Base symbol conversions. More...

Public Types
enum	base { NONE =0, ADENINE =1, CYTOSINE =2, AMINO =3, THYMINE =4, WEAK =5, PYRIMIDINE =6, NOT_GUANINE =7, GUANINE =8, PURINE =9, STRONG =10, NOT_THYMINE =11, KETO =12, NOT_CYTOSINE =13, NOT_ADENINE =14, ANY =15 }
	Nucleotide enum (bitmask).

enum	packed_base { PCK_ADENINE =0, PCK_CYTOSINE =1, PCK_GUANINE =2, PCK_THYMINE =3, PCK_ANY =4, PCK_NONE =5, PCK_PURINE =6, PCK_PYRIMIDINE =7, PCK_KETO =8, PCK_AMINO =9, PCK_WEAK =10, PCK_STRONG =11, PCK_NOT_THYMINE =12, PCK_NOT_GUANINE =13, PCK_NOT_CYTOSINE =14, PCK_NOT_ADENINE =15 }
	Nucleotide enum using fewer bits for frequent symbols.

Static Public Member Functions
static char	enc (const base b)
	Gets the IUPAC base symbol.

static std::string	s_enc (const base b)
	Gets the nucleotide name.

static char	rna_enc (const base b)
	Gets the IUPAC base symbol.

static std::string	rna_s_enc (const base b)
	Gets the nucleotide name.

static base	comp (const base b)
	Gets the complementary base (circular shift on the bitmask).

static base	km_class (const base b)
	Change base, but stay in the keto or amino class.

static base	ry_class (const base b)
	Change base, but stay in the pyrimdine or purine class.

static base	tr (const base b, const base replacewhat, const base replacewith)
	Substitute a base by another. More...

static base	dec (const unsigned char abbr)
	Gets the base id corresponding to the given IUPAC symbol. More...

static base	s_dec (const std::string &name)
	Gets the base id corresponding to the given nucleotide name.

static int	amb (const base b)
	Get the level of ambiguity for a base id.

static int	gc (const base b)
	Single base GC content. More...

static packed_base	pack (const base b)

static base	unpack (const packed_base b)

template<typename Iter >
static bool	is_nucleic_acid (Iter beg, Iter end, typename boost::enable_if< boost::is_same< typename std::iterator_traits< Iter >::value_type, char > >::type *dummy=0)
	Test if a character sequence represents a nucleotide sequence.

template<typename Iter >
static bool	is_plain_nucleic_acid (Iter beg, Iter end, typename boost::enable_if< boost::is_same< typename std::iterator_traits< Iter >::value_type, char > >::type *dummy=0)
	Test if a character sequence represents a nucleotide sequence without ambiguous IUPAC symbols.

template<typename Iter >
static bool	is_rc_palindrome (Iter b, Iter e, typename boost::enable_if< boost::is_same< typename std::iterator_traits< Iter >::value_type, base > >::type *dummy=0)
	Test if the sequence in the range is a bio palindrome.

template<typename Iter >
static bool	is_rc_palindrome (Iter b, Iter e, typename boost::enable_if< boost::is_same< typename std::iterator_traits< Iter >::value_type, packed_base > >::type *dummy=0)
	Test if the sequence in the range is a bio palindrome.

template<typename Iter >
static bool	is_rc_palindrome (Iter b, Iter e, typename boost::enable_if< boost::is_same< typename std::iterator_traits< Iter >::value_type, char > >::type *dummy=0)
	Test if the sequence in the range is a bio palindrome.

static void	rcomp (std::string &seq)
	Reverse complements a sequence (in place).

template<typename Iter >
static void	to_string (Iter beg, Iter end, std::string &res)

template<typename Iter >
static std::string	to_string (Iter beg, Iter end)

template<typename Iter >
static void	unpack_to_string (Iter beg, Iter end, std::string &res)

template<typename Iter >
static Iter	unpack_to_string (Iter beg, Iter end, std::string &res, size_t nmax)

template<typename Iter >
static std::string	unpack_to_string (Iter beg, Iter end)

Detailed Description

Base symbol conversions.

Member Function Documentation

static base shore::nuc::dec ( const unsigned char abbr)

inlinestatic

Gets the base id corresponding to the given IUPAC symbol.

Upper and lower case symbols supported; 'U' is treated as 'T'. Invalid symbols or gaps convert to NONE.

static int shore::nuc::gc ( const base b)

inlinestatic

Single base GC content.

Returns: 0 -> 0.0, 2 -> 1/3, 3 -> 1/2, 4 -> 2/3, 6 -> 1.0

static base shore::nuc::tr	(	const base	b,
		const base	replacewhat,
		const base	replacewith
	)

inlinestatic

Substitute a base by another.

Only meaningful for ambiguous symbols.

The documentation for this class was generated from the following file:

shore/datatype/nucleotide.hpp

Public Types

Static Public Member Functions

Detailed Description

Member Function Documentation