LocARNA-1.9.2
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Public Member Functions
LocARNA::McC_ali_matrices_t Class Reference

Alifold-McCaskill matrices. More...

#include <mcc_matrices.hh>

Inheritance diagram for LocARNA::McC_ali_matrices_t:
LocARNA::McC_matrices_base

List of all members.

Public Member Functions

 McC_ali_matrices_t (vrna_fold_compound_t *vc)
 Construct from fold compound.
virtual ~McC_ali_matrices_t ()
 destruct
short pscore (size_t i, size_t j) const
 Access matrix pscore.
short S (size_t s, size_t i) const
 Read access to sequence encoding S.
short S3 (size_t s, size_t i) const
 Read access to sequence encoding S3.
short S5 (size_t s, size_t i) const
 Read access to sequence encoding S5.
short a2s (size_t s, size_t i) const
 Read access to a2s.
char * Ss (size_t s) const

Detailed Description

Alifold-McCaskill matrices.


Constructor & Destructor Documentation

LocARNA::McC_ali_matrices_t::McC_ali_matrices_t ( vrna_fold_compound_t *  vc) [explicit]

Construct from fold compound.

Parameters:
vcvrna 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:
ssequence index
ibase 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:
ifirst index
jsecond 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:
ssequence index
ibase 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:
ssequence index
ibase 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:
ssequence index
ibase index
Returns:
encoding of base i in sequence s

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