Provide match probabilities calculated by pf approach. More...
#include <edge_probs.hh>
Inheritance diagram for LocARNA::PFMatchProbs< pf_score_t >:
Collaboration diagram for LocARNA::PFMatchProbs< pf_score_t >:
Public Types | |
| using | size_type = EdgeProbs::size_type |
| size type | |
 Public Types inherited from LocARNA::EdgeProbs | |
| using | size_type = size_t |
| size | |
Public Member Functions | |
| PFMatchProbs (const RnaData &rnaA, const RnaData &rnaB, const TraceController &trace_controller, const Matrix< double > &sim_mat, const Alphabet< char, 4 > &alphabet, double gap_opening, double gap_extension, double pf_struct_weight, double temp, const FreeEndgaps &free_endgaps, bool flag_local) | |
| construct; run computation of pfs and probabilities More... | |
| bool | fail () const |
| const pf_score_t & | z () const |
| Public Member Functions inherited from LocARNA::MatchProbs | |
| MatchProbs (std::istream &in, size_type lenA, size_type lenB) | |
| construct from input stream (sparse format) | |
| Public Member Functions inherited from LocARNA::EdgeProbs | |
| EdgeProbs (std::istream &in, size_type lenA, size_type lenB) | |
| construct from input stream (sparse format) | |
| std::ostream & | write_sparse (std::ostream &out, double threshold) const |
| size_type | lenA () const |
| get the length of the first sequence | |
| size_type | lenB () const |
| get the length of the second sequence | |
| double | prob (size_t i, size_t j) const |
| return the match probability for the two bases | |
Additional Inherited Members | |
| Protected Member Functions inherited from LocARNA::EdgeProbs | |
| std::istream & | read_sparse (std::istream &in, size_type lenA, size_type lenB) |
| void | read_sparse (const std::string &filename, size_type lenA, size_type lenB) |
| Protected Attributes inherited from LocARNA::EdgeProbs | |
| Matrix< double > | probs_ |
| the base match probabilities | |
Detailed Description
template<class pf_score_t>
class LocARNA::PFMatchProbs< pf_score_t >
Provide match probabilities calculated by pf approach.
Similar to proba/probalign, use statistical-mechanics-like model. Assume alignments are Boltzman distributed, calc match probs via partition function. This approach supports Stral-like scoring (using pf_struct_weight as "alpha")
Constructor & Destructor Documentation
◆ PFMatchProbs()
template<class pf_score_t >
| LocARNA::PFMatchProbs< pf_score_t >::PFMatchProbs | ( | const RnaData & | rnaA, |
| const RnaData & | rnaB, | ||
| const TraceController & | trace_controller, | ||
| const Matrix< double > & | sim_mat, | ||
| const Alphabet< char, 4 > & | alphabet, | ||
| double | gap_opening, | ||
| double | gap_extension, | ||
| double | pf_struct_weight, | ||
| double | temp, | ||
| const FreeEndgaps & | free_endgaps, | ||
| bool | flag_local | ||
| ) |
construct; run computation of pfs and probabilities
- Parameters
-
rnaA rna data of first RNA rnaB rna data of second RNA sim_mat similarity matrix for scoring base matches; e.g.
- See also
- Ribosum::get_basematch_scores()
- Parameters
-
alphabet the alphabet of the similiarity matrix gap_opening score for opening a gap gap_extension score for extending a gap pf_struct_weight weight of structure (vs. sequence) temp temperature for computing the Boltzmann weights flag_local compute probabilities from local alignments
- Note
- unlike the integer scores in locarna, the scores passed to this function are not scaled by factor 100. (Consequently, the integer scores and the structure weight are usually divided by 100.)
The documentation for this class was generated from the following file:
- src/LocARNA/edge_probs.hh
