LocARNA::PFGotoh< pf_score_t > Class Template Reference

Provide Gotoh partition functions. More...

#include <edge_probs.hh>

Inheritance diagram for LocARNA::PFGotoh< pf_score_t >:

Collaboration diagram for LocARNA::PFGotoh< pf_score_t >:

Public Types
using	size_type = size_t
	size

Public Member Functions
	PFGotoh (const RnaData &rnaA, const RnaData &rnaB, const TraceController &trace_controller, const Matrix< double > &sim_mat, const Alphabet< char, 4 > &alphabet, double gap_opening, double gap_extension, double pf_struct_weight, double temp, const FreeEndgaps &free_endgaps, bool flag_local)
	Construct to provide partial partition functions from Gotoh-like matrices. More...
const pf_score_t &	z () const
	Get the partition function. More...

Protected Member Functions
void	pf_gotoh (Matrix< pf_score_t > &zM, Matrix< pf_score_t > &zA, Matrix< pf_score_t > &zB, const TraceController &trace_controller, const StralScore &score, const FreeEndgaps &free_endgaps)
	perform the partition version of Gotoh's algorithm More...
bool	fail () const

Protected Attributes
size_type	lenA_
size_type	lenB_
double	temp_
bool	flag_local_
pf_score_t	z_
Matrix< pf_score_t >	zM_
	pfs over alignments ending in match i~j
Matrix< pf_score_t >	zA_
	pfs over alignments ending w/ gap in A
Matrix< pf_score_t >	zB_
	pfs over alignments ending w/ gap in B
Matrix< pf_score_t >	zMr_
	reverse zM_
Matrix< pf_score_t >	zAr_
	reverse zA_
Matrix< pf_score_t >	zBr_
	reverse zB_

Detailed Description

template<class pf_score_t>
class LocARNA::PFGotoh< pf_score_t >

Provide Gotoh partition functions.

Implements a partition function variant of the Gotoh algorithm

In contrast to the standard Gotoh algorithm, we need to make the algorithm non-ambiguous. This means that ZM is only for alignments that do not end in gaps. We achieve this by reducing ZM_ij to ZM_i-1,j-1, ZA_i-1,j-1, and ZB_i-1,j-1

The matrices ZA and ZB represent alignments that end in a gap in seqA or seqB, resp.

Constructor & Destructor Documentation

PFGotoh()

template<class pf_score_t >

LocARNA::PFGotoh< pf_score_t >::PFGotoh	(	const RnaData &	rnaA,
		const RnaData &	rnaB,
		const TraceController &	trace_controller,
		const Matrix< double > &	sim_mat,
		const Alphabet< char, 4 > &	alphabet,
		double	gap_opening,
		double	gap_extension,
		double	pf_struct_weight,
		double	temp,
		const FreeEndgaps &	free_endgaps,
		bool	flag_local
	)

Construct to provide partial partition functions from Gotoh-like matrices.

Runs the Gotoh partition function variant

Parameters

rnaA	RnaData of RNA A
rnaB	RnaData of RNA B
trace_controller	controller limiting possible traces
sim_mat	similarity matrix for scoring base matches; e.g.

See also

Ribosum::get_basematch_scores()

Parameters

alphabet	the alphabet of the similiarity matrix
gap_opening	score for opening a gap
gap_extension	score for extending a gap
pf_struct_weight	weight of structure (vs. sequence)
temp	temperature for computing the Boltzmann weights
free_endgaps	which end gaps should be cost free
flag_local	whether to run local alignment

Member Function Documentation

pf_gotoh()

template<class pf_score_t >

void LocARNA::PFGotoh< pf_score_t >::pf_gotoh ( Matrix< pf_score_t > &  zM, Matrix< pf_score_t > &  zA, Matrix< pf_score_t > &  zB, const TraceController &  trace_controller, const StralScore &  score, const FreeEndgaps &  free_endgaps  )

protected

perform the partition version of Gotoh's algorithm

Parameters

[out]	zM	matrix for alignments ending in match
[out]	zA	matrix for alignments ending with gapped pos in sequence A
[out]	zB	matrix for alignments ending with gapped pos in sequence B @score stral scoring object
	free_endgaps	which end gaps should be cost free

this method does not use sequence objects; the sequence information is provided by the scoring object

z()

template<class pf_score_t >

const pf_score_t& LocARNA::PFGotoh< pf_score_t >::z ( ) const

inline

Get the partition function.

Returns

partition function

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

• src/LocARNA/edge_probs.hh