Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PhmmerAction	27	12	5	0.00%	Show methods
PhmmerAction.Builder	29	4	2	0.00%	Show methods

Class PhmmerAction

Class PhmmerAction	Line # 27	Total Statements 12	Complexity 5	TOTAL Coverage 0.00%
newBuilder(AlignmentWebServiceClientI) : Builder   newBuilder(AlignmentWebServiceClientI) : Builder	4646	1.01	1.01	0.0 0.00%
PhmmerAction(Builder)   PhmmerAction(Builder)	5353	2.02	1.01	0.0 0.00%
perform(AlignmentViewport,List<ArgumentI>,Credentials,TaskEventListener<AlignmentI>) : TaskI<AlignmentI>   perform(AlignmentViewport,List<ArgumentI>,Credentials,TaskEventListener<AlignmentI>) : TaskI<AlignmentI>	5959	7.07	1.01	0.0 0.00%
createTask(AlignViewportI,List<ArgumentI>,Credentials) : PhmmerTask   createTask(AlignViewportI,List<ArgumentI>,Credentials) : PhmmerTask	7171	1.01	1.01	0.0 0.00%
isActive(AlignmentViewport) : boolean   isActive(AlignmentViewport) : boolean	7777	1.01	1.01	0.0 0.00%

 

Class PhmmerAction.Builder

Class PhmmerAction.Builder	Line # 29	Total Statements 4	Complexity 2	TOTAL Coverage 0.00%
Builder(AlignmentWebServiceClientI)   Builder(AlignmentWebServiceClientI)	3333	3.03	1.01	0.0 0.00%
build() : PhmmerAction   build() : PhmmerAction	4040	1.01	1.01	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws2.actions.hmmer;
2
3		import java.util.List;
4		import java.util.Objects;
5
6		import jalview.api.AlignViewportI;
7		import jalview.datamodel.AlignmentI;
8		import jalview.viewmodel.AlignmentViewport;
9		import jalview.ws.params.ArgumentI;
10		import jalview.ws2.actions.BaseAction;
11		import jalview.ws2.actions.PollingTaskExecutor;
12		import jalview.ws2.actions.api.TaskEventListener;
13		import jalview.ws2.actions.api.TaskI;
14		import jalview.ws2.api.Credentials;
15		import jalview.ws2.client.api.AlignmentWebServiceClientI;
16		import jalview.ws2.client.api.WebServiceClientI;
17
18		/**
19		* Implementation of the {@link BaseAction} for the phmmer client. This is NOT
20		* how you should implement it. The action should be more generic and cover
21		* range of similar services.
22		*
23		* @author mmwarowny
24		*
25		*/
26		// FIXME: Not an alignment action (temporary hack)
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.42
27		public class PhmmerAction extends BaseAction<AlignmentI>
28		{
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
29		public static class Builder extends BaseAction.Builder<PhmmerAction>
30		{
31		protected AlignmentWebServiceClientI client;
32
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
33	0	private Builder(AlignmentWebServiceClientI client)...
34		{
35	0	super();
36	0	Objects.requireNonNull(client);
37	0	this.client = client;
38		}
39
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
40	0	public PhmmerAction build()...
41		{
42	0	return new PhmmerAction(this);
43		}
44		}
45
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
46	0	public static Builder newBuilder(AlignmentWebServiceClientI client)...
47		{
48	0	return new Builder(client);
49		}
50
51		protected final AlignmentWebServiceClientI client;
52
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
53	0	public PhmmerAction(Builder builder)...
54		{
55	0	super(builder);
56	0	client = builder.client;
57		}
58
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
59	0	public TaskI<AlignmentI> perform(AlignmentViewport viewport,...
60		List<ArgumentI> args, Credentials credentials,
61		TaskEventListener<AlignmentI> handler)
62		{
63	0	var task = createTask(viewport, args, credentials);
64	0	task.addTaskEventListener(handler);
65	0	var executor = PollingTaskExecutor.fromPool(viewport.getServiceExecutor());
66	0	var future = executor.submit(task);
67	0	task.setCancelAction(() -> { future.cancel(true); });
68	0	return task;
69		}
70
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	public PhmmerTask createTask(AlignViewportI viewport,...
72		List<ArgumentI> args, Credentials credentials)
73		{
74	0	return new PhmmerTask(client, args, credentials, viewport.getAlignmentView(true));
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@Override...
78		public boolean isActive(AlignmentViewport viewport)
79		{
80	0	return false;
81		}
82		}