a class for the representation of exact pattern matches (EPM) More...

#include <exact_matcher.hh>

Public Types
typedef BasePairs__Arc	Arc
	arc class of BasePairs

typedef SparsificationMapper::seq_pos_t	seqpos_t
	a type for a sequence position

typedef SparseTraceController::matpos_t	matpos_t
	a type for a position in a sparsified matrix

typedef SparsificationMapper::ArcIdx	ArcIdx
	arc index

typedef SparseTraceController::pair_seqpos_t	pair_seqpos_t
	pair of positions in sequence A and B

typedef std::pair< ArcIdx, ArcIdx >	PairArcIdx
	pair of arc indices

typedef std::vector< PairArcIdx >	PairArcIdxVec
	a vector of pairs of arc indices

typedef triple< seqpos_t, seqpos_t, char >	el_pat_vec
	type for elements of the pattern vector, <position in seq A, position in sequence B, structure>

typedef std::vector< el_pat_vec >	pat_vec_t
	type for pattern vector

Public Member Functions
	EPM ()
	Constructor.

virtual	~EPM ()
	destructor

score_t	get_score () const
	returns the score of the EPM

int	get_state () const
	return the current matrix state of the EPM

const matpos_t &	get_cur_pos () const
	returns the current matrix position of the EPM

const score_t &	get_max_tol_left () const
	returns the maximal tolerance that is left for the EPM

bool	get_first_insertion () const
	returns whether it is the first insertion into the EPM

bool	is_invalid () const

void	set_score (score_t score_)

void	set_state (int state_)

void	set_cur_pos (matpos_t cur_pos_)

void	set_max_tol_left (score_t tol)

void	set_first_insertion (bool first_insertion_)

void	set_invalid ()
	sets the flag invalid for the EPM

const PairArcIdx &	get_am (PairArcIdxVec::size_type idx) const

PairArcIdxVec::size_type	number_of_am ()

void	clear_am_to_do ()
	deletes the list am_to_do

PairArcIdxVec::const_iterator	am_begin () const

PairArcIdxVec::const_iterator	am_end () const

el_pat_vec	pat_vec_at (pat_vec_t::size_type idx) const

pat_vec_t::size_type	pat_vec_size () const

pat_vec_t::const_iterator	begin () const

pat_vec_t::const_iterator	end () const

pair_seqpos_t	last_matched_pos ()

void	add (seqpos_t posA, seqpos_t posB, char c)

void	overwrite (seqpos_t posA, seqpos_t posB, char c, pat_vec_t::size_type pos)

void	add_am (const Arc &a, const Arc &b)

void	store_am (const Arc &a, const Arc &b)

PairArcIdx	next_arcmatch ()

void	sort_patVec ()

void	sort_am_to_do ()

void	insert_epm (const EPM &epm_to_insert)

bool	includes (const EPM &epm_to_test) const

bool	includes_am (const EPM &epm_to_test) const

void	print_epm (std::ostream &out, bool verbose) const

Detailed Description

a class for the representation of exact pattern matches (EPM)

Member Function Documentation

void LocARNA::EPM::add	(	seqpos_t	posA,
		seqpos_t	posB,
		char	c
	)

inline

adds an element to the pattern vector

Parameters

posA	position in sequence A that is added to the pattern vector
posB	position in sequence B that is added to the pattern vector
c	char that specifies the match (sequential match '.', structural match '(' or ')' )

void LocARNA::EPM::add_am	(	const Arc &	a,
		const Arc &	b
	)

inline

appends an arc match to the EPM

Parameters

a	arc in sequence A
b	arc in sequence B

PairArcIdxVec::const_iterator LocARNA::EPM::am_begin ( ) const

inline

begin of vector that stores the pairs of arc indices that need to be computed

Returns: an iterator to the beginning of am_to_do

PairArcIdxVec::const_iterator LocARNA::EPM::am_end ( ) const

inline

end of vector that stores the pairs of arc indices that need to be computed

Returns: an iterator to the end of am_to_do

pat_vec_t::const_iterator LocARNA::EPM::begin ( ) const

inline

begin of pattern vector

Returns: an iterator to the beginning of the pattern vector pat_vec

pat_vec_t::const_iterator LocARNA::EPM::end ( ) const

inline

end of pattern vector

Returns: an iterator to the end of the pattern vector pat_vec

const PairArcIdx& LocARNA::EPM::get_am ( PairArcIdxVec::size_type idx ) const

inline

returns the pair of arc indices at position pos

Parameters

idx	index in the PairArcIdxVec

Returns: returns the PairArcIdx at the index idx in the am_to_do vector

bool LocARNA::EPM::includes ( const EPM & epm_to_test ) const

inline

checks whether the current EPM includes the EPM epm_to_test

Parameters

epm_to_test EPM that is checked

Returns: true, if the current EPM includes the EPM epm_to_test false, otherwise

bool LocARNA::EPM::includes_am ( const EPM & epm_to_test ) const

inline

checks whether the arcmatches of the current EPM includes the arcmatches of the epm_to_test

Parameters

epm_to_test EPM that is checked

Returns: true, if the arcmatches of the current EPM includes the arcmatches of the EPM epm_to_test false, otherwise

void LocARNA::EPM::insert_epm ( const EPM & epm_to_insert )

inline

inserts the pattern vector of the EPM epm_to_insert into the current EPM

Parameters

epm_to_insert EPM that is inserted

bool LocARNA::EPM::is_invalid ( ) const

inline

returns whether the EPM is invalid (only used in the suboptimal traceback when inexact structural matches are allowed)

pair_seqpos_t LocARNA::EPM::last_matched_pos ( )

inline

returns the last sequence position that is matched in the EPM

Returns: the last sequence position that is matched in the EPM

PairArcIdx LocARNA::EPM::next_arcmatch ( )

inline

returns a pair of arc indices that is processed

Returns: the pair of arc indices that is processed next

PairArcIdxVec::size_type LocARNA::EPM::number_of_am ( )

inline

returns the number of pairs of arc indices that need to be computed

Returns: the number of arc matches in am_to_do

void LocARNA::EPM::overwrite	(	seqpos_t	posA,
		seqpos_t	posB,
		char	c,
		pat_vec_t::size_type	pos
	)

inline

overwrites the element at position pos of the pattern vector

Parameters

posA	position in sequence A that is added to the pattern vector
posB	position in sequence B that is added to the pattern vector
c	char that specifies the match (sequential match '.', structural match '(' or ')' )
pos	position in the pattern vector

el_pat_vec LocARNA::EPM::pat_vec_at ( pat_vec_t::size_type idx ) const

inline

returns the element of the pattern vector at position pos

Parameters

idx index

Returns: the element of the pattern vector at idx

pat_vec_t::size_type LocARNA::EPM::pat_vec_size ( ) const

inline

return the size of the pattern vector

Returns: the size of the pattern vector pat_vec

void LocARNA::EPM::print_epm	(	std::ostream &	out,
		bool	verbose
	)		const

inline

prints the EPM

Parameters

out	output stream object
verbose	whether to write additional information

void LocARNA::EPM::set_cur_pos ( matpos_t cur_pos_ )

inline

sets the matrix position of the EPM

Parameters

cur_pos_ matrix position

void LocARNA::EPM::set_first_insertion ( bool first_insertion_ )

inline

sets the flag first_insertion for the EPM

Parameters

first_insertion_ whether it is the first_insertion

void LocARNA::EPM::set_max_tol_left ( score_t tol )

inline

sets the maximal tolerance that is left for the EPM

Parameters

tol	maximal tolerance

void LocARNA::EPM::set_score ( score_t score_ )

inline

sets the score of the EPM

Parameters

score_ score

void LocARNA::EPM::set_state ( int state_ )

inline

sets the matrix state of the EPM

Parameters

state_ matrix state

void LocARNA::EPM::sort_am_to_do ( )

inline

sorts the list of arcmatches am_to_do, such that includes_am works

void LocARNA::EPM::sort_patVec ( )

inline

sorts the pattern vector according to the positions in the first sequence (automatically also sorted according to the positions in the second sequence)

void LocARNA::EPM::store_am	(	const Arc &	a,
		const Arc &	b
	)

inline

stores an arc match in the am_to_do data structure

Parameters

a	arc in sequence A
b	arc in sequence B

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

src/LocARNA/exact_matcher.hh

Public Types

Public Member Functions

Detailed Description

Member Function Documentation