Inheritance diagram for ymir::DiNucInsertionModel:

Public Member Functions
	DiNucInsertionModel (prob_t err_prob)

	DiNucInsertionModel (std::vector< prob_t >::const_iterator start, prob_t err_prob=0)

	DiNucInsertionModel (const event_matrix_t &mat, prob_t err_prob=0)

	DiNucInsertionModel (const DiNucInsertionModel &other)

DiNucInsertionModel &	operator= (const DiNucInsertionModel &other)

sequence_t	generate (seq_len_t len, std::default_random_engine &rg, char first_char=NULL_CHAR, bool reverse=false) const

prob_t	operator() (uint8_t row, uint8_t col) const


prob_t	nucProbability (const std::string &sequence, char first_char=NULL_CHAR, bool with_errors=false) const
	Probability of the given nucleotide sequence.

prob_t	nucProbability (std::string::const_iterator start, seq_len_t sequence_len, char first_char=NULL_CHAR, bool with_errors=false) const

prob_t	nucProbability (std::string::const_reverse_iterator start, seq_len_t sequence_len, char first_char=NULL_CHAR, bool with_errors=false) const


prob_t	aaProbability (const std::string &sequence, char first_char=NULL_CHAR) const

prob_t	aaProbability (std::string::const_iterator start, seq_len_t sequence_len, char first_char=NULL_CHAR) const

prob_t	aaProbability (std::string::const_reverse_iterator start, seq_len_t sequence_len, char first_char=NULL_CHAR) const

Public Member Functions inherited from ymir::AbstractInsertionModel
	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)

prob_t	err_prob () const

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

prob_t	operator[] (uint8_t index) const

Protected Member Functions
void	updateProbabilitiesMatrix (const event_matrix_t &mat)

void	updateProbabilitiesMatrix (const event_matrix_t &mat, prob_t err_prob)

Protected Member Functions inherited from ymir::AbstractInsertionModel
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)

Additional Inherited Members
Public Types inherited from ymir::AbstractInsertionModel
typedef unique_ptr< prob_t[]>	prob_array_t

Protected Attributes inherited from ymir::AbstractInsertionModel
prob_array_t	_arr

prob_t	_err_prob

uint8_t	_size

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

Ymir/src/insertionmodel.h

Public Member Functions

Protected Member Functions

Additional Inherited Members