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 alphabet_type &	string_alphabet () const

const Alphabet< char > &	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 Attributes
matrix_t	base_probs_
	matrix of base probabilities

matrix_t	base_nonstruct_probs_
	matrix of base probabilities in non-structural context

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...

alphabet_type	basename_alphabet
	alphabet of base names

alphabet_type	arcname_alphabet
	alphabet of arc names

Alphabet< char >	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

Protected Types inherited from LocARNA::Ribosum
typedef Alphabet< std::string >	alphabet_type
	type of alphabet

Protected Member Functions inherited from LocARNA::Ribosum
std::istream &	read_matrix (std::istream &in, matrix_t &mat, const alphabet_type &names) const

std::ostream &	write_matrix (std::ostream &out, const matrix_t &mat, const alphabet_type &alph) const

	Ribosum ()
	Construct empty.

void	read_ribosum (std::istream &in)

Alphabet< char >	make_char_alphabet () const
	transform the basename alphabet to alphabet over characters

void	set_basename_alphabet (const std::string a[])

void	set_arcname_alphabet (const std::string a[])

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

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

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

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

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

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

Public Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation