vdj_pipe::Seq_fls< N, S > Class Template Reference

store short sequence in an integer More...

#include <sequence_fls.hpp>

Public Types
typedef Seq_fls	self_type

Public Member Functions
	Seq_fls ()
	Seq_fls (const boost::string_ref seq)
	Seq_fls (self_type const &ss)
std::size_t	size () const
self_type &	operator= (self_type const &ss)
self_type &	operator= (const boost::string_ref seq)
bool	operator== (self_type const &sf) const
bool	operator!= (self_type const &sf) const
Nucleotide	operator[] (const std::size_t i) const
void	set (const unsigned i, const Nucleotide n)
std::string	to_string (std::size_t n=self_type::length()) const
std::ostream &	print (std::ostream &os, std::size_t n=self_type::length()) const

Static Public Member Functions
static std::size_t	length ()

Static Public Attributes
static const unsigned	alphabet_size = N

Private Member Functions
void	assign (const boost::string_ref seq)

Private Attributes
S	val_

Static Private Attributes
static const unsigned	BITS_PER_CHAR = boost::static_log2<N>::value
static const unsigned	MAX_CHARS = sizeof(S) * 8 / BITS_PER_CHAR
static const unsigned	MASK = ~(~0 << BITS_PER_CHAR)

Friends
std::size_t	hash_value (self_type const &seq)
std::ostream &	operator<< (std::ostream &os, self_type const &seq)
bool	assign (self_type &seq1, const boost::string_ref seq2)

Detailed Description

template<unsigned N = 4, typename S = boost::uint_least32_t>
class vdj_pipe::Seq_fls< N, S >

store short sequence in an integer

Template Parameters

N	alphabet size
storage	type

Member Typedef Documentation

template<unsigned N = 4, typename S = boost::uint_least32_t>

typedef Seq_fls vdj_pipe::Seq_fls< N, S >::self_type

Constructor & Destructor Documentation

template<unsigned N = 4, typename S = boost::uint_least32_t>

vdj_pipe::Seq_fls< N, S >::Seq_fls ( )

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

vdj_pipe::Seq_fls< N, S >::Seq_fls ( const boost::string_ref  seq )

inlineexplicit

template<unsigned N = 4, typename S = boost::uint_least32_t>

vdj_pipe::Seq_fls< N, S >::Seq_fls ( self_type const &  ss )

inline

Member Function Documentation

template<unsigned N = 4, typename S = boost::uint_least32_t>

void vdj_pipe::Seq_fls< N, S >::assign ( const boost::string_ref  seq )

inlineprivate

template<unsigned N = 4, typename S = boost::uint_least32_t>

static std::size_t vdj_pipe::Seq_fls< N, S >::length ( )

inlinestatic

template<unsigned N = 4, typename S = boost::uint_least32_t>

bool vdj_pipe::Seq_fls< N, S >::operator!= ( self_type const &  sf ) const

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

self_type& vdj_pipe::Seq_fls< N, S >::operator= ( self_type const &  ss )

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

self_type& vdj_pipe::Seq_fls< N, S >::operator= ( const boost::string_ref  seq )

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

bool vdj_pipe::Seq_fls< N, S >::operator== ( self_type const &  sf ) const

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

Nucleotide vdj_pipe::Seq_fls< N, S >::operator[] ( const std::size_t  i ) const

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

std::ostream& vdj_pipe::Seq_fls< N, S >::print ( std::ostream &  os, std::size_t  n = self_type::length()  ) const

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

void vdj_pipe::Seq_fls< N, S >::set ( const unsigned  i, const Nucleotide  n  )

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

std::size_t vdj_pipe::Seq_fls< N, S >::size ( ) const

inline

template<unsigned N = 4, typename S = boost::uint_least32_t>

std::string vdj_pipe::Seq_fls< N, S >::to_string ( std::size_t  n = self_type::length() ) const

inline

Friends And Related Function Documentation

template<unsigned N = 4, typename S = boost::uint_least32_t>

bool assign ( self_type &  seq1, const boost::string_ref  seq2  )

friend

Assign seq2 to seq1

Parameters

seq1[out]	compressed sequence
seq2[in]	regular sequence

Returns

true if seq2 can fit into seq1 and the alphabet of seq1 can accommodate all characters of seq2

template<unsigned N = 4, typename S = boost::uint_least32_t>

std::size_t hash_value ( self_type const &  seq )

friend

template<unsigned N = 4, typename S = boost::uint_least32_t>

std::ostream& operator<< ( std::ostream &  os, self_type const &  seq  )

friend

Member Data Documentation

template<unsigned N = 4, typename S = boost::uint_least32_t>

const unsigned vdj_pipe::Seq_fls< N, S >::alphabet_size = N

static

template<unsigned N = 4, typename S = boost::uint_least32_t>

const unsigned vdj_pipe::Seq_fls< N, S >::BITS_PER_CHAR = boost::static_log2<N>::value

staticprivate

template<unsigned N = 4, typename S = boost::uint_least32_t>

const unsigned vdj_pipe::Seq_fls< N, S >::MASK = ~(~0 << BITS_PER_CHAR)

staticprivate

template<unsigned N = 4, typename S = boost::uint_least32_t>

const unsigned vdj_pipe::Seq_fls< N, S >::MAX_CHARS = sizeof(S) * 8 / BITS_PER_CHAR

staticprivate

template<unsigned N = 4, typename S = boost::uint_least32_t>

S vdj_pipe::Seq_fls< N, S >::val_

private

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

• include/vdj_pipe/sequence_fls.hpp