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

Detailed description

template< typename AlignerType, typename PipelineType>
struct nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >

A scoring stream, fetching the input hits to score from the hit queue indexed by the input sorting order, and assigning them their score and sink attributes.

Definition at line 54 of file score_all_inl.h.

#include <score_all_inl.h>

Inheritance diagram for nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >:
nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType >

Public Types

typedef AlignmentStreamBase
< SCORE_STREAM, AlignerType,
PipelineType > 
base_type
 
typedef base_type::context_type context_type
 
typedef base_type::scheme_type scheme_type
 
- Public Types inherited from nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType >
typedef AlignmentStrings
< AlignerType, PipelineType > 
strings_type
 
typedef PipelineType::scheme_type scheme_type
 
typedef AlignerType aligner_type
 

Public Methods

 AllScoreStream (const uint32 _band_len, const PipelineType _pipeline, const AlignerType _aligner, const ParamsPOD _params, const uint32 _buffer_offset, const uint32 _buffer_size, uint32 *_counter)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
max_pattern_length () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
max_text_length () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
size () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
init_context (const uint32 i, context_type *context) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
output (const uint32 i, const context_type *context) const
 
- Public Methods inherited from nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType >
 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

const uint32 m_band_len
 
const uint32 m_buffer_offset
 
const uint32 m_buffer_size
 
uint32m_counter
 
- Public Members inherited from nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType >
PipelineType m_pipeline
 the pipeline object More...
 
aligner_type m_aligner
 the aligner More...
 
ParamsPOD m_params
 global parameters More...
 

Member Typedef Documentation

template<typename AlignerType , typename PipelineType >
typedef AlignmentStreamBase<SCORE_STREAM,AlignerType,PipelineType> nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::base_type

Definition at line 56 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
typedef base_type::context_type nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::context_type

Definition at line 57 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
typedef base_type::scheme_type nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::scheme_type

Definition at line 58 of file score_all_inl.h.

Constructor & Destructor Documentation

template<typename AlignerType , typename PipelineType >
nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::AllScoreStream ( const uint32  _band_len,
const PipelineType  _pipeline,
const AlignerType  _aligner,
const ParamsPOD  _params,
const uint32  _buffer_offset,
const uint32  _buffer_size,
uint32 _counter 
)
inline

constructor

Parameters
_band_leneffective band length; NOTE: this value must match the template BAND_LEN parameter used for instantiating aln::BatchedBandedAlignmentScore.
_pipelinethe pipeline object
_alignerthe aligner object

Definition at line 70 of file score_all_inl.h.

Member Function Documentation

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::init_context ( const uint32  i,
context_type context 
) const
inline

initialize the i-th context

Definition at line 101 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::max_pattern_length ( ) const
inline

return the maximum pattern length

Definition at line 86 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::max_text_length ( ) const
inline

return the maximum text length

Definition at line 91 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::output ( const uint32  i,
const context_type context 
) const
inline

handle the output

Definition at line 134 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::size ( void  ) const
inline

return the stream size

Definition at line 96 of file score_all_inl.h.

Member Data Documentation

template<typename AlignerType , typename PipelineType >
const uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::m_band_len

Definition at line 158 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
const uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::m_buffer_offset

Definition at line 159 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
const uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::m_buffer_size

Definition at line 160 of file score_all_inl.h.

template<typename AlignerType , typename PipelineType >
uint32* nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::m_counter

Definition at line 161 of file score_all_inl.h.


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