gatb.core-API-0.0.0: CountProcessorChain< span

#include <CountProcessorChain.hpp>

Inheritance diagram for CountProcessorChain:

Public Member Functions
	CountProcessorChain (const std::vector< CountProcessor * > items, std::vector< bool > &solidVec)

	CountProcessorChain (CountProcessor *first,...)

virtual	~CountProcessorChain ()

void	begin (const Configuration &config)

void	end ()

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=0)

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

std::vector< CountProcessor * >	getInstances () const

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

virtual	~CountProcessorAbstract ()

virtual void	beginPass (size_t passId)

virtual void	endPass (size_t passId)

virtual std::string	getName () const

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

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 ()

Protected Member Functions
CountNumber	computeSum (const CountVector &count) const

Protected Member Functions inherited from SmartPointer
	SmartPointer ()

virtual	~SmartPointer ()

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

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

Detailed Description

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

The CountProcessorChain implementation allows to link several instances of ICountProcessor. When such an instance is called via 'process', the first item of the list is called via 'process'; if it returns true, the next item in the list is called and so on; if it returns false, the chain is stopped. This class is used for the definition of the "DSK" count processor (histogram -> solidity -> dump)

Constructor & Destructor Documentation

CountProcessorChain	(	const std::vector< CountProcessor * >	items,
		std::vector< bool > &	solidVec
	)

inline

Constructor.

CountProcessorChain	(	CountProcessor *	first,
			...
	)

inline

Constructor.

virtual ~CountProcessorChain ( )

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

Clone the instance. An instance can be cloned N times in order to use the cloned instance in one thread.

Returns: the cloned instance.

Implements ICountProcessor.

CountNumber computeSum ( const CountVector & count ) const

inlineprotected

void end ( )

inlinevirtual

Called just after the mainloop of SortingCountAlgorithm.

Reimplemented from CountProcessorAbstract.

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.

std::vector<CountProcessor*> getInstances ( ) const

inlinevirtual

Get a vector of instances in case of the current object is a composite.

Returns: a vector of ICountProcessor instance.

Reimplemented from CountProcessorAbstract.

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

inlinevirtual

Get some properties about the count processor.

Returns: properties.

Reimplemented from CountProcessorAbstract.

bool process	(	size_t	partId,
		const Type &	kmer,
		const CountVector &	count,
		CountNumber	sum = `0`
	)

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/CountProcessorChain.hpp

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

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