#include <objtools/edit/apply_object.hpp>

Inheritance diagram for CApplyObject:

Collaboration diagram for CApplyObject:

Public Member Functions
	CApplyObject (CSeq_entry_Handle seh, CConstRef< CObject > orig, CRef< CObject > editable)

	CApplyObject (CBioseq_Handle bsh, const CSeqdesc &desc)

	CApplyObject (CBioseq_Handle bsh, CSeqdesc::E_Choice subtype)

	CApplyObject (CBioseq_Handle bsh, const string &user_label)

	CApplyObject (CBioseq_Handle bsh, const CSeq_feat &feat)

	CApplyObject (CBioseq_Handle bsh)

bool	PreExists () const

CObject &	SetObject ()

const CObject &	GetObject () const

const CObject *	GetOriginalObject () const

void	ReplaceEditable (CObject &edit)

void	DeleteEditable (bool do_delete=true)

CSeq_entry_Handle	GetSEH () const

void	ApplyChange ()

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 Attributes
CSeq_entry_Handle	m_SEH

CConstRef< CObject >	m_Original

CRef< CObject >	m_Editable

bool	m_Delete

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 50 of file apply_object.hpp.

Constructor & Destructor Documentation

◆ CApplyObject() [1/6]

CApplyObject::CApplyObject	(	CSeq_entry_Handle	seh,
		CConstRef< CObject >	orig,
		CRef< CObject >	editable
	)

inline

Definition at line 53 of file apply_object.hpp.

◆ CApplyObject() [2/6]

CApplyObject::CApplyObject	(	CBioseq_Handle	bsh,
		const CSeqdesc &	desc
	)

Definition at line 49 of file apply_object.cpp.

References CSerialObject::Assign(), CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetClass(), CBioseq_set_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CRef< C, Locker >::GetPointer(), CBioseq_set_Handle::IsSetClass(), and CSeq_entry_Handle::Reset().

◆ CApplyObject() [3/6]

CApplyObject::CApplyObject	(	CBioseq_Handle	bsh,
		CSeqdesc::E_Choice	subtype
	)

Definition at line 66 of file apply_object.cpp.

References CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Title, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_Handle::GetParentEntry(), CBioseq_set_Handle::GetParentEntry(), CRef< C, Locker >::GetPointer(), CBioseq_set_Handle::IsSetClass(), m_Editable, m_Original, m_SEH, CConstRef< C, Locker >::Reset(), and CSeqdesc_Base::Select().

◆ CApplyObject() [4/6]

CApplyObject::CApplyObject	(	CBioseq_Handle	bsh,
		const string &	user_label
	)

Definition at line 83 of file apply_object.cpp.

References CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_Handle::GetParentEntry(), CBioseq_set_Handle::GetParentEntry(), CRef< C, Locker >::GetPointer(), CBioseq_set_Handle::IsSetClass(), m_Editable, m_Original, m_SEH, CConstRef< C, Locker >::Reset(), CUser_object_Base::SetType(), and CSeqdesc_Base::SetUser().

◆ CApplyObject() [5/6]

CApplyObject::CApplyObject	(	CBioseq_Handle	bsh,
		const CSeq_feat &	feat
	)

Definition at line 98 of file apply_object.cpp.

References CSerialObject::Assign(), CBioseq_Handle::GetParentEntry(), CRef< C, Locker >::GetPointer(), m_Editable, m_Original, m_SEH, and CConstRef< C, Locker >::Reset().

◆ CApplyObject() [6/6]

CApplyObject::CApplyObject ( CBioseq_Handle bsh )

Definition at line 108 of file apply_object.cpp.

References CSerialObject::Assign(), CBioseq_Handle::GetCompleteBioseq(), CBioseq_Handle::GetParentEntry(), CConstRef< C, Locker >::GetPointer(), CRef< C, Locker >::GetPointer(), m_Editable, m_Original, m_SEH, and CConstRef< C, Locker >::Reset().

Member Function Documentation

◆ ApplyChange()

void CApplyObject::ApplyChange ( )

Definition at line 118 of file apply_object.cpp.

References CSeq_annot_EditHandle::AddFeat(), CSeq_entry_EditHandle::AddSeqdesc(), CSerialObject::Assign(), CSeq_entry_EditHandle::AttachAnnot(), CBioseq_set_Base::eClass_nuc_prot, CSeq_annot_CI::eSearch_entry, ftable, CSeq_feat_Handle::GetAnnot(), CSeq_feat_EditHandle::GetAnnot(), CScope::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetData(), CBioseq_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CBioseq_Handle::GetParentBioseq_set(), CSeq_entry_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CSeq_annot_Handle::GetParentEntry(), CSeq_annot_EditHandle::GetParentEntry(), CConstRef< C, Locker >::GetPointer(), CRef< C, Locker >::GetPointer(), CSeq_feat_Base::GetProduct(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetSeq(), CScope::GetSeq_featHandle(), GetSeqEntryForSeqdesc(), CSeq_entry_Handle::GetSet(), CSeqFeatData_Base::IsCdregion(), CSeq_entry_Handle::IsSet(), CBioseq_set_Handle::IsSetClass(), CSeq_feat_Base::IsSetData(), CSeq_feat_Handle::IsSetData(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Handle::IsSetProduct(), m_Delete, m_Editable, m_Original, m_SEH, CSeq_feat_EditHandle::Remove(), CSeq_entry_EditHandle::RemoveSeqdesc(), CSeq_feat_EditHandle::Replace(), CSeq_annot_Base::SetData(), CBioseq_EditHandle::SetInst(), and CSeq_annot_EditHandle::TakeFeat().

◆ DeleteEditable()

void CApplyObject::DeleteEditable ( bool do_delete = true )

inline

Definition at line 67 of file apply_object.hpp.

◆ GetObject()

const CObject& CApplyObject::GetObject ( void ) const

inline

Definition at line 64 of file apply_object.hpp.

◆ GetOriginalObject()

const CObject* CApplyObject::GetOriginalObject ( ) const

inline

Definition at line 65 of file apply_object.hpp.

Referenced by GetCommandFromApplyObject().

◆ GetSEH()

CSeq_entry_Handle CApplyObject::GetSEH ( ) const

inline

Definition at line 68 of file apply_object.hpp.

Referenced by GetCommandFromApplyObject().

◆ PreExists()

bool CApplyObject::PreExists ( ) const

inline

Definition at line 62 of file apply_object.hpp.

Referenced by GetCommandFromApplyObject().

◆ ReplaceEditable()

void CApplyObject::ReplaceEditable ( CObject & edit )

inline

Definition at line 66 of file apply_object.hpp.

◆ SetObject()

CObject& CApplyObject::SetObject ( void )

inline

Definition at line 63 of file apply_object.hpp.

Referenced by GetCommandFromApplyObject().

Member Data Documentation

◆ m_Delete

bool CApplyObject::m_Delete

protected

Definition at line 75 of file apply_object.hpp.

Referenced by ApplyChange().

◆ m_Editable

CRef<CObject> CApplyObject::m_Editable

protected

Definition at line 74 of file apply_object.hpp.

Referenced by ApplyChange(), and CApplyObject().

◆ m_Original

CConstRef<CObject> CApplyObject::m_Original

protected

Definition at line 73 of file apply_object.hpp.

Referenced by ApplyChange(), and CApplyObject().

◆ m_SEH

CSeq_entry_Handle CApplyObject::m_SEH

protected

Definition at line 72 of file apply_object.hpp.

Referenced by ApplyChange(), and CApplyObject().

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

include/objtools/edit/apply_object.hpp
src/objtools/edit/apply_object.cpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CApplyObject() [1/6]

◆ CApplyObject() [2/6]

◆ CApplyObject() [3/6]

◆ CApplyObject() [4/6]

◆ CApplyObject() [5/6]

◆ CApplyObject() [6/6]

Member Function Documentation

◆ ApplyChange()

◆ DeleteEditable()

◆ GetObject()

◆ GetOriginalObject()

◆ GetSEH()

◆ PreExists()

◆ ReplaceEditable()

◆ SetObject()

Member Data Documentation

◆ m_Delete

◆ m_Editable

◆ m_Original

◆ m_SEH