodR.setToolTipText(JvSwingUtils.wrapTooltip(
315 + (preset.isModifiable() ? MessageManager
316 .getString("label.user_preset")
318 .getString("label.service_preset"))
319 + "</strong><br/>" + preset.getDescription()
321 methodR.addActionListener(new ActionListener()
323 public void actionPerformed(ActionEvent e)
325 AlignmentView msa = alignFrame
326 .gatherSequencesForAlignment();
327 new MsaWSClient(service, preset, alignFrame.getTitle(),
328 msa, false, true, alignFrame.getViewport()
329 .getAlignment().getDataset(), alignFrame);
334 presetlist.add(methodR);
336 msawsmenu.add(presetlist);
339 if (!submitGaps && canSubmitGaps())