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.AlignmentI;
25 import jalview.datamodel.AlignmentView;
26 import jalview.datamodel.SequenceI;
27 import jalview.gui.AlignFrame;
28 import jalview.gui.Desktop;
29 import jalview.gui.JvSwingUtils;
30 import jalview.util.MessageManager;
31 import jalview.ws.jws2.jabaws2.Jws2Instance;
32 import jalview.ws.params.WsParamSetI;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.awt.event.MouseAdapter;
37 import java.awt.event.MouseEvent;
38 import java.util.List;
40 import javax.swing.JMenu;
41 import javax.swing.JMenuItem;
42 import javax.swing.JOptionPane;
43 import javax.swing.ToolTipManager;
45 import compbio.data.msa.MsaWS;
46 import compbio.metadata.Argument;
54 public class MsaWSClient extends Jws2Client
57 * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
61 public MsaWSClient(Jws2Instance sh, String altitle,
62 jalview.datamodel.AlignmentView msa, boolean submitGaps,
63 boolean preserveOrder, Alignment seqdataset,
64 AlignFrame _alignFrame)
66 this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
67 seqdataset, _alignFrame);
68 // TODO Auto-generated constructor stub
71 public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
72 jalview.datamodel.AlignmentView msa, boolean submitGaps,
73 boolean preserveOrder, Alignment seqdataset,
74 AlignFrame _alignFrame)
76 this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
77 seqdataset, _alignFrame);
78 // TODO Auto-generated constructor stub
82 * Creates a new MsaWSClient object that uses a service given by an externally
83 * retrieved ServiceHandle
86 * service handle of type AbstractName(MsaWS)
93 * @param preserveOrder
97 public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
98 List<Argument> arguments, boolean editParams, String altitle,
99 jalview.datamodel.AlignmentView msa, boolean submitGaps,
100 boolean preserveOrder, Alignment seqdataset,
101 AlignFrame _alignFrame)
103 super(_alignFrame, preset, arguments);
104 if (!processParams(sh, editParams))
109 if (!(sh.service instanceof MsaWS))
111 // redundant at mo - but may change
112 JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
113 .formatMessage("label.service_called_is_not_msa_service",
115 { sh.serviceType }), MessageManager
116 .getString("label.internal_jalview_error"),
117 JOptionPane.WARNING_MESSAGE);
121 server = (MsaWS) sh.service;
122 if ((wsInfo = setWebService(sh, false)) == null)
124 JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
125 .formatMessage("label.msa_service_is_unknown", new String[]
126 { sh.serviceType }), MessageManager
127 .getString("label.internal_jalview_error"),
128 JOptionPane.WARNING_MESSAGE);
132 startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
139 // add a class reference to the list
142 private void startMsaWSClient(String altitle, AlignmentView msa,
143 boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
145 // if (!locateWebService())
150 wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
151 + " of " + altitle + "\nJob details\n");
152 String jobtitle = WebServiceName.toLowerCase();
153 if (jobtitle.endsWith("alignment"))
156 && (!jobtitle.endsWith("realignment") || jobtitle
157 .indexOf("profile") == -1))
159 int pos = jobtitle.indexOf("alignment");
160 jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
165 jobtitle = WebServiceName + " of " + altitle;
170 jobtitle = WebServiceName + (submitGaps ? " re" : " ")
171 + "alignment of " + altitle;
174 MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
175 WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
176 submitGaps, preserveOrder, seqdataset);
177 wsInfo.setthisService(msathread);
178 if (isValidAlignment(alignFrame.getCurrentView().getAlignment()))
185 private boolean isValidAlignment(AlignmentI seqdataset)
187 String header = wsInfo.getInfoText()
188 + "\nValidating submited Alignment...";
189 wsInfo.setInfoText(header);
190 int validSeqCount = 0;
191 List<SequenceI> seqs = seqdataset.getSequences();
194 wsInfo.setInfoText(header
195 + "\nA minimum of two sequences is required to perform this operation");
199 for (SequenceI seq : seqs)
202 if (seq.getSequenceAsString().matches(
203 "([(a-zA-Z?)(-?)(.?)]+)?[a-zA-Z]([(a-zA-Z?)(-?)(.?)]+)?"))
207 if (validSeqCount > 1)
209 wsInfo.setInfoText(header
210 + "\nAlignment sequences was successfully validated");
215 wsInfo.setInfoText(header
216 + "\nA minimum of two sequences with at least one non-gap character in each sequence is required to perform this operation");
220 public static void main(String[] args)
224 .matches("([(a-zA-Z?)(-?)(.?)]+)?[a-zA-Z]([(a-zA-Z?)(-?)(.?)]+)?"));
229 protected String getServiceActionKey()
234 protected String getServiceActionDescription()
236 return "Multiple Sequence Alignment";
240 * look at ourselves and work out if we are a service that can take a profile
243 * @return true if we can send gapped sequences to the alignment service
245 private boolean canSubmitGaps()
247 // TODO: query service or extract service handle props to check if we can
249 return (WebServiceName.indexOf("lustal") > -1); // cheat!
252 public void attachWSMenuEntry(JMenu rmsawsmenu,
253 final Jws2Instance service, final AlignFrame alignFrame)
255 if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
257 // Alignment dependent analysis calculation WS gui
260 setWebService(service, true); // headless
261 boolean finished = true, submitGaps = false;
262 JMenu msawsmenu = rmsawsmenu;
263 String svcname = WebServiceName;
264 if (svcname.endsWith("WS"))
266 svcname = svcname.substring(0, svcname.length() - 2);
268 String calcName = svcname + " ";
271 msawsmenu = new JMenu(svcname);
272 rmsawsmenu.add(msawsmenu);
275 boolean hasparams = service.hasParameters();
278 String action = "Align ";
279 if (submitGaps == true)
282 msawsmenu = new JMenu(MessageManager.formatMessage(
283 "label.realign_with_params", new String[]
285 msawsmenu.setToolTipText(MessageManager
286 .getString("label.align_sequences_to_existing_alignment"));
287 rmsawsmenu.add(msawsmenu);
289 final boolean withGaps = submitGaps;
291 JMenuItem method = new JMenuItem(MessageManager.formatMessage(
292 "label.calcname_with_default_settings", new String[]
294 method.setToolTipText(MessageManager.formatMessage(
295 "label.action_with_default_settings", new String[]
298 method.addActionListener(new ActionListener()
300 public void actionPerformed(ActionEvent e)
302 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
303 new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
304 true, alignFrame.getViewport().getAlignment()
305 .getDataset(), alignFrame);
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
317 .getString("label.view_and_change_parameters_before_alignment"));
319 method.addActionListener(new ActionListener()
321 public void actionPerformed(ActionEvent e)
323 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
324 new MsaWSClient(service, null, null, true, alignFrame
325 .getTitle(), msa, withGaps, true, alignFrame
326 .getViewport().getAlignment().getDataset(), alignFrame);
330 msawsmenu.add(method);
331 List<WsParamSetI> presets = service.getParamStore().getPresets();
332 if (presets != null && presets.size() > 0)
334 JMenu presetlist = new JMenu(MessageManager.formatMessage(
335 "label.run_with_preset_params", new String[]
338 final int showToolTipFor = ToolTipManager.sharedInstance()
340 for (final WsParamSetI preset : presets)
342 final JMenuItem methodR = new JMenuItem(preset.getName());
343 final int QUICK_TOOLTIP = 1500;
344 // JAL-1582 shorten tooltip display time in these menu items as
345 // they can obscure other options
346 methodR.addMouseListener(new MouseAdapter()
349 public void mouseEntered(MouseEvent e)
351 ToolTipManager.sharedInstance().setDismissDelay(
356 public void mouseExited(MouseEvent e)
358 ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
362 methodR.setToolTipText(JvSwingUtils.wrapTooltip(
365 + (preset.isModifiable() ? MessageManager
366 .getString("label.user_preset")
368 .getString("label.service_preset"))
369 + "</strong><br/>" + preset.getDescription()
371 methodR.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
375 AlignmentView msa = alignFrame
376 .gatherSequencesForAlignment();
377 new MsaWSClient(service, preset, alignFrame.getTitle(),
378 msa, false, true, alignFrame.getViewport()
379 .getAlignment().getDataset(), alignFrame);
384 presetlist.add(methodR);
386 msawsmenu.add(presetlist);
389 if (!submitGaps && canSubmitGaps())