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

queues	scoring queues
read_index	index of this read
selector	input/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_index

output 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.

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

• E:/git/nvbio/nvBowtie/bowtie2/cuda/scoring_queues.h
• E:/git/nvbio/nvBowtie/bowtie2/cuda/scoring_queues_inl.h