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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 "amino-acid.hpp"
- #include <type_traits>
-
- namespace genetics {
-
- /// Functions which operate on sequences of IUPAC amino acid symbols.
- namespace protein {
-
- /**
- * Returns the percent identity between two proteins.
- *
- * @param first1,last1 Range of IUPAC amino acids which constitute the first protein.
- * @param first2 Beginning of the range of IUPAC amino acids which constitute the second protein.
- * @return Percent identity between the two proteins.
- */
- template <class T, class ForwardIt1, class ForwardIt2>
- T identity(ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2);
-
- /**
- * Scores two proteins using a substitution matrix.
- *
- * @param first1,last1 Range of IUPAC amino acid codes which constitute the first protein.
- * @param first2 Beginning of the range 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, const Matrix& matrix);
-
- /**
- * Returns the percent similarity between two proteins.
- *
- * @param first1,last1 Range of IUPAC amino acids which constitute the first protein.
- * @param first2 Beginning of the range of IUPAC amino acids which constitute the second protein.
- * @return Percent similarity between the two proteins.
- */
- 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
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