Family of Ribofit matrices. More...
#include <ribofit.hh>
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_t & | get_basematch_scores (double identity, matrix_t &basematch_scores) const |
Get base match scores. | |
Protected Attributes | |
Alphabet< char > | alphabet_ |
alphabet of base names as characters |
Family of Ribofit matrices.
Represents a function of sequence identities to matrices of base and arc match scores. Abstract base class.
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
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 |
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
i | character in sequence A |
j | character in sequence B |
identity | sequence identity |
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.
identity | sequence identity | |
[out] | basematch_scores | matrix to hold basematch scores |