Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JPred4WSDiscoverer	18	32	10	0.00%	Show methods

Class JPred4WSDiscoverer

Class JPred4WSDiscoverer	Line # 18	Total Statements 32	Complexity 10	TOTAL Coverage 0.00%
<clinit>, line 21()   <clinit>, line 21()	2121	3.03	2.02	0.0 0.00%
JPred4WSDiscoverer()   JPred4WSDiscoverer()	3636	0.00	1.01	-1.0 -1.0 -
getInstance() : JPred4WSDiscoverer   getInstance() : JPred4WSDiscoverer	4040	3.03	2.02	0.0 0.00%
setParamManager(ParamManager) : void   setParamManager(ParamManager) : void	4747	1.01	1.01	0.0 0.00%
getStatusForUrl(URL) : int   getStatusForUrl(URL) : int	5252	1.01	1.01	0.0 0.00%
getUrlsPropertyKey() : String   getUrlsPropertyKey() : String	5959	1.01	1.01	0.0 0.00%
getDefaultUrl() : URL   getDefaultUrl() : URL	6565	1.01	1.01	0.0 0.00%
fetchServices(URL) : List<WebService<?>>   fetchServices(URL) : List<WebService<?>>	7171	22.022	1.01	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws2.client.jpred4;
2
3		import java.io.IOException;
4		import java.net.MalformedURLException;
5		import java.net.URL;
6		import java.util.Collections;
7		import java.util.List;
8
9		import jalview.ws.params.ArgumentI;
10		import jalview.ws.params.ParamManager;
11		import jalview.ws2.actions.secstructpred.SecStructPredAction;
12		import jalview.ws2.api.WebService;
13		import jalview.ws2.client.api.AbstractWebServiceDiscoverer;
14		import jalview.ws2.client.ebi.JobDispatcherWSDiscoverer;
15		import jalview.ws2.params.SimpleParamDatastore;
16		import uk.ac.dundee.compbio.jpred.JPredClient;
17
		0% Uncovered Elements: 42 (42) Complexity: 10 Complexity Density: 0.31
18		public class JPred4WSDiscoverer extends AbstractWebServiceDiscoverer
19		{
20		private static final URL DEFAULT_URL;
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
21	0	static...
22		{
23	0	try
24		{
25	0	DEFAULT_URL = new URL("https://www.compbio.dundee.ac.uk/jpred4/");
26		} catch (MalformedURLException e)
27		{
28	0	throw new ExceptionInInitializerError(e);
29		}
30		}
31
32		private static JPred4WSDiscoverer instance = null;
33
34		private static ParamManager paramManager = null;
35
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
36	0	private JPred4WSDiscoverer()...
37		{
38		}
39
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
40	0	public static JPred4WSDiscoverer getInstance()...
41		{
42	0	if (instance == null)
43	0	instance = new JPred4WSDiscoverer();
44	0	return instance;
45		}
46
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	public static void setParamManager(ParamManager manager)...
48		{
49	0	paramManager = manager;
50		}
51
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	@Override...
53		public int getStatusForUrl(URL url)
54		{
55		// TODO: implement actual status check
56	0	return STATUS_OK;
57		}
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	@Override...
60		public String getUrlsPropertyKey()
61		{
62	0	return null;
63		}
64
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
65	0	@Override...
66		protected URL getDefaultUrl()
67		{
68	0	return DEFAULT_URL;
69		}
70
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
71	0	@Override...
72		protected List<WebService<?>> fetchServices(URL url) throws IOException
73		{
74	0	JPredClient client = new JPredClient(url);
75	0	var wsBuilder = WebService.<SecStructPredAction> newBuilder();
76	0	wsBuilder.url(url);
77	0	wsBuilder.clientName("jpred4");
78	0	wsBuilder.category("Secondary structure prediction");
79	0	wsBuilder.name("jpred4");
80	0	wsBuilder.description("JPred4 Secondary Structure Prediction.");
81	0	wsBuilder.interactive(false);
82
83	0	wsBuilder
84		.paramDatastore(new SimpleParamDatastore(url, Collections.emptyList(),
85		Collections.emptyList(), paramManager));
86	0	wsBuilder.actionClass(SecStructPredAction.class);
87	0	var webService = wsBuilder.build();
88
89	0	var actionBuilder = SecStructPredAction.newBuilder(
90		new JPred4WSClient(client, false));
91	0	actionBuilder.webService(webService);
92	0	actionBuilder.msaMode(false);
93	0	actionBuilder.name("JPred4 (Single sequence)");
94	0	webService.addAction(actionBuilder.build());
95
96	0	var actionBuilderMsa = SecStructPredAction.newBuilder(
97		new JPred4WSClient(client, true));
98	0	actionBuilderMsa.webService(webService);
99	0	actionBuilderMsa.msaMode(true);
100	0	actionBuilderMsa.name("JPred4 (MSA)");
101	0	webService.addAction(actionBuilderMsa.build());
102
103	0	return List.of(webService);
104		}
105		}