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NCBI C++ ToolKit: include/sra/data_loaders/wgs/impl/wgsloader_impl.hpp Source File

& prefix);

& prefix);

& prefix);

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Call>

retry_count = 0);

& prefix);

& prefix);

vector<CSeq_id_Handle>

;

unique_ptr<CDeadline> m_IndexUpdateDeadline;

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Adaptation of CThread class repeatedly running some job.

CWGSBlobId(const string &str)

string ToString(void) const

Get string representation of blob id.

bool operator<(const CBlobId &id) const

void FromString(CTempString str)

bool operator==(const CBlobId &id) const

CWGSResolver & GetResolver(void)

CWGSDataLoader_Impl(const CWGSDataLoader::SLoaderParams &params)

CDataLoader::TTSE_LockSet GetRecordsOnce(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

CDataLoader::SHashFound GetSequenceHash(const CSeq_id_Handle &idh)

CDataLoader::TTSE_LockSet GetRecords(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

TTaxId GetTaxIdOnce(const CSeq_id_Handle &idh)

vector< CSeq_id_Handle > TIds

TTaxId GetTaxId(const CSeq_id_Handle &idh)

CDataLoader::STypeFound GetSequenceTypeOnce(const CSeq_id_Handle &idh)

unsigned m_IndexUpdateDelay

CRef< CThreadNonStop > m_IndexUpdateThread

CRef< CWGSFileInfo > OpenWGSFile(SWGSFileInfoSlot &slot, const string &prefix)

CRef< CWGSFileInfo > GetWGSFile(const string &acc)

map< string, CRef< SWGSFileInfoSlot > > TFixedFiles

CDataLoader::SAccVerFound GetAccVerOnce(const CSeq_id_Handle &idh)

CRef< CWGSBlobId > GetBlobIdOnce(const CSeq_id_Handle &idh)

SAccFileInfo GetFileInfoByProtAcc(const CTextseq_id &text_id)

unsigned m_FileReopenTime

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

SAccFileInfo GetFileInfoByAcc(const CTextseq_id &text_id)

CDataLoader::STypeFound GetSequenceType(const CSeq_id_Handle &idh)

CDataLoader::SGiFound GetGi(const CSeq_id_Handle &idh)

void GetChunkOnce(const CWGSBlobId &blob_id, CTSE_Chunk_Info &chunk)

CDataLoader::SHashFound GetSequenceHashOnce(const CSeq_id_Handle &idh)

CDataLoader::SGiFound GetGiOnce(const CSeq_id_Handle &idh)

CRef< CWGSFileInfo > x_GetFileInfo(SWGSFileInfoSlot &info_slot, const string &prefix)

CRef< CWGSFileInfo > OpenWGSFileOnce(SWGSFileInfoSlot &slot, const string &prefix)

SAccFileInfo GetFileInfoByGi(TGi gi)

CTSE_LoadLock GetBlobById(CDataSource *data_source, const CWGSBlobId &blob_id)

CRef< CWGSBlobId > GetBlobId(const CSeq_id_Handle &idh)

void GetChunk(const CWGSBlobId &blob_id, CTSE_Chunk_Info &chunk)

atomic< bool > m_ResolverCreated

CDataLoader::SAccVerFound GetAccVer(const CSeq_id_Handle &idh)

TSeqPos GetSequenceLengthOnce(const CSeq_id_Handle &idh)

CTSE_LoadLock GetBlobByIdOnce(CDataSource *data_source, const CWGSBlobId &blob_id)

void GetIds(const CSeq_id_Handle &idh, TIds &ids)

CWGSFileInfo::SAccFileInfo SAccFileInfo

CFastMutex m_ResolverMutex

CRef< CWGSResolver > m_Resolver

CVDBCacheWithExpiration TFoundFiles

bool GetAddWGSMasterDescr(void) const

SAccFileInfo GetFileInfoByGeneral(const CDbtag &dbtag)

TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

void SetAddWGSMasterDescr(bool flag)

CRef< CWGSFileInfo > GetFileInfo(const CWGSBlobId &blob_id)

~CWGSDataLoader_Impl(void)

CVDBCacheWithExpiration::CSlot SWGSFileInfoSlot

void LoadBlob(const CWGSBlobId &blob_id, CTSE_LoadLock &load_lock)

unsigned m_FileRecheckTime

void GetIdsOnce(const CSeq_id_Handle &idh, TIds &ids)

bool FindProtAcc(SAccFileInfo &info, const CTextseq_id &text_id)

void x_Initialize(const CWGSDataLoader_Impl &impl, const string &prefix)

void Open(const CWGSDataLoader_Impl &impl, const string &prefix)

CWGSFileInfo(const CWGSDataLoader_Impl &impl, const string &prefix)

CWGSProteinIterator GetProteinIterator(const CWGSBlobId &blob_id) const

CWGSSeqIterator GetContigIterator(const CWGSBlobId &blob_id) const

bool FindGi(SAccFileInfo &info, TGi gi)

void LoadChunk(const CWGSBlobId &blob_id, CTSE_Chunk_Info &chunk) const

void LoadBlob(const CWGSBlobId &blob_id, CTSE_LoadLock &load_lock) const

CWGSScaffoldIterator GetScaffoldIterator(const CWGSBlobId &blob_id) const

const string & GetWGSPrefix(void) const

const CWGSDb & GetDb(void) const

void x_InitMasterDescr(void)

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

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

EChoice

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

#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.

Multi-threading – mutexes; rw-locks; semaphore.

Defines: CTimeFormat - storage class for time format.

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,...

CWGSProteinIterator GetProteinIterator(void) const

bool IsProtein(void) const

CWGSSeqIterator GetContigIterator(void) const

bool ValidateAcc(const CTextseq_id &text_id)

bool IsContig(void) const

DECLARE_OPERATOR_BOOL_REF(file)

bool IsMigrated(const CWGSProteinIterator &iter) const

SAccFileInfo GetRootFileInfo(void) const

bool IsScaffold(void) const

CRef< CWGSFileInfo > file

CWGSScaffoldIterator GetScaffoldIterator(void) const

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