Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ShmrRestClient	10	16	1	1.0100%	Show methods

Class ShmrRestClient

Class ShmrRestClient	Line # 10	Total Statements 16	Complexity 1	TOTAL Coverage 1.0100%
makeShmmrRestClient() : RestClient   makeShmmrRestClient() : RestClient	1313	16.016	1.01	1.0 1.0100%

 

Contributing tests

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1		package jalview.ws.rest.clientdefs;
2
3		import jalview.io.packed.DataProvider.JvDataType;
4		import jalview.util.MessageManager;
5		import jalview.ws.rest.InputType;
6		import jalview.ws.rest.RestClient;
7		import jalview.ws.rest.RestServiceDescription;
8		import java.util.Hashtable;
9
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06
10		public class ShmrRestClient
11		{
12
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06
13	13	public static RestClient makeShmmrRestClient()...
14		{
15	13	String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
16		.getString("label.multiharmony");
17	13	Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
18	13	jalview.ws.rest.params.JobConstant toolp;
19		// toolp = new jalview.ws.rest.JobConstant("tool","jalview");
20		// iparams.put(toolp.token, toolp);
21		// toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
22		// iparams.put(toolp.token, toolp);
23		// toolp = new
24		// jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
25		// iparams.put(toolp.token, toolp);
26		// toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
27		// iparams.put(toolp.token, toolp);
28		// toolp = new jalview.ws.rest.params.JobConstant("blast","0");
29		// iparams.put(toolp.token, toolp);
30
31	13	jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
32		// SHMR server has a 65K limit for content pasted into the 'ali' parameter,
33		// so we always upload our files.
34	13	aliinput.token = "ali_file";
35	13	aliinput.writeAsFile = true;
36	13	iparams.put(aliinput.token, aliinput);
37	13	jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
38	13	sgroups.setMinsize(2);
39	13	sgroups.min = 2;// need at least two group defined to make a partition
40	13	iparams.put("groups", sgroups);
41	13	sgroups.token = "groups";
42	13	sgroups.sep = " ";
43	13	RestServiceDescription shmrService = new RestServiceDescription(
44		action,
45		description,
46		name,
47		"https://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
48		"?tool=jalview", iparams, true, false, '-');
49		// a priori knowledge of the data returned from the service
50	13	shmrService.addResultDatatype(JvDataType.ANNOTATION);
51	13	return new RestClient(shmrService);
52		}
53
54		}