NVBIO: nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler > Struct Template Reference

Detailed description

template< typename stream_type>
struct nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler >

DeviceStagedThreadScheduler specialization of BatchedAlignmentScore.

Template Parameters

stream_type the stream of alignment jobs

Definition at line 533 of file batched_inl.h.

#include <batched_inl.h>

Public Types
typedef stream_type::aligner_type	aligner_type

typedef checkpoint_storage_type < aligner_type >::type	cell_type

Public Methods
void	enact (stream_type stream, uint64 temp_size=0u, uint8 *temp=NULL)

Static Public Methods
static uint32	column_storage (const uint32 max_pattern_len, const uint32 max_text_len)

static uint64	min_temp_storage (const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size)

static uint64	max_temp_storage (const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size)

Static Public Members
static const uint32	BLOCKDIM = 128

Member Typedef Documentation

template<typename stream_type >

typedef stream_type::aligner_type nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler >::aligner_type

Definition at line 537 of file batched_inl.h.

template<typename stream_type >

typedef checkpoint_storage_type<aligner_type>::type nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler >::cell_type

Definition at line 538 of file batched_inl.h.

Member Function Documentation

template<typename stream_type >

static uint32 nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler >::column_storage	(	const uint32	max_pattern_len,
		const uint32	max_text_len
	)

inlinestatic

return the per-element column storage size

Definition at line 542 of file batched_inl.h.

template<typename stream_type >

void nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler >::enact	(	stream_type	stream,
		uint64	temp_size = `0u`,
		uint8 *	temp = `NULL`
	)

inline

enact the batch execution

Definition at line 567 of file batched_inl.h.

template<typename stream_type >

static uint64 nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler >::max_temp_storage	(	const uint32	max_pattern_len,
		const uint32	max_text_len,
		const uint32	stream_size
	)

inlinestatic

return the maximum number of bytes required by the algorithm

Definition at line 560 of file batched_inl.h.

template<typename stream_type >

static uint64 nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler >::min_temp_storage	(	const uint32	max_pattern_len,
		const uint32	max_text_len,
		const uint32	stream_size
	)

inlinestatic

return the minimum number of bytes required by the algorithm

Definition at line 553 of file batched_inl.h.

Member Data Documentation

template<typename stream_type >

const uint32 nvbio::aln::BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler >::BLOCKDIM = 128

static

Definition at line 535 of file batched_inl.h.

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

E:/git/nvbio/nvbio/alignment/batched_inl.h