PE Namespace Reference

Functions
void	PEUnroll (score_vec_t(&dp_mem)[PE_NUM+1][3], const input_char_block_t qry, const input_char_block_t ref, const Penalties penalties, tbp_vec_t &tbp)
	Unrolls the array of PE. More...
void	PEUnrollSep (dp_mem_block_t &dp_mem, const input_char_block_t &qry, const input_char_block_t &ref, const Penalties penalties, wavefront_scores_inf_t &score, tbp_vec_t &tbp)
	Unrolls the array of PE, saparating the score input buffer and the score output buffer. Used in the rectangular kernel. More...
void	PEUnrollFixedSep (const dp_mem_block_t dp_mem, const input_char_block_t qry, const input_char_block_t ref, const Penalties penalties, wavefront_scores_inf_t &score, tbp_vec_t &tbp)
	Unrolls the array of PE, saparating the score input buffer and the score output buffer. Used in the fixed banded kernel. More...

Function Documentation

void PE::PEUnroll	(	score_vec_t(&)	dp_mem[PE_NUM+1][3],
		const input_char_block_t	qry,
		const input_char_block_t	ref,
		const Penalties	penalties,
		tbp_vec_t &	tbp
	)

Unrolls the array of PE.

Deprecated:

Parameters

dp_mem	DP Memory of Three Wavefronts
qry	Local Query
ref	Local Reference
penalties	Penalties
tbp	Traceback Pointer Out

void PE::PEUnrollFixedSep	(	const dp_mem_block_t	dp_mem,
		const input_char_block_t	qry,
		const input_char_block_t	ref,
		const Penalties	penalties,
		wavefront_scores_inf_t &	score,
		tbp_vec_t &	tbp
	)

Unrolls the array of PE, saparating the score input buffer and the score output buffer. Used in the fixed banded kernel.

Parameters

dp_mem	DP Memory of Three Wavefronts
qry	Local Query
ref	Local Reference
penalties	Penalties
score	Scores Out Buffer
tbp	Traceback Poitner Out

void PE::PEUnrollSep	(	dp_mem_block_t &	dp_mem,
		const input_char_block_t &	qry,
		const input_char_block_t &	ref,
		const Penalties	penalties,
		wavefront_scores_inf_t &	score,
		tbp_vec_t &	tbp
	)

Unrolls the array of PE, saparating the score input buffer and the score output buffer. Used in the rectangular kernel.

Parameters

dp_mem	DP Memory of Three Wavefronts
qry	Local Query
ref	Local Reference
penalties	Penalties
score	Scores Out Buffer
tbp	Traceback Poitner Out