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Coverage Report

  1. Project Clover database Thu Dec 4 2025 16:11:35 GMT
  2. Package jalview.ws.jws1

File SeqSearchWSClient.java

 

Coverage histogram

../../../img/srcFileCovDistChart1.png
57% of files have more coverage

Code metrics

38
85
12
1
337
234
36
0.42
7.08
12
3

Classes

Class Line # Actions
SeqSearchWSClient 53 85 36
0.029629633%
 

Contributing tests

This file is covered by 3 tests. .

Source view

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.bin.Console;
24    import jalview.datamodel.AlignmentI;
25    import jalview.datamodel.AlignmentView;
26    import jalview.gui.AlignFrame;
27    import jalview.gui.Desktop;
28    import jalview.gui.JvOptionPane;
29    import jalview.gui.WebserviceInfo;
30    import jalview.util.MessageManager;
31   
32    import java.awt.Component;
33    import java.awt.event.ActionEvent;
34    import java.awt.event.ActionListener;
35    import java.util.Enumeration;
36    import java.util.Hashtable;
37    import java.util.StringTokenizer;
38    import java.util.Vector;
39   
40    import javax.swing.JMenu;
41    import javax.swing.JMenuItem;
42   
43    import ext.vamsas.SeqSearchServiceLocator;
44    import ext.vamsas.SeqSearchServiceSoapBindingStub;
45    import ext.vamsas.ServiceHandle;
46   
47    /**
48    * DOCUMENT ME!
49    *
50    * @author $author$
51    * @version $Revision$
52    */
 
53    public class SeqSearchWSClient extends WS1Client
54    {
55    /**
56    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
57    */
58    ext.vamsas.SeqSearchI server;
59   
60    /**
61    * Creates a new MsaWSClient object that uses a service given by an externally
62    * retrieved ServiceHandle
63    *
64    * @param sh
65    * service handle of type AbstractName(MsaWS)
66    * @param altitle
67    * DOCUMENT ME!
68    * @param msa
69    * DOCUMENT ME!
70    * @param submitGaps
71    * DOCUMENT ME!
72    * @param preserveOrder
73    * DOCUMENT ME!
74    */
75   
 
76  0 toggle public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
77    jalview.datamodel.AlignmentView msa, String db,
78    AlignmentI seqdataset, AlignFrame _alignFrame)
79    {
80  0 super();
81  0 alignFrame = _alignFrame;
82    // can generalise the two errors below for metadata mapping from interface
83    // name to service client name
84  0 if (!sh.getAbstractName().equals(this.getServiceActionKey()))
85    {
86  0 JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
87    MessageManager.formatMessage(
88    "label.service_called_is_not_seq_search_service",
89    new String[]
90    { sh.getName() }),
91    MessageManager.getString("label.internal_jalview_error"),
92    JvOptionPane.WARNING_MESSAGE);
93   
94  0 return;
95    }
96   
97  0 if ((wsInfo = setWebService(sh)) == null)
98    {
99  0 JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
100    MessageManager.formatMessage(
101    "label.seq_search_service_is_unknown", new String[]
102    { sh.getName() }),
103    MessageManager.getString("label.internal_jalview_error"),
104    JvOptionPane.WARNING_MESSAGE);
105   
106  0 return;
107    }
108  0 startSeqSearchClient(altitle, msa, db, seqdataset);
109   
110    }
111   
112    /**
113    * non-process web service interaction - use this for calling HEADLESS
114    * synchronous service methods
115    *
116    * @param sh
117    */
 
118  0 toggle public SeqSearchWSClient(ServiceHandle sh)
119    {
120  0 setWebService(sh, true);
121    }
122   
 
123  6 toggle public SeqSearchWSClient()
124    {
125   
126  6 super();
127    // add a class reference to the list
128    }
129   
 
130  0 toggle private void startSeqSearchClient(String altitle, AlignmentView msa,
131    String db, AlignmentI seqdataset)
132    {
133  0 if (!locateWebService())
134    {
135  0 return;
136    }
137  0 String visdb = (db == null || db == "") ? "default" : db; // need a visible
138    // name for a
139    // sequence db
140  0 boolean profileSearch = msa.getSequences().length > 2 ? true : false;
141    // single sequence or profile from alignment view
142  0 wsInfo.setProgressText("Searching " + visdb
143  0 + (!profileSearch
144    ? " with sequence "
145    + msa.getSequences()[0].getRefSeq().getName()
146    : " with profile")
147    + " from " + altitle + "\nJob details\n");
148   
149  0 String jobtitle = WebServiceName
150  0 + ((WebServiceName.indexOf("earch") > -1) ? " " : " search ")
151    + " of " + visdb
152  0 + (!profileSearch
153    ? " with sequence "
154    + msa.getSequences()[0].getRefSeq().getName()
155    : " with profile")
156    + " from " + altitle;
157  0 SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL,
158    wsInfo, alignFrame, WebServiceName, jobtitle, msa, db,
159    seqdataset);
160  0 wsInfo.setthisService(ssthread);
161  0 ssthread.start();
162    }
163   
164    /**
165    * Initializes the server field with a valid service implementation.
166    *
167    * @return true if service was located.
168    */
 
169  0 toggle private boolean locateWebService()
170    {
171    // this can be abstracted using reflection
172    // TODO: MuscleWS transmuted to generic MsaWS client
173  0 SeqSearchServiceLocator loc = new SeqSearchServiceLocator(); // Default
174   
175  0 try
176    {
177  0 this.server = loc.getSeqSearchService(new java.net.URL(WsURL));
178  0 ((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One
179    // minute
180    // timeout
181    } catch (Exception ex)
182    {
183  0 wsInfo.setProgressText("Serious! " + WebServiceName
184    + " Service location failed\nfor URL :" + WsURL + "\n"
185    + ex.getMessage());
186  0 wsInfo.setStatus(WebserviceInfo.ERROR);
187  0 ex.printStackTrace();
188   
189  0 return false;
190    }
191   
192  0 loc.getEngine().setOption("axis", "1");
193   
194  0 return true;
195    }
196   
 
197  0 toggle protected String getServiceActionKey()
198    {
199  0 return "SeqSearch";
200    }
201   
 
202  0 toggle protected String getServiceActionDescription()
203    {
204  0 return "Sequence Database Search";
205    }
206   
207    // simple caching of db parameters for each service endpoint
208    private static Hashtable dbParamsForEndpoint;
 
209  6 toggle static
210    {
211  6 dbParamsForEndpoint = new Hashtable();
212    }
213   
 
214  0 toggle public String[] getSupportedDatabases() throws Exception
215    {
216   
217    // check that we haven't already been to this service endpoint
218  0 if (dbParamsForEndpoint.containsKey(WsURL))
219    {
220  0 return (String[]) dbParamsForEndpoint.get(WsURL);
221    }
222  0 if (!locateWebService())
223    {
224  0 throw new Exception(MessageManager.formatMessage(
225    "exception.cannot_contact_service_endpoint_at", new String[]
226    { WsURL }));
227    }
228  0 String database = server.getDatabase();
229  0 if (database == null)
230    {
231  0 dbParamsForEndpoint.put(WsURL, new String[] {});
232  0 return null;
233    }
234  0 StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
235  0 String[] dbs = new String[en.countTokens()];
236  0 for (int i = 0; i < dbs.length; i++)
237    {
238  0 dbs[i++] = en.nextToken().trim();
239    }
240  0 dbParamsForEndpoint.put(WsURL, dbs);
241  0 return dbs;
242    }
243   
 
244  0 toggle @Override
245    public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
246    final AlignFrame af)
247    {
248    // look for existing database service submenus on wsmenu
249  0 Hashtable dbsrchs = new Hashtable();
250  0 Vector newdbsrch = new Vector();
251  0 Component entries[] = wsmenu.getComponents();
252  0 for (int i = 0; entries != null && i < entries.length; i++)
253    {
254  0 if (entries[i] instanceof JMenu)
255    {
256  0 dbsrchs.put(entries[i].getName(), entries[i]);
257    }
258    }
259  0 JMenu defmenu = (JMenu) dbsrchs.get("Default Database");
260  0 if (defmenu == null)
261    {
262  0 dbsrchs.put("Default Database",
263    defmenu = new JMenu("Default Database"));
264  0 newdbsrch.addElement(defmenu);
265    }
266   
267  0 String dbs[] = null;
268  0 try
269    {
270  0 dbs = new jalview.ws.jws1.SeqSearchWSClient(sh)
271    .getSupportedDatabases();
272    } catch (Exception e)
273    {
274  0 Console.warn(
275    "Database list request failed, so disabling SeqSearch Service client "
276    + sh.getName() + " at " + sh.getEndpointURL(),
277    e);
278  0 return;
279    }
280  0 JMenuItem method;
281    // do default entry
282  0 defmenu.add(method = new JMenuItem(sh.getName()));
283  0 method.setToolTipText(sh.getEndpointURL());
284  0 method.addActionListener(new ActionListener()
285    {
 
286  0 toggle @Override
287    public void actionPerformed(ActionEvent e)
288    {
289    // use same input gatherer as for secondary structure prediction
290    // we could actually parameterise the gatherer method here...
291  0 AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
292  0 new jalview.ws.jws1.SeqSearchWSClient(sh, af.getTitle(), msa, null,
293    af.getViewport().getAlignment().getDataset(), af);
294    }
295    });
296    // add entry for each database the service supports
297  0 for (int db = 0; dbs != null && db < dbs.length; db++)
298    {
299  0 JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);
300  0 if (dbmenu == null)
301    {
302  0 dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));
303  0 newdbsrch.addElement(dbmenu);
304    }
305    // add the client handler code for this service
306  0 dbmenu.add(method = new JMenuItem(sh.getName()));
307  0 method.setToolTipText(sh.getEndpointURL());
308  0 final String searchdb = dbs[db];
309  0 method.addActionListener(new ActionListener()
310    {
 
311  0 toggle @Override
312    public void actionPerformed(ActionEvent e)
313    {
314  0 AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
315  0 new jalview.ws.jws1.SeqSearchWSClient(sh, af.getTitle(), msa,
316    searchdb, af.getViewport().getAlignment().getDataset(),
317    af);
318    }
319    });
320    }
321    // add the databases onto the seqsearch menu
322  0 Enumeration e = newdbsrch.elements();
323  0 while (e.hasMoreElements())
324    {
325  0 Object el = e.nextElement();
326  0 if (el instanceof JMenu)
327    {
328  0 wsmenu.add((JMenu) el);
329    }
330    else
331    {
332  0 wsmenu.add((JMenuItem) el);
333    }
334    }
335   
336    }
337    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 16:21:53 GMT using coverage data from Thu Dec 4 2025 16:21:39 GMT.
  • OpenClover is free and open-source software.