LocARNA::Ribosum Class Reference

Represents ribosum similarity matrices. More...

#include <ribosum.hh>

Inheritance diagram for LocARNA::Ribosum:

List of all members.

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

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Detailed Description

Represents ribosum similarity matrices.

Reads ribosum data from file and provides access.

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Constructor & Destructor Documentation

LocARNA::Ribosum::Ribosum

(

const std::string &

filename

)

[explicit]

Construct from file

Parameters:

filename

name of the input file

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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[]

)

[inline, protected]

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[]

)

[inline, protected]

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

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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

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Member Data Documentation

matrix_t LocARNA::Ribosum::am [protected]

16x16 matrix

scores for basepair/arc matches,

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

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