Alphabets

Detailed Description

This module provides various operators to work with the following alphabets:

DNA	4-letter DNA alphabet	A,C,G,T
DNA_N	5-letter DNA + N alphabet	A,C,G,T,N
DNA_IUPAC	16-letter DNA IUPAC alphabet	=,A,C,M,G,R,S,V,T,W,Y,H,K,D,B,N
PROTEIN	24-letter Protein alphabet	A,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,V,W,Y,B,Z,X
RNA	4-letter RNA alphabet	A,C,G,U
RNA_N	5-letter RNA + N alphabet	A,C,G,U,N

Classes
struct	nvbio::AlphabetTraits< ALPHABET >
struct	nvbio::AlphabetTraits< DNA >
struct	nvbio::AlphabetTraits< DNA_N >
struct	nvbio::AlphabetTraits< DNA_IUPAC >
struct	nvbio::AlphabetTraits< PROTEIN >
struct	nvbio::AlphabetTraits< RNA >
struct	nvbio::AlphabetTraits< RNA_N >
struct	nvbio::AlphabetTraits< ASCII >
struct	nvbio::to_char_functor< ALPHABET >
struct	nvbio::from_char_functor< ALPHABET >

Enumerations
enum	nvbio::Alphabet {   nvbio::DNA = 0u, nvbio::DNA_N = 1u, nvbio::DNA_IUPAC = 2u, nvbio::PROTEIN = 3u,   nvbio::RNA = 4u, nvbio::RNA_N = 5u, nvbio::ASCII = 6u }

Functions
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::bits_per_symbol (const Alphabet alphabet)
template<Alphabet ALPHABET>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	nvbio::to_char (const uint8 c)
template<Alphabet ALPHABET>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	nvbio::from_char (const char c)
template<Alphabet ALPHABET, typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::to_string (const SymbolIterator begin, const uint32 n, char *string)
template<Alphabet ALPHABET, typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::to_string (const SymbolIterator begin, const SymbolIterator end, char *string)
template<Alphabet ALPHABET, typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::from_string (const char *begin, const char *end, SymbolIterator symbols)
template<Alphabet ALPHABET, typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::from_string (const char *begin, SymbolIterator symbols)
template<Alphabet ALPHABET, typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE transform_iterator< Iterator, to_char_functor< ALPHABET > >	nvbio::to_string (Iterator it)
template<Alphabet ALPHABET, typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE transform_iterator< Iterator, from_char_functor< ALPHABET > >	nvbio::from_string (Iterator it)

Enumeration Type Documentation

enum nvbio::Alphabet

The supported sequence alphabet types

Enumerator
DNA	4-letter DNA alphabet { A,C,G,T }
DNA_N	5-letter DNA + N alphabet { A,C,G,T,N }
DNA_IUPAC	16-letter DNA IUPAC alphabet { =,A,C,M,G,R,S,V,T,W,Y,H,K,D,B,N }
PROTEIN	24-letter Protein alphabet { A,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,V,W,Y,B,Z,X }
RNA	4-letter RNA alphabet { A,C,G,U }
RNA_N	5-letter RNA + N alphabet { A,C,G,U,N }
ASCII	standard ASCII alphabet

Definition at line 68 of file alphabet.h.

Function Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bits_per_symbol

(

const Alphabet

alphabet)

return the number of bits per symbol for a given alphabet

Definition at line 212 of file alphabet.h.

template<Alphabet ALPHABET>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::from_char

(

const char

c)

convert a given symbol to its ASCII character

Definition at line 145 of file alphabet_inl.h.

template<Alphabet ALPHABET, typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::from_string	(	const char *	begin,
		const char *	end,
		SymbolIterator	symbols
	)

convert from an ASCII string to the given alphabet

Definition at line 196 of file alphabet_inl.h.

template<Alphabet ALPHABET, typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::from_string	(	const char *	begin,
		SymbolIterator	symbols
	)

convert from an ASCII string to the given alphabet

Definition at line 208 of file alphabet_inl.h.

template<Alphabet ALPHABET, typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE transform_iterator< Iterator, from_char_functor<ALPHABET> > nvbio::from_string

(

Iterator

it)

convert an ASCII string iterator to a given alphabet string iterator

Definition at line 306 of file alphabet.h.

template<Alphabet ALPHABET>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char nvbio::to_char

(

const uint8

c)

convert a given symbol to its ASCII character

Definition at line 122 of file alphabet_inl.h.

template<Alphabet ALPHABET, typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::to_string	(	const SymbolIterator	begin,
		const uint32	n,
		char *	string
	)

convert from the given alphabet to an ASCII string

Definition at line 168 of file alphabet_inl.h.

template<Alphabet ALPHABET, typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::to_string	(	const SymbolIterator	begin,
		const SymbolIterator	end,
		char *	string
	)

convert from the given alphabet to an ASCII string

Definition at line 182 of file alphabet_inl.h.

template<Alphabet ALPHABET, typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE transform_iterator< Iterator, to_char_functor<ALPHABET> > nvbio::to_string

(

Iterator

it)

convert a string iterator from a given alphabet to an ASCII string iterator

Definition at line 296 of file alphabet.h.