amino-acid.hpp

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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/>.
 */
 
#ifndef ANTKEEPER_GENETICS_AMINO_ACID_HPP
#define ANTKEEPER_GENETICS_AMINO_ACID_HPP
 
#include <type_traits>
 
namespace genetics {
 
namespace amino_acid {
 
template <class Matrix>
typename std::remove_all_extents<Matrix>::type score(char a, char b, const Matrix& matrix);
 
template <class Matrix>
typename std::remove_all_extents<Matrix>::type score(char a, char b, const Matrix& matrix)
{
    int i = (a < 'A' || a > 'Z') ? ((a == '*') ? 26 : -1) : a - 'A';
    int j = (b < 'A' || b > 'Z') ? ((b == '*') ? 26 : -1) : b - 'A';
    
    if (i < 0 || j < 0)
        return 0;
    
    return matrix[i][j];
}
 
} // namspace amino_acid
} // namespace genetics
 
#endif // ANTKEEPER_GENETICS_AMINO_ACID_HPP