Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignCalcWorker	39	28	11	22	0.4761904847.6%	Show methods

Class AlignCalcWorker

Class AlignCalcWorker	Line # 39	Total Statements 28	Complexity 11	Uncovered Elements 22	TOTAL Coverage 0.4761904847.6%
AlignCalcWorker(AlignViewportI,AlignmentViewPanel)   AlignCalcWorker(AlignViewportI,AlignmentViewPanel)	5252	3.03	1.01	0.00	1.0 1.0100%
abortAndDestroy() : void   abortAndDestroy() : void	6060	5.05	2.02	1.01	0.85714287 0.8571428785.7%
involves(AlignmentAnnotation) : boolean   involves(AlignmentAnnotation) : boolean	7272	1.01	1.01	0.00	1.0 1.0100%
removeAnnotation() : void   removeAnnotation() : void	8282	6.06	3.03	8.08	0.0 0.00%
isDeletable() : boolean   isDeletable() : boolean	102102	1.01	1.01	1.01	0.0 0.00%
setGraphMinMax(AlignmentAnnotation,Annotation[]) : void   setGraphMinMax(AlignmentAnnotation,Annotation[]) : void	116116	12.012	3.03	10.010	0.375 0.37537.5%

 

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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.AlignCalcManagerI;
24		import jalview.api.AlignCalcWorkerI;
25		import jalview.api.AlignViewportI;
26		import jalview.api.AlignmentViewPanel;
27		import jalview.datamodel.AlignmentAnnotation;
28		import jalview.datamodel.AlignmentI;
29		import jalview.datamodel.Annotation;
30
31		import java.util.List;
32
33		/**
34		* Base class for alignment calculation workers
35		*
36		* @author jimp
37		*
38		*/
		47.6% Uncovered Elements: 22 (42) Complexity: 11 Complexity Density: 0.39
39		public abstract class AlignCalcWorker implements AlignCalcWorkerI
40		{
41		/**
42		* manager and data source for calculations
43		*/
44		protected AlignViewportI alignViewport;
45
46		protected AlignCalcManagerI calcMan;
47
48		protected AlignmentViewPanel ap;
49
50		protected List<AlignmentAnnotation> ourAnnots;
51
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
52	380	public AlignCalcWorker(AlignViewportI alignViewport,...
53		AlignmentViewPanel alignPanel)
54		{
55	380	this.alignViewport = alignViewport;
56	380	calcMan = alignViewport.getCalcManager();
57	380	ap = alignPanel;
58		}
59
		85.7% Uncovered Elements: 1 (7) Complexity: 2 Complexity Density: 0.4
60	1	protected void abortAndDestroy()...
61		{
62	1	if (calcMan != null)
63		{
64	1	calcMan.workerComplete(this);
65		}
66	1	alignViewport = null;
67	1	calcMan = null;
68	1	ap = null;
69
70		}
71
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
72	274	@Override...
73		public boolean involves(AlignmentAnnotation i)
74		{
75	274	return ourAnnots != null && ourAnnots.contains(i);
76		}
77
78		/**
79		* Permanently removes from the alignment all annotation rows managed by this
80		* worker
81		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
82	0	@Override...
83		public void removeAnnotation()
84		{
85	0	if (ourAnnots != null && alignViewport != null)
86		{
87	0	AlignmentI alignment = alignViewport.getAlignment();
88	0	synchronized (ourAnnots)
89		{
90	0	for (AlignmentAnnotation aa : ourAnnots)
91		{
92	0	alignment.deleteAnnotation(aa, true);
93		}
94		}
95	0	ourAnnots.clear();
96		}
97		}
98
99		// TODO: allow GUI to query workers associated with annotation to add items to
100		// annotation label panel popup menu
101
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
102	0	@Override...
103		public boolean isDeletable()
104		{
105	0	return false;
106		}
107
108		/**
109		* Calculate min and max values of annotations and set as graphMin, graphMax
110		* on the AlignmentAnnotation. This is needed because otherwise, well, bad
111		* things happen.
112		*
113		* @param ann
114		* @param anns
115		*/
		37.5% Uncovered Elements: 10 (16) Complexity: 3 Complexity Density: 0.25
116	2	protected void setGraphMinMax(AlignmentAnnotation ann, Annotation[] anns)...
117		{
118		// TODO feels like this belongs inside AlignmentAnnotation!
119	2	float max = Float.MIN_VALUE;
120	2	float min = Float.MAX_VALUE;
121	2	boolean set = false;
122	2	for (Annotation a : anns)
123		{
124	0	if (a != null)
125		{
126	0	set = true;
127	0	float val = a.value;
128	0	max = Math.max(max, val);
129	0	min = Math.min(min, val);
130		}
131		}
132	2	if (set)
133		{
134	0	ann.graphMin = min;
135	0	ann.graphMax = max;
136		}
137		}
138
139		}