protein.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_PROTEIN_HPP
#define ANTKEEPER_GENETICS_PROTEIN_HPP
 
#include <engine/genetics/amino-acid.hpp>
#include <type_traits>
 
namespace genetics {
 
namespace protein {
 
template <class T, class ForwardIt1, class ForwardIt2>
T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2);
 
template <class ForwardIt1, class ForwardIt2, class Matrix>
typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix);
 
template <class T, class ForwardIt1, class ForwardIt2, class Matrix>
typename T similarity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix);
 
template <class T, class ForwardIt1, class ForwardIt2>
T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2)
{
    auto length = std::distance(first1, last1);
    
    T sum = 0;
    for (; first1 != last1; ++first1, ++first2)
        if (*first1 == *first2)
            ++sum;
    
    return sum / static_cast<T>(length);
}
 
template <class ForwardIt1, class ForwardIt2, class Matrix>
typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix)
{
    typename std::remove_all_extents<Matrix>::type result = 0;
    for (; first1 != last1; ++first1, ++first2)
        result += amino_acid::score(*first1, *first2, matrix);
    return result;
}
 
template <class T, class ForwardIt1, class ForwardIt2, class Matrix>
typename T similarity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix)
{
    T length = static_cast<T>(std::distance(first1, last1));
    T positive_count = T(0);
    
    for (; first1 != last1; ++first1, ++first2)
        if (amino_acid::score(*first1, *first2, matrix) > 0)
            ++positive_count;
    
    return positive_count / length;
}
 
} // namespace protein
} // namespace genetics
 
#endif // ANTKEEPER_GENETICS_PROTEIN_HPP