LocARNA::McC_matrices_base Class Reference

Inheritance diagram for LocARNA::McC_matrices_base:

Public Member Functions
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...

Protected Member Functions
	McC_matrices_base (vrna_fold_compound_t *vc)
	construct empty

Protected Attributes
vrna_fold_compound_t *	vc_
	vrna fold compound More...

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

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