jalviewX
File CodonComparator.java
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| CodonComparator | 35 | 16 | 15 | 0 |
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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; | |
| 22 | ||
| 23 | import jalview.datamodel.AlignedCodon; | |
| 24 | ||
| 25 | import java.util.Comparator; | |
| 26 | ||
| 27 | /** | |
| 28 | * Implements rules for comparing two aligned codons, i.e. determining whether | |
| 29 | * they should occupy the same position in a translated protein alignment, or | |
| 30 | * one or the other should 'follow' (by preceded by a gap). | |
| 31 | * | |
| 32 | * @author gmcarstairs | |
| 33 | * | |
| 34 | */ | |
| 35 | public final class CodonComparator implements Comparator<AlignedCodon> | |
| 36 | { | |
| 37 | ||
| 38 | 3520 |  @Override |
| 39 | public int compare(AlignedCodon ac1, AlignedCodon ac2) | |
| 40 | { | |
| 41 | 3520 | if (ac1 == null || ac2 == null || ac1.equals(ac2)) |
| 42 | { | |
| 43 | 1749 | return 0; |
| 44 | } | |
| 45 | ||
| 46 | /** | |
| 47 | * <pre> | |
| 48 | * Case 1: if one starts before the other, and doesn't end after it, then it | |
| 49 | * precedes. We ignore the middle base position here. | |
| 50 | * A--GT | |
| 51 | * -CT-G | |
| 52 | * </pre> | |
| 53 | */ | |
| 54 | 1771 | if (ac1.pos1 < ac2.pos1 && ac1.pos3 <= ac2.pos3) |
| 55 | { | |
| 56 | 235 | return -1; |
| 57 | } | |
| 58 | 1536 | if (ac2.pos1 < ac1.pos1 && ac2.pos3 <= ac1.pos3) |
| 59 | { | |
| 60 | 1485 | return 1; |
| 61 | } | |
| 62 | ||
| 63 | /** | |
| 64 | * <pre> | |
| 65 | * Case 2: if one ends after the other, and doesn't start before it, then it | |
| 66 | * follows. We ignore the middle base position here. | |
| 67 | * -TG-A | |
| 68 | * G-TC | |
| 69 | * </pre> | |
| 70 | */ | |
| 71 | 51 | if (ac1.pos3 > ac2.pos3 && ac1.pos1 >= ac2.pos1) |
| 72 | { | |
| 73 | 15 | return 1; |
| 74 | } | |
| 75 | 36 | if (ac2.pos3 > ac1.pos3 && ac2.pos1 >= ac1.pos1) |
| 76 | { | |
| 77 | 12 | return -1; |
| 78 | } | |
| 79 | ||
| 80 | /* | |
| 81 | * Case 3: if start and end match, compare middle base positions. | |
| 82 | */ | |
| 83 | 24 | if (ac1.pos1 == ac2.pos1 && ac1.pos3 == ac2.pos3) |
| 84 | { | |
| 85 | 6 | return Integer.compare(ac1.pos2, ac2.pos2); |
| 86 | } | |
| 87 | ||
| 88 | /* | |
| 89 | * That just leaves the 'enclosing' case - one codon starts after but ends | |
| 90 | * before the other. If the middle bases don't match, use their comparison | |
| 91 | * (majority vote). | |
| 92 | */ | |
| 93 | 18 | int compareMiddles = Integer.compare(ac1.pos2, ac2.pos2); |
| 94 | 18 | if (compareMiddles != 0) |
| 95 | { | |
| 96 | 12 | return compareMiddles; |
| 97 | } | |
| 98 | ||
| 99 | /** | |
| 100 | * <pre> | |
| 101 | * Finally just leaves overlap with matching middle base, e.g. | |
| 102 | * -A-A-A | |
| 103 | * G--GG | |
| 104 | * In this case the choice is arbitrary whether to compare based on | |
| 105 | * first or last base position. We pick the first. Note this preserves | |
| 106 | * symmetricality of the comparison. | |
| 107 | * </pre> | |
| 108 | */ | |
| 109 | 6 | return Integer.compare(ac1.pos1, ac2.pos1); |
| 110 | } | |
| 111 | } |