genetics::protein Namespace Reference

Functions which operate on sequences of IUPAC amino acid symbols. More...

Functions
template<class T , class ForwardIt1 , class ForwardIt2 >
T	identity (ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2)
	Returns the percent identity between two proteins. More...
template<class ForwardIt1 , class ForwardIt2 , class Matrix >
std::remove_all_extents< Matrix >::type	score (ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix &matrix)
	Scores two proteins using a substitution matrix. More...
template<class T , class ForwardIt1 , class ForwardIt2 , class Matrix >
T	similarity (ForwardIt1 first1, ForwardIt1 last1, ForwardIt2 first2, const Matrix &matrix)
	Returns the percent similarity between two proteins. More...

Detailed Description

Functions which operate on sequences of IUPAC amino acid symbols.

Function Documentation

identity()

template<class T , class ForwardIt1 , class ForwardIt2 >

T genetics::protein::identity	(	ForwardIt1	first1,
		ForwardIt1	last1,
		ForwardIt2	first2
	)

Returns the percent identity between two proteins.

Parameters

first1,last1	Range of IUPAC amino acids which constitute the first protein.
first2	Beginning of the range of IUPAC amino acids which constitute the second protein.

Returns

Percent identity between the two proteins.

Definition at line 63 of file protein.hpp.

score()

template<class ForwardIt1 , class ForwardIt2 , class Matrix >

std::remove_all_extents< Matrix >::type genetics::protein::score	(	ForwardIt1	first1,
		ForwardIt1	last1,
		ForwardIt2	first2,
		const Matrix &	matrix
	)

Scores two proteins using a substitution matrix.

Parameters

first1,last1	Range of IUPAC amino acid codes which constitute the first protein.
first2	Beginning of the range of IUPAC amino acid codes which constitute the second protein.
matrix	Substitution matrix.

Returns

Score of the two proteins.

Definition at line 76 of file protein.hpp.

similarity()

template<class T , class ForwardIt1 , class ForwardIt2 , class Matrix >

T genetics::protein::similarity	(	ForwardIt1	first1,
		ForwardIt1	last1,
		ForwardIt2	first2,
		const Matrix &	matrix
	)

Returns the percent similarity between two proteins.

Parameters

first1,last1	Range of IUPAC amino acids which constitute the first protein.
first2	Beginning of the range of IUPAC amino acids which constitute the second protein.

Returns

Percent similarity between the two proteins.

Definition at line 85 of file protein.hpp.