Alifold-McCaskill matrices. More...

#include <mcc_matrices.hh>

Inheritance diagram for LocARNA::McC_ali_matrices_t:

Collaboration diagram for LocARNA::McC_ali_matrices_t:

Public Member Functions
	McC_ali_matrices_t (const MultipleAlignment &ma, const PFoldParams &params)
	Construct from multiple alignment. More...

virtual	~McC_ali_matrices_t ()
	destruct

short	pscore (size_t i, size_t j) const
	Access matrix pscore. More...

short	S (size_t s, size_t i) const
	Read access to sequence encoding S. More...

short	S3 (size_t s, size_t i) const
	Read access to sequence encoding S3. More...

short	S5 (size_t s, size_t i) const
	Read access to sequence encoding S5. More...

short	a2s (size_t s, size_t i) const
	Read access to a2s. More...

char *	Ss (size_t s) const

Public Member Functions inherited from LocARNA::McC_matrices_base
virtual	~McC_matrices_base ()
	Destructor. More...

size_t	iidx (size_t i, size_t j) const
	index in triagonal matrix

size_t	jidx (size_t i, size_t j) const
	index in triagonal matrix

FLT_OR_DBL	bppm (size_t i, size_t j) const
	Read access matrix bppm. More...

FLT_OR_DBL	qb (size_t i, size_t j) const
	Read access matrix qb. More...

FLT_OR_DBL	qm (size_t i, size_t j) const
	Read access matrix qm. More...

vrna_exp_param_t *	exp_params () const
	exp params

FLT_OR_DBL	scale (size_t i) const
	scale More...

FLT_OR_DBL	expMLbase (size_t i) const
	expMLbase More...

FLT_OR_DBL	kT () const
	kT More...

FLT_OR_DBL	q1k (size_t k) const
	Read access matrix q1k. More...

FLT_OR_DBL	qln (size_t l) const
	Read access matrix qln. More...

int	pair (size_t c, size_t d) const
	Read access matrix pair. More...

int	rtype (size_t x) const

vrna_fold_compound_t *	vc ()

Additional Inherited Members
Protected Member Functions inherited from LocARNA::McC_matrices_base
	McC_matrices_base (vrna_fold_compound_t *vc=nullptr)
	construct with fold compound

Protected Attributes inherited from LocARNA::McC_matrices_base
vrna_fold_compound_t *	vc_
	vrna fold compound The fold compound holds the DP matrices, input and model details.

Detailed Description

Alifold-McCaskill matrices.

Constructor & Destructor Documentation

◆ McC_ali_matrices_t()

LocARNA::McC_ali_matrices_t::McC_ali_matrices_t	(	const MultipleAlignment &	ma,
		const PFoldParams &	params
	)

Construct from multiple alignment.

Parameters

ma	the multiple alignment
params	locarna partition fold parameters

Member Function Documentation

◆ a2s()

short LocARNA::McC_ali_matrices_t::a2s	(	size_t	s,
		size_t	i
	)		const

inline

Read access to a2s.

Parameters

s	sequence index
i	base index

Returns: encoding of base i in sequence s

◆ pscore()

short LocARNA::McC_ali_matrices_t::pscore	(	size_t	i,
		size_t	j
	)		const

inline

Access matrix pscore.

Parameters

i	first index
j	second index

Returns: matrix entry

◆ S()

short LocARNA::McC_ali_matrices_t::S	(	size_t	s,
		size_t	i
	)		const

inline

Read access to sequence encoding S.

Parameters

s	sequence index
i	base index

Returns: encoding of base i in sequence s

◆ S3()

short LocARNA::McC_ali_matrices_t::S3	(	size_t	s,
		size_t	i
	)		const

inline

Read access to sequence encoding S3.

Parameters

s	sequence index
i	base index

Returns: encoding of base i in sequence s

◆ S5()

short LocARNA::McC_ali_matrices_t::S5	(	size_t	s,
		size_t	i
	)		const

inline

Read access to sequence encoding S5.

Parameters

s	sequence index
i	base index

Returns: encoding of base i in sequence s

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

src/LocARNA/mcc_matrices.hh
src/LocARNA/mcc_matrices.cc

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ McC_ali_matrices_t()

Member Function Documentation

◆ a2s()

◆ pscore()

◆ S()

◆ S3()

◆ S5()