bvector<> serialization

Collaboration diagram for bvector<> serialization:

Data Structures
class	bm::serializer< BV >
	Bit-vector serialization class. More...
class	bm::deseriaizer_base< DEC, BLOCK_IDX >
	Base deserialization class. More...
class	bm::deserializer< BV, DEC >
	Deserializer for bit-vector. More...
class	bm::serial_stream_iterator< DEC, BLOCK_IDX >
	Serialization stream iterator. More...
class	bm::operation_deserializer< BV >
	Deserializer, performs logical operations between bit-vector and serialized bit-vector. More...

Enumerations
enum	bm::serialization_flags { bm::BM_NO_BYTE_ORDER = 1 , bm::BM_NO_GAP_LENGTH = (1 << 1) }
	Bit mask flags for serialization algorithm <> More...

Functions
template<class BV >
size_t	bm::serialize (const BV &bv, unsigned char *buf, bm::word_t *temp_block=0, unsigned serialization_flags=0)
	Saves bitvector into memory. More...
template<class BV >
size_t	bm::serialize (BV &bv, unsigned char *buf, unsigned serialization_flags=0)
	Saves bitvector into memory. Allocates temporary memory block for bvector. More...
template<class BV >
size_t	bm::deserialize (BV &bv, const unsigned char *buf, bm::word_t *temp_block=0, const bm::bv_ref_vector< BV > *ref_vect=0)
	Bitvector deserialization from a memory BLOB. More...
template<class BV >
void	bm::deserialize_range (BV &bv, const unsigned char *buf, typename BV::size_type from, typename BV::size_type to, const bm::bv_ref_vector< BV > *ref_vect=0)
	Bitvector range deserialization from a memory BLOB. More...

Detailed Description

Serialization for bvector<> container

Enumeration Type Documentation

serialization_flags

enum bm::serialization_flags

Bit mask flags for serialization algorithm <>

Enumerator
BM_NO_BYTE_ORDER	save no byte-order info (save some space)
BM_NO_GAP_LENGTH	save no GAP info (save some space)

Definition at line 3026 of file bmserial.h.

Function Documentation

deserialize()

template<class BV >

size_t bm::deserialize	(	BV &	bv,
		const unsigned char *	buf,
		bm::word_t *	temp_block = 0,
		const bm::bv_ref_vector< BV > *	ref_vect = 0
	)

Bitvector deserialization from a memory BLOB.

Parameters

bv	- target bvector
buf	- pointer on memory which keeps serialized bvector
temp_block	- pointer on temporary block, if NULL bvector allocates own.
ref_vect	- [in] optional pointer to a list of reference vectors used for XOR compression.

Returns

Number of bytes consumed by deserializer.

Function deserializes bitvector from memory block containig results of previous serialization. Function does not remove bits which are currently set. Effectively it is OR logical operation between the target bit-vector and serialized one.

See also

deserialize_range

Examples

inv_list.cpp, sample14.cpp, sample4.cpp, xsample01.cpp, and xsample07a.cpp.

Definition at line 3140 of file bmserial.h.

References bm::BigEndian, BM_ASSERT, bm::BM_HM_NO_BO, bm::globals< T >::byte_order(), bm::deserializer< BV, DEC >::deserialize(), bm::decoder_base::get_8(), bm::LittleEndian, and bm::deserializer< BV, DEC >::set_ref_vectors().

Referenced by assign_to_best_cluster(), assign_to_best_cluster_union(), compute_group(), compute_seq_group_union(), convert_bv2bvs(), bm::compressed_collection_deserializer< CBC >::deserialize(), CSequenceColl::deserialize_k_mers(), CSeqClusters::elect_leaders(), main(), and read_bvector().

deserialize_range()

template<class BV >

void bm::deserialize_range	(	BV &	bv,
		const unsigned char *	buf,
		typename BV::size_type	from,
		typename BV::size_type	to,
		const bm::bv_ref_vector< BV > *	ref_vect = 0
	)

Bitvector range deserialization from a memory BLOB.

Parameters

bv	- target bvector
buf	- pointer on memory which keeps serialized bvector
from	- bit-vector index to deserialize from
to	- bit-vector index to deserialize to
ref_vect	- [in] optional pointer to a list of reference vectors used for XOR compression.

Function deserializes bitvector from memory block containig results of previous serialization. Function does not remove bits which are currently set. Effectively it is OR logical operation between the target bit-vector and serialized one.

See also

deserialize

Examples

sample22.cpp.

Definition at line 3203 of file bmserial.h.

References bm::BigEndian, BM_ASSERT, bm::BM_HM_NO_BO, bm::globals< T >::byte_order(), bm::deserializer< BV, DEC >::deserialize(), bm::decoder_base::get_8(), bm::LittleEndian, bm::deserializer< BV, DEC >::set_range(), and bm::deserializer< BV, DEC >::set_ref_vectors().

Referenced by bm::operation_deserializer< BV >::deserialize_range(), and main().

serialize() [1/2]

template<class BV >

size_t bm::serialize	(	BV &	bv,
		unsigned char *	buf,
		unsigned	serialization_flags = 0
	)

Saves bitvector into memory. Allocates temporary memory block for bvector.

Parameters

bv	- source bvecor
buf	- pointer on target memory area. No range checking in the function. It is responsibility of programmer to allocate sufficient amount of memory using information from calc_stat function.
serialization_flags	Flags controlling serilization (bit-mask) (use OR-ed serialization flags)

Definition at line 3108 of file bmserial.h.

References bm::serialize().

serialize() [2/2]

template<class BV >

size_t bm::serialize	(	const BV &	bv,
		unsigned char *	buf,
		bm::word_t *	temp_block = 0,
		unsigned	serialization_flags = 0
	)

Saves bitvector into memory.

Function serializes content of the bitvector into memory. Serialization adaptively uses compression(variation of GAP encoding) when it is benefitial.

Parameters

bv	- source bvecor
buf	- pointer on target memory area. No range checking in the function. It is responsibility of programmer to allocate sufficient amount of memory using information from calc_stat function.
temp_block	- pointer on temporary memory block. Cannot be 0; If you want to save memory across multiple bvectors allocate temporary block using allocate_tempblock and pass it to serialize. (Serialize does not deallocate temp_block.)
serialization_flags	Flags controlling serilization (bit-mask) (use OR-ed serialization flags)

Returns

Size of serialization block.

See also

calc_stat, serialization_flags

Serialization format:

| HEADER | BLOCKS |

Header structure:
  BYTE : Serialization header (bit mask of BM_HM_*)
  BYTE : Byte order ( 0 - Big Endian, 1 - Little Endian)
  INT16: Reserved (0)
  INT16: Reserved Flags (0)

Definition at line 3074 of file bmserial.h.

References bm::BM_NO_BYTE_ORDER, bm::BM_NO_GAP_LENGTH, bm::serializer< BV >::byte_order_serialization(), bm::serializer< BV >::gap_length_serialization(), and bm::serializer< BV >::serialize().

Referenced by bm::serializer< BV >::optimize_serialize_destroy(), bm::serialize(), and bm::serializer< BV >::serialize().