Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ComplementConsensusThread	39	14	12	0.00%	Show methods

Class ComplementConsensusThread

Class ComplementConsensusThread	Line # 39	Total Statements 14	Complexity 12	TOTAL Coverage 0.00%
ComplementConsensusThread(AlignViewportI,AlignmentViewPanel)   ComplementConsensusThread(AlignViewportI,AlignmentViewPanel)	4242	1.01	1.01	0.0 0.00%
getConsensusAnnotation() : AlignmentAnnotation   getConsensusAnnotation() : AlignmentAnnotation	4848	1.01	1.01	0.0 0.00%
getViewportConsensus() : Hashtable<String, Object>[]   getViewportConsensus() : Hashtable<String, Object>[]	5454	1.01	1.01	0.0 0.00%
computeConsensus(AlignmentI) : void   computeConsensus(AlignmentI) : void	6363	6.06	3.03	0.0 0.00%
deriveConsensus(AlignmentAnnotation,Hashtable<String, Object>[]) : void   deriveConsensus(AlignmentAnnotation,Hashtable<String, Object>[]) : void	100100	1.01	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	107107	4.04	5.05	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.AAFrequency;
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.ConcurrentModificationException;
30		import java.util.Hashtable;
31
32		/**
33		* A thread to recompute the consensus of the cDNA complement for a linked
34		* protein alignment.
35		*
36		* @author gmcarstairs
37		*
38		*/
		0% Uncovered Elements: 24 (24) Complexity: 12 Complexity Density: 0.86
39		public class ComplementConsensusThread extends ConsensusThread
40		{
41
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
42	0	public ComplementConsensusThread(AlignViewportI alignViewport,...
43		AlignmentViewPanel alignPanel)
44		{
45	0	super(alignViewport, alignPanel);
46		}
47
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
48	0	@Override...
49		protected AlignmentAnnotation getConsensusAnnotation()
50		{
51	0	return alignViewport.getComplementConsensusAnnotation();
52		}
53
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	@Override...
55		protected Hashtable<String, Object>[] getViewportConsensus()
56		{
57	0	return alignViewport.getComplementConsensusHash();
58		}
59
60		/**
61		* Calculate the cDNA consensus and store it on the Viewport
62		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
63	0	@Override...
64		protected void computeConsensus(AlignmentI alignment)
65		{
66	0	@SuppressWarnings("unchecked")
67		Hashtable<String, Object>[] hconsensus = new Hashtable[alignment
68		.getWidth()];
69
70		// SequenceI[] aseqs = getSequences();
71
72		/*
73		* Allow 3 tries at this, since this thread can start up while we are still
74		* modifying protein-codon mappings on the alignment
75		*/
76	0	for (int i = 0; i < 3; i++)
77		{
78	0	try
79		{
80	0	AAFrequency.calculateCdna(alignment, hconsensus);
81	0	break;
82		} catch (ConcurrentModificationException e)
83		{
84		// try again
85		}
86		}
87
88	0	alignViewport.setComplementConsensusHash(hconsensus);
89		}
90
91		/**
92		* Convert the computed consensus data into the desired annotation for
93		* display.
94		*
95		* @param consensusAnnotation
96		* the annotation to be populated
97		* @param consensusData
98		* the computed consensus data
99		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
100	0	protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,...
101		Hashtable<String, Object>[] consensusData)
102		{
103	0	AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
104		alignViewport.isShowSequenceLogo(), getSequences().length);
105		}
106
		0% Uncovered Elements: 6 (6) Complexity: 5 Complexity Density: 1.25
107	0	@Override...
108		public void updateResultAnnotation(boolean immediate)
109		{
110	0	AlignmentAnnotation consensus = getConsensusAnnotation();
111	0	Hashtable<String, Object>[] hconsensus = getViewportConsensus();
112	0	if (immediate || !calcMan.isWorking(this) && consensus != null
113		&& hconsensus != null)
114		{
115	0	deriveConsensus(consensus, hconsensus);
116		}
117		}
118
119		}