Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ConservationThread	32	28	19	0.00%	Show methods

Class ConservationThread

Class ConservationThread	Line # 32	Total Statements 28	Complexity 19	TOTAL Coverage 0.00%
ConservationThread(AlignViewportI,AlignmentViewPanel)   ConservationThread(AlignViewportI,AlignmentViewPanel)	3838	2.02	1.01	0.0 0.00%
run() : void   run() : void	5151	22.022	11.011	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	101101	3.03	6.06	0.0 0.00%
updateAnnotation() : void   updateAnnotation() : void	111111	1.01	1.01	0.0 0.00%

 

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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.analysis.Conservation;
24		import jalview.api.AlignViewportI;
25		import jalview.api.AlignmentViewPanel;
26		import jalview.datamodel.AlignmentAnnotation;
27		import jalview.datamodel.AlignmentI;
28
29		import java.util.ArrayList;
30		import java.util.List;
31
		0% Uncovered Elements: 42 (42) Complexity: 19 Complexity Density: 0.68
32		public class ConservationThread extends AlignCalcWorker
33		{
34
35		private int ConsPercGaps = 25; // JBPNote : This should be a configurable
36		// property!
37
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
38	0	public ConservationThread(AlignViewportI alignViewport,...
39		AlignmentViewPanel alignPanel)
40		{
41	0	super(alignViewport, alignPanel);
42	0	ConsPercGaps = alignViewport.getConsPercGaps();
43		}
44
45		private Conservation cons;
46
47		AlignmentAnnotation conservation, quality;
48
49		int alWidth;
50
		0% Uncovered Elements: 30 (30) Complexity: 11 Complexity Density: 0.5
51	0	@Override...
52		public void run()
53		{
54	0	if ((alignViewport == null) || (calcMan == null)
55		|| (alignViewport.isClosed()))
56		{
57	0	abortAndDestroy();
58	0	return;
59		}
60	0	List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
61	0	AlignmentI alignment = alignViewport.getAlignment();
62	0	conservation = alignViewport.getAlignmentConservationAnnotation();
63	0	quality = alignViewport.getAlignmentQualityAnnot();
64	0	ourAnnot.add(conservation);
65	0	ourAnnot.add(quality);
66	0	ourAnnots = ourAnnot;
67	0	ConsPercGaps = alignViewport.getConsPercGaps();
68		// AlignViewport.UPDATING_CONSERVATION = true;
69
70	0	if (alignment == null || (alWidth = alignment.getWidth()) < 0)
71		{
72		// .updatingConservation = false;
73		// AlignViewport.UPDATING_CONSERVATION = false;
74	0	return;
75		}
76	0	try
77		{
78	0	cons = Conservation.calculateConservation("All",
79		alignment.getSequences(), 0, alWidth - 1, false,
80		ConsPercGaps, quality != null);
81		} catch (IndexOutOfBoundsException x)
82		{
83		// probable race condition. just finish and return without any fuss.
84	0	return;
85		}
86	0	updateResultAnnotation(true);
87
88	0	if ((alignViewport == null) || (calcMan == null)
89		|| (alignViewport.isClosed()))
90		{
91	0	abortAndDestroy();
92	0	return;
93		}
94	0	if (ap != null)
95		{
96	0	ap.paintAlignment(true, true);
97		}
98
99		}
100
		0% Uncovered Elements: 5 (5) Complexity: 6 Complexity Density: 2
101	0	private void updateResultAnnotation(boolean b)...
102		{
103	0	if (b || !calcMan.isWorking(this) && cons != null
104		&& conservation != null && quality != null)
105		{
106	0	alignViewport.setConservation(cons);
107	0	cons.completeAnnotations(conservation, quality, 0, alWidth);
108		}
109		}
110
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
111	0	@Override...
112		public void updateAnnotation()
113		{
114	0	updateResultAnnotation(false);
115
116		}
117		}