vdj_pipe::Seq_file_entry Class Reference

#include <sequence_file_entry.hpp>

Collaboration diagram for vdj_pipe::Seq_file_entry:

Classes
struct	Err

Public Types
typedef std::map< Val_id, value_variant >	map_t
typedef map_t::const_iterator	iterator
typedef map_t::const_iterator	const_iterator
typedef map_t::value_type	value_type

Public Member Functions
	Seq_file_entry (map_t const &m, Input_manager const &im, Value_map const &vm)
const_iterator	begin () const
const_iterator	end () const
bool	is_paired () const
bool	has_emid () const
bool	has_quality () const
bool	has_qual_file () const
std::string const &	sequence () const
std::string const &	quality () const
std::string const &	seq_rev () const
std::string const &	qual_rev () const
std::string const &	mid () const
std::string const &	mid_rev () const

Private Types
enum	qual_type { none, qual, fastq }

Private Member Functions
void	check (Input_manager const &im)
std::string const &	get_str (const Val_id id, std::string const &msg) const

Private Attributes
qual_type	qt_
Val_id	seq_
Val_id	qual_
Val_id	seq_rev_
Val_id	qual_rev_
Val_id	mid_
Val_id	mid_rev_
map_t	map_

Detailed Description

Tuple of sequence data files that should be processed in parallel and associated info. Examples:

• single FASTA file name
• two FASTA/Qual pairs for paired reads and a sample name

Member Typedef Documentation

typedef map_t::const_iterator vdj_pipe::Seq_file_entry::const_iterator

typedef map_t::const_iterator vdj_pipe::Seq_file_entry::iterator

typedef std::map<Val_id, value_variant> vdj_pipe::Seq_file_entry::map_t

typedef map_t::value_type vdj_pipe::Seq_file_entry::value_type

Member Enumeration Documentation

enum vdj_pipe::Seq_file_entry::qual_type

private

Enumerator
none
qual
fastq

Constructor & Destructor Documentation

vdj_pipe::Seq_file_entry::Seq_file_entry	(	map_t const &	m,
		Input_manager const &	im,
		Value_map const &	vm
	)

Member Function Documentation

const_iterator vdj_pipe::Seq_file_entry::begin ( ) const

inline

void vdj_pipe::Seq_file_entry::check ( Input_manager const &  im )

private

const_iterator vdj_pipe::Seq_file_entry::end ( ) const

inline

std::string const& vdj_pipe::Seq_file_entry::get_str ( const Val_id  id, std::string const &  msg  ) const

inlineprivate

bool vdj_pipe::Seq_file_entry::has_emid ( ) const

inline

bool vdj_pipe::Seq_file_entry::has_qual_file ( ) const

inline

bool vdj_pipe::Seq_file_entry::has_quality ( ) const

inline

bool vdj_pipe::Seq_file_entry::is_paired ( ) const

inline

std::string const& vdj_pipe::Seq_file_entry::mid ( ) const

inline

std::string const& vdj_pipe::Seq_file_entry::mid_rev ( ) const

inline

std::string const& vdj_pipe::Seq_file_entry::qual_rev ( ) const

inline

std::string const& vdj_pipe::Seq_file_entry::quality ( ) const

inline

std::string const& vdj_pipe::Seq_file_entry::seq_rev ( ) const

inline

std::string const& vdj_pipe::Seq_file_entry::sequence ( ) const

inline

Member Data Documentation

map_t vdj_pipe::Seq_file_entry::map_

private

Val_id vdj_pipe::Seq_file_entry::mid_

private

Val_id vdj_pipe::Seq_file_entry::mid_rev_

private

qual_type vdj_pipe::Seq_file_entry::qt_

private

Val_id vdj_pipe::Seq_file_entry::qual_

private

Val_id vdj_pipe::Seq_file_entry::qual_rev_

private

Val_id vdj_pipe::Seq_file_entry::seq_

private

Val_id vdj_pipe::Seq_file_entry::seq_rev_

private

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

• include/vdj_pipe/sequence_file_entry.hpp
• lib/sequence_file_entry.cpp