💿🐜 Antkeeper source code
https://antkeeper.com
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99 lines
2.3 KiB
99 lines
2.3 KiB
/*
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* Copyright (C) 2021 Christopher J. Howard
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*
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* This file is part of Antkeeper source code.
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*
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* Antkeeper source code is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Antkeeper source code is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Antkeeper source code. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include "base.hpp"
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namespace genetics {
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namespace base {
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/**
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* Decodes an IUPAC degenerate base symbol into a bit mask representing the possible bases represented by the symbol.
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*
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* @param symbol IUPAC degenerate base symbol.
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* @return Bit mask representing the possible bases represented by the symbol.
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*/
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static inline unsigned char decode(char symbol)
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{
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static constexpr unsigned char bases[25] =
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{
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0b0001, // A
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0b1110, // B
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0b0010, // C
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0b1101, // D
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0, // E
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0, // F
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0b0100, // G
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0b1011, // H
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0, // I
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0, // J
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0b1100, // K
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0, // L
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0b0011, // M
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0b1111, // N
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0, // O
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0, // P
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0, // Q
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0b0101, // R
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0b0110, // S
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0b1000, // T
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0b1000, // U
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0b0111, // V
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0b1001, // W
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0, // X
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0b1010, // Y
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};
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return (symbol < 'A' || symbol >= 'Z') ? 0 : bases[symbol - 'A'];
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}
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int compare(char a, char b)
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{
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static constexpr int popcount[16] =
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{
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0, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4
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};
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return popcount[decode(a) & decode(b)];
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}
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char transcribe(char symbol)
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{
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return (symbol == 'T') ? 'U' : (symbol == 'U') ? 'T' : symbol;
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}
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namespace dna
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{
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char complement(char symbol)
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{
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static constexpr char* complements = "TVGHZZCDZZMZKNZZZYSAABWZR";
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return (symbol < 'A' || symbol >= 'Z') ? 'Z' : complements[symbol - 'A'];
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}
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}
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namespace rna
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{
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char complement(char symbol)
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{
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static constexpr char* complements = "UVGHZZCDZZMZKNZZZYSAABWZR";
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return (symbol < 'A' || symbol >= 'Z') ? 'Z' : complements[symbol - 'A'];
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}
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}
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} // namespace base
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} // namespace genetics
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