gatb.core-API-0.0.0
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#include <CountProcessorCutoff.hpp>
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 | |
CountProcessorCutoff (size_t nbBanks) | |
CountProcessorCutoff (const std::vector< CountProcessorHistogram< span > * > &histogramProcessors) | |
virtual | ~CountProcessorCutoff () |
CountProcessorAbstract< span > * | clone () |
void | endPass (size_t passId) |
bool | process (size_t partId, const 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 | begin (const Configuration &config) |
virtual void | end () |
virtual void | beginPass (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 () |
The CountProcessorCutoff 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).
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inline |
Constructor for the prototype instance.
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inline |
Constructor for the cloned instances.
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inlinevirtual |
Destructor.
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inlinevirtual |
Clone the instance. An instance can be cloned N times in order to use the cloned instance in one thread.
Implements ICountProcessor< span >.
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inlinevirtual |
Called just after the mainloop of SortingCountAlgorithm.
Reimplemented from CountProcessorAbstract< span >.
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inlinevirtual |
Get some properties about the count processor.
Reimplemented from CountProcessorAbstract< span >.
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inlinevirtual |
Notification that a [kmer,counts] is available and can be handled by the count processor.
[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 >.