CountProcessorAbstract< span > Class Template Reference

#include <CountProcessorAbstract.hpp>

Inheritance diagram for CountProcessorAbstract< span >:

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

Public Member Functions
	CountProcessorAbstract (const std::string &name="processor")
virtual	~CountProcessorAbstract ()
virtual void	begin (const Configuration &config)
virtual void	end ()
virtual void	beginPass (size_t passId)
virtual void	endPass (size_t passId)
virtual void	finishClones (std::vector< ICountProcessor< span > * > &clones)
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 tools::misc::impl::Properties	getProperties () const
virtual std::vector< ICountProcessor< span > * >	getInstances () const
Public Member Functions inherited from ICountProcessor< span >
virtual ICountProcessor *	clone ()=0
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>
class gatb::core::kmer::impl::CountProcessorAbstract< span >

Abstract implementation of ICountProcessor interface.

Member Typedef Documentation

typedef Kmer<span>::Type Type

Shortcuts.

Constructor & Destructor Documentation

CountProcessorAbstract ( const std::string &  name = "processor" )

inline

Constructor.

virtual ~CountProcessorAbstract ( )

inlinevirtual

Destructor.

Member Function Documentation

virtual void begin ( const Configuration &  config )

inlinevirtual

Called just before the mainloop of SortingCountAlgorithm.

Parameters

[in]

config

: configuration of the SortingCountAlgorithm.

Implements ICountProcessor< span >.

Reimplemented in CountProcessorSolidityAbstract< span, Derived >, CountProcessorSolidityAbstract< span, CountProcessorSoliditySum< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityOne< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityCustom< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityAll< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityMax< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityMin< span > >, CountProcessorDump< span >, CountProcessorDumpKff< span >, and CountProcessorChain< span >.

virtual 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.

Implements ICountProcessor< span >.

Reimplemented in CountProcessorDump< span >, CountProcessorDumpKff< span >, and CountProcessorChain< span >.

virtual void beginPass ( size_t  passId )

inlinevirtual

Called just after the mainloop of SortingCountAlgorithm.

Implements ICountProcessor< span >.

virtual void end ( )

inlinevirtual

Called just after the mainloop of SortingCountAlgorithm.

Implements ICountProcessor< span >.

Reimplemented in CountProcessorHistogram< span >, and CountProcessorChain< span >.

virtual 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.

Implements ICountProcessor< span >.

Reimplemented in CountProcessorDumpKff< span >, CountProcessorDump< span >, and CountProcessorChain< span >.

virtual void endPass ( size_t  passId )

inlinevirtual

Called just after the mainloop of SortingCountAlgorithm.

Implements ICountProcessor< span >.

Reimplemented in CountProcessorCutoff< span >.

virtual 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

Implements ICountProcessor< span >.

Reimplemented in CountProcessorSolidityAbstract< span, Derived >, CountProcessorSolidityAbstract< span, CountProcessorSoliditySum< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityOne< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityCustom< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityAll< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityMax< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityMin< span > >, CountProcessorDump< span >, CountProcessorDumpKff< span >, and CountProcessorChain< span >.

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

inlinevirtual

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

Returns

a vector of ICountProcessor instance.

Implements ICountProcessor< span >.

Reimplemented in CountProcessorChain< span >.

virtual std::string getName ( ) const

inlinevirtual

Get a name for the count processor.

Returns

the count processor name.

Implements ICountProcessor< span >.

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

inlinevirtual

Get some properties about the count processor.

Returns

properties.

Implements ICountProcessor< span >.

Reimplemented in CountProcessorDumpKff< span >, CountProcessorHistogram< span >, CountProcessorDump< span >, CountProcessorSolidityAbstract< span, Derived >, CountProcessorSolidityAbstract< span, CountProcessorSoliditySum< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityOne< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityCustom< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityAll< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityMax< span > >, CountProcessorSolidityAbstract< span, CountProcessorSolidityMin< span > >, CountProcessorChain< span >, and CountProcessorCutoff< span >.

virtual 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.

Implements ICountProcessor< span >.

Reimplemented in CountProcessorDumpKff< span >, CountProcessorHistogram< span >, CountProcessorDump< span >, CountProcessorChain< span >, and CountProcessorCutoff< span >.

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

inlinevirtual

Set a name for the count processor.

Parameters

[in]

name

: the count processor name.

Implements ICountProcessor< span >.

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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/CountProcessorAbstract.hpp