AbstractBank Class Reference

Abstract implementation of IBank for factorizing common behavior. More...

#include <AbstractBank.hpp>

Inheritance diagram for AbstractBank:

Public Member Functions
	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 IBank
virtual std::string	getId ()=0
virtual tools::dp::Iterator< Sequence > *	iterator ()=0
virtual void	insert (const Sequence &item)=0
virtual u_int64_t	getSize ()=0
virtual void	estimate (u_int64_t &number, u_int64_t &totalSize, u_int64_t &maxSize)=0
Public Member Functions inherited from Iterable< Sequence >
void	iterate (Functor f)
virtual int64_t	getNbItems ()=0
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)
virtual void	flush ()=0
Public Member Functions inherited from SmartPointer
void	use ()
void	forget ()

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

Detailed Description

Abstract implementation of IBank for factorizing common behavior.

This abstract implementation of the IBank interface provides some methods having the same behavior for most implementations.

Note that it implements the system::ISmartPointer interface as well, so it can be used as a smart pointer.

Constructor & Destructor Documentation

AbstractBank ( )

inline

Constructor.

Member Function Documentation

int64_t estimateNbItems ( )

inlinevirtual

Shortcut to 'estimate' method.

Returns

estimation of the number of sequences

Implements IBank.

Reimplemented in BankDelegate.

int64_t estimateNbItemsBanki ( int  i )

inlinevirtual

In case of a composite bank,

Returns

estimation of the number of sequences of sub bank i

Implements IBank.

Reimplemented in BankDelegate, and BankComposite.

u_int64_t estimateSequencesSize ( )

inlinevirtual

Shortcut to 'estimate' method.

Returns

estimation of the size of sequences

Implements IBank.

Reimplemented in BankDelegate.

void finalize ( )

inlinevirtual

Method that may be called when the bank is done. It is called by BankFasta destructor for instance. It will close fclose() or something equivalent. You don't need to call this function yourself.

Implements IBank.

Reimplemented in BankFasta.

const std::vector<IBank*> getBanks ( ) const

inlinevirtual

Return the vector of sub IBank objects (in case of bank composite), or a vector containing only the bank itself

Returns

the IBank objects.

Implements IBank.

Reimplemented in BankComposite.

size_t getCompositionNb ( )

inlinevirtual

In case of a composite bank, return the number of sub banks.

Returns

number of sub banks.

Implements IBank.

Reimplemented in BankComposite.

u_int64_t getEstimateThreshold ( )

inlinevirtual

Returns

the number of sequences read from the bank for computing estimated information

Implements IBank.

Reimplemented in BankDelegate.

std::string getIdNb ( int  i )

inlinevirtual

In case of a composite bank, return the id of bank i

Returns

id of sub bank i

Implements IBank.

Reimplemented in BankComposite, and BankDelegate.

void remove ( )

inlinevirtual

Remove physically the bank. This method will have non-empty implementation for banks using file system for instance.

Implements IBank.

Reimplemented in BankComposite, BankAlbum, and BankBinary.

void setEstimateThreshold ( u_int64_t  nbSeq )

inlinevirtual

Set the number of sequences read from the bank for computing estimated information

Parameters

[in]

nbSeq

: the number of sequences to be read.

Implements IBank.

Reimplemented in BankDelegate.

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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/bank/impl/AbstractBank.hpp