NVBIO: nvbio::aln::ScoreStream< stream_type > Struct Template Reference

Detailed description

template< typename stream_type>
struct nvbio::aln::ScoreStream< stream_type >

A work-stream class to be used with a WorkQueue. This class implements the context to fetch and run parallel alignment jobs.

In particular, it provides utilities for accessing all the temporary alignment storage bound to a given queue slot, which is represented by vectors with a strided memory layout in order to favor read/write coalescing.

Template Parameters

stream_type the underlying BatchedAlignmentScore stream_type (see Batch Alignments and BatchedAlignmentScore).

Definition at line 54 of file batched_stream.h.

#include <batched_stream.h>

Public Types
typedef stream_type::aligner_type	aligner_type
	the aligner type More...

typedef checkpoint_storage_type < aligner_type >::type	cell_type
	the DP cell type More...

typedef strided_iterator < cell_type * >	checkpoint_type
	the strided DP checkpoint type More...

typedef strided_iterator < cell_type * >	column_type
	the strided DP column type More...

Public Methods
	ScoreStream (const stream_type _stream, uint8 _columns, uint8 _checkpoints, const uint32 _stride)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	size () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE checkpoint_type	checkpoint (const uint32 i) const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE column_type	column (const uint32 i) const

template<typename score_unit_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	get (const uint32 job_id, score_unit_type *unit, const uint2 queue_slot) const

Public Members
stream_type	stream
	alignment stream More...

cell_type *	columns
	temporary columns storage More...

cell_type *	checkpoints
	temporary checkpoints storage More...

uint32	stride
	memory stride More...

Member Typedef Documentation

template<typename stream_type>

typedef stream_type::aligner_type nvbio::aln::ScoreStream< stream_type >::aligner_type

the aligner type

Definition at line 56 of file batched_stream.h.

template<typename stream_type>

typedef checkpoint_storage_type<aligner_type>::type nvbio::aln::ScoreStream< stream_type >::cell_type

the DP cell type

Definition at line 57 of file batched_stream.h.

template<typename stream_type>

typedef strided_iterator<cell_type*> nvbio::aln::ScoreStream< stream_type >::checkpoint_type

the strided DP checkpoint type

Definition at line 58 of file batched_stream.h.

template<typename stream_type>

typedef strided_iterator<cell_type*> nvbio::aln::ScoreStream< stream_type >::column_type

the strided DP column type

Definition at line 59 of file batched_stream.h.

Constructor & Destructor Documentation

template<typename stream_type>

nvbio::aln::ScoreStream< stream_type >::ScoreStream	(	const stream_type	_stream,
		uint8 *	_columns,
		uint8 *	_checkpoints,
		const uint32	_stride
	)

inline

constructor

Definition at line 63 of file batched_stream.h.

Member Function Documentation

template<typename stream_type>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE checkpoint_type nvbio::aln::ScoreStream< stream_type >::checkpoint ( const uint32 i) const

inline

return the i-th checkpoint

Definition at line 78 of file batched_stream.h.

template<typename stream_type>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE column_type nvbio::aln::ScoreStream< stream_type >::column ( const uint32 i) const

inline

return the i-th checkpoint

Definition at line 86 of file batched_stream.h.

template<typename stream_type>

template<typename score_unit_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::ScoreStream< stream_type >::get	(	const uint32	job_id,
		score_unit_type *	unit,
		const uint2	queue_slot
	)		const

inline

get the i-th work unit

Definition at line 95 of file batched_stream.h.

template<typename stream_type>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::aln::ScoreStream< stream_type >::size ( void ) const

inline

stream size

Definition at line 73 of file batched_stream.h.

Member Data Documentation

template<typename stream_type>

cell_type* nvbio::aln::ScoreStream< stream_type >::checkpoints

temporary checkpoints storage

Definition at line 103 of file batched_stream.h.

template<typename stream_type>

cell_type* nvbio::aln::ScoreStream< stream_type >::columns

temporary columns storage

Definition at line 102 of file batched_stream.h.

template<typename stream_type>

stream_type nvbio::aln::ScoreStream< stream_type >::stream

alignment stream

Definition at line 101 of file batched_stream.h.

template<typename stream_type>

uint32 nvbio::aln::ScoreStream< stream_type >::stride

memory stride

Definition at line 104 of file batched_stream.h.

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

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