#include <sequence_file_map.hpp>

Collaboration diagram for vdj_pipe::Seq_file_map:

Classes
struct	Err

struct	Pair

Public Types
typedef Seq_file	value_type

typedef file_map::iterator	iterator

typedef file_map::const_iterator	const_iterator

Public Member Functions
	Seq_file_map ()

std::size_t	size () const

const_iterator	begin () const

const_iterator	end () const

bool	empty () const

Seq_file const &	operator[] (const Path_id id) const

Seq_file const &	at (const Path_id id) const

Seq_file const *	find (std::string const &path) const

void	erase (const Path_id id)

void	clear ()

std::pair< Path_id, bool >	insert (Seq_file const &file)

void	set_seq_qual (const Path_id seq_id, const Path_id qual_id)

void	set_paired (const Path_id frw_id, const Path_id rev_id)

void	set_mid (const Path_id seq_id, const Path_id mid_id)

Path_id	qual2seq (const Path_id qual_id) const

Path_id	seq2qual (const Path_id seq_id) const

Path_id	rev2frw (const Path_id rev_id) const

Path_id	frw2rev (const Path_id frw_id) const

Path_id	mid2seq (const Path_id mid_id) const

Path_id	seq2mid (const Path_id seq_id) const

Private Types
typedef boost::multi_index_container< Seq_file, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::tag< struct id_tag >, boost::multi_index::const_mem_fun< Seq_file, Path_id,&Seq_file::id > >, boost::multi_index::ordered_unique< boost::multi_index::tag< struct path_tag >, boost::multi_index::const_mem_fun< File, std::string const &,&Seq_file::path > > > >	file_map

typedef file_map::index< id_tag >::type	id_index

typedef id_index::const_iterator	id_iterator

typedef file_map::index< path_tag >::type	path_index

typedef path_index::const_iterator	path_iterator

typedef boost::multi_index_container< Pair, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< Pair, Path_id,&Pair::one_ > >, boost::multi_index::ordered_unique< boost::multi_index::member< Pair, Path_id,&Pair::two_ > > > >	pair_map

typedef pair_map::nth_index< 0 >::type	index1

typedef index1::const_iterator	citer1

typedef pair_map::nth_index< 1 >::type	index2

typedef index2::const_iterator	citer2

Static Private Member Functions
template<int N>
static Path_id	get (const Path_id pid, pair_map const &pm)

Private Attributes
Id_iterator< Path_id >	i_

file_map	map_

pair_map	sqm_

pair_map	frm_

pair_map	smm_

Member Typedef Documentation

typedef index1::const_iterator vdj_pipe::Seq_file_map::citer1

private

typedef index2::const_iterator vdj_pipe::Seq_file_map::citer2

private

typedef file_map::const_iterator vdj_pipe::Seq_file_map::const_iterator

typedef boost::multi_index_container< Seq_file, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::tag<struct id_tag>, boost::multi_index::const_mem_fun< Seq_file, Path_id, &Seq_file::id > >, boost::multi_index::ordered_unique< boost::multi_index::tag<struct path_tag>, boost::multi_index::const_mem_fun< File, std::string const&, &Seq_file::path > > > > vdj_pipe::Seq_file_map::file_map

private

typedef file_map::index<id_tag>::type vdj_pipe::Seq_file_map::id_index

private

typedef id_index::const_iterator vdj_pipe::Seq_file_map::id_iterator

private

typedef pair_map::nth_index<0>::type vdj_pipe::Seq_file_map::index1

private

typedef pair_map::nth_index<1>::type vdj_pipe::Seq_file_map::index2

private

typedef file_map::iterator vdj_pipe::Seq_file_map::iterator

typedef boost::multi_index_container< Pair, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member<Pair, Path_id, &Pair::one_> >, boost::multi_index::ordered_unique< boost::multi_index::member<Pair, Path_id, &Pair::two_> > > > vdj_pipe::Seq_file_map::pair_map

private

typedef file_map::index<path_tag>::type vdj_pipe::Seq_file_map::path_index

private

typedef path_index::const_iterator vdj_pipe::Seq_file_map::path_iterator

private

typedef Seq_file vdj_pipe::Seq_file_map::value_type

Constructor & Destructor Documentation

vdj_pipe::Seq_file_map::Seq_file_map ( )

inline

Member Function Documentation

Seq_file const& vdj_pipe::Seq_file_map::at ( const Path_id id ) const

inline

const_iterator vdj_pipe::Seq_file_map::begin ( ) const

inline

void vdj_pipe::Seq_file_map::clear ( )

inline

bool vdj_pipe::Seq_file_map::empty ( ) const

inline

const_iterator vdj_pipe::Seq_file_map::end ( ) const

inline

void vdj_pipe::Seq_file_map::erase ( const Path_id id )

inline

Seq_file const* vdj_pipe::Seq_file_map::find ( std::string const & path ) const

inline

Path_id vdj_pipe::Seq_file_map::frw2rev ( const Path_id frw_id ) const

inline

template<int N>

static Path_id vdj_pipe::Seq_file_map::get	(	const Path_id	pid,
		pair_map const &	pm
	)

inlinestaticprivate

std::pair<Path_id, bool> vdj_pipe::Seq_file_map::insert ( Seq_file const & file )

inline

Path_id vdj_pipe::Seq_file_map::mid2seq ( const Path_id mid_id ) const

inline

Seq_file const& vdj_pipe::Seq_file_map::operator[] ( const Path_id id ) const

inline

Path_id vdj_pipe::Seq_file_map::qual2seq ( const Path_id qual_id ) const

inline

Path_id vdj_pipe::Seq_file_map::rev2frw ( const Path_id rev_id ) const

inline

Path_id vdj_pipe::Seq_file_map::seq2mid ( const Path_id seq_id ) const

inline

Path_id vdj_pipe::Seq_file_map::seq2qual ( const Path_id seq_id ) const

inline

void vdj_pipe::Seq_file_map::set_mid	(	const Path_id	seq_id,
		const Path_id	mid_id
	)

inline

void vdj_pipe::Seq_file_map::set_paired	(	const Path_id	frw_id,
		const Path_id	rev_id
	)

inline

void vdj_pipe::Seq_file_map::set_seq_qual	(	const Path_id	seq_id,
		const Path_id	qual_id
	)

inline

std::size_t vdj_pipe::Seq_file_map::size ( ) const

inline

Member Data Documentation

pair_map vdj_pipe::Seq_file_map::frm_

private

forward reverse pairs

Id_iterator<Path_id> vdj_pipe::Seq_file_map::i_

private

file_map vdj_pipe::Seq_file_map::map_

private

pair_map vdj_pipe::Seq_file_map::smm_

private

sequence eMID pairs

pair_map vdj_pipe::Seq_file_map::sqm_

private

sequence quality pairs

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

include/vdj_pipe/sequence_file_map.hpp

Classes

Public Types

Public Member Functions

Private Types

Static Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation