💿🐜 Antkeeper source code
https://antkeeper.com
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100 lines
3.6 KiB
100 lines
3.6 KiB
/*
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* Copyright (C) 2021 Christopher J. Howard
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*
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* This file is part of Antkeeper source code.
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*
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* Antkeeper source code is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Antkeeper source code is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Antkeeper source code. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef ANTKEEPER_GENETICS_PROTEIN_HPP
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#define ANTKEEPER_GENETICS_PROTEIN_HPP
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#include "amino-acid.hpp"
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#include <type_traits>
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namespace genetics {
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/// Functions which operate on sequences of IUPAC amino acid symbols.
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namespace protein {
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/**
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* Returns the percent identity between two proteins.
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*
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* @param first1,last1 Range of IUPAC amino acids which constitute the first protein.
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* @param first2 Beginning of the range of IUPAC amino acids which constitute the second protein.
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* @return Percent identity between the two proteins.
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*/
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template <class T, class ForwardIt1, class ForwardIt2>
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T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2);
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/**
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* Scores two proteins using a substitution matrix.
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*
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* @param first1,last1 Range of IUPAC amino acid codes which constitute the first protein.
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* @param first2 Beginning of the range of IUPAC amino acid codes which constitute the second protein.
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* @param matrix Substitution matrix.
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* @return Score of the two proteins.
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*/
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template <class ForwardIt1, class ForwardIt2, class Matrix>
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typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix);
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/**
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* Returns the percent similarity between two proteins.
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*
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* @param first1,last1 Range of IUPAC amino acids which constitute the first protein.
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* @param first2 Beginning of the range of IUPAC amino acids which constitute the second protein.
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* @return Percent similarity between the two proteins.
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*/
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template <class T, class ForwardIt1, class ForwardIt2, class Matrix>
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typename T similarity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix);
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template <class T, class ForwardIt1, class ForwardIt2>
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T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2)
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{
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auto length = std::distance(first1, last1);
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T sum = 0;
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for (; first1 != last1; ++first1, ++first2)
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if (*first1 == *first2)
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++sum;
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return sum / static_cast<T>(length);
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}
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template <class ForwardIt1, class ForwardIt2, class Matrix>
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typename std::remove_all_extents<Matrix>::type score(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix)
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{
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typename std::remove_all_extents<Matrix>::type result = 0;
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for (; first1 != last1; ++first1, ++first2)
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result += amino_acid::score(*first1, *first2, matrix);
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return result;
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}
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template <class T, class ForwardIt1, class ForwardIt2, class Matrix>
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typename T similarity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix& matrix)
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{
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T length = static_cast<T>(std::distance(first1, last1));
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T positive_count = T(0);
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for (; first1 != last1; ++first1, ++first2)
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if (amino_acid::score(*first1, *first2, matrix) > 0)
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++positive_count;
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return positive_count / length;
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}
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} // namespace protein
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} // namespace genetics
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#endif // ANTKEEPER_GENETICS_PROTEIN_HPP
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