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NCBI C++ ToolKit: include/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp Source File

<

Call>

retry_count = 0);

shared_ptr<SPsgBioseqInfo> x_GetBioseqInfo(

& idh);

shared_ptr<SPsgBlobInfo> x_GetBlobInfo(

* data_source,

& blob_id);

pair<shared_ptr<SPsgBioseqInfo>,

pair<size_t, CRef<CPSGL_Processor>>

x_GetBulkBioseqInfo(

& ids,

pair<size_t, CRef<CPSGL_Processor>>

x_GetBulkBioseqAndBlobInfo(

* data_source,

x_CheckAnnotCache(

& name,

pair<size_t, CRef<CPSGL_Processor>>

TBioseqAndBlobInfo& ret,

id_index = 0);

TBioseqAndBlobInfo& ret,

m_AddWGSMasterDescr =

;

std::invoke_result< Call >::type CallWithRetry(Call &&call, const char *name, int retry_count=0)

pair< string, int > GetAccVer(const CAlignModel &a, CScope &scope)

unique_ptr< CThreadPool > m_ThreadPool

CDataLoader::TSequenceStates TSequenceStates

pair< shared_ptr< SPsgBioseqInfo >, pair< shared_ptr< SPsgBlobInfo >, EPSG_Status > > TBioseqAndBlobInfo

psgl::CPSGL_QueueGuard CPSGL_QueueGuard

CRef< CRequestContext > m_RequestContext

CDataLoader::TBulkIds TBulkIds

psgl::CPSGCaches CPSGCaches

psgl::SPsgBlobInfo SPsgBlobInfo

CDataLoader::TTSE_LockSets TTSE_LockSets

CDataLoader::TSequenceHashes TSequenceHashes

set< CSeq_id_Handle > TLoadedSeqIds

CDataLoader::TSeqIdSets TSeqIdSets

vector< shared_ptr< SPsgBioseqInfo > > TBioseqInfos

CDataLoader::TSequenceLengths TSequenceLengths

psgl::CPSGL_ResultGuard CPSGL_ResultGuard

CRef< CPSG_PrefetchCDD_Task > m_CDDPrefetchTask

unique_ptr< CPSGCaches > m_Caches

vector< TBioseqAndBlobInfo > TBioseqAndBlobInfos

psgl::CPSGL_Processor CPSGL_Processor

CRef< CPSGL_Queue > m_Queue

psgl::CPSGL_Queue CPSGL_Queue

CDataLoader::TLabels TLabels

CDataLoader::TSequenceTypes TSequenceTypes

unsigned int m_RetryCount

unsigned int m_BulkRetryCount

CDataLoader::TLoaded TLoaded

CDataLoader::TTaxIds TTaxIds

psgl::SPsgBioseqInfo SPsgBioseqInfo

CDataLoader::THashKnown THashKnown

CIncreasingTime m_WaitTime

CDataLoader::TCDD_Locks TCDD_Locks

Blob data meta information.

EIncludeData

Specify which info and data is needed.

@ eSmartTSE

If ID2 split is available, return split info blob only.

@ eWholeTSE

If ID2 split is available, return all split blobs.

Main class implementing functionality of pool of threads.

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

vector< TSeqPos > TSequenceLengths

vector< CTSE_Lock > TCDD_Locks

vector< CSeq_id_Handle > TIds

vector< bool > THashKnown

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

vector< CSeq_inst::TMol > TSequenceTypes

vector< vector< CSeq_id_Handle > > TSeqIdSets

vector< bool > TLoaded

Bulk loading interface for a small pieces of information per id.

vector< int > TSequenceStates

vector< int > TSequenceHashes

vector< TChunk > TChunkSet

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XLOADER_GENBANK_EXPORT

const GenericPointer< typename T::ValueType > T2 value

EPSG_Status

Retrieval result.

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

Return a (corrected) set of flags identifying the sequence type.

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

shared_ptr< SPsgBlobInfo > blob_info

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