Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StrucConsensusThread	33	49	25	0.660%	Show methods

Class StrucConsensusThread

Class StrucConsensusThread	Line # 33	Total Statements 49	Complexity 25	TOTAL Coverage 0.660%
StrucConsensusThread(AlignViewportI,AlignmentViewPanel)   StrucConsensusThread(AlignViewportI,AlignmentViewPanel)	3535	1.01	1.01	1.0 1.0100%
run() : void   run() : void	4747	45.045	18.018	0.5846154 0.584615458.5%
updateAnnotation() : void   updateAnnotation() : void	152152	1.01	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	158158	2.02	5.05	0.75 0.7575%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.6	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
		60% Uncovered Elements: 30 (75) Complexity: 25 Complexity Density: 0.51
33		public class StrucConsensusThread extends AlignCalcWorker
34		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
35	3	public StrucConsensusThread(AlignViewportI alignViewport,...
36		AlignmentViewPanel alignPanel)
37		{
38	3	super(alignViewport, alignPanel);
39		}
40
41		AlignmentAnnotation strucConsensus;
42
43		Hashtable[] hStrucConsensus;
44
45		private long nseq = -1;
46
		58.5% Uncovered Elements: 27 (65) Complexity: 18 Complexity Density: 0.4
47	5	@Override...
48		public void run()
49		{
50	5	try
51		{
52	5	if (calcMan.isPending(this))
53		{
54	0	return;
55		}
56	5	calcMan.notifyStart(this);
57	5	while (!calcMan.notifyWorking(this))
58		{
59	0	try
60		{
61	0	if (ap != null)
62		{
63		// ap.paintAlignment(false);
64		}
65
66	0	Thread.sleep(200);
67		} catch (Exception ex)
68		{
69	0	ex.printStackTrace();
70		}
71		}
72	5	if (alignViewport.isClosed())
73		{
74	0	abortAndDestroy();
75	0	return;
76		}
77	5	AlignmentI alignment = alignViewport.getAlignment();
78
79	5	int aWidth = -1;
80
81	?	if (alignment == null || (aWidth = alignment.getWidth()) < 0)
82		{
83	0	calcMan.workerComplete(this);
84	0	return;
85		}
86	5	strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
87	5	hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
88	5	strucConsensus.annotations = null;
89	5	strucConsensus.annotations = new Annotation[aWidth];
90
91	5	hStrucConsensus = new Hashtable[aWidth];
92
93	5	AlignmentAnnotation[] aa = alignViewport.getAlignment()
94		.getAlignmentAnnotation();
95	5	AlignmentAnnotation rnaStruc = null;
96		// select rna struct to use for calculation
97	5	if (aa != null)
98		{
99	5	for (int i = 0; i < aa.length; i++)
100		{
101	5	if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
102		{
103	5	rnaStruc = aa[i];
104	5	break;
105		}
106		}
107		}
108		// check to see if its valid
109
110	5	if (rnaStruc == null || !rnaStruc.isValidStruc())
111		{
112	0	calcMan.workerComplete(this);
113	0	return;
114		}
115
116	5	try
117		{
118	5	final SequenceI[] arr = alignment.getSequencesArray();
119	5	nseq = arr.length;
120	5	jalview.analysis.StructureFrequency.calculate(arr, 0,
121		alignment.getWidth(), hStrucConsensus, true, rnaStruc);
122		} catch (ArrayIndexOutOfBoundsException x)
123		{
124	0	calcMan.workerComplete(this);
125	0	return;
126		}
127	5	alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
128		// TODO AlignmentAnnotation rnaStruc!!!
129	5	updateResultAnnotation(true);
130		} catch (OutOfMemoryError error)
131		{
132	0	calcMan.disableWorker(this);
133
134		// consensus = null;
135		// hconsensus = null;
136	0	ap.raiseOOMWarning("calculating RNA structure consensus", error);
137		} finally
138		{
139	5	calcMan.workerComplete(this);
140	5	if (ap != null)
141		{
142	5	ap.paintAlignment(true, true);
143		}
144		}
145
146		}
147
148		/**
149		* update the consensus annotation from the sequence profile data using
150		* current visualization settings.
151		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
152	0	@Override...
153		public void updateAnnotation()
154		{
155	0	updateResultAnnotation(false);
156		}
157
		75% Uncovered Elements: 1 (4) Complexity: 5 Complexity Density: 2.5
158	5	public void updateResultAnnotation(boolean immediate)...
159		{
160	5	if (immediate || !calcMan.isWorking(this) && strucConsensus != null
161		&& hStrucConsensus != null)
162		{
163	5	StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
164		0, hStrucConsensus.length,
165		alignViewport.isIgnoreGapsConsensus(),
166		alignViewport.isShowSequenceLogo(), nseq);
167		}
168		}
169
170		}