Public Member Functions
	MAAGForwardBackwardAlgorithm (const MAAG &maag, ErrorMode error_mode=NO_ERRORS)

bool	process (const MAAG &maag, ErrorMode error_mode=NO_ERRORS)

event_pair_t	nextEvent ()

bool	is_empty ()

bool	status () const

prob_t	fullProbability () const

prob_t	bfullProbability () const

const vector< event_pair_t > &	event_pairs () const

prob_t *	VJ_nuc_probs ()

prob_t *	VD_nuc_probs ()

prob_t *	DJ_nuc_probs ()

prob_t	err_prob ()

Protected Member Functions
void	fillZero (ProbMMC *mmc, uint start_node=0)

void	inferInsertionNucleotides (const MAAG &maag, node_ind_t ins_node, seq_len_t left_start_pos, seq_len_t left_end_pos, seq_len_t right_start_pos, seq_len_t right_end_pos, prob_t *nuc_arr, bool reversed=false)

void	vectorise_pair_map (const MAAG &maag)

void	forward_vj (const MAAG &maag, event_ind_t j_ind)

void	backward_vj (const MAAG &maag, event_ind_t j_ind)

void	forward_backward_vj (const MAAG &maag)

void	forward_vdj (const MAAG &maag, event_ind_t d_ind, event_ind_t j_ind, bool recompute_d_gen_fi)

void	backward_vdj (const MAAG &maag, event_ind_t d_ind, event_ind_t j_ind)

void	forward_backward_vdj (const MAAG &maag)


void	pushEventValue (event_ind_t event_index, prob_t prob_value)
	Access to a hash map which maps event probabilities to event indices.

void	pushEventPair (const MAAG &maag, node_ind_t node_i, matrix_ind_t maag_mat_i, dim_t maag_row_i, dim_t maag_col_i, matrix_ind_t fb_mat_i, dim_t fb_row_i, dim_t fb_col_i)

void	pushEventPairs (const MAAG &maag, node_ind_t node_i, matrix_ind_t maag_mat_i, matrix_ind_t fb_mat_i)

void	pushEventPairsWithErrors (const MAAG &maag, node_ind_t node_i, matrix_ind_t maag_mat_i, matrix_ind_t fb_mat_i, node_ind_t err_node_i)

Protected Attributes
bool	_status

bool	_vectorised

pProbMMC	_forward_acc

pProbMMC	_backward_acc

prob_t	_full_prob

prob_t	_back_full_prob

vector< event_pair_t >	_pairs

size_t	_pairs_i

unordered_map< event_ind_t, prob_t >	_pair_map

prob_t	_nuc_arr1 [16]

prob_t	_nuc_arr2 [16]

prob_t	_err_prob

ErrorMode	_err_mode

Member Data Documentation

prob_t ymir::MAAGForwardBackwardAlgorithm::_back_full_prob

protected

Full generation probability of the input MAAG.

prob_t ymir::MAAGForwardBackwardAlgorithm::_full_prob

protected

Temporary MMC for storing forward and backward probabilities correspond.

vector<event_pair_t> ymir::MAAGForwardBackwardAlgorithm::_pairs

protected

Full generation probability of the input MAAG obtained with backward algorithm. Just for testing purposes.

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

Public Member Functions