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File CodingUtils.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| CodingUtils | 29 | 51 | 20 |
Contributing tests
This file is covered by 22 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; | |
| 22 | ||
| 23 | /** | |
| 24 | * A utility class to provide encoding/decoding schemes for data. | |
| 25 | * | |
| 26 | * @author gmcarstairs | |
| 27 | * | |
| 28 | */ | |
| 29 | public class CodingUtils | |
| 30 | { | |
| 31 | ||
| 32 | /* | |
| 33 | * Number of bits used when encoding codon characters. 2 is enough for ACGT. | |
| 34 | * To accommodate more (e.g. ambiguity codes), simply increase this number | |
| 35 | * (and adjust unit tests to match). | |
| 36 | */ | |
| 37 | private static final int CODON_ENCODING_BITSHIFT = 2; | |
| 38 | ||
| 39 | /** | |
| 40 | * Encode a codon from e.g. ['A', 'G', 'C'] to a number in the range 0 - 63. | |
| 41 | * Converts lower to upper case, U to T, then assembles a binary value by | |
| 42 | * encoding A/C/G/T as 00/01/10/11 respectively and shifting. | |
| 43 | * | |
| 44 | * @param codon | |
| 45 | * @return the encoded codon, or a negative number if unexpected characters | |
| 46 | * found | |
| 47 | */ | |
| 48 | 10675 |  public static int encodeCodon(char[] codon) |
| 49 | { | |
| 50 | 10675 | if (codon == null) |
| 51 | { | |
| 52 | 1 | return -1; |
| 53 | } | |
| 54 | 10674 | return encodeCodon(codon[2]) |
| 55 | + (encodeCodon(codon[1]) << CODON_ENCODING_BITSHIFT) | |
| 56 | + (encodeCodon(codon[0]) << (2 * CODON_ENCODING_BITSHIFT)); | |
| 57 | } | |
| 58 | ||
| 59 | /** | |
| 60 | * Encodes aA/cC/gG/tTuU as 0/1/2/3 respectively. Returns Integer.MIN_VALUE (a | |
| 61 | * large negative value) for any other character. | |
| 62 | * | |
| 63 | * @param c | |
| 64 | * @return | |
| 65 | */ | |
| 66 | 32033 | public static int encodeCodon(char c) |
| 67 | { | |
| 68 | 32033 | int result = Integer.MIN_VALUE; |
| 69 | 32033 | switch (c) |
| 70 | { | |
| 71 | 9172 | case 'A': |
| 72 | 4 | case 'a': |
| 73 | 9176 | result = 0; |
| 74 | 9176 | break; |
| 75 | 7473 | case 'C': |
| 76 | 5 | case 'c': |
| 77 | 7478 | result = 1; |
| 78 | 7478 | break; |
| 79 | 7390 | case 'G': |
| 80 | 5 | case 'g': |
| 81 | 7395 | result = 2; |
| 82 | 7395 | break; |
| 83 | 7974 | case 'T': |
| 84 | 7 | case 't': |
| 85 | 1 | case 'U': |
| 86 | 1 | case 'u': |
| 87 | 7983 | result = 3; |
| 88 | 7983 | break; |
| 89 | } | |
| 90 | 32033 | return result; |
| 91 | } | |
| 92 | ||
| 93 | /** | |
| 94 | * Converts a binary encoded codon into an ['A', 'C', 'G'] (or 'T') triplet. | |
| 95 | * | |
| 96 | * The two low-order bits encode for A/C/G/T as 0/1/2/3, etc. | |
| 97 | * | |
| 98 | * @param encoded | |
| 99 | * @return | |
| 100 | */ | |
| 101 | 1966 | public static char[] decodeCodon(int encoded) |
| 102 | { | |
| 103 | 1966 | char[] result = new char[3]; |
| 104 | 1966 | result[2] = decodeNucleotide(encoded & 3); |
| 105 | 1966 | encoded = encoded >>> CODON_ENCODING_BITSHIFT; |
| 106 | 1966 | result[1] = decodeNucleotide(encoded & 3); |
| 107 | 1966 | encoded = encoded >>> CODON_ENCODING_BITSHIFT; |
| 108 | 1966 | result[0] = decodeNucleotide(encoded & 3); |
| 109 | 1966 | return result; |
| 110 | } | |
| 111 | ||
| 112 | 0 | public static void decodeCodon2(int encoded, char[] result) |
| 113 | { | |
| 114 | 0 | result[2] = decodeNucleotide(encoded & 3); |
| 115 | 0 | encoded = encoded >>> CODON_ENCODING_BITSHIFT; |
| 116 | 0 | result[1] = decodeNucleotide(encoded & 3); |
| 117 | 0 | encoded = encoded >>> CODON_ENCODING_BITSHIFT; |
| 118 | 0 | result[0] = decodeNucleotide(encoded & 3); |
| 119 | } | |
| 120 | ||
| 121 | /** | |
| 122 | * Convert value 0/1/2/3 to 'A'/'C'/'G'/'T' | |
| 123 | * | |
| 124 | * @param i | |
| 125 | * @return | |
| 126 | */ | |
| 127 | 5903 | public static char decodeNucleotide(int i) |
| 128 | { | |
| 129 | 5903 | char result = '0'; |
| 130 | 5903 | switch (i) |
| 131 | { | |
| 132 | 1652 | case 0: |
| 133 | 1652 | result = 'A'; |
| 134 | 1652 | break; |
| 135 | 1320 | case 1: |
| 136 | 1320 | result = 'C'; |
| 137 | 1320 | break; |
| 138 | 1311 | case 2: |
| 139 | 1311 | result = 'G'; |
| 140 | 1311 | break; |
| 141 | 1619 | case 3: |
| 142 | 1619 | result = 'T'; |
| 143 | 1619 | break; |
| 144 | } | |
| 145 | 5903 | return result; |
| 146 | } | |
| 147 | ||
| 148 | } |