Search Toolkit Book for CSeq_entry_Info

#include <objmgr/impl/seq_entry_info.hpp>

Inheritance diagram for CSeq_entry_Info:

Collaboration diagram for CSeq_entry_Info:

Public Types
typedef CSeq_entry	TObject

typedef TObject::E_Choice	E_Choice

typedef CBioseq_set_Info	TSet

typedef CBioseq_Info	TSeq

typedef CSeq_descr	TDescr

typedef CSeq_descr::Tdata::const_iterator	TDesc_CI

typedef unsigned	TDescTypeMask

typedef vector< CRef< CSeq_annot_Info > >	TAnnot

typedef vector< CSeq_id_Handle >	TSeqIds

Public Types inherited from CTSE_Info_Object
enum	ENeedUpdateAux { kNeedUpdate_bits = 8 }

enum	ENeedUpdate { fNeedUpdate_this = (1<<kNeedUpdate_bits)-1 , fNeedUpdate_children = fNeedUpdate_this<<kNeedUpdate_bits , fNeedUpdate_descr = 1<<0 , fNeedUpdate_annot = 1<<1 , fNeedUpdate_seq_data = 1<<2 , fNeedUpdate_core = 1<<3 , fNeedUpdate_assembly = 1<<4 , fNeedUpdate_bioseq = 1<<5 , fNeedUpdate_children_descr = fNeedUpdate_descr <<kNeedUpdate_bits , fNeedUpdate_children_annot = fNeedUpdate_annot <<kNeedUpdate_bits , fNeedUpdate_children_seq_data = fNeedUpdate_seq_data<<kNeedUpdate_bits , fNeedUpdate_children_core = fNeedUpdate_core <<kNeedUpdate_bits , fNeedUpdate_children_assembly = fNeedUpdate_assembly<<kNeedUpdate_bits , fNeedUpdate_children_bioseq = fNeedUpdate_bioseq <<kNeedUpdate_bits }

typedef map< CConstRef< CObject >, CRef< CObject > >	TObjectCopyMap

typedef int	TNeedUpdateFlags

typedef int	TChunkId

typedef vector< TChunkId >	TChunkIds

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
	CSeq_entry_Info (void)

	CSeq_entry_Info (const CSeq_entry_Info &info, TObjectCopyMap *copy_map)

	CSeq_entry_Info (CSeq_entry &entry)

virtual	~CSeq_entry_Info (void)

const CBioseq_set_Info &	GetParentBioseq_set_Info (void) const

CBioseq_set_Info &	GetParentBioseq_set_Info (void)

const CSeq_entry_Info &	GetParentSeq_entry_Info (void) const

CSeq_entry_Info &	GetParentSeq_entry_Info (void)

const CSeq_entry_Info &	GetXrefTSE () const

virtual const CBioObjectId &	GetBioObjectId (void) const

bool	HasNoSeq_entry (void) const

CConstRef< TObject >	GetCompleteSeq_entry (void) const

CConstRef< TObject >	GetSeq_entryCore (void) const

CConstRef< TObject >	GetSeq_entrySkeleton (void) const

E_Choice	Which (void) const

void	x_CheckWhich (E_Choice which) const

void	Reset (void)

bool	IsSet (void) const

const TSet &	GetSet (void) const

TSet &	SetSet (void)

TSet &	SelectSet (void)

TSet &	SelectSet (TSet &seqset)

TSet &	SelectSet (CBioseq_set &seqset)

bool	IsSeq (void) const

const TSeq &	GetSeq (void) const

TSeq &	SetSeq (void)

TSeq &	SelectSeq (TSeq &seq)

TSeq &	SelectSeq (CBioseq &seq)

bool	IsSetDescr (void) const

const TDescr &	GetDescr (void) const

void	ResetDescr (void)

void	SetDescr (TDescr &v)

TDescr &	SetDescr (void)

bool	AddSeqdesc (CSeqdesc &d)

CRef< CSeqdesc >	RemoveSeqdesc (const CSeqdesc &d)

CRef< CSeqdesc >	ReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc)

void	AddSeq_descr (const TDescr &v)

const CBioseq_Base_Info &	x_GetBaseInfo (void) const

bool	x_IsEndDesc (TDesc_CI iter) const

TDesc_CI	x_GetFirstDesc (TDescTypeMask types) const

TDesc_CI	x_GetNextDesc (TDesc_CI iter, TDescTypeMask types) const

CRef< CSeq_annot_Info >	AddAnnot (CSeq_annot &annot)

void	AddAnnot (CRef< CSeq_annot_Info > annot)

void	RemoveAnnot (CRef< CSeq_annot_Info > annot)

const TAnnot &	GetLoadedAnnot (void) const

CRef< CSeq_entry_Info >	AddEntry (CSeq_entry &entry, int index=-1)

void	AddEntry (CRef< CSeq_entry_Info > entry, int index=-1)

void	RemoveEntry (CRef< CSeq_entry_Info > entry)

void	x_ParentAttach (CBioseq_set_Info &parent)

void	x_ParentDetach (CBioseq_set_Info &parent)

virtual void	x_DSAttachContents (CDataSource &ds)

virtual void	x_DSDetachContents (CDataSource &ds)

virtual void	x_TSEAttachContents (CTSE_Info &tse_info)

virtual void	x_TSEDetachContents (CTSE_Info &tse_info)

void	UpdateAnnotIndex (void) const

void	x_SetBioseqChunkId (TChunkId chunk_id)

void	x_GetBioseqsIds (TSeqIds &ids) const

virtual void	GetBioseqsIds (TSeqIds &ids) const

void	x_GetAnnotIds (TSeqIds &ids) const

virtual void	GetAnnotIds (TSeqIds &ids) const

virtual void	GetSeqAndAnnotIds (TSeqIds &seq_ids, TSeqIds &annot_ids) const

Public Member Functions inherited from CTSE_Info_Object
	CTSE_Info_Object (void)

	CTSE_Info_Object (const CTSE_Info_Object &src, TObjectCopyMap *copy_map)

virtual	~CTSE_Info_Object (void)

virtual void	SetBioObjectId (const CBioObjectId &id)

bool	HasDataSource (void) const

CDataSource &	GetDataSource (void) const

bool	HasTSE_Info (void) const

bool	BelongsToTSE_Info (const CTSE_Info &tse) const

const CTSE_Info &	GetTSE_Info (void) const

CTSE_Info &	GetTSE_Info (void)

bool	HasParent_Info (void) const

const CTSE_Info_Object &	GetBaseParent_Info (void) const

CTSE_Info_Object &	GetBaseParent_Info (void)

void	x_DSAttach (CDataSource &ds)

void	x_DSDetach (CDataSource &ds)

void	x_TSEAttach (CTSE_Info &tse)

void	x_TSEDetach (CTSE_Info &tse)

bool	x_DirtyAnnotIndex (void) const

void	x_SetDirtyAnnotIndex (void)

void	x_SetParentDirtyAnnotIndex (void)

void	x_ResetDirtyAnnotIndex (void)

virtual void	x_SetDirtyAnnotIndexNoParent (void)

virtual void	x_ResetDirtyAnnotIndexNoParent (void)

void	x_UpdateAnnotIndex (CTSE_Info &tse)

bool	x_NeedUpdate (ENeedUpdate flag) const

void	x_SetNeedUpdate (TNeedUpdateFlags flags)

virtual void	x_SetNeedUpdateParent (TNeedUpdateFlags flags)

void	x_Update (TNeedUpdateFlags flags) const

void	x_UpdateComplete (void) const

void	x_UpdateCore (void) const

void	x_LoadChunk (TChunkId chunk_id) const

void	x_LoadChunks (const TChunkIds &chunk_ids) const

virtual string	GetDescription (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

Protected Member Functions
void	x_AttachContents (void)

void	x_DetachContents (void)

TObject &	x_GetObject (void)

const TObject &	x_GetObject (void) const

void	x_SetObject (TObject &obj)

void	x_SetObject (const CSeq_entry_Info &info, TObjectCopyMap *copy_map)

void	x_Select (CSeq_entry::E_Choice which, CBioseq_Base_Info *contents)

void	x_Select (CSeq_entry::E_Choice which, CRef< CBioseq_Base_Info > contents)

void	x_DSMapObject (CConstRef< TObject > obj, CDataSource &ds)

void	x_DSUnmapObject (CConstRef< TObject > obj, CDataSource &ds)

void	x_UpdateAnnotIndexContents (CTSE_Info &tse)

void	x_UpdateSkeleton () const

void	x_Update (TNeedUpdateFlags flags) const

void	x_DoUpdate (TNeedUpdateFlags flags)

void	x_SetNeedUpdateContents (TNeedUpdateFlags flags)

CSeq_entry_Info &	operator= (const CSeq_entry_Info &)

Protected Member Functions inherited from CTSE_Info_Object
void	x_BaseParentAttach (CTSE_Info_Object &parent)

void	x_BaseParentDetach (CTSE_Info_Object &parent)

void	x_AttachObject (CTSE_Info_Object &object)

void	x_DetachObject (CTSE_Info_Object &object)

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

Static Protected Member Functions
static CRef< TObject >	sx_ShallowCopy (TObject &obj)

Protected Attributes
CRef< TObject >	m_Object

E_Choice	m_Which

CRef< CBioseq_Base_Info >	m_Contents

Private Types
typedef CTSE_Info_Object	TParent

Friends
class	CScope_Impl

class	CDataSource

class	CAnnot_Collector

class	CSeq_annot_CI

class	CTSE_Info

class	CBioseq_Base_Info

class	CBioseq_Info

class	CBioseq_set_Info

class	CSeq_annot_Info

Additional Inherited Members
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 72 of file seq_entry_info.hpp.

Member Typedef Documentation

◆ E_Choice

typedef TObject::E_Choice CSeq_entry_Info::E_Choice

Definition at line 102 of file seq_entry_info.hpp.

◆ TAnnot

typedef vector< CRef<CSeq_annot_Info> > CSeq_entry_Info::TAnnot

Definition at line 153 of file seq_entry_info.hpp.

◆ TDesc_CI

typedef CSeq_descr::Tdata::const_iterator CSeq_entry_Info::TDesc_CI

Definition at line 143 of file seq_entry_info.hpp.

◆ TDescr

typedef CSeq_descr CSeq_entry_Info::TDescr

Definition at line 126 of file seq_entry_info.hpp.

◆ TDescTypeMask

typedef unsigned CSeq_entry_Info::TDescTypeMask

Definition at line 144 of file seq_entry_info.hpp.

◆ TObject

typedef CSeq_entry CSeq_entry_Info::TObject

Definition at line 94 of file seq_entry_info.hpp.

◆ TParent

typedef CTSE_Info_Object CSeq_entry_Info::TParent

private

Definition at line 74 of file seq_entry_info.hpp.

◆ TSeq

typedef CBioseq_Info CSeq_entry_Info::TSeq

Definition at line 117 of file seq_entry_info.hpp.

◆ TSeqIds

typedef vector<CSeq_id_Handle> CSeq_entry_Info::TSeqIds

Definition at line 176 of file seq_entry_info.hpp.

◆ TSet

typedef CBioseq_set_Info CSeq_entry_Info::TSet

Definition at line 107 of file seq_entry_info.hpp.

Constructor & Destructor Documentation

◆ CSeq_entry_Info() [1/3]

CSeq_entry_Info::CSeq_entry_Info ( void )

Definition at line 58 of file seq_entry_info.cpp.

◆ CSeq_entry_Info() [2/3]

CSeq_entry_Info::CSeq_entry_Info	(	const CSeq_entry_Info &	info,
		TObjectCopyMap *	copy_map
	)

explicit

Definition at line 71 of file seq_entry_info.cpp.

References info, and x_SetObject().

◆ CSeq_entry_Info() [3/3]

CSeq_entry_Info::CSeq_entry_Info ( CSeq_entry & entry )

explicit

Definition at line 64 of file seq_entry_info.cpp.

References x_SetObject().

◆ ~CSeq_entry_Info()

CSeq_entry_Info::~CSeq_entry_Info ( void )

virtual

Definition at line 83 of file seq_entry_info.cpp.

Member Function Documentation

◆ AddAnnot() [1/2]

void CSeq_entry_Info::AddAnnot ( CRef< CSeq_annot_Info > annot )

Definition at line 625 of file seq_entry_info.cpp.

References CBioseq_Base_Info::AddAnnot(), and m_Contents.

◆ AddAnnot() [2/2]

CRef< CSeq_annot_Info > CSeq_entry_Info::AddAnnot ( CSeq_annot & annot )

Definition at line 619 of file seq_entry_info.cpp.

References CBioseq_Base_Info::AddAnnot(), and m_Contents.

Referenced by CTSE_ScopeInfo::AddAnnot(), CDataSource::AttachAnnot(), and CScope_Impl::x_AttachAnnot().

◆ AddEntry() [1/2]

void CSeq_entry_Info::AddEntry	(	CRef< CSeq_entry_Info >	entry,
		int	index = `-1`
	)

Definition at line 656 of file seq_entry_info.cpp.

References CBioseq_set_Info::AddEntry(), CSeq_entry_Base::e_Set, SetSet(), and x_CheckWhich().

◆ AddEntry() [2/2]

CRef< CSeq_entry_Info > CSeq_entry_Info::AddEntry	(	CSeq_entry &	entry,
		int	index = `-1`
	)

Definition at line 648 of file seq_entry_info.cpp.

References CBioseq_set_Info::AddEntry(), CSeq_entry_Base::e_Set, SetSet(), and x_CheckWhich().

◆ AddSeq_descr()

void CSeq_entry_Info::AddSeq_descr ( const TDescr & v )

Definition at line 591 of file seq_entry_info.cpp.

References CBioseq_Base_Info::AddSeq_descr(), CTSE_Info_Object::fNeedUpdate_descr, m_Contents, and x_Update().

Referenced by CSeq_entry_EditHandle::x_RealAddSeq_descr().

◆ AddSeqdesc()

bool CSeq_entry_Info::AddSeqdesc ( CSeqdesc & d )

Definition at line 562 of file seq_entry_info.cpp.

References CBioseq_Base_Info::AddSeqdesc(), CTSE_Info_Object::fNeedUpdate_descr, m_Contents, and x_Update().

Referenced by CSeq_entry_EditHandle::x_RealAddSeqdesc().

◆ GetAnnotIds()

void CSeq_entry_Info::GetAnnotIds ( TSeqIds & ids ) const

virtual

Reimplemented in CTSE_Info.

Definition at line 745 of file seq_entry_info.cpp.

References CTSE_Info_Object::GetTSE_Info(), CTSE_Info::UpdateAnnotIndex(), and x_GetAnnotIds().

Referenced by GetSeqAndAnnotIds().

◆ GetBioObjectId()

const CBioObjectId & CSeq_entry_Info::GetBioObjectId ( void ) const

virtual

Reimplemented from CTSE_Info_Object.

Definition at line 669 of file seq_entry_info.cpp.

References CTSE_Info_Object::GetBioObjectId(), and m_Contents.

Referenced by CSeq_entry_Handle::GetBioObjectId().

◆ GetBioseqsIds()

void CSeq_entry_Info::GetBioseqsIds ( TSeqIds & ids ) const

virtual

Reimplemented in CTSE_Info.

Definition at line 738 of file seq_entry_info.cpp.

References x_GetBioseqsIds().

Referenced by GetSeqAndAnnotIds().

◆ GetCompleteSeq_entry()

CConstRef< CSeq_entry > CSeq_entry_Info::GetCompleteSeq_entry ( void ) const

Definition at line 302 of file seq_entry_info.cpp.

References m_Object, and CTSE_Info_Object::x_UpdateComplete().

Referenced by CSeq_entry_Handle::GetCompleteSeq_entry(), CTSE_Info::GetCompleteTSE(), and CTSE_Handle::GetCompleteTSE().

◆ GetDescr()

const CSeq_descr & CSeq_entry_Info::GetDescr ( void ) const

Definition at line 534 of file seq_entry_info.cpp.

References CTSE_Info_Object::fNeedUpdate_descr, CBioseq_Base_Info::GetDescr(), m_Contents, and x_Update().

Referenced by CSeq_entry_Handle::GetDescr().

◆ GetLoadedAnnot()

const CSeq_entry_Info::TAnnot & CSeq_entry_Info::GetLoadedAnnot ( void ) const

Definition at line 676 of file seq_entry_info.cpp.

References _ASSERT, CBioseq_Base_Info::GetLoadedAnnot(), m_Contents, and NCBI_THROW.

Referenced by CSeq_annot_Finder::Find().

◆ GetParentBioseq_set_Info() [1/2]

CBioseq_set_Info & CSeq_entry_Info::GetParentBioseq_set_Info ( void )

Definition at line 94 of file seq_entry_info.cpp.

References CTSE_Info_Object::GetBaseParent_Info().

◆ GetParentBioseq_set_Info() [2/2]

const CBioseq_set_Info & CSeq_entry_Info::GetParentBioseq_set_Info ( void ) const

Definition at line 88 of file seq_entry_info.cpp.

References CTSE_Info_Object::GetBaseParent_Info().

Referenced by CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentBioseq_set(), GetParentSeq_entry_Info(), GetXrefTSE(), CDataSource::RemoveEntry(), CTSE_ScopeInfo::RemoveEntry(), and CBioseq_Base_Info::x_SearchFirstDesc().

◆ GetParentSeq_entry_Info() [1/2]

CSeq_entry_Info & CSeq_entry_Info::GetParentSeq_entry_Info ( void )

Definition at line 106 of file seq_entry_info.cpp.

References GetParentBioseq_set_Info(), and CBioseq_Base_Info::GetParentSeq_entry_Info().

◆ GetParentSeq_entry_Info() [2/2]

const CSeq_entry_Info & CSeq_entry_Info::GetParentSeq_entry_Info ( void ) const

Definition at line 100 of file seq_entry_info.cpp.

References GetParentBioseq_set_Info(), and CBioseq_Base_Info::GetParentSeq_entry_Info().

◆ GetSeq()

const CBioseq_Info & CSeq_entry_Info::GetSeq ( void ) const

Definition at line 164 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_Seq, CTSE_Info_Object::fNeedUpdate_bioseq, m_Contents, x_CheckWhich(), and x_Update().

Referenced by CScope_Impl::AddBioseq(), CScope_Impl::AddSharedBioseq(), x_GetBioseqsIds(), and CBioseq_CI::x_Settle().

◆ GetSeq_entryCore()

CConstRef< CSeq_entry > CSeq_entry_Info::GetSeq_entryCore ( void ) const

Definition at line 309 of file seq_entry_info.cpp.

References m_Object, and CTSE_Info_Object::x_UpdateCore().

Referenced by CSeq_entry_Handle::GetSeq_entryCore(), CTSE_Info::GetTSECore(), and CTSE_Handle::GetTSECore().

◆ GetSeq_entrySkeleton()

CConstRef< CSeq_entry > CSeq_entry_Info::GetSeq_entrySkeleton ( void ) const

Definition at line 498 of file seq_entry_info.cpp.

References m_Object, and x_UpdateSkeleton().

Referenced by CDataLoaderPatcher::x_PatchLock().

◆ GetSeqAndAnnotIds()

void CSeq_entry_Info::GetSeqAndAnnotIds	(	TSeqIds &	seq_ids,
		TSeqIds &	annot_ids
	)		const

virtual

Definition at line 753 of file seq_entry_info.cpp.

References GetAnnotIds(), and GetBioseqsIds().

Referenced by CScope_Impl::x_ClearCacheOnNewData().

◆ GetSet()

const CBioseq_set_Info & CSeq_entry_Info::GetSet ( void ) const

Definition at line 182 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_Set, m_Contents, and x_CheckWhich().

Referenced by CScope_Impl::AddSeq_annot(), CScope_Impl::AddSharedSeq_annot(), CWGSMasterSupport::AddWGSMaster(), CTSE_Info::GetTopLevelSeq_submit(), GetXrefTSE(), CDataSource::x_CollectBioseqs(), x_GetAnnotIds(), x_GetBioseqsIds(), CScope_Impl::x_IsDummyTSE(), CBioseq_CI::x_PushEntry(), and CAnnot_Collector::x_SearchAll().

◆ GetXrefTSE()

const CSeq_entry_Info & CSeq_entry_Info::GetXrefTSE ( void ) const

Definition at line 127 of file seq_entry_info.cpp.

References CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, CBioseq_set_Info::GetClass(), GetParentBioseq_set_Info(), CBioseq_Base_Info::GetParentSeq_entry_Info(), GetSet(), CTSE_Info_Object::HasParent_Info(), and IsSet().

Referenced by CSeq_annot_Info::GetXrefTSE(), and CTSE_Info::x_GetFeaturesByLocus().

◆ HasNoSeq_entry()

bool CSeq_entry_Info::HasNoSeq_entry ( void ) const

inline

Definition at line 250 of file seq_entry_info.hpp.

References m_Object.

Referenced by x_CreateEmptyLocalCDDEntry().

◆ IsSeq()

bool CSeq_entry_Info::IsSeq ( void ) const

inline

Definition at line 264 of file seq_entry_info.hpp.

References CSeq_entry_Base::e_Seq, and Which().

Referenced by CScope_Impl::AddSharedBioseq(), and x_GetBioseqsIds().

◆ IsSet()

bool CSeq_entry_Info::IsSet ( void ) const

inline

Definition at line 257 of file seq_entry_info.hpp.

References CSeq_entry_Base::e_Set, and Which().

Referenced by CScope_Impl::AddSharedSeq_annot(), CWGSMasterSupport::AddWGSMaster(), CTSE_Info::GetTopLevelSeq_submit(), GetXrefTSE(), SelectSet(), CDataSource::x_CollectBioseqs(), x_GetAnnotIds(), x_GetBioseqsIds(), CScope_Impl::x_IsDummyTSE(), and CAnnot_Collector::x_SearchAll().

◆ IsSetDescr()

bool CSeq_entry_Info::IsSetDescr ( void ) const

Definition at line 526 of file seq_entry_info.cpp.

References CBioseq_Base_Info::IsSetDescr(), m_Contents, and x_UpdateSkeleton().

Referenced by CSeq_entry_Handle::IsSetDescr().

◆ operator=()

CSeq_entry_Info& CSeq_entry_Info::operator= ( const CSeq_entry_Info & )

protected

◆ RemoveAnnot()

void CSeq_entry_Info::RemoveAnnot ( CRef< CSeq_annot_Info > annot )

Definition at line 631 of file seq_entry_info.cpp.

References m_Contents, and CBioseq_Base_Info::RemoveAnnot().

◆ RemoveEntry()

void CSeq_entry_Info::RemoveEntry ( CRef< CSeq_entry_Info > entry )

Definition at line 663 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_Set, CBioseq_set_Info::RemoveEntry(), SetSet(), and x_CheckWhich().

◆ RemoveSeqdesc()

CRef< CSeqdesc > CSeq_entry_Info::RemoveSeqdesc ( const CSeqdesc & d )

Definition at line 569 of file seq_entry_info.cpp.

References CTSE_Info_Object::fNeedUpdate_descr, m_Contents, CBioseq_Base_Info::RemoveSeqdesc(), and x_Update().

Referenced by CSeq_entry_EditHandle::x_RealRemoveSeqdesc().

◆ ReplaceSeqdesc()

CRef< CSeqdesc > CSeq_entry_Info::ReplaceSeqdesc	(	const CSeqdesc &	old_desc,
		CSeqdesc &	new_desc
	)

Definition at line 576 of file seq_entry_info.cpp.

References CTSE_Info_Object::fNeedUpdate_descr, m_Contents, CBioseq_Base_Info::ReplaceSeqdesc(), and x_Update().

Referenced by CSeq_entry_EditHandle::x_RealReplaceSeqdesc().

◆ Reset()

void CSeq_entry_Info::Reset ( void )

Definition at line 232 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_not_set, CTSE_Info_Object::GetTSE_Info(), CTSE_Info_Object::SetBioObjectId(), and x_Select().

Referenced by CTSE_Info::SetSeq_entry().

◆ ResetDescr()

void CSeq_entry_Info::ResetDescr ( void )

Definition at line 555 of file seq_entry_info.cpp.

References CTSE_Info_Object::fNeedUpdate_descr, m_Contents, CBioseq_Base_Info::ResetDescr(), and x_Update().

Referenced by CSeq_entry_EditHandle::x_RealResetDescr().

◆ SelectSeq() [1/2]

CBioseq_Info & CSeq_entry_Info::SelectSeq ( CBioseq & seq )

Definition at line 276 of file seq_entry_info.cpp.

References CBioseq_Info, and SelectSeq().

◆ SelectSeq() [2/2]

CBioseq_Info & CSeq_entry_Info::SelectSeq ( TSeq & seq )

Definition at line 265 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_not_set, CSeq_entry_Base::e_Seq, NCBI_THROW, SetSeq(), Which(), and x_Select().

Referenced by SelectSeq(), CTSE_ScopeInfo::SelectSeq(), and CScope_Impl::x_SelectSeq().

◆ SelectSet() [1/3]

CBioseq_set_Info & CSeq_entry_Info::SelectSet ( CBioseq_set & seqset )

Definition at line 250 of file seq_entry_info.cpp.

References CBioseq_set_Info, and SelectSet().

◆ SelectSet() [2/3]

CBioseq_set_Info & CSeq_entry_Info::SelectSet ( TSet & seqset )

Definition at line 239 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_not_set, CSeq_entry_Base::e_Set, NCBI_THROW, SetSet(), Which(), and x_Select().

◆ SelectSet() [3/3]

CBioseq_set_Info & CSeq_entry_Info::SelectSet ( void )

Definition at line 256 of file seq_entry_info.cpp.

References IsSet(), and SetSet().

Referenced by SelectSet(), CTSE_ScopeInfo::SelectSet(), and CScope_Impl::x_SelectSet().

◆ SetDescr() [1/2]

void CSeq_entry_Info::SetDescr ( TDescr & v )

Definition at line 541 of file seq_entry_info.cpp.

References CTSE_Info_Object::fNeedUpdate_descr, m_Contents, CBioseq_Base_Info::SetDescr(), and x_Update().

Referenced by CSeq_entry_EditHandle::SetDescr(), and CSeq_entry_EditHandle::x_RealSetDescr().

◆ SetDescr() [2/2]

CSeq_entry_Info::TDescr & CSeq_entry_Info::SetDescr ( void )

Definition at line 548 of file seq_entry_info.cpp.

References CTSE_Info_Object::fNeedUpdate_descr, m_Contents, CBioseq_Base_Info::SetDescr(), and x_Update().

◆ SetSeq()

CBioseq_Info & CSeq_entry_Info::SetSeq ( void )

Definition at line 173 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_Seq, CTSE_Info_Object::fNeedUpdate_bioseq, m_Contents, x_CheckWhich(), and x_Update().

Referenced by SelectSeq(), and x_Select().

◆ SetSet()

CBioseq_set_Info & CSeq_entry_Info::SetSet ( void )

Definition at line 190 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_Set, m_Contents, and x_CheckWhich().

Referenced by AddEntry(), RemoveEntry(), SelectSet(), CLDS2_DataLoader::x_LoadTSE(), and x_Select().

◆ sx_ShallowCopy()

static CRef<TObject> CSeq_entry_Info::sx_ShallowCopy ( TObject & obj )

staticprotected

◆ UpdateAnnotIndex()

void CSeq_entry_Info::UpdateAnnotIndex ( void ) const

Definition at line 458 of file seq_entry_info.cpp.

References CTSE_Info_Object::GetTSE_Info(), CTSE_Info::UpdateAnnotIndex(), and CTSE_Info_Object::x_DirtyAnnotIndex().

Referenced by CDataSource::UpdateAnnotIndex(), and CAnnot_Collector::x_SearchAll().

◆ Which()

CSeq_entry::E_Choice CSeq_entry_Info::Which ( void ) const

Definition at line 491 of file seq_entry_info.cpp.

References m_Which, and x_UpdateSkeleton().

Referenced by IsSeq(), IsSet(), CTSE_ScopeInfo::SelectSeq(), SelectSeq(), CTSE_ScopeInfo::SelectSet(), SelectSet(), CSeq_entry_Handle::Which(), x_CheckWhich(), x_DoUpdate(), x_GetAnnotIds(), and x_Select().

◆ x_AttachContents()

void CSeq_entry_Info::x_AttachContents ( void )

protected

Definition at line 440 of file seq_entry_info.cpp.

References m_Contents, CTSE_Info_Object::x_AttachObject(), and CBioseq_Base_Info::x_ParentAttach().

Referenced by x_Select(), and x_SetObject().

◆ x_CheckWhich()

void CSeq_entry_Info::x_CheckWhich ( E_Choice which ) const

Definition at line 112 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, eGet, NCBI_THROW, and Which().

Referenced by AddEntry(), GetSeq(), GetSet(), RemoveEntry(), SetSeq(), and SetSet().

◆ x_DetachContents()

void CSeq_entry_Info::x_DetachContents ( void )

protected

Definition at line 449 of file seq_entry_info.cpp.

References m_Contents, CTSE_Info_Object::x_DetachObject(), and CBioseq_Base_Info::x_ParentDetach().

Referenced by CTSE_Info::SetSeq_entry(), and x_Select().

◆ x_DoUpdate()

void CSeq_entry_Info::x_DoUpdate ( TNeedUpdateFlags flags )

protectedvirtual

Reimplemented from CTSE_Info_Object.

Reimplemented in CTSE_Info.

Definition at line 282 of file seq_entry_info.cpp.

References _ASSERT, flags, CTSE_Info_Object::fNeedUpdate_bioseq, CTSE_Info_Object::fNeedUpdate_children, kBioseqChunkId, CTSE_Info_Object::kNeedUpdate_bits, m_Contents, m_Object, Which(), CTSE_Info_Object::x_DoUpdate(), CTSE_Info_Object::x_LoadChunk(), and CTSE_Info_Object::x_Update().

Referenced by CTSE_Info::x_DoUpdate().

◆ x_DSAttachContents()

void CSeq_entry_Info::x_DSAttachContents ( CDataSource & ds )

virtual

Reimplemented from CTSE_Info_Object.

Reimplemented in CTSE_Info.

Definition at line 354 of file seq_entry_info.cpp.

References m_Contents, m_Object, CTSE_Info_Object::x_DSAttach(), CTSE_Info_Object::x_DSAttachContents(), and x_DSMapObject().

Referenced by CTSE_Info::x_DSAttachContents().

◆ x_DSDetachContents()

void CSeq_entry_Info::x_DSDetachContents ( CDataSource & ds )

virtual

Reimplemented from CTSE_Info_Object.

Reimplemented in CTSE_Info.

Definition at line 366 of file seq_entry_info.cpp.

References m_Contents, m_Object, CTSE_Info_Object::x_DSDetach(), CTSE_Info_Object::x_DSDetachContents(), and x_DSUnmapObject().

Referenced by CTSE_Info::x_DSDetachContents().

◆ x_DSMapObject()

void CSeq_entry_Info::x_DSMapObject	(	CConstRef< TObject >	obj,
		CDataSource &	ds
	)

protected

Definition at line 378 of file seq_entry_info.cpp.

References CDataSource::x_Map().

Referenced by x_DSAttachContents(), CTSE_Info::x_DSMapObject(), and x_SetObject().

◆ x_DSUnmapObject()

void CSeq_entry_Info::x_DSUnmapObject	(	CConstRef< TObject >	obj,
		CDataSource &	ds
	)

protected

Definition at line 384 of file seq_entry_info.cpp.

References CDataSource::x_Unmap().

Referenced by x_DSDetachContents(), and CTSE_Info::x_DSUnmapObject().

◆ x_GetAnnotIds()

void CSeq_entry_Info::x_GetAnnotIds ( TSeqIds & ids ) const

Definition at line 710 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_not_set, CBioseq_Base_Info::GetAnnot(), CBioseq_set_Info::GetSeq_set(), GetSet(), IsSet(), ITERATE, Which(), and x_GetBaseInfo().

Referenced by GetAnnotIds().

◆ x_GetBaseInfo()

const CBioseq_Base_Info & CSeq_entry_Info::x_GetBaseInfo ( void ) const

Definition at line 519 of file seq_entry_info.cpp.

References m_Contents, and x_UpdateSkeleton().

Referenced by CWGSMasterSupport::AddWGSMaster(), x_GetAnnotIds(), ITSE_Assigner::x_GetBase(), and CAnnot_Collector::x_SearchAll().

◆ x_GetBioseqsIds()

void CSeq_entry_Info::x_GetBioseqsIds ( TSeqIds & ids ) const

Definition at line 695 of file seq_entry_info.cpp.

References CBioseq_Info::GetId(), GetSeq(), CBioseq_set_Info::GetSeq_set(), GetSet(), IsSeq(), IsSet(), and ITERATE.

Referenced by GetBioseqsIds().

◆ x_GetFirstDesc()

CSeq_entry_Info::TDesc_CI CSeq_entry_Info::x_GetFirstDesc ( TDescTypeMask types ) const

Definition at line 606 of file seq_entry_info.cpp.

References m_Contents, types, and CBioseq_Base_Info::x_GetFirstDesc().

◆ x_GetNextDesc()

CSeq_entry_Info::TDesc_CI CSeq_entry_Info::x_GetNextDesc	(	TDesc_CI	iter,
		TDescTypeMask	types
	)		const

Definition at line 613 of file seq_entry_info.cpp.

References m_Contents, types, and CBioseq_Base_Info::x_GetNextDesc().

◆ x_GetObject() [1/2]

CSeq_entry & CSeq_entry_Info::x_GetObject ( void )

protected

Definition at line 505 of file seq_entry_info.cpp.

References m_Object, and x_UpdateSkeleton().

Referenced by x_ParentAttach(), CBioseq_Info::x_ParentAttach(), CBioseq_set_Info::x_ParentAttach(), and x_Select().

◆ x_GetObject() [2/2]

const CSeq_entry & CSeq_entry_Info::x_GetObject ( void ) const

protected

Definition at line 512 of file seq_entry_info.cpp.

References m_Object, and x_UpdateSkeleton().

◆ x_IsEndDesc()

bool CSeq_entry_Info::x_IsEndDesc ( TDesc_CI iter ) const

Definition at line 599 of file seq_entry_info.cpp.

References m_Contents, and CBioseq_Base_Info::x_IsEndDesc().

◆ x_ParentAttach()

void CSeq_entry_Info::x_ParentAttach ( CBioseq_set_Info & parent )

Definition at line 315 of file seq_entry_info.cpp.

References _ASSERT, CBioseq_Base_Info::GetParentSeq_entry_Info(), CTSE_Info_Object::HasParent_Info(), m_Object, CTSE_Info_Object::x_BaseParentAttach(), and x_GetObject().

◆ x_ParentDetach()

void CSeq_entry_Info::x_ParentDetach ( CBioseq_set_Info & parent )

Definition at line 329 of file seq_entry_info.cpp.

References m_Object, and CTSE_Info_Object::x_BaseParentDetach().

◆ x_Select() [1/2]

void CSeq_entry_Info::x_Select	(	CSeq_entry::E_Choice	which,
		CBioseq_Base_Info *	contents
	)

inlineprotected

Definition at line 225 of file seq_entry_info.cpp.

References Ref().

Referenced by Reset(), SelectSeq(), SelectSet(), and x_SetObject().

◆ x_Select() [2/2]

void CSeq_entry_Info::x_Select	(	CSeq_entry::E_Choice	which,
		CRef< CBioseq_Base_Info >	contents
	)

protected

Definition at line 198 of file seq_entry_info.cpp.

References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, m_Contents, m_Object, m_Which, CRef< C, Locker >::Reset(), SetSeq(), SetSet(), Which(), x_AttachContents(), x_DetachContents(), and x_GetObject().

◆ x_SetBioseqChunkId()

void CSeq_entry_Info::x_SetBioseqChunkId ( TChunkId chunk_id )

Definition at line 637 of file seq_entry_info.cpp.

References _ASSERT, CSeq_entry_Base::e_Seq, CTSE_Info_Object::fNeedUpdate_bioseq, kBioseqChunkId, m_Contents, m_Object, m_Which, and CTSE_Info_Object::x_SetNeedUpdate().

Referenced by CTSE_Default_Assigner::AddBioseqPlace().

◆ x_SetNeedUpdateContents()

void CSeq_entry_Info::x_SetNeedUpdateContents ( TNeedUpdateFlags flags )

protected

Definition at line 296 of file seq_entry_info.cpp.

References flags, and CTSE_Info_Object::x_SetNeedUpdate().

◆ x_SetObject() [1/2]

void CSeq_entry_Info::x_SetObject	(	const CSeq_entry_Info &	info,
		TObjectCopyMap *	copy_map
	)

protected

Definition at line 414 of file seq_entry_info.cpp.

References _ASSERT, CBioseq_Info, CBioseq_set_Info, CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CTSE_Info_Object::GetDataSource(), CTSE_Info_Object::HasDataSource(), info, m_Contents, m_Object, CRef< C, Locker >::Reset(), x_DSMapObject(), and x_Select().

◆ x_SetObject() [2/2]

void CSeq_entry_Info::x_SetObject ( TObject & obj )

protected

◆ x_TSEAttachContents()

void CSeq_entry_Info::x_TSEAttachContents ( CTSE_Info & tse_info )

virtual

Reimplemented from CTSE_Info_Object.

Definition at line 336 of file seq_entry_info.cpp.

References m_Contents, CTSE_Info_Object::x_TSEAttach(), and CTSE_Info_Object::x_TSEAttachContents().

◆ x_TSEDetachContents()

void CSeq_entry_Info::x_TSEDetachContents ( CTSE_Info & tse_info )

virtual

Reimplemented from CTSE_Info_Object.

Definition at line 345 of file seq_entry_info.cpp.

References m_Contents, CTSE_Info_Object::x_TSEDetach(), and CTSE_Info_Object::x_TSEDetachContents().

◆ x_Update()

void CSeq_entry_Info::x_Update ( TNeedUpdateFlags flags ) const

protected

Definition at line 484 of file seq_entry_info.cpp.

References flags, CTSE_Info_Object::x_Update(), and x_UpdateSkeleton().

Referenced by AddSeq_descr(), AddSeqdesc(), CTSE_Info::CTSE_Info(), GetDescr(), GetSeq(), RemoveSeqdesc(), ReplaceSeqdesc(), ResetDescr(), SetDescr(), and SetSeq().

◆ x_UpdateAnnotIndexContents()

void CSeq_entry_Info::x_UpdateAnnotIndexContents ( CTSE_Info & tse )

protectedvirtual

Reimplemented from CTSE_Info_Object.

Reimplemented in CTSE_Info.

Definition at line 466 of file seq_entry_info.cpp.

References m_Contents, CTSE_Info_Object::x_UpdateAnnotIndex(), and CTSE_Info_Object::x_UpdateAnnotIndexContents().

Referenced by CTSE_Info::x_UpdateAnnotIndexContents().

◆ x_UpdateSkeleton()

void CSeq_entry_Info::x_UpdateSkeleton ( ) const

inlineprotected

Definition at line 476 of file seq_entry_info.cpp.

References CTSE_Info_Object::GetTSE_Info(), m_Object, and CTSE_Info::x_LoadDelayedMainChunk().

Referenced by GetSeq_entrySkeleton(), IsSetDescr(), Which(), x_GetBaseInfo(), x_GetObject(), and x_Update().

Friends And Related Function Documentation

◆ CAnnot_Collector

friend class CAnnot_Collector

friend

Definition at line 193 of file seq_entry_info.hpp.

◆ CBioseq_Base_Info

friend class CBioseq_Base_Info

friend

Definition at line 197 of file seq_entry_info.hpp.

◆ CBioseq_Info

friend class CBioseq_Info

friend

Definition at line 198 of file seq_entry_info.hpp.

Referenced by SelectSeq(), and x_SetObject().

◆ CBioseq_set_Info

friend class CBioseq_set_Info

friend

Definition at line 199 of file seq_entry_info.hpp.

Referenced by SelectSet(), and x_SetObject().

◆ CDataSource

friend class CDataSource

friend

Definition at line 191 of file seq_entry_info.hpp.

◆ CScope_Impl

friend class CScope_Impl

friend

Definition at line 190 of file seq_entry_info.hpp.

◆ CSeq_annot_CI

friend class CSeq_annot_CI

friend

Definition at line 194 of file seq_entry_info.hpp.

◆ CSeq_annot_Info

friend class CSeq_annot_Info

friend

Definition at line 200 of file seq_entry_info.hpp.

◆ CTSE_Info

friend class CTSE_Info ( void )

friend

Definition at line 196 of file seq_entry_info.hpp.

Member Data Documentation

◆ m_Contents

CRef<CBioseq_Base_Info> CSeq_entry_Info::m_Contents

protected

◆ m_Object

CRef<TObject> CSeq_entry_Info::m_Object

protected

Definition at line 230 of file seq_entry_info.hpp.

Referenced by GetCompleteSeq_entry(), GetSeq_entryCore(), GetSeq_entrySkeleton(), HasNoSeq_entry(), CTSE_Info::SetBlobVersion(), CTSE_Info::SetSeq_entry(), x_DoUpdate(), x_DSAttachContents(), x_DSDetachContents(), x_GetObject(), x_ParentAttach(), x_ParentDetach(), CTSE_Info::x_Reset(), x_Select(), x_SetBioseqChunkId(), x_SetObject(), and x_UpdateSkeleton().

◆ m_Which

E_Choice CSeq_entry_Info::m_Which

protected

Definition at line 233 of file seq_entry_info.hpp.

Referenced by CTSE_Info::SetSeq_entry(), Which(), CTSE_Info::x_Reset(), x_Select(), x_SetBioseqChunkId(), and x_SetObject().

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

include/objmgr/impl/seq_entry_info.hpp
src/objmgr/seq_entry_info.cpp

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Types

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ E_Choice

◆ TAnnot

◆ TDesc_CI

◆ TDescr

◆ TDescTypeMask

◆ TObject

◆ TParent

◆ TSeq

◆ TSeqIds

◆ TSet

Constructor & Destructor Documentation

◆ CSeq_entry_Info() [1/3]

◆ CSeq_entry_Info() [2/3]

◆ CSeq_entry_Info() [3/3]

◆ ~CSeq_entry_Info()

Member Function Documentation

◆ AddAnnot() [1/2]

◆ AddAnnot() [2/2]

◆ AddEntry() [1/2]

◆ AddEntry() [2/2]

◆ AddSeq_descr()

◆ AddSeqdesc()

◆ GetAnnotIds()

◆ GetBioObjectId()

◆ GetBioseqsIds()

◆ GetCompleteSeq_entry()

◆ GetDescr()

◆ GetLoadedAnnot()

◆ GetParentBioseq_set_Info() [1/2]

◆ GetParentBioseq_set_Info() [2/2]

◆ GetParentSeq_entry_Info() [1/2]

◆ GetParentSeq_entry_Info() [2/2]

◆ GetSeq()

◆ GetSeq_entryCore()

◆ GetSeq_entrySkeleton()

◆ GetSeqAndAnnotIds()

◆ GetSet()

◆ GetXrefTSE()

◆ HasNoSeq_entry()

◆ IsSeq()

◆ IsSet()

◆ IsSetDescr()

◆ operator=()

◆ RemoveAnnot()

◆ RemoveEntry()

◆ RemoveSeqdesc()

◆ ReplaceSeqdesc()

◆ Reset()

◆ ResetDescr()

◆ SelectSeq() [1/2]

◆ SelectSeq() [2/2]

◆ SelectSet() [1/3]

◆ SelectSet() [2/3]

◆ SelectSet() [3/3]

◆ SetDescr() [1/2]

◆ SetDescr() [2/2]

◆ SetSeq()

◆ SetSet()

◆ sx_ShallowCopy()

◆ UpdateAnnotIndex()

◆ Which()

◆ x_AttachContents()

◆ x_CheckWhich()

◆ x_DetachContents()

◆ x_DoUpdate()

◆ x_DSAttachContents()

◆ x_DSDetachContents()

◆ x_DSMapObject()

◆ x_DSUnmapObject()

◆ x_GetAnnotIds()