vdj_pipe::Seq_store Class Reference

Store sequence and related information. More...

#include <sequence_store.hpp>

Collaboration diagram for vdj_pipe::Seq_store:

Public Types
typedef detail::Id_map< Seq_id, Seq_entry >	seq_map
typedef boost::shared_ptr< seq_map >	seq_map_ptr
typedef detail::Vector_set< sub_seq >	sub_seq_set
typedef detail::Vector_set< super_seq >	super_seq_set
typedef seq_index::iterator	iterator
typedef seq_index::const_iterator	const_iterator

Public Member Functions
	Seq_store ()
std::size_t	size () const
const_iterator	begin () const
const_iterator	end () const
bool	empty () const
Seq_entry const &	operator[] (const Seq_id sid) const
boost::shared_ptr< seq_map >	sequence_map ()
size_range	by_size () const
size_range	by_size (const unsigned size) const
size_range	by_size_range (const unsigned from, const unsigned to=std::numeric_limits< unsigned >::max()) const
Seq_id	insert (const Read_id rid, const boost::string_ref seq)
	insert name and sequence checking for duplicates More...
template<class Super_seqs >
void	remove_subsequence (const Seq_id sid, Super_seqs const &ss)
super_seq_set const &	maps_to (const Read_id iid) const
sub_seq_set const &	maps_from (const Seq_id sid) const

Private Types
typedef detail::Getter< seq_map, Seq_id, Seq_entry, std::string const &,&Seq_entry::sequence >	get_seq
typedef detail::Getter< seq_map, Seq_id, Seq_entry, unsigned,&Seq_entry::size >	get_size
typedef boost::multi_index_container< Seq_id, boost::multi_index::indexed_by< boost::multi_index::hashed_unique< boost::multi_index::tag< struct seq_tag >, get_seq >, boost::multi_index::ordered_non_unique< boost::multi_index::tag< struct size_tag >, get_size > > >	seq_mi_t
typedef seq_mi_t::index< seq_tag >::type	seq_index
typedef seq_mi_t::index< size_tag >::type	size_index
typedef detail::Id_map< Seq_id, sub_seq_set >	seq_to_info
typedef detail::Id_map< Read_id, super_seq_set >	info_to_seq
typedef size_index::const_iterator	size_iterator
typedef boost::iterator_range< size_iterator >	size_range

Static Private Member Functions
static seq_mi_t::ctor_args_list	seq_index_init (seq_map const &sm)

Private Attributes
seq_map_ptr	sm_
seq_mi_t	si_
seq_to_info	s2i_
info_to_seq	i2s_

Detailed Description

Store sequence and related information.

Member Typedef Documentation

typedef seq_index::const_iterator vdj_pipe::Seq_store::const_iterator

typedef detail::Getter< seq_map, Seq_id, Seq_entry, std::string const&, &Seq_entry::sequence > vdj_pipe::Seq_store::get_seq

private

typedef detail::Getter< seq_map, Seq_id, Seq_entry, unsigned, &Seq_entry::size > vdj_pipe::Seq_store::get_size

private

typedef detail::Id_map<Read_id, super_seq_set> vdj_pipe::Seq_store::info_to_seq

private

typedef seq_index::iterator vdj_pipe::Seq_store::iterator

typedef seq_mi_t::index<seq_tag>::type vdj_pipe::Seq_store::seq_index

private

typedef detail::Id_map<Seq_id, Seq_entry> vdj_pipe::Seq_store::seq_map

typedef boost::shared_ptr<seq_map> vdj_pipe::Seq_store::seq_map_ptr

typedef boost::multi_index_container< Seq_id, boost::multi_index::indexed_by< boost::multi_index::hashed_unique< boost::multi_index::tag<struct seq_tag>, get_seq >, boost::multi_index::ordered_non_unique< boost::multi_index::tag<struct size_tag>, get_size > > > vdj_pipe::Seq_store::seq_mi_t

private

typedef detail::Id_map<Seq_id, sub_seq_set> vdj_pipe::Seq_store::seq_to_info

private

typedef seq_mi_t::index<size_tag>::type vdj_pipe::Seq_store::size_index

private

typedef size_index::const_iterator vdj_pipe::Seq_store::size_iterator

private

typedef boost::iterator_range<size_iterator> vdj_pipe::Seq_store::size_range

private

typedef detail::Vector_set<sub_seq> vdj_pipe::Seq_store::sub_seq_set

typedef detail::Vector_set<super_seq> vdj_pipe::Seq_store::super_seq_set

Constructor & Destructor Documentation

vdj_pipe::Seq_store::Seq_store ( )

inline

Member Function Documentation

const_iterator vdj_pipe::Seq_store::begin ( ) const

inline

size_range vdj_pipe::Seq_store::by_size ( ) const

inline

Returns

range of all sequence info IDs ordered by size

size_range vdj_pipe::Seq_store::by_size ( const unsigned  size ) const

inline

Returns

range of sequence info IDs of % size size

size_range vdj_pipe::Seq_store::by_size_range ( const unsigned  from, const unsigned  to = std::numeric_limits<unsigned>::max()  ) const

inline

Returns

range of sequence info IDs that have % size in the range [from, to)

bool vdj_pipe::Seq_store::empty ( ) const

inline

const_iterator vdj_pipe::Seq_store::end ( ) const

inline

Seq_id vdj_pipe::Seq_store::insert ( const Read_id  rid, const boost::string_ref  seq  )

inline

insert name and sequence checking for duplicates

sub_seq_set const& vdj_pipe::Seq_store::maps_from ( const Seq_id  sid ) const

inline

super_seq_set const& vdj_pipe::Seq_store::maps_to ( const Read_id  iid ) const

inline

Seq_entry const& vdj_pipe::Seq_store::operator[] ( const Seq_id  sid ) const

inline

template<class Super_seqs >

void vdj_pipe::Seq_store::remove_subsequence ( const Seq_id  sid, Super_seqs const &  ss  )

inline

static seq_mi_t::ctor_args_list vdj_pipe::Seq_store::seq_index_init ( seq_map const &  sm )

inlinestaticprivate

boost::shared_ptr<seq_map> vdj_pipe::Seq_store::sequence_map ( )

inline

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

inline

Member Data Documentation

info_to_seq vdj_pipe::Seq_store::i2s_

private

seq_to_info vdj_pipe::Seq_store::s2i_

private

seq_mi_t vdj_pipe::Seq_store::si_

private

seq_map_ptr vdj_pipe::Seq_store::sm_

private

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

• include/vdj_pipe/sequence_store.hpp