Classes

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

Class DistanceScoreModel

Class DistanceScoreModel	Line # 28	Total Statements 6	Complexity 2	TOTAL Coverage 0.00%
findSimilarities(AlignmentView,SimilarityParamsI) : MatrixI   findSimilarities(AlignmentView,SimilarityParamsI) : MatrixI	3434	3.03	1.01	0.0 0.00%
distanceToSimilarity(MatrixI) : MatrixI   distanceToSimilarity(MatrixI) : MatrixI	5252	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 DistanceScoreModel implements ScoreModelI
29		{
30		/**
31		* A similarity score is calculated by first computing a distance score, and
32		* then reversing the min-max range of the score values
33		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
34	0	@Override...
35		public MatrixI findSimilarities(AlignmentView seqData,
36		SimilarityParamsI options)
37		{
38	0	MatrixI distances = findDistances(seqData, options);
39
40	0	MatrixI similarities = distanceToSimilarity(distances);
41
42	0	return similarities;
43		}
44
45		/**
46		* Converts distance scores to similarity scores, by reversing the range of
47		* score values so that max becomes min and vice versa. The input matrix is
48		* not modified.
49		*
50		* @param distances
51		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
52	0	public static MatrixI distanceToSimilarity(MatrixI distances)...
53		{
54	0	MatrixI similarities = distances.copy();
55
56	0	similarities.reverseRange(false);
57
58	0	return similarities;
59		}
60		}