Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentComparisonThread	48	36	21	0.00%	Show methods

Class AlignmentComparisonThread

Class AlignmentComparisonThread	Line # 48	Total Statements 36	Complexity 21	TOTAL Coverage 0.00%
AlignmentComparisonThread(AlignViewportI,AlignmentViewPanel)   AlignmentComparisonThread(AlignViewportI,AlignmentViewPanel)	5151	1.01	1.01	0.0 0.00%
run() : void   run() : void	6262	15.015	8.08	0.0 0.00%
computeColumnCorrespondence(AlignViewportI,AlignViewportI) : void   computeColumnCorrespondence(AlignViewportI,AlignViewportI) : void	9494	14.014	7.07	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	122122	5.05	4.04	0.0 0.00%
updateAnnotation() : void   updateAnnotation() : void	133133	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: 55 (55) Complexity: 21 Complexity Density: 0.58
48		public class AlignmentComparisonThread extends AlignCalcWorker
49		{
50
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
51	0	public AlignmentComparisonThread(AlignViewportI alignViewport,...
52		AlignmentViewPanel alignPanel)
53		{
54	0	super(alignViewport, alignPanel);
55		}
56
57		Annotation[] correspondence = new Annotation[1];
58		AlignmentAnnotation comparisonAnnot=null;
59		int alWidth;
60		private int maxCor=1;
61
		0% Uncovered Elements: 21 (21) Complexity: 8 Complexity Density: 0.53
62	0	@Override...
63		public void run()
64		{
65	0	comparisonAnnot = alignViewport.getComparisonAnnotation();
66	0	if ((alignViewport == null) || (calcMan == null)
67		|| (alignViewport.isClosed()))
68		{
69	0	return;
70		}
71	0	List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
72
73	0	AlignmentI alignment = alignViewport.getAlignment();
74	0	AlignViewportI codingComplement = alignViewport.getCodingComplement();
75	0	if (alignment == null || (alWidth = alignment.getWidth()) < 0
76		|| (codingComplement == null))
77		{
78	0	return;
79		}
80
81	0	comparisonAnnot.annotations=correspondence;
82	0	ourAnnot.add(comparisonAnnot);
83	0	ourAnnots = ourAnnot;
84	0	computeColumnCorrespondence(alignViewport, codingComplement);
85	0	updateResultAnnotation(true);
86
87	0	if (ap != null)
88		{
89	0	ap.paintAlignment(true, true);
90		}
91
92		}
93
		0% Uncovered Elements: 20 (20) Complexity: 7 Complexity Density: 0.5
94	0	private void computeColumnCorrespondence(AlignViewportI alignViewport,...
95		AlignViewportI codingComplement)
96		{
97	0	List<SequenceI> us = alignViewport.getAlignment().getSequences();
98	0	List<AlignedCodonFrame> ourMappings = alignViewport.getAlignment()
99		.getCodonFrames();
100	0	List<SequenceI> them = codingComplement.getAlignment().getSequences();
101	0	if (us == null || them == null || us.isEmpty() || them.isEmpty())
102		{
103	0	return;
104		}
105
106	0	int colEnd = alignViewport.getAlignment().getWidth();
107	0	Annotation[] colCorrsp = new Annotation[colEnd];
108	0	maxCor=0;
109	0	for (int col = 0; col < colEnd; col++)
110		{
111	0	int[] theirWidth = MappingUtils.findMappedColumns(col, ourMappings,
112		us, them, alignViewport.getGapCharacter());
113	0	int wid =theirWidth != null ? Math.abs(theirWidth[1] - theirWidth[0])
114		: 0;
115	0	colCorrsp[col] = new Annotation(
116		wid);
117	0	maxCor = Math.max(maxCor, wid);
118		}
119	0	correspondence=colCorrsp;
120		}
121
		0% Uncovered Elements: 7 (7) Complexity: 4 Complexity Density: 0.8
122	0	private void updateResultAnnotation(boolean b)...
123		{
124	0	if (b || !calcMan.isWorking(this) && correspondence!=null)
125		{
126	0	comparisonAnnot.annotations = correspondence;
127	0	comparisonAnnot.graphMax=(float)maxCor;
128	0	comparisonAnnot.validateRangeAndDisplay();
129	0	ap.paintAlignment(false, false);
130		}
131		}
132
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	@Override...
134		public void updateAnnotation()
135		{
136	0	updateResultAnnotation(false);
137
138		}
139
140		}