Implements the stral-like scoring function. More...
#include <stral_score.hh>
Public Member Functions | |
StralScore (const RnaData &rnaA, const RnaData &rnaB, const Matrix< double > &sim_mat_, const Alphabet< char > &alphabet_, double pf_struct_weight_, double gap_opening_, double gap_extension_) | |
double | sigma (size_type i, size_type j) const |
Compute STRAL-like similarity of two residues in the two RNAs. | |
double | alpha () const |
Read gap opening cost. | |
double | beta () const |
Read gap extension cost. | |
void | reverse () |
Reverse the scoring. |
Implements the stral-like scoring function.
LocARNA::StralScore::StralScore | ( | const RnaData & | rnaA, |
const RnaData & | rnaB, | ||
const Matrix< double > & | sim_mat_, | ||
const Alphabet< char > & | alphabet_, | ||
double | pf_struct_weight_, | ||
double | gap_opening_, | ||
double | gap_extension_ | ||
) |
Construct for pair of RNAs with parameters for alignment
rnaA | data of first RNA |
rnaB | data of second RNA |
sim_mat_ | similarity matrix for bases |
alphabet_ | alphabet |
pf_struct_weight_ | structure weight |
gap_opening_ | gap opening cost |
gap_extension_ | gap extension cost |
double LocARNA::StralScore::alpha | ( | ) | const [inline] |
Read gap opening cost.
double LocARNA::StralScore::beta | ( | ) | const [inline] |
Read gap extension cost.
void LocARNA::StralScore::reverse | ( | ) |
Reverse the scoring.
double LocARNA::StralScore::sigma | ( | size_type | i, |
size_type | j | ||
) | const |
Compute STRAL-like similarity of two residues in the two RNAs.
i | position in sequence A |
j | position in sequence B |