LocARNA::BasePairs Class Reference

Describes sequence and structure ensemble of an RNA. More...

#include <basepairs.hh>

Classes
class	LeftAdjEntry
	Entry in a left adjacency list. More...
class	RightAdjEntry
	Entry in a right adjacency list. More...

Public Types
typedef size_t	size_type
	size
typedef BasePairs__Arc	Arc
	arc
typedef std::vector< Arc >	arc_vec_t
	Vector of arcs.
typedef std::vector< LeftAdjEntry >	LeftAdjList
	type of left adjacency list
typedef std::vector< RightAdjEntry >	RightAdjList
	type of right adjacency list
typedef SparseMatrix< int >	arc_matrix_t
	type for matrix of arcs (actually arc indices)
typedef std::pair< size_type, size_type >	bpair_t
	type for pair of positions (base pairs)
typedef std::set< bpair_t >	bpair_set_t
	type for set of position pairs

Public Member Functions
	BasePairs (const RnaData *rna_data, double min_prob)
	BasePairs (size_type len, const bpair_set_t &bps)
	Construct from a set of base pairs. More...
void	register_arc (int i, int j)
	registers an arc (i,j) More...
const LeftAdjList &	left_adjlist_s (size_type i) const
	Get left adjacency list with sentinel. More...
const RightAdjList &	right_adjlist_s (size_type i) const
	Get right adjacency list with sentinel. More...
const Arc &	arc (int i, int j) const
	accesses basepair by (i,j)
const Arc &	arc (size_type idx) const
bool	exists_arc (int i, int j) const
	returns whether basepair (i,j) exists
size_type	num_bps () const
	returns number of basepairs in the object
size_type	seqlen () const
	returns length of sequence
double	prob_min () const
	return minimal probability

Detailed Description

Describes sequence and structure ensemble of an RNA.

Stores and maintains the list of potential base pairs together with their score contributions in arc matches.

In contrast to RnaData, which stores the raw data for an RNA, a BasePairs object knows about sparsification of base pairs by a probability threshold and provides traversal of base pairs suited for alignment algorithms.

If the base pairs object is constructed from an RnaData object, it knows about its corresponding RnaData object.

Constructor & Destructor Documentation

BasePairs() [1/2]

LocARNA::BasePairs::BasePairs	(	const RnaData *	rna_data,
		double	min_prob
	)

Construct from rna data

Parameters

rna_data	rna data
min_prob	minimal probability for filtering base pairs

Note

while rna data maintains base pairs regardless of their probability, an object of BasePairs represents the sparsified set of base pairs (due to min_prob_)

BasePairs() [2/2]

LocARNA::BasePairs::BasePairs	(	size_type	len,
		const bpair_set_t &	bps
	)

Construct from a set of base pairs.

Parameters

len	length of sequence
bps	set of base pairs

Member Function Documentation

arc()

const Arc& LocARNA::BasePairs::arc ( size_type  idx ) const

inline

Parameters

idx	an arc index

Returns

arc with index idx

left_adjlist_s()

const LeftAdjList& LocARNA::BasePairs::left_adjlist_s ( size_type  i ) const

inline

Get left adjacency list with sentinel.

Parameters

i

position

Returns

list of arcs with left end i

register_arc()

void LocARNA::BasePairs::register_arc	(	int	i,
		int	j
	)

registers an arc (i,j)

registers a basepair (i,j), maintains the basepair access data structures

right_adjlist_s()

const RightAdjList& LocARNA::BasePairs::right_adjlist_s ( size_type  i ) const

inline

Get right adjacency list with sentinel.

Parameters

i

position

Returns

list of arcs with right end i

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

• src/LocARNA/basepairs.hh
• src/LocARNA/basepairs.cc