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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/reader_8hpp_source.html below:

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

InitParams(

& conf,

& driver_name,

default_max_conn);

vector<CSeq_id_Handle>

;

&

)

;

SetMaximumConnections(

);

SetMaximumConnections(

,

default_max);

GetMaximumConnections(

)

;

GetMaximumConnectionsLimit(

)

;

SetPreopenConnection(

preopen =

);

GetPreopenConnection(

)

;

OpenInitialConnection(

force);

GetConst(

& const_name)

;

SetMaximumRetryCount(

retry_count);

GetRetryCount(

)

;

MayBeSkippedOnErrors(

)

;

ResetCache(

);

OpenConnection(

);

WaitBeforeNewConnection(

);

ConnectSucceeds(

);

ConnectFailed(

);

SetNewConnectionDelayMicroSec(

micro_sec);

SetIncludeHUP(

include_hup =

,

<

T>

x_ReportDisconnect(

* reader,

* server,

m_IncludeHUP = include_hup;

x_AllocConnection(

oldest =

);

x_ReleaseConnection(

,

retry_delay = 0);

x_ReleaseClosedConnection(

);

x_AddConnection(

);

x_RemoveConnection(

);

Release(

);

Restart(

);

m_Result != 0;

ncbi::TMaskedQueryRegions mask

void operator=(CReaderAllocatedConnection &)

CReaderAllocatedConnection(const CReaderAllocatedConnection &)

CReaderRequestResult * m_Result

bool IsAllocated(void) const

bool GetEnableSNP(void) const

void SetEnableCDD(CNullable< bool > enable)

bool GetEnableCDD(void) const

CNullable< bool > m_EnableWGS

CNullable< bool > m_EnableCDD

bool GetEnableWGS(void) const

bool IsSetEnableCDD(void) const

void SetEnableWGS(CNullable< bool > enable)

CNullable< bool > m_EnableSNP

void SetEnableSNP(CNullable< bool > enable)

bool IsSetEnableSNP(void) const

void SetEnableWGS(bool enable)

void SetEnableSNP(bool enable)

bool IsSetEnableWGS(void) const

void SetEnableCDD(bool enable)

friend CDebugPrinter & operator<<(CDebugPrinter &pr, const T &obj)

virtual bool LoadSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

CDataLoader::STypeFound TSequenceType

CSemaphore m_NumFreeConnections

vector< CSeq_id_Handle > TSeqIds

CReadDispatcher * m_Dispatcher

CReaderAllocatedConnection CConn

virtual void x_ConnectAtSlot(TConn conn)=0

vector< CBlob_Info > TBlobIds

TFreeConnections m_FreeConnections

void operator=(const CReader &)

CIncreasingTime m_WaitTime

void x_SetIncludeHUP(bool include_hup)

virtual bool LoadBlob(CReaderRequestResult &result, const CBlob_id &blob_id)=0

atomic< int > m_ConnectFailCount

TConn m_NextNewConnection

vector< TSeqPos > TLengths

vector< pair< TBlobId, TChunkIds > > TBlobChunkIds

vector< CSeq_inst::EMol > TTypes

vector< CSeq_id_Handle > TIds

CDataLoader::SAccVerFound TSequenceAcc

CDataLoader::SHashFound TSequenceHash

virtual bool LoadBlobState(CReaderRequestResult &result, const TBlobId &blob_id)=0

virtual void x_AddConnectionSlot(TConn conn)=0

list< SConnSlot > TFreeConnections

bool HasHUPIncluded() const

vector< TChunkId > TChunkIds

virtual bool LoadBlobVersion(CReaderRequestResult &result, const TBlobId &blob_id)=0

CMutex m_ConnectionsMutex

vector< CBlob_id > TPlainBlobIds

virtual void x_RemoveConnectionSlot(TConn conn)=0

CDataLoader::SGiFound TSequenceGi

definition of a Culling tree

static CS_CONNECTION * conn

bool IsNull(void) const

Check if the object is unassigned.

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TValue & GetValue(void) const

Get a const reference to the current value.

#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.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

virtual void SetParams()

Called at the beginning of Run, before creating thread pool.

#define NCBI_XREADER_EXPORT

static const char label[]

Interfaces for a local cache of versioned binary large objects (BLOBS).

const string version

version string

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

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Defines: CTimeFormat - storage class for time format.

CReader::CDebugPrinter CDebugPrinter

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,...

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