Traceback Namespace Reference

Functions
void	Traceback (tbp_t(&tbmat)[MAX_QUERY_LENGTH][MAX_REFERENCE_LENGTH], tbr_t(&traceback_out)[MAX_REFERENCE_LENGTH+MAX_QUERY_LENGTH], const int max_row, const int max_col)
	Traceback function. It extract the traceback path from a matrix of traceback pointers. More...
void	TracebackOptimized (tbp_t(&tbmat)[PE_NUM][TBMEM_SIZE], traceback_buf_t(&traceback_out), idx_t(&ck_start_col)[MAX_QUERY_LENGTH/PE_NUM], idx_t(&ck_end_col)[MAX_QUERY_LENGTH/PE_NUM], int ck_idx, int pe_idx, int col_idx, int v_row, int v_col)
	Traceback function. It extract the traceback path from a matrix of traceback pointers. More...
template<int VIRTUAL_CHUNK_WIDTH>
void	NextAddressFixedSize (tbr_t &nav, int &chunk, int &pe, int &col, int &v_row, int &v_col)
template<int CHUNK_WIDTH>
void	TracebackFixedSize (tbp_t(&tbmat)[PE_NUM][TBMEM_SIZE], traceback_buf_t(&traceback_out), int ck_idx, int pe_idx, int col_idx, int v_row, int v_col)
void	pointer_to_coordinate (tbp_t tbp, TB_STATE &state, int &row, int &column)
	A traceback pointer to coordinate mapping function. The traceback function is implemeted as a state machine. The state represents the matrix the traceback is tracing in. To increase the customizability, the function that maps a traceback pointer with it's current state to the next coordinate and the state the next step goes to shall be overrite by the user. More...
void	state_initial (tbp_t tbp, TB_STATE &state)
	Function used to set the initial state of the traceback, according to the ruls of the traceback pointer set by the user. More...
tbp_t	extract_direction (tbp_t tbp)
	Private helper function that extract the direction bit of the traceback pointer. More...
tbr_t	state_to_path (TB_STATE state)
void	NextAddress (tbr_t &nagivation, idx_t(&ck_start_idx)[CK_NUM], idx_t(&ck_end_idx)[CK_NUM], int &chunk, int &pe, int &col, int &v_row, int &v_col)

Function Documentation

tbp_t Traceback::extract_direction

(

tbp_t

tbp

)

Private helper function that extract the direction bit of the traceback pointer.

Parameters

tbp	: Traceback Pointer.

void Traceback::NextAddress	(	tbr_t &	nagivation,
		idx_t(&)	ck_start_idx[CK_NUM],
		idx_t(&)	ck_end_idx[CK_NUM],
		int &	chunk,
		int &	pe,
		int &	col,
		int &	v_row,
		int &	v_col
	)

template<int VIRTUAL_CHUNK_WIDTH>

void Traceback::NextAddressFixedSize	(	tbr_t &	nav,
		int &	chunk,
		int &	pe,
		int &	col,
		int &	v_row,
		int &	v_col
	)

void Traceback::pointer_to_coordinate	(	tbp_t	tbp,
		TB_STATE &	state,
		int &	row,
		int &	column
	)

A traceback pointer to coordinate mapping function. The traceback function is implemeted as a state machine. The state represents the matrix the traceback is tracing in. To increase the customizability, the function that maps a traceback pointer with it's current state to the next coordinate and the state the next step goes to shall be overrite by the user.

Parameters

tbp	: A traceback pointer
state	: The state of the traceback at the pointer.
row	: Row index of the poiner.
column	: Column index of the pointer.

void Traceback::state_initial	(	tbp_t	tbp,
		TB_STATE &	state
	)

Function used to set the initial state of the traceback, according to the ruls of the traceback pointer set by the user.

Parameters

tbp	: initial traceback pointer.

tbr_t Traceback::state_to_path

(

TB_STATE

state

)

Parameters

state

: Current state of the state machine.

Returns

Number corresponding to the traceback navigation.

void Traceback::Traceback	(	tbp_t(&)	tbmat[MAX_QUERY_LENGTH][MAX_REFERENCE_LENGTH],
		tbr_t(&)	traceback_out[MAX_REFERENCE_LENGTH+MAX_QUERY_LENGTH],
		const int	max_row,
		const int	max_col
	)

Traceback function. It extract the traceback path from a matrix of traceback pointers.

Parameters

max_row	: Row index of the maximum element to start the traceback.
max_col	: Column index of the maximum element to start the traceback.

template<int CHUNK_WIDTH>

void Traceback::TracebackFixedSize	(	tbp_t(&)	tbmat[PE_NUM][TBMEM_SIZE],
		traceback_buf_t &	traceback_out,
		int	ck_idx,
		int	pe_idx,
		int	col_idx,
		int	v_row,
		int	v_col
	)

void Traceback::TracebackOptimized	(	tbp_t(&)	tbmat[PE_NUM][TBMEM_SIZE],
		traceback_buf_t &	traceback_out,
		idx_t(&)	ck_start_col[MAX_QUERY_LENGTH/PE_NUM],
		idx_t(&)	ck_end_col[MAX_QUERY_LENGTH/PE_NUM],
		int	ck_idx,
		int	pe_idx,
		int	col_idx,
		int	v_row,
		int	v_col
	)

Traceback function. It extract the traceback path from a matrix of traceback pointers.

Parameters

max_row	: Row index of the maximum element to start the traceback.
max_col	: Column index of the maximum element to start the traceback.