LocARNA::McC_matrices_base Class Reference

Inheritance diagram for LocARNA::McC_matrices_base:

List of all members.

Public Member Functions
virtual	~McC_matrices_base ()
	Destructor.
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.
FLT_OR_DBL	qb (size_t i, size_t j) const
	Read access matrix qb.
FLT_OR_DBL	qm (size_t i, size_t j) const
	Read access matrix qm.
vrna_exp_param_t *	exp_params () const
	exp params
FLT_OR_DBL	scale (size_t i) const
	scale
FLT_OR_DBL	expMLbase (size_t i) const
	expMLbase
FLT_OR_DBL	kT () const
	kT
FLT_OR_DBL	q1k (size_t k) const
	Read access matrix q1k.
FLT_OR_DBL	qln (size_t l) const
	Read access matrix qln.
int	pair (size_t c, size_t d) const
	Read access matrix pair.
Protected Member Functions
	McC_matrices_base (vrna_fold_compound_t *vc)
	construct empty
Protected Attributes
vrna_fold_compound_t *	vc_
	vrna fold compound

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Constructor & Destructor Documentation

LocARNA::McC_matrices_base::~McC_matrices_base

(

)

[virtual]

Destructor.

Frees the fold compound

---

Member Function Documentation

FLT_OR_DBL LocARNA::McC_matrices_base::bppm	(	size_t	i,
		size_t	j
	)		const [inline]

Read access matrix bppm.

Parameters:

i	first indexb
j	second index

Returns:

matrix entry

FLT_OR_DBL LocARNA::McC_matrices_base::expMLbase

(

size_t

i

)

const [inline]

expMLbase

Parameters:

i

index

Returns:

contribution to pf for base i in ML

FLT_OR_DBL LocARNA::McC_matrices_base::kT

(

)

const [inline]

kT

Returns:

k times temperature

int LocARNA::McC_matrices_base::pair	(	size_t	c,
		size_t	d
	)		const [inline]

Read access matrix pair.

Parameters:

c	first base code
d	second base code

Returns:

matrix entry

FLT_OR_DBL LocARNA::McC_matrices_base::q1k

(

size_t

k

)

const [inline]

Read access matrix q1k.

Parameters:

k

index

Returns:

matrix entry

FLT_OR_DBL LocARNA::McC_matrices_base::qb	(	size_t	i,
		size_t	j
	)		const [inline]

Read access matrix qb.

Parameters:

i	first index
j	second index

Returns:

matrix entry

FLT_OR_DBL LocARNA::McC_matrices_base::qln

(

size_t

l

)

const [inline]

Read access matrix qln.

Parameters:

l

index

Returns:

matrix entry

FLT_OR_DBL LocARNA::McC_matrices_base::qm	(	size_t	i,
		size_t	j
	)		const [inline]

Read access matrix qm.

Parameters:

i	first index
j	second index

Returns:

matrix entry

FLT_OR_DBL LocARNA::McC_matrices_base::scale

(

size_t

i

)

const [inline]

scale

Parameters:

i

length

Returns:

scaling factor for fragment of length i

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Member Data Documentation

vrna_fold_compound_t* LocARNA::McC_matrices_base::vc_ [protected]

vrna fold compound

The fold compound holds the DP matrices, input and model details. It is freed on destruction of the McC_matrices_base object.

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

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