LocARNA-1.9.2
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Public Member Functions | Protected Member Functions | Protected Attributes
LocARNA::McC_matrices_base Class Reference
Inheritance diagram for LocARNA::McC_matrices_base:
LocARNA::McC_ali_matrices_t LocARNA::McC_matrices_t

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

Constructor & Destructor Documentation

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:
ifirst indexb
jsecond index
Returns:
matrix entry
FLT_OR_DBL LocARNA::McC_matrices_base::expMLbase ( size_t  i) const [inline]

expMLbase

Parameters:
iindex
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:
cfirst base code
dsecond base code
Returns:
matrix entry
FLT_OR_DBL LocARNA::McC_matrices_base::q1k ( size_t  k) const [inline]

Read access matrix q1k.

Parameters:
kindex
Returns:
matrix entry
FLT_OR_DBL LocARNA::McC_matrices_base::qb ( size_t  i,
size_t  j 
) const [inline]

Read access matrix qb.

Parameters:
ifirst index
jsecond index
Returns:
matrix entry
FLT_OR_DBL LocARNA::McC_matrices_base::qln ( size_t  l) const [inline]

Read access matrix qln.

Parameters:
lindex
Returns:
matrix entry
FLT_OR_DBL LocARNA::McC_matrices_base::qm ( size_t  i,
size_t  j 
) const [inline]

Read access matrix qm.

Parameters:
ifirst index
jsecond index
Returns:
matrix entry
FLT_OR_DBL LocARNA::McC_matrices_base::scale ( size_t  i) const [inline]

scale

Parameters:
ilength
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.


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