BankStrings Class Reference

IBank defined by constant strings. More...

#include <BankStrings.hpp>

Inheritance diagram for BankStrings:

Public Member Functions
std::string	getId ()
	BankStrings (const std::vector< std::string > &sequencesData)
	BankStrings (const char *sequencesData[], size_t nb)
	BankStrings (const char *seq,...)
tools::dp::Iterator< Sequence > *	iterator ()
int64_t	getNbItems ()
void	insert (const Sequence &item)
void	flush ()
u_int64_t	getSize ()
void	estimate (u_int64_t &number, u_int64_t &totalSize, u_int64_t &maxSize)
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 ()

Static Public Member Functions
static const char *	name ()

Protected Attributes
std::vector< Sequence >	_sequences

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

Detailed Description

IBank defined by constant strings.

This class allows to define banks with some nucleotides strings.

Instances of this class are located in memory only.

This class is mainly used for tests.

Constructor & Destructor Documentation

BankStrings ( const std::vector< std::string > &  sequencesData )

inline

Constructor.

BankStrings ( const char *  sequencesData[], size_t  nb  )

inline

Constructor.

BankStrings ( const char *  seq,   ...  )

inline

Constructor.

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

Constructor.

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 Sequence &  item )

inlinevirtual

Insert an item into the bag.

Parameters

[in]

item

: the item to be inserted.

Implements IBank.

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

inlinevirtual

Create an iterator for the given Iterable instance.

Returns

the new iterator.

Implements IBank.

static const char* name ( )

inlinestatic

Returns the name of the bank format.

Member Data Documentation

std::vector<Sequence> _sequences

protected

Sequences.

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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/BankStrings.hpp