gatb.core-API-1.4.2
CountProcessorHistogram< span > Class Template Reference

#include <CountProcessorHistogram.hpp>

Inheritance diagram for CountProcessorHistogram< span >:
Inheritance graph

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::IHistogramgetHistogram ()
 
- 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 >.


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