LocARNA-1.9.2
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Public Types | Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Friends
LocARNA::Ribosum Class Reference

Represents ribosum similarity matrices. More...

#include <ribosum.hh>

Inheritance diagram for LocARNA::Ribosum:
LocARNA::RibosumFreq

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_tget_basematch_scores () const
 Get base match scores.
const matrix_tget_arcmatch_scores () const
const alphabet_typestring_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)

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:
filenamename 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:
ileft character of first arc
jright character of first arc
kleft character of second arc
lright 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:
icharacter of first nucleotide
jcharacter of second nucleotide
Returns:
ribosum score for matching nucleotides i and j.

Get arc match scores

Returns:
the matrix of arc match scores

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:
ininput stream
[out]matmatrix to be read
namesalphabet 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:
ininput stream
void LocARNA::Ribosum::set_arcname_alphabet ( const std::string  a[]) [inline, protected]

Set alphabet of base names

Parameters:
aarray 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:
aarray of strings of the base names
Postcondition:
basename_alphabet and char_basename_alphabet are initialized

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:
outoutput stream
matmatrix to be written
alphalphabet 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:
outoutput stream
ribosumRibosum to be written to stream
Returns:
output stream after writing

Member Data Documentation

16x16 matrix

scores for basepair/arc matches,


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