Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StrucConsensusThread	33	32	19	0.770%	Show methods

Class StrucConsensusThread

Class StrucConsensusThread	Line # 33	Total Statements 32	Complexity 19	TOTAL Coverage 0.770%
StrucConsensusThread(AlignViewportI,AlignmentViewPanel)   StrucConsensusThread(AlignViewportI,AlignmentViewPanel)	3535	1.01	1.01	1.0 1.0100%
run() : void   run() : void	4747	28.028	12.012	0.7 0.770%
updateAnnotation() : void   updateAnnotation() : void	112112	1.01	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	118118	2.02	5.05	0.75 0.7575%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.7	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS

 

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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.StructureFrequency;
24		import jalview.api.AlignViewportI;
25		import jalview.api.AlignmentViewPanel;
26		import jalview.datamodel.AlignmentAnnotation;
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.Annotation;
29		import jalview.datamodel.SequenceI;
30
31		import java.util.Hashtable;
32
		70% Uncovered Elements: 15 (50) Complexity: 19 Complexity Density: 0.59
33		public class StrucConsensusThread extends AlignCalcWorker
34		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
35	2	public StrucConsensusThread(AlignViewportI alignViewport,...
36		AlignmentViewPanel alignPanel)
37		{
38	2	super(alignViewport, alignPanel);
39		}
40
41		AlignmentAnnotation strucConsensus;
42
43		Hashtable[] hStrucConsensus;
44
45		private long nseq = -1;
46
		70% Uncovered Elements: 12 (40) Complexity: 12 Complexity Density: 0.43
47	2	@Override...
48		public void run()
49		{
50	2	if (alignViewport.isClosed())
51		{
52	0	abortAndDestroy();
53	0	return;
54		}
55	2	AlignmentI alignment = alignViewport.getAlignment();
56
57	2	int aWidth = -1;
58
59	?	if (alignment == null || (aWidth = alignment.getWidth()) < 0)
60		{
61	0	return;
62		}
63	2	strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
64	2	hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
65	2	strucConsensus.annotations = null;
66	2	strucConsensus.annotations = new Annotation[aWidth];
67
68	2	hStrucConsensus = new Hashtable[aWidth];
69
70	2	AlignmentAnnotation[] aa = alignViewport.getAlignment()
71		.getAlignmentAnnotation();
72	2	AlignmentAnnotation rnaStruc = null;
73		// select rna struct to use for calculation
74	2	if (aa != null)
75		{
76	2	for (int i = 0; i < aa.length; i++)
77		{
78	2	if (aa[i].isForDisplay() && aa[i].isRNA() && aa[i].isValidStruc())
79		{
80	2	rnaStruc = aa[i];
81	2	break;
82		}
83		}
84		}
85		// check to see if its valid
86
87	2	if (rnaStruc == null || !rnaStruc.isValidStruc())
88		{
89	0	return;
90		}
91
92	2	try
93		{
94	2	final SequenceI[] arr = alignment.getSequencesArray();
95	2	nseq = arr.length;
96	2	jalview.analysis.StructureFrequency.calculate(arr, 0,
97		alignment.getWidth(), hStrucConsensus, true, rnaStruc);
98		} catch (ArrayIndexOutOfBoundsException x)
99		{
100	0	return;
101		}
102	2	alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
103		// TODO AlignmentAnnotation rnaStruc!!!
104	2	updateResultAnnotation(true);
105
106		}
107
108		/**
109		* update the consensus annotation from the sequence profile data using
110		* current visualization settings.
111		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	@Override...
113		public void updateAnnotation()
114		{
115	0	updateResultAnnotation(false);
116		}
117
		75% Uncovered Elements: 1 (4) Complexity: 5 Complexity Density: 2.5
118	2	public void updateResultAnnotation(boolean immediate)...
119		{
120	2	if (immediate || !calcMan.isWorking(this) && strucConsensus != null
121		&& hStrucConsensus != null)
122		{
123	2	StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
124		0, hStrucConsensus.length,
125		alignViewport.isIgnoreGapsConsensus(),
126		alignViewport.isShowSequenceLogo(), nseq);
127		}
128		}
129
130		}