#include <scoring.hh>

Inheritance diagram for LocARNA::PFScoring< T >:

Collaboration diagram for LocARNA::PFScoring< T >:

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Public Types
using	pf_score_t = T

using	PFScoreVector = std::vector< pf_score_t >
	Vector of partition functions.

using	PFScoreMatrix = Matrix< pf_score_t >
	Matrix of partition functions.

Public Types inherited from LocARNA::Scoring
typedef BasePairs__Arc	Arc
	arc

Public Member Functions
	PFScoring (const Sequence &seqA, const Sequence &seqB, const RnaData &rna_dataA, const RnaData &rna_dataB, const ArcMatches &arc_matches, const MatchProbs *match_probs, const ScoringParams &params)
	construct scoring object More...

pf_score_t	exp_basematch (size_type i, size_type j) const
	Boltzmann weight of score of a base match (without structure) More...

pf_score_t	exp_arcmatch (const ArcMatch &am) const
	Boltzmann weight of score of arc match. More...

pf_score_t	exp_gapA (size_type posA) const
	Boltzmann weight of score of deletion. More...

pf_score_t	exp_gapB (size_type posB) const
	Boltzmann weight of score of insertion. More...

pf_score_t	exp_indel_opening () const
	exp of cost to begin a new indel

pf_score_t	exp_indel_opening_loop () const
	exp of cost to begin a new indel in loops

Public Member Functions inherited from LocARNA::Scoring
	Scoring (const Sequence &seqA, const Sequence &seqB, const RnaData &rna_dataA, const RnaData &rna_dataB, const ArcMatches &arc_matches, const MatchProbs *match_probs, const ScoringParams &params)
	construct scoring object More...

void	modify_by_parameter (score_t lambda)
	modify scoring by a parameter lambda. More...

void	apply_unpaired_penalty ()

score_t	lambda () const
	Get factor lambda for normalized alignment. More...

score_t	basematch (size_type i, size_type j) const
	Score of a match of bases (without structure) More...

score_t	arcmatch (const ArcMatch &am, bool stacked=false) const
	Score of arc match, support explicit arc match scores. More...

score_t	arcmatch (const BasePairs__Arc &arcA, const BasePairs__Arc &arcB, bool stacked=false) const
	Score of arc match, given two arcs. More...

const ArcMatches *	arc_matches () const

template<bool gapAorB>
score_t	arcDel (const BasePairs__Arc &arc, bool stacked=false) const
	Very basic interface, score of aligning a basepair to gap. More...

score_t	arcmatch_stacked (const ArcMatch &am) const
	Score of stacked arc match. More...

template<bool gapInA>
score_t	gapX (size_type alignedToGap) const

score_t	gapA (size_type posA) const

score_t	gapB (size_type posB) const

score_t	exclusion () const
	cost of an exclusion

score_t	indel_opening () const
	cost to begin a new indel

score_t	loop_indel_score (const score_t score) const
	multiply an score by the ratio of indel_loop/indel

score_t	indel_opening_loop () const
	cost to begin a new indel

double	prob_exp (size_type len) const
	Expected base pair probability. More...

bool	stacking () const
	Query stacking flag. More...

bool	is_stackable_arcA (const Arc &a) const
	Is arc of A stackable. More...

bool	is_stackable_arcB (const Arc &a) const
	Is arc of B stackable. More...

bool	is_stackable_am (const ArcMatch &am) const
	Is arc match stackable. More...

template<>
score_t	gapX (size_type alignedToGap) const

template<>
score_t	gapX (size_type alignedToGap) const

Protected Member Functions
void	precompute_exp_gapcost ()
	Precompute the tables for Boltzmann weights of gapcost.

void	precompute_exp_sigma ()
	Precompute all Boltzmann weights of base similarities. More...

pf_score_t	boltzmann_weight (score_t s) const

Protected Member Functions inherited from LocARNA::Scoring
void	precompute_sequence_identities ()

score_t	round2score (double d) const
	Round a double to score_t. More...

score_t	sigma_ (int i, int j) const
	Compute base similarity. More...

void	precompute_sigma ()
	Precompute all base similarities. More...

void	precompute_gapcost ()
	Precompute the tables for gapcost.

void	precompute_weights ()
	Precompute weights/stacked weights for all arcs in A and B.

void	precompute_weights (const RnaData &rna_data, const BasePairs &bps, double exp_prob, std::vector< score_t > &weights, std::vector< score_t > &stack_weights)
	Helper for precompute_weights (does job for one rna) More...

score_t	probToWeight (double p, double prob_exp) const
	convert probability to weight for scoring More...

double	ribosum_arcmatch_prob (const Arc &arcA, const Arc &arcB) const

score_t	riboX_arcmatch_score (const Arc &arcA, const Arc &arcB) const
	ribofit or ribosum arcmatch score contribution More...

void	subtract (std::vector< score_t > &v, score_t x) const
	subtract from each element of a score_t vector v a value x

void	subtract (Matrix< score_t > &m, score_t x) const
	subtract from each element of a score_t Matrix m a value x

Additional Inherited Members
Protected Attributes inherited from LocARNA::Scoring
const ScoringParams *	params
	a collection of parameters for scoring

const ArcMatches *	arc_matches_
	arc matches

const MatchProbs *	match_probs
	base match probabilities

const RnaData &	rna_dataA
	rna data for RNA A

const RnaData &	rna_dataB
	rna data for RNA B

const Sequence &	seqA
	sequence A

const Sequence &	seqB
	sequence B

score_t	lambda_

Matrix< score_t >	sigma_tab
	precomputed table of base match similarities

std::vector< score_t >	gapcost_tabA
	table for gapcost in A

std::vector< score_t >	gapcost_tabB
	table for gapcost in B

std::vector< score_t >	weightsA

std::vector< score_t >	weightsB

std::vector< score_t >	stack_weightsA

std::vector< score_t >	stack_weightsB

Matrix< size_t >	identity
	sequence identities in percent

Detailed Description

template<typename T>
class LocARNA::PFScoring< T >

Scoring for partition function alignment

Parameters

T	type of the partition functions (like float, double, or long double)

Constructor & Destructor Documentation

◆ PFScoring()

template<typename T >

LocARNA::PFScoring< T >::PFScoring	(	const Sequence &	seqA,
		const Sequence &	seqB,
		const RnaData &	rna_dataA,
		const RnaData &	rna_dataB,
		const ArcMatches &	arc_matches,
		const MatchProbs *	match_probs,
		const ScoringParams &	params
	)

construct scoring object

Parameters

seqA	first sequence
seqB	second sequence
rna_dataA	probability data of first sequence
rna_dataB	probability data of second sequence
arc_matches	the (significant) arc matches between the sequences
match_probs	pointer to base match probabilities (can be nullptr for non-mea scores)
params	a collection of parameters for scoring

Member Function Documentation

◆ exp_arcmatch()

template<typename T >

pf_score_t LocARNA::PFScoring< T >::exp_arcmatch ( const ArcMatch & am ) const

inline

Boltzmann weight of score of arc match.

Parameters

am arc match

Returns: Boltzmann weight of score of arc match am

◆ exp_basematch()

template<typename T >

pf_score_t LocARNA::PFScoring< T >::exp_basematch	(	size_type	i,
		size_type	j
	)		const

inline

Boltzmann weight of score of a base match (without structure)

Parameters

i	position in A
j	position in B

Returns: Boltzmann weight of score of base match i~j

◆ exp_gapA()

template<typename T >

pf_score_t LocARNA::PFScoring< T >::exp_gapA ( size_type posA ) const

inline

Boltzmann weight of score of deletion.

Parameters

posA	position in A

Returns: Boltzmann weight of score of deletion of posA after posB

◆ exp_gapB()

template<typename T >

pf_score_t LocARNA::PFScoring< T >::exp_gapB ( size_type posB ) const

inline

Boltzmann weight of score of insertion.

Parameters

posB	position in B

Returns: Boltzmann weight of score of insertion of posB after posA

◆ precompute_exp_sigma()

template<typename T >

void LocARNA::PFScoring< T >::precompute_exp_sigma

protected

Precompute all Boltzmann weights of base similarities.

Precomputed similarities are stored in the exp_sigma table.

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

src/LocARNA/scoring.hh

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

template<typename T> class LocARNA::PFScoring< T >

Constructor & Destructor Documentation

◆ PFScoring()

Member Function Documentation

◆ exp_arcmatch()

◆ exp_basematch()

◆ exp_gapA()

◆ exp_gapB()

◆ precompute_exp_sigma()

template<typename T>
class LocARNA::PFScoring< T >