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NCBI C++ ToolKit: src/app/pubseq_gateway/server/wgs_client.hpp Source File

shared_ptr<SWGSData>

(

objects::CSeq_id& seq_id);

shared_ptr<SWGSData>

(

& id2info,

chunk_id);

(

seq_id_type,

& seq_id);

(

&

,

seq_id_type,

& seq_id);

objects::CWGSDb

(

& prefix);

objects::CTextseq_id&

,

skip_lookup =

);

skip_lookup =

);

objects::CAsnBinData&

)

;

User-defined methods of the data storage class.

static void SetSeqId(CSeq_id &id, int seq_id_type, const string &seq_id)

shared_ptr< SWGSData > GetChunk(const string &id2info, int64_t chunk_id)

bool GetCompress(SWGSProcessor_Config::ECompressData comp, const SWGSSeqInfo &seq, const objects::CAsnBinData &data) const

SWGSSeqInfo ResolveBlobId(const objects::CID2_Blob_Id &id, bool skip_lookup=false)

SWGSSeqInfo ResolveGi(TGi gi, bool skip_lookup=false)

static bool IsOSGBlob(const CID2_Blob_Id &blob_id)

shared_ptr< SWGSData > GetBlobByBlobId(const string &blob_id)

bool IsCorrectVersion(SWGSSeqInfo &seq, int version)

void ResetIteratorCache(SWGSSeqInfo &seq)

void GetWGSData(shared_ptr< SWGSData > &data, SWGSSeqInfo &seq0)

static string GetPSGBlobId(const CID2_Blob_Id &blob_id)

CRef< objects::CSeq_id > GetAccVer(SWGSSeqInfo &seq)

CWGSClient(const SWGSProcessor_Config &config)

CFastMutex m_ResolverMutex

SWGSSeqInfo & GetRootSeq(SWGSSeqInfo &seq0)

static bool CanBeWGS(int seq_id_type, const string &seq_id)

objects::CWGSScaffoldIterator & GetScaffoldIterator(SWGSSeqInfo &seq)

CVDBCacheWithExpiration TWGSDbCache

shared_ptr< SWGSData > ResolveSeqId(const objects::CSeq_id &seq_id)

TGi GetGi(SWGSSeqInfo &seq)

shared_ptr< SWGSData > GetSeqInfoBySeqId(const objects::CSeq_id &seq_id, SWGSSeqInfo &seq, const TBlobIds &excluded)

CRef< objects::CWGSResolver > m_Resolver

bool IsValidRowId(SWGSSeqInfo &seq)

CRef< objects::CWGSResolver > GetWGSResolver(void)

SWGSSeqInfo ResolveAcc(const objects::CTextseq_id &id, bool skip_lookup=false)

SWGSSeqInfo Resolve(const objects::CSeq_id &id, bool skip_lookup=false)

bool HasMigrated(SWGSSeqInfo &seq)

objects::CID2_Blob_Id & GetBlobId(SWGSSeqInfo &id)

static SParsedId2Info ParsePSGId2Info(const string &idsss2_info)

objects::CWGSDb GetWGSDb(const string &prefix)

CRef< objects::CSeq_id > GetGeneral(SWGSSeqInfo &seq)

bool CanProcessRequest(CPSGS_Request &request)

int GetID2BlobState(SWGSSeqInfo &seq)

objects::CWGSSeqIterator & GetContigIterator(SWGSSeqInfo &seq)

vector< string > TBlobIds

NCBI_gb_state GetGBState(SWGSSeqInfo &seq0)

void GetBioseqInfo(shared_ptr< SWGSData > &data, SWGSSeqInfo &seq)

objects::CWGSProteinIterator & GetProteinIterator(SWGSSeqInfo &seq)

static CRef< CID2_Blob_Id > ParsePSGBlobId(const SPSGS_BlobId &blob_id)

void x_RegisterTiming(psg_time_point_t start, EPSGOperation operation, EPSGOperationStatus status)

SWGSSeqInfo ResolveWGSAcc(const string &acc, const objects::CTextseq_id &id, TAllowSeqType allow_seq_type, bool skip_lookup=false)

bool HasSpecialState(SWGSSeqInfo &seq, NCBI_gb_state special_state)

SWGSSeqInfo ResolveGeneral(const objects::CDbtag &dbtag, bool skip_lookup=false)

SWGSSeqInfo ResolveProtAcc(const objects::CTextseq_id &id, bool skip_lookup=false)

SWGSProcessor_Config m_Config

void GetSeqIds(SWGSSeqInfo &seq, list< CRef< objects::CSeq_id > > &ids)

CRef< CThreadNonStop > m_IndexUpdateThread

uint8_t Uint1

1-byte (8-bit) unsigned integer

operation

Bit operations.

Generic map with size limited by some number.

const string version

version string

psg_clock_t::time_point psg_time_point_t

TID2SplitVersion split_version

DECLARE_OPERATOR_BOOL_REF(tse_id)

CRef< CID2_Blob_Id > tse_id

AutoPtr< SWGSSeqInfo > m_RootSeq

objects::CWGSProteinIterator m_ProteinIter

bool IsProtein(void) const

bool IsMaster(void) const

objects::CWGSScaffoldIterator m_ScaffoldIter

objects::CWGSSeqIterator m_ContigIter

DECLARE_OPERATOR_BOOL(m_ValidWGS)

objects::TVDBRowId m_RowId

CRef< objects::CID2_Blob_Id > m_BlobId

bool IsContig(void) const

bool IsScaffold(void) const

int TPSGS_BioseqIncludeData

SPSGS_ResolveRequest::TPSGS_BioseqIncludeData TBioseqInfoFlags

shared_ptr< CBioseqInfoRecord > m_BioseqInfo

CRef< objects::CAsnBinData > m_Data

int GetPSGBioseqState() const

TBioseqInfoFlags m_BioseqInfoFlags

int GetID2BlobState(void) const

CRef< objects::CID2_Blob_Id > m_Id2BlobId

unsigned m_IndexUpdateDelay

unsigned m_FileReopenTime

unsigned m_FileRecheckTime

ECompressData m_CompressData

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