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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCId1ReaderBase.html below:

NCBI C++ ToolKit: CId1ReaderBase Class Reference

Search Toolkit Book for CId1ReaderBase

#include <objtools/data_loaders/genbank/impl/reader_id1_base.hpp>

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
} 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 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...
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) virtual void GetBlobState (CReaderRequestResult &result, const CBlob_id &blob_id)=0 virtual void GetBlobVersion (CReaderRequestResult &result, const CBlob_id &blob_id)=0 virtual void GetBlob (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id)=0 CReader (void) virtual ~CReader (void) void InitParams (CConfig &conf, const string &driver_name, int default_max_conn) virtual bool LoadSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel) All LoadXxx() methods should return false if there is no requested data in the reader. More...
virtual bool LoadSeq_idSeq_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0 virtual bool LoadSeq_idGi (CReaderRequestResult &result, const CSeq_id_Handle &seq_id) 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 virtual int GetMaximumConnectionsLimit (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) 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...
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

Definition at line 44 of file reader_id1_base.hpp.

◆ ESat Enumerator eSat_ANNOT_CDD eSat_ANNOT eSat_TRACE eSat_TRACE_ASSM eSat_TR_ASSM_CH eSat_TRACE_CHGR

Definition at line 75 of file reader_id1_base.hpp.

◆ ESubSat Enumerator eSubSat_main eSubSat_SNP eSubSat_SNP_graph eSubSat_CDD eSubSat_MGC eSubSat_HPRD eSubSat_STS eSubSat_tRNA eSubSat_microRNA eSubSat_Exon

Definition at line 84 of file reader_id1_base.hpp.

◆ CId1ReaderBase() ◆ ~CId1ReaderBase() ◆ CreateExtAnnotBlob_ids() void CId1ReaderBase::CreateExtAnnotBlob_ids ( TBlobIds & blob_ids, TIntId gi, int ext_feat ) static ◆ GetAnnotSat() ◆ GetBlob() ◆ GetBlobState() ◆ GetBlobVersion() ◆ GetExtAnnotGi() ◆ GetExtAnnotSubSat() ◆ GetNextExtAnnotBit() int CId1ReaderBase::GetNextExtAnnotBit ( int & ext_feat ) static ◆ IsAnnotSat() bool CId1ReaderBase::IsAnnotSat ( int sat ) static ◆ LoadBlob() ◆ LoadBlobState() ◆ LoadBlobVersion() ◆ LoadChunk() ◆ SetExtAnnotBlob_id()

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

include/objtools/data_loaders/genbank/impl/reader_id1_base.hpp
src/objtools/data_loaders/genbank/reader_id1_base.cpp

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