#include <objtools/data_loaders/genbank/writer.hpp>

Inheritance diagram for CWriter:

Collaboration diagram for CWriter:

Classes
class	CBlobStream

Public Types
enum	EType { eBlobWriter , eIdWriter }

typedef CBlob_id	TBlobId

typedef int	TChunkId

typedef int	TBlobState

typedef int	TBlobVersion

typedef int	TProcessorTag

typedef vector< char >	TOctetString

typedef list< TOctetString * >	TOctetStringSequence

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...

Public Member Functions
virtual	~CWriter (void)

virtual void	SaveSeq_idSeq_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

virtual void	SaveSeq_idGi (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

virtual void	SaveSeq_idAccVer (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

virtual void	SaveSeq_idLabel (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

virtual void	SaveSeq_idTaxId (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

virtual void	SaveSequenceHash (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

virtual void	SaveSequenceLength (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

virtual void	SaveSequenceType (CReaderRequestResult &result, const CSeq_id_Handle &seq_id)=0

virtual void	SaveSeq_idBlob_ids (CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel)=0

virtual void	SaveBlobState (CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state)=0

virtual void	SaveBlobVersion (CReaderRequestResult &result, const TBlobId &blob_id, TBlobVersion version)=0

virtual CRef< CBlobStream >	OpenBlobStream (CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, const CProcessor &processor)=0

virtual bool	CanWrite (EType type) const =0

virtual void	InitializeCache (CReaderCacheManager &cache_manager, const TPluginManagerParamTree *params)

virtual void	ResetCache (void)

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

Static Public Member Functions
static void	WriteInt (CNcbiOstream &stream, int value)

static void	WriteBytes (CNcbiOstream &stream, CRef< CByteSource > bs)

static void	WriteBytes (CNcbiOstream &stream, CRef< CByteSourceReader > rdr)

static void	WriteBytes (CNcbiOstream &stream, const TOctetString &data)

static void	WriteBytes (CNcbiOstream &stream, const TOctetStringSequence &data)

static void	WriteProcessorTag (CNcbiOstream &stream, const CProcessor &processor)

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)

Additional Inherited Members
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...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 55 of file writer.hpp.

Member Typedef Documentation

◆ TBlobId

typedef CBlob_id CWriter::TBlobId

Definition at line 58 of file writer.hpp.

◆ TBlobState

typedef int CWriter::TBlobState

Definition at line 60 of file writer.hpp.

◆ TBlobVersion

typedef int CWriter::TBlobVersion

Definition at line 61 of file writer.hpp.

◆ TChunkId

typedef int CWriter::TChunkId

Definition at line 59 of file writer.hpp.

◆ TOctetString

typedef vector<char> CWriter::TOctetString

Definition at line 117 of file writer.hpp.

◆ TOctetStringSequence

typedef list<TOctetString*> CWriter::TOctetStringSequence

Definition at line 118 of file writer.hpp.

◆ TProcessorTag

typedef int CWriter::TProcessorTag

Definition at line 62 of file writer.hpp.

Member Enumeration Documentation

◆ EType

enum CWriter::EType ( void )

Enumerator
eBlobWriter
eIdWriter

Definition at line 64 of file writer.hpp.

Constructor & Destructor Documentation

◆ ~CWriter()

CWriter::~CWriter ( void )

virtual

Definition at line 42 of file writer.cpp.

Member Function Documentation

◆ CanWrite()

virtual bool CWriter::CanWrite ( EType type ) const

pure virtual

Implemented in CCacheWriter.

◆ InitializeCache()

void CWriter::InitializeCache	(	CReaderCacheManager &	cache_manager,
		const TPluginManagerParamTree *	params
	)

virtual

Reimplemented in CCacheWriter.

Definition at line 107 of file writer.cpp.

Referenced by CGBDataLoader_Native::x_CreateWriter().

◆ OpenBlobStream()

virtual CRef<CBlobStream> CWriter::OpenBlobStream	(	CReaderRequestResult &	result,
		const TBlobId &	blob_id,
		TChunkId	chunk_id,
		const CProcessor &	processor
	)

pure virtual

Implemented in CCacheWriter.

◆ ResetCache()

void CWriter::ResetCache ( void )

virtual

Reimplemented in CCacheWriter.

Definition at line 113 of file writer.cpp.

◆ SaveBlobState()

virtual void CWriter::SaveBlobState	(	CReaderRequestResult &	result,
		const TBlobId &	blob_id,
		TBlobState	blob_state
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveBlobVersion()

virtual void CWriter::SaveBlobVersion	(	CReaderRequestResult &	result,
		const TBlobId &	blob_id,
		TBlobVersion	version
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSeq_idAccVer()

virtual void CWriter::SaveSeq_idAccVer	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSeq_idBlob_ids()

virtual void CWriter::SaveSeq_idBlob_ids	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id,
		const SAnnotSelector *	sel
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSeq_idGi()

virtual void CWriter::SaveSeq_idGi	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSeq_idLabel()

virtual void CWriter::SaveSeq_idLabel	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSeq_idSeq_ids()

virtual void CWriter::SaveSeq_idSeq_ids	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSeq_idTaxId()

virtual void CWriter::SaveSeq_idTaxId	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSequenceHash()

virtual void CWriter::SaveSequenceHash	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSequenceLength()

virtual void CWriter::SaveSequenceLength	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

pure virtual

Implemented in CCacheWriter.

◆ SaveSequenceType()

virtual void CWriter::SaveSequenceType	(	CReaderRequestResult &	result,
		const CSeq_id_Handle &	seq_id
	)

pure virtual

Implemented in CCacheWriter.

◆ WriteBytes() [1/4]

void CWriter::WriteBytes	(	CNcbiOstream &	stream,
		const TOctetString &	data
	)

static

Definition at line 90 of file writer.cpp.

References data.

◆ WriteBytes() [2/4]

void CWriter::WriteBytes	(	CNcbiOstream &	stream,
		const TOctetStringSequence &	data
	)

static

Definition at line 81 of file writer.cpp.

References data, ITERATE, and WriteBytes().

◆ WriteBytes() [3/4]

void CWriter::WriteBytes	(	CNcbiOstream &	stream,
		CRef< CByteSource >	bs
	)

static

Definition at line 53 of file writer.cpp.

References CByteSource::Open().

Referenced by CProcessor_ID1::SaveBlob(), CProcessor_St_SE::SaveBlob(), and WriteBytes().

◆ WriteBytes() [4/4]

void CWriter::WriteBytes	(	CNcbiOstream &	stream,
		CRef< CByteSourceReader >	rdr
	)

static

Definition at line 60 of file writer.cpp.

References buffer, BUFFER_SIZE, cnt, CByteSourceReader::EndOfData(), NCBI_THROW, and CByteSourceReader::Read().

◆ WriteInt()

void CWriter::WriteInt	(	CNcbiOstream &	stream,
		int	value
	)

static

Definition at line 47 of file writer.cpp.

References rapidjson::value.

Referenced by WriteProcessorTag().

◆ WriteProcessorTag()

void CWriter::WriteProcessorTag	(	CNcbiOstream &	stream,
		const CProcessor &	processor
	)

static

Definition at line 99 of file writer.cpp.

References CProcessor::GetMagic(), CProcessor::GetType(), and WriteInt().

Referenced by CCacheWriter::OpenBlobStream().

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

include/objtools/data_loaders/genbank/writer.hpp
src/objtools/data_loaders/genbank/writer.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TBlobId

◆ TBlobState

◆ TBlobVersion

◆ TChunkId

◆ TOctetString

◆ TOctetStringSequence

◆ TProcessorTag

Member Enumeration Documentation

◆ EType

Constructor & Destructor Documentation

◆ ~CWriter()

Member Function Documentation

◆ CanWrite()

◆ InitializeCache()

◆ OpenBlobStream()

◆ ResetCache()

◆ SaveBlobState()

◆ SaveBlobVersion()

◆ SaveSeq_idAccVer()

◆ SaveSeq_idBlob_ids()

◆ SaveSeq_idGi()

◆ SaveSeq_idLabel()

◆ SaveSeq_idSeq_ids()

◆ SaveSeq_idTaxId()

◆ SaveSequenceHash()

◆ SaveSequenceLength()

◆ SaveSequenceType()

◆ WriteBytes() [1/4]

◆ WriteBytes() [2/4]

◆ WriteBytes() [3/4]

◆ WriteBytes() [4/4]

◆ WriteInt()

◆ WriteProcessorTag()