nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type > Struct Template Reference

Detailed description

template< typename ConfigType, uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type>
struct nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >

Definition at line 353 of file sufsort_inl.h.

#include <sufsort_inl.h>

Public Types
typedef std::iterator_traits < storage_type >::value_type	word_type
typedef ConfigType::string_set_handler	string_set_handler_type
typedef ConfigType::bucket_type	bucket_type
typedef ConfigType::suffix_bucketer	suffix_bucketer_type
typedef ConcatenatedStringSet < typename PackedStream < storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 >::iterator, uint64 * >	string_set_type

Static Public Methods
static uint32	max_subbucket_size (const thrust::host_vector< uint32 > &h_buckets, const uint64 max_super_block_size, const uint32 limit, LargeBWTStatus *status)
static void	build_subbuckets (const thrust::host_vector< uint32 > &h_buckets, thrust::host_vector< uint32 > &h_subbuckets, const uint64 max_super_block_size, const uint32 max_block_size)
template<typename output_handler >
static LargeBWTStatus	enact (const string_set_type string_set, output_handler &output, BWTParams *params)

Member Typedef Documentation

template<typename ConfigType , uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type >

typedef ConfigType::bucket_type nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >::bucket_type

Definition at line 357 of file sufsort_inl.h.

template<typename ConfigType , uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type >

typedef ConfigType::string_set_handler nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >::string_set_handler_type

Definition at line 356 of file sufsort_inl.h.

template<typename ConfigType , uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type >

typedef ConcatenatedStringSet< typename PackedStream<storage_type,uint8,SYMBOL_SIZE,BIG_ENDIAN,uint64>::iterator, uint64*> nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >::string_set_type

Definition at line 362 of file sufsort_inl.h.

template<typename ConfigType , uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type >

typedef ConfigType::suffix_bucketer nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >::suffix_bucketer_type

Definition at line 358 of file sufsort_inl.h.

template<typename ConfigType , uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type >

typedef std::iterator_traits<storage_type>::value_type nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >::word_type

Definition at line 355 of file sufsort_inl.h.

Member Function Documentation

template<typename ConfigType , uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type >

static void nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >::build_subbuckets ( const thrust::host_vector< uint32 > &  h_buckets, thrust::host_vector< uint32 > &  h_subbuckets, const uint64  max_super_block_size, const uint32  max_block_size  )

inlinestatic

Definition at line 419 of file sufsort_inl.h.

template<typename ConfigType , uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type >

template<typename output_handler >

static LargeBWTStatus nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >::enact ( const string_set_type  string_set, output_handler &  output, BWTParams *  params  )

inlinestatic

Definition at line 470 of file sufsort_inl.h.

template<typename ConfigType , uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type >

static uint32 nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >::max_subbucket_size ( const thrust::host_vector< uint32 > &  h_buckets, const uint64  max_super_block_size, const uint32  limit, LargeBWTStatus *  status  )

inlinestatic

Definition at line 366 of file sufsort_inl.h.

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

• E:/git/nvbio/nvbio/sufsort/sufsort_inl.h