Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignCalcWorkerAdapter	19	48	19	0.00%	Show methods
AlignCalcWorkerAdapter.WorkerListener	160	0	3	0.00%	Show methods

Class AlignCalcWorkerAdapter

Class AlignCalcWorkerAdapter	Line # 19	Total Statements 48	Complexity 19	TOTAL Coverage 0.00%
taskCompleted(TaskI,AnnotationResult) : void   taskCompleted(TaskI,AnnotationResult) : void	3535	13.013	3.03	0.0 0.00%
AlignCalcWorkerAdapter(AlignViewportI,AlignmentViewPanel,AnnotationAction,List<ArgumentI>,Credentials)   AlignCalcWorkerAdapter(AlignViewportI,AlignmentViewPanel,AnnotationAction,List<ArgumentI>,Credentials)	6666	4.04	1.01	0.0 0.00%
getCalcName() : String   getCalcName() : String	7575	1.01	1.01	0.0 0.00%
updateAnnotation() : void   updateAnnotation() : void	8181	0.00	1.01	-1.0 -1.0 -
updateOurAnnots(List<AlignmentAnnotation>) : void   updateOurAnnots(List<AlignmentAnnotation>) : void	8787	8.08	3.03	0.0 0.00%
startUp() : void   startUp() : void	9999	8.08	2.02	0.0 0.00%
poll() : boolean   poll() : boolean	114114	1.01	1.01	0.0 0.00%
cancel() : void   cancel() : void	120120	4.04	1.01	0.0 0.00%
done() : void   done() : void	133133	4.04	2.02	0.0 0.00%
isDeletable() : boolean   isDeletable() : boolean	148148	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	154154	1.01	1.01	0.0 0.00%
setWorkerListener(WorkerListener) : void   setWorkerListener(WorkerListener) : void	181181	3.03	2.02	0.0 0.00%

 

Class AlignCalcWorkerAdapter.WorkerListener

Class AlignCalcWorkerAdapter.WorkerListener	Line # 160	Total Statements 0	Complexity 3	TOTAL Coverage 0.00%
workerStarted(AlignCalcWorkerAdapter) : void   workerStarted(AlignCalcWorkerAdapter) : void	162162	0.00	1.01	-1.0 -1.0 -
workerStopped(AlignCalcWorkerAdapter) : void   workerStopped(AlignCalcWorkerAdapter) : void	166166	0.00	1.01	-1.0 -1.0 -
workerHasResult(AlignCalcWorkerAdapter,AnnotationResult) : void   workerHasResult(AlignCalcWorkerAdapter,AnnotationResult) : void	170170	0.00	1.01	-1.0 -1.0 -

 

Contributing tests

Source view

1		package jalview.ws2.actions.annotation;
2
3		import java.util.ArrayList;
4		import java.util.Collections;
5		import java.util.List;
6
7		import jalview.analysis.AlignmentAnnotationUtils;
8		import jalview.api.AlignViewportI;
9		import jalview.api.AlignmentViewPanel;
10		import jalview.api.PollableAlignCalcWorkerI;
11		import jalview.datamodel.AlignmentAnnotation;
12		import jalview.datamodel.AlignmentI;
13		import jalview.workers.AlignCalcWorker;
14		import jalview.ws.params.ArgumentI;
15		import jalview.ws2.actions.api.TaskEventListener;
16		import jalview.ws2.actions.api.TaskI;
17		import jalview.ws2.api.Credentials;
18
		0% Uncovered Elements: 72 (72) Complexity: 19 Complexity Density: 0.4
19		public class AlignCalcWorkerAdapter extends AlignCalcWorker implements PollableAlignCalcWorkerI
20		{
21		private static int calcCount = 0;
22
23		private final int calcNumber = calcCount++;
24
25		private final AnnotationAction action;
26
27		private final List<ArgumentI> args;
28
29		private final Credentials credentials;
30
31		private TaskI<AnnotationResult> currentTask = null;
32
33		private TaskEventListener<AnnotationResult> taskListener = new TaskEventListener<>()
34		{
		0% Uncovered Elements: 17 (17) Complexity: 3 Complexity Density: 0.23
35	0	@Override...
36		public void taskCompleted(TaskI source, AnnotationResult result)
37		{
38	0	int graphGroup = alignViewport.getAlignment().getLastGraphGroup();
39	0	List<AlignmentAnnotation> annotations = new ArrayList<>();
40	0	for (AlignmentAnnotation ala : result.getAnnotations())
41		{
42	0	if (ala.graphGroup > 0)
43	0	ala.graphGroup += graphGroup;
44	0	var newAnnot = alignViewport.getAlignment()
45		.updateFromOrCopyAnnotation(ala);
46	0	if (newAnnot.sequenceRef != null)
47		{
48	0	newAnnot.sequenceRef.addAlignmentAnnotation(newAnnot);
49	0	newAnnot.adjustForAlignment();
50	0	AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(
51		newAnnot, newAnnot.label, newAnnot.getCalcId());
52		}
53	0	annotations.add(newAnnot);
54		}
55	0	updateOurAnnots(annotations);
56	0	listener.workerHasResult(
57		AlignCalcWorkerAdapter.this,
58		new AnnotationResult(
59		annotations,
60		result.hasFeatures,
61		result.featureColours,
62		result.featureFilters));
63		}
64		};
65
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
66	0	public AlignCalcWorkerAdapter(AlignViewportI alignViewport, AlignmentViewPanel alignPanel, AnnotationAction action,...
67		List<ArgumentI> args, Credentials credentials)
68		{
69	0	super(alignViewport, alignPanel);
70	0	this.action = action;
71	0	this.args = args;
72	0	this.credentials = credentials;
73		}
74
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	@Override...
76		public String getCalcName()
77		{
78	0	return action.getWebService().getName();
79		}
80
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
81	0	@Override...
82		public void updateAnnotation()
83		{
84
85		}
86
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
87	0	private void updateOurAnnots(List<AlignmentAnnotation> newAnnots)...
88		{
89	0	List<AlignmentAnnotation> oldAnnots = ourAnnots != null ? ourAnnots : List.of();
90	0	AlignmentI alignment = alignViewport.getAlignment();
91	0	for (AlignmentAnnotation annotation : oldAnnots)
92	0	if (!newAnnots.contains(annotation))
93	0	alignment.deleteAnnotation(annotation);
94	0	for (AlignmentAnnotation annotation : newAnnots)
95	0	alignment.validateAnnotation(annotation);
96	0	ourAnnots = Collections.synchronizedList(newAnnots);
97		}
98
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
99	0	@Override...
100		public synchronized void startUp() throws Throwable
101		{
102	0	if (alignViewport.isClosed())
103		{
104	0	calcMan.disableWorker(this);
105	0	abortAndDestroy();
106	0	throw new IllegalStateException("Starting calculation for closed viewport");
107		}
108	0	currentTask = action.createTask(alignViewport, args, credentials);
109	0	currentTask.addTaskEventListener(taskListener);
110	0	currentTask.init();
111	0	listener.workerStarted(this);
112		}
113
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
114	0	@Override...
115		public boolean poll() throws Throwable
116		{
117	0	return currentTask.poll();
118		}
119
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
120	0	@Override...
121		public synchronized void cancel()
122		{
123	0	try
124		{
125	0	currentTask.cancel();
126		} finally
127		{
128	0	currentTask.removeTaskEventListener(taskListener);
129	0	listener.workerStopped(this);
130		}
131		}
132
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
133	0	@Override...
134		public synchronized void done()
135		{
136	0	try
137		{
138	0	currentTask.complete();
139		} catch (Exception e)
140		{
141		} finally
142		{
143	0	currentTask.removeTaskEventListener(taskListener);
144	0	listener.workerStopped(this);
145		}
146		}
147
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
148	0	@Override...
149		public boolean isDeletable()
150		{
151	0	return true;
152		}
153
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
154	0	@Override...
155		public String toString()
156		{
157	0	return "AlignCalcWorkerAdapter-" + calcNumber + " for " + getCalcName();
158		}
159
		0% Uncovered Elements: 3 (3) Complexity: 3 Complexity Density: -
160		public interface WorkerListener extends java.util.EventListener
161		{
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
162	0	default void workerStarted(AlignCalcWorkerAdapter source)...
163		{
164		};
165
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
166	0	default void workerStopped(AlignCalcWorkerAdapter source)...
167		{
168		};
169
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
170	0	default void workerHasResult(AlignCalcWorkerAdapter source, AnnotationResult result)...
171		{
172		};
173
174		static final WorkerListener NULL_LISTENER = new WorkerListener()
175		{
176		};
177		}
178
179		private WorkerListener listener = WorkerListener.NULL_LISTENER;
180
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
181	0	public void setWorkerListener(WorkerListener listener)...
182		{
183	0	if (listener == null) listener = WorkerListener.NULL_LISTENER;
184	0	this.listener = listener;
185		}
186		}