Functions and structures related to sequences of IUPAC degenerate base symbols. More...

Namespaces
	dna
	Functions which operate on sequences of IUPAC degenerate DNA base symbols.

	rna
	Functions which operate on sequences of IUPAC degenerate RNA base symbols.

Classes
struct	orf
	Open reading frame (ORF), defined by a start codon and stop codon, with the distance between divisible by three. More...

Functions
template<class ForwardIt1 , class ForwardIt2 , class URBG >
ForwardIt2	crossover (ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, URBG &&g)
	Exchanges elements between two ranges, starting at a random offset. More...

template<class ForwardIt1 , class ForwardIt2 , class Size , class URBG >
void	crossover_n (ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, Size count, URBG &&g)
	Exchanges elements between two ranges multiple times, starting at a random offset each time. More...

template<class ForwardIt >
orf< ForwardIt >	find_orf (ForwardIt first, ForwardIt last, const codon::table &table)
	Searches a sequence for an open reading frame (ORF). More...

template<class ForwardIt , class UnaryOperation , class URBG >
ForwardIt	mutate (ForwardIt first, ForwardIt last, UnaryOperation unary_op, URBG &&g)
	Applies the given function to a randomly selected element in a range. More...

template<class ForwardIt , class Size , class UnaryOperation , class URBG >
void	mutate_n (ForwardIt first, ForwardIt last, Size count, UnaryOperation unary_op, URBG &&g)
	Applies the given function to a random selection of elements in a range. More...

template<class ForwardIt1 , class ForwardIt2 >
ForwardIt1	search (ForwardIt1 first, ForwardIt1 last, ForwardIt2 s_first, ForwardIt2 s_last, typename std::iterator_traits< ForwardIt1 >::difference_type stride)
	Searches a sequence of IUPAC base symbols for a pattern matching a search string of IUPAC degenerate base symbols. More...

template<class InputIt , class OutputIt >
OutputIt	transcribe (InputIt first, InputIt last, OutputIt d_first)
	Transcribes a sequence of IUPAC base symbols between DNA and RNA, swapping `T` for `U` or `U` for `T`. More...

template<class InputIt , class OutputIt >
OutputIt	translate (InputIt first, InputIt last, OutputIt d_first, const codon::table &table)
	Translates a sequence of codons into amino acids. More...

Detailed Description

Functions and structures related to sequences of IUPAC degenerate base symbols.

Function Documentation

◆ crossover()

template<class ForwardIt1 , class ForwardIt2 , class URBG >

ForwardIt2 genetics::sequence::crossover	(	ForwardIt1	first1,
		ForwardIt1	last1,
		ForwardIt2	first2,
		URBG &&	g
	)

Exchanges elements between two ranges, starting at a random offset.

Parameters

first1,last1	First range of elements to crossover.
first2	Beginning of the second range of elements to crossover.
g	Uniform random bit generator.

Returns: Iterator to the start of the crossover in the second range.

Definition at line 164 of file sequence.hpp.

◆ crossover_n()

template<class ForwardIt1 , class ForwardIt2 , class Size , class URBG >

void genetics::sequence::crossover_n	(	ForwardIt1	first1,
		ForwardIt1	last1,
		ForwardIt2	first2,
		Size	count,
		URBG &&	g
	)

Exchanges elements between two ranges multiple times, starting at a random offset each time.

Parameters

first1,last1	First range of elements to crossover.
first2	Beginning of the second range of elements to crossover.
count	Number of times to crossover.
g	Uniform random bit generator.

Definition at line 176 of file sequence.hpp.

◆ find_orf()

template<class ForwardIt >

orf< ForwardIt > genetics::sequence::find_orf	(	ForwardIt	first,
		ForwardIt	last,
		const codon::table &	table
	)

Searches a sequence for an open reading frame (ORF).

Parameters

first,last	Range of elements to search.
table	Genetic code translation table.

Returns: First ORF in the sequence, or {last, last} if no ORF was found.

Definition at line 198 of file sequence.hpp.

◆ mutate()

template<class ForwardIt , class UnaryOperation , class URBG >

ForwardIt genetics::sequence::mutate	(	ForwardIt	first,
		ForwardIt	last,
		UnaryOperation	unary_op,
		URBG &&	g
	)

Applies the given function to a randomly selected element in a range.

Parameters

first,last	Range of elements to mutate.
unary_op	Unary operation function object that will be applied.
g	Uniform random bit generator.

Returns: Iterator to the mutated element.

Definition at line 247 of file sequence.hpp.

◆ mutate_n()

template<class ForwardIt , class Size , class UnaryOperation , class URBG >

void genetics::sequence::mutate_n	(	ForwardIt	first,
		ForwardIt	last,
		Size	count,
		UnaryOperation	unary_op,
		URBG &&	g
	)

Applies the given function to a random selection of elements in a range.

Parameters

first,last	Range of elements to mutate.
count	Number of elements to mutate.
unary_op	Unary operation function object that will be applied.
g	Uniform random bit generator.

Definition at line 262 of file sequence.hpp.

◆ search()

template<class ForwardIt1 , class ForwardIt2 >

ForwardIt1 genetics::sequence::search	(	ForwardIt1	first,
		ForwardIt1	last,
		ForwardIt2	s_first,
		ForwardIt2	s_last,
		typename std::iterator_traits< ForwardIt1 >::difference_type	stride
	)

Searches a sequence of IUPAC base symbols for a pattern matching a search string of IUPAC degenerate base symbols.

Parameters

first,last	Sequence of IUPAC base symbols to search.
s_first,s_last	Search string of IUPAC degenerate base symbols.
stride	Distance between consecutive searches.

Returns: Iterator to the beginning of the first subsequence matching [s_first, s_last) in the sequence [first, last). If no such occurrence is found, last is returned.

Definition at line 282 of file sequence.hpp.

◆ transcribe()

template<class InputIt , class OutputIt >

OutputIt genetics::sequence::transcribe	(	InputIt	first,
		InputIt	last,
		OutputIt	d_first
	)

inline

Transcribes a sequence of IUPAC base symbols between DNA and RNA, swapping T for U or U for T.

Parameters

first,last	Range of elements to transcribe.
d_first	Beginning of the destination range.

Returns: Output iterator to the element past the last element transcribed.

Definition at line 307 of file sequence.hpp.

◆ translate()

template<class InputIt , class OutputIt >

OutputIt genetics::sequence::translate	(	InputIt	first,
		InputIt	last,
		OutputIt	d_first,
		const codon::table &	table
	)

Translates a sequence of codons into amino acids.

Parameters

first,last	Open reading frame.
d_first	Beginning of destination range.
table	Genetic code translation table.

Returns: Output iterator to the element past the last element translated.

Definition at line 313 of file sequence.hpp.

Namespaces

Classes

Functions

Detailed Description

Function Documentation

◆ crossover()

◆ crossover_n()

◆ find_orf()

◆ mutate()

◆ mutate_n()

◆ search()

◆ transcribe()

◆ translate()