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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
iproblem index
window_beginpattern window to load
window_endpattern window to load
contextinitialized context
stringsoutput 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.


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