jalviewX
File AlignedCodon.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| AlignedCodon | 33 | 18 | 11 | 10 |
Contributing tests
This file is covered by 19 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.datamodel; | |
| 22 | ||
| 23 | /** | |
| 24 | * Holds the aligned column positions (base 0) for one codon in a nucleotide | |
| 25 | * sequence, and (optionally) its peptide translation. The object is immutable | |
| 26 | * once created. | |
| 27 | * | |
| 28 | * Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8). | |
| 29 | * | |
| 30 | * @author gmcarstairs | |
| 31 | * | |
| 32 | */ | |
| 33 | public final class AlignedCodon | |
| 34 | { | |
| 35 | // base 1 aligned sequence position (base 0) | |
| 36 | public final int pos1; | |
| 37 | ||
| 38 | // base 2 aligned sequence position (base 0) | |
| 39 | public final int pos2; | |
| 40 | ||
| 41 | // base 3 aligned sequence position (base 0) | |
| 42 | public final int pos3; | |
| 43 | ||
| 44 | // peptide aligned sequence position (base 0) | |
| 45 | public final int peptideCol; | |
| 46 | ||
| 47 | // peptide coded for by this codon | |
| 48 | public final String product; | |
| 49 | ||
| 50 | 2057 |  public AlignedCodon(int i, int j, int k) |
| 51 | { | |
| 52 | 2057 | this(i, j, k, null, 0); |
| 53 | } | |
| 54 | ||
| 55 | 2107 | public AlignedCodon(int i, int j, int k, String prod, int prodCol) |
| 56 | { | |
| 57 | 2107 | pos1 = i; |
| 58 | 2107 | pos2 = j; |
| 59 | 2107 | pos3 = k; |
| 60 | 2107 | product = prod; |
| 61 | 2107 | peptideCol = prodCol; |
| 62 | } | |
| 63 | ||
| 64 | /** | |
| 65 | * Returns the column position for the given base (1, 2, 3). | |
| 66 | * | |
| 67 | * @param base | |
| 68 | * @return | |
| 69 | * @throws IllegalArgumentException | |
| 70 | * if an argument value other than 1, 2 or 3 is supplied | |
| 71 | */ | |
| 72 | 0 | public int getBaseColumn(int base) |
| 73 | { | |
| 74 | 0 | if (base < 1 || base > 3) |
| 75 | { | |
| 76 | 0 | throw new IllegalArgumentException(Integer.toString(base)); |
| 77 | } | |
| 78 | 0 | return base == 1 ? pos1 : (base == 2 ? pos2 : pos3); |
| 79 | } | |
| 80 | ||
| 81 | /** | |
| 82 | * Two aligned codons are equal if all their base positions are the same. We | |
| 83 | * don't care about the protein product. This test is required for correct | |
| 84 | * alignment of translated gapped dna alignments (the same codon positions in | |
| 85 | * different sequences occupy the same column in the translated alignment). | |
| 86 | */ | |
| 87 | 4663 | @Override |
| 88 | public boolean equals(Object o) | |
| 89 | { | |
| 90 | /* | |
| 91 | * Equality with null value required for consistency with | |
| 92 | * Dna.compareCodonPos | |
| 93 | */ | |
| 94 | 4663 | if (o == null) |
| 95 | { | |
| 96 | 1 | return true; |
| 97 | } | |
| 98 | 4662 | if (!(o instanceof AlignedCodon)) |
| 99 | { | |
| 100 | 1 | return false; |
| 101 | } | |
| 102 | 4661 | AlignedCodon ac = (AlignedCodon) o; |
| 103 | 4661 | return (pos1 == ac.pos1 && pos2 == ac.pos2 && pos3 == ac.pos3); |
| 104 | } | |
| 105 | ||
| 106 | 184 | @Override |
| 107 | public String toString() | |
| 108 | { | |
| 109 | 184 | StringBuilder sb = new StringBuilder(); |
| 110 | 184 | sb.append("[").append(pos1).append(", ").append(pos2).append(", ") |
| 111 | .append(pos3).append("]"); | |
| 112 | 184 | return sb.toString(); |
| 113 | } | |
| 114 | } |