vdj_pipe::match::Match_element_ambiguous Class Reference

Find best match between DNA sequence interval and a set of sequences without gaps that may include ambiguous nucleotides. More...

#include <me_ambiguous.hpp>

Collaboration diagram for vdj_pipe::match::Match_element_ambiguous:

Classes
struct	Err

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

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

Private Attributes
Value_map	vm_
Val_id	name_val_id_
Val_id	score_val_id_
Seq_map_full	sm_
Relative_interval	ri_
scoring_matrix_t const *	scoring_matrix_
int	min_score_
bool	require_best_

Detailed Description

Find best match between DNA sequence interval and a set of sequences without gaps that may include ambiguous nucleotides.

Member Typedef Documentation

typedef Qual_record::quality vdj_pipe::match::Match_element_ambiguous::quality

typedef boost::string_ref vdj_pipe::match::Match_element_ambiguous::sequence

Constructor & Destructor Documentation

vdj_pipe::match::Match_element_ambiguous::Match_element_ambiguous ( Value_map const &  vm, std::string const &  match_value_name, std::string const &  score_value_name, Relative_interval const &  ri, detail::name_seq_vector const &  sv, const int  min_score, const bool  ignore_dups, const bool  require_best, const bool  track_mismatches  )

inline

Member Function Documentation

void vdj_pipe::match::Match_element_ambiguous::finish ( )

inline

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

inline

Member Data Documentation

int vdj_pipe::match::Match_element_ambiguous::min_score_

private

Val_id vdj_pipe::match::Match_element_ambiguous::name_val_id_

private

bool vdj_pipe::match::Match_element_ambiguous::require_best_

private

Relative_interval vdj_pipe::match::Match_element_ambiguous::ri_

private

Val_id vdj_pipe::match::Match_element_ambiguous::score_val_id_

private

scoring_matrix_t const* vdj_pipe::match::Match_element_ambiguous::scoring_matrix_

private

Seq_map_full vdj_pipe::match::Match_element_ambiguous::sm_

private

Value_map vdj_pipe::match::Match_element_ambiguous::vm_

private

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

• lib/me_ambiguous.hpp