Provides probabilities for alignment egdes (match or trace probabilities etc). More...
#include <edge_probs.hh>
Inheritance diagram for LocARNA::EdgeProbs:
Collaboration diagram for LocARNA::EdgeProbs:
Public Types | |
| using | size_type = size_t |
| size | |
Public Member Functions | |
| 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 | |
Protected Member Functions | |
| 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 | |
| Matrix< double > | probs_ |
| the base match probabilities | |
Detailed Description
Provides probabilities for alignment egdes (match or trace probabilities etc).
The probabilities must be read in from an input stream.
Member Function Documentation
◆ read_sparse() [1/2]
|
protected |
read the probabilities from a file read 'sparse' format "i j p"
◆ read_sparse() [2/2]
|
protected |
read the probabilities from a stream read 'sparse' format "i j p"
◆ write_sparse()
| std::ostream & LocARNA::EdgeProbs::write_sparse | ( | std::ostream & | out, |
| double | threshold | ||
| ) | const |
write the probabilities to a stream, only probs >= threshold use format "i j p"
The documentation for this class was generated from the following files:
- src/LocARNA/edge_probs.hh
- src/LocARNA/edge_probs.cc
