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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.io

File WSWUBlastClient.java

 

Coverage histogram

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

Code metrics

34
99
8
3
323
228
29
0.29
12.38
2.67
3.62

Classes

Class Line # Actions
WSWUBlastClient 54 48 15
0.00%
WSWUBlastClient.ImageTwirler 193 14 7
0.00%
WSWUBlastClient.BlastThread 242 37 7
0.00%
 

Contributing tests

No tests hitting this source file were found.

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.List;
36    import java.util.StringTokenizer;
37    import java.util.Vector;
38   
39    import javax.swing.ImageIcon;
40   
41    import uk.ac.ebi.www.Data;
42    import uk.ac.ebi.www.InputParams;
43    import uk.ac.ebi.www.WSFile;
44    import uk.ac.ebi.www.WSWUBlast;
45    import uk.ac.ebi.www.WSWUBlastService;
46    import uk.ac.ebi.www.WSWUBlastServiceLocator;
47   
48    /**
49    * DOCUMENT ME!
50    *
51    * @author $author$
52    * @version $Revision$
53    */
 
54    public class WSWUBlastClient
55    {
56    AlignmentPanel ap;
57   
58    AlignmentI al;
59   
60    CutAndPasteTransfer output = new CutAndPasteTransfer();
61   
62    int jobsRunning = 0;
63   
64    Vector suggestedIds = new Vector();
65   
66    /**
67    * Creates a new WSWUBlastClient object.
68    *
69    * @param al
70    * DOCUMENT ME!
71    * @param ids
72    * DOCUMENT ME!
73    */
 
74  0 toggle public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
75    {
76  0 this.ap = ap;
77  0 this.al = al;
78  0 output.setText(
79    MessageManager.getString("label.wswublast_client_credits"));
80   
81  0 Desktop.addInternalFrame(output, MessageManager.getString(
82    "label.blasting_for_unidentified_sequence"), 800, 300);
83   
84  0 for (int i = 0; i < ids.size(); i++)
85    {
86  0 Sequence sequence = (Sequence) ids.get(i);
87  0 System.out.println(sequence.getName());
88   
89  0 BlastThread thread = new BlastThread(sequence);
90  0 thread.start();
91  0 jobsRunning++;
92    }
93   
94  0 ImageTwirler thread = new ImageTwirler();
95  0 thread.start();
96    }
97   
98    /**
99    * DOCUMENT ME!
100    *
101    * @param id1
102    * DOCUMENT ME!
103    * @param res
104    * DOCUMENT ME!
105    */
 
106  0 toggle void parseResult(Sequence seq, String res)
107    {
108  0 StringTokenizer st = new StringTokenizer(res, "\n");
109  0 String data;
110  0 String id2;
111  0 int maxFound = 90;
112  0 StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
113   
114  0 while (st.hasMoreTokens())
115    {
116  0 data = st.nextToken();
117   
118  0 if (data.indexOf(">UNIPROT") > -1)
119    {
120  0 int index = data.indexOf(">UNIPROT") + 9;
121  0 id2 = data.substring(index, data.indexOf(" ", index));
122   
123  0 boolean identitiesFound = false;
124  0 while (!identitiesFound)
125    {
126  0 data = st.nextToken();
127   
128  0 if (data.indexOf("Identities") > -1)
129    {
130  0 identitiesFound = true;
131   
132  0 int value = Integer.parseInt(data
133    .substring(data.indexOf("(") + 1, data.indexOf("%")));
134   
135  0 if (value >= maxFound)
136    {
137  0 maxFound = value;
138  0 buffer.append(" " + id2 + " " + value + "%; ");
139  0 suggestedIds.addElement(new Object[] { seq, id2 });
140    }
141    }
142    }
143    }
144    }
145   
146  0 output.appendText(buffer.toString());
147    }
148   
 
149  0 toggle void updateIds()
150    {
151    // This must be outside the run() body as java 1.5
152    // will not return any value from the OptionPane to the expired thread.
153  0 int reply = JvOptionPane.showConfirmDialog(Desktop.desktop,
154    "Automatically update suggested ids?",
155    "Auto replace sequence ids", JvOptionPane.YES_NO_OPTION);
156   
157  0 if (reply == JvOptionPane.YES_OPTION)
158    {
159  0 Enumeration keys = suggestedIds.elements();
160  0 while (keys.hasMoreElements())
161    {
162  0 Object[] object = (Object[]) keys.nextElement();
163   
164  0 Sequence oldseq = (Sequence) object[0];
165   
166  0 oldseq.setName(object[1].toString());
167   
168    // Oldseq is actually in the dataset, we must find the
169    // Visible seq and change its name also.
170  0 for (int i = 0; i < al.getHeight(); i++)
171    {
172  0 if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
173    {
174  0 al.getSequenceAt(i).setName(oldseq.getName());
175  0 break;
176    }
177    }
178   
179  0 List<DBRefEntry> entries = oldseq.getDBRefs();
180    // BH 2019.01.25 check for 0-length was missing here
181  0 if (entries != null && entries.size() > 0)
182    {
183  0 oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
184    jalview.datamodel.DBRefSource.UNIPROT, "0",
185    entries.get(0).getAccessionId()));
186    }
187    }
188    }
189  0 ap.paintAlignment(true, false);
190   
191    }
192   
 
193    class ImageTwirler extends Thread
194    {
195    ImageIcon[] imageIcon;
196   
197    int imageIndex = 0;
198   
 
199  0 toggle public ImageTwirler()
200    {
201  0 imageIcon = new ImageIcon[9];
202   
203  0 for (int i = 0; i < 9; i++)
204    {
205  0 java.net.URL url = getClass()
206    .getResource("/images/dna" + (i + 1) + ".gif");
207   
208  0 if (url != null)
209    {
210  0 imageIcon[i] = new ImageIcon(url);
211    }
212    }
213    }
214   
 
215  0 toggle @Override
216    public void run()
217    {
218  0 while (jobsRunning > 0)
219    {
220  0 try
221    {
222  0 Thread.sleep(100);
223  0 imageIndex++;
224  0 imageIndex %= 9;
225  0 output.setFrameIcon(imageIcon[imageIndex]);
226  0 output.setTitle(MessageManager.formatMessage(
227    "label.blasting_for_unidentified_sequence_jobs_running",
228    new String[]
229    { Integer.valueOf(jobsRunning).toString() }));
230    } catch (Exception ex)
231    {
232    }
233    }
234   
235  0 if (jobsRunning == 0)
236    {
237  0 updateIds();
238    }
239    }
240    }
241   
 
242    class BlastThread extends Thread
243    {
244    Sequence sequence;
245   
246    String jobid;
247   
248    boolean jobComplete = false;
249   
 
250  0 toggle BlastThread(Sequence sequence)
251    {
252  0 System.out.println("blasting for: " + sequence.getName());
253  0 this.sequence = sequence;
254    }
255   
 
256  0 toggle @Override
257    public void run()
258    {
259  0 StartJob();
260   
261  0 while (!jobComplete)
262    {
263  0 try
264    {
265  0 WSWUBlastService service = new WSWUBlastServiceLocator();
266  0 WSWUBlast wublast = service.getWSWUBlast();
267  0 WSFile[] results = wublast.getResults(jobid);
268   
269  0 if (results != null)
270    {
271  0 String result = new String(wublast.poll(jobid, "tooloutput"));
272  0 parseResult(sequence, result);
273  0 jobComplete = true;
274  0 jobsRunning--;
275    }
276    else
277    {
278  0 Thread.sleep(10000);
279  0 System.out.println("WSWuBlastClient: I'm alive "
280    + sequence.getName() + " " + jobid); // log.debug
281    }
282    } catch (Exception ex)
283    {
284    }
285    }
286    }
287   
 
288  0 toggle void StartJob()
289    {
290  0 InputParams params = new InputParams();
291   
292  0 params.setProgram("blastp");
293  0 params.setDatabase("uniprot");
294  0 params.setMatrix("pam10");
295   
296  0 params.setNumal(5);
297  0 params.setSensitivity("low");
298  0 params.setSort("totalscore");
299  0 params.setOutformat("txt");
300  0 params.setAsync(true);
301   
302  0 try
303    {
304  0 Data inputs[] = new Data[1];
305  0 Data input = new Data();
306  0 input.setType("sequence");
307  0 input.setContent(AlignSeq.extractGaps("-. ",
308    sequence.getSequenceAsString()));
309  0 inputs[0] = input;
310   
311  0 WSWUBlastService service = new WSWUBlastServiceLocator();
312  0 WSWUBlast wublast = service.getWSWUBlast();
313  0 jobid = wublast.runWUBlast(params, inputs);
314    } catch (Exception exp)
315    {
316  0 jobComplete = true;
317  0 jobsRunning--;
318  0 System.err.println("WSWUBlastClient error:\n" + exp.toString());
319  0 exp.printStackTrace();
320    }
321    }
322    }
323    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.