NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Public Types | Public Methods | Public Members | Static Public Members | List of all members
nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > > Struct Template Reference

Detailed description

template< uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type>
struct nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >

A SetBWTOutputHandler class to output a string-set BWT to a (potentially packed) host string

Definition at line 189 of file sufsort_utils.h.

#include <sufsort_utils.h>

Inheritance diagram for nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >:
nvbio::SetBWTHandler

Public Types

typedef PackedStream
< word_type *, uint8,
SYMBOL_SIZE, BIG_ENDIAN,
uint64
OutputIterator
 

Public Methods

 HostBWTHandler (OutputIterator _output)
 
template<typename bwt_iterator >
void do_process (const uint32 n_suffixes, const bwt_iterator bwt)
 
void process (const uint32 n_suffixes, const uint32 bits_per_symbol, const uint32 *bwt, const uint32 n_dollars, const uint64 *dollar_pos, const uint64 *dollar_ids)
 
void process (const uint32 n_suffixes, const uint8 *bwt, const uint32 n_dollars, const uint64 *dollar_pos, const uint64 *dollar_ids)
 
- Public Methods inherited from nvbio::SetBWTHandler
virtual ~SetBWTHandler ()
 

Public Members

OutputIterator output
 
uint64 offset
 

Static Public Members

static const uint32 WORD_SIZE = uint32( 8u * sizeof(word_type) )
 
static const uint32 SYMBOLS_PER_WORD = WORD_SIZE / SYMBOL_SIZE
 

Member Typedef Documentation

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
typedef PackedStream<word_type*,uint8,SYMBOL_SIZE,BIG_ENDIAN,uint64> nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::OutputIterator

Definition at line 191 of file sufsort_utils.h.

Constructor & Destructor Documentation

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::HostBWTHandler ( OutputIterator  _output)
inline

constructor

Definition at line 199 of file sufsort_utils.h.

Member Function Documentation

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
template<typename bwt_iterator >
void nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::do_process ( const uint32  n_suffixes,
const bwt_iterator  bwt 
)
inline

process a batch of BWT symbols

Definition at line 204 of file sufsort_utils.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
void nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::process ( const uint32  n_suffixes,
const uint32  bits_per_symbol,
const uint32 bwt,
const uint32  n_dollars,
const uint64 dollar_pos,
const uint64 dollar_ids 
)
inlinevirtual

process a batch of BWT symbols

Reimplemented from nvbio::SetBWTHandler.

Definition at line 266 of file sufsort_utils.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
void nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::process ( const uint32  n_suffixes,
const uint8 bwt,
const uint32  n_dollars,
const uint64 dollar_pos,
const uint64 dollar_ids 
)
inlinevirtual

process a batch of BWT symbols

Reimplemented from nvbio::SetBWTHandler.

Definition at line 284 of file sufsort_utils.h.

Member Data Documentation

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
uint64 nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::offset

Definition at line 295 of file sufsort_utils.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
OutputIterator nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::output

Definition at line 294 of file sufsort_utils.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
const uint32 nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::SYMBOLS_PER_WORD = WORD_SIZE / SYMBOL_SIZE
static

Definition at line 194 of file sufsort_utils.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename word_type >
const uint32 nvbio::HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >::WORD_SIZE = uint32( 8u * sizeof(word_type) )
static

Definition at line 193 of file sufsort_utils.h.


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