vdj_pipe::Seq_map_full Class Reference

#include <sequence_map_full.hpp>

Collaboration diagram for vdj_pipe::Seq_map_full:

Classes
struct	Err

Public Types
typedef std::vector< Nucleotide >	seq_type
typedef Best_match_pair< Mid_id, int >	match_type
typedef Id_iterator< Mid_id >	iterator
typedef iterator	const_iterator

Public Member Functions
	Seq_map_full (const bool allow_duplicate_seq=false)
iterator	begin () const
iterator	end () const
seq_type	seq (const Mid_id id) const
std::string	seq_string (const Mid_id id) const
std::string const &	name (const Mid_id id) const
Mid_id	max_id () const
std::size_t	min_len () const
std::size_t	max_len () const
Mid_id const *	find_exact (seq_type const &seq) const
Mid_id const *	find_exact (const boost::string_ref seq) const
template<class Seq >
bool	find_closest (const Seq s, match_type &m, scoring_matrix_t const &sm) const
Mid_id	insert (std::string name, std::string const &seq)

Static Public Member Functions
static std::string	to_string (seq_type const &sv)

Private Types
typedef detail::Id_bimap< Mid_id, seq_type >	seq_map
typedef detail::Id_map< Mid_id, std::string >	name_map

Static Private Member Functions
static seq_type	to_vector (const boost::string_ref s)

Private Attributes
seq_map	seqs_
name_map	names_
bool	allow_duplicate_seq_
std::size_t	min_len_
std::size_t	max_len_

Member Typedef Documentation

typedef iterator vdj_pipe::Seq_map_full::const_iterator

typedef Id_iterator<Mid_id> vdj_pipe::Seq_map_full::iterator

typedef Best_match_pair<Mid_id, int> vdj_pipe::Seq_map_full::match_type

typedef detail::Id_map<Mid_id, std::string> vdj_pipe::Seq_map_full::name_map

private

typedef detail::Id_bimap<Mid_id, seq_type> vdj_pipe::Seq_map_full::seq_map

private

typedef std::vector<Nucleotide> vdj_pipe::Seq_map_full::seq_type

Constructor & Destructor Documentation

vdj_pipe::Seq_map_full::Seq_map_full ( const bool  allow_duplicate_seq = false )

inlineexplicit

Member Function Documentation

iterator vdj_pipe::Seq_map_full::begin ( ) const

inline

iterator vdj_pipe::Seq_map_full::end ( ) const

inline

template<class Seq >

bool vdj_pipe::Seq_map_full::find_closest ( const Seq  s, match_type &  m, scoring_matrix_t const &  sm  ) const

inline

Mid_id const* vdj_pipe::Seq_map_full::find_exact ( seq_type const &  seq ) const

inline

Mid_id const* vdj_pipe::Seq_map_full::find_exact ( const boost::string_ref  seq ) const

inline

Mid_id vdj_pipe::Seq_map_full::insert ( std::string  name, std::string const &  seq  )

inline

Mid_id vdj_pipe::Seq_map_full::max_id ( ) const

inline

std::size_t vdj_pipe::Seq_map_full::max_len ( ) const

inline

std::size_t vdj_pipe::Seq_map_full::min_len ( ) const

inline

std::string const& vdj_pipe::Seq_map_full::name ( const Mid_id  id ) const

inline

seq_type vdj_pipe::Seq_map_full::seq ( const Mid_id  id ) const

inline

std::string vdj_pipe::Seq_map_full::seq_string ( const Mid_id  id ) const

inline

static std::string vdj_pipe::Seq_map_full::to_string ( seq_type const &  sv )

inlinestatic

static seq_type vdj_pipe::Seq_map_full::to_vector ( const boost::string_ref  s )

inlinestaticprivate

Member Data Documentation

bool vdj_pipe::Seq_map_full::allow_duplicate_seq_

private

std::size_t vdj_pipe::Seq_map_full::max_len_

private

std::size_t vdj_pipe::Seq_map_full::min_len_

private

name_map vdj_pipe::Seq_map_full::names_

private

seq_map vdj_pipe::Seq_map_full::seqs_

private

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

• lib/sequence_map_full.hpp