Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SmithWatermanModel	37	19	11	0.00%	Show methods

Class SmithWatermanModel

Class SmithWatermanModel	Line # 37	Total Statements 19	Complexity 11	TOTAL Coverage 0.00%
SmithWatermanModel()   SmithWatermanModel()	4646	0.00	1.01	-1.0 -1.0 -
findSimilarities(AlignmentView,SimilarityParamsI) : MatrixI   findSimilarities(AlignmentView,SimilarityParamsI) : MatrixI	5050	14.014	5.05	0.0 0.00%
getName() : String   getName() : String	8282	1.01	1.01	0.0 0.00%
isDNA() : boolean   isDNA() : boolean	8888	1.01	1.01	0.0 0.00%
isProtein() : boolean   isProtein() : boolean	9494	1.01	1.01	0.0 0.00%
getDescription() : String   getDescription() : String	100100	1.01	1.01	0.0 0.00%
getInstance(AlignmentViewPanel) : ScoreModelI   getInstance(AlignmentViewPanel) : ScoreModelI	106106	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.analysis.scoremodels;
22
23		import jalview.analysis.AlignSeq;
24		import jalview.api.AlignmentViewPanel;
25		import jalview.api.analysis.ScoreModelI;
26		import jalview.api.analysis.SimilarityParamsI;
27		import jalview.datamodel.AlignmentView;
28		import jalview.datamodel.SequenceI;
29		import jalview.math.Matrix;
30		import jalview.math.MatrixI;
31		import jalview.util.Comparison;
32
33		/**
34		* A class that computes pairwise similarity scores using the Smith-Waterman
35		* alignment algorithm
36		*/
		0% Uncovered Elements: 34 (34) Complexity: 11 Complexity Density: 0.58
37		public class SmithWatermanModel extends SimilarityScoreModel
38		{
39		private static final String NAME = "Smith Waterman Score";
40
41		private String description;
42
43		/**
44		* Constructor
45		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
46	0	public SmithWatermanModel()...
47		{
48		}
49
		0% Uncovered Elements: 22 (22) Complexity: 5 Complexity Density: 0.36
50	0	@Override...
51		public MatrixI findSimilarities(AlignmentView seqData,
52		SimilarityParamsI options)
53		{
54	0	SequenceI[] sequenceString = seqData
55		.getVisibleAlignment(Comparison.GAP_SPACE).getSequencesArray();
56	0	int noseqs = sequenceString.length;
57	0	double[][] distances = new double[noseqs][noseqs];
58
59	0	double max = -1;
60
61	0	for (int i = 0; i < (noseqs - 1); i++)
62		{
63	0	for (int j = i; j < noseqs; j++)
64		{
65	0	AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j],
66	0	seqData.isNa() ? "dna" : "pep");
67	0	as.calcScoreMatrix();
68	0	as.traceAlignment();
69	0	as.printAlignment(System.out);
70	0	distances[i][j] = as.maxscore;
71
72	0	if (max < distances[i][j])
73		{
74	0	max = distances[i][j];
75		}
76		}
77		}
78
79	0	return new Matrix(distances);
80		}
81
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
82	0	@Override...
83		public String getName()
84		{
85	0	return NAME;
86		}
87
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
88	0	@Override...
89		public boolean isDNA()
90		{
91	0	return true;
92		}
93
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
94	0	@Override...
95		public boolean isProtein()
96		{
97	0	return true;
98		}
99
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
100	0	@Override...
101		public String getDescription()
102		{
103	0	return description;
104		}
105
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
106	0	@Override...
107		public ScoreModelI getInstance(AlignmentViewPanel avp)
108		{
109	0	return this;
110		}
111		}