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LocARNA-1.9.2
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LocARNA-1.9.2
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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 |
1.7.6.1
