gatb.core-API-0.0.0: BloomNeighborCoherent< Item

Bloom filter implementation with cache consideration. More...

#include <Bloom.hpp>

Inheritance diagram for BloomNeighborCoherent< Item >:

Public Member Functions
	BloomNeighborCoherent (u_int64_t tai_bloom, size_t kmersize, size_t nbHash=4, size_t block_nbits=12)

void	insert (const Item &item)

std::string	getName () const

u_int64_t	getBitSize ()

bool	contains (const Item &item)

std::bitset< 4 >	contains4 (const Item &item, bool right)

std::bitset< 8 >	contains8 (const Item &item)

Public Member Functions inherited from BloomCacheCoherent< Item >
	BloomCacheCoherent (u_int64_t tai_bloom, size_t nbHash=4, size_t block_nbits=12)

unsigned long	weight ()

Public Member Functions inherited from Bloom< Item >
	Bloom (u_int64_t tai_bloom, size_t nbHash=4)

void	flush ()

void	dump (const char *filename)

Public Member Functions inherited from BloomContainer< Item >
	BloomContainer (u_int64_t tai_bloom, size_t nbHash=4)

virtual	~BloomContainer ()

size_t	getNbHash () const

virtual u_int8_t *&	getArray ()

virtual u_int64_t	getSize ()

Public Member Functions inherited from IBloom< Item >
virtual	~IBloom ()

Public Member Functions inherited from Container< Item >
virtual	~Container ()

Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()

Public Member Functions inherited from Bag< Item >
virtual void	insert (const std::vector< Item > &items, size_t length=0)

virtual void	insert (const Item *items, size_t length)

Public Member Functions inherited from SmartPointer
void	use ()

void	forget ()

Additional Inherited Members
Protected Member Functions inherited from SmartPointer
	SmartPointer ()

virtual	~SmartPointer ()

Detailed Description

template<typename Item>
class gatb::core::tools::collections::impl::BloomNeighborCoherent< Item >

Bloom filter implementation with cache consideration.

This implementation improve memory locality in the Bloom filter between a kmer and its neighbors. This means that this implementation should be used only with Item being a kmer.

In particular, it implements contains4 and contains8 in a clever way.

Constructor & Destructor Documentation

BloomNeighborCoherent	(	u_int64_t	tai_bloom,
		size_t	kmersize,
		size_t	nbHash = `4`,
		size_t	block_nbits = `12`
	)

inline

Constructor.

Parameters

[in]	tai_bloom	: size (in bits) of the bloom filter.
[in]	kmersize	: kmer size
[in]	nbHash	: number of hash functions to use
[in]	block_nbits	: size of the block (actual 2^nbits)

Member Function Documentation

bool contains ( const Item & item )

inlinevirtual

Reimplemented from BloomCacheCoherent< Item >.

std::bitset<4> contains4	(	const Item &	item,
		bool	right
	)

inlinevirtual

Tells whether the 4 neighbors of the given item are in the Bloom filter. The 4 neighbors are computed from the given item by adding successively nucleotides 'A', 'C', 'T' and 'G' Note: some implementation may not provide this service.

Parameters

[in]	item	: starting item from which neighbors are computed.
[in]	right	: if true, successors are computed, otherwise predecessors are computed.

Returns: a bitset with a boolean for the 'contains' status of each neighbor

Reimplemented from BloomContainer< Item >.

std::bitset<8> contains8 ( const Item & item )

inlinevirtual

Tells whether the 8 neighbors of the given item are in the Bloom filter. A default implementation may be two calls to contains4 with right==true and right==left and by concatenating the two bitsets. Note: some implementation may not provide this service.

Parameters

[in] item : starting item from which neighbors are computed.