Search Toolkit Book for bm::sparse_vector_deserializer

sparse vector de-serializer More...

#include <util/bitset/bmsparsevec_serial.h>

Inheritance diagram for bm::sparse_vector_deserializer< SV >:

Collaboration diagram for bm::sparse_vector_deserializer< SV >:

Public Types
typedef SV::bvector_type	bvector_type

typedef const bvector_type *	bvector_type_const_ptr

typedef bvector_type *	bvector_type_ptr

typedef SV::value_type	value_type

typedef SV::size_type	size_type

typedef bvector_type::allocator_type::allocator_pool_type	allocator_pool_type

typedef bm::serializer< bvector_type >::bv_ref_vector_type	bv_ref_vector_type

Public Member Functions
	sparse_vector_deserializer ()

	~sparse_vector_deserializer ()

void	set_finalization (bm::finalization is_final)
	Set deserialization finalization to force deserialized vectors into READONLY (or READWRITE) mode. More...

void	set_xor_ref (bv_ref_vector_type *bv_ref_ptr)
	Set external XOR reference vectors (data frame referenece vectors) More...

void	deserialize (SV &sv, const unsigned char *buf, bool clear_sv=true)

void	deserialize_range (SV &sv, const unsigned char *buf, size_type from, size_type to, bool clear_sv=true)

void	deserialize (SV &sv, const unsigned char *buf, size_type from, size_type to)

void	deserialize (SV &sv, const unsigned char *buf, const bvector_type &mask_bv)

void	deserialize_structure (SV &sv, const unsigned char *buf)

Protected Types
typedef bvector_type::allocator_type	alloc_type

Protected Member Functions
unsigned	load_header (bm::decoder &dec, SV &sv, unsigned char &matr_s_ser)
	Deserialize header/version and other common info. More...

void	deserialize_sv (SV &sv, const unsigned char buf, const bvector_type mask_bv, bool clear_sv)

void	deserialize_planes (SV &sv, unsigned planes, const unsigned char buf, const bvector_type mask_bv=0)
	deserialize bit-vector planes More...

void	load_planes_off_table (const unsigned char *buf, bm::decoder &dec, unsigned planes)
	load offset table More...

int	load_null_plane (SV &sv, int planes, const unsigned char buf, const bvector_type mask_bv)
	load NULL bit-plane (returns new planes count) More...

void	load_remap (SV &sv, const unsigned char *remap_buf_ptr)
	load string remap dict More...

void	setup_xor_compression ()
	setup deserializers More...

void	clear_xor_compression ()
	unset XOR compression vectors More...

Static Protected Member Functions
static void	raise_invalid_header ()
	throw error on incorrect deserialization More...

static void	raise_invalid_64bit ()
	throw error on incorrect deserialization More...

static void	raise_invalid_bitdepth ()
	throw error on incorrect deserialization More...

static void	raise_invalid_format ()
	throw error on incorrect deserialization More...

static void	raise_missing_remap_matrix ()
	throw error on incorrect deserialization More...

Protected Attributes
bm::finalization	is_final_ = bm::finalization::UNDEFINED

const unsigned char *	remap_buf_ptr_ = 0

alloc_type	alloc_

bm::word_t *	temp_block_ = 0

allocator_pool_type	pool_

bvector_type	plane_digest_bv_

bm::id64_t	sv_size_

bm::id64_t	digest_offset_

bm::deserializer< bvector_type, bm::decoder >	deserial_

bm::operation_deserializer< bvector_type >	op_deserial_

bm::rank_compressor< bvector_type >	rsc_compressor_

bvector_type	not_null_mask_bv_

bvector_type	rsc_mask_bv_

bm::heap_vector< size_t, alloc_type, true >	off_vect_

bm::heap_vector< unsigned, alloc_type, true >	off32_vect_

rlen_vector_type	remap_rlen_vect_

bv_ref_vector_type	bv_ref_
	reference vector More...

bv_ref_vector_type *	bv_ref_ptr_ = 0
	external ref bit-vect More...

bool	idx_range_set_ = false

size_type	idx_range_from_

size_type	idx_range_to_

Private Types
typedef bm::heap_vector< unsigned, alloc_type, true >	rlen_vector_type

Private Member Functions
	sparse_vector_deserializer (const sparse_vector_deserializer &)=delete

sparse_vector_deserializer &	operator= (const sparse_vector_deserializer &)=delete

Detailed Description

template<typename SV>
class bm::sparse_vector_deserializer< SV >

sparse vector de-serializer

Definition at line 326 of file bmsparsevec_serial.h.

Member Typedef Documentation

◆ alloc_type

template<typename SV >

typedef bvector_type::allocator_type bm::sparse_vector_deserializer< SV >::alloc_type

protected

Definition at line 427 of file bmsparsevec_serial.h.

◆ allocator_pool_type

template<typename SV >

typedef bvector_type::allocator_type::allocator_pool_type bm::sparse_vector_deserializer< SV >::allocator_pool_type

Definition at line 334 of file bmsparsevec_serial.h.

◆ bv_ref_vector_type

template<typename SV >

typedef bm::serializer<bvector_type>::bv_ref_vector_type bm::sparse_vector_deserializer< SV >::bv_ref_vector_type

Definition at line 335 of file bmsparsevec_serial.h.

◆ bvector_type

template<typename SV >

typedef SV::bvector_type bm::sparse_vector_deserializer< SV >::bvector_type

Definition at line 329 of file bmsparsevec_serial.h.

◆ bvector_type_const_ptr

template<typename SV >

typedef const bvector_type* bm::sparse_vector_deserializer< SV >::bvector_type_const_ptr

Definition at line 330 of file bmsparsevec_serial.h.

◆ bvector_type_ptr

template<typename SV >

typedef bvector_type* bm::sparse_vector_deserializer< SV >::bvector_type_ptr

Definition at line 331 of file bmsparsevec_serial.h.

◆ rlen_vector_type

template<typename SV >

typedef bm::heap_vector<unsigned, alloc_type, true> bm::sparse_vector_deserializer< SV >::rlen_vector_type

private

Definition at line 478 of file bmsparsevec_serial.h.

◆ size_type

template<typename SV >

typedef SV::size_type bm::sparse_vector_deserializer< SV >::size_type

Definition at line 333 of file bmsparsevec_serial.h.

◆ value_type

template<typename SV >

typedef SV::value_type bm::sparse_vector_deserializer< SV >::value_type

Definition at line 332 of file bmsparsevec_serial.h.

Constructor & Destructor Documentation

◆ sparse_vector_deserializer() [1/2]

template<typename SV >

bm::sparse_vector_deserializer< SV >::sparse_vector_deserializer

Definition at line 1156 of file bmsparsevec_serial.h.

◆ ~sparse_vector_deserializer()

template<typename SV >

bm::sparse_vector_deserializer< SV >::~sparse_vector_deserializer

Definition at line 1166 of file bmsparsevec_serial.h.

◆ sparse_vector_deserializer() [2/2]

template<typename SV >

bm::sparse_vector_deserializer< SV >::sparse_vector_deserializer ( const sparse_vector_deserializer< SV > & )

privatedelete

Member Function Documentation

◆ clear_xor_compression()

template<typename SV >

void bm::sparse_vector_deserializer< SV >::clear_xor_compression

protected

unset XOR compression vectors

Definition at line 1195 of file bmsparsevec_serial.h.

◆ deserialize() [1/3]

template<typename SV >

void bm::sparse_vector_deserializer< SV >::deserialize	(	SV &	sv,
		const unsigned char *	buf,
		bool	clear_sv = `true`
	)

Deserialize sparse vector

Parameters

sv	- [out] target sparse vector to populate
buf	- input BLOB source memory pointer
clear_sv	- if true clears the target vector (sv)

See also: deserialize_range

Definition at line 1222 of file bmsparsevec_serial.h.

References BM_ASSERT, and buf.

Referenced by CSeqDictionary< Alphabet >::Deserialize(), CDataFrame< MAX_SIZE >::Deserialize(), NVcfUtil::DeserializeColumn(), CVcfHistogram::Init(), bm::sparse_vector_deserialize(), test_chr21(), TestCompressSparseVectorSerial(), TestSignedSparseVectorSerial(), TestSparseVectorSerial(), TestSparseVectorSerialization2(), TestStrSparseVector_FindEq(), TestStrSparseVectorSerial(), CVCFVariantsBase::x_DeserializeDescr_All(), CVCFVariantsBase::x_DeserializeDescr_Range(), and CVCFVariantsBase::x_DeserializeIndexVectors().

◆ deserialize() [2/3]

template<typename SV >

void bm::sparse_vector_deserializer< SV >::deserialize	(	SV &	sv,
		const unsigned char *	buf,
		const bvector_type &	mask_bv
	)

inline

Deserialize sparse vector using address mask vector Address mask defines (by set bits) which vector elements to be extracted from the compressed BLOB

Parameters

sv	- [out] target sparse vector to populate
buf	- source memory pointer
mask_bv	- AND mask bit-vector (address gather vector)

Definition at line 409 of file bmsparsevec_serial.h.

◆ deserialize() [3/3]

template<typename SV >

void bm::sparse_vector_deserializer< SV >::deserialize	(	SV &	sv,
		const unsigned char *	buf,
		size_type	from,
		size_type	to
	)

inline

Better use deserialize_range()

See also: deserialize_range

Definition at line 392 of file bmsparsevec_serial.h.

◆ deserialize_planes()

template<typename SV >

void bm::sparse_vector_deserializer< SV >::deserialize_planes	(	SV &	sv,
		unsigned	planes,
		const unsigned char *	buf,
		const bvector_type *	mask_bv = `0`
	)

protected

deserialize bit-vector planes

Definition at line 1472 of file bmsparsevec_serial.h.

References BM_ASSERT, buf, i, offset, and bm::READONLY.

◆ deserialize_range()

template<typename SV >

void bm::sparse_vector_deserializer< SV >::deserialize_range	(	SV &	sv,
		const unsigned char *	buf,
		size_type	from,
		size_type	to,
		bool	clear_sv = `true`
	)

Deserialize sparse vector for the range [from, to]

Parameters

sv	- [out] target sparse vector to populate
buf	- input BLOB source memory pointer
from	- start vector index for deserialization range
to	- end vector index for deserialization range
clear_sv	- if true clears the target vector

Definition at line 1261 of file bmsparsevec_serial.h.

References buf.

Referenced by bm::sparse_vector_deserializer< bm::str_sparse_vector >::deserialize(), TestCompressSparseVectorSerial(), TestSparseVectorSerialization2(), TestStrSparseVectorSerial(), and CVCFVariantsBase::x_DeserializeDescr_Range().

◆ deserialize_structure()

template<typename SV >

void bm::sparse_vector_deserializer< SV >::deserialize_structure	(	SV &	sv,
		const unsigned char *	buf
	)

Load serialization descriptor, create vectors but DO NOT perform full deserialization

Parameters

sv	- [out] target sparse vector to populate
buf	- source memory pointer

Definition at line 1235 of file bmsparsevec_serial.h.

References BM_ASSERT, buf, and i.

Referenced by test_chr21(), test_str_sv_des_fnc(), TestSparseVectorSerialization2(), TestStrSparseVectorSerial(), VCF_des_test(), CVCFVariantsBase::x_DeserializeDescr_All(), and CVCFVariantsBase::x_DeserializeDescr_Range().

◆ deserialize_sv()

template<typename SV >

void bm::sparse_vector_deserializer< SV >::deserialize_sv	(	SV &	sv,
		const unsigned char *	buf,
		const bvector_type *	mask_bv,
		bool	clear_sv
	)

protected

Definition at line 1333 of file bmsparsevec_serial.h.

References BM_ASSERT, and buf.

Referenced by bm::sparse_vector_deserializer< bm::str_sparse_vector >::deserialize().

◆ load_header()

template<typename SV >

unsigned bm::sparse_vector_deserializer< SV >::load_header	(	bm::decoder &	dec,
		SV &	sv,
		unsigned char &	matr_s_ser
	)

protected

Deserialize header/version and other common info.

Returns: number of bit-planes

Definition at line 1417 of file bmsparsevec_serial.h.

References BM_ASSERT, bm::decoder::get_64(), bm::decoder_base::get_8(), and rapidjson::value.

◆ load_null_plane()

template<typename SV >

int bm::sparse_vector_deserializer< SV >::load_null_plane	(	SV &	sv,
		int	planes,
		const unsigned char *	buf,
		const bvector_type *	mask_bv
	)

protected

load NULL bit-plane (returns new planes count)

Definition at line 1559 of file bmsparsevec_serial.h.

References BM_ASSERT, buf, i, offset, and bm::READONLY.

◆ load_planes_off_table()

template<typename SV >

void bm::sparse_vector_deserializer< SV >::load_planes_off_table	(	const unsigned char *	buf,
		bm::decoder &	dec,
		unsigned	planes
	)

protected

load offset table

Definition at line 1631 of file bmsparsevec_serial.h.

References bm::bit_in< TDecoder >::bic_decode_u32_cm(), BM_ASSERT, buf, bm::decoder::get_32(), bm::decoder::get_64(), bm::decoder_base::get_8(), i, and offset.

◆ load_remap()

template<typename SV >

void bm::sparse_vector_deserializer< SV >::load_remap	(	SV &	sv,
		const unsigned char *	remap_buf_ptr
	)

protected

load string remap dict

Definition at line 1703 of file bmsparsevec_serial.h.

References BM_ASSERT, BMRESTRICT, cnt, bm::bit_in< TDecoder >::gamma(), bm::decoder::get_16(), bm::decoder::get_32(), bm::decoder::get_64(), bm::decoder_base::get_8(), bm::decoder_base::memcpy(), r(), and row.

◆ operator=()

template<typename SV >

sparse_vector_deserializer& bm::sparse_vector_deserializer< SV >::operator= ( const sparse_vector_deserializer< SV > & )

privatedelete