nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler > Struct Template Reference

Detailed description

template< uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type>
struct nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >

DeviceThreadScheduler specialization of BatchedAlignmentTraceback.

Template Parameters

stream_type

the stream of alignment jobs

Definition at line 336 of file batched_banded_inl.h.

#include <batched_banded_inl.h>

Public Types
typedef stream_type::aligner_type	aligner_type
typedef column_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	checkpoint_storage (const uint32 max_pattern_len, const uint32 max_text_len)
static uint32	submatrix_storage (const uint32 max_pattern_len, const uint32 max_text_len)
static uint32	element_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<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

typedef stream_type::aligner_type nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::aligner_type

Definition at line 340 of file batched_banded_inl.h.

template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

typedef column_storage_type<aligner_type>::type nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::cell_type

Definition at line 341 of file batched_banded_inl.h.

Member Function Documentation

template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

static uint32 nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::checkpoint_storage ( const uint32  max_pattern_len, const uint32  max_text_len  )

inlinestatic

return the per-element checkpoint storage size

Definition at line 345 of file batched_banded_inl.h.

template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

static uint32 nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::element_storage ( const uint32  max_pattern_len, const uint32  max_text_len  )

inlinestatic

return the per-element storage size

Definition at line 362 of file batched_banded_inl.h.

template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

void nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::enact	(	stream_type	stream,
		uint64	temp_size = 0u,
		uint8 *	temp = NULL
	)

enact the batch execution

Definition at line 400 of file batched_banded_inl.h.

template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

uint64 nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::max_temp_storage ( const uint32  max_pattern_len, const uint32  max_text_len, const uint32  stream_size  )

static

return the maximum number of bytes required by the algorithm

Definition at line 392 of file batched_banded_inl.h.

template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

uint64 nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::min_temp_storage ( const uint32  max_pattern_len, const uint32  max_text_len, const uint32  stream_size  )

static

return the minimum number of bytes required by the algorithm

Definition at line 384 of file batched_banded_inl.h.

template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

static uint32 nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::submatrix_storage ( const uint32  max_pattern_len, const uint32  max_text_len  )

inlinestatic

return the per-element submatrix storage size

Definition at line 352 of file batched_banded_inl.h.

Member Data Documentation

template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type >

const uint32 nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >::BLOCKDIM = 128

static

Definition at line 338 of file batched_banded_inl.h.

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

• E:/git/nvbio/nvbio/alignment/batched_banded_inl.h