LocARNA::McC_ali_matrices_t Class Reference

Alifold-McCaskill matrices. More...

#include <mcc_matrices.hh>

Inheritance diagram for LocARNA::McC_ali_matrices_t:

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

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Detailed Description

Alifold-McCaskill matrices.

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Constructor & Destructor Documentation

LocARNA::McC_ali_matrices_t::McC_ali_matrices_t

(

vrna_fold_compound_t *

vc

)

[explicit]

Construct from fold compound.

Parameters:

vc	vrna fold compound (alignment)

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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