#include <counting_bloom_filter.hpp>

Public Member Functions
	CountingBloomFilter ()

	CountingBloomFilter (size_t bytes, unsigned hash_num, std::string hash_fn="")

	CountingBloomFilter (const std::string &path)

	CountingBloomFilter (const CountingBloomFilter &)=delete

	CountingBloomFilter (CountingBloomFilter &&)=delete

CountingBloomFilter &	operator= (const CountingBloomFilter &)=delete

CountingBloomFilter &	operator= (CountingBloomFilter &&)=delete

void	insert (const uint64_t *hashes, T n=1)

void	insert (const std::vector< uint64_t > &hashes, T n=1)

void	remove (const uint64_t *hashes)

void	remove (const std::vector< uint64_t > &hashes)

void	clear (const uint64_t *hashes)

void	clear (const std::vector< uint64_t > &hashes)

T	contains (const uint64_t *hashes) const

T	contains (const std::vector< uint64_t > &hashes) const

T	contains_insert (const uint64_t *hashes, T n=1)

T	contains_insert (const std::vector< uint64_t > &hashes, T n=1)

T	insert_contains (const uint64_t *hashes, T n=1)

T	insert_contains (const std::vector< uint64_t > &hashes, T n=1)

T	insert_thresh_contains (const uint64_t *hashes, T threshold)

T	insert_thresh_contains (const std::vector< uint64_t > &hashes, const T threshold)

T	contains_insert_thresh (const uint64_t *hashes, T threshold)

T	contains_insert_thresh (const std::vector< uint64_t > &hashes, const T threshold)

size_t	get_bytes () const

uint64_t	get_pop_cnt (T threshold=1) const

double	get_occupancy (T threshold=1) const

unsigned	get_hash_num () const

double	get_fpr (T threshold=1) const

const std::string &	get_hash_fn () const

void	save (const std::string &path)

Static Public Member Functions
static bool	is_bloom_file (const std::string &path)

Friends
class	KmerCountingBloomFilter< T >

Detailed Description

template<typename T>
class btllib::CountingBloomFilter< T >

Counting Bloom filter data structure. Provides CountingBloomFilter8, CountingBloomFilter16, and CountingBloomFilter32 classes with corresponding bit-size counters.

Constructor & Destructor Documentation

◆ CountingBloomFilter() [1/3]

template<typename T >

btllib::CountingBloomFilter< T >::CountingBloomFilter ( )

inline

Construct a dummy k-mer Bloom filter (e.g. as a default argument).

◆ CountingBloomFilter() [2/3]

template<typename T >

btllib::CountingBloomFilter< T >::CountingBloomFilter	(	size_t	bytes,
		unsigned	hash_num,
		std::string	hash_fn = "" )

inline

Construct an empty Counting Bloom filter of given size.

Parameters

bytes	Filter size in bytes.
hash_num	Number of hash values per element.
hash_fn	Name of the hash function used. Used for metadata. Optional.

◆ CountingBloomFilter() [3/3]

template<typename T >

btllib::CountingBloomFilter< T >::CountingBloomFilter ( const std::string & path )

inlineexplicit

Load a Counting Bloom filter from a file.

Parameters

path	Filepath to load from.

Member Function Documentation

◆ clear() [1/2]

template<typename T >

void btllib::CountingBloomFilter< T >::clear ( const std::vector< uint64_t > & hashes )

inline

Set the count of an element to zero.

Parameters

hashes Integer vector of the element's hash values.

◆ clear() [2/2]

template<typename T >

void btllib::CountingBloomFilter< T >::clear ( const uint64_t * hashes )

Set the count of an element to zero.

Parameters

hashes Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.

◆ contains() [1/2]

template<typename T >

T btllib::CountingBloomFilter< T >::contains ( const std::vector< uint64_t > & hashes ) const

inline

Get the count of an element.

Parameters

hashes Integer vector of the element's hash values.

Returns: The count of the queried element.

◆ contains() [2/2]

template<typename T >

T btllib::CountingBloomFilter< T >::contains ( const uint64_t * hashes ) const

inline

Get the count of an element.

Parameters

hashes Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.

Returns: The count of the queried element.

◆ contains_insert() [1/2]

template<typename T >

T btllib::CountingBloomFilter< T >::contains_insert	(	const std::vector< uint64_t > &	hashes,
		T	n = 1 )

inline

Get the count of an element and then increment the count.

Parameters

hashes	Integer vector of the element's hash values.
n	Increment value

Returns: The count of the queried element before insertion.

◆ contains_insert() [2/2]

template<typename T >

T btllib::CountingBloomFilter< T >::contains_insert	(	const uint64_t *	hashes,
		T	n = 1 )

inline

Get the count of an element and then increment the count.

Parameters

hashes	Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.
n	Increment value

Returns: The count of the queried element before insertion.

◆ contains_insert_thresh() [1/2]

template<typename T >

T btllib::CountingBloomFilter< T >::contains_insert_thresh	(	const std::vector< uint64_t > &	hashes,
		const T	threshold )

inline

Get the count of an element and then increment the count if it's not above the threshold.

Parameters

hashes	Integer vector of the element's hash values.
threshold	The threshold.

Returns: The count of the queried element before insertion.

◆ contains_insert_thresh() [2/2]

template<typename T >

T btllib::CountingBloomFilter< T >::contains_insert_thresh	(	const uint64_t *	hashes,
		T	threshold )

inline

Get the count of an element and then increment the count if it's not above the threshold.

Parameters

hashes	Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.
threshold	The threshold.

Returns: The count of the queried element before insertion.

◆ get_bytes()

template<typename T >

size_t btllib::CountingBloomFilter< T >::get_bytes ( ) const

inline

Get filter size in bytes.

◆ get_fpr()

template<typename T >

double btllib::CountingBloomFilter< T >::get_fpr ( T threshold = 1 ) const

inline

Get the query false positive rate for elements with count >= threshold.

Parameters

threshold The threshold.

Returns: The false positive rate.

◆ get_hash_fn()

template<typename T >

const std::string & btllib::CountingBloomFilter< T >::get_hash_fn ( ) const

inline

Get the name of the hash function used.

◆ get_hash_num()

template<typename T >

unsigned btllib::CountingBloomFilter< T >::get_hash_num ( ) const

inline

Get the number of hash values per element.

◆ get_occupancy()

template<typename T >

double btllib::CountingBloomFilter< T >::get_occupancy ( T threshold = 1 ) const

inline

Get the fraction of the filter occupied by >= threshold counters.

◆ get_pop_cnt()

template<typename T >

uint64_t btllib::CountingBloomFilter< T >::get_pop_cnt ( T threshold = 1 ) const

inline

Get population count, i.e. the number of counters >= threshold in the filter.

◆ insert() [1/2]

template<typename T >

void btllib::CountingBloomFilter< T >::insert	(	const std::vector< uint64_t > &	hashes,
		T	n = 1 )

inline

Insert an element.

Parameters

hashes	Integer vector of the element's hash values.
n	Increment value

◆ insert() [2/2]

template<typename T >

void btllib::CountingBloomFilter< T >::insert	(	const uint64_t *	hashes,
		T	n = 1 )

inline

Insert an element.

Parameters

hashes	Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.
n	Increment value

◆ insert_contains() [1/2]

template<typename T >

T btllib::CountingBloomFilter< T >::insert_contains	(	const std::vector< uint64_t > &	hashes,
		T	n = 1 )

inline

Increment an element's count and then return the count.

Parameters

hashes	Integer vector of the element's hash values.
n	Increment value

Returns: The count of the queried element after insertion.

◆ insert_contains() [2/2]

template<typename T >

T btllib::CountingBloomFilter< T >::insert_contains	(	const uint64_t *	hashes,
		T	n = 1 )

inline

Increment an element's count and then return the count.

Parameters

hashes	Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.
n	Increment value

Returns: The count of the queried element after insertion.

◆ insert_thresh_contains() [1/2]

template<typename T >

T btllib::CountingBloomFilter< T >::insert_thresh_contains	(	const std::vector< uint64_t > &	hashes,
		const T	threshold )

inline

Increment an element's count if it's not above the threshold and then return the count.

Parameters

hashes	Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.
threshold	The threshold.

Returns: The count of the queried element after insertion.

◆ insert_thresh_contains() [2/2]

template<typename T >

T btllib::CountingBloomFilter< T >::insert_thresh_contains	(	const uint64_t *	hashes,
		T	threshold )

inline

Increment an element's count if it's not above the threshold and then return the count.

Parameters

hashes	Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.
threshold	The threshold.

Returns: The count of the queried element after insertion.

◆ is_bloom_file()

template<typename T >

static bool btllib::CountingBloomFilter< T >::is_bloom_file ( const std::string & path )

inlinestatic

Check whether the file at the given path is a saved Counting Bloom filter.

Parameters

path	Filepath to check.

◆ remove() [1/2]

template<typename T >

void btllib::CountingBloomFilter< T >::remove ( const std::vector< uint64_t > & hashes )

inline

Delete an element.

Parameters

hashes Integer vector of the element's hash values.

◆ remove() [2/2]

template<typename T >

void btllib::CountingBloomFilter< T >::remove ( const uint64_t * hashes )

inline

Delete an element.

Parameters

hashes Integer array of the element's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.

◆ save()

template<typename T >

void btllib::CountingBloomFilter< T >::save ( const std::string & path )

inline

Save the Bloom filter to a file that can be loaded in the future.

Parameters

path	Filepath to store filter at.

The documentation for this class was generated from the following files:

include/btllib/counting_bloom_filter.hpp
include/btllib/counting_bloom_filter-inl.hpp

Public Member Functions

Static Public Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ CountingBloomFilter() [1/3]

◆ CountingBloomFilter() [2/3]

◆ CountingBloomFilter() [3/3]

Member Function Documentation

◆ clear() [1/2]

◆ clear() [2/2]

◆ contains() [1/2]

◆ contains() [2/2]

◆ contains_insert() [1/2]

◆ contains_insert() [2/2]

◆ contains_insert_thresh() [1/2]

◆ contains_insert_thresh() [2/2]

◆ get_bytes()

◆ get_fpr()

◆ get_hash_fn()

◆ get_hash_num()

◆ get_occupancy()

◆ get_pop_cnt()

◆ insert() [1/2]

◆ insert() [2/2]

◆ insert_contains() [1/2]

◆ insert_contains() [2/2]

◆ insert_thresh_contains() [1/2]

◆ insert_thresh_contains() [2/2]

◆ is_bloom_file()

◆ remove() [1/2]

◆ remove() [2/2]

◆ save()