/*
 * Copyright (C) 2020  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_PROTEIN_HPP
#define ANTKEEPER_GENETICS_PROTEIN_HPP

#include "amino-acid.hpp"
#include <type_traits>

namespace genetics {
namespace protein {

/**
 * Scores two proteins using a substitution matrix.
 *
 * @param first1,last1 Sequence of IUPAC amino acid codes which constitute the first protein.
 * @param first2,last2 Sequence of IUPAC amino acid codes which constitute the second protein.
 * @param matrix Substitution matrix.
 * @return Score of the two proteins.
 */
template <class ForwardIt1, class ForwardIt2, class Matrix>
typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, ForwardIt2 last2, const Matrix& matrix);

template <class ForwardIt1, class ForwardIt2, class Matrix>
typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, ForwardIt2 last2, const Matrix& matrix)
{
	typename std::remove_all_extents<Matrix>::type result = 0;
	for (; first1 != last1 && first2 != last2; ++first1, ++first2)
		result += amino_acid::score(*first1, *first2, matrix);
	return result;
}

} // namespace protein
} // namespace genetics

#endif // ANTKEEPER_GENETICS_PROTEIN_HPP