Generalized DNA suffix tree. More...

#include <gdst.hpp>

Collaboration diagram for vdj_pipe::gdst::Gdst:

[legend]

Classes
struct	Err

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 ()

	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)

Private Types
typedef detail::Id_map< Branch_id, Branch >	branch_map

typedef detail::Id_map< Leaf_id, Leaf >	leaf_map

typedef detail::Id_map< Children_id, Children >	children_map

typedef boost::string_ref	seq_type

Private Member Functions
void	collect_sequences (const gdst::Branch_id nid, detail::Vector_set< Seq_id > &vs) const

void	suffix_link (const Branch_id bid1, const Branch_id bid2)

Branch_id	suffix_link (const Branch_id bid) const

unsigned	edge_length (const Branch_id bid, const Nucleotide n) const

unsigned	edge_length (const Branch_id bid, const seq_type suff) const

void	check_edge (Branch_id &an, unsigned &aei, unsigned &al, const boost::string_ref seq) const

void	add_to_leaf (const Branch_id bid, const Seq_id sid)

Branch_id	leaf_from_branch (const Branch_id bid1, const Nucleotide n1, const unsigned i, const Seq_id sid)

Branch_id	split_edge (const Branch_id bid1, const Nucleotide n1, const unsigned i, const Nucleotide n2)

Private Attributes
seq_map_ptr	ss_

branch_map	bm_

children_map	cm_

leaf_map	lm_

Branch_id	root_

Friends
class	Gdst_stats

class	Common_substrings

class	Ukkonen_inserter

Detailed Description

Generalized DNA suffix tree.

Member Typedef Documentation

typedef detail::Id_map<Branch_id, Branch> vdj_pipe::gdst::Gdst::branch_map

private

typedef detail::Id_map<Children_id, Children> vdj_pipe::gdst::Gdst::children_map

private

typedef detail::Id_map<Leaf_id, Leaf> vdj_pipe::gdst::Gdst::leaf_map

private

typedef Seq_pos<Seq_id> vdj_pipe::gdst::Gdst::match_type

typedef std::vector<match_type> vdj_pipe::gdst::Gdst::match_vector

typedef detail::Id_map<Seq_id, Seq_entry> vdj_pipe::gdst::Gdst::seq_map

typedef boost::shared_ptr<seq_map> vdj_pipe::gdst::Gdst::seq_map_ptr

typedef boost::string_ref vdj_pipe::gdst::Gdst::seq_type

private

Constructor & Destructor Documentation

vdj_pipe::gdst::Gdst::Gdst ( )

inline

vdj_pipe::gdst::Gdst::Gdst ( seq_map_ptr ss )

inlineexplicit

Member Function Documentation

void vdj_pipe::gdst::Gdst::add_to_leaf	(	const Branch_id	bid,
		const Seq_id	sid
	)

inlineprivate

void vdj_pipe::gdst::Gdst::check_edge	(	Branch_id &	an,
		unsigned &	aei,
		unsigned &	al,
		const boost::string_ref	seq
	)		const

inlineprivate

Branch_id vdj_pipe::gdst::Gdst::child	(	const Branch_id	bid1,
		const Nucleotide	n
	)		const

inline

Branch_id vdj_pipe::gdst::Gdst::child	(	const Branch_id	bid1,
		const seq_type	seq
	)		const

inline

void vdj_pipe::gdst::Gdst::child	(	const Branch_id	bid1,
		const Nucleotide	n,
		const Branch_id	bid2
	)

inline

void vdj_pipe::gdst::Gdst::collect_sequences	(	const gdst::Branch_id	nid,
		detail::Vector_set< Seq_id > &	vs
	)		const

inlineprivate

Depth_iter vdj_pipe::gdst::Gdst::depth_first ( ) const

inline

unsigned vdj_pipe::gdst::Gdst::edge_length	(	const Branch_id	bid,
		const Nucleotide	n
	)		const

inlineprivate

unsigned vdj_pipe::gdst::Gdst::edge_length	(	const Branch_id	bid,
		const seq_type	suff
	)		const

inlineprivate

Match vdj_pipe::gdst::Gdst::find	(	const seq_type	seq,
		const Branch_id	bid,
		unsigned	min_d = `0`
	)		const

inline

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

Returns: set of sequence IDs that have overlaps with seq

void vdj_pipe::gdst::Gdst::insert ( const Seq_id sid )

Leaf const& vdj_pipe::gdst::Gdst::leaf ( const Branch_id bid ) const

inline

Branch_id vdj_pipe::gdst::Gdst::leaf_from_branch	(	const Branch_id	bid1,
		const Nucleotide	n1,
		const unsigned	i,
		const Seq_id	sid
	)

inlineprivate

Nucleotide vdj_pipe::gdst::Gdst::letter	(	const Branch_id	bid,
		const unsigned	i
	)		const

inline

Nucleotide vdj_pipe::gdst::Gdst::letter	(	const Branch_id	bid,
		const Nucleotide	n,
		const unsigned	i
	)		const

inline

Branch const& vdj_pipe::gdst::Gdst::operator[] ( const Branch_id bid ) const

inline

Leaf const& vdj_pipe::gdst::Gdst::operator[] ( const Leaf_id lid ) const

inline

Seq_entry const& vdj_pipe::gdst::Gdst::operator[] ( const Seq_id sid ) const

inline

Branch_id vdj_pipe::gdst::Gdst::root ( ) const

inline

seq_map const& vdj_pipe::gdst::Gdst::sequence_map ( ) const

inline

seq_map& vdj_pipe::gdst::Gdst::sequence_map ( )

inline

std::size_t vdj_pipe::gdst::Gdst::size ( ) const

inline

Branch_id vdj_pipe::gdst::Gdst::split_edge	(	const Branch_id	bid1,
		const Nucleotide	n1,
		const unsigned	i,
		const Nucleotide	n2
	)

inlineprivate

const seq_type vdj_pipe::gdst::Gdst::suffix	(	const Seq_id	sid,
		const unsigned	len
	)		const

inline

const seq_type vdj_pipe::gdst::Gdst::suffix	(	const Leaf_id	lid,
		const unsigned	len
	)		const

inline

const seq_type vdj_pipe::gdst::Gdst::suffix ( Branch const & b ) const

inline

const seq_type vdj_pipe::gdst::Gdst::suffix ( const Branch_id bid ) const

inline

void vdj_pipe::gdst::Gdst::suffix_link	(	const Branch_id	bid1,
		const Branch_id	bid2
	)

inlineprivate

Branch_id vdj_pipe::gdst::Gdst::suffix_link ( const Branch_id bid ) const

inlineprivate

Friends And Related Function Documentation

friend class Common_substrings

friend

friend class Gdst_stats

friend

friend class Ukkonen_inserter

friend

Member Data Documentation

branch_map vdj_pipe::gdst::Gdst::bm_

private

children_map vdj_pipe::gdst::Gdst::cm_

private

leaf_map vdj_pipe::gdst::Gdst::lm_

private

Branch_id vdj_pipe::gdst::Gdst::root_

private

seq_map_ptr vdj_pipe::gdst::Gdst::ss_

private

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

include/vdj_pipe/gdst/gdst.hpp
lib/gdst.cpp

Classes

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation