LocARNA::Ribosum Class Reference

Represents ribosum similarity matrices. More...

#include <ribosum.hh>

Inheritance diagram for LocARNA::Ribosum:

Collaboration diagram for LocARNA::Ribosum:

Public Types
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

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 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
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
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 Ribosum &ribosum)

Detailed Description

Represents ribosum similarity matrices.

Reads ribosum data from file and provides access.

Constructor & Destructor Documentation

Ribosum()

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

explicit

Construct from file

Parameters

filename

name of the input file

Member Function Documentation

alphabet()

const char_alphabet_type& LocARNA::Ribosum::alphabet ( ) const

inline

Get the basename alphabet as alphabet over characters

Returns

basename alphabet

arcmatch_score()

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.

basematch_score()

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.

get_arcmatch_scores()

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

inline

Get arc match scores

Returns

the matrix of arc match scores

get_basematch_scores()

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

inline

Get base match scores.

Returns

the matrix of base match scores

get_name()

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

inline

Get name of ribosum

Returns

name of ribosum

read_matrix()

template<size_t N>

std::istream & LocARNA::Ribosum::read_matrix ( std::istream &  in, matrix_t &  mat, const Alphabet< std::string, N > &  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

read_ribosum()

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

protected

reads the standard ribosum file format

Parameters

in	input stream

set_arcname_alphabet()

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

inlineprotected

Set alphabet of base names

Parameters

a	array of strings of the arc names

Postcondition

arcname_alphabet is initialized

set_basename_alphabet()

void LocARNA::Ribosum::set_basename_alphabet ( const std::array< std::string, 4 > &  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

string_alphabet()

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

inline

Get the basename alphabet as alphabet over strings

Returns

alphabet of strings

write_matrix()

template<size_t N>

std::ostream & LocARNA::Ribosum::write_matrix ( std::ostream &  out, const matrix_t &  mat, const Alphabet< std::string, N > &  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

operator<<

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

am_

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