LocARNA::ArcMatchesIndexed Class Reference

class ArcMatches with additional mapping More...

#include <arc_matches.hh>

Inheritance diagram for LocARNA::ArcMatchesIndexed:

List of all members.

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
	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.
const ArcMatch::idx_type	invalid_am_index () const
	the invalid arc match index
const ArcMatch::idx_type	am_index (const size_type &arcAIdx, const size_type &arcBIdx) const
	Lookup arc match index by pair of arc indices.
const ArcMatch &	am_index (const Arc &arcA, const Arc &arcB) const
	Lookup arc match by pair of arcs.

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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.

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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

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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

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

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