LocARNA::McC_ali_matrices_t Class Reference

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 (vrna_fold_compound_t *vc)
	Construct from fold compound. 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...

Additional Inherited Members
Protected Member Functions inherited from LocARNA::McC_matrices_base
	McC_matrices_base (vrna_fold_compound_t *vc)
	construct empty
Protected Attributes inherited from LocARNA::McC_matrices_base
vrna_fold_compound_t *	vc_
	vrna fold compound More...

Detailed Description

Alifold-McCaskill matrices.

Constructor & Destructor Documentation

LocARNA::McC_ali_matrices_t::McC_ali_matrices_t

(

vrna_fold_compound_t *

vc

)

Construct from fold compound.

Parameters

vc	vrna fold compound (alignment)

Member Function Documentation

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

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

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

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

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

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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