Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SecondaryStructureConsensusThread	33	53	28	0.00%	Show methods

Class SecondaryStructureConsensusThread

Class SecondaryStructureConsensusThread	Line # 33	Total Statements 53	Complexity 28	TOTAL Coverage 0.00%
SecondaryStructureConsensusThread(AlignViewportI,AlignmentViewPanel)   SecondaryStructureConsensusThread(AlignViewportI,AlignmentViewPanel)	3535	1.01	1.01	0.0 0.00%
run() : void   run() : void	4141	30.030	12.012	0.0 0.00%
eraseSSConsensus(int) : void   eraseSSConsensus(int) : void	115115	3.03	2.02	0.0 0.00%
computeSSConsensus(AlignmentI) : void   computeSSConsensus(AlignmentI) : void	127127	5.05	1.01	0.0 0.00%
getSequences() : SequenceI[]   getSequences() : SequenceI[]	142142	1.01	1.01	0.0 0.00%
setColourSchemeConsensus(ProfilesI) : void   setColourSchemeConsensus(ProfilesI) : void	150150	3.03	2.02	0.0 0.00%
getSSConsensusAnnotation() : AlignmentAnnotation   getSSConsensusAnnotation() : AlignmentAnnotation	164164	1.01	1.01	0.0 0.00%
updateAnnotation() : void   updateAnnotation() : void	174174	1.01	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	180180	5.05	5.05	0.0 0.00%
deriveSSConsensus(AlignmentAnnotation,ProfilesI) : void   deriveSSConsensus(AlignmentAnnotation,ProfilesI) : void	202202	2.02	1.01	0.0 0.00%
getViewportSSConsensus() : Object   getViewportSSConsensus() : Object	218218	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: 84 (84) Complexity: 28 Complexity Density: 0.53
33		public class SecondaryStructureConsensusThread extends AlignCalcWorker
34		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
35	0	public SecondaryStructureConsensusThread(AlignViewportI alignViewport,...
36		AlignmentViewPanel alignPanel)
37		{
38	0	super(alignViewport, alignPanel);
39		}
40
		0% Uncovered Elements: 44 (44) Complexity: 12 Complexity Density: 0.4
41	0	@Override...
42		public void run()
43		{
44	0	if (calcMan.isPending(this))
45		{
46	0	return;
47		}
48	0	calcMan.notifyStart(this);
49		// long started = System.currentTimeMillis();
50	0	try
51		{
52	0	AlignmentAnnotation ssConsensus = getSSConsensusAnnotation();
53	0	if ((ssConsensus == null) || calcMan.isPending(this))
54		{
55	0	calcMan.workerComplete(this);
56	0	return;
57		}
58	0	while (!calcMan.notifyWorking(this))
59		{
60	0	try
61		{
62	0	if (ap != null)
63		{
64	0	ap.paintAlignment(false, false);
65		}
66	0	Thread.sleep(200);
67		} catch (Exception ex)
68		{
69	0	ex.printStackTrace();
70		}
71		}
72	0	if (alignViewport.isClosed())
73		{
74	0	abortAndDestroy();
75	0	return;
76		}
77	0	AlignmentI alignment = alignViewport.getAlignment();
78
79	0	int aWidth = -1;
80
81	0	if (alignment == null || (aWidth = alignment.getWidth()) < 0)
82		{
83	0	calcMan.workerComplete(this);
84	0	return;
85		}
86
87	0	eraseSSConsensus(aWidth);
88	0	computeSSConsensus(alignment);
89	0	updateResultAnnotation(true);
90
91	0	if (ap != null)
92		{
93	0	ap.paintAlignment(true, true);
94		}
95		} catch (OutOfMemoryError error)
96		{
97	0	calcMan.disableWorker(this);
98	0	ap.raiseOOMWarning("calculating consensus", error);
99		} finally
100		{
101		/*
102		* e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
103		* - alignment was edited at same time as calculation was running
104		*/
105	0	calcMan.workerComplete(this);
106		}
107		}
108
109		/**
110		* Clear out any existing consensus annotations
111		*
112		* @param aWidth
113		* the width (number of columns) of the annotated alignment
114		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
115	0	protected void eraseSSConsensus(int aWidth)...
116		{
117	0	AlignmentAnnotation ssConsensus = getSSConsensusAnnotation();
118	0	if (ssConsensus != null)
119		{
120	0	ssConsensus.annotations = new Annotation[aWidth];
121		}
122		}
123
124		/**
125		* @param alignment
126		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
127	0	protected void computeSSConsensus(AlignmentI alignment)...
128		{
129
130	0	SequenceI[] aseqs = getSequences();
131	0	int width = alignment.getWidth();
132	0	ProfilesI hSSConsensus = AAFrequency.calculateSS(aseqs, width, 0, width,
133		true);
134
135	0	alignViewport.setSequenceSSConsensusHash(hSSConsensus);
136	0	setColourSchemeConsensus(hSSConsensus);
137		}
138
139		/**
140		* @return
141		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	protected SequenceI[] getSequences()...
143		{
144	0	return alignViewport.getAlignment().getSequencesArray();
145		}
146
147		/**
148		* @param hconsensus
149		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
150	0	protected void setColourSchemeConsensus(ProfilesI hSSconsensus)...
151		{
152	0	ResidueShaderI cs = alignViewport.getResidueShading();
153	0	if (cs != null)
154		{
155	0	cs.setSsConsensus(hSSconsensus);
156		}
157		}
158
159		/**
160		* Get the Consensus annotation for the alignment
161		*
162		* @return
163		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
164	0	protected AlignmentAnnotation getSSConsensusAnnotation()...
165		{
166	0	return alignViewport
167		.getAlignmentSecondaryStructureConsensusAnnotation();
168		}
169
170		/**
171		* update the consensus annotation from the sequence profile data using
172		* current visualization settings.
173		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
174	0	@Override...
175		public void updateAnnotation()
176		{
177	0	updateResultAnnotation(false);
178		}
179
		0% Uncovered Elements: 7 (7) Complexity: 5 Complexity Density: 1
180	0	public void updateResultAnnotation(boolean immediate)...
181		{
182	0	AlignmentAnnotation ssConsensus = getSSConsensusAnnotation();
183	0	ProfilesI hSSConsensus = (ProfilesI) getViewportSSConsensus();
184	0	if (immediate || !calcMan.isWorking(this) && ssConsensus != null
185		&& hSSConsensus != null)
186		{
187	0	deriveSSConsensus(ssConsensus, hSSConsensus);
188
189	0	ssConsensus.hasData=hSSConsensus.getCount()>0;
190		}
191		}
192
193		/**
194		* Convert the computed consensus data into the desired annotation for
195		* display.
196		*
197		* @param consensusAnnotation
198		* the annotation to be populated
199		* @param hconsensus
200		* the computed consensus data
201		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
202	0	protected void deriveSSConsensus(...
203		AlignmentAnnotation ssConsensusAnnotation, ProfilesI hSSConsensus)
204		{
205
206	0	long nseq = getSequences().length;
207	0	AAFrequency.completeSSConsensus(ssConsensusAnnotation, hSSConsensus,
208		hSSConsensus.getStartColumn(), hSSConsensus.getEndColumn() + 1,
209		alignViewport.isIgnoreGapsConsensus(),
210		alignViewport.isShowSequenceLogo(), nseq);
211		}
212
213		/**
214		* Get the consensus data stored on the viewport.
215		*
216		* @return
217		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
218	0	protected Object getViewportSSConsensus()...
219		{
220		// TODO convert ComplementConsensusThread to use Profile
221	0	return alignViewport.getSequenceSSConsensusHash();
222		}
223		}