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MsaWSClient | 49 | 50 | 21 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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. | |
11 | * | |
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. | |
16 | * | |
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. | |
20 | */ | |
21 | package jalview.ws.jws1; | |
22 | ||
23 | import java.util.Locale; | |
24 | ||
25 | import jalview.datamodel.AlignmentI; | |
26 | import jalview.datamodel.AlignmentView; | |
27 | import jalview.gui.AlignFrame; | |
28 | import jalview.gui.Desktop; | |
29 | import jalview.gui.JvOptionPane; | |
30 | import jalview.gui.WebserviceInfo; | |
31 | import jalview.util.MessageManager; | |
32 | ||
33 | import java.awt.event.ActionEvent; | |
34 | import java.awt.event.ActionListener; | |
35 | ||
36 | import javax.swing.JMenu; | |
37 | import javax.swing.JMenuItem; | |
38 | ||
39 | import ext.vamsas.MuscleWSServiceLocator; | |
40 | import ext.vamsas.MuscleWSSoapBindingStub; | |
41 | import ext.vamsas.ServiceHandle; | |
42 | ||
43 | /** | |
44 | * DOCUMENT ME! | |
45 | * | |
46 | * @author $author$ | |
47 | * @version $Revision$ | |
48 | */ | |
49 | public class MsaWSClient extends WS1Client | |
50 | { | |
51 | /** | |
52 | * server is a WSDL2Java generated stub for an archetypal MsaWSI service. | |
53 | */ | |
54 | ext.vamsas.MuscleWS server; | |
55 | ||
56 | AlignFrame alignFrame; | |
57 | ||
58 | /** | |
59 | * Creates a new MsaWSClient object that uses a service given by an externally | |
60 | * retrieved ServiceHandle | |
61 | * | |
62 | * @param sh | |
63 | * service handle of type AbstractName(MsaWS) | |
64 | * @param altitle | |
65 | * DOCUMENT ME! | |
66 | * @param msa | |
67 | * DOCUMENT ME! | |
68 | * @param submitGaps | |
69 | * DOCUMENT ME! | |
70 | * @param preserveOrder | |
71 | * DOCUMENT ME! | |
72 | */ | |
73 | ||
74 | 0 | public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, |
75 | jalview.datamodel.AlignmentView msa, boolean submitGaps, | |
76 | boolean preserveOrder, AlignmentI seqdataset, | |
77 | AlignFrame _alignFrame) | |
78 | { | |
79 | 0 | super(); |
80 | 0 | alignFrame = _alignFrame; |
81 | 0 | if (!sh.getAbstractName().equals("MsaWS")) |
82 | { | |
83 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
84 | MessageManager.formatMessage( | |
85 | "label.service_called_is_not_msa_service", | |
86 | new String[] | |
87 | { sh.getName() }), | |
88 | MessageManager.getString("label.internal_jalview_error"), | |
89 | JvOptionPane.WARNING_MESSAGE); | |
90 | ||
91 | 0 | return; |
92 | } | |
93 | ||
94 | 0 | if ((wsInfo = setWebService(sh)) == null) |
95 | { | |
96 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager |
97 | .formatMessage("label.msa_service_is_unknown", new String[] | |
98 | { sh.getName() }), | |
99 | MessageManager.getString("label.internal_jalview_error"), | |
100 | JvOptionPane.WARNING_MESSAGE); | |
101 | ||
102 | 0 | return; |
103 | } | |
104 | 0 | startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset); |
105 | ||
106 | } | |
107 | ||
108 | 6 | public MsaWSClient() |
109 | { | |
110 | 6 | super(); |
111 | // add a class reference to the list | |
112 | } | |
113 | ||
114 | 0 | private void startMsaWSClient(String altitle, AlignmentView msa, |
115 | boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset) | |
116 | { | |
117 | 0 | if (!locateWebService()) |
118 | { | |
119 | 0 | return; |
120 | } | |
121 | ||
122 | 0 | wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") |
123 | + " of " + altitle + "\nJob details\n"); | |
124 | 0 | String jobtitle = WebServiceName.toLowerCase(Locale.ROOT); |
125 | 0 | if (jobtitle.endsWith("alignment")) |
126 | { | |
127 | 0 | if (submitGaps && (!jobtitle.endsWith("realignment") |
128 | || jobtitle.indexOf("profile") == -1)) | |
129 | { | |
130 | 0 | int pos = jobtitle.indexOf("alignment"); |
131 | 0 | jobtitle = WebServiceName.substring(0, pos) + "re-alignment of " |
132 | + altitle; | |
133 | } | |
134 | else | |
135 | { | |
136 | 0 | jobtitle = WebServiceName + " of " + altitle; |
137 | } | |
138 | } | |
139 | else | |
140 | { | |
141 | 0 | jobtitle = WebServiceName + (submitGaps ? " re" : " ") |
142 | + "alignment of " + altitle; | |
143 | } | |
144 | ||
145 | 0 | MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo, |
146 | alignFrame, WebServiceName, jobtitle, msa, submitGaps, | |
147 | preserveOrder, seqdataset); | |
148 | 0 | wsInfo.setthisService(msathread); |
149 | 0 | msathread.start(); |
150 | } | |
151 | ||
152 | /** | |
153 | * Initializes the server field with a valid service implementation. | |
154 | * | |
155 | * @return true if service was located. | |
156 | */ | |
157 | 0 | private boolean locateWebService() |
158 | { | |
159 | // TODO: MuscleWS transmuted to generic MsaWS client | |
160 | 0 | MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default |
161 | ||
162 | 0 | try |
163 | { | |
164 | 0 | this.server = loc.getMuscleWS(new java.net.URL(WsURL)); |
165 | 0 | ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute |
166 | // timeout | |
167 | } catch (Exception ex) | |
168 | { | |
169 | 0 | wsInfo.setProgressText("Serious! " + WebServiceName |
170 | + " Service location failed\nfor URL :" + WsURL + "\n" | |
171 | + ex.getMessage()); | |
172 | 0 | wsInfo.setStatus(WebserviceInfo.ERROR); |
173 | 0 | ex.printStackTrace(); |
174 | ||
175 | 0 | return false; |
176 | } | |
177 | ||
178 | 0 | loc.getEngine().setOption("axis", "1"); |
179 | ||
180 | 0 | return true; |
181 | } | |
182 | ||
183 | 0 | protected String getServiceActionKey() |
184 | { | |
185 | 0 | return "MsaWS"; |
186 | } | |
187 | ||
188 | 0 | protected String getServiceActionDescription() |
189 | { | |
190 | 0 | return "Multiple Sequence Alignment"; |
191 | } | |
192 | ||
193 | /** | |
194 | * look at ourselves and work out if we are a service that can take a profile | |
195 | * and align to it | |
196 | * | |
197 | * @return true if we can send gapped sequences to the alignment service | |
198 | */ | |
199 | 0 | private boolean canSubmitGaps() |
200 | { | |
201 | // TODO: query service or extract service handle props to check if we can | |
202 | // realign | |
203 | 0 | return (WebServiceName.indexOf("lustal") > -1); // cheat! |
204 | } | |
205 | ||
206 | 0 | @Override |
207 | public void attachWSMenuEntry(JMenu msawsmenu, | |
208 | final ServiceHandle serviceHandle, final AlignFrame alignFrame) | |
209 | { | |
210 | 0 | setWebService(serviceHandle, true); // headless |
211 | 0 | JMenuItem method = new JMenuItem(WebServiceName); |
212 | 0 | method.setToolTipText(WsURL); |
213 | 0 | method.addActionListener(new ActionListener() |
214 | { | |
215 | 0 | @Override |
216 | public void actionPerformed(ActionEvent e) | |
217 | { | |
218 | 0 | AlignmentView msa = alignFrame.gatherSequencesForAlignment(); |
219 | 0 | new jalview.ws.jws1.MsaWSClient(serviceHandle, |
220 | alignFrame.getTitle(), msa, false, true, | |
221 | alignFrame.getViewport().getAlignment().getDataset(), | |
222 | alignFrame); | |
223 | ||
224 | } | |
225 | ||
226 | }); | |
227 | 0 | msawsmenu.add(method); |
228 | 0 | if (canSubmitGaps()) |
229 | { | |
230 | // We know that ClustalWS can accept partial alignments for refinement. | |
231 | 0 | final JMenuItem methodR = new JMenuItem( |
232 | serviceHandle.getName() + " Realign"); | |
233 | 0 | methodR.setToolTipText(WsURL); |
234 | 0 | methodR.addActionListener(new ActionListener() |
235 | { | |
236 | 0 | @Override |
237 | public void actionPerformed(ActionEvent e) | |
238 | { | |
239 | 0 | AlignmentView msa = alignFrame.gatherSequencesForAlignment(); |
240 | 0 | new jalview.ws.jws1.MsaWSClient(serviceHandle, |
241 | alignFrame.getTitle(), msa, true, true, | |
242 | alignFrame.getViewport().getAlignment().getDataset(), | |
243 | alignFrame); | |
244 | ||
245 | } | |
246 | ||
247 | }); | |
248 | 0 | msawsmenu.add(methodR); |
249 | ||
250 | } | |
251 | ||
252 | } | |
253 | } |