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- /*
- * Copyright (C) 2021 Christopher J. Howard
- *
- * This file is part of Antkeeper source code.
- *
- * Antkeeper source code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * Antkeeper source code is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Antkeeper source code. If not, see <http://www.gnu.org/licenses/>.
- */
-
- #include "codon.hpp"
-
- namespace genetics {
- namespace codon {
-
- /**
- * Returns the index of a nucleobase for use with a translation table.
- *
- * @param base IUPAC code of nucleobase, either `U`, `T`, `C`, `A`, or `G`.
- * @return Index of the nucleobase, or a negative value if a non-standard nucleobase was supplied.
- */
- static inline int base_index(char base)
- {
- switch (base)
- {
- case 'U':
- case 'T':
- return 0;
- case 'C':
- return 1;
- case 'A':
- return 2;
- case 'G':
- return 3;
- }
-
- return ~3;
- }
-
- /**
- * Returns the index of a codon for use with a translation table.
- *
- * @param base1 IUPAC code of first nucleobase, either `U`, `T`, `C`, `A`, or `G`.
- * @param base2 IUPAC code of second nucleobase, either `U`, `T`, `C`, `A`, or `G`.
- * @param base3 IUPAC code of third nucleobase, either `U`, `T`, `C`, `A`, or `G`.
- * @return Index of codon, or a negative value if a non-standard nucleobase was supplied.
- */
- static inline int codon_index(char base1, char base2, char base3)
- {
- int i = base_index(base1);
- int j = base_index(base2);
- int k = base_index(base3);
- return (i << 4) | (j << 2) | k;
- }
-
- inline char translate(char base1, char base2, char base3, const char* aas)
- {
- int index = codon_index(base1, base2, base3);
- if (index < 0)
- return '-';
- return aas[index];
- }
-
- bool is_start(char base1, char base2, char base3, const char* starts)
- {
- char aa = translate(base1, base2, base3, starts);
- return ((aa != '-') && (aa != '*'));
- }
-
- bool is_stop(char base1, char base2, char base3, const char* aas)
- {
- char aa = translate(base1, base2, base3, aas);
- return (aa == '*');
- }
-
- } // namspace codon
- } // namespace genetics
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