LocARNA::Ribofit_will2014 Class Reference

Inheritance diagram for LocARNA::Ribofit_will2014:

Collaboration diagram for LocARNA::Ribofit_will2014:

Public Member Functions
	Ribofit_will2014 ()
	Construct.
	~Ribofit_will2014 ()
	destructor
Public Member Functions inherited from LocARNA::Ribofit
	Ribofit (std::array< char, 4 > alphabet)
	Construct.
virtual	~Ribofit ()
	virtual destructor
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 Member Functions
double	basematch_score (char i, char j, double identity) const
	ribofit base match score for specific identity More...
double	arcmatch_score (char i, char j, char k, char l, double identity) const
	ribofit arc match score for specific identity More...

Additional Inherited Members
Public Types inherited from LocARNA::Ribofit
typedef Matrix< double >	matrix_t
	type of a matrix
using	base_alphabet_type = Alphabet< char, 4 >
Protected Attributes inherited from LocARNA::Ribofit
base_alphabet_type	alphabet_
	alphabet of base names as characters

Member Function Documentation

arcmatch_score()

double LocARNA::Ribofit_will2014::arcmatch_score ( char  i, char  j, char  k, char  l, double  identity  ) const

inlineprotectedvirtual

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

Returns

ribofit arc match score

Implements LocARNA::Ribofit.

basematch_score()

double LocARNA::Ribofit_will2014::basematch_score ( char  i, char  j, double  identity  ) const

inlineprotectedvirtual

ribofit base match score for specific identity

Parameters

i	character in sequence A
j	character in sequence B
identity	sequence identity

Returns

ribofit base match score

Implements LocARNA::Ribofit.

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

• src/LocARNA/ribofit.hh