Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationWorker	37	35	12	0.6734693667.3%	Show methods

Class AnnotationWorker

Class AnnotationWorker	Line # 37	Total Statements 35	Complexity 12	TOTAL Coverage 0.6734693667.3%
AnnotationWorker(AlignViewportI,AlignmentViewPanel,AnnotationProviderI)   AnnotationWorker(AlignViewportI,AlignmentViewPanel,AnnotationProviderI)	5050	4.04	1.01	1.0 1.0100%
run() : void   run() : void	5959	30.030	9.09	0.675 0.67567.5%
updateAnnotation() : void   updateAnnotation() : void	131131	0.00	1.01	-1.0 -1.0 -
isDeletable() : boolean   isDeletable() : boolean	142142	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.67346936	jalview.workers.AlignCalcManagerTest.testRemoveWorkerForAnnotationjalview.workers.AlignCalcManagerTest.testRemoveWorkerForAnnotation	1PASS

 

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.workers;
22
23		import jalview.api.AlignViewportI;
24		import jalview.api.AlignmentViewPanel;
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.AlignmentI;
27		import jalview.renderer.seqfeatures.FeatureRenderer;
28
29		import java.util.ArrayList;
30		import java.util.List;
31
32		/**
33		* A class to create and update one or more alignment annotations, given a
34		* 'calculator'. Intended to support a 'plug-in' annotation worker which
35		* implements the AnnotationProviderI interface.
36		*/
		67.3% Uncovered Elements: 16 (49) Complexity: 12 Complexity Density: 0.34
37		class AnnotationWorker extends AlignCalcWorker
38		{
39		/*
40		* the provider of the annotation calculations
41		*/
42		AnnotationProviderI counter;
43
44		/**
45		* Constructor
46		*
47		* @param af
48		* @param counter
49		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
50	2	public AnnotationWorker(AlignViewportI viewport, AlignmentViewPanel panel,...
51		AnnotationProviderI counter)
52		{
53	2	super(viewport, panel);
54	2	ourAnnots = new ArrayList<>();
55	2	this.counter = counter;
56	2	calcMan.registerWorker(this);
57		}
58
		67.5% Uncovered Elements: 13 (40) Complexity: 9 Complexity Density: 0.3
59	2	@Override...
60		public void run()
61		{
62	2	try
63		{
64	2	calcMan.notifyStart(this);
65
66	2	while (!calcMan.notifyWorking(this))
67		{
68	0	try
69		{
70	0	Thread.sleep(200);
71		} catch (InterruptedException ex)
72		{
73	0	ex.printStackTrace();
74		}
75		}
76	2	if (alignViewport.isClosed())
77		{
78	0	abortAndDestroy();
79	0	return;
80		}
81
82		// removeAnnotation();
83	2	AlignmentI alignment = alignViewport.getAlignment();
84	2	if (alignment != null)
85		{
86	2	try
87		{
88	2	List<AlignmentAnnotation> anns = counter.calculateAnnotation(
89		alignment, new FeatureRenderer(alignViewport));
90	2	for (AlignmentAnnotation ann : anns)
91		{
92	2	AlignmentAnnotation theAnn = alignment.findOrCreateAnnotation(
93		ann.label, ann.description, false, null, null);
94	2	theAnn.showAllColLabels = true;
95	2	theAnn.graph = AlignmentAnnotation.BAR_GRAPH;
96	2	theAnn.scaleColLabel = true;
97	2	theAnn.annotations = ann.annotations;
98	2	setGraphMinMax(theAnn, theAnn.annotations);
99	2	theAnn.validateRangeAndDisplay();
100	2	if (!ourAnnots.contains(theAnn))
101		{
102	2	ourAnnots.add(theAnn);
103		}
104		// alignment.addAnnotation(ann);
105		}
106		} catch (IndexOutOfBoundsException x)
107		{
108		// probable race condition. just finish and return without any fuss.
109	0	return;
110		}
111		}
112		} catch (OutOfMemoryError error)
113		{
114	0	ap.raiseOOMWarning("calculating annotations", error);
115	0	calcMan.disableWorker(this);
116		} finally
117		{
118	2	calcMan.workerComplete(this);
119		}
120
121	2	if (ap != null)
122		{
123	2	ap.adjustAnnotationHeight();
124		// TODO: only need to update colour and geometry if panel height changes
125		// and view is coloured by annotation, and the annotation is actually
126		// changed!
127	2	ap.paintAlignment(true, true);
128		}
129		}
130
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
131	0	@Override...
132		public void updateAnnotation()
133		{
134		// do nothing
135		}
136
137		/**
138		* Answers true to indicate that if this worker's annotation is deleted from
139		* the display, the worker should also be removed. This prevents it running
140		* and recreating the annotation when the alignment changes.
141		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	@Override...
143		public boolean isDeletable()
144		{
145	0	return true;
146		}
147		}