#include <CountProcessorDumpKff.hpp>
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| CountProcessorDumpKff (std::string prefix, tools::storage::impl::Group &group, const size_t kmerSize, system::ISynchronizer *synchronizer=0, tools::storage::impl::Partition< Count > *solidCounts=0, size_t nbPartsPerPass=0) |
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virtual | ~CountProcessorDumpKff () |
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void | begin (const Configuration &config) |
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CountProcessorAbstract< span > * | clone () |
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void | finishClones (std::vector< ICountProcessor< span > * > &clones) |
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void | beginPart (size_t passId, size_t partId, size_t cacheSize, const char *name) |
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void | endPart (size_t passId, size_t partId) |
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bool | process (size_t partId, const Type &kmer, const CountVector &count, CountNumber sum) |
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tools::misc::impl::Properties | getProperties () const |
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u_int64_t | getNbItems () |
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| CountProcessorAbstract (const std::string &name="processor") |
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virtual | ~CountProcessorAbstract () |
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virtual void | end () |
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virtual void | beginPass (size_t passId) |
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virtual void | endPass (size_t passId) |
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virtual std::string | getName () const |
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virtual void | setName (const std::string &name) |
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virtual std::vector< ICountProcessor< span > * > | getInstances () const |
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template<typename T > |
T * | get () const |
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void | use () |
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void | forget () |
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virtual | ~ISmartPointer () |
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template<size_t span = KMER_DEFAULT_SPAN>
class gatb::core::kmer::impl::CountProcessorDumpKff< span >
The CountProcessorDumpKff
see CountProcessorDump for a real doc
void begin |
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const Configuration & |
config | ) |
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inlinevirtual |
void beginPart |
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size_t |
passId, |
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size_t |
partId, |
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size_t |
cacheSize, |
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const char * |
name |
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) |
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inlinevirtual |
Called at the beginning of a new kmers partition processing.
- Parameters
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[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. |
Reimplemented from CountProcessorAbstract< span >.
void endPart |
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size_t |
passId, |
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size_t |
partId |
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) |
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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
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[in] | clones | : the N cloned instances |
Reimplemented from CountProcessorAbstract< span >.
Get the number of items.
- Returns
- the total number of items in the partition.
Notification that a [kmer,counts] is available and can be handled by the count processor.
- Parameters
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[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:
- /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/kmer/impl/CountProcessorDumpKff.hpp