CountProcessorHistogram< span > Class Template Reference

#include <CountProcessorHistogram.hpp>

Inheritance diagram for CountProcessorHistogram< span >:

Public Types
typedef Kmer< span >::Type	Type
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
	CountProcessorHistogram (tools::storage::impl::Group *group=0, size_t histoMax=10000, size_t min_auto_threshold=3, bool histo2Dmode=false, bool histo1Dmode=false, std::string histo2Dfilename="histo2Dfile", std::string histo1Dfilename="histo1Dfile")
	CountProcessorHistogram (tools::storage::impl::Group *group, tools::misc::IHistogram *histogram, size_t min_auto_threshold=3, bool histo2Dmode=false, bool histo1Dmode=false, std::string histo2Dfilename="histo2Dfile", std::string histo1Dfilename="histo1Dfile")
virtual	~CountProcessorHistogram ()
void	end ()
CountProcessorAbstract< span > *	clone ()
bool	process (size_t partId, const Type &kmer, const CountVector &count, CountNumber sum)
tools::misc::impl::Properties	getProperties () const
gatb::core::tools::misc::IHistogram *	getHistogram ()
Public Member Functions inherited from CountProcessorAbstract< span >
	CountProcessorAbstract (const std::string &name="processor")
virtual	~CountProcessorAbstract ()
virtual void	begin (const Configuration &config)
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 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::CountProcessorHistogram< span >

The CountProcessorHistogram implementation collects information about the kmers distribution. It feeds a IHistogram instance during the 'process' method.

At the end of the algorithm, it provides information such as the best cutoff (ie a "good" abundance min parameter).

Member Typedef Documentation

typedef Kmer<span>::Type Type

Shortcuts.

Constructor & Destructor Documentation

CountProcessorHistogram ( tools::storage::impl::Group *  group = 0, size_t  histoMax = 10000, size_t  min_auto_threshold = 3, bool  histo2Dmode = false, bool  histo1Dmode = false, std::string  histo2Dfilename = "histo2Dfile", std::string  histo1Dfilename = "histo1Dfile"  )

inline

Constructor.

CountProcessorHistogram ( tools::storage::impl::Group *  group, tools::misc::IHistogram *  histogram, size_t  min_auto_threshold = 3, bool  histo2Dmode = false, bool  histo1Dmode = false, std::string  histo2Dfilename = "histo2Dfile", std::string  histo1Dfilename = "histo1Dfile"  )

inline

Constructor.

virtual ~CountProcessorHistogram ( )

inlinevirtual

Destructor.

Member Function Documentation

CountProcessorAbstract<span>* 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< span >.

void end ( )

inlinevirtual

Called just after the mainloop of SortingCountAlgorithm.

Reimplemented from CountProcessorAbstract< span >.

gatb::core::tools::misc::IHistogram* getHistogram ( )

inline

Get the histogram.

Returns

the histogram instance.

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 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< 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/CountProcessorHistogram.hpp