Inheritance diagram for vdj_pipe::detail::External_mid_base:

Collaboration diagram for vdj_pipe::detail::External_mid_base:

Protected Member Functions
	VDJ_PIPE_KEYWORD_STRUCT (kwds,(fasta_path)(pairs_path)(value_name)(min_score)(max_mismatches)(require_best))

std::size_t	mid_size () const

void	find_mid (const boost::string_ref seq, Value_map &vm)

Private Types
typedef Best_match_pair< Mid_id, int >	match_type

Private Attributes
boost::shared_ptr< Seq_map_short >	sms_

boost::shared_ptr< Seq_map_full >	smf_

scoring_matrix_t const *	scoring_matrix_

int	min_score_

bool	require_best_

Val_id	name_val_id_

Val_id	score_val_id_

Member Typedef Documentation

private

Member Function Documentation

void vdj_pipe::detail::External_mid_base::find_mid	(	const boost::string_ref	seq,
		Value_map &	vm
	)

protected

Attempt to assign sequence to one of the MIDs, gather statistics;

std::size_t vdj_pipe::detail::External_mid_base::mid_size ( ) const

protected

vdj_pipe::detail::External_mid_base::VDJ_PIPE_KEYWORD_STRUCT	(	kwds	,
		(fasta_path)(pairs_path)(value_name)(min_score)(max_mismatches)(require_best)
	)

protected

int vdj_pipe::detail::External_mid_base::min_score_

private

Val_id vdj_pipe::detail::External_mid_base::name_val_id_

private

bool vdj_pipe::detail::External_mid_base::require_best_

private

Val_id vdj_pipe::detail::External_mid_base::score_val_id_

private

scoring_matrix_t const* vdj_pipe::detail::External_mid_base::scoring_matrix_

private

boost::shared_ptr<Seq_map_full> vdj_pipe::detail::External_mid_base::smf_

private

boost::shared_ptr<Seq_map_short> vdj_pipe::detail::External_mid_base::sms_

private

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