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nvbio::aln::BandedScoreUnit< BAND_LEN, stream_type > Struct Template Reference

Detailed description

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

A staged scoring work unit, implemented inheriting from StagedAlignmentUnitBase

Definition at line 252 of file batched_stream.h.

#include <batched_stream.h>

Inheritance diagram for nvbio::aln::BandedScoreUnit< BAND_LEN, stream_type >:
nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >

Public Types

typedef ScoreStream
< stream_type >::cell_type 
cell_type
 
typedef ScoreStream
< stream_type >
::checkpoint_type 
checkpoint_type
 
typedef ScoreStream
< stream_type >::column_type 
column_type
 
- Public Types inherited from nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >
typedef stream_type::context_type context_type
 
typedef stream_type::strings_type strings_type
 
typedef stream_type::aligner_type aligner_type
 

Public Methods

template<typename pattern_string , typename qual_string , typename text_string , typename sink_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
execute (const ScoreStream< stream_type > &score_stream, const uint32 queue_slot, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink)
 
- Public Methods inherited from nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
setup (const uint32 _job_id, const uint32 _queue_slot, const stream_type &stream)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
run (const ScoreStream< stream_type > &score_stream)
 

Additional Inherited Members

- Public Members inherited from nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >
uint32 job_id
 the job id More...
 
uint32 queue_slot
 the job's execution slot More...
 
context_type context
 the alignment context More...
 
strings_type strings
 the strings to be aligned More...
 
volatile uint32 window_begin
 the beginning of the pattern window More...
 
volatile bool valid
 valid flag More...
 
- Static Public Members inherited from nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >
static const uint32 WINDOW_SIZE = 32
 

Member Typedef Documentation

template<uint32 BAND_LEN, typename stream_type >
typedef ScoreStream<stream_type>::cell_type nvbio::aln::BandedScoreUnit< BAND_LEN, stream_type >::cell_type

Definition at line 257 of file batched_stream.h.

template<uint32 BAND_LEN, typename stream_type >
typedef ScoreStream<stream_type>::checkpoint_type nvbio::aln::BandedScoreUnit< BAND_LEN, stream_type >::checkpoint_type

Definition at line 258 of file batched_stream.h.

template<uint32 BAND_LEN, typename stream_type >
typedef ScoreStream<stream_type>::column_type nvbio::aln::BandedScoreUnit< BAND_LEN, stream_type >::column_type

Definition at line 259 of file batched_stream.h.

Member Function Documentation

template<uint32 BAND_LEN, typename stream_type >
template<typename pattern_string , typename qual_string , typename text_string , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::aln::BandedScoreUnit< BAND_LEN, stream_type >::execute ( const ScoreStream< stream_type > &  score_stream,
const uint32  queue_slot,
const pattern_string  pattern,
const qual_string  quals,
const text_string  text,
const int32  min_score,
const uint32  window_begin,
const uint32  window_end,
sink_type &  sink 
)
inline

Definition at line 268 of file batched_stream.h.


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