💿🐜 Antkeeper source code
https://antkeeper.com
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94 lines
2.7 KiB
94 lines
2.7 KiB
/*
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* Copyright (C) 2020 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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#ifndef ANTKEEPER_TRANSLATE_HPP
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#define ANTKEEPER_TRANSLATE_HPP
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#include <algorithm>
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#include <cstdint>
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#include <iterator>
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namespace dna
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{
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constexpr char* standard_code =
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"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" // Amino acid
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"---M------**--*----M---------------M----------------------------" // Start/stop
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"TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG" // Base 1
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"TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG" // Base 2
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"TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"; // Base 3
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/**
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* Translates codons into amino acids until a stop codon is read or the end of the sequence is reached.
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*
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* @param first,last Range of codons to translate.
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* @param t_first Beginning of the translation table.
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* @param d_first Beginning of the destination range.
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* @return Output iterator to the amino acid in the destination range, one past the last amino acid translated.
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*/
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template <class InputIt1, class InputIt2, class OutputIt>
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OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_first)
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{
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InputIt1 second = first;
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++second;
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InputIt1 third = second;
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++third;
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InputIt2 base1_first = t_first;
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std::advance(base1_first, 128);
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InputIt2 base2_first = base1_first;
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std::advance(base2_first, 64);
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InputIt2 base3_first = base2_first;
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std::advance(base3_first, 64);
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while (first != last && second != last && third != last)
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{
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InputIt2 aa = t_first;
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InputIt2 base1 = base1_first;
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InputIt2 base2 = base2_first;
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InputIt2 base3 = base3_first;
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for (std::uint_fast8_t i = 0; i < 64; ++i)
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{
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if (*first == *base1 && *second == *base2 && *third == *base3)
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{
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if (*aa == '*')
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return d_first;
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*(d_first++) = *aa;
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break;
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}
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++aa;
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++base1;
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++base2;
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++base3;
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}
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first = ++third;
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second = ++third;
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++third;
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}
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return d_first;
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}
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} // namespace dna
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#endif // ANTKEEPER_TRANSLATE_HPP
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