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

#include <ribosum.hh>

Inheritance diagram for LocARNA::RibosumFreq:

Collaboration diagram for LocARNA::RibosumFreq:

[legend]

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 More...

double	basematch_score_corrected (char i, char j) const
	Get corrected score for a base match. More...

void	print_basematch_scores_corrected (std::ostream &out) const
	Print the corrected score of base matches. More...

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

Public Member Functions inherited from LocARNA::Ribosum
	Ribosum (const std::string &filename)

virtual	~Ribosum ()
	virtual destructor

const matrix_t &	get_basematch_scores () const
	Get base match scores. More...

const matrix_t &	get_arcmatch_scores () const

const base_alphabet_type &	string_alphabet () const

const char_alphabet_type &	alphabet () const

const std::string &	get_name () const

double	basematch_score (char i, char j) const
	Get base match score. More...

double	arcmatch_score (char i, char j, char k, char l) const
	Get arc match score. More...

Protected Member Functions
void	write_CC_matrix (std::ostream &out, const std::string &ribname, const std::string &matname, int x, int y, const Ribosum::matrix_t &m) const

Protected Member Functions inherited from LocARNA::Ribosum
template<size_t N>
std::istream &	read_matrix (std::istream &in, matrix_t &mat, const Alphabet< std::string, N > &names) const

template<size_t N>
std::ostream &	write_matrix (std::ostream &out, const matrix_t &mat, const Alphabet< std::string, N > &alph) const

	Ribosum ()
	Construct empty.

void	read_ribosum (std::istream &in)

char_alphabet_type	make_char_alphabet () const
	transform the basename alphabet to alphabet over characters

void	set_basename_alphabet (const std::array< std::string, 4 > &a)

void	set_arcname_alphabet (const std::array< std::string, 16 > &a)

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

Protected Attributes inherited from LocARNA::Ribosum
std::string	name_
	name of ribosum

matrix_t	bm_
	scores for base matches, 4x4 matrix

matrix_t	am_
	16x16 matrix More...

base_alphabet_type	basename_alphabet_
	alphabet of base names

arc_alphabet_type	arcname_alphabet_
	alphabet of arc names

char_alphabet_type	char_basename_alphabet_
	alphabet of base names as characters

Friends
std::ostream &	operator<< (std::ostream &out, const RibosumFreq &ribosum)

Additional Inherited Members
Public Types inherited from LocARNA::Ribosum
typedef Matrix< double >	matrix_t
	type of a matrix

typedef Alphabet< std::string, 4 >	base_alphabet_type
	type of alphabet

typedef Alphabet< char, 4 >	char_alphabet_type
	type of alphabet

typedef Alphabet< std::string, 16 >	arc_alphabet_type
	type of alphabet

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

Constructor & Destructor Documentation

◆ RibosumFreq()

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.

Member Function Documentation

◆ arcmatch_prob()

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.

◆ base_nonstruct_prob()

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

◆ base_prob()

double LocARNA::RibosumFreq::base_prob ( char i ) const

inline

Get probability of a base

Parameters

i	nucleotide character

Returns: probability of nucleotide character

◆ base_unpaired_prob()

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

◆ basematch_prob()

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

◆ basematch_score_corrected()

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.

◆ basepair_prob()

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

◆ get_arcmatch_probs()

const matrix_t& LocARNA::RibosumFreq::get_arcmatch_probs ( ) const

inline

Get arcmatch prob matrix @ return matrix of arc match probabilities

◆ get_base_nonstruct_probs()

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

◆ get_base_probs()

const matrix_t& LocARNA::RibosumFreq::get_base_probs ( ) const

inline

Get base prob matrix

Returns: matrix of probabilities of all bases/nucleotides

◆ get_basematch_probs()

const matrix_t& LocARNA::RibosumFreq::get_basematch_probs ( ) const

inline

Get basematch prob matrix

Returns: matrix of probabilities of base matches

◆ get_basepair_probs()

const matrix_t& LocARNA::RibosumFreq::get_basepair_probs ( ) const

inline

Get base pair prob matrix

Returns: matrix of probabilities of base pairs

◆ print_basematch_scores_corrected()

void LocARNA::RibosumFreq::print_basematch_scores_corrected ( std::ostream & out ) const

Print the corrected score of base matches.

See also: basematch_score_corrected()

◆ read_matrix()

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

◆ write_ICC_code()

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()

◆ write_matrix()

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

Friends And Related Function Documentation

◆ operator<<

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

Member Data Documentation

◆ base_nonstruct_probs_

matrix_t LocARNA::RibosumFreq::base_nonstruct_probs_

protected

matrix of base probabilities in non-structural context

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RibosumFreq()

Member Function Documentation

◆ arcmatch_prob()

◆ base_nonstruct_prob()

◆ base_prob()

◆ base_unpaired_prob()

◆ basematch_prob()

◆ basematch_score_corrected()

◆ basepair_prob()

◆ get_arcmatch_probs()

◆ get_base_nonstruct_probs()

◆ get_base_probs()

◆ get_basematch_probs()

◆ get_basepair_probs()

◆ print_basematch_scores_corrected()

◆ read_matrix()

◆ write_ICC_code()

◆ write_matrix()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ base_nonstruct_probs_