💿🐜 Antkeeper source code
https://antkeeper.com
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78 lines
3.0 KiB
78 lines
3.0 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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#ifndef ANTKEEPER_GENETICS_CODON_HPP
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#define ANTKEEPER_GENETICS_CODON_HPP
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namespace genetics {
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/// Functions and structures related to triplets of IUPAC base symbols.
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namespace codon {
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/**
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* Table for translating codons to amino acids.
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*
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* @see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
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*/
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struct table
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{
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/// String of 64 IUPAC amino acid base symbols, in TCAG order.
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const char* aas;
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/// String of 64 IUPAC amino acid base symbols, in TCAG order, where symbols other than `-` and `*` indicate a start codon and its amino acid.
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const char* starts;
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};
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/**
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* Returns `true` if a codon is a start codon.
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*
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* @param base1 IUPAC base code of first nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param base2 IUPAC base code of second nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param base3 IUPAC base code of third nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param starts String of 64 IUPAC amino acid codes, in TCAG order.
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* @return `true` if the codon is a start codon, `false` otherwise.
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*/
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bool is_start(char base1, char base2, char base3, const char* starts);
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/**
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* Returns `true` if a codon is a stop codon.
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*
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* @param base1 IUPAC base code of first nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param base2 IUPAC base code of second nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param base3 IUPAC base code of third nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param aas String of 64 IUPAC amino acid codes, in TCAG order.
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* @return `true` if the codon is a stop codon, `false` otherwise.
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*/
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bool is_stop(char base1, char base2, char base3, const char* aas);
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/**
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* Translates a codon into an amino acid.
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*
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* @param base1 IUPAC base code of first nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param base2 IUPAC base code of second nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param base3 IUPAC base code of third nucleobase, either `U`, `T`, `C`, `A`, or `G`.
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* @param aas String of 64 IUPAC amino acid codes, in TCAG order.
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* @return IUPAC amino acid code of corresponding amino acid, or `-` if an invalid codon was supplied.
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*/
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char translate(char base1, char base2, char base3, const char* aas);
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} // namspace codon
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} // namespace genetics
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#endif // ANTKEEPER_GENETICS_CODON_HPP
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