class ArcMatches with additional mapping More...

#include <arc_matches.hh>

Inheritance diagram for LocARNA::ArcMatchesIndexed:

Collaboration diagram for LocARNA::ArcMatchesIndexed:

[legend]

Public Member Functions
	ArcMatchesIndexed (const Sequence &seqA_, const Sequence &seqB_, const std::string &arcmatch_scores_file, int probability_scale, size_type max_length_diff, size_type max_diff_at_am, const MatchController &trace_controller, const AnchorConstraints &constraints)
	construct with explicit arc match score list More...

	ArcMatchesIndexed (const RnaData &rnadataA, const RnaData &rnadataB, double min_prob, size_type max_length_diff, size_type max_diff_at_am, const MatchController &trace_controller, const AnchorConstraints &constraints)
	construct from single base pair probabilities. More...

const ArcMatch::idx_type	invalid_am_index () const
	the invalid arc match index More...

const ArcMatch::idx_type	am_index (const size_type &arcAIdx, const size_type &arcBIdx) const
	Lookup arc match index by pair of arc indices. More...

const ArcMatch &	am_index (const Arc &arcA, const Arc &arcB) const
	Lookup arc match by pair of arcs. More...

Public Member Functions inherited from LocARNA::ArcMatches
	ArcMatches (const Sequence &seqA_, const Sequence &seqB_, const std::string &arcmatch_scores_file, int probability_scale, size_type max_length_diff, size_type max_diff_at_am, const MatchController &trace_controller, const AnchorConstraints &constraints)
	construct with explicit arc match score list More...

	ArcMatches (const RnaData &rnadataA, const RnaData &rnadataB, double min_prob, size_type max_length_diff, size_type max_diff_at_am, const MatchController &trace_controller, const AnchorConstraints &constraints)
	construct from single base pair probabilities. More...

	~ArcMatches ()
	clean up base pair objects

void	read_arcmatch_scores (const std::string &arcmatch_scores_file, int probability_scale)
	Reads scores for arc matches. More...

void	write_arcmatch_scores (const std::string &arcmatch_scores_file, const Scoring &scoring) const

const BasePairs &	get_base_pairsA () const
	returns the base pairs object for RNA A

const BasePairs &	get_base_pairsB () const
	returns the base pairs object for RNA B

bool	explicit_scores () const
	true, if arc match scores are explicit (because they are read in from a list)

void	make_scores_explicit (const Scoring &scoring)
	Make arcmatch scores explicit. More...

score_t	get_score (const ArcMatch &am) const

size_type	num_arc_matches () const
	total number of arc matches

const ArcMatch &	arcmatch (size_type idx) const
	get arc match by its index

const ArcMatchIdxVec &	common_right_end_list (size_type i, size_type j) const
	list of all arc matches that share the common right end (i,j)

const ArcMatchIdxVec &	common_left_end_list (size_type i, size_type j) const
	list of all arc matches that share the common left end (i,j)

void	get_max_right_ends (size_type al, size_type bl, size_type max_ar, size_type max_br, bool no_lonely_pairs) const
	get the maximal right ends of any arc match with left ends (al,bl). More...

void	get_min_right_ends (size_type al, size_type bl, size_type min_ar, size_type min_br) const

bool	exists_inner_arc_match (const ArcMatch &am) const

const ArcMatch &	inner_arc_match (const ArcMatch &am) const

void	sort_right_adjacency_lists ()

const_iterator	begin () const
	begin of arc matches vector

const_iterator	end () const
	end of arc matches vector

Additional Inherited Members
Public Types inherited from LocARNA::ArcMatches
typedef std::vector< int >::size_type	size_type
	size

typedef BasePairs__Arc	Arc
	arc

typedef ArcMatchVec::const_iterator	const_iterator
	const iterator over arc matches

Protected Member Functions inherited from LocARNA::ArcMatches
bool	is_valid_arcmatch (const Arc &arcA, const Arc &arcB) const

void	init_inner_arc_matchs ()
	initialize the vector of inner arc match indices

Protected Attributes inherited from LocARNA::ArcMatches
size_type	lenA
	length of sequence A

size_type	lenB
	length of sequence B

BasePairs *	bpsA
	base pairs of RNA A

BasePairs *	bpsB
	base pairs of RNA B

size_type	max_length_diff
	for max-diff-am heuristics

size_type	max_diff_at_am
	for max diff at arc matches heuristics

const MatchController &	match_controller
	allowed alignment traces by max-diff heuristics

const AnchorConstraints &	constraints
	for constraints

bool	maintain_explicit_scores
	whether scores are maintained explicitely or computed from pair probabilities

ArcMatchVec	arc_matches_vec
	vector of all maintained arc matches

size_type	number_of_arcmatches

std::vector< score_t >	scores
	vector of scores (of arc matches with the same index)

Matrix< ArcMatchIdxVec >	common_right_end_lists
	for each (i,j) maintain vector of the indices of the arc matchs that share the common right end (i,j)

Matrix< ArcMatchIdxVec >	common_left_end_lists
	for each (i,j) maintain vector of the indices of the arc matchs that share the common left end (i,j)

ArcMatchIdxVec	inner_arcmatch_idxs
	vector of indices of inner arc matches

Detailed Description

class ArcMatches with additional mapping

Like ArcMatches, maintain the relevant arc matches and their scores. Additionally, build an index to support mapping from pairs of arcs to arc matches.

Constructor & Destructor Documentation

LocARNA::ArcMatchesIndexed::ArcMatchesIndexed	(	const Sequence &	seqA_,
		const Sequence &	seqB_,
		const std::string &	arcmatch_scores_file,
		int	probability_scale,
		size_type	max_length_diff,
		size_type	max_diff_at_am,
		const MatchController &	trace_controller,
		const AnchorConstraints &	constraints
	)

inline

construct with explicit arc match score list

construct from seqnames and explicit list of all scored arc matches together with their score.

Note: registers constraints and heuristics and then calls read_arcmatch_scores. The constructed object explicitely represents/maintains the scores of arc matchs.

Parameters

seqA_	sequence A
seqB_	sequence B
arcmatch_scores_file	file containing arc match scores
probability_scale	if >=0 read probabilities and multiply them by probability_scale
max_length_diff	accept arc matches only up to maximal length difference
trace_controller	accept only due to trace controller
constraints	accept only due to constraints

LocARNA::ArcMatchesIndexed::ArcMatchesIndexed	(	const RnaData &	rnadataA,
		const RnaData &	rnadataB,
		double	min_prob,
		size_type	max_length_diff,
		size_type	max_diff_at_am,
		const MatchController &	trace_controller,
		const AnchorConstraints &	constraints
	)

inline

construct from single base pair probabilities.

In this case, the object filters for relevant base pairs/arcs by min_prob. Registers constraints and heuristics and then calls read_arcmatch_scores. Constructs BasePairs objects for each single object and registers them. Generates adjacency lists of arc matches for internal use and sorts them. Lists contain only valid arc matches according to constraints and heuristics (see is_valid_arcmatch()). The constructed object does not explicitely represent/maintain the scores of arc matchs.

Parameters

rnadataA	data for RNA A
rnadataB	data for RNA B
min_prob	consider only arcs with this minimal probability
max_length_diff	consider arc matches only up to maximal length difference
trace_controller	arc matches only due to trace controller
constraints	arc matches only due to constraints

Member Function Documentation

const ArcMatch::idx_type LocARNA::ArcMatchesIndexed::am_index	(	const size_type &	arcAIdx,
		const size_type &	arcBIdx
	)		const

inline

Lookup arc match index by pair of arc indices.

Parameters

arcAIdx	index of arc in A
arcBIdx	index of arc in B

Returns: index of arcmatch of arcA and arcB or invalid_am_index()

const ArcMatch& LocARNA::ArcMatchesIndexed::am_index	(	const Arc &	arcA,
		const Arc &	arcB
	)		const

inline

Lookup arc match by pair of arcs.

Parameters

arcA	arc in A
arcB	arc in B

Returns: arcmatch of arcA and arcB (or an invalid arc match with index invalid_am_index())

const ArcMatch::idx_type LocARNA::ArcMatchesIndexed::invalid_am_index ( ) const

inline

the invalid arc match index

Returns: invalid arc match index

Note: this index is returned by am_index if the queried pair of arcs does not correspond to a valid arcmatch

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

src/LocARNA/arc_matches.hh
src/LocARNA/arc_matches.cc

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation