Represents ribosum similarity matrices. More...

#include <ribosum.hh>

Inheritance diagram for LocARNA::Ribosum:

Collaboration diagram for LocARNA::Ribosum:

[legend]

Public Types
typedef Matrix< double >	matrix_t
	type of a matrix

Public Member Functions
	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 Types
typedef Alphabet< std::string >	alphabet_type
	type of alphabet

Protected Member Functions
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[])

Protected Attributes
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 Ribosum &ribosum)

Detailed Description

Represents ribosum similarity matrices.

Reads ribosum data from file and provides access.

Constructor & Destructor Documentation

LocARNA::Ribosum::Ribosum ( const std::string & filename )

explicit

Construct from file

Parameters

filename name of the input file

Member Function Documentation

const Alphabet<char>& LocARNA::Ribosum::alphabet ( ) const

inline

Get the basename alphabet as alphabet over characters

Returns: basename alphabet

double LocARNA::Ribosum::arcmatch_score	(	char	i,
		char	j,
		char	k,
		char	l
	)		const

inline

Get arc match score.

Parameters

i	left character of first arc
j	right character of first arc
k	left character of second arc
l	right character of second arc

Returns: ribosum score for matching an arc of nucleotides i and j with an arc of nucleotides k and l.

double LocARNA::Ribosum::basematch_score	(	char	i,
		char	j
	)		const

inline

Get base match score.

Parameters

i	character of first nucleotide
j	character of second nucleotide

Returns: ribosum score for matching nucleotides i and j.

const matrix_t& LocARNA::Ribosum::get_arcmatch_scores ( ) const

inline

Get arc match scores

Returns: the matrix of arc match scores

const matrix_t& LocARNA::Ribosum::get_basematch_scores ( ) const

inline

Get base match scores.

Returns: the matrix of base match scores

const std::string& LocARNA::Ribosum::get_name ( ) const

inline

Get name of ribosum

Returns: name of ribosum

std::istream & LocARNA::Ribosum::read_matrix	(	std::istream &	in,
		matrix_t &	mat,
		const alphabet_type &	names
	)		const

protected

Read matrix from input stream

Parameters

	in	input stream
[out]	mat	matrix to be read
	names	alphabet names provided as Alphabet (of strings)

Returns: input stream after reading

void LocARNA::Ribosum::read_ribosum ( std::istream & in )

protected

reads the standard ribosum file format

Parameters

in	input stream

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

inlineprotected

Set alphabet of base names

Parameters

a	array of strings of the arc names

Postcondition: arcname_alphabet is initialized

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

inlineprotected

Set alphabet of base names

Parameters

a	array of strings of the base names

Postcondition: basename_alphabet and char_basename_alphabet are initialized

const alphabet_type& LocARNA::Ribosum::string_alphabet ( ) const

inline

Get the basename alphabet as alphabet over strings

Returns: alphabet of strings

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

protected

Write matrix to output stream

Parameters

out	output stream
mat	matrix to be written
alph	alphabet names provided as Alphabet (of strings)

Returns: output stream after writing

Friends And Related Function Documentation

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

friend

Output operator

Parameters

out	output stream
ribosum	Ribosum to be written to stream

Returns: output stream after writing

Member Data Documentation

matrix_t LocARNA::Ribosum::am

protected

16x16 matrix

scores for basepair/arc matches,

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

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

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation