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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.ws.jws1

File SeqSearchWSClient.java

 

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53% of files have more coverage

Code metrics

38
85
12
1
338
234
36
0.42
7.08
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3

Classes

Class Line # Actions
SeqSearchWSClient 52 85 36 131
0.029629633%
 

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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 jalview.datamodel.AlignmentI;
24    import jalview.datamodel.AlignmentView;
25    import jalview.gui.AlignFrame;
26    import jalview.gui.Desktop;
27    import jalview.gui.JvOptionPane;
28    import jalview.gui.WebserviceInfo;
29    import jalview.util.MessageManager;
30   
31    import java.awt.Component;
32    import java.awt.event.ActionEvent;
33    import java.awt.event.ActionListener;
34    import java.util.Enumeration;
35    import java.util.Hashtable;
36    import java.util.StringTokenizer;
37    import java.util.Vector;
38   
39    import javax.swing.JMenu;
40    import javax.swing.JMenuItem;
41   
42    import ext.vamsas.SeqSearchServiceLocator;
43    import ext.vamsas.SeqSearchServiceSoapBindingStub;
44    import ext.vamsas.ServiceHandle;
45   
46    /**
47    * DOCUMENT ME!
48    *
49    * @author $author$
50    * @version $Revision$
51    */
 
52    public class SeqSearchWSClient extends WS1Client
53    {
54    /**
55    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
56    */
57    ext.vamsas.SeqSearchI server;
58   
59    AlignFrame alignFrame;
60   
61    /**
62    * Creates a new MsaWSClient object that uses a service given by an externally
63    * retrieved ServiceHandle
64    *
65    * @param sh
66    * service handle of type AbstractName(MsaWS)
67    * @param altitle
68    * DOCUMENT ME!
69    * @param msa
70    * DOCUMENT ME!
71    * @param submitGaps
72    * DOCUMENT ME!
73    * @param preserveOrder
74    * DOCUMENT ME!
75    */
76   
 
77  0 toggle public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
78    jalview.datamodel.AlignmentView msa, String db,
79    AlignmentI seqdataset, AlignFrame _alignFrame)
80    {
81  0 super();
82  0 alignFrame = _alignFrame;
83    // can generalise the two errors below for metadata mapping from interface
84    // name to service client name
85  0 if (!sh.getAbstractName().equals(this.getServiceActionKey()))
86    {
87  0 JvOptionPane.showMessageDialog(Desktop.desktop,
88    MessageManager.formatMessage(
89    "label.service_called_is_not_seq_search_service",
90    new String[]
91    { sh.getName() }),
92    MessageManager.getString("label.internal_jalview_error"),
93    JvOptionPane.WARNING_MESSAGE);
94   
95  0 return;
96    }
97   
98  0 if ((wsInfo = setWebService(sh)) == null)
99    {
100  0 JvOptionPane.showMessageDialog(Desktop.desktop,
101    MessageManager.formatMessage(
102    "label.seq_search_service_is_unknown", new String[]
103    { sh.getName() }),
104    MessageManager.getString("label.internal_jalview_error"),
105    JvOptionPane.WARNING_MESSAGE);
106   
107  0 return;
108    }
109  0 startSeqSearchClient(altitle, msa, db, seqdataset);
110   
111    }
112   
113    /**
114    * non-process web service interaction - use this for calling HEADLESS
115    * synchronous service methods
116    *
117    * @param sh
118    */
 
119  0 toggle public SeqSearchWSClient(ServiceHandle sh)
120    {
121  0 setWebService(sh, true);
122    }
123   
 
124  1 toggle public SeqSearchWSClient()
125    {
126   
127  1 super();
128    // add a class reference to the list
129    }
130   
 
131  0 toggle private void startSeqSearchClient(String altitle, AlignmentView msa,
132    String db, AlignmentI seqdataset)
133    {
134  0 if (!locateWebService())
135    {
136  0 return;
137    }
138  0 String visdb = (db == null || db == "") ? "default" : db; // need a visible
139    // name for a
140    // sequence db
141  0 boolean profileSearch = msa.getSequences().length > 2 ? true : false;
142    // single sequence or profile from alignment view
143  0 wsInfo.setProgressText("Searching " + visdb
144  0 + (!profileSearch
145    ? " with sequence "
146    + msa.getSequences()[0].getRefSeq().getName()
147    : " with profile")
148    + " from " + altitle + "\nJob details\n");
149   
150  0 String jobtitle = WebServiceName
151  0 + ((WebServiceName.indexOf("earch") > -1) ? " " : " search ")
152    + " of " + visdb
153  0 + (!profileSearch
154    ? " with sequence "
155    + msa.getSequences()[0].getRefSeq().getName()
156    : " with profile")
157    + " from " + altitle;
158  0 SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL,
159    wsInfo, alignFrame, WebServiceName, jobtitle, msa, db,
160    seqdataset);
161  0 wsInfo.setthisService(ssthread);
162  0 ssthread.start();
163    }
164   
165    /**
166    * Initializes the server field with a valid service implementation.
167    *
168    * @return true if service was located.
169    */
 
170  0 toggle private boolean locateWebService()
171    {
172    // this can be abstracted using reflection
173    // TODO: MuscleWS transmuted to generic MsaWS client
174  0 SeqSearchServiceLocator loc = new SeqSearchServiceLocator(); // Default
175   
176  0 try
177    {
178  0 this.server = loc.getSeqSearchService(new java.net.URL(WsURL));
179  0 ((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One
180    // minute
181    // timeout
182    } catch (Exception ex)
183    {
184  0 wsInfo.setProgressText("Serious! " + WebServiceName
185    + " Service location failed\nfor URL :" + WsURL + "\n"
186    + ex.getMessage());
187  0 wsInfo.setStatus(WebserviceInfo.ERROR);
188  0 ex.printStackTrace();
189   
190  0 return false;
191    }
192   
193  0 loc.getEngine().setOption("axis", "1");
194   
195  0 return true;
196    }
197   
 
198  0 toggle protected String getServiceActionKey()
199    {
200  0 return "SeqSearch";
201    }
202   
 
203  0 toggle protected String getServiceActionDescription()
204    {
205  0 return "Sequence Database Search";
206    }
207   
208    // simple caching of db parameters for each service endpoint
209    private static Hashtable dbParamsForEndpoint;
 
210  1 toggle static
211    {
212  1 dbParamsForEndpoint = new Hashtable();
213    }
214   
 
215  0 toggle public String[] getSupportedDatabases() throws Exception
216    {
217   
218    // check that we haven't already been to this service endpoint
219  0 if (dbParamsForEndpoint.containsKey(WsURL))
220    {
221  0 return (String[]) dbParamsForEndpoint.get(WsURL);
222    }
223  0 if (!locateWebService())
224    {
225  0 throw new Exception(MessageManager.formatMessage(
226    "exception.cannot_contact_service_endpoint_at", new String[]
227    { WsURL }));
228    }
229  0 String database = server.getDatabase();
230  0 if (database == null)
231    {
232  0 dbParamsForEndpoint.put(WsURL, new String[] {});
233  0 return null;
234    }
235  0 StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
236  0 String[] dbs = new String[en.countTokens()];
237  0 for (int i = 0; i < dbs.length; i++)
238    {
239  0 dbs[i++] = en.nextToken().trim();
240    }
241  0 dbParamsForEndpoint.put(WsURL, dbs);
242  0 return dbs;
243    }
244   
 
245  0 toggle @Override
246    public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
247    final AlignFrame af)
248    {
249    // look for existing database service submenus on wsmenu
250  0 Hashtable dbsrchs = new Hashtable();
251  0 Vector newdbsrch = new Vector();
252  0 Component entries[] = wsmenu.getComponents();
253  0 for (int i = 0; entries != null && i < entries.length; i++)
254    {
255  0 if (entries[i] instanceof JMenu)
256    {
257  0 dbsrchs.put(entries[i].getName(), entries[i]);
258    }
259    }
260  0 JMenu defmenu = (JMenu) dbsrchs.get("Default Database");
261  0 if (defmenu == null)
262    {
263  0 dbsrchs.put("Default Database",
264    defmenu = new JMenu("Default Database"));
265  0 newdbsrch.addElement(defmenu);
266    }
267   
268  0 String dbs[] = null;
269  0 try
270    {
271  0 dbs = new jalview.ws.jws1.SeqSearchWSClient(sh)
272    .getSupportedDatabases();
273    } catch (Exception e)
274    {
275  0 jalview.bin.Cache.log.warn(
276    "Database list request failed, so disabling SeqSearch Service client "
277    + sh.getName() + " at " + sh.getEndpointURL(),
278    e);
279  0 return;
280    }
281  0 JMenuItem method;
282    // do default entry
283  0 defmenu.add(method = new JMenuItem(sh.getName()));
284  0 method.setToolTipText(sh.getEndpointURL());
285  0 method.addActionListener(new ActionListener()
286    {
 
287  0 toggle @Override
288    public void actionPerformed(ActionEvent e)
289    {
290    // use same input gatherer as for secondary structure prediction
291    // we could actually parameterise the gatherer method here...
292  0 AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
293  0 new jalview.ws.jws1.SeqSearchWSClient(sh, af.getTitle(), msa, null,
294    af.getViewport().getAlignment().getDataset(), af);
295    }
296    });
297    // add entry for each database the service supports
298  0 for (int db = 0; dbs != null && db < dbs.length; db++)
299    {
300  0 JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);
301  0 if (dbmenu == null)
302    {
303  0 dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));
304  0 newdbsrch.addElement(dbmenu);
305    }
306    // add the client handler code for this service
307  0 dbmenu.add(method = new JMenuItem(sh.getName()));
308  0 method.setToolTipText(sh.getEndpointURL());
309  0 final String searchdb = dbs[db];
310  0 method.addActionListener(new ActionListener()
311    {
 
312  0 toggle @Override
313    public void actionPerformed(ActionEvent e)
314    {
315  0 AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
316  0 new jalview.ws.jws1.SeqSearchWSClient(sh, af.getTitle(), msa,
317    searchdb, af.getViewport().getAlignment().getDataset(),
318    af);
319    }
320    });
321    }
322    // add the databases onto the seqsearch menu
323  0 Enumeration e = newdbsrch.elements();
324  0 while (e.hasMoreElements())
325    {
326  0 Object el = e.nextElement();
327  0 if (el instanceof JMenu)
328    {
329  0 wsmenu.add((JMenu) el);
330    }
331    else
332    {
333  0 wsmenu.add((JMenuItem) el);
334    }
335    }
336   
337    }
338    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.