Coverage Report
File SimilarityScoreModel.java
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44% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| SimilarityScoreModel | 28 | 6 | 2 |
Contributing tests
This file is covered by 8 tests.
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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 | ||
| 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 | */ | |
| 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 | */ | |
| 54 | 11 | public static MatrixI similarityToDistance(MatrixI similarities) |
| 55 | { | |
| 56 | 11 | MatrixI distances = similarities.copy(); |
| 57 | ||
| 58 | 11 | distances.reverseRange(true); |
| 59 | ||
| 60 | 11 | return distances; |
| 61 | } | |
| 62 | ||
| 63 | } |