Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationWorker	37	26	9	0.736842173.7%	Show methods

Class AnnotationWorker

Class AnnotationWorker	Line # 37	Total Statements 26	Complexity 9	TOTAL Coverage 0.736842173.7%
AnnotationWorker(AlignViewportI,AlignmentViewPanel,AnnotationProviderI)   AnnotationWorker(AlignViewportI,AlignmentViewPanel,AnnotationProviderI)	5050	4.04	1.01	1.0 1.0100%
run() : void   run() : void	5959	21.021	6.06	0.7586207 0.758620775.9%
updateAnnotation() : void   updateAnnotation() : void	109109	0.00	1.01	-1.0 -1.0 -
isDeletable() : boolean   isDeletable() : boolean	120120	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.7368421	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		*/
		73.7% Uncovered Elements: 10 (38) Complexity: 9 Complexity Density: 0.35
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
		75.9% Uncovered Elements: 7 (29) Complexity: 6 Complexity Density: 0.29
59	2	@Override...
60		public void run()
61		{
62	2	if (alignViewport.isClosed())
63		{
64	0	abortAndDestroy();
65	0	return;
66		}
67
68		// removeAnnotation();
69	2	AlignmentI alignment = alignViewport.getAlignment();
70	2	if (alignment != null)
71		{
72	2	try
73		{
74	2	List<AlignmentAnnotation> anns = counter.calculateAnnotation(
75		alignment, new FeatureRenderer(alignViewport));
76	2	for (AlignmentAnnotation ann : anns)
77		{
78	2	AlignmentAnnotation theAnn = alignment.findOrCreateAnnotation(
79		ann.label, ann.description, false, null, null);
80	2	theAnn.showAllColLabels = true;
81	2	theAnn.graph = AlignmentAnnotation.BAR_GRAPH;
82	2	theAnn.scaleColLabel = true;
83	2	theAnn.annotations = ann.annotations;
84	2	setGraphMinMax(theAnn, theAnn.annotations);
85	2	theAnn.validateRangeAndDisplay();
86	2	if (!ourAnnots.contains(theAnn))
87		{
88	2	ourAnnots.add(theAnn);
89		}
90		// alignment.addAnnotation(ann);
91		}
92		} catch (IndexOutOfBoundsException x)
93		{
94		// probable race condition. just finish and return without any fuss.
95	0	return;
96		}
97		}
98
99	2	if (ap != null)
100		{
101	2	ap.adjustAnnotationHeight();
102		// TODO: only need to update colour and geometry if panel height changes
103		// and view is coloured by annotation, and the annotation is actually
104		// changed!
105	2	ap.paintAlignment(true, true);
106		}
107		}
108
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
109	0	@Override...
110		public void updateAnnotation()
111		{
112		// do nothing
113		}
114
115		/**
116		* Answers true to indicate that if this worker's annotation is deleted from
117		* the display, the worker should also be removed. This prevents it running
118		* and recreating the annotation when the alignment changes.
119		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
120	0	@Override...
121		public boolean isDeletable()
122		{
123	0	return true;
124		}
125		}