Collaboration diagram for vdj_pipe::match::Element_proto:

Public Member Functions
	Element_proto (bpt::ptree const &pt, Input_manager const &in)

Truncate	truncation () const

Relative_interval	interval () const

void	parse_position (bpt::ptree const &pt)

void	parse_csv_file (bpt::ptree const &pt, Input_manager const &in)

Public Attributes
bool	start_defined_

bool	re_start_

std::string	name_

std::string	value_name_

std::string	score_name_

std::string	identity_name_

std::string	re_name_

boost::optional< int >	pos_

boost::optional< int >	len_

boost::optional< int >	min_score_

boost::optional< unsigned >	min_match_length_

bool	track_mismatches_

bool	allow_gaps_

bool	required_

bool	ignore_dups_

bool	require_best_

detail::name_seq_vector	seqs_

boost::optional< detail::Seq_props >	sp_

Cut_proto	cut_lo_

Cut_proto	cut_up_

Static Public Attributes
static const int	unset = std::numeric_limits<int>::min()

Constructor & Destructor Documentation

vdj_pipe::match::Element_proto::Element_proto	(	bpt::ptree const &	pt,
		Input_manager const &	in
	)

Member Function Documentation

Relative_interval vdj_pipe::match::Element_proto::interval ( ) const

void vdj_pipe::match::Element_proto::parse_csv_file	(	bpt::ptree const &	pt,
		Input_manager const &	in
	)

void vdj_pipe::match::Element_proto::parse_position ( bpt::ptree const & pt )

Truncate vdj_pipe::match::Element_proto::truncation ( ) const

inline

bool vdj_pipe::match::Element_proto::allow_gaps_

Cut_proto vdj_pipe::match::Element_proto::cut_lo_

Cut_proto vdj_pipe::match::Element_proto::cut_up_

std::string vdj_pipe::match::Element_proto::identity_name_

bool vdj_pipe::match::Element_proto::ignore_dups_

ignore duplicate sequences for short matches

boost::optional<int> vdj_pipe::match::Element_proto::len_

boost::optional<unsigned> vdj_pipe::match::Element_proto::min_match_length_

boost::optional<int> vdj_pipe::match::Element_proto::min_score_

std::string vdj_pipe::match::Element_proto::name_

boost::optional<int> vdj_pipe::match::Element_proto::pos_

std::string vdj_pipe::match::Element_proto::re_name_

bool vdj_pipe::match::Element_proto::re_start_

bool vdj_pipe::match::Element_proto::require_best_

bool vdj_pipe::match::Element_proto::required_

std::string vdj_pipe::match::Element_proto::score_name_

detail::name_seq_vector vdj_pipe::match::Element_proto::seqs_

boost::optional<detail::Seq_props> vdj_pipe::match::Element_proto::sp_

bool vdj_pipe::match::Element_proto::start_defined_

bool vdj_pipe::match::Element_proto::track_mismatches_

interpret min_score_ as maximum number of mismatches

const int vdj_pipe::match::Element_proto::unset = std::numeric_limits<int>::min()

static

std::string vdj_pipe::match::Element_proto::value_name_

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