Search Toolkit Book for CTopLevelSeqEntryContext

#include <objtools/format/context.hpp>

Inheritance diagram for CTopLevelSeqEntryContext:

Collaboration diagram for CTopLevelSeqEntryContext:

Public Member Functions
	CTopLevelSeqEntryContext (const CSeq_entry_Handle &entry_handle, bool useIndexedFasterSets=false)

void	x_InitSeqs (const CSeq_entry &sep)

bool	GetCanSourcePubsBeFused (void) const

bool	GetHasSmallGenomeSet (void) const

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

Private Attributes
bool	m_CanSourcePubsBeFused

bool	m_HasSmallGenomeSet

Additional Inherited Members
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 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...

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

Detailed Description

Definition at line 504 of file context.hpp.

Constructor & Destructor Documentation

◆ CTopLevelSeqEntryContext()

CTopLevelSeqEntryContext::CTopLevelSeqEntryContext	(	const CSeq_entry_Handle &	entry_handle,
		bool	useIndexedFasterSets = `false`
	)

Definition at line 1303 of file context.cpp.

References CBioseq_set_Handle::CanGetClass(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CBioseq_set_Base::eClass_small_genome_set, CSeq_entry_CI::eRecursive, CTextseq_id_Base::GetAccession(), CBioseq_set_Handle::GetClass(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetId(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetSeq_entryCore(), CSeq_entry_Handle::GetSet(), CSeq_id::GetTextseq_Id(), CSeq_entry_Handle::GetTopLevelEntry(), CConstRef< C, Locker >::IsNull(), CSeq_entry_Handle::IsSet(), CTextseq_id_Base::IsSetAccession(), ITERATE, m_CanSourcePubsBeFused, m_HasSmallGenomeSet, CSeq_id_Base::Which(), and x_InitSeqs().

Member Function Documentation

◆ GetCanSourcePubsBeFused()

bool CTopLevelSeqEntryContext::GetCanSourcePubsBeFused ( void ) const

inline

Definition at line 510 of file context.hpp.

References m_CanSourcePubsBeFused.

◆ GetHasSmallGenomeSet()

bool CTopLevelSeqEntryContext::GetHasSmallGenomeSet ( void ) const

inline

Definition at line 511 of file context.hpp.

References m_HasSmallGenomeSet.

◆ x_InitSeqs()

void CTopLevelSeqEntryContext::x_InitSeqs ( const CSeq_entry & sep )

Member Data Documentation

◆ m_CanSourcePubsBeFused

bool CTopLevelSeqEntryContext::m_CanSourcePubsBeFused

private

Definition at line 514 of file context.hpp.

Referenced by CTopLevelSeqEntryContext(), GetCanSourcePubsBeFused(), and x_InitSeqs().

◆ m_HasSmallGenomeSet

bool CTopLevelSeqEntryContext::m_HasSmallGenomeSet

private

Definition at line 515 of file context.hpp.

Referenced by CTopLevelSeqEntryContext(), GetHasSmallGenomeSet(), and x_InitSeqs().

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

include/objtools/format/context.hpp
src/objtools/format/context.cpp

Public Member Functions

Private Attributes

Additional Inherited Members