gatb.core-API-0.0.0: CountProcessorDump< span

#include <CountProcessorDump.hpp>

Inheritance diagram for CountProcessorDump:

Public Types
typedef Kmer< span >::Count	Count

Public Types inherited from CountProcessorAbstract< span >
typedef Kmer< span >::Type	Type

Public Types inherited from ICountProcessor< span >
typedef kmer::impl::Kmer< span >::Type	Type

Public Member Functions
	CountProcessorDump (tools::storage::impl::Group &group, size_t kmerSize, system::ISynchronizer synchronizer=0, tools::storage::impl::Partition< Count > solidCounts=0, size_t nbPartsPerPass=0)

virtual	~CountProcessorDump ()

void	begin (const Configuration &config)

CountProcessorAbstract< span > *	clone ()

void	finishClones (std::vector< ICountProcessor< span > * > &clones)

void	beginPart (size_t passId, size_t partId, size_t cacheSize, const char *name)

void	endPart (size_t passId, size_t partId)

bool	process (size_t partId, const Type &kmer, const CountVector &count, CountNumber sum)

tools::misc::impl::Properties	getProperties () const

tools::storage::impl::Partition< Count > *	getSolidCounts ()

u_int64_t	getNbItems ()

Public Member Functions inherited from CountProcessorAbstract< span >
	CountProcessorAbstract (const std::string &name="processor")

virtual	~CountProcessorAbstract ()

virtual void	end ()

virtual void	beginPass (size_t passId)

virtual void	endPass (size_t passId)

virtual std::string	getName () const

virtual void	setName (const std::string &name)

virtual std::vector< ICountProcessor< span > * >	getInstances () const

Public Member Functions inherited from ICountProcessor< span >
template<typename T >
T *	get () const

Public Member Functions inherited from SmartPointer
void	use ()

void	forget ()

Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()

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

virtual	~SmartPointer ()

Detailed Description

template<size_t span = KMER_DEFAULT_SPAN>
class gatb::core::kmer::impl::CountProcessorDump

The CountProcessorDump implementation dumps kmers on file system through a Partition object.

The number of partitions is not known at creation and is received through a call to the 'begin' method; there, the number of partitions is used to configure the Partition object.

A clone instance is dedicated to one partition, which is configured when the method 'beginPart' is called on a cloned instance.

The CountProcessorDump implementation is likely to be used in a CountProcessorChain, like this : solidity -> dump. It allows to dump on file system only solid kmers.

Member Typedef Documentation

typedef Kmer::Count Count

Shortcuts.

Constructor & Destructor Documentation

CountProcessorDump	(	tools::storage::impl::Group &	group,
		size_t	kmerSize,
		system::ISynchronizer *	synchronizer = `0`,
		tools::storage::impl::Partition< Count > *	solidCounts = `0`,
		size_t	nbPartsPerPass = `0`
	)

inline

Constructor

virtual ~CountProcessorDump ( )

inlinevirtual

Destructor

Member Function Documentation

void begin ( const Configuration & config )

inlinevirtual

Called just before the mainloop of SortingCountAlgorithm.

Parameters

[in] config : configuration of the SortingCountAlgorithm.

Reimplemented from CountProcessorAbstract.

void beginPart	(	size_t	passId,
		size_t	partId,
		size_t	cacheSize,
		const char *	name
	)

inlinevirtual

Called at the beginning of a new kmers partition processing.

Parameters

[in]	passId	: index of the current pass in the SortingCountAlgorithm.
[in]	passId	: index of the current kmers partition in the SortingCountAlgorithm.
[in]	cacheSize	: memory size used for the current kmers partition
[in]	name	: class name of the child PartitionsCommand class.

Reimplemented from CountProcessorAbstract.

CountProcessorAbstract* clone ( )

inlinevirtual

Implements ICountProcessor.

void endPart	(	size_t	passId,
		size_t	partId
	)

inlinevirtual

Called at the end of a new kmers partition processing.

Parameters

[in]	passId	: index of the current pass in the SortingCountAlgorithm.
[in]	passId	: index of the current kmers partition in the SortingCountAlgorithm.

Reimplemented from CountProcessorAbstract.

void finishClones ( std::vector< ICountProcessor * > & clones )

inlinevirtual

Called when N partitions have been processed through N clones. This should be the last time these clones are available before being deleted. It can be the opportunity to the prototype instance to gather information from the clones.

Parameters

[in] clones : the N cloned instances

Reimplemented from CountProcessorAbstract.

u_int64_t getNbItems ( )

inline

Get the number of items.

Returns: the total number of items in the partition.

tools::misc::impl::Properties getProperties ( ) const

inlinevirtual

Get some properties about the count processor.

Returns: properties.

Reimplemented from CountProcessorAbstract.

tools::storage::impl::Partition<Count>* getSolidCounts ( )

inline

Get the partition of counts.

Returns: the Partition<Count> instance

bool process	(	size_t	partId,
		const Type &	kmer,
		const CountVector &	count,
		CountNumber	sum
	)

inlinevirtual

Notification that a [kmer,counts] is available and can be handled by the count processor.

Parameters

[in]	partId	: index of the current partition
[in]	kmer	: kmer for which we are receiving counts
[in]	count	: vector of counts of the kmer, one count per bank
[in]	sum	: sum of the occurrences for all bank.

Reimplemented from CountProcessorAbstract.

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

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

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

template<size_t span = KMER_DEFAULT_SPAN> class gatb::core::kmer::impl::CountProcessorDump< span >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

template<size_t span = KMER_DEFAULT_SPAN>
class gatb::core::kmer::impl::CountProcessorDump< span >