base.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/base.hpp>
 
namespace genetics {
namespace base {
 
static inline unsigned char decode(char symbol)
{
    static constexpr unsigned char bases[25] =
    {
        0b0001, // A
        0b1110, // B
        0b0010, // C
        0b1101, // D
        0,      // E
        0,      // F
        0b0100, // G
        0b1011, // H
        0,      // I
        0,      // J
        0b1100, // K
        0,      // L
        0b0011, // M
        0b1111, // N
        0,      // O
        0,      // P
        0,      // Q
        0b0101, // R
        0b0110, // S
        0b1000, // T
        0b1000, // U
        0b0111, // V
        0b1001, // W
        0,      // X
        0b1010, // Y
    };
    
    return (symbol < 'A' || symbol >= 'Z') ? 0 : bases[symbol - 'A'];
}
 
int compare(char a, char b)
{
    static constexpr int popcount[16] =
    {
        0, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4
    };
    
    return popcount[decode(a) & decode(b)];
}
 
char transcribe(char symbol)
{
    return (symbol == 'T') ? 'U' : (symbol == 'U') ? 'T' : symbol;
}
 
namespace dna
{
    char complement(char symbol)
    {
        constexpr const char* complements = "TVGHZZCDZZMZKNZZZYSAABWZR";
        return (symbol < 'A' || symbol >= 'Z') ? 'Z' : complements[symbol - 'A'];
    }
}
 
namespace rna
{
    char complement(char symbol)
    {
        constexpr const char* complements = "UVGHZZCDZZMZKNZZZYSAABWZR";
        return (symbol < 'A' || symbol >= 'Z') ? 'Z' : complements[symbol - 'A'];
    }
}
 
} // namespace base
} // namespace genetics