McCaskill matrices. More...

Inheritance diagram for LocARNA::McC_matrices_t:

Collaboration diagram for LocARNA::McC_matrices_t:

Public Member Functions
	McC_matrices_t (const MultipleAlignment &sequence, const PFoldParams &params)
	Construct from sequence. More...

virtual	~McC_matrices_t ()
	destruct, optionally free local copy

char	ptype (size_t i, size_t j) const
	Access matrix ptype. More...

char	rev_ptype (size_t i, size_t j) const
	Reverse ptype. More...

short	S1 (size_t i) const
	Read access to sequence encoding S1. More...

char *	sequence () 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

McCaskill matrices.

Holds vrna fold compound with DP matrices

Constructor & Destructor Documentation

LocARNA::McC_matrices_t::McC_matrices_t	(	const MultipleAlignment &	sequence,
		const PFoldParams &	params
	)

Construct from sequence.

Parameters

sequence	the sequence
params	locarna partition fold parameters

char LocARNA::McC_matrices_t::ptype	(	size_t	i,
		size_t	j
	)		const

inline

Access matrix ptype.

Parameters

i	first index
j	second index

char LocARNA::McC_matrices_t::rev_ptype	(	size_t	i,
		size_t	j
	)		const

inline

Reverse ptype.

Parameters

i	first index
j	second index

short LocARNA::McC_matrices_t::S1 ( size_t i ) const

inline

Read access to sequence encoding S1.

Parameters

i index

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