ymir::AbstractInsertionModel Class Reference

Class for representing VJ / VD / DJ insertions models - either a mono-nucleotide or a di-nucleotide model. More...

#include <insertionmodel.h>

Inheritance diagram for ymir::AbstractInsertionModel:

Public Types
typedef unique_ptr< prob_t[]>	prob_array_t

Public Member Functions
	AbstractInsertionModel (uint8_t size, prob_t err_prob=0)
	AbstractInsertionModel (uint8_t size, std::vector< prob_t >::const_iterator start, prob_t err_prob=0)
	AbstractInsertionModel (const AbstractInsertionModel &other)
AbstractInsertionModel &	operator= (const AbstractInsertionModel &other)
virtual sequence_t	generate (seq_len_t len, std::default_random_engine &rg, char first_char=NULL_CHAR, bool reverse=false) const =0
prob_t	err_prob () const
virtual prob_t	nucProbability (const std::string &sequence, char first_char=NULL_CHAR, bool with_errors=false) const =0
	Probability of the given nucleotide sequence.
virtual prob_t	nucProbability (std::string::const_iterator start, seq_len_t sequence_len, char first_char=NULL_CHAR, bool with_errors=false) const =0
virtual prob_t	nucProbability (std::string::const_reverse_iterator start, seq_len_t sequence_len, char first_char=NULL_CHAR, bool with_errors=false) const =0
virtual prob_t	aaProbability (const std::string &sequence, seq_len_t first_nuc_pos, seq_len_t last_nuc_pos, char first_char=NULL_CHAR) const =0
virtual prob_t	aaProbability (std::string::const_iterator start, seq_len_t first_nuc_pos, seq_len_t last_nuc_pos, char first_char=NULL_CHAR) const =0
virtual prob_t	aaProbability (std::string::const_reverse_iterator start, seq_len_t first_nuc_pos, seq_len_t last_nuc_pos, char first_char=NULL_CHAR) const =0
Event probability access.
prob_t	operator[] (uint8_t index) const

Protected Member Functions
Update chain probabilities.
Update internal std::vector of nucleotide joint probabilities. Parameters start Iterator to std::vector, in which each 4 elements are rows in nucleotide joint probability matrix, i.e. row for prev-A-nucleotide, row for prev-C-nucleotide and so on. mat Matrix with nucleotide joint probabilities with rows for prev nucleotide and columns for next nucleotide.
void	updateProbabilities (std::vector< prob_t >::const_iterator start)
void	updateProbabilities (prob_t *start)
void	updateProbabilities (std::vector< prob_t >::const_iterator start, prob_t err_prob)
void	updateProbabilities (prob_t *start, prob_t err_prob)

Protected Attributes
prob_array_t	_arr
prob_t	_err_prob
uint8_t	_size

Detailed Description

Class for representing VJ / VD / DJ insertions models - either a mono-nucleotide or a di-nucleotide model.

Member Data Documentation

prob_t ymir::AbstractInsertionModel::_err_prob

protected

Representation for a std::vector (#elements = 4) or a matrix (#elements = 16) with transition probabilities; rows and cols are for A-C-G-T (sequentially).

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The documentation for this class was generated from the following file:

• Ymir/src/insertionmodel.h