Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
WSWUBlastClient	54	48	15	0.00%	Show methods
WSWUBlastClient.ImageTwirler	193	14	7	0.00%	Show methods
WSWUBlastClient.BlastThread	242	37	7	0.00%	Show methods

Class WSWUBlastClient

Class WSWUBlastClient	Line # 54	Total Statements 48	Complexity 15	TOTAL Coverage 0.00%
WSWUBlastClient(AlignmentPanel,AlignmentI,ArrayList)   WSWUBlastClient(AlignmentPanel,AlignmentI,ArrayList)	7474	12.012	2.02	0.0 0.00%
parseResult(Sequence,String) : void   parseResult(Sequence,String) : void	106106	21.021	6.06	0.0 0.00%
updateIds() : void   updateIds() : void	149149	15.015	7.07	0.0 0.00%

 

Class WSWUBlastClient.ImageTwirler

Class WSWUBlastClient.ImageTwirler	Line # 193	Total Statements 14	Complexity 7	TOTAL Coverage 0.00%
ImageTwirler()   ImageTwirler()	199199	5.05	3.03	0.0 0.00%
run() : void   run() : void	215215	9.09	4.04	0.0 0.00%

 

Class WSWUBlastClient.BlastThread

Class WSWUBlastClient.BlastThread	Line # 242	Total Statements 37	Complexity 7	TOTAL Coverage 0.00%
BlastThread(Sequence)   BlastThread(Sequence)	250250	2.02	1.01	0.0 0.00%
run() : void   run() : void	256256	13.013	4.04	0.0 0.00%
StartJob() : void   StartJob() : void	288288	22.022	2.02	0.0 0.00%

 

Contributing 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.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		*/
		0% Uncovered Elements: 73 (73) Complexity: 15 Complexity Density: 0.31
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		*/
		0% Uncovered Elements: 14 (14) Complexity: 2 Complexity Density: 0.17
74	0	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	jalview.bin.Console.outPrintln(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		*/
		0% Uncovered Elements: 31 (31) Complexity: 6 Complexity Density: 0.29
106	0	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
		0% Uncovered Elements: 25 (25) Complexity: 7 Complexity Density: 0.47
149	0	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
		0% Uncovered Elements: 24 (24) Complexity: 7 Complexity Density: 0.5
193		class ImageTwirler extends Thread
194		{
195		ImageIcon[] imageIcon;
196
197		int imageIndex = 0;
198
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
199	0	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
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.44
215	0	@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
		0% Uncovered Elements: 44 (44) Complexity: 7 Complexity Density: 0.19
242		class BlastThread extends Thread
243		{
244		Sequence sequence;
245
246		String jobid;
247
248		boolean jobComplete = false;
249
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
250	0	BlastThread(Sequence sequence)...
251		{
252	0	jalview.bin.Console.outPrintln("blasting for: " + sequence.getName());
253	0	this.sequence = sequence;
254		}
255
		0% Uncovered Elements: 17 (17) Complexity: 4 Complexity Density: 0.31
256	0	@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	jalview.bin.Console.outPrintln("WSWuBlastClient: I'm alive "
280		+ sequence.getName() + " " + jobid); // log.debug
281		}
282		} catch (Exception ex)
283		{
284		}
285		}
286		}
287
		0% Uncovered Elements: 22 (22) Complexity: 2 Complexity Density: 0.09
288	0	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	jalview.bin.Console
319		.errPrintln("WSWUBlastClient error:\n" + exp.toString());
320	0	exp.printStackTrace();
321		}
322		}
323		}
324		}