💿🐜 Antkeeper source code
https://antkeeper.com
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56 lines
1.7 KiB
56 lines
1.7 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_AMINO_ACID_HPP
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#define ANTKEEPER_GENETICS_AMINO_ACID_HPP
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#include <type_traits>
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namespace genetics {
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/// Functions which operate on IUPAC amino acid symbols.
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namespace amino_acid {
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/**
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* Scores two amino acids using a substitution matrix.
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*
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* @param a IUPAC amino acid code of first amino acid.
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* @param b IUPAC amino acid code of second amino acid.
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* @param matrix Substitution matrix.
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* @return Score of the two amino acids.
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*/
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template <class Matrix>
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typename std::remove_all_extents<Matrix>::type score(char a, char b, const Matrix& matrix);
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template <class Matrix>
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typename std::remove_all_extents<Matrix>::type score(char a, char b, const Matrix& matrix)
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{
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int i = (a < 'A' || a > 'Z') ? ((a == '*') ? 26 : -1) : a - 'A';
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int j = (b < 'A' || b > 'Z') ? ((b == '*') ? 26 : -1) : b - 'A';
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if (i < 0 || j < 0)
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return 0;
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return matrix[i][j];
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}
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} // namspace amino_acid
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} // namespace genetics
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#endif // ANTKEEPER_GENETICS_AMINO_ACID_HPP
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