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nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler > Struct Template Reference

Detailed description

template< uint32 BAND_LEN, typename stream_type>
struct nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler >

HostThreadScheduler specialization of BatchedBandedAlignmentScore.

Template Parameters
stream_typethe stream of alignment jobs

Definition at line 98 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 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, typename stream_type >
typedef stream_type::aligner_type nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler >::aligner_type

Definition at line 102 of file batched_banded_inl.h.

template<uint32 BAND_LEN, typename stream_type >
typedef column_storage_type<aligner_type>::type nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler >::cell_type

Definition at line 103 of file batched_banded_inl.h.

Member Function Documentation

template<uint32 BAND_LEN, typename stream_type >
void nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler >::enact ( stream_type  stream,
uint64  temp_size = 0u,
uint8 temp = NULL 
)

enact the batch execution

Definition at line 121 of file batched_banded_inl.h.

template<uint32 BAND_LEN, typename stream_type >
static uint64 nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler >::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 111 of file batched_banded_inl.h.

template<uint32 BAND_LEN, typename stream_type >
static uint64 nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler >::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 107 of file batched_banded_inl.h.

Member Data Documentation

template<uint32 BAND_LEN, typename stream_type >
const uint32 nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler >::BLOCKDIM = 128
static

Definition at line 100 of file batched_banded_inl.h.


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