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

Family of Ribofit matrices. More...

#include <ribofit.hh>

Inheritance diagram for LocARNA::Ribofit:
LocARNA::Ribofit_will2014

List of all members.

Public Types

typedef Matrix< double > matrix_t
 type of a matrix

Public Member Functions

 Ribofit (const char *alphabet)
 Construct.
virtual ~Ribofit ()
 virtual destructor
virtual double basematch_score (char i, char j, double identity) const =0
 ribofit base match score for specific identity
virtual double arcmatch_score (char i, char j, char k, char l, double identity) const =0
 ribofit arc match score for specific identity
const Alphabet< char > & alphabet () const
const matrix_tget_basematch_scores (double identity, matrix_t &basematch_scores) const
 Get base match scores.

Protected Attributes

Alphabet< char > alphabet_
 alphabet of base names as characters

Detailed Description

Family of Ribofit matrices.

Represents a function of sequence identities to matrices of base and arc match scores. Abstract base class.


Member Function Documentation

virtual double LocARNA::Ribofit::arcmatch_score ( char  i,
char  j,
char  k,
char  l,
double  identity 
) const [pure virtual]

ribofit arc match score for specific identity

Parameters:
ileft character of first arc
jright character of first arc
kleft character of second arc
lright character of second arc
identitysequence identity
Returns:
ribofit arc match score

Implemented in LocARNA::Ribofit_will2014.

virtual double LocARNA::Ribofit::basematch_score ( char  i,
char  j,
double  identity 
) const [pure virtual]

ribofit base match score for specific identity

Parameters:
icharacter in sequence A
jcharacter in sequence B
identitysequence identity
Returns:
ribofit base match score

Implemented in LocARNA::Ribofit_will2014.

const Ribofit::matrix_t & LocARNA::Ribofit::get_basematch_scores ( double  identity,
matrix_t basematch_scores 
) const

Get base match scores.

Parameters:
identitysequence identity
[out]basematch_scoresmatrix to hold basematch scores
Returns:
the matrix of base match scores at given identity

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