Family of Ribofit matrices. More...

#include <ribofit.hh>

Inheritance diagram for LocARNA::Ribofit:

Collaboration diagram for LocARNA::Ribofit:

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

using	base_alphabet_type = Alphabet< char, 4 >

Public Member Functions
	Ribofit (std::array< char, 4 > 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 More...

virtual double	arcmatch_score (char i, char j, char k, char l, double identity) const =0
	ribofit arc match score for specific identity More...

const base_alphabet_type &	alphabet () const

const matrix_t &	get_basematch_scores (double identity, matrix_t &basematch_scores) const
	Get base match scores. More...

Protected Attributes
base_alphabet_type	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

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

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

pure virtual

ribofit base match score for specific identity

Parameters

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

Get base match scores.

Parameters

	identity	sequence identity
[out]	basematch_scores	matrix to hold basematch scores

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