Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SimilarityScoreModel	28	6	2	0.00%	Show methods

Class SimilarityScoreModel

Class SimilarityScoreModel	Line # 28	Total Statements 6	Complexity 2	TOTAL Coverage 0.00%
findDistances(AlignmentView,SimilarityParamsI) : MatrixI   findDistances(AlignmentView,SimilarityParamsI) : MatrixI	3636	3.03	1.01	0.0 0.00%
similarityToDistance(MatrixI) : MatrixI   similarityToDistance(MatrixI) : MatrixI	5454	3.03	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.api.analysis.ScoreModelI;
24		import jalview.api.analysis.SimilarityParamsI;
25		import jalview.datamodel.AlignmentView;
26		import jalview.math.MatrixI;
27
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
28		public abstract class SimilarityScoreModel implements ScoreModelI
29		{
30
31		/**
32		* Computed similarity scores are converted to distance scores by subtracting
33		* every value from the maximum value. That is, maximum similarity corresponds
34		* to zero distance, and smaller similarities to larger distances.
35		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
36	0	@Override...
37		public MatrixI findDistances(AlignmentView seqData,
38		SimilarityParamsI options)
39		{
40	0	MatrixI similarities = findSimilarities(seqData, options);
41
42	0	MatrixI distances = similarityToDistance(similarities);
43
44	0	return distances;
45		}
46
47		/**
48		* Converts a matrix of similarity scores to distance scores, by reversing the
49		* range of the scores, mapping the maximum to zero. The input matrix is not
50		* modified.
51		*
52		* @param similarities
53		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
54	0	public static MatrixI similarityToDistance(MatrixI similarities)...
55		{
56	0	MatrixI distances = similarities.copy();
57
58	0	distances.reverseRange(true);
59
60	0	return distances;
61		}
62
63		}