Maintains the relevant arc matches and their scores. More...

#include <arc_matches.hh>

Inheritance diagram for LocARNA::ArcMatches:

Collaboration diagram for LocARNA::ArcMatches:

[legend]

Classes
class	lex_greater_left_ends
	Compare two arc match indices by lexicographically comparing their left ends. More...

class	tuple5

Public Types
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

Public Member Functions
	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

Protected Member Functions
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
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

Maintains the relevant arc matches and their scores.

It works as an interface between the source of arc match scoring information, i.e. dot plots of the single sequences or explicit listing of all arc matches, and the use of this information in the class Scoring and in the alignment algorithm. For the latter purpose, it allows to generate the necessary objects of class BasePairs for the iteration of base pairs in the single structures.

ArcMatches knows about all arc matches that shall be considered for the alignment. Each arc match gets an index between 0..(number of arc_matches-1). The index is used to access the arc match score, the single arcs of the match, the matrix D, ...

The object offers iteration over 1.) all arc matches 2.) all arc matches that share left ends/right ends (i,j) During iteration the index of the current arc match is known, thus one never needs to infer the arc match index from the arc ends or arc indices! (This could be done in constant time using an O(n^2) lookup table.)

Constructor & Destructor Documentation

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

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::ArcMatches::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.

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

bool LocARNA::ArcMatches::exists_inner_arc_match ( const ArcMatch & am ) const

inline

whether there is an inner (valid) arc match for the arc with the given index

void LocARNA::ArcMatches::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).

Precondition: max_ar, max_br are initialized with smallest possible values

Parameters

	al	left and in sequence A
	bl	left and in sequence B
[in,out]	max_ar	maximal right end in sequence A
[in,out]	max_br	maximal right end in sequence B
	no_lonely_pairs	whether in lonely pair mode

Returns: out parameters max_ar, max_br are set to the maximal right ends

Determine minimal max_ar and max_br such that there is no arc match with left ends al, bl and larger right ends ar>max_ar or al>max_br. In lonely pair mode, consider only arc matchs that have an immediately enclosing arc match.

void LocARNA::ArcMatches::get_min_right_ends	(	size_type	al,
		size_type	bl,
		size_type *	min_ar,
		size_type *	min_br
	)		const

get the minimal right ends of any arc match with left ends (al,bl). pre: min_ar, min_br are initialized with largest possible values returns result in out parameters min_ar, min_br

Note: Does not support noLP like get_max_right_ends() yet

score_t LocARNA::ArcMatches::get_score ( const ArcMatch & am ) const

inline

get the score of an arc match

Parameters

am arc match

Returns: score of arc match

Precondition: object represents arc match scores explicitely

const ArcMatch& LocARNA::ArcMatches::inner_arc_match ( const ArcMatch & am ) const

inline

index of inner arc match for the arc with the given index. Call only if there is such an arc match

bool LocARNA::ArcMatches::is_valid_arcmatch	(	const Arc &	arcA,
		const Arc &	arcB
	)		const

protected

decide according to constraints and heuristics whether an arc match is valid.

Parameters

arcA	arc (i,j) in first sequence
arcB	arc (k.l) in second sequence

Returns: whether match of arcA and arcB is valid An arc match is valid, if and only if: 1.) matches i~k and j~l are valid due to trace_controller (max-diff-match heuristic) and constraints (anchor constraints) 2.) length difference of arcs <= max_length_diff 3.) max diff at am ends ok

void LocARNA::ArcMatches::make_scores_explicit ( const Scoring & scoring )

Make arcmatch scores explicit.

Parameters

scoring An scoring object

void LocARNA::ArcMatches::read_arcmatch_scores	(	const std::string &	arcmatch_scores_file,
		int	probability_scale
	)

Reads scores for arc matches.

Reads from a file reads a list i j k l score, where score is the score for matching arcs (i,j) and (k,l).

Parameters

arcmatch_scores_file	file containing arc match scores
probability_scale	if >=0 read probabilities and multiply them by probability_scale

Note: All registered arc matches are valid (is_valid_arcmatch()).

void LocARNA::ArcMatches::sort_right_adjacency_lists ( )

sort the lists of arc matches with common right ends in "common_right_end_list" by their left ends in lexicographically descending order. Additionally, generate data structure for optimized traversal.

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

write arc match scores to a file (this is useful after the scores are generated from base pair probabilities)

Member Data Documentation

size_type LocARNA::ArcMatches::number_of_arcmatches

protected

the number of valid arc matches

Note: this number can differ from the size of arc_matches_vec

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

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

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation