ppALIGN API documentation
HmmWeight Class Reference
#include <weights.hpp>
Inheritance diagram for HmmWeight:
Public Member Functions | |
| HmmWeight (const Alphabet &, const Alphabet &, const std::string &name, double gap_open, double gap_extension, AlignmentType t, bool _allow_DI=true, bool _allow_ID=false) | |
| HmmWeight (const ScoreMatrix &matrix, double _scale, const Frequencies &freq1, const Frequencies &freq2, double gap_open, double gap_extension, AlignmentType t, bool _allow_DI=true, bool _allow_ID=false) | |
| HmmWeight (const ScoreMatrix &matrix, const Sequence &seq1, const Sequence &seq2, double gap_open, double gap_extension, AlignmentType t, bool _allow_DI=true, bool _allow_ID=false) | |
Detailed Description
The weights of a pair HMM.
- Examples:
Definition at line 373 of file weights.hpp.
Constructor & Destructor Documentation
| HmmWeight::HmmWeight | ( | const Alphabet & | , | |
| const Alphabet & | , | |||
| const std::string & | name, | |||
| double | gap_open, | |||
| double | gap_extension, | |||
| AlignmentType | t, | |||
| bool | _allow_DI = true, |
|||
| bool | _allow_ID = false | |||
| ) |
Construct pair probability weights from matrix name
- Parameters:
-
a1 alphabet of the first sequence a2 alphabet of the second sequence name name of the matrix (e.g. blosum62) gap_open gap open penalty gap_extension gap extension penalty t alignment type _allow_DI transitions from deletion to insertion possible _allow_ID transitions from insertion to deletion possible
The documentation for this class was generated from the following file:
- src/weights.hpp