LocARNA::EPM Class Reference

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

#include <exact_matcher.hh>

List of all members.

Classes
struct	compare_el_am_to_do
struct	compare_el_pat_vec
	compare two elements of the pattern vector
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
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 (const 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 Typedef Documentation

typedef triple<seqpos_t, seqpos_t, char> LocARNA::EPM::el_pat_vec

type for elements of the pattern vector, <position in seq A, position in sequence B, structure>

---

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

(

const 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

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

• src/LocARNA/exact_matcher.hh