💿🐜 Antkeeper source code
https://antkeeper.com
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136 lines
3.7 KiB
136 lines
3.7 KiB
/*
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* Copyright (C) 2020 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_DNA_FRAME_HPP
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#define ANTKEEPER_DNA_FRAME_HPP
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#include <iterator>
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namespace dna {
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/**
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* Finds the first start codon in a sequence.
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*
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* @param first,last Range of elements to search.
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* @param n Number of elements per codon.
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* @param p Binary predicate which returns `true` if a subrange of length @p n is a start codon.
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* @return Iterator to the first element in the start codon, or @p last if no start codon was found.
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*/
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template <class InputIt, class Size, class BinaryPredicate>
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InputIt find_start(InputIt first, InputIt last, Size n, BinaryPredicate p)
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{
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auto length = std::distance(first, last);
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if (length >= n)
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{
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InputIt next = first;
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std::advance(next, n);
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do
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{
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if (p(first, next))
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return first;
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++first;
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++next;
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--length;
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}
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while (length >= n);
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}
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return last;
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}
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/**
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* Searches the range `[first, last)` for a sequence of @p n elements which satifies predicate @p p.
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*
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* @param first,last Range of elements to search.
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* @param n Number of elements in the sequence.
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* @param stride Number of elements between searches.
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* @param p
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*/
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template <class InputIt, class Size, class BinaryPredicate>
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InputIt find_sequence(InputIt first, InputIt last, Size n, Size stride, BinaryPredicate p)
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{
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if (auto length = std::distance(first, last); length >= n)
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{
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Size offset = n + stride;
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InputIt next = first;
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std::advance(next, n);
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do
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{
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if (p(first, next))
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return first;
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if (length < offset)
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break;
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std::advance(first, stride);
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std::advance(next, stride);
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length -= offset;
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}
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while (1);
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}
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return last;
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}
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/**
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* Finds the first stop codon in a sequence.
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*
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* @param first,last Range of elements to search.
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* @param n Number of elements per codon.
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* @param p Binary predicate which returns `true` if a subrange of length @p n is a stop codon.
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* @return Iterator to the first element in the stop codon, or @p last if no stop codon was found.
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*/
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template <class InputIt, class Size, class BinaryPredicate>
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InputIt find_stop(InputIt first, InputIt last, Size n, BinaryPredicate p)
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{
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for (auto length = std::distance(first, last); length >= n; length -= n)
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{
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InputIt next = first;
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std::advance(next, n);
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if (p(first, next))
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return first;
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first = next;
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}
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return last;
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}
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/**
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* Finds the first open reading frame (ORF) in a range of elements.
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*
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* @param[in,out] first Iterator to the beginning of the sequence, which will point to th
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*
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* @param start_p Binary predicate which returns `true` if a subrange of length @p n is a start codon.
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* @param stop_p Binary predicate which returns `true` if a subrange of length @p n is a stop codon.
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*/
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template <class InputIt, class Size, class BinaryPredicate1, class BinaryPredicate2>
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void find_orf(InputIt& first, InputIt& last, Size n, BinaryPredicate1 start_p, BinaryPredicate2 stop_p)
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{
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first = find_start(first, last, n, start_p);
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if (first != last)
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last = find_stop(first, last, n, stop_p);
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}
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} // namespace dna
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#endif // ANTKEEPER_DNA_FRAME_HPP
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