Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ConsensusThread	33	49	27	0.00%	Show methods

Class ConsensusThread

Class ConsensusThread	Line # 33	Total Statements 49	Complexity 27	TOTAL Coverage 0.00%
ConsensusThread(AlignViewportI,AlignmentViewPanel)   ConsensusThread(AlignViewportI,AlignmentViewPanel)	3535	1.01	1.01	0.0 0.00%
run() : void   run() : void	4141	16.016	7.07	0.0 0.00%
eraseConsensus(int) : void   eraseConsensus(int) : void	8080	6.06	3.03	0.0 0.00%
computeConsensus(AlignmentI) : void   computeConsensus(AlignmentI) : void	9797	5.05	1.01	0.0 0.00%
getSequences() : SequenceI[]   getSequences() : SequenceI[]	112112	1.01	1.01	0.0 0.00%
setColourSchemeConsensus(ProfilesI) : void   setColourSchemeConsensus(ProfilesI) : void	120120	3.03	2.02	0.0 0.00%
getConsensusAnnotation() : AlignmentAnnotation   getConsensusAnnotation() : AlignmentAnnotation	134134	1.01	1.01	0.0 0.00%
getGapAnnotation() : AlignmentAnnotation   getGapAnnotation() : AlignmentAnnotation	144144	1.01	1.01	0.0 0.00%
updateAnnotation() : void   updateAnnotation() : void	153153	1.01	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	159159	7.07	6.06	0.0 0.00%
deriveConsensus(AlignmentAnnotation,ProfilesI) : void   deriveConsensus(AlignmentAnnotation,ProfilesI) : void	184184	3.03	1.01	0.0 0.00%
deriveGap(AlignmentAnnotation,ProfilesI) : void   deriveGap(AlignmentAnnotation,ProfilesI) : void	206206	3.03	1.01	0.0 0.00%
getViewportConsensus() : Object   getViewportConsensus() : Object	221221	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.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.Annotation;
29		import jalview.datamodel.ProfilesI;
30		import jalview.datamodel.SequenceI;
31		import jalview.renderer.ResidueShaderI;
32
		0% Uncovered Elements: 80 (80) Complexity: 27 Complexity Density: 0.55
33		public class ConsensusThread extends AlignCalcWorker
34		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
35	0	public ConsensusThread(AlignViewportI alignViewport,...
36		AlignmentViewPanel alignPanel)
37		{
38	0	super(alignViewport, alignPanel);
39		}
40
		0% Uncovered Elements: 24 (24) Complexity: 7 Complexity Density: 0.44
41	0	@Override...
42		public void run()
43		{
44	0	AlignmentAnnotation consensus = getConsensusAnnotation();
45	0	AlignmentAnnotation gap = getGapAnnotation();
46	0	if ((consensus == null && gap == null))
47		{
48	0	return;
49		}
50	0	if (alignViewport.isClosed())
51		{
52	0	abortAndDestroy();
53	0	return;
54		}
55	0	AlignmentI alignment = alignViewport.getAlignment();
56
57	0	int aWidth = -1;
58
59	0	if (alignment == null || (aWidth = alignment.getWidth()) < 0)
60		{
61	0	return;
62		}
63
64	0	eraseConsensus(aWidth);
65	0	computeConsensus(alignment);
66	0	updateResultAnnotation(true);
67
68	0	if (ap != null)
69		{
70	0	ap.paintAlignment(true, true);
71		}
72		}
73
74		/**
75		* Clear out any existing consensus annotations
76		*
77		* @param aWidth
78		* the width (number of columns) of the annotated alignment
79		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
80	0	protected void eraseConsensus(int aWidth)...
81		{
82	0	AlignmentAnnotation consensus = getConsensusAnnotation();
83	0	if (consensus != null)
84		{
85	0	consensus.annotations = new Annotation[aWidth];
86		}
87	0	AlignmentAnnotation gap = getGapAnnotation();
88	0	if (gap != null)
89		{
90	0	gap.annotations = new Annotation[aWidth];
91		}
92		}
93
94		/**
95		* @param alignment
96		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
97	0	protected void computeConsensus(AlignmentI alignment)...
98		{
99
100	0	SequenceI[] aseqs = getSequences();
101	0	int width = alignment.getWidth();
102	0	ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
103		true);
104
105	0	alignViewport.setSequenceConsensusHash(hconsensus);
106	0	setColourSchemeConsensus(hconsensus);
107		}
108
109		/**
110		* @return
111		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	protected SequenceI[] getSequences()...
113		{
114	0	return alignViewport.getAlignment().getSequencesArray();
115		}
116
117		/**
118		* @param hconsensus
119		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
120	0	protected void setColourSchemeConsensus(ProfilesI hconsensus)...
121		{
122	0	ResidueShaderI cs = alignViewport.getResidueShading();
123	0	if (cs != null)
124		{
125	0	cs.setConsensus(hconsensus);
126		}
127		}
128
129		/**
130		* Get the Consensus annotation for the alignment
131		*
132		* @return
133		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
134	0	protected AlignmentAnnotation getConsensusAnnotation()...
135		{
136	0	return alignViewport.getAlignmentConsensusAnnotation();
137		}
138
139		/**
140		* Get the Gap annotation for the alignment
141		*
142		* @return
143		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
144	0	protected AlignmentAnnotation getGapAnnotation()...
145		{
146	0	return alignViewport.getAlignmentGapAnnotation();
147		}
148
149		/**
150		* update the consensus annotation from the sequence profile data using
151		* current visualization settings.
152		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
153	0	@Override...
154		public void updateAnnotation()
155		{
156	0	updateResultAnnotation(false);
157		}
158
		0% Uncovered Elements: 11 (11) Complexity: 6 Complexity Density: 0.86
159	0	public void updateResultAnnotation(boolean immediate)...
160		{
161	0	AlignmentAnnotation consensus = getConsensusAnnotation();
162	0	ProfilesI hconsensus = (ProfilesI) getViewportConsensus();
163	0	if (immediate || !calcMan.isWorking(this) && consensus != null
164		&& hconsensus != null)
165		{
166	0	deriveConsensus(consensus, hconsensus);
167	0	AlignmentAnnotation gap = getGapAnnotation();
168	0	if (gap != null)
169		{
170	0	deriveGap(gap, hconsensus);
171		}
172		}
173		}
174
175		/**
176		* Convert the computed consensus data into the desired annotation for
177		* display.
178		*
179		* @param consensusAnnotation
180		* the annotation to be populated
181		* @param hconsensus
182		* the computed consensus data
183		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
184	0	protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,...
185		ProfilesI hconsensus)
186		{
187	0	long nseq = getSequences().length;
188	0	consensusAnnotation.setNoOfSequencesIncluded(nseq);
189	0	AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
190		hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
191		alignViewport.isIgnoreGapsConsensus(),
192		alignViewport.isShowSequenceLogo(), nseq);
193		// TODO: JAL-4425 - from JAL-4392 - uncommenting this line will mean consensus annotation is hidden if only one sequence is shown.
194		// consensusAnnotation.hasData=hconsensus.getCount()>1;
195
196		}
197
198		/**
199		* Convert the computed consensus data into a gap annotation row for display.
200		*
201		* @param gapAnnotation
202		* the annotation to be populated
203		* @param hconsensus
204		* the computed consensus data
205		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
206	0	protected void deriveGap(AlignmentAnnotation gapAnnotation,...
207		ProfilesI hconsensus)
208		{
209	0	long nseq = getSequences().length;
210	0	gapAnnotation.setNoOfSequencesIncluded(nseq);
211	0	AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
212		hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
213		nseq);
214		}
215
216		/**
217		* Get the consensus data stored on the viewport.
218		*
219		* @return
220		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
221	0	protected Object getViewportConsensus()...
222		{
223		// TODO convert ComplementConsensusThread to use Profile
224	0	return alignViewport.getSequenceConsensusHash();
225		}
226		}