CountProcessorSolidityAbstract< span, Derived > Class Template Reference

#include <CountProcessorSolidity.hpp>

Inheritance diagram for CountProcessorSolidityAbstract< span, Derived >:

Public Member Functions
	CountProcessorSolidityAbstract ()
	CountProcessorSolidityAbstract (const std::vector< tools::misc::CountRange > &thresholds, std::vector< bool > &solidVec)
virtual	~CountProcessorSolidityAbstract ()
void	begin (const Configuration &config)
CountProcessorAbstract< span > *	clone ()
void	finishClones (std::vector< ICountProcessor< span > * > &clones)
bool	process (size_t partId, const typename Kmer< span >::Type &kmer, const CountVector &count, CountNumber sum)
tools::misc::impl::Properties	getProperties () const
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 void	beginPart (size_t passId, size_t partId, size_t cacheSize, const char *name)
virtual void	endPart (size_t passId, size_t partId)
virtual bool	process (size_t partId, const Type &kmer, const CountVector &count, CountNumber sum=0)
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
Public Types inherited from CountProcessorAbstract< span >
typedef Kmer< span >::Type	Type
Public Types inherited from ICountProcessor< span >
typedef kmer::impl::Kmer< span >::Type	Type
Protected Member Functions inherited from SmartPointer
	SmartPointer ()
virtual	~SmartPointer ()

Detailed Description

template<size_t span, class Derived>
class gatb::core::kmer::impl::CountProcessorSolidityAbstract< span, Derived >

The CountProcessorSolidityAbstract is an abstract class that factories stuff for telling whether a kmer is solid or not.

Inherited classes provides (through the 'check' method) the way the kmer solidity is computed. There is one subclass per kind of kmer solidity.

Technically, static polymorphism is used here through the 'check' method.

Note that there exists a factory class CountProcessorSolidityFactory that manages the creation of the correct instance according to some user information.

Constructor & Destructor Documentation

CountProcessorSolidityAbstract ( )

inline

Constructor for prototype instance.

CountProcessorSolidityAbstract ( const std::vector< tools::misc::CountRange > &  thresholds, std::vector< bool > &  solidVec  )

inline

Constructor for clone instance.

virtual ~CountProcessorSolidityAbstract ( )

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< span >.

CountProcessorAbstract<span>* clone ( )

inlinevirtual

Implements ICountProcessor< span >.

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

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

inlinevirtual

Get some properties about the count processor.

Returns

properties.

Reimplemented from CountProcessorAbstract< span >.

bool process ( size_t  partId, const typename Kmer< span >::Type &  kmer, const CountVector &  count, CountNumber  sum  )

inline

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.

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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/CountProcessorSolidity.hpp