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string_set.h File Reference
#include <nvbio/strings/string.h>
#include <nvbio/basic/packedstream.h>
#include <nvbio/basic/vector_view.h>
#include <nvbio/basic/strided_iterator.h>
#include <nvbio/basic/cached_iterator.h>
#include <nvbio/basic/iterator.h>
#include <nvbio/strings/string_set_inl.h>

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Classes

struct  nvbio::concatenated_string_set_tag
 
struct  nvbio::sparse_string_set_tag
 
struct  nvbio::strided_string_set_tag
 
struct  nvbio::strided_packed_string_set_tag
 
struct  nvbio::StringSetIterator< StringSetType >
 
struct  nvbio::ConcatenatedStringSet< StringIterator, OffsetIterator >
 
struct  nvbio::SparseStringSet< StringIterator, RangeIterator >
 
struct  nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >
 
struct  nvbio::StridedStringSet< StringIterator, LengthIterator >
 
struct  nvbio::string_set_length_functor< string_set_type >
 
struct  nvbio::CachedPackedConcatStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, value_type >
 
struct  nvbio::CachedPackedConcatStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint4 >
 
struct  nvbio::CachedPackedConcatStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint32 >
 
struct  nvbio::CachedPackedSparseStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, value_type >
 
struct  nvbio::CachedPackedSparseStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint4 >
 
struct  nvbio::CachedPackedSparseStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint32 >
 

Namespaces

 nvbio
 Define a vector_view POD type and plain_view() for std::vector.
 
 nvbio::cuda
 

Functions

template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
StringSetIterator< StringSet >
::difference_type 
nvbio::operator- (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
StringSetIterator< StringSet > 
nvbio::operator+ (const StringSetIterator< StringSet > &it, const int32 d)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
StringSetIterator< StringSet > 
nvbio::operator- (const StringSetIterator< StringSet > &it, const int32 d)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
StringSetIterator< StringSet > & 
nvbio::operator+= (StringSetIterator< StringSet > &it, const int32 d)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
StringSetIterator< StringSet > & 
nvbio::operator-= (StringSetIterator< StringSet > &it, const int32 d)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::operator< (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::operator> (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::operator<= (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::operator>= (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::operator== (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
 
template<typename StringSet >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::operator!= (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
 
template<typename InStringSet , typename StringIterator , typename OffsetIterator >
void nvbio::cuda::copy (const InStringSet &in_string_set, ConcatenatedStringSet< StringIterator, OffsetIterator > &out_string_set)
 
template<typename InStringSet , typename StringIterator , typename LengthIterator >
void nvbio::cuda::copy (const InStringSet &in_string_set, StridedStringSet< StringIterator, LengthIterator > &out_string_set)
 
template<typename InStringSet , typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >
void nvbio::cuda::copy (const InStringSet &in_string_set, StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator > &out_string_set)
 
template<typename InStringSet , typename StringIterator , typename OffsetIterator >
void nvbio::copy (const InStringSet &in_string_set, ConcatenatedStringSet< StringIterator, OffsetIterator > &out_string_set)
 
template<typename InStringSet , typename StringIterator , typename LengthIterator >
void nvbio::copy (const InStringSet &in_string_set, StridedStringSet< StringIterator, LengthIterator > &out_string_set)
 
template<typename InStringSet , typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >
void nvbio::copy (const InStringSet &in_string_set, StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator > &out_string_set)
 
template<typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >
CachedPackedSparseStringSet
< StreamIterator, SymbolType,
SYMBOL_SIZE_T, BIG_ENDIAN_T,
LengthIterator, typename
std::iterator_traits
< StreamIterator >::value_type >
::cached_string_set 
nvbio::make_cached_string_set (const SparseStringSet< PackedStream< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T >, LengthIterator > string_set)
 
template<typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >
CachedPackedConcatStringSet
< StreamIterator, SymbolType,
SYMBOL_SIZE_T, BIG_ENDIAN_T,
LengthIterator, typename
std::iterator_traits
< StreamIterator >::value_type >
::cached_string_set 
nvbio::make_cached_string_set (const ConcatenatedStringSet< PackedStream< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T >, LengthIterator > string_set)