LocARNA::RibosumFreq Class Reference

Represents ribosum similarity matrices including raw frequencies. More...

#include <ribosum.hh>

Inheritance diagram for LocARNA::RibosumFreq:

List of all members.

Public Member Functions
	RibosumFreq (const std::string &filename)
double	base_prob (char i) const
double	base_nonstruct_prob (char i) const
const matrix_t &	get_base_probs () const
const matrix_t &	get_base_nonstruct_probs () const
double	basepair_prob (char i, char j) const
const matrix_t &	get_basepair_probs () const
double	basematch_prob (char i, char j) const
const matrix_t &	get_basematch_probs () const
double	arcmatch_prob (char i, char j, char k, char l) const
const matrix_t &	get_arcmatch_probs () const
double	base_unpaired_prob (char i) const
	probability that a nucleotide/base occurs unpaired
double	basematch_score_corrected (char i, char j) const
	Get corrected score for a base match.
void	print_basematch_scores_corrected (std::ostream &out) const
	Print the corrected score of base matches.
void	read_matrix (std::istream &in, const std::string &header, matrix_t &mat, size_t xdim, size_t ydim)
void	write_ICC_code (std::ostream &out, const std::string &ribname) const
std::ostream &	write_matrix (std::ostream &out, const std::string &name, const Matrix< double > &mat) const
Protected Attributes
matrix_t	base_probs_
	matrix of base probabilities
matrix_t	base_nonstruct_probs_
matrix_t	basepair_probs_
	matrix of base pair probabilities
matrix_t	basematch_probs_
	matrix of base match probabilties
matrix_t	arcmatch_probs_
	matrix of arc match probabilities
Friends
std::ostream &	operator<< (std::ostream &out, const RibosumFreq &ribosum)

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Detailed Description

Represents ribosum similarity matrices including raw frequencies.

Extension of the ribosum class that maintains additional "raw" information in particular frequencies of bases, basematches, basepairs, and arcmatches

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Constructor & Destructor Documentation

LocARNA::RibosumFreq::RibosumFreq

(

const std::string &

filename

)

[explicit]

Construct from file

Parameters:

filename

Name of input file

Note:

The file has to be in an extended ribosum file format including frequencies.

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Member Function Documentation

double LocARNA::RibosumFreq::arcmatch_prob	(	char	i,
		char	j,
		char	k,
		char	l
	)		const [inline]

Get the probability of an arcmatch

Parameters:

i	left nucleotide character of first base pair
j	right nucleotide character of first base pair
k	left nucleotide character of second base pair
l	right nucleotide character of second base pair

Returns:

probability of matching a

probability for matching an arc of nucleotides i and j with an arc of nucleotides k and l.

double LocARNA::RibosumFreq::base_nonstruct_prob

(

char

i

)

const [inline]

Get probability of a base occuring in a non-structural match

Parameters:

i	nucleotide character

Returns:

probability of nucleotide character in non-structural matches

double LocARNA::RibosumFreq::base_prob

(

char

i

)

const [inline]

Get probability of a base

Parameters:

i	nucleotide character

Returns:

probability of nucleotide character

double LocARNA::RibosumFreq::base_unpaired_prob

(

char

i

)

const

probability that a nucleotide/base occurs unpaired

Parameters:

i	nucleotide character

Returns:

probability that nucleotide is unpaired

double LocARNA::RibosumFreq::basematch_prob	(	char	i,
		char	j
	)		const [inline]

Get the probability of a base match

Parameters:

i	left nucleotide character
j	right nucleotide character

Returns:

probability of match of nucleotides i and j

double LocARNA::RibosumFreq::basematch_score_corrected	(	char	i,
		char	j
	)		const

Get corrected score for a base match.

Parameters:

i	first nucleotide character
j	second nucleotide character

Returns:

corrected score that i and j are matched

Note:

the score is computed as log odd of frequencies for seeing i and j matched without incident structure divided by the background to see i and j without incident structure.

The arguments are characters of the alphabet/nucleotides.

Currently, not tabellized. Thus, we have some computational overhead.

double LocARNA::RibosumFreq::basepair_prob	(	char	i,
		char	j
	)		const [inline]

Get probability of a basepair

Parameters:

i	left nucleotide character
j	right nucleotide character

Returns:

probability of base pair of nucleotides i and j

const matrix_t& LocARNA::RibosumFreq::get_arcmatch_probs

(

)

const [inline]

Get arcmatch prob matrix @ return matrix of arc match probabilities

const matrix_t& LocARNA::RibosumFreq::get_base_nonstruct_probs

(

)

const [inline]

Get base nonstruct prob matrix

Returns:

matrix of probabilities of all bases/nucleotides in nonstructural matches

const matrix_t& LocARNA::RibosumFreq::get_base_probs

(

)

const [inline]

Get base prob matrix

Returns:

matrix of probabilities of all bases/nucleotides

const matrix_t& LocARNA::RibosumFreq::get_basematch_probs

(

)

const [inline]

Get basematch prob matrix

Returns:

matrix of probabilities of base matches

const matrix_t& LocARNA::RibosumFreq::get_basepair_probs

(

)

const [inline]

Get base pair prob matrix

Returns:

matrix of probabilities of base pairs

void LocARNA::RibosumFreq::print_basematch_scores_corrected

(

std::ostream &

out

)

const

Print the corrected score of base matches.

See also:

basematch_score_corrected()

void LocARNA::RibosumFreq::read_matrix	(	std::istream &	in,
		const std::string &	header,
		matrix_t &	mat,
		size_t	xdim,
		size_t	ydim
	)

Read one matrix in ribosum input

Parameters:

	in	input stream
	header	header string
[out]	mat	matrix object to be read into
	xdim	first dimension of matrix
	ydim	second dimension of matrix

void LocARNA::RibosumFreq::write_ICC_code	(	std::ostream &	out,
		const std::string &	ribname
	)		const

Write the ribosum matrices as C++ code

Parameters:

out	output stream
ribname	Name of ribosum

Note:

this is used to precompile ribosum matrices, such that their parameters can be linked to the code and we do not have to depend on data files.

See also:

write_HH_code()

std::ostream & LocARNA::RibosumFreq::write_matrix	(	std::ostream &	out,
		const std::string &	name,
		const Matrix< double > &	mat
	)		const

Write single matrix to output stream

Parameters:

out	output stream
name	name of matrix
mat	matrix

Returns:

output stream after writing

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Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const RibosumFreq &	ribosum
	)		[friend]

Output operator

Parameters:

out	output stream
ribosum	Ribosum to be written to stream

Returns:

output stream after writing

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Member Data Documentation

matrix_t LocARNA::RibosumFreq::base_nonstruct_probs_ [protected]

matrix of base probabilities in non-structural context

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

• src/LocARNA/ribosum.hh
• src/LocARNA/ribosum.cc