LocARNA::ExactMatcher Class Reference

Computes exact pattern matchings (EPM) between two RNA sequences. More...

#include <exact_matcher.hh>

List of all members.

Public Member Functions
	ExactMatcher (const Sequence &seqA_, const Sequence &seqB_, const RnaData &rna_dataA_, const RnaData &rna_dataB_, const ArcMatches &arc_matches_, const SparseTraceController &sparse_trace_controller_, PatternPairMap &foundEPMs_, int alpha_1_, int alpha_2_, int alpha_3_, score_t difference_to_opt_score_, score_t min_score_, long int max_number_of_EPMs_, bool inexact_struct_match_, score_t struct_mismatch_score_, bool apply_filter_, bool verbose_)
	Constructor.
void	compute_arcmatch_score ()
void	test_arcmatch_score ()
	for debugging
void	trace_EPMs (bool suboptimal)
	computes the traceback and traces all EPMs

---

Detailed Description

Computes exact pattern matchings (EPM) between two RNA sequences.

There exist two different tracebacks: the heuristic and the suboptimal one. The heuristic traceback computes one EPM that ends at a position in the matrix F, if it is maximally extended. The suboptimal traceback enumerates all suboptimal EPMs up to a certain score (--diff-to-opt-score) or enumerates a certain number of EPMs (--number-of-EPMs).

The list of all traced EPMs can either be written in a file or handed over to the PatternPairMap to do the chaining in order to find the best set of EPMs that can be simultaneously be part of an alignment.

---

Constructor & Destructor Documentation

LocARNA::ExactMatcher::ExactMatcher	(	const Sequence &	seqA_,
		const Sequence &	seqB_,
		const RnaData &	rna_dataA_,
		const RnaData &	rna_dataB_,
		const ArcMatches &	arc_matches_,
		const SparseTraceController &	sparse_trace_controller_,
		PatternPairMap &	foundEPMs_,
		int	alpha_1_,
		int	alpha_2_,
		int	alpha_3_,
		score_t	difference_to_opt_score_,
		score_t	min_score_,
		long int	max_number_of_EPMs_,
		bool	inexact_struct_match_,
		score_t	struct_mismatch_score_,
		bool	apply_filter_,
		bool	verbose_
	)

Constructor.

Parameters:

seqA_	sequence A
seqB_	sequence B
rna_dataA_	sparsified data of RNA ensemble for sequence A
rna_dataB_	sparsified data of RNA ensemble for sequence B
arc_matches_	arc matches
sparse_trace_controller_	trace controller combined with the sparsification mapper
foundEPMs_	pattern pair map to store the list of all EPMs
alpha_1_	sequential weight
alpha_2_	structural weight
alpha_3_	stacking weight
difference_to_opt_score_	all EPMs with a score difference not more than difference_to_opt_score_ from the optimal score are traced
min_score_	the minimal score of an EPMs that is traced
max_number_of_EPMs_	maximal number of EPMs for the suboptimal traceback
inexact_struct_match_	whether to allow inexact structure matches
struct_mismatch_score_	the mismatch score for two nucleotides in an arcmatch (only used if inexact_struct_match_ is set)
apply_filter_	whether to apply an additional filter when allowing inexact structure matches
verbose_	whether to write additional information

---

Member Function Documentation

void LocARNA::ExactMatcher::compute_arcmatch_score

(

)

fills matrix D (i.e. computes all arc match scores) by filling matrices L, G_A and LR

void LocARNA::ExactMatcher::trace_EPMs

(

bool

suboptimal

)

computes the traceback and traces all EPMs

Parameters:

suboptimal

whether to compute the suboptimal or heuristic traceback

---

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

• src/LocARNA/exact_matcher.hh
• src/LocARNA/exact_matcher.cc