Generalized DNA suffix tree. More...

#include <gdst.hpp>

Public Types
typedef detail::Id_map< Seq_id, Seq_entry >	seq_map

typedef boost::shared_ptr< seq_map >	seq_map_ptr

typedef Seq_pos< Seq_id >	match_type

typedef std::vector< match_type >	match_vector

Public Member Functions
	Gdst (seq_map_ptr ss)

std::size_t	size () const

Depth_iter	depth_first () const

Branch_id	root () const

seq_map const &	sequence_map () const

seq_map &	sequence_map ()

Branch const &	operator[] (const Branch_id bid) const

Leaf const &	operator[] (const Leaf_id lid) const

Seq_entry const &	operator[] (const Seq_id sid) const

Leaf const &	leaf (const Branch_id bid) const

const seq_type	suffix (const Seq_id sid, const unsigned len) const

const seq_type	suffix (const Leaf_id lid, const unsigned len) const

const seq_type	suffix (Branch const &b) const

const seq_type	suffix (const Branch_id bid) const

Nucleotide	letter (const Branch_id bid, const unsigned i) const

Nucleotide	letter (const Branch_id bid, const Nucleotide n, const unsigned i) const

Branch_id	child (const Branch_id bid1, const Nucleotide n) const

Branch_id	child (const Branch_id bid1, const seq_type seq) const

void	child (const Branch_id bid1, const Nucleotide n, const Branch_id bid2)

Common_subseq	find_longest (const seq_type seq, std::size_t min_len=0) const

void	find_overlaping (const boost::string_ref seq, detail::Vector_set< Seq_id > &vs, std::size_t min_overlap=0) const

Match	find (const seq_type seq, const Branch_id bid, unsigned min_d=0) const

void	insert (const Seq_id sid)

Detailed Description

Generalized DNA suffix tree.

Member Function Documentation

Common_subseq vdj_pipe::gdst::Gdst::find_longest	(	const seq_type	seq,
		std::size_t	min_len = `0`
	)		const

find longest common substring

Parameters

seq	DNA sequence, no ambiguous characters
min_len	minimal common substring length; if min_len == 0, only complete matches are considered

void vdj_pipe::gdst::Gdst::find_overlaping	(	const boost::string_ref	seq,
		detail::Vector_set< Seq_id > &	vs,
		std::size_t	min_overlap = `0`
	)		const

Parameters

seq	sequence of non-ambiguous nucleotides
min_overlap	minimal overlap size; if min_overlap == 0, only fully matching sequences will be returned

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