String Sets

Detailed Description

This module defines various types of string sets which vary for the internal representation. For a deeper explanation, see the string_page page.

Modules
	Private

Classes
struct	nvbio::Infix< StringType, CoordType >
struct	nvbio::InfixSet< SequenceType, InfixIterator >
struct	nvbio::Prefix< StringType, CoordType >
struct	nvbio::PrefixSet< SequenceType, PrefixIterator >
struct	nvbio::uniform_seeds_functor< index_type >
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::Suffix< StringType, CoordType >
struct	nvbio::SuffixSet< SequenceType, SuffixIterator >

Typedefs
typedef uint32_2	nvbio::string_infix_coord_type
typedef uint64_2	nvbio::long_string_infix_coord_type
typedef uint32_4	nvbio::string_set_infix_coord_type
typedef uint64_4	nvbio::long_string_set_infix_coord_type
typedef uint32	nvbio::string_prefix_coord_type
typedef uint64	nvbio::long_string_prefix_coord_type
typedef uint32_2	nvbio::string_set_prefix_coord_type
typedef uint64_2	nvbio::long_string_set_prefix_coord_type
typedef uint32	nvbio::string_suffix_coord_type
typedef uint64	nvbio::long_string_suffix_coord_type
typedef uint32_2	nvbio::string_set_suffix_coord_type
typedef uint64_2	nvbio::long_string_set_suffix_coord_type

Functions
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix < StringType, CoordType >	nvbio::make_infix (const StringType string, const CoordType coords)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::infix_begin (const uint32_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::infix_end (const uint32_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::length (const uint32_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	nvbio::infix_begin (const uint64_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	nvbio::infix_end (const uint64_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	nvbio::length (const uint64_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::infix_begin (const uint32_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::infix_end (const uint32_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::length (const uint32_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	nvbio::infix_begin (const uint64_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	nvbio::infix_end (const uint64_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	nvbio::length (const uint64_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::string_id (const uint32_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	nvbio::string_id (const uint64_4 &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix < StringType, CoordType > ::index_type	nvbio::infix_begin (const Infix< StringType, CoordType > &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix < StringType, CoordType > ::index_type	nvbio::infix_end (const Infix< StringType, CoordType > &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::string_id (const InfixCore< StringType, CoordType, 4u > &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::length (const Infix< StringType, CoordType > &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Prefix < StringType, CoordType >	nvbio::make_prefix (const StringType string, const CoordType coords)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::string_id (const PrefixCore< StringType, CoordType, 2u > &prefix)
template<typename StringType , typename CoordType , uint32 CoordDim>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::length (const PrefixCore< StringType, CoordType, CoordDim > &prefix)
template<typename index_type , typename seed_functor , typename index_vector_type >
index_type	nvbio::enumerate_string_seeds (const index_type string_len, const seed_functor seeder, index_vector_type &indices)
template<typename string_set_type , typename seed_functor , typename index_vector_type >
uint64	nvbio::enumerate_string_set_seeds (const string_set_type string_set, const seed_functor seeder, index_vector_type &indices)
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 StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Suffix < StringType, CoordType >	nvbio::make_suffix (const StringType string, const CoordType coords)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::string_id (const SuffixCore< StringType, CoordType, 2u > &suffix)
template<typename StringType , typename CoordType , uint32 CoordDim>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::length (const SuffixCore< StringType, CoordType, CoordDim > &suffix)
template<typename string_set_type >
int32	nvbio::compare_suffixes (const string_set_type string_set, const uint2 suffix1, const uint2 suffix2)
template<typename StringIterator , typename OffsetIterator >
ConcatenatedStringSet < StringIterator, OffsetIterator >	make_concatenated_string_set (const uint32 size, const StringIterator string, const OffsetIterator offsets)
template<typename StringIterator , typename RangeIterator >
SparseStringSet < StringIterator, RangeIterator >	make_sparse_string_set (const uint32 size, const StringIterator string, const RangeIterator offsets)

Typedef Documentation

typedef uint64_2 nvbio::long_string_infix_coord_type

64-bit string infix coordinates type

Definition at line 47 of file infix.h.

typedef uint64 nvbio::long_string_prefix_coord_type

64-bit string prefix coordinates type

Definition at line 47 of file prefix.h.

typedef uint64_4 nvbio::long_string_set_infix_coord_type

64-bit string-set infix coordinates type

Definition at line 55 of file infix.h.

typedef uint64_2 nvbio::long_string_set_prefix_coord_type

64-bit string-set prefix coordinates type

Definition at line 55 of file prefix.h.

typedef uint64_2 nvbio::long_string_set_suffix_coord_type

64-bit string-set suffix coordinates type

Definition at line 55 of file suffix.h.

typedef uint64 nvbio::long_string_suffix_coord_type

64-bit string suffix coordinates type

Definition at line 47 of file suffix.h.

typedef uint32_2 nvbio::string_infix_coord_type

32-bit string infix coordinates type

Definition at line 43 of file infix.h.

typedef uint32 nvbio::string_prefix_coord_type

32-bit string prefix coordinates type

Definition at line 43 of file prefix.h.

typedef uint32_4 nvbio::string_set_infix_coord_type

32-bit string-set infix coordinates type

Definition at line 51 of file infix.h.

typedef uint32_2 nvbio::string_set_prefix_coord_type

32-bit string-set prefix coordinates type

Definition at line 51 of file prefix.h.

typedef uint32_2 nvbio::string_set_suffix_coord_type

32-bit string-set suffix coordinates type

Definition at line 51 of file suffix.h.

typedef uint32 nvbio::string_suffix_coord_type

32-bit string suffix coordinates type

Definition at line 43 of file suffix.h.

Function Documentation

template<typename string_set_type >

int32 nvbio::compare_suffixes	(	const string_set_type	string_set,
		const uint2	suffix1,
		const uint2	suffix2
	)

compare string-set suffixes

Definition at line 495 of file suffix.h.

template<typename InStringSet , typename StringIterator , typename OffsetIterator >

void nvbio::cuda::copy	(	const InStringSet &	in_string_set,
		ConcatenatedStringSet< StringIterator, OffsetIterator > &	out_string_set
	)

copy a generic string set into a concatenated one

Parameters

in_string_set	input string set
out_string_set	output string set

Definition at line 2128 of file string_set_inl.h.

template<typename InStringSet , typename StringIterator , typename LengthIterator >

void nvbio::cuda::copy	(	const InStringSet &	in_string_set,
		StridedStringSet< StringIterator, LengthIterator > &	out_string_set
	)

copy a generic string set into a strided one

Parameters

in_string_set	input string set
out_string_set	output string set

Definition at line 2146 of file string_set_inl.h.

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
	)

copy a generic string set into a strided-packed one

Parameters

in_string_set	input string set
out_string_set	output string set

Definition at line 2167 of file string_set_inl.h.

template<typename InStringSet , typename StringIterator , typename OffsetIterator >

void nvbio::copy	(	const InStringSet &	in_string_set,
		ConcatenatedStringSet< StringIterator, OffsetIterator > &	out_string_set
	)

copy a generic string set into a concatenated one

Parameters

in_string_set	input string set
out_string_set	output string set

Definition at line 2128 of file string_set_inl.h.

template<typename InStringSet , typename StringIterator , typename LengthIterator >

void nvbio::copy	(	const InStringSet &	in_string_set,
		StridedStringSet< StringIterator, LengthIterator > &	out_string_set
	)

copy a generic string set into a strided one

Parameters

in_string_set	input string set
out_string_set	output string set

Definition at line 2146 of file string_set_inl.h.

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
	)

copy a generic string set into a strided-packed one

Parameters

in_string_set	input string set
out_string_set	output string set

Definition at line 2167 of file string_set_inl.h.

template<typename index_type , typename seed_functor , typename index_vector_type >

index_type nvbio::enumerate_string_seeds	(	const index_type	string_len,
		const seed_functor	seeder,
		index_vector_type &	indices
	)

extract a set of seed coordinates out of a string, according to a given seeding functor

Template Parameters

index_type	the type of string indices: uint32 or uint64
seed_functor	a class providing the following interface: struct seed_functor { typedef uint32 argument_type; typedef uint32 result_type; // return the number of seeds produced for a given string length uint32 operator() (const uint32 length) const; // return the coordinate of the i-th seed produced for a given string length uint2 seed(const uint32 length, const uint32 i) const; };
index_vector_type	a dynamic vector of uint2 coordinates

Parameters

seeder	the seeding functor
indices	the vector of output uint32 or uint2 indices: in the first case, only the starting seed coordinates will be retained

Definition at line 167 of file seeds_inl.h.

template<typename string_set_type , typename seed_functor , typename index_vector_type >

uint64 nvbio::enumerate_string_set_seeds	(	const string_set_type	string_set,
		const seed_functor	seeder,
		index_vector_type &	indices
	)

extract a set of seed coordinates out of a string-set, according to a given seeding functor

Template Parameters

string_set_type	the string-set type
seed_functor	a Seeding Functor
index_vector_type	a dynamic vector of uint2 coordinates

Parameters

string_set	the string set to seed
seeder	the seeding functor
indices	the vector of output uint2 or uint4 indices: in the first case, only the starting seed coordinates will be retained

Definition at line 193 of file seeds_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::infix_begin

(

const uint32_2 &

infix)

return the string begin of a given infix

Definition at line 430 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::infix_begin

(

const uint64_2 &

infix)

return the string begin of a given infix

Definition at line 445 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::infix_begin

(

const uint32_4 &

infix)

return the string begin of a given infix

Definition at line 460 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::infix_begin

(

const uint64_4 &

infix)

return the string begin of a given infix

Definition at line 475 of file infix.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix<StringType,CoordType>::index_type nvbio::infix_begin

(

const Infix< StringType, CoordType > &

infix)

return the string begin of a given infix

Definition at line 501 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::infix_end

(

const uint32_2 &

infix)

return the string begin of a given infix

Definition at line 435 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::infix_end

(

const uint64_2 &

infix)

return the string begin of a given infix

Definition at line 450 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::infix_end

(

const uint32_4 &

infix)

return the string begin of a given infix

Definition at line 465 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::infix_end

(

const uint64_4 &

infix)

return the string begin of a given infix

Definition at line 480 of file infix.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix<StringType,CoordType>::index_type nvbio::infix_end

(

const Infix< StringType, CoordType > &

infix)

return the string end of a given infix

Definition at line 507 of file infix.h.

template<typename StringType , typename CoordType , uint32 CoordDim>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::length

(

const PrefixCore< StringType, CoordType, CoordDim > &

prefix)

return the length of a given prefix

Definition at line 419 of file prefix.h.

template<typename StringType , typename CoordType , uint32 CoordDim>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::length

(

const SuffixCore< StringType, CoordType, CoordDim > &

suffix)

return the length of a given suffix

Definition at line 421 of file suffix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::length

(

const uint32_2 &

infix)

return the length a given infix

Definition at line 440 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::length

(

const uint64_2 &

infix)

return the length a given infix

Definition at line 455 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::length

(

const uint32_4 &

infix)

return the length a given infix

Definition at line 470 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::length

(

const uint64_4 &

infix)

return the length a given infix

Definition at line 485 of file infix.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::length

(

const Infix< StringType, CoordType > &

infix)

return the length a given infix

Definition at line 519 of file infix.h.

template<typename StringIterator , typename OffsetIterator >

ConcatenatedStringSet< StringIterator, OffsetIterator > make_concatenated_string_set ( const uint32  size, const StringIterator  string, const OffsetIterator  offsets  )

related

A utility function to make a ConcatenatedStringSet

Definition at line 566 of file string_set.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix<StringType,CoordType> nvbio::make_infix	(	const StringType	string,
		const CoordType	coords
	)

make an infix, i.e. a substring of a given string

Template Parameters

StringType	the underlying string type
CoordType	the coordinates type, either string_infix_coord_type or string_set_infix_coord_type

Parameters

string	the underlying string object
coords	the infix coordinates

Definition at line 302 of file infix.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Prefix<StringType,CoordType> nvbio::make_prefix	(	const StringType	string,
		const CoordType	coords
	)

make a prefix, i.e. a substring of a given string

Template Parameters

StringType	the underlying string type
CoordType	the coordinates type, either string_prefix_coord_type or string_set_prefix_coord_type

Parameters

string	the underlying string object
coords	the prefix coordinates

Definition at line 284 of file prefix.h.

template<typename StringIterator , typename RangeIterator >

SparseStringSet< StringIterator, RangeIterator > make_sparse_string_set ( const uint32  size, const StringIterator  string, const RangeIterator  offsets  )

related

A utility function to make a SparseStringSet

Definition at line 699 of file string_set.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Suffix<StringType,CoordType> nvbio::make_suffix	(	const StringType	string,
		const CoordType	coords
	)

make a suffix, i.e. a substring of a given string

Template Parameters

StringType	the underlying string type
CoordType	the coordinates type, either string_suffix_coord_type or string_set_suffix_coord_type

Parameters

string	the underlying string object
coords	the suffix coordinates

Definition at line 286 of file suffix.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator!=	(	const StringSetIterator< StringSet > &	it1,
		const StringSetIterator< StringSet > &	it2
	)

operator!=

Definition at line 393 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator<StringSet> nvbio::operator+	(	const StringSetIterator< StringSet > &	it,
		const int32	d
	)

operator+

Definition at line 292 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator<StringSet>& nvbio::operator+=	(	StringSetIterator< StringSet > &	it,
		const int32	d
	)

operator+=

Definition at line 314 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator<StringSet>::difference_type nvbio::operator-	(	const StringSetIterator< StringSet > &	it1,
		const StringSetIterator< StringSet > &	it2
	)

difference operator

Definition at line 281 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator<StringSet> nvbio::operator-	(	const StringSetIterator< StringSet > &	it,
		const int32	d
	)

operator-

Definition at line 303 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator<StringSet>& nvbio::operator-=	(	StringSetIterator< StringSet > &	it,
		const int32	d
	)

operator-=

Definition at line 326 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator<	(	const StringSetIterator< StringSet > &	it1,
		const StringSetIterator< StringSet > &	it2
	)

operator<

Definition at line 338 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator<=	(	const StringSetIterator< StringSet > &	it1,
		const StringSetIterator< StringSet > &	it2
	)

operator<=

Definition at line 360 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator==	(	const StringSetIterator< StringSet > &	it1,
		const StringSetIterator< StringSet > &	it2
	)

operator==

Definition at line 382 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator>	(	const StringSetIterator< StringSet > &	it1,
		const StringSetIterator< StringSet > &	it2
	)

operator>

Definition at line 349 of file string_set.h.

template<typename StringSet >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator>=	(	const StringSetIterator< StringSet > &	it1,
		const StringSetIterator< StringSet > &	it2
	)

operator>=

Definition at line 371 of file string_set.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::string_id

(

const PrefixCore< StringType, CoordType, 2u > &

prefix)

return the string index of a given prefix

Definition at line 413 of file prefix.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::string_id

(

const SuffixCore< StringType, CoordType, 2u > &

suffix)

return the string index of a given suffix

Definition at line 415 of file suffix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::string_id

(

const uint32_4 &

infix)

return the string index of a given infix

Definition at line 490 of file infix.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::string_id

(

const uint64_4 &

infix)

return the string index of a given infix

Definition at line 495 of file infix.h.

template<typename StringType , typename CoordType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::string_id

(

const InfixCore< StringType, CoordType, 4u > &

infix)

return the string index of a given infix

Definition at line 513 of file infix.h.