CId1Reader Class Reference

Search Toolkit Book for CId1Reader

#include <objtools/data_loaders/genbank/id1/reader_id1.hpp>

Inheritance diagram for CId1Reader:

Collaboration diagram for CId1Reader:

Public Member Functions
	CId1Reader (int max_connections=0)
	CId1Reader (const TPluginManagerParamTree *params, const string &driver_name)
	~CId1Reader ()
int	GetMaximumConnectionsLimit (void) const
bool	LoadSeq_idGi (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)
bool	LoadSeq_idSeq_ids (CReaderRequestResult &result, const CSeq_id_Handle &id)
bool	LoadGiSeq_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)
bool	LoadSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &id, const SAnnotSelector *sel)
	All LoadXxx() methods should return false if there is no requested data in the reader. More...
bool	LoadGiBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel)
void	GetBlobState (CReaderRequestResult &result, const CBlob_id &blob_id)
void	GetBlobVersion (CReaderRequestResult &result, const CBlob_id &blob_id)
void	GetBlob (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id)
Public Member Functions inherited from CId1ReaderBase
	CId1ReaderBase (void)
	~CId1ReaderBase (void)
bool	LoadBlob (CReaderRequestResult &result, const TBlobId &blob_id)
bool	LoadBlobState (CReaderRequestResult &result, const TBlobId &blob_id)
bool	LoadBlobVersion (CReaderRequestResult &result, const TBlobId &blob_id)
bool	LoadChunk (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id)
Public Member Functions inherited from CReader
	CReader (void)
virtual	~CReader (void)
void	InitParams (CConfig &conf, const string &driver_name, int default_max_conn)
virtual bool	LoadSeq_idAccVer (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)
virtual bool	LoadSeq_idLabel (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)
virtual bool	LoadSeq_idTaxId (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)
virtual bool	LoadSequenceHash (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)
virtual bool	LoadSequenceLength (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)
virtual bool	LoadSequenceType (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)
virtual bool	LoadBulkIds (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TBulkIds &ret)
virtual bool	LoadAccVers (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TIds &ret)
virtual bool	LoadGis (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TGis &ret)
virtual bool	LoadLabels (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLabels &ret)
virtual bool	LoadTaxIds (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTaxIds &ret)
virtual bool	LoadHashes (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, THashes &ret, TKnown &known)
virtual bool	LoadLengths (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLengths &ret)
virtual bool	LoadTypes (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTypes &ret)
virtual bool	LoadStates (CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TStates &ret)
virtual bool	LoadBlobs (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TContentsMask mask, const SAnnotSelector *sel)
virtual bool	LoadBlobs (CReaderRequestResult &result, const CLoadLockBlobIds &lock, TContentsMask mask, const SAnnotSelector *sel)
virtual bool	LoadBlob (CReaderRequestResult &result, const CBlob_Info &blob_info)
virtual bool	LoadChunks (CReaderRequestResult &result, const TBlobId &blob_id, const TChunkIds &chunk_ids)
virtual bool	LoadChunks (CReaderRequestResult &result, const TBlobChunkIds &chunk_ids)
virtual bool	LoadBlobSet (CReaderRequestResult &result, const TSeqIds &seq_ids)
virtual bool	LoadBlobs (CReaderRequestResult &result, const TBlobIds &blob_infos)
void	SetAndSaveSeq_idSeq_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const CFixedSeq_ids &seq_ids) const
void	SetAndSaveNoSeq_idSeq_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TState state) const
void	SetAndSaveSeq_idAccVer (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceAcc &acc_id) const
void	SetAndSaveSeq_idGi (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceGi &gi) const
void	SetAndSaveSeq_idAccFromSeqIds (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const CLoadLockSeqIds &seq_ids) const
void	SetAndSaveSeq_idGiFromSeqIds (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const CLoadLockSeqIds &seq_ids) const
void	SetAndSaveSeq_idSeq_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const CLoadLockSeqIds &seq_ids) const
void	SetAndSaveNoSeq_idSeq_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const CLoadLockGi &gi_lock) const
void	SetAndSaveSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, CLoadLockBlobIds &lock, const CLoadLockBlobIds &blob_ids) const
void	SetAndSaveNoSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, const CLoadLockGi &gi_lock) const
void	SetAndSaveSeq_idTaxId (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TTaxId taxid) const
void	SetAndSaveSequenceHash (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceHash &hash) const
void	SetAndSaveSequenceLength (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TSeqPos length) const
void	SetAndSaveSequenceType (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceType &type) const
void	SetAndSaveSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, const CFixedBlob_ids &blob_ids) const
void	SetAndSaveNoSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, TBlobState state) const
void	SetAndSaveBlobState (CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state) const
void	SetAndSaveBlobVersion (CReaderRequestResult &result, const TBlobId &blob_id, TBlobVersion version) const
void	SetAndSaveNoBlob (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, TBlobState blob_state)
void	SetAndSaveSeq_idLabelFromSeqIds (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const CLoadLockSeqIds &seq_ids) const
void	SetAndSaveSeq_idLabel (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const string &label) const
void	SetAndSaveSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, CLoadLockBlobIds &lock, const CFixedBlob_ids &blob_ids) const
void	SetAndSaveNoSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, CLoadLockBlobIds &lock, TBlobState state) const
int	SetMaximumConnections (int max)
void	SetMaximumConnections (int max, int default_max)
int	GetMaximumConnections (void) const
void	SetPreopenConnection (bool preopen=true)
bool	GetPreopenConnection (void) const
void	OpenInitialConnection (bool force)
virtual int	GetConst (const string &const_name) const
void	SetMaximumRetryCount (int retry_count)
virtual int	GetRetryCount (void) const
virtual bool	MayBeSkippedOnErrors (void) const
virtual void	InitializeCache (CReaderCacheManager &cache_manager, const TPluginManagerParamTree *params)
virtual void	ResetCache (void)
virtual void	OpenConnection (TConn conn)
virtual void	WaitBeforeNewConnection (TConn conn)
virtual void	ConnectSucceeds (TConn conn)
virtual void	ConnectFailed (TConn conn)
virtual void	SetNewConnectionDelayMicroSec (unsigned long micro_sec)
virtual void	SetIncludeHUP (bool include_hup=true, const string &web_cookie=NcbiEmptyString)
bool	HasHUPIncluded () const
virtual void	SetParams (const CReaderParams &params)
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Protected Types
typedef map< TConn, CReaderServiceConnector::SConnInfo >	TConnections
Protected Types inherited from CReader
typedef CReaderAllocatedConnection	CConn

Protected Member Functions
virtual void	x_AddConnectionSlot (TConn conn)
virtual void	x_RemoveConnectionSlot (TConn conn)
virtual void	x_DisconnectAtSlot (TConn conn, bool failed)
virtual void	x_ConnectAtSlot (TConn conn)
string	x_ConnDescription (CConn_IOStream &stream) const
CConn_IOStream *	x_GetConnection (TConn conn)
TBlobState	x_ResolveId (CReaderRequestResult &result, CID1server_back &id1_reply, CID1server_request &id1_request)
void	x_SendRequest (TConn conn, CID1server_request &request)
void	x_ReceiveReply (TConn conn, CID1server_back &reply)
void	x_SendRequest (const CBlob_id &blob_id, TConn conn)
void	x_SetParams (CID1server_maxcomplex &params, const CBlob_id &blob_id)
void	x_SetBlobRequest (CID1server_request &request, const CBlob_id &blob_id)
CRef< CTSE_Info >	x_ReceiveMainBlob (CConn_IOStream *stream)
Protected Member Functions inherited from CReader
void	x_ReportDisconnect (const char *reader, const char *server, TConn conn, bool failed) const
void	x_SetIncludeHUP (bool include_hup)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
CReaderServiceConnector	m_Connector
TConnections	m_Connections
Protected Attributes inherited from CReader
CReadDispatcher *	m_Dispatcher

Additional Inherited Members
Public Types inherited from CId1ReaderBase
enum	ESat {   eSat_ANNOT_CDD = 10 , eSat_ANNOT = 26 , eSat_TRACE = 28 , eSat_TRACE_ASSM = 29 ,   eSat_TR_ASSM_CH = 30 , eSat_TRACE_CHGR = 31 }
enum	ESubSat {   eSubSat_main = 0 , eSubSat_SNP = 1<<0 , eSubSat_SNP_graph = 1<<2 , eSubSat_CDD = 1<<3 ,   eSubSat_MGC = 1<<4 , eSubSat_HPRD = 1<<5 , eSubSat_STS = 1<<6 , eSubSat_tRNA = 1<<7 ,   eSubSat_microRNA = 1<<8 , eSubSat_Exon = 1<<9 }
Public Types inherited from CReader
typedef unsigned	TConn
typedef CBlob_id	TBlobId
typedef int	TState
typedef int	TBlobState
typedef int	TBlobVersion
typedef int	TBlobSplitVersion
typedef int	TChunkId
typedef int	TContentsMask
typedef vector< TChunkId >	TChunkIds
typedef vector< CSeq_id_Handle >	TSeqIds
typedef vector< CBlob_Info >	TBlobIds
typedef vector< CSeq_id_Handle >	TIds
typedef vector< bool >	TLoaded
typedef vector< TIds >	TBulkIds
typedef vector< TGi >	TGis
typedef vector< string >	TLabels
typedef vector< TTaxId >	TTaxIds
typedef vector< int >	TStates
typedef vector< int >	THashes
typedef vector< bool >	TKnown
typedef vector< TSeqPos >	TLengths
typedef vector< CSeq_inst::EMol >	TTypes
typedef vector< CBlob_id >	TPlainBlobIds
typedef vector< pair< TBlobId, TChunkIds > >	TBlobChunkIds
typedef CDataLoader::SAccVerFound	TSequenceAcc
typedef CDataLoader::SGiFound	TSequenceGi
typedef CDataLoader::STypeFound	TSequenceType
typedef CDataLoader::SHashFound	TSequenceHash
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...
Static Public Member Functions inherited from CId1ReaderBase
static bool	IsAnnotSat (int sat)
static ESat	GetAnnotSat (int subsat)
static void	CreateExtAnnotBlob_ids (TBlobIds &blob_ids, TIntId gi, int ext_feat)
static int	GetNextExtAnnotBit (int &ext_feat)
static void	SetExtAnnotBlob_id (CBlob_id &blob_id, TIntId gi, int bit)
static TIntId	GetExtAnnotGi (const CBlob_id &blob_id)
static int	GetExtAnnotSubSat (const CBlob_id &blob_id)
Static Public Member Functions inherited from CReader
static int	ReadInt (CNcbiIstream &stream)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Definition at line 44 of file reader_id1.hpp.

Member Typedef Documentation

TConnections

typedef map< TConn, CReaderServiceConnector::SConnInfo > CId1Reader::TConnections

protected

Definition at line 112 of file reader_id1.hpp.

Constructor & Destructor Documentation

CId1Reader() [1/2]

CId1Reader::CId1Reader

(

int

max_connections = 0

)

Definition at line 129 of file reader_id1.cpp.

References DEFAULT_NUM_CONN, ERR_POST_X_ONCE, and CReader::SetMaximumConnections().

CId1Reader() [2/2]

CId1Reader::CId1Reader	(	const TPluginManagerParamTree *	params,
		const string &	driver_name
	)

Definition at line 137 of file reader_id1.cpp.

References DEFAULT_NUM_CONN, CConfig::eErr_NoThrow, ERR_POST_X_ONCE, CConfig::GetString(), CReader::InitParams(), CReaderServiceConnector::InitTimeouts(), kEmptyStr, m_Connector, NCBI, NCBI_GBLOADER_READER_ID1_PARAM_SERVICE_NAME, NCBI_PARAM_TYPE, and CReaderServiceConnector::SetServiceName().

~CId1Reader()

CId1Reader::~CId1Reader

(

)

Definition at line 159 of file reader_id1.cpp.

Member Function Documentation

GetBlob()

void CId1Reader::GetBlob ( CReaderRequestResult &  result, const TBlobId &  blob_id, TChunkId  chunk_id  )

virtual

Implements CId1ReaderBase.

Definition at line 652 of file reader_id1.cpp.

References conn, CId1ReaderBase::eSubSat_SNP, CProcessor::eType_ID1, CProcessor::eType_ID1_SNP, CReadDispatcher::GetProcessor(), CBlob_id::GetSubSat(), CLoadLockBlob::IsLoadedChunk(), CReader::m_Dispatcher, NCBI_RETHROW, CProcessor::ProcessStream(), result, x_ConnDescription(), x_GetConnection(), x_SendRequest(), and x_SetBlobRequest().

GetBlobState()

void CId1Reader::GetBlobState ( CReaderRequestResult &  result, const CBlob_id &  blob_id  )

virtual

Implements CId1ReaderBase.

Definition at line 562 of file reader_id1.cpp.

References GetBlobVersion(), and result.

GetBlobVersion()

void CId1Reader::GetBlobVersion ( CReaderRequestResult &  result, const CBlob_id &  blob_id  )

virtual

Implements CId1ReaderBase.

Definition at line 569 of file reader_id1.cpp.

References abs, CID1server_back_Base::e_Error, CID1server_back_Base::e_Gotblobinfo, CID1server_back_Base::e_Gotsewithinfo, ERR_POST_X, CBioseq_Handle::fState_dead, CID1SeqEntry_info_Base::GetBlob_info(), CID1blob_info_Base::GetBlob_state(), CID1server_back_Base::GetGotblobinfo(), CID1server_back_Base::GetGotsewithinfo(), NCBI_THROW, result, CReader::SetAndSaveBlobState(), CReader::SetAndSaveBlobVersion(), CID1server_request_Base::SetGetblobinfo(), version, CID1server_back_Base::Which(), x_ResolveId(), and x_SetParams().

Referenced by GetBlobState().

GetMaximumConnectionsLimit()

int CId1Reader::GetMaximumConnectionsLimit ( void  ) const

virtual

Reimplemented from CReader.

Definition at line 164 of file reader_id1.cpp.

References MAX_MT_CONN.

LoadGiBlob_ids()

bool CId1Reader::LoadGiBlob_ids	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id,
		const SAnnotSelector *	sel
	)

Definition at line 466 of file reader_id1.cpp.

References _ASSERT, CProcessor::ConvertGiFromOM(), CId1ReaderBase::CreateExtAnnotBlob_ids(), CSeq_id_Base::e_Gi, eEntry_complexities_entry, eTakeOwnership, fBlobHasAllLocal, CBioseq_Handle::fState_confidential, CBioseq_Handle::fState_dead, CBioseq_Handle::fState_other_error, CBioseq_Handle::fState_suppress_perm, CBioseq_Handle::fState_suppress_temp, CBioseq_Handle::fState_withdrawn, CSeq_id_Handle::GetGi(), CSeq_id_Base::GetGi(), CID1server_back_Base::GetGotblobinfo(), CSeq_id_Handle::GetSeqId(), GI_TO, info, CSeq_id_Handle::IsGi(), CID1server_back_Base::IsGotblobinfo(), LOG_POST_X, result, CReader::SetAndSaveNoSeq_idBlob_ids(), CReader::SetAndSaveSeq_idBlob_ids(), CID1server_request_Base::SetGetblobinfo(), CID1server_maxcomplex_Base::SetGi(), CID1server_maxcomplex_Base::SetMaxplex(), CLoadLockBlobIds::SetNoBlob_ids(), CProcessor::TrySNPSplit(), Warning(), CSeq_id_Handle::Which(), x_ResolveId(), and ZERO_GI.

Referenced by LoadSeq_idBlob_ids().

LoadGiSeq_ids()

bool CId1Reader::LoadGiSeq_ids	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

Definition at line 341 of file reader_id1.cpp.

References _ASSERT, CSeq_id_Base::e_Gi, eTakeOwnership, CSeq_id_Handle::GetGi(), CSeq_id_Base::GetGi(), CSeq_id_Handle::GetHandle(), CID1server_back_Base::GetIds(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::IsGi(), CID1server_back_Base::IsIds(), ITERATE, result, CReader::SetAndSaveNoSeq_idSeq_ids(), CReader::SetAndSaveSeq_idSeq_ids(), CID1server_request_Base::SetGetseqidsfromgi(), CSeq_id_Handle::Which(), x_ResolveId(), and ZERO_GI.

Referenced by LoadSeq_idSeq_ids().

LoadSeq_idBlob_ids()

bool CId1Reader::LoadSeq_idBlob_ids ( CReaderRequestResult &  result, const CSeq_id_Handle &  seq_id, const SAnnotSelector *  sel  )

virtual

All LoadXxx() methods should return false if there is no requested data in the reader.

This will notify dispatcher that there is no sense to retry.

Reimplemented from CReader.

Definition at line 397 of file reader_id1.cpp.

References CProcessor::ConvertGiFromOM(), data, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CId1ReaderBase::eSat_ANNOT, CId1ReaderBase::eSat_ANNOT_CDD, eTakeOwnership, fBlobHasAllLocal, CDbtag_Base::GetDb(), CLoadLockGi::GetGi(), CSeq_id_Handle::GetGiHandle(), SAnnotSelector::GetNamedAnnotAccessions(), CSeq_id_Handle::GetSeqId(), GI_FROM, GI_TO, SAnnotSelector::IsIncludedAnyNamedAnnotAccession(), LoadGiBlob_ids(), CReadDispatcher::LoadSeq_idBlob_ids(), CReader::LoadSeq_idBlob_ids(), CReadDispatcher::LoadSeq_idGi(), CReader::m_Dispatcher, result, CReader::SetAndSaveNoSeq_idBlob_ids(), CReader::SetAndSaveSeq_idBlob_ids(), CLoadLockBlobIds::SetLoadedBlob_ids(), sx_IsSNPOnly(), CSeq_id_Handle::Which(), and ZERO_GI.

LoadSeq_idGi()

bool CId1Reader::LoadSeq_idGi ( CReaderRequestResult &  result, const CSeq_id_Handle &  seq_id  )

virtual

Reimplemented from CReader.

Definition at line 268 of file reader_id1.cpp.

References CID1server_back_Base::GetGotgi(), CSeq_id_Handle::GetSeqId(), CDataLoader::SGiFound::gi, CID1server_back_Base::IsGotgi(), CLoadLockGi::IsLoadedGi(), result, CDataLoader::SGiFound::sequence_found, CReader::SetAndSaveSeq_idGi(), CID1server_request_Base::SetGetgi(), x_ResolveId(), and ZERO_GI.

LoadSeq_idSeq_ids()

bool CId1Reader::LoadSeq_idSeq_ids ( CReaderRequestResult &  result, const CSeq_id_Handle &  id  )

virtual

Implements CReader.

Definition at line 292 of file reader_id1.cpp.

References data, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, eTakeOwnership, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CLoadLockGi::GetGi(), CSeq_id_Handle::GetGiHandle(), CObject_id::GetId8(), CSeq_id_Handle::GetSeqId(), CDbtag_Base::GetTag(), CLoadLockGi::IsFound(), LoadGiSeq_ids(), CReadDispatcher::LoadSeq_idGi(), CReadDispatcher::LoadSeq_idSeq_ids(), CReader::m_Dispatcher, result, CReader::SetAndSaveNoSeq_idSeq_ids(), CReader::SetAndSaveSeq_idSeq_ids(), CLoadLockSeqIds::SetLoadedSeq_ids(), and CSeq_id_Handle::Which().

x_AddConnectionSlot()

void CId1Reader::x_AddConnectionSlot ( TConn  conn )

protectedvirtual

Implements CReader.

Definition at line 174 of file reader_id1.cpp.

References _ASSERT, conn, and m_Connections.

x_ConnDescription()

string CId1Reader::x_ConnDescription ( CConn_IOStream &  stream ) const

protected

Definition at line 211 of file reader_id1.cpp.

References CReaderServiceConnector::GetConnDescription(), and m_Connector.

Referenced by GetBlob(), x_ConnectAtSlot(), x_ReceiveReply(), and x_SendRequest().

x_ConnectAtSlot()

void CId1Reader::x_ConnectAtSlot ( TConn  conn )

protectedvirtual

Implements CReader.

Definition at line 217 of file reader_id1.cpp.

References conn, CONN_SetTimeout(), CReaderServiceConnector::Connect(), eIO_Close, eIO_ReadWrite, eTraceOpen, CConn_IOStream::GetCONN(), GetDebugLevel(), m_Connections, m_Connector, CReaderServiceConnector::SConnInfo::m_Stream, NCBI_THROW, STimeoutTag::sec, SetRandomFail, CReaderServiceConnector::SetTimeoutTo(), STimeoutTag::usec, and x_ConnDescription().

x_DisconnectAtSlot()

void CId1Reader::x_DisconnectAtSlot ( TConn  conn, bool  failed  )

protectedvirtual

Reimplemented from CReader.

Definition at line 187 of file reader_id1.cpp.

References _ASSERT, conn, failed, m_Connections, m_Connector, CReaderServiceConnector::SConnInfo::m_Stream, CReaderServiceConnector::RememberIfBad(), AutoPtr< X, Del >::reset(), and CReader::x_ReportDisconnect().

x_GetConnection()

CConn_IOStream * CId1Reader::x_GetConnection ( TConn  conn )

protected

Definition at line 199 of file reader_id1.cpp.

References _VERIFY, conn, AutoPtr< X, Del >::get(), m_Connections, CReaderServiceConnector::SConnInfo::m_Stream, and CReader::OpenConnection().

Referenced by GetBlob(), x_ReceiveReply(), and x_SendRequest().

x_ReceiveMainBlob()

CRef<CTSE_Info> CId1Reader::x_ReceiveMainBlob ( CConn_IOStream *  stream )

protected

x_ReceiveReply()

void CId1Reader::x_ReceiveReply ( TConn  conn, CID1server_back &  reply  )

protected

Definition at line 756 of file reader_id1.cpp.

References Begin(), conn, eTraceASN, eTraceConn, GetDebugLevel(), in(), MSerial_AsnText, NCBI_RETHROW, CProcessor::OffsetAllGisToOM(), SetRandomFail, x_ConnDescription(), and x_GetConnection().

Referenced by x_ResolveId().

x_RemoveConnectionSlot()

void CId1Reader::x_RemoveConnectionSlot ( TConn  conn )

protectedvirtual

Implements CReader.

Definition at line 181 of file reader_id1.cpp.

References _VERIFY, conn, map_checker< Container >::erase(), and m_Connections.

x_ResolveId()

CReader::TBlobVersion CId1Reader::x_ResolveId ( CReaderRequestResult &  result, CID1server_back &  id1_reply, CID1server_request &  id1_request  )

protected

Definition at line 611 of file reader_id1.cpp.

References conn, CBioseq_Handle::fState_confidential, CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_not_found, CBioseq_Handle::fState_withdrawn, CID1server_back_Base::GetError(), CID1server_back_Base::IsError(), NCBI_THROW_FMT, result, x_ReceiveReply(), and x_SendRequest().

Referenced by GetBlobVersion(), LoadGiBlob_ids(), LoadGiSeq_ids(), and LoadSeq_idGi().

x_SendRequest() [1/2]

void CId1Reader::x_SendRequest ( const CBlob_id &  blob_id, TConn  conn  )

protected

Definition at line 711 of file reader_id1.cpp.

References conn, CID1server_request_Base::SetGetsefromgi(), x_SendRequest(), and x_SetParams().

x_SendRequest() [2/2]

void CId1Reader::x_SendRequest ( TConn  conn, CID1server_request &  request  )

protected

Definition at line 719 of file reader_id1.cpp.

References Begin(), conn, eTraceASN, eTraceConn, GetDebugLevel(), MSerial_AsnText, NCBI_RETHROW, CProcessor::OffsetAllGisFromOM(), out(), SetRandomFail, x_ConnDescription(), and x_GetConnection().

Referenced by GetBlob(), x_ResolveId(), and x_SendRequest().

x_SetBlobRequest()

void CId1Reader::x_SetBlobRequest ( CID1server_request &  request, const CBlob_id &  blob_id  )

protected

Definition at line 687 of file reader_id1.cpp.

References CID1server_request_Base::SetGetsewithinfo(), and x_SetParams().

Referenced by GetBlob().

x_SetParams()

void CId1Reader::x_SetParams ( CID1server_maxcomplex &  params, const CBlob_id &  blob_id  )

protected

Definition at line 694 of file reader_id1.cpp.

References eEntry_complexities_entry, CId1ReaderBase::GetExtAnnotGi(), CId1ReaderBase::GetExtAnnotSubSat(), CBlob_id::GetSat(), CBlob_id::GetSatKey(), GI_FROM, CId1ReaderBase::IsAnnotSat(), NStr::NumericToString(), CID1server_maxcomplex_Base::SetEnt(), CID1server_maxcomplex_Base::SetGi(), CID1server_maxcomplex_Base::SetMaxplex(), CID1server_maxcomplex_Base::SetSat(), and ZERO_GI.

Referenced by GetBlobVersion(), x_SendRequest(), and x_SetBlobRequest().

Member Data Documentation

m_Connections

TConnections CId1Reader::m_Connections

protected

Definition at line 113 of file reader_id1.hpp.

Referenced by x_AddConnectionSlot(), x_ConnectAtSlot(), x_DisconnectAtSlot(), x_GetConnection(), and x_RemoveConnectionSlot().

m_Connector

CReaderServiceConnector CId1Reader::m_Connector

protected

Definition at line 110 of file reader_id1.hpp.

Referenced by CId1Reader(), x_ConnDescription(), x_ConnectAtSlot(), and x_DisconnectAtSlot().

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The documentation for this class was generated from the following files:

• include/objtools/data_loaders/genbank/id1/reader_id1.hpp
• src/objtools/data_loaders/genbank/id1/reader_id1.cpp