vdj_pipe::match::Match_element_aligned Class Reference

Identify DNA sequence interval by finding the best alignment. More...

#include <me_aligned.hpp>

Collaboration diagram for vdj_pipe::match::Match_element_aligned:

Classes
struct	Err

Public Types
typedef boost::string_ref	sequence
typedef Qual_record::quality	quality

Public Member Functions
	Match_element_aligned (Value_map const &vm, std::string const &match_value_name, std::string const &score_value_name, std::string const &identity_value_name, Relative_interval const &ri, detail::name_seq_vector const &sv, const int min_score, const unsigned min_match_len, const bool track_mismatches)
sequence_interval	operator() (const sequence seq, quality const &, sequence_interval const &si)
void	finish ()

Private Attributes
Value_map	vm_
Val_id	name_val_id_
Val_id	score_val_id_
Val_id	identity_val_id_
Seq_map_aligned	gsm_
Relative_interval	ri_
int	min_score_
std::size_t	min_match_len_
bool	track_mismatches_

Detailed Description

Identify DNA sequence interval by finding the best alignment.

Member Typedef Documentation

typedef Qual_record::quality vdj_pipe::match::Match_element_aligned::quality

typedef boost::string_ref vdj_pipe::match::Match_element_aligned::sequence

Constructor & Destructor Documentation

vdj_pipe::match::Match_element_aligned::Match_element_aligned ( Value_map const &  vm, std::string const &  match_value_name, std::string const &  score_value_name, std::string const &  identity_value_name, Relative_interval const &  ri, detail::name_seq_vector const &  sv, const int  min_score, const unsigned  min_match_len, const bool  track_mismatches  )

inline

Member Function Documentation

void vdj_pipe::match::Match_element_aligned::finish ( )

inline

sequence_interval vdj_pipe::match::Match_element_aligned::operator() ( const sequence  seq, quality const &  , sequence_interval const &  si  )

inline

Member Data Documentation

Seq_map_aligned vdj_pipe::match::Match_element_aligned::gsm_

private

Val_id vdj_pipe::match::Match_element_aligned::identity_val_id_

private

std::size_t vdj_pipe::match::Match_element_aligned::min_match_len_

private

int vdj_pipe::match::Match_element_aligned::min_score_

private

Val_id vdj_pipe::match::Match_element_aligned::name_val_id_

private

Relative_interval vdj_pipe::match::Match_element_aligned::ri_

private

Val_id vdj_pipe::match::Match_element_aligned::score_val_id_

private

bool vdj_pipe::match::Match_element_aligned::track_mismatches_

private

Value_map vdj_pipe::match::Match_element_aligned::vm_

private

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

• lib/me_aligned.hpp