Coverage Report
File SimilarityParamsI.java
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| SimilarityParamsI | 27 | 0 | 0 |
Contributing tests
Source view
| 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.api.analysis; | |
| 22 | ||
| 23 | /** | |
| 24 | * A description of options when computing percentage identity of two aligned | |
| 25 | * sequences | |
| 26 | */ | |
| 27 | public interface SimilarityParamsI | |
| 28 | { | |
| 29 | /** | |
| 30 | * Answers true if gap-gap aligned positions should be included in the | |
| 31 | * calculation | |
| 32 | * | |
| 33 | * @return | |
| 34 | */ | |
| 35 | boolean includeGappedColumns(); | |
| 36 | ||
| 37 | /** | |
| 38 | * Answers true if gap-residue alignment is considered a match | |
| 39 | * | |
| 40 | * @return | |
| 41 | */ | |
| 42 | // TODO is this specific to a PID score only? | |
| 43 | // score matrix will compute whatever is configured for gap-residue | |
| 44 | boolean matchGaps(); | |
| 45 | ||
| 46 | /** | |
| 47 | * Answers true if gaps are included in the calculation. This may affect the | |
| 48 | * calculated score, the denominator (normalisation factor) of the score, or | |
| 49 | * both. Gap-gap positions are included if this and includeGappedColumns both | |
| 50 | * answer true. | |
| 51 | * | |
| 52 | * @return | |
| 53 | */ | |
| 54 | boolean includeGaps(); | |
| 55 | ||
| 56 | /** | |
| 57 | * Answers true if only the shortest sequence length is used to divide the | |
| 58 | * total score, false if the longest sequence length | |
| 59 | * | |
| 60 | * @return | |
| 61 | */ | |
| 62 | boolean denominateByShortestLength(); | |
| 63 | } |