NVBIO: nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type > Struct Template Reference

Detailed description

template< typename stream_type, typename derived_type>
struct nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >

This class provides the fundamental mechanisms to perform a staged job. In order to allow for configuration, it is templated over a derived_type which must implement the method:

bool execute(
    const ScoreStream<stream_type>& stream,
    const uint32                    queue_slot,
    pattern_string                  pattern,
    qual_string                     quals,
    text_string                     text,
    const int32                     min_score,
    const uint32                    window_begin,
    const uint32                    window_end,
    sink_type&                      sink);

Definition at line 126 of file batched_stream.h.

#include <batched_stream.h>

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

Public Types
typedef stream_type::context_type	context_type

typedef stream_type::strings_type	strings_type

typedef stream_type::aligner_type	aligner_type

Public Methods
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)

Public Members
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
static const uint32	WINDOW_SIZE = 32

Member Typedef Documentation

template<typename stream_type, typename derived_type>

typedef stream_type::aligner_type nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::aligner_type

Definition at line 132 of file batched_stream.h.

template<typename stream_type, typename derived_type>

typedef stream_type::context_type nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::context_type

Definition at line 130 of file batched_stream.h.

template<typename stream_type, typename derived_type>

typedef stream_type::strings_type nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::strings_type

Definition at line 131 of file batched_stream.h.

Member Function Documentation

template<typename stream_type, typename derived_type>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::run ( const ScoreStream< stream_type > & score_stream)

inline

Definition at line 157 of file batched_stream.h.

template<typename stream_type, typename derived_type>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::setup	(	const uint32	_job_id,
		const uint32	_queue_slot,
		const stream_type &	stream
	)

inline

Definition at line 136 of file batched_stream.h.

Member Data Documentation

template<typename stream_type, typename derived_type>

context_type nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::context

the alignment context

Definition at line 196 of file batched_stream.h.

template<typename stream_type, typename derived_type>

uint32 nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::job_id

the job id

Definition at line 194 of file batched_stream.h.

template<typename stream_type, typename derived_type>

uint32 nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::queue_slot

the job's execution slot

Definition at line 195 of file batched_stream.h.

template<typename stream_type, typename derived_type>

strings_type nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::strings

the strings to be aligned

Definition at line 197 of file batched_stream.h.

template<typename stream_type, typename derived_type>

volatile bool nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::valid

valid flag

Definition at line 199 of file batched_stream.h.

template<typename stream_type, typename derived_type>

volatile uint32 nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::window_begin

the beginning of the pattern window

Definition at line 198 of file batched_stream.h.

template<typename stream_type, typename derived_type>

const uint32 nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >::WINDOW_SIZE = 32

static

Definition at line 128 of file batched_stream.h.

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

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