BankKmers Class Reference

Bank whose sequences are all the possible kmers of a kmer model. More...

#include <BankKmers.hpp>

Inheritance diagram for BankKmers:

Public Member Functions
	BankKmers (size_t kmerSize)
std::string	getId ()
int64_t	getNbItems ()
void	estimate (u_int64_t &number, u_int64_t &totalSize, u_int64_t &maxSize)
void	insert (const bank::Sequence &item)
void	flush ()
u_int64_t	getSize ()
tools::dp::Iterator< bank::Sequence > *	iterator ()
Public Member Functions inherited from AbstractBank
	AbstractBank ()
std::string	getIdNb (int i)
int64_t	estimateNbItemsBanki (int i)
const std::vector< IBank * >	getBanks () const
int64_t	estimateNbItems ()
u_int64_t	estimateSequencesSize ()
u_int64_t	getEstimateThreshold ()
void	setEstimateThreshold (u_int64_t nbSeq)
void	remove ()
void	finalize ()
size_t	getCompositionNb ()
Public Member Functions inherited from Iterable< Sequence >
void	iterate (Functor f)
virtual Sequence *	getItems (Sequence *&buffer)
virtual size_t	getItems (Sequence *&buffer, size_t start, size_t nb)
Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()
Public Member Functions inherited from Bag< Sequence >
virtual void	insert (const Sequence &item)=0
virtual void	insert (const std::vector< Sequence > &items, size_t length=0)
virtual void	insert (const Sequence *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

Bank whose sequences are all the possible kmers of a kmer model.

For instance, for a kmer size of 3, the bank will iterate the 3^4 possible kmers.

Constructor & Destructor Documentation

BankKmers ( size_t  kmerSize )

inline

Constructor.

Parameters

[in]

kmerSize

: size of the kmers to be iterated.

Member Function Documentation

void estimate ( u_int64_t &  number, u_int64_t &  totalSize, u_int64_t &  maxSize  )

inlinevirtual

Give an estimation of sequences information in the bank.

Parameters

[out]	number	: sequences number
[out]	totalSize	: sequences size (in bytes)
[out]	maxSize	: max size size (in bytes)

Implements IBank.

void flush ( )

inlinevirtual

Flush the current content. May be useful for implementation that uses a cache.

Implements Bag< Sequence >.

std::string getId ( )

inlinevirtual

Get an unique identifier for the bank (could be the URI of a FASTA file for instance).

Returns

the identifier

Implements IBank.

int64_t getNbItems ( )

inlinevirtual

Return the number of items. If a specific implementation doesn't know the value, it should return -1 by convention.

Returns

the number of items if known, -1 otherwise.

Implements Iterable< Sequence >.

u_int64_t getSize ( )

inlinevirtual

Return the size of the bank (comments + data)

The returned value may be an approximation in some case. For instance, if we use a zipped bank, an implementation may be not able to give accurate answer to the size of the original file.

Returns

the bank size in bytes.

Implements IBank.

void insert ( const bank::Sequence &  item )

inlinevirtual

Insert an item into the bag.

Parameters

[in]

item

: the item to be inserted.

Implements IBank.

tools::dp::Iterator<bank::Sequence>* iterator ( )

inlinevirtual

Create an iterator for the given Iterable instance.

Returns

the new iterator.

Implements IBank.

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

• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/kmer/impl/BankKmers.hpp