codon.cpp

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/*
 * Copyright (C) 2023  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 <engine/genetics/codon.hpp>
 
namespace genetics {
namespace codon {
 
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;
}
 
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