Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentComparisonThread	48	56	30	0.00%	Show methods

Class AlignmentComparisonThread

Class AlignmentComparisonThread	Line # 48	Total Statements 56	Complexity 30	TOTAL Coverage 0.00%
AlignmentComparisonThread(AlignViewportI,AlignmentViewPanel)   AlignmentComparisonThread(AlignViewportI,AlignmentViewPanel)	5151	2.02	1.01	0.0 0.00%
run() : void   run() : void	6363	33.033	17.017	0.0 0.00%
computeColumnCorrespondence(AlignViewportI,AlignViewportI) : void   computeColumnCorrespondence(AlignViewportI,AlignViewportI) : void	142142	15.015	7.07	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	172172	5.05	4.04	0.0 0.00%
updateAnnotation() : void   updateAnnotation() : void	183183	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.analysis.Conservation;
25		import jalview.analysis.scoremodels.ScoreModels;
26		import jalview.api.AlignViewportI;
27		import jalview.api.AlignmentViewPanel;
28		import jalview.bin.Console;
29		import jalview.datamodel.AlignedCodonFrame;
30		import jalview.datamodel.AlignmentAnnotation;
31		import jalview.datamodel.AlignmentI;
32		import jalview.datamodel.Annotation;
33		import jalview.datamodel.SequenceI;
34		import jalview.util.MappingUtils;
35
36		import java.util.ArrayList;
37		import java.util.ConcurrentModificationException;
38		import java.util.Hashtable;
39		import java.util.List;
40
41		/**
42		* A thread to compute the columnwise correspondence between aligned positions
43		* and their positions in a linked alignment
44		*
45		* @author jprocter
46		*
47		*/
		0% Uncovered Elements: 81 (81) Complexity: 30 Complexity Density: 0.54
48		public class AlignmentComparisonThread extends AlignCalcWorker
49		{
50
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
51	0	public AlignmentComparisonThread(AlignViewportI alignViewport,...
52		AlignmentViewPanel alignPanel)
53		{
54	0	super(alignViewport, alignPanel);
55	0	comparisonAnnot = alignViewport.getComparisonAnnotation();
56		}
57
58		Annotation[] correspondence = new Annotation[1];
59		AlignmentAnnotation comparisonAnnot=null;
60		int alWidth;
61		private int maxCor=1;
62
		0% Uncovered Elements: 45 (45) Complexity: 17 Complexity Density: 0.52
63	0	@Override...
64		public void run()
65		{
66	0	try
67		{
68	0	calcMan.notifyStart(this); // updatingConservation = true;
69
70	0	while ((calcMan != null) && (!calcMan.notifyWorking(this)))
71		{
72	0	try
73		{
74	0	if (ap != null)
75		{
76		// ap.paintAlignment(false);
77		}
78	0	Thread.sleep(200);
79		} catch (Exception ex)
80		{
81	0	ex.printStackTrace();
82		}
83		}
84	0	if ((alignViewport == null) || (calcMan == null)
85		|| (alignViewport.isClosed()))
86		{
87	0	abortAndDestroy();
88	0	return;
89		}
90	0	List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
91
92	0	AlignmentI alignment = alignViewport.getAlignment();
93	0	AlignViewportI codingComplement = alignViewport.getCodingComplement();
94	0	if (alignment == null || (alWidth = alignment.getWidth()) < 0
95		|| (codingComplement == null))
96		{
97	0	calcMan.workerComplete(this);
98		// .updatingConservation = false;
99		// AlignViewport.UPDATING_CONSERVATION = false;
100
101	0	return;
102		}
103
104	0	comparisonAnnot.annotations=correspondence;
105	0	ourAnnot.add(comparisonAnnot);
106	0	ourAnnots = ourAnnot;
107
108	0	try
109		{
110	0	computeColumnCorrespondence(alignViewport, codingComplement);
111		} catch (Throwable x)
112		{
113	0	Console.error("Unexpected error computing similarity of alignments",x);
114		// probable race condition. just finish and return without any fuss.
115	0	calcMan.workerComplete(this);
116	0	return;
117		}
118	0	updateResultAnnotation(true);
119		} catch (OutOfMemoryError error)
120		{
121	0	ap.raiseOOMWarning("calculating conservation", error);
122	0	calcMan.disableWorker(this);
123		// alignViewport.conservation = null;
124		// this.alignViewport.quality = null;
125
126		}
127	0	calcMan.workerComplete(this);
128
129	0	if ((alignViewport == null) || (calcMan == null)
130		|| (alignViewport.isClosed()))
131		{
132	0	abortAndDestroy();
133	0	return;
134		}
135	0	if (ap != null)
136		{
137	0	ap.paintAlignment(true, true);
138		}
139
140		}
141
		0% Uncovered Elements: 21 (21) Complexity: 7 Complexity Density: 0.47
142	0	private void computeColumnCorrespondence(AlignViewportI alignViewport,...
143		AlignViewportI codingComplement)
144		{
145	0	List<SequenceI> us = alignViewport.getAlignment().getSequences();
146	0	List<AlignedCodonFrame> ourMappings = alignViewport.getAlignment()
147		.getCodonFrames();
148	0	List<SequenceI> them = codingComplement.getAlignment().getSequences();
149	0	List<AlignedCodonFrame> theirMappings = codingComplement.getAlignment()
150		.getCodonFrames();
151	0	if (us == null || them == null || us.isEmpty() || them.isEmpty())
152		{
153	0	return;
154		}
155
156	0	int colEnd = alignViewport.getAlignment().getWidth();
157	0	Annotation[] colCorrsp = new Annotation[colEnd];
158	0	maxCor=0;
159	0	for (int col = 0; col < colEnd; col++)
160		{
161	0	int[] theirWidth = MappingUtils.findMappedColumns(col, ourMappings,
162		us, them, alignViewport.getGapCharacter());
163	0	int wid =theirWidth != null ? Math.abs(theirWidth[1] - theirWidth[0])
164		: 0;
165	0	colCorrsp[col] = new Annotation(
166		wid);
167	0	maxCor = Math.max(maxCor, wid);
168		}
169	0	correspondence=colCorrsp;
170		}
171
		0% Uncovered Elements: 7 (7) Complexity: 4 Complexity Density: 0.8
172	0	private void updateResultAnnotation(boolean b)...
173		{
174	0	if (b || !calcMan.isWorking(this) && correspondence!=null)
175		{
176	0	comparisonAnnot.annotations = correspondence;
177	0	comparisonAnnot.graphMax=(float)maxCor;
178	0	comparisonAnnot.validateRangeAndDisplay();
179	0	ap.paintAlignment(false, false);
180		}
181		}
182
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
183	0	@Override...
184		public void updateAnnotation()
185		{
186	0	updateResultAnnotation(false);
187
188		}
189
190		}