Access to value map for paired read pipeline and processing steps. More...

#include <value_map_access_paired.hpp>

Inheritance diagram for vdj_pipe::Vm_access_paired:

Collaboration diagram for vdj_pipe::Vm_access_paired:

Classes
struct	Err

Public Types
typedef Seq_record::sequence	seq_type

typedef Qual_record::quality	qual_type

Public Types inherited from vdj_pipe::Value_map
typedef map_type::iterator	iterator

typedef iterator	const_iterator

Public Member Functions
	Vm_access_paired ()

std::string const &	description_fwd () const

void	description_fwd (std::string const &descr)

std::string const &	description_rev () const

void	description_rev (std::string const &descr)

seq_type const &	sequence_fwd () const

std::string	sequence_fwd (const bool trim) const

void	sequence_fwd (seq_type const &seq)

seq_type const &	sequence_rev () const

std::string	sequence_rev (const bool trim, const bool reverse) const

void	sequence_rev (seq_type const &seq)

qual_type const &	quality_fwd () const

qual_type	quality_fwd (const bool trim) const

void	quality_fwd (qual_type const &qual)

qual_type const &	quality_rev () const

qual_type	quality_rev (const bool trim, const bool reverse) const

void	quality_rev (qual_type const &qual)

sequence_interval	interval_fwd () const

void	interval_fwd (sequence_interval const &si)

sequence_interval	interval_rev () const

void	interval_rev (sequence_interval const &si)

std::string const &	sequence_path_fwd () const

void	sequence_path_fwd (std::string const &s)

std::string const &	sequence_path_rev () const

void	sequence_path_rev (std::string const &s)

std::string const &	quality_path_fwd () const

void	quality_path_fwd (std::string const &s)

std::string const &	quality_path_rev () const

void	quality_path_rev (std::string const &s)

Public Member Functions inherited from vdj_pipe::Value_map
	Value_map ()

iterator	begin () const

iterator	end () const

std::size_t	size () const

void	clear_values ()

std::string const &	name (const Val_id vid) const

Val_id	insert_name (std::string const &name)

Val_id	insert_new_name (std::string const &name)

Val_id const *	find_id (std::string const &name) const

Val_id	value_id (std::string const &name) const

value_variant const &	operator[] (const Val_id vid) const

value_variant &	operator[] (const Val_id vid)

long	read_count () const

void	read_count_reset ()

void	read_count_incr ()

long	file_read_count () const

void	file_read_count_reset ()

void	file_read_count_incr ()

std::string const &	seq_file_name () const

void	seq_file_name (std::string const &fn)

std::string const &	read_id_nothrow () const

std::string const &	read_id () const

void	read_id (std::string const &id)

template<typename T >
T const &	value (std::string const &name) const

template<typename T >
T const *	value_ptr (std::string const &name) const

template<typename T >
T const &	value (const Val_id id) const

template<typename T >
T const *	value_ptr (const Val_id id) const

std::string const &	str_nothrow (const Val_id id) const

Protected Attributes
Value_ids_paired	ids_

Additional Inherited Members
Protected Member Functions inherited from vdj_pipe::Value_map
std::string	sequence (const Val_id seq_id, const Val_id trim_id, const bool trimmed, const bool reverse_compl) const

Qual_record::quality	quality (const Val_id qual_id, const Val_id trim_id, const bool trimmed, const bool reverse_compl) const

Detailed Description

Access to value map for paired read pipeline and processing steps.

Member Typedef Documentation

typedef Qual_record::quality vdj_pipe::Vm_access_paired::qual_type

typedef Seq_record::sequence vdj_pipe::Vm_access_paired::seq_type

Constructor & Destructor Documentation

vdj_pipe::Vm_access_paired::Vm_access_paired ( )

inline

Member Function Documentation

std::string const& vdj_pipe::Vm_access_paired::description_fwd ( ) const

inline

void vdj_pipe::Vm_access_paired::description_fwd ( std::string const & descr )

inline

std::string const& vdj_pipe::Vm_access_paired::description_rev ( ) const

inline

void vdj_pipe::Vm_access_paired::description_rev ( std::string const & descr )

inline

sequence_interval vdj_pipe::Vm_access_paired::interval_fwd ( ) const

inline

void vdj_pipe::Vm_access_paired::interval_fwd ( sequence_interval const & si )

inline

sequence_interval vdj_pipe::Vm_access_paired::interval_rev ( ) const

inline

void vdj_pipe::Vm_access_paired::interval_rev ( sequence_interval const & si )

inline

qual_type const& vdj_pipe::Vm_access_paired::quality_fwd ( ) const

inline

qual_type vdj_pipe::Vm_access_paired::quality_fwd ( const bool trim ) const

inline

void vdj_pipe::Vm_access_paired::quality_fwd ( qual_type const & qual )

inline

std::string const& vdj_pipe::Vm_access_paired::quality_path_fwd ( ) const

inline

void vdj_pipe::Vm_access_paired::quality_path_fwd ( std::string const & s )

inline

std::string const& vdj_pipe::Vm_access_paired::quality_path_rev ( ) const

inline

void vdj_pipe::Vm_access_paired::quality_path_rev ( std::string const & s )

inline

qual_type const& vdj_pipe::Vm_access_paired::quality_rev ( ) const

inline

qual_type vdj_pipe::Vm_access_paired::quality_rev	(	const bool	trim,
		const bool	reverse
	)		const

inline

void vdj_pipe::Vm_access_paired::quality_rev ( qual_type const & qual )

inline

seq_type const& vdj_pipe::Vm_access_paired::sequence_fwd ( ) const

inline

std::string vdj_pipe::Vm_access_paired::sequence_fwd ( const bool trim ) const

inline

void vdj_pipe::Vm_access_paired::sequence_fwd ( seq_type const & seq )

inline

std::string const& vdj_pipe::Vm_access_paired::sequence_path_fwd ( ) const

inline

void vdj_pipe::Vm_access_paired::sequence_path_fwd ( std::string const & s )

inline

std::string const& vdj_pipe::Vm_access_paired::sequence_path_rev ( ) const

inline

void vdj_pipe::Vm_access_paired::sequence_path_rev ( std::string const & s )

inline

seq_type const& vdj_pipe::Vm_access_paired::sequence_rev ( ) const

inline

std::string vdj_pipe::Vm_access_paired::sequence_rev	(	const bool	trim,
		const bool	reverse
	)		const

inline

void vdj_pipe::Vm_access_paired::sequence_rev ( seq_type const & seq )

inline

Member Data Documentation

Value_ids_paired vdj_pipe::Vm_access_paired::ids_

protected

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

include/vdj_pipe/value_map_access_paired.hpp

Classes

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation