Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SecondaryStructureConsensusThread	40	65	34	0.00%	Show methods

Class SecondaryStructureConsensusThread

Class SecondaryStructureConsensusThread	Line # 40	Total Statements 65	Complexity 34	TOTAL Coverage 0.00%
SecondaryStructureConsensusThread(AlignViewportI,AlignmentViewPanel)   SecondaryStructureConsensusThread(AlignViewportI,AlignmentViewPanel)	4242	1.01	1.01	0.0 0.00%
run() : void   run() : void	4848	16.016	6.06	0.0 0.00%
eraseSSConsensus(int) : void   eraseSSConsensus(int) : void	8888	4.04	2.02	0.0 0.00%
computeSSConsensus(AlignmentI) : void   computeSSConsensus(AlignmentI) : void	103103	9.09	1.01	0.0 0.00%
getSequences() : SequenceI[]   getSequences() : SequenceI[]	124124	1.01	1.01	0.0 0.00%
setColourSchemeConsensus(Map<String, ProfilesI>) : void   setColourSchemeConsensus(Map<String, ProfilesI>) : void	132132	3.03	2.02	0.0 0.00%
getSSConsensusAnnotation() : List<AlignmentAnnotation>   getSSConsensusAnnotation() : List<AlignmentAnnotation>	147147	1.01	1.01	0.0 0.00%
getSecondaryStructureSources() : List<String>   getSecondaryStructureSources() : List<String>	153153	1.01	1.01	0.0 0.00%
getGapAnnotation() : AlignmentAnnotation   getGapAnnotation() : AlignmentAnnotation	163163	1.01	1.01	0.0 0.00%
updateAnnotation() : void   updateAnnotation() : void	172172	1.01	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	178178	24.024	15.015	0.0 0.00%
deriveSSConsensus(AlignmentAnnotation,ProfilesI) : void   deriveSSConsensus(AlignmentAnnotation,ProfilesI) : void	242242	2.02	1.01	0.0 0.00%
getViewportSSConsensus() : Map<String, ProfilesI>   getViewportSSConsensus() : Map<String, ProfilesI>	258258	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 java.util.Collections;
24		import java.util.HashMap;
25		import java.util.List;
26		import java.util.Map;
27
28		import jalview.analysis.AAFrequency;
29		import jalview.api.AlignViewportI;
30		import jalview.api.AlignmentViewPanel;
31		import jalview.datamodel.AlignmentAnnotation;
32		import jalview.datamodel.AlignmentI;
33		import jalview.datamodel.Annotation;
34		import jalview.datamodel.ProfilesI;
35		import jalview.datamodel.SequenceI;
36		import jalview.renderer.ResidueShaderI;
37		import jalview.util.Constants;
38		import jalview.util.MessageManager;
39
		0% Uncovered Elements: 106 (106) Complexity: 34 Complexity Density: 0.52
40		public class SecondaryStructureConsensusThread extends AlignCalcWorker
41		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
42	0	public SecondaryStructureConsensusThread(AlignViewportI alignViewport,...
43		AlignmentViewPanel alignPanel)
44		{
45	0	super(alignViewport, alignPanel);
46		}
47
		0% Uncovered Elements: 24 (24) Complexity: 6 Complexity Density: 0.38
48	0	@Override...
49		public void run()
50		{
51	0	List<AlignmentAnnotation> ssConsensus = getSSConsensusAnnotation();
52	0	if (ssConsensus == null)
53		{
54	0	return;
55		}
56	0	if (alignViewport.isClosed())
57		{
58	0	abortAndDestroy();
59	0	return;
60		}
61
62	0	AlignmentI alignment = alignViewport.getAlignment();
63
64	0	int aWidth = -1;
65
66	0	if (alignment == null || (aWidth = alignment.getWidth()) < 0)
67		{
68	0	return;
69		}
70
71	0	alignViewport.setSecondaryStructureSources();
72	0	eraseSSConsensus(aWidth);
73	0	computeSSConsensus(alignment);
74	0	updateResultAnnotation(true);
75
76	0	if (ap != null)
77		{
78	0	ap.adjustAnnotationHeight();
79		}
80		}
81
82		/**
83		* Clear out any existing consensus annotations
84		*
85		* @param aWidth
86		* the width (number of columns) of the annotated alignment
87		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
88	0	protected void eraseSSConsensus(int aWidth)...
89		{
90	0	List<AlignmentAnnotation> ssConsensuses = getSSConsensusAnnotation();
91	0	for (AlignmentAnnotation ssConsensus : ssConsensuses)
92		{
93	0	if (ssConsensus != null)
94		{
95	0	ssConsensus.annotations = new Annotation[aWidth];
96		}
97		}
98		}
99
100		/**
101		* @param alignment
102		*/
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11
103	0	protected void computeSSConsensus(AlignmentI alignment)...
104		{
105
106	0	SequenceI[] aseqs = getSequences();
107	0	int width = alignment.getWidth();
108	0	Map<String, ProfilesI> hSSConsensusProfileMap = new HashMap<String, ProfilesI>();
109	0	List<String> ssSources = getSecondaryStructureSources();
110	0	for (String ssSource : ssSources)
111		{
112	0	ProfilesI hSSConsensus = AAFrequency.calculateSS(aseqs, width, 0,
113		width, true, ssSource, null);
114	0	hSSConsensusProfileMap.put(ssSource, hSSConsensus);
115		}
116
117	0	alignViewport.setSequenceSSConsensusHash(hSSConsensusProfileMap);
118	0	setColourSchemeConsensus(hSSConsensusProfileMap);
119		}
120
121		/**
122		* @return
123		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
124	0	protected SequenceI[] getSequences()...
125		{
126	0	return alignViewport.getAlignment().getSequencesArray();
127		}
128
129		/**
130		* @param hconsensus
131		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
132	0	protected void setColourSchemeConsensus(...
133		Map<String, ProfilesI> ssConsensusProfileMap)
134		{
135	0	ResidueShaderI cs = alignViewport.getResidueShading();
136	0	if (cs != null)
137		{
138	0	cs.setSSConsensusProfileMap(ssConsensusProfileMap);
139		}
140		}
141
142		/**
143		* Get the Consensus annotation for the alignment
144		*
145		* @return
146		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
147	0	protected List<AlignmentAnnotation> getSSConsensusAnnotation()...
148		{
149	0	return alignViewport
150		.getAlignmentSecondaryStructureConsensusAnnotation();
151		}
152
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
153	0	protected List<String> getSecondaryStructureSources()...
154		{
155	0	return alignViewport.getSecondaryStructureSources();
156		}
157
158		/**
159		* Get the Gap annotation for the alignment
160		*
161		* @return
162		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
163	0	protected AlignmentAnnotation getGapAnnotation()...
164		{
165	0	return alignViewport.getAlignmentGapAnnotation();
166		}
167
168		/**
169		* update the consensus annotation from the sequence profile data using
170		* current visualization settings.
171		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
172	0	@Override...
173		public void updateAnnotation()
174		{
175	0	updateResultAnnotation(false);
176		}
177
		0% Uncovered Elements: 40 (40) Complexity: 15 Complexity Density: 0.62
178	0	public void updateResultAnnotation(boolean immediate)...
179		{
180	0	List<AlignmentAnnotation> ssConsensuses = getSSConsensusAnnotation();
181	0	Map<String, ProfilesI> ssConsensusProfileMap = getViewportSSConsensus();
182
183		// we might be called when there is no SS available..
184	0	if (ssConsensuses==null || ssConsensusProfileMap==null)
185		{
186	0	return;
187		}
188	0	boolean singleProvider = false;
189
190	0	if(ssConsensusProfileMap.keySet() != null && ssConsensusProfileMap.keySet().size() == 2)
191		{
192	0	singleProvider = true; //Single provider if size is 2 (All, Provider 1)
193		}
194
195	0	for (AlignmentAnnotation ssConsensus : ssConsensuses)
196		{
197	0	ProfilesI ssConsensusProfile = null;
198	0	for (String source : ssConsensusProfileMap.keySet())
199		{
200	0	if (ssConsensus.description.startsWith(source))
201		{
202	0	ssConsensusProfile = ssConsensusProfileMap.get(source);
203	0	ssConsensus.visible = source.equals(Constants.SS_ALL_PROVIDERS) && singleProvider ? false : true;
204
205	0	break;
206		}
207		}
208	0	if (ssConsensusProfile == null)
209		{
210	0	continue;
211		}
212	0	if (immediate || !calcMan.isWorking(this) && ssConsensus != null
213		&& ssConsensusProfile != null)
214		{
215	0	deriveSSConsensus(ssConsensus, ssConsensusProfile);
216
217	0	if (ssConsensusProfile.get(1) != null)
218		{
219	0	ssConsensus.setNoOfSequencesIncluded(
220		ssConsensusProfile.get(1).getSeqWithSSCount());
221		}
222	0	ssConsensus.setNoOfTracksIncluded(ssConsensusProfile.getCount());
223	0	ssConsensus.hasData=ssConsensusProfile.getCount()>0;
224	0	if (!ssConsensus.hasData) {
225	0	ssConsensus.visible = false;
226		}
227		}
228
229
230		}
231		}
232
233		/**
234		* Convert the computed consensus data into the desired annotation for
235		* display.
236		*
237		* @param consensusAnnotation
238		* the annotation to be populated
239		* @param hconsensus
240		* the computed consensus data
241		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
242	0	protected void deriveSSConsensus(AlignmentAnnotation ssConsensus,...
243		ProfilesI hSSConsensus)
244		{
245
246	0	long nseq = getSequences().length;
247	0	AAFrequency.completeSSConsensus(ssConsensus, hSSConsensus,
248		hSSConsensus.getStartColumn(), hSSConsensus.getEndColumn() + 1,
249		alignViewport.isIgnoreGapsConsensus(),
250		alignViewport.isShowSequenceLogo(), nseq);
251		}
252
253		/**
254		* Get the consensus data stored on the viewport.
255		*
256		* @return
257		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
258	0	protected Map<String, ProfilesI> getViewportSSConsensus()...
259		{
260		// TODO convert ComplementConsensusThread to use Profile
261	0	return alignViewport.getSequenceSSConsensusHash();
262		}
263		}