Provide match probabilities calculated by pf approach. More...
#include <edge_probs.hh>
Inheritance diagram for LocARNA::PFTraceProbs< pf_score_t >:
Collaboration diagram for LocARNA::PFTraceProbs< pf_score_t >:
Public Types | |
| using | size_type = TraceProbs::size_type |
| size type | |
 Public Types inherited from LocARNA::EdgeProbs | |
| using | size_type = size_t |
| size | |
Public Member Functions | |
| PFTraceProbs (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::TraceProbs | |
| TraceProbs (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::PFTraceProbs< pf_score_t >
Provide match probabilities calculated by pf approach.
- See also
- PFMatchProbs
Constructor & Destructor Documentation
◆ PFTraceProbs()
template<class pf_score_t >
| LocARNA::PFTraceProbs< pf_score_t >::PFTraceProbs | ( | 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 free_endgaps which end gaps should be cost free flag_local compute probabilities from local alignments
- See also
- PFMatchProbs::PFMatchProbs::()
The documentation for this class was generated from the following file:
- src/LocARNA/edge_probs.hh
