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nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType > Struct Template Reference

Detailed description

template< typename ScoringQueuesType>
struct nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >

A reference to the collection of hits bound to a given read (in the input queue)

Definition at line 448 of file scoring_queues.h.

#include <scoring_queues.h>

Public Types

typedef
ScoringQueuesType::read_hits_index_type 
read_hits_index_type
 
typedef
ScoringQueuesType::hits_storage_type 
hits_storage_type
 
typedef HitReference
< hits_storage_type
reference
 

Public Methods

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE ReadHitsReference (ScoringQueuesType &queues, const uint32 read_index=uint32(-1))
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
bind (const uint32 read_index)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
size () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE HitReference
< hits_storage_type
operator[] (const uint32 i) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE packed_read 
read_info () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
slot (const uint32 i) const
 

Member Typedef Documentation

template<typename ScoringQueuesType>
typedef ScoringQueuesType::hits_storage_type nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::hits_storage_type

Definition at line 451 of file scoring_queues.h.

template<typename ScoringQueuesType>
typedef ScoringQueuesType::read_hits_index_type nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::read_hits_index_type

Definition at line 450 of file scoring_queues.h.

template<typename ScoringQueuesType>
typedef HitReference<hits_storage_type> nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::reference

Definition at line 452 of file scoring_queues.h.

Constructor & Destructor Documentation

template<typename ScoringQueuesType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::ReadHitsReference ( ScoringQueuesType &  queues,
const uint32  read_index = uint32(-1) 
)

constructor

Parameters
queuesscoring queues
read_indexindex of this read
selectorinput/output queue selector

Definition at line 228 of file scoring_queues_inl.h.

Member Function Documentation

template<typename ScoringQueuesType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::bind ( const uint32  read_index)

bind this object to a given index

Parameters
read_indexoutput index of this read

Definition at line 270 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE ReadHitsReference< ScoringQueuesType >::reference nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::operator[] ( const uint32  i) const

return the i-th element NOTE: this method is only valid after the i-th hit has been bound.

Definition at line 248 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE packed_read nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::read_info ( ) const

access the packed_read info in the selected queue

Definition at line 279 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::size ( void  ) const

size of the hits vector

Definition at line 237 of file scoring_queues_inl.h.

template<typename ScoringQueuesType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::ReadHitsReference< ScoringQueuesType >::slot ( const uint32  i) const

return the slot where the i-th element is stored

Definition at line 260 of file scoring_queues_inl.h.


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