gatb.core-API-0.0.0
CountProcessorAbstract< span > Class Template Reference

#include <CountProcessorAbstract.hpp>

Inheritance diagram for CountProcessorAbstract< span >:
Inheritance graph

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 ICountProcessorclone ()=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 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 >, 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 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
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 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 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 >.


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