Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PaSiMapModel	38	7	6	0.00%	Show methods

Class PaSiMapModel

Class PaSiMapModel	Line # 38	Total Statements 7	Complexity 6	TOTAL Coverage 0.00%
constructModel() : PaSiMap   constructModel() : PaSiMap	4141	1.01	1.01	0.0 0.00%
PaSiMapModel(AlignmentViewport,SequenceI[],boolean,ScoreModelI)   PaSiMapModel(AlignmentViewport,SequenceI[],boolean,ScoreModelI)	4646	1.01	1.01	0.0 0.00%
calculate(PairwiseAlignPanel) : void   calculate(PairwiseAlignPanel) : void	5656	2.02	1.01	0.0 0.00%
setInputData(AlignmentViewport) : void   setInputData(AlignmentViewport) : void	6161	1.01	1.01	0.0 0.00%
getPasimapData() : PaSiMap   getPasimapData() : PaSiMap	6565	1.01	1.01	0.0 0.00%
setPasimapData(PaSiMap) : void   setPasimapData(PaSiMap) : void	6969	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.viewmodel;
22
23		import jalview.analysis.PCA;
24		import jalview.analysis.PaSiMap;
25		import jalview.api.RotatableCanvasI;
26		import jalview.api.analysis.ScoreModelI;
27		import jalview.api.analysis.SimilarityParamsI;
28		import jalview.datamodel.AlignmentView;
29		import jalview.datamodel.Point;
30		import jalview.datamodel.SequenceI;
31		import jalview.datamodel.SequencePoint;
32		import jalview.gui.PairwiseAlignPanel;
33		import jalview.viewmodel.AlignmentViewport;
34
35		import java.util.List;
36		import java.util.Vector;
37
		0% Uncovered Elements: 13 (13) Complexity: 6 Complexity Density: 0.86
38		public class PaSiMapModel extends SpatialModel<PaSiMap>
39		{
40		PairwiseAlignPanel pap = null;
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
41	0	@Override...
42		public PaSiMap constructModel()
43		{
44	0	return new PaSiMap(av, scoreModel, pap);
45		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
46	0	public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs,...
47		boolean nuc, ScoreModelI modelName)
48		{
49	0	super(seqData,null,sqs,nuc, modelName,null);
50		}
51
52		/**
53		* Performs the PaSiMap calculation (in the same thread) and extracts result
54		* data needed for visualisation by PaSiMapPanel
55		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
56	0	public void calculate(PairwiseAlignPanel pap)...
57		{
58	0	this.pap = pap;
59	0	calculate();
60		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	public void setInputData(AlignmentViewport data)...
62		{
63	0	av = data;
64		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
65	0	public PaSiMap getPasimapData()...
66		{
67	0	return outputModel;
68		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
69	0	public void setPasimapData(PaSiMap pasimapData)...
70		{
71	0	outputModel = pasimapData;
72		}
73
74		}