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

NCBI C++ ToolKit: CProcessor Class Reference

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

enum EType {
  eType_ID1 , eType_ID1_SNP , eType_Seq_entry , eType_Seq_entry_SNP ,
  eType_St_Seq_entry , eType_St_Seq_entry_SNPT , eType_ID2 , eType_ID2AndSkel ,
  eType_ID2_SE , eType_ID2_Split , eType_ID2_Chunk , eType_ID2_SNP ,
  eType_ExtAnnot , eType_AnnotInfo
} typedef CBlob_id TBlobId typedef int TBlobState typedef int TBlobVersion typedef int TChunkId typedef unsigned TMagic 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...
virtual ~CProcessor (void) virtual EType GetType (void) const =0 virtual TMagic GetMagic (void) const =0 virtual void ProcessStream (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CNcbiIstream &stream) const virtual void ProcessObjStream (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const void ProcessBlobFromID2Data (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, const CID2_Reply_Data &data) const 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 static void RegisterAllProcessors (CReadDispatcher &dispatcher) static bool TryStringPack (void) static bool TrySNPSplit (void) static bool TrySNPTable (void) static void SetSeqEntryReadHooks (CObjectIStream &in) static void SetSNPReadHooks (CObjectIStream &in) static void SetLoaded (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CLoadLockBlob &blob) static TIntId GetGiOffset (void) static void OffsetGi (TGi &gi, TIntId gi_offset) static void OffsetGi (TIntId &gi, TIntId gi_offset) static bool OffsetId (CSeq_id &id, TIntId gi_offset) static bool OffsetId (CSeq_id_Handle &id, TIntId gi_offset) static void OffsetAllGis (CBeginInfo obj, TIntId gi_offset) static void OffsetAllGis (CTSE_SetObjectInfo &set_info, TIntId gi_offset) static TGi ConvertGiFromOM (TGi gi) static TGi ConvertGiToOM (TGi gi) static CSeq_id_Handle ConvertIdFromOM (CSeq_id_Handle id) static void OffsetGiToOM (TGi &gi) static void OffsetIdToOM (CSeq_id &id) static void OffsetAllGisFromOM (CBeginInfo obj) static void OffsetAllGisToOM (CBeginInfo obj, CTSE_SetObjectInfo *set_info=0) 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 void EnableDebugDump (bool on) static int CollectStatistics (void) static void LogStat (CReaderRequestResultRecursion &recursion, const CBlob_id &blob_id, CGBRequestStatistics::EStatType stat_type, const char *descr, double size) static void LogStat (CReaderRequestResultRecursion &recursion, const CBlob_id &blob_id, int chunk_id, CGBRequestStatistics::EStatType stat_type, const char *descr, double size) static void LogStat (CReaderRequestResultRecursion &recursion, const CBlob_id &blob_id, CGBRequestStatistics::EStatType stat_type, const char *descr, CNcbiStreampos size) static void LogStat (CReaderRequestResultRecursion &recursion, const CBlob_id &blob_id, int chunk_id, CGBRequestStatistics::EStatType stat_type, const char *descr, CNcbiStreampos size) static void LogStat (CReaderRequestResultRecursion &recursion, const CBlob_id &blob_id, CGBRequestStatistics::EStatType stat_type, const char *descr, size_t size) static void LogStat (CReaderRequestResultRecursion &recursion, const CBlob_id &blob_id, int chunk_id, CGBRequestStatistics::EStatType stat_type, const char *descr, size_t size)

Definition at line 61 of file processor.hpp.

◆ TBlobId ◆ TBlobState ◆ TBlobVersion ◆ TChunkId ◆ TMagic ◆ EType Enumerator eType_ID1 eType_ID1_SNP eType_Seq_entry eType_Seq_entry_SNP eType_St_Seq_entry eType_St_Seq_entry_SNPT eType_ID2 eType_ID2AndSkel eType_ID2_SE eType_ID2_Split eType_ID2_Chunk eType_ID2_SNP eType_ExtAnnot eType_AnnotInfo

Definition at line 68 of file processor.hpp.

◆ ~CProcessor() CProcessor::~CProcessor ( void ) virtual

Definition at line 232 of file processors.cpp.

◆ CProcessor() ◆ CollectStatistics() int CProcessor::CollectStatistics ( void ) inlinestaticprotected ◆ ConvertGiFromOM() ◆ ConvertGiToOM() ◆ ConvertIdFromOM() ◆ GetGiOffset() TIntId CProcessor::GetGiOffset ( void ) static ◆ GetMagic() virtual TMagic CProcessor::GetMagic ( void ) const pure virtual

Implemented in CProcessor_AnnotInfo, CProcessor_ExtAnnot, CProcessor_ID2AndSkel, CProcessor_ID2_Split, CProcessor_ID2, CProcessor_St_SE_SNPT, CProcessor_St_SE, CProcessor_SE_SNP, CProcessor_SE, CProcessor_ID1_SNP, and CProcessor_ID1.

Referenced by CWriter::WriteProcessorTag(), and CCacheReader::x_ProcessBlob().

◆ GetType() virtual EType CProcessor::GetType ( void ) const pure virtual

Referenced by CReadDispatcher::InsertProcessor(), CWriter::WriteProcessorTag(), and CCacheReader::x_ProcessBlob().

◆ GetWriter() ◆ LogStat() [1/6] ◆ LogStat() [2/6]

Definition at line 2479 of file processors.cpp.

References cmd, CReaderRequestResultRecursion::GetResult(), CReadDispatcher::LogStat(), and ncbi::grid::netcache::search::fields::size.

Referenced by LogStat(), CProcessor_ID2::ProcessData(), CProcessor_ID1::ProcessObjStream(), CProcessor_ID1_SNP::ProcessObjStream(), CProcessor_SE::ProcessObjStream(), CProcessor_SE_SNP::ProcessObjStream(), CProcessor_St_SE::ProcessObjStream(), CProcessor_ID2::ProcessObjStream(), CProcessor_ID2_Split::ProcessObjStream(), CProcessor_ID2AndSkel::ProcessObjStream(), and CProcessor_St_SE_SNPT::ProcessStream().

◆ LogStat() [3/6] ◆ LogStat() [4/6] ◆ LogStat() [5/6] ◆ LogStat() [6/6] ◆ OffsetAllGis() [1/2]

Definition at line 499 of file processors.cpp.

Referenced by OffsetAllGisFromOM(), and OffsetAllGisToOM().

◆ OffsetAllGis() [2/2] ◆ OffsetAllGisFromOM() void CProcessor::OffsetAllGisFromOM ( CBeginInfo obj ) static ◆ OffsetAllGisToOM() ◆ OffsetGi() [1/2] ◆ OffsetGi() [2/2] ◆ OffsetGiToOM() static void CProcessor::OffsetGiToOM ( TGi & gi ) inlinestatic ◆ OffsetId() [1/2]

Definition at line 429 of file processors.cpp.

References NStr::eNocase, NStr::EqualNocase(), NStr::fConvErr_NoThrow, CDbtag_Base::GetDb(), GI_FROM, NPOS, NStr::NumericToString(), CDbtag_Base::SetTag(), NStr::StartsWith(), NStr::StringToNumeric(), tag, and ZERO_GI.

Referenced by ConvertIdFromOM(), OffsetAllGis(), OffsetId(), and OffsetIdToOM().

◆ OffsetId() [2/2] ◆ OffsetIdToOM() ◆ ProcessBlobFromID2Data() ◆ ProcessObjStream() ◆ ProcessStream() ◆ RegisterAllProcessors() ◆ SetLoaded() ◆ SetSeqEntryReadHooks() ◆ SetSNPReadHooks() ◆ TrySNPSplit() bool CProcessor::TrySNPSplit ( void ) static ◆ TrySNPTable() bool CProcessor::TrySNPTable ( void ) static ◆ TryStringPack() bool CProcessor::TryStringPack ( void ) static ◆ m_Dispatcher

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

include/objtools/data_loaders/genbank/impl/processor.hpp
src/objtools/data_loaders/genbank/processors.cpp

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