Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ComplementConsensusThread	40	15	12	2	0.9292%	Show methods

Class ComplementConsensusThread

Class ComplementConsensusThread	Line # 40	Total Statements 15	Complexity 12	Uncovered Elements 2	TOTAL Coverage 0.9292%
ComplementConsensusThread(AlignViewportI,AlignmentViewPanel)   ComplementConsensusThread(AlignViewportI,AlignmentViewPanel)	4343	1.01	1.01	0.00	1.0 1.0100%
getConsensusAnnotation() : AlignmentAnnotation   getConsensusAnnotation() : AlignmentAnnotation	4949	1.01	1.01	0.00	1.0 1.0100%
getViewportConsensus() : Hashtable[]   getViewportConsensus() : Hashtable[]	5555	1.01	1.01	0.00	1.0 1.0100%
computeConsensus(AlignmentI) : void   computeConsensus(AlignmentI) : void	6464	7.07	3.03	1.01	0.8888889 0.888888988.9%
deriveConsensus(AlignmentAnnotation,Hashtable[]) : void   deriveConsensus(AlignmentAnnotation,Hashtable[]) : void	9999	1.01	1.01	0.00	1.0 1.0100%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	106106	4.04	5.05	1.01	0.8333333 0.833333383.3%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.92	jalview.io.FeaturesFileTest.simpleGff3FileLoaderjalview.io.FeaturesFileTest.simpleGff3FileLoader	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.AAFrequency;
24		import jalview.api.AlignViewportI;
25		import jalview.api.AlignmentViewPanel;
26		import jalview.datamodel.AlignmentAnnotation;
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.SequenceI;
29
30		import java.util.ConcurrentModificationException;
31		import java.util.Hashtable;
32
33		/**
34		* A thread to recompute the consensus of the cDNA complement for a linked
35		* protein alignment.
36		*
37		* @author gmcarstairs
38		*
39		*/
		92% Uncovered Elements: 2 (25) Complexity: 12 Complexity Density: 0.8
40		public class ComplementConsensusThread extends ConsensusThread
41		{
42
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
43	1	public ComplementConsensusThread(AlignViewportI alignViewport,...
44		AlignmentViewPanel alignPanel)
45		{
46	1	super(alignViewport, alignPanel);
47		}
48
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
49	3	@Override...
50		protected AlignmentAnnotation getConsensusAnnotation()
51		{
52	3	return alignViewport.getComplementConsensusAnnotation();
53		}
54
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
55	1	@Override...
56		protected Hashtable[] getViewportConsensus()
57		{
58	1	return alignViewport.getComplementConsensusHash();
59		}
60
61		/**
62		* Calculate the cDNA consensus and store it on the Viewport
63		*/
		88.9% Uncovered Elements: 1 (9) Complexity: 3 Complexity Density: 0.43
64	1	@Override...
65		protected void computeConsensus(AlignmentI alignment)
66		{
67	1	Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
68
69	1	SequenceI[] aseqs = getSequences();
70
71		/*
72		* Allow 3 tries at this, since this thread can start up while we are still
73		* modifying protein-codon mappings on the alignment
74		*/
75	1	for (int i = 0; i < 3; i++)
76		{
77	1	try
78		{
79	1	AAFrequency.calculateCdna(alignment, hconsensus);
80	1	break;
81		} catch (ConcurrentModificationException e)
82		{
83		// try again
84		}
85		}
86
87	1	alignViewport.setComplementConsensusHash(hconsensus);
88		}
89
90		/**
91		* Convert the computed consensus data into the desired annotation for
92		* display.
93		*
94		* @param consensusAnnotation
95		* the annotation to be populated
96		* @param consensusData
97		* the computed consensus data
98		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
99	1	protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,...
100		Hashtable[] consensusData)
101		{
102	1	AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
103		alignViewport.isShowSequenceLogo(), getSequences().length);
104		}
105
		83.3% Uncovered Elements: 1 (6) Complexity: 5 Complexity Density: 1.25
106	1	@Override...
107		public void updateResultAnnotation(boolean immediate)
108		{
109	1	AlignmentAnnotation consensus = getConsensusAnnotation();
110	1	Hashtable[] hconsensus = getViewportConsensus();
111	1	if (immediate || !calcMan.isWorking(this) && consensus != null
112		&& hconsensus != null)
113		{
114	1	deriveConsensus(consensus, hconsensus);
115		}
116		}
117
118		}