nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType > Struct Template Reference

Detailed description

template< AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>
struct nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >

A base stream class to be used in conjunction with the aln::BatchedAlignmentScore class. This class implements the load_strings() method, which performs read and genome loading, and defers the implementation of init_context() to its inheritors, BestScoreStream, BestAnchorScoreStream, and BestOppositeScoreStream.

Definition at line 274 of file alignment_utils.h.

#include <alignment_utils.h>

Classes
struct	context_type

Public Types
typedef AlignmentStrings < AlignerType, PipelineType >	strings_type
typedef PipelineType::scheme_type	scheme_type
typedef AlignerType	aligner_type

Public Methods
	AlignmentStreamBase (const PipelineType _pipeline, const aligner_type _aligner, const ParamsPOD _params)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const aligner_type &	aligner () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	pattern_length (const uint32 i, const context_type *context) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	text_length (const uint32 i, const context_type *context) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	load_strings (const uint32 i, const uint32 window_begin, const uint32 window_end, const context_type *context, strings_type *strings) const

Public Members
PipelineType	m_pipeline
	the pipeline object More...
aligner_type	m_aligner
	the aligner More...
ParamsPOD	m_params
	global parameters More...

Member Typedef Documentation

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

typedef AlignerType nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::aligner_type

Definition at line 278 of file alignment_utils.h.

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

typedef PipelineType::scheme_type nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::scheme_type

Definition at line 277 of file alignment_utils.h.

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

typedef AlignmentStrings<AlignerType,PipelineType> nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::strings_type

Definition at line 276 of file alignment_utils.h.

Constructor & Destructor Documentation

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::AlignmentStreamBase ( const PipelineType  _pipeline, const aligner_type  _aligner, const ParamsPOD  _params  )

inline

constructor

Definition at line 296 of file alignment_utils.h.

Member Function Documentation

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const aligner_type& nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::aligner ( ) const

inline

get the aligner

Definition at line 305 of file alignment_utils.h.

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::load_strings ( const uint32  i, const uint32  window_begin, const uint32  window_end, const context_type *  context, strings_type *  strings  ) const

inline

initialize the strings corresponding to the i-th context

Parameters

i	problem index
window_begin	pattern window to load
window_end	pattern window to load
context	initialized context
strings	output strings

Definition at line 331 of file alignment_utils.h.

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::pattern_length ( const uint32  i, const context_type *  context  ) const

inline

return the pattern length

Definition at line 310 of file alignment_utils.h.

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::text_length ( const uint32  i, const context_type *  context  ) const

inline

return the text length

Definition at line 318 of file alignment_utils.h.

Member Data Documentation

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

aligner_type nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::m_aligner

the aligner

Definition at line 343 of file alignment_utils.h.

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

ParamsPOD nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::m_params

global parameters

Definition at line 344 of file alignment_utils.h.

template<AlignmentStreamType TYPE, typename AlignerType, typename PipelineType>

PipelineType nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::m_pipeline

the pipeline object

Definition at line 342 of file alignment_utils.h.

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

• E:/git/nvbio/nvBowtie/bowtie2/cuda/alignment_utils.h