#include <value_map_access_single.hpp>

Inheritance diagram for vdj_pipe::Vm_access_single:

Collaboration diagram for vdj_pipe::Vm_access_single:

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_single (Value_names::single_read_names const &names)

	Vm_access_single (Value_map const &vm, Value_names::single_read_names const &names)

	Vm_access_single (Value_map const &vm, Value_ids_single const &ids)

void	reset (Value_ids_single const &ids)

std::string const &	description () const

void	description (std::string const &descr)

seq_type const &	sequence () const

void	sequence (seq_type const &seq)

qual_type const &	quality () const

void	quality (qual_type const &qual)

sequence_interval	interval () const

void	interval (sequence_interval const &si)

void	set_empty ()

void	trim (sequence_interval const &si)

bool	is_reverse () const

void	set_reverse (const bool rev)

std::string	sequence (const bool trimmed, const bool reverse_compl) const

qual_type	quality (const bool trimmed, const bool reverse_compl) const

std::string const &	sequence_path () const

void	sequence_path (std::string const &s)

std::string const &	quality_path () const

void	quality_path (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

Private Attributes
Value_ids_single	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

Member Typedef Documentation

typedef Qual_record::quality vdj_pipe::Vm_access_single::qual_type

typedef Seq_record::sequence vdj_pipe::Vm_access_single::seq_type

Constructor & Destructor Documentation

vdj_pipe::Vm_access_single::Vm_access_single ( Value_names::single_read_names const & names )

inline

vdj_pipe::Vm_access_single::Vm_access_single	(	Value_map const &	vm,
		Value_names::single_read_names const &	names
	)

inline

vdj_pipe::Vm_access_single::Vm_access_single	(	Value_map const &	vm,
		Value_ids_single const &	ids
	)

inline

Member Function Documentation

std::string const& vdj_pipe::Vm_access_single::description ( ) const

inline

void vdj_pipe::Vm_access_single::description ( std::string const & descr )

inline

sequence_interval vdj_pipe::Vm_access_single::interval ( ) const

inline

Returns: sequence interval

void vdj_pipe::Vm_access_single::interval ( sequence_interval const & si )

inline

Parameters

si	set read sequence interval to si

bool vdj_pipe::Vm_access_single::is_reverse ( ) const

inline

Returns: true if read sequence marked as reverse

qual_type const& vdj_pipe::Vm_access_single::quality ( ) const

inline

void vdj_pipe::Vm_access_single::quality ( qual_type const & qual )

inline

qual_type vdj_pipe::Vm_access_single::quality	(	const bool	trimmed,
		const bool	reverse_compl
	)		const

inline

std::string const& vdj_pipe::Vm_access_single::quality_path ( ) const

inline

void vdj_pipe::Vm_access_single::quality_path ( std::string const & s )

inline

void vdj_pipe::Vm_access_single::reset ( Value_ids_single const & ids )

inline

seq_type const& vdj_pipe::Vm_access_single::sequence ( ) const

inline

void vdj_pipe::Vm_access_single::sequence ( seq_type const & seq )

inline

std::string vdj_pipe::Vm_access_single::sequence	(	const bool	trimmed,
		const bool	reverse_compl
	)		const

inline

Parameters

trimmed
reverse_compl

Returns: sequence complete or within interval() if trimmed, and reverse-complemented if is_reverse() and reverse_compl

std::string const& vdj_pipe::Vm_access_single::sequence_path ( ) const

inline

void vdj_pipe::Vm_access_single::sequence_path ( std::string const & s )

inline

void vdj_pipe::Vm_access_single::set_empty ( )

inline

void vdj_pipe::Vm_access_single::set_reverse ( const bool rev )

inline

void vdj_pipe::Vm_access_single::trim ( sequence_interval const & si )

inline

Member Data Documentation

Value_ids_single vdj_pipe::Vm_access_single::ids_

private

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

include/vdj_pipe/value_map_access_single.hpp

Classes

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation