NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Public Types | Public Methods | List of all members
nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType > Struct Template Reference
SeedHits

Detailed description

template< typename SeedHitDequeArrayType>
struct nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >

Implements a reference to a hit deque bound to a read. Provides methods for atomically allocating the deque's storage, as well as a deque and plain array interface.

Definition at line 57 of file seed_hit_deque_array.h.

#include <seed_hit_deque_array.h>

Public Types

typedef vector_view< SeedHit * > hit_vector_type
 
typedef priority_deque
< SeedHit, hit_vector_type,
hit_compare > 		hit_deque_type
 

Public Methods

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHitDequeReference (SeedHitDequeArrayType &deques, const uint32 read_id)
 
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE ~SeedHitDequeReference ()
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE SeedHit * 		alloc (const uint32 size)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		resize (const uint32 size)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 		size () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE SeedHit * 		get_data () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE float * 		get_probs () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		erase ()
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
hit_deque_type 		get_deque (bool build_heap=false) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		push (const SeedHit hit)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		pop_top ()
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		pop_bottom ()
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		pop ()
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE const
SeedHit & 		top () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE const
SeedHit & 		bottom () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE SeedHit & 		operator[] (const uint32 i)
 

Member Typedef Documentation

template<typename SeedHitDequeArrayType >
typedef priority_deque<SeedHit, hit_vector_type, hit_compare> nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::hit_deque_type

Definition at line 241 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
typedef vector_view<SeedHit*> nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::hit_vector_type

Definition at line 240 of file seed_hit_deque_array.h.

Constructor & Destructor Documentation

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::SeedHitDequeReference ( SeedHitDequeArrayType &  deques,
const uint32  read_id 
)
inline

constructor

Definition at line 246 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::~SeedHitDequeReference ( )
inline

destructor

Definition at line 254 of file seed_hit_deque_array.h.

Member Function Documentation

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHit* nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::alloc ( const uint32  size)
inline

allocate some storage for the deque bound to a given read

Definition at line 263 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const SeedHit& nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::bottom ( ) const
inline

bottom

Definition at line 334 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::erase ( )
inline

erase the set of hits bound to a read. NOTE: this method doesn't release the previously allocated memory!

Definition at line 299 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHit* nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::get_data ( ) const
inline

get the storage for the hit vector bound to a given read

Definition at line 288 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE hit_deque_type nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::get_deque ( bool  build_heap = false) const
inline

return the deque bound to a given read

Definition at line 304 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float* nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::get_probs ( ) const
inline

get the storage for the hit vector bound to a given read

Definition at line 293 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SeedHit& nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::operator[] ( const uint32  i)
inline

return the i-th seed-hit (unsorted)

Definition at line 339 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::pop ( void  )
inline

pop from the top

Definition at line 324 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::pop_bottom ( void  )
inline

pop from the front

Definition at line 319 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::pop_top ( void  )
inline

pop from the front

Definition at line 314 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::push ( const SeedHit  hit)
inline

push a seed-hit

Definition at line 309 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::resize ( const uint32  size)
inline

allocate some storage for the deque bound to a given read NOTE: this method doesn't expand or release the previously allocated memory!

Definition at line 274 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::size ( void  ) const
inline

get the size of the hit vector bound to a given read

Definition at line 283 of file seed_hit_deque_array.h.

template<typename SeedHitDequeArrayType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const SeedHit& nvbio::bowtie2::cuda::SeedHitDequeReference< SeedHitDequeArrayType >::top ( void  ) const
inline

top

Definition at line 329 of file seed_hit_deque_array.h.

The documentation for this struct was generated from the following file:
Generated on Wed Feb 25 2015 08:34:12 for NVBIO by   doxygen 1.8.4