LocARNA::SparsificationMapper Class Reference

Represents the mapping for sparsification. More...

#include <sparsification_mapper.hh>

List of all members.

Classes
struct	info_for_pos
Public Types
typedef BasePairs__Arc	Arc
	type of arc
typedef size_t	ArcIdx
	type of arc index
typedef std::vector< ArcIdx >	ArcIdxVec
	vector of arc indices
typedef pos_type	matidx_t
	type for a matrix position
typedef pos_type	seq_pos_t
	type for a sequence position
typedef size_t	index_t
	type for an index
typedef std::vector< info_for_pos >	InfoForPosVec
Public Member Functions
	SparsificationMapper (const BasePairs &bps_, const ExtRnaData &rnadata_, double prob_unpaired_in_loop_threshold_, double prob_basepair_in_loop_threshold_, bool index_left_ends)
size_type	get_max_info_vec_size () const
const InfoForPosVec &	valid_seq_positions (index_t idx) const
const ArcIdxVec &	valid_arcs_right_adj (index_t idx, matidx_t pos) const
matidx_t	first_valid_mat_pos_before_eq (index_t index, seq_pos_t pos, index_t left_end=std::numeric_limits< index_t >::max()) const
matidx_t	first_valid_mat_pos_before (index_t index, seq_pos_t pos, index_t left_end=std::numeric_limits< index_t >::max()) const
seq_pos_t	get_pos_in_seq_new (index_t idx, matidx_t pos) const
size_type	number_of_valid_mat_pos (index_t idx) const
bool	pos_unpaired (index_t idx, matidx_t pos) const
bool	matching_without_gap_possible (const Arc &arc, seq_pos_t pos) const
const ArcIdxVec &	valid_arcs_left_adj (const Arc &arc, seq_pos_t pos) const
virtual	~SparsificationMapper ()
	class destructor
matidx_t	idx_geq (index_t index, seq_pos_t min_col, index_t left_end=std::numeric_limits< index_t >::max()) const
matidx_t	idx_after_leq (index_t index, seq_pos_t max_col, index_t left_end=std::numeric_limits< index_t >::max()) const
bool	is_valid_pos (const Arc &arc, seq_pos_t pos) const
bool	is_valid_pos_external (seq_pos_t pos) const

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Detailed Description

Represents the mapping for sparsification.

The datastructures are either indexed by the ArcIdx (in Exparna_P) or by the common left end (Locarna_ng).

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Member Typedef Documentation

typedef std::vector<info_for_pos> LocARNA::SparsificationMapper::InfoForPosVec

vector of struct info_for_pos that is assigned to the index (either common left end or arc index)

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Constructor & Destructor Documentation

LocARNA::SparsificationMapper::SparsificationMapper	(	const BasePairs &	bps_,
		const ExtRnaData &	rnadata_,
		double	prob_unpaired_in_loop_threshold_,
		double	prob_basepair_in_loop_threshold_,
		bool	index_left_ends
	)		[inline]

Constructor

Parameters:

bps_	BasePairs
rnadata_	RnaData
prob_unpaired_in_loop_threshold_	probability threshold for unpaired position under a loop
prob_basepair_in_loop_threshold_	probability threshold for basepair under a loop
index_left_ends	specifies whether the datastructures are indexed by the common left end (true) or by the arc index (false)

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Member Function Documentation

matidx_t LocARNA::SparsificationMapper::first_valid_mat_pos_before	(	index_t	index,
		seq_pos_t	pos,
		index_t	left_end = std::numeric_limits<index_t>::max()
	)		const [inline]

gives the first valid matrix position before a sequence position

Parameters:

index	index
pos	sequence position
left_end	the index left end;if not set, it is set to the index (for example when indexing by the left end is used)

Returns:

the first valid matrix position before the position pos at the index left_end

matidx_t LocARNA::SparsificationMapper::first_valid_mat_pos_before_eq	(	index_t	index,
		seq_pos_t	pos,
		index_t	left_end = std::numeric_limits<index_t>::max()
	)		const [inline]

gives the first valid matrix position before or equal to a sequence position

Parameters:

index	index
pos	sequence position
left_end	the index left end; if not set, it is set to the index (for example when indexing by the left end is used)

Returns:

the first valid matrix position before or equal to the position pos at the index left_end

size_type LocARNA::SparsificationMapper::get_max_info_vec_size

(

)

const [inline]

returns the maximal size of the info vectors

seq_pos_t LocARNA::SparsificationMapper::get_pos_in_seq_new	(	index_t	idx,
		matidx_t	pos
	)		const [inline]

maps a matrix position to the corresponding sequence position

Parameters:

idx	index
pos	matrix position

Returns:

the sequence position that corresponds to the matrix position at the index idx

matidx_t LocARNA::SparsificationMapper::idx_after_leq	(	index_t	index,
		seq_pos_t	max_col,
		index_t	left_end = std::numeric_limits<index_t>::max()
	)		const [inline]

gives the index position after the index position that stores the first sequence position that is less than or equal to max_col if it does not exist return 0

Parameters:

index	index
max_col	the maximal column in the non-sparsified matrix
left_end	the index left end; if not set, it is set to the index (for example when indexing by the left end is used)

Returns:

matrix position that stores the first sequence position that is less than or equal to max_col

matidx_t LocARNA::SparsificationMapper::idx_geq	(	index_t	index,
		seq_pos_t	min_col,
		index_t	left_end = std::numeric_limits<index_t>::max()
	)		const [inline]

gives the index that stores the first sequence position that is greater than or equal to min_col if it does not exist, return the number of valid matrix positions num_pos

Parameters:

index	index
min_col	the minimal column in the non-sparsified matrix
left_end	the index left end; if not set, it is set to the index (for example when indexing by the left end is used)

Returns:

matrix position that stores the first sequence position that is greater than or equal to min_col

bool LocARNA::SparsificationMapper::is_valid_pos	(	const Arc &	arc,
		seq_pos_t	pos
	)		const [inline]

Is position pos valid?

Parameters:

arc	Arc
pos	sequence position

Returns:

true, if the probability that the inner_arc occurs in the loop closed by the arc is greater or equal to the threshold for a basepair under a loop
false, otherwise

bool LocARNA::SparsificationMapper::is_valid_pos_external

(

seq_pos_t

pos

)

const [inline]

Is position pos a valid external position?

Parameters:

pos	sequence position

Returns:

true, if the sequence position pos has a probability to be external greater than or equal to prob_unpaired_in_loop_threshold

bool LocARNA::SparsificationMapper::matching_without_gap_possible	(	const Arc &	arc,
		seq_pos_t	pos
	)		const [inline]

Is a matrix position unpaired?

Parameters:

arc	arc that is used as an index
pos	sequence position

Returns:

true, if matching without a gap is possible from pos for the arc index
false, otherwise
matching without a gap is possible from pos if the sequence position that corresponds to the first valid matrix position before pos is directly adjacent to pos

size_type LocARNA::SparsificationMapper::number_of_valid_mat_pos

(

index_t

idx

)

const [inline]

gives the number of valid matrix positions for the index

Parameters:

idx

index

Returns:

the number of valid matrix positions for idx

bool LocARNA::SparsificationMapper::pos_unpaired	(	index_t	idx,
		matidx_t	pos
	)		const [inline]

Is a matrix position unpaired?

Parameters:

idx	index
pos	matrix position

Returns:

true, if pos can occur unpaired
false, otherwise

const ArcIdxVec& LocARNA::SparsificationMapper::valid_arcs_left_adj	(	const Arc &	arc,
		seq_pos_t	pos
	)		const [inline]

gives all valid arcs with common left end from a sequence position

Parameters:

arc	arc that is used as an index
pos	sequence position

Returns:

vector of all valid arcs with common left end pos for the arc index

const ArcIdxVec& LocARNA::SparsificationMapper::valid_arcs_right_adj	(	index_t	idx,
		matidx_t	pos
	)		const [inline]

gives all valid arcs that end at a matrix position

Parameters:

idx	index
pos	matrix position

Returns:

vector of all valid arcs with the common right end pos

const InfoForPosVec& LocARNA::SparsificationMapper::valid_seq_positions

(

index_t

idx

)

const [inline]

gives all valid positions with additional information for an index

Parameters:

idx

index

Returns:

vector of all valid positions with additional information at index

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

• src/LocARNA/sparsification_mapper.hh
• src/LocARNA/sparsification_mapper.cc