vdj_pipe::match Namespace Reference

Namespaces
	anonymous_namespace{me_battery.cpp}
	anonymous_namespace{me_factory.cpp}

Classes
struct	Cut_proto
struct	Element_proto
class	Match_combination
class	Match_element_aligned
	Identify DNA sequence interval by finding the best alignment. More...
class	Match_element_ambiguous
	Find best match between DNA sequence interval and a set of sequences without gaps that may include ambiguous nucleotides. More...
class	Match_element_battery
class	Match_element_factory
class	Match_element_positional
	Identify DNA sequence interval by position only. More...
class	Match_element_short
	Find best match between DNA sequence interval and a set of short sequences without gaps. More...
class	Match_element_visitor
class	Relative_interval
class	Relative_position
	Sequence position defined relatively to an interval. More...
class	Truncate

Typedefs
typedef boost::variant< Match_element_aligned, Match_element_ambiguous, Match_element_positional, Match_element_short >	me_variant
typedef std::vector< me_variant >	variant_vector
typedef std::vector< Truncate >	truncate_vector
typedef std::vector< Match_combination >	combination_vector
typedef std::vector< sequence_interval >	interval_vector

Functions
void	make_element_index (std::vector< std::string > const &me_names, std::vector< std::string > const &all_me_names, std::vector< std::size_t > &mev)
void	make_column_inds (std::string const &line, std::vector< std::string > const &col_names, std::vector< int > &col_inds)
void	parse_csv_combination (std::istream &is, std::vector< int > const &col_inds, detail::string_table &st)
void	parse_csv_combination (bpt::ptree const &pt, Input_manager const &in, std::vector< std::string > const &me_names, std::vector< std::size_t > &mev, detail::string_table &st)
Match_combination	make_combination (Value_map const &vm, bpt::ptree const &pt, Input_manager const &in, std::vector< std::string > const &me_names)

Typedef Documentation

typedef std::vector<Match_combination> vdj_pipe::match::combination_vector

typedef std::vector<sequence_interval> vdj_pipe::match::interval_vector

typedef boost::variant< Match_element_aligned, Match_element_ambiguous, Match_element_positional, Match_element_short > vdj_pipe::match::me_variant

typedef std::vector<Truncate> vdj_pipe::match::truncate_vector

typedef std::vector<me_variant> vdj_pipe::match::variant_vector

Function Documentation

void vdj_pipe::match::make_column_inds	(	std::string const &	line,
		std::vector< std::string > const &	col_names,
		std::vector< int > &	col_inds
	)

Match_combination vdj_pipe::match::make_combination	(	Value_map const &	vm,
		bpt::ptree const &	pt,
		Input_manager const &	in,
		std::vector< std::string > const &	me_names
	)

void vdj_pipe::match::make_element_index	(	std::vector< std::string > const &	me_names,
		std::vector< std::string > const &	all_me_names,
		std::vector< std::size_t > &	mev
	)

VDJ_PIPE_DECL void vdj_pipe::match::parse_csv_combination	(	std::istream &	is,
		std::vector< int > const &	col_inds,
		detail::string_table &	st
	)

Parameters

is
col_inds	show where to put each column
st	string table

VDJ_PIPE_DECL void vdj_pipe::match::parse_csv_combination	(	bpt::ptree const &	pt,
		Input_manager const &	in,
		std::vector< std::string > const &	all_me_names,
		std::vector< std::size_t > &	mev,
		detail::string_table &	st
	)