2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.ws.jws2;
20 import java.awt.event.ActionEvent;
21 import java.awt.event.ActionListener;
22 import java.util.List;
26 import jalview.datamodel.*;
28 import compbio.data.msa.MsaWS;
29 import compbio.metadata.Argument;
30 import jalview.util.MessageManager;
31 import jalview.ws.jws2.jabaws2.Jws2Instance;
32 import jalview.ws.params.WsParamSetI;
40 public class MsaWSClient extends Jws2Client
43 * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
47 public MsaWSClient(Jws2Instance sh, String altitle,
48 jalview.datamodel.AlignmentView msa, boolean submitGaps,
49 boolean preserveOrder, Alignment seqdataset,
50 AlignFrame _alignFrame)
52 this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
53 seqdataset, _alignFrame);
54 // TODO Auto-generated constructor stub
57 public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
58 jalview.datamodel.AlignmentView msa, boolean submitGaps,
59 boolean preserveOrder, Alignment seqdataset,
60 AlignFrame _alignFrame)
62 this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
63 seqdataset, _alignFrame);
64 // TODO Auto-generated constructor stub
68 * Creates a new MsaWSClient object that uses a service given by an externally
69 * retrieved ServiceHandle
72 * service handle of type AbstractName(MsaWS)
79 * @param preserveOrder
83 public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
84 List<Argument> arguments, boolean editParams, String altitle,
85 jalview.datamodel.AlignmentView msa, boolean submitGaps,
86 boolean preserveOrder, Alignment seqdataset,
87 AlignFrame _alignFrame)
89 super(_alignFrame, preset, arguments);
90 if (!processParams(sh, editParams))
95 if (!(sh.service instanceof MsaWS))
97 // redundant at mo - but may change
101 "The Service called \n"
103 + "\nis not a \nMultiple Sequence Alignment Service !",
104 "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
108 server = (MsaWS) sh.service;
109 if ((wsInfo = setWebService(sh, false)) == null)
111 JOptionPane.showMessageDialog(Desktop.desktop,
112 "The Multiple Sequence Alignment Service named "
113 + sh.serviceType + " is unknown",
114 "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 setWebService(service, true); // headless
194 boolean finished = true, submitGaps = false;
195 JMenu msawsmenu = rmsawsmenu;
196 String svcname = WebServiceName;
197 if (svcname.endsWith("WS"))
199 svcname = svcname.substring(0, svcname.length() - 2);
201 String calcName = svcname + " ";
204 msawsmenu = new JMenu(svcname);
205 rmsawsmenu.add(msawsmenu);
208 boolean hasparams = service.hasParameters();
211 String action = "Align ";
212 if (submitGaps == true)
215 msawsmenu = new JMenu(MessageManager.formatMessage("label.realign_with_params", new String[]{svcname}));
217 .setToolTipText(MessageManager.getString("label.align_sequences_to_existing_alignment"));
218 rmsawsmenu.add(msawsmenu);
220 final boolean withGaps = submitGaps;
222 JMenuItem method = new JMenuItem(MessageManager.formatMessage("label.calcname_with_default_settings", new String[]{calcName}));
223 method.setToolTipText(MessageManager.formatMessage("label.action_with_default_settings", new String[]{action}));
225 method.addActionListener(new ActionListener()
227 public void actionPerformed(ActionEvent e)
229 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
230 new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
231 true, alignFrame.getViewport().getAlignment()
232 .getDataset(), alignFrame);
236 msawsmenu.add(method);
239 // only add these menu options if the service has user-modifiable
241 method = new JMenuItem(MessageManager.getString("label.edit_settings_and_run"));
242 method.setToolTipText(MessageManager.getString("label.view_and_change_parameters_before_alignment"));
244 method.addActionListener(new ActionListener()
246 public void actionPerformed(ActionEvent e)
248 AlignmentView msa = alignFrame.gatherSequencesForAlignment();
249 new MsaWSClient(service, null, null, true, alignFrame
250 .getTitle(), msa, withGaps, true, alignFrame
251 .getViewport().getAlignment().getDataset(), alignFrame);
255 msawsmenu.add(method);
256 List<WsParamSetI> presets = service.getParamStore().getPresets();
257 if (presets != null && presets.size() > 0)
259 JMenu presetlist = new JMenu(MessageManager.formatMessage("label.run_with_preset_params", new String[]{calcName}));
261 for (final WsParamSetI preset : presets)
263 final JMenuItem methodR = new JMenuItem(preset.getName());
264 methodR.setToolTipText("<html><p>"
265 + JvSwingUtils.wrapTooltip("<strong>"
266 + (preset.isModifiable() ? "User Preset"
267 : "Service Preset") + "</strong><br/>"
268 + preset.getDescription() + "</p>") + "</html>");
269 methodR.addActionListener(new ActionListener()
271 public void actionPerformed(ActionEvent e)
273 AlignmentView msa = alignFrame
274 .gatherSequencesForAlignment();
275 new MsaWSClient(service, preset, alignFrame.getTitle(),
276 msa, false, true, alignFrame.getViewport()
277 .getAlignment().getDataset(), alignFrame);
282 presetlist.add(methodR);
284 msawsmenu.add(presetlist);
287 if (!submitGaps && canSubmitGaps())