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jalviewX

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

File WSWUBlastClient.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
56% of files have more coverage

Code metrics

34
99
8
3
321
227
28
0.28
12.38
2.67
3.5

Classes

Class Line # Actions
WSWUBlastClient 53 48 14 73
0.00%
WSWUBlastClient.ImageTwirler 191 14 7 24
0.00%
WSWUBlastClient.BlastThread 240 37 7 44
0.00%
 

Contributing tests

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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.io;
22   
23    import jalview.analysis.AlignSeq;
24    import jalview.datamodel.AlignmentI;
25    import jalview.datamodel.DBRefEntry;
26    import jalview.datamodel.Sequence;
27    import jalview.gui.AlignmentPanel;
28    import jalview.gui.CutAndPasteTransfer;
29    import jalview.gui.Desktop;
30    import jalview.gui.JvOptionPane;
31    import jalview.util.MessageManager;
32   
33    import java.util.ArrayList;
34    import java.util.Enumeration;
35    import java.util.StringTokenizer;
36    import java.util.Vector;
37   
38    import javax.swing.ImageIcon;
39   
40    import uk.ac.ebi.www.Data;
41    import uk.ac.ebi.www.InputParams;
42    import uk.ac.ebi.www.WSFile;
43    import uk.ac.ebi.www.WSWUBlast;
44    import uk.ac.ebi.www.WSWUBlastService;
45    import uk.ac.ebi.www.WSWUBlastServiceLocator;
46   
47    /**
48    * DOCUMENT ME!
49    *
50    * @author $author$
51    * @version $Revision$
52    */
 
53    public class WSWUBlastClient
54    {
55    AlignmentPanel ap;
56   
57    AlignmentI al;
58   
59    CutAndPasteTransfer output = new CutAndPasteTransfer();
60   
61    int jobsRunning = 0;
62   
63    Vector suggestedIds = new Vector();
64   
65    /**
66    * Creates a new WSWUBlastClient object.
67    *
68    * @param al
69    * DOCUMENT ME!
70    * @param ids
71    * DOCUMENT ME!
72    */
 
73  0 toggle public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
74    {
75  0 this.ap = ap;
76  0 this.al = al;
77  0 output.setText(
78    MessageManager.getString("label.wswublast_client_credits"));
79   
80  0 Desktop.addInternalFrame(output, MessageManager.getString(
81    "label.blasting_for_unidentified_sequence"), 800, 300);
82   
83  0 for (int i = 0; i < ids.size(); i++)
84    {
85  0 Sequence sequence = (Sequence) ids.get(i);
86  0 System.out.println(sequence.getName());
87   
88  0 BlastThread thread = new BlastThread(sequence);
89  0 thread.start();
90  0 jobsRunning++;
91    }
92   
93  0 ImageTwirler thread = new ImageTwirler();
94  0 thread.start();
95    }
96   
97    /**
98    * DOCUMENT ME!
99    *
100    * @param id1
101    * DOCUMENT ME!
102    * @param res
103    * DOCUMENT ME!
104    */
 
105  0 toggle void parseResult(Sequence seq, String res)
106    {
107  0 StringTokenizer st = new StringTokenizer(res, "\n");
108  0 String data;
109  0 String id2;
110  0 int maxFound = 90;
111  0 StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
112   
113  0 while (st.hasMoreTokens())
114    {
115  0 data = st.nextToken();
116   
117  0 if (data.indexOf(">UNIPROT") > -1)
118    {
119  0 int index = data.indexOf(">UNIPROT") + 9;
120  0 id2 = data.substring(index, data.indexOf(" ", index));
121   
122  0 boolean identitiesFound = false;
123  0 while (!identitiesFound)
124    {
125  0 data = st.nextToken();
126   
127  0 if (data.indexOf("Identities") > -1)
128    {
129  0 identitiesFound = true;
130   
131  0 int value = Integer.parseInt(data
132    .substring(data.indexOf("(") + 1, data.indexOf("%")));
133   
134  0 if (value >= maxFound)
135    {
136  0 maxFound = value;
137  0 buffer.append(" " + id2 + " " + value + "%; ");
138  0 suggestedIds.addElement(new Object[] { seq, id2 });
139    }
140    }
141    }
142    }
143    }
144   
145  0 output.appendText(buffer.toString());
146    }
147   
 
148  0 toggle void updateIds()
149    {
150    // This must be outside the run() body as java 1.5
151    // will not return any value from the OptionPane to the expired thread.
152  0 int reply = JvOptionPane.showConfirmDialog(Desktop.desktop,
153    "Automatically update suggested ids?",
154    "Auto replace sequence ids", JvOptionPane.YES_NO_OPTION);
155   
156  0 if (reply == JvOptionPane.YES_OPTION)
157    {
158  0 Enumeration keys = suggestedIds.elements();
159  0 while (keys.hasMoreElements())
160    {
161  0 Object[] object = (Object[]) keys.nextElement();
162   
163  0 Sequence oldseq = (Sequence) object[0];
164   
165  0 oldseq.setName(object[1].toString());
166   
167    // Oldseq is actually in the dataset, we must find the
168    // Visible seq and change its name also.
169  0 for (int i = 0; i < al.getHeight(); i++)
170    {
171  0 if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
172    {
173  0 al.getSequenceAt(i).setName(oldseq.getName());
174  0 break;
175    }
176    }
177   
178  0 DBRefEntry[] entries = oldseq.getDBRefs();
179  0 if (entries != null)
180    {
181  0 oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
182    jalview.datamodel.DBRefSource.UNIPROT, "0",
183    entries[0].getAccessionId()));
184    }
185    }
186    }
187  0 ap.paintAlignment(true, false);
188   
189    }
190   
 
191    class ImageTwirler extends Thread
192    {
193    ImageIcon[] imageIcon;
194   
195    int imageIndex = 0;
196   
 
197  0 toggle public ImageTwirler()
198    {
199  0 imageIcon = new ImageIcon[9];
200   
201  0 for (int i = 0; i < 9; i++)
202    {
203  0 java.net.URL url = getClass()
204    .getResource("/images/dna" + (i + 1) + ".gif");
205   
206  0 if (url != null)
207    {
208  0 imageIcon[i] = new ImageIcon(url);
209    }
210    }
211    }
212   
 
213  0 toggle @Override
214    public void run()
215    {
216  0 while (jobsRunning > 0)
217    {
218  0 try
219    {
220  0 Thread.sleep(100);
221  0 imageIndex++;
222  0 imageIndex %= 9;
223  0 output.setFrameIcon(imageIcon[imageIndex]);
224  0 output.setTitle(MessageManager.formatMessage(
225    "label.blasting_for_unidentified_sequence_jobs_running",
226    new String[]
227    { Integer.valueOf(jobsRunning).toString() }));
228    } catch (Exception ex)
229    {
230    }
231    }
232   
233  0 if (jobsRunning == 0)
234    {
235  0 updateIds();
236    }
237    }
238    }
239   
 
240    class BlastThread extends Thread
241    {
242    Sequence sequence;
243   
244    String jobid;
245   
246    boolean jobComplete = false;
247   
 
248  0 toggle BlastThread(Sequence sequence)
249    {
250  0 System.out.println("blasting for: " + sequence.getName());
251  0 this.sequence = sequence;
252    }
253   
 
254  0 toggle @Override
255    public void run()
256    {
257  0 StartJob();
258   
259  0 while (!jobComplete)
260    {
261  0 try
262    {
263  0 WSWUBlastService service = new WSWUBlastServiceLocator();
264  0 WSWUBlast wublast = service.getWSWUBlast();
265  0 WSFile[] results = wublast.getResults(jobid);
266   
267  0 if (results != null)
268    {
269  0 String result = new String(wublast.poll(jobid, "tooloutput"));
270  0 parseResult(sequence, result);
271  0 jobComplete = true;
272  0 jobsRunning--;
273    }
274    else
275    {
276  0 Thread.sleep(10000);
277  0 System.out.println("WSWuBlastClient: I'm alive "
278    + sequence.getName() + " " + jobid); // log.debug
279    }
280    } catch (Exception ex)
281    {
282    }
283    }
284    }
285   
 
286  0 toggle void StartJob()
287    {
288  0 InputParams params = new InputParams();
289   
290  0 params.setProgram("blastp");
291  0 params.setDatabase("uniprot");
292  0 params.setMatrix("pam10");
293   
294  0 params.setNumal(5);
295  0 params.setSensitivity("low");
296  0 params.setSort("totalscore");
297  0 params.setOutformat("txt");
298  0 params.setAsync(true);
299   
300  0 try
301    {
302  0 Data inputs[] = new Data[1];
303  0 Data input = new Data();
304  0 input.setType("sequence");
305  0 input.setContent(AlignSeq.extractGaps("-. ",
306    sequence.getSequenceAsString()));
307  0 inputs[0] = input;
308   
309  0 WSWUBlastService service = new WSWUBlastServiceLocator();
310  0 WSWUBlast wublast = service.getWSWUBlast();
311  0 jobid = wublast.runWUBlast(params, inputs);
312    } catch (Exception exp)
313    {
314  0 jobComplete = true;
315  0 jobsRunning--;
316  0 System.err.println("WSWUBlastClient error:\n" + exp.toString());
317  0 exp.printStackTrace();
318    }
319    }
320    }
321    }
  • 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.