Search Toolkit Book for CBioseq_set_EditHandle

#include <objmgr/bioseq_set_handle.hpp>

Inheritance diagram for CBioseq_set_EditHandle:

Collaboration diagram for CBioseq_set_EditHandle:

Public Types
enum	ERemoveMode { eRemoveSeq_entry , eKeepSeq_entry }

Public Types inherited from CBioseq_set_Handle
typedef CBioseq_set	TObject
	Unified interface for templates. More...

typedef CBioseq_set::TId	TId

typedef CBioseq_set::TColl	TColl

typedef CBioseq_set::TLevel	TLevel

typedef CBioseq_set::TClass	TClass

typedef CBioseq_set::TRelease	TRelease

typedef CBioseq_set::TDate	TDate

typedef CBioseq_set::TDescr	TDescr

Public Member Functions
	CBioseq_set_EditHandle (void)

	CBioseq_set_EditHandle (const CBioseq_set_Handle &h)
	create edit interface class to the object which already allows editing throw an exception if the argument is not in editing mode More...

CSeq_entry_EditHandle	GetParentEntry (void) const
	Navigate object tree. More...

void	ResetId (void) const

void	SetId (TId &id) const

void	ResetColl (void) const

void	SetColl (TColl &v) const

void	ResetLevel (void) const

void	SetLevel (TLevel v) const

void	ResetClass (void) const

void	SetClass (TClass v) const

void	ResetRelease (void) const

void	SetRelease (TRelease &v) const

void	ResetDate (void) const

void	SetDate (TDate &v) const

void	ResetDescr (void) const

void	SetDescr (TDescr &v) const

TDescr &	SetDescr (void) const

bool	AddSeqdesc (CSeqdesc &d) const

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

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

void	AddSeq_descr (TDescr &v) const

CSeq_entry_EditHandle	AddNewEntry (int index) const
	Create new empty seq-entry. More...

CSeq_annot_EditHandle	AttachAnnot (CSeq_annot &annot) const
	Attach an annotation. More...

CSeq_annot_EditHandle	CopyAnnot (const CSeq_annot_Handle &annot) const
	Attach a copy of the annotation. More...

CSeq_annot_EditHandle	TakeAnnot (const CSeq_annot_EditHandle &annot) const
	Remove the annotation from its location and attach to current one. More...

CBioseq_EditHandle	AttachBioseq (CBioseq &seq, int index=-1) const
	Attach a bioseq. More...

CBioseq_EditHandle	CopyBioseq (const CBioseq_Handle &seq, int index=-1) const
	Attach a copy of the bioseq. More...

CBioseq_EditHandle	TakeBioseq (const CBioseq_EditHandle &seq, int index=-1) const
	Remove bioseq from its location and attach to current one. More...

CSeq_entry_EditHandle	AttachEntry (CSeq_entry &entry, int index=-1) const
	Attach an existing seq-entry. More...

CSeq_entry_EditHandle	AttachEntry (CRef< CSeq_entry_Info > entry, int index=-1) const

CSeq_entry_EditHandle	CopyEntry (const CSeq_entry_Handle &entry, int index=-1) const
	Attach a copy of the existing seq-entry. More...

CSeq_entry_EditHandle	TakeEntry (const CSeq_entry_EditHandle &entry, int index=-1) const
	Remove seq-entry from its location and attach to current one. More...

CSeq_entry_EditHandle	AttachEntry (const CSeq_entry_EditHandle &entry, int index=-1) const
	Attach seq-entry previously removed from another place. More...

void	Remove (ERemoveMode mode=eRemoveSeq_entry) const
	Remove current seqset-entry from its location. More...

TScopeInfo &	x_GetScopeInfo (void) const

CBioseq_set_Info &	x_GetInfo (void) const

void	x_RealResetDescr (void) const

void	x_RealSetDescr (TDescr &v) const

bool	x_RealAddSeqdesc (CSeqdesc &d) const

CRef< CSeqdesc >	x_RealRemoveSeqdesc (const CSeqdesc &d) const

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

void	x_RealAddSeq_descr (TDescr &v) const

void	x_RealResetId (void) const

void	x_RealSetId (TId &id) const

void	x_RealResetColl (void) const

void	x_RealSetColl (TColl &v) const

void	x_RealResetLevel (void) const

void	x_RealSetLevel (TLevel v) const

void	x_RealResetClass (void) const

void	x_RealSetClass (TClass v) const

void	x_RealResetRelease (void) const

void	x_RealSetRelease (TRelease &v) const

void	x_RealResetDate (void) const

void	x_RealSetDate (TDate &v) const

Public Member Functions inherited from CBioseq_set_Handle
	CBioseq_set_Handle (void)

CScope &	GetScope (void) const
	Get scope this handle belongs to. More...

CSeq_entry_Handle	GetParentEntry (void) const
	Return a handle for the parent seq-entry of the bioseq. More...

CBioseq_set_Handle	GetParentBioseq_set (void) const
	Return a handle for the parent Bioseq-set, or null handle. More...

CSeq_entry_Handle	GetTopLevelEntry (void) const
	Return a handle for the top-level seq-entry. More...

CBioseq_set_EditHandle	GetEditHandle (void) const
	Get 'edit' version of handle. More...

CConstRef< CBioseq_set >	GetCompleteBioseq_set (void) const
	Return the complete bioseq-set object. More...

CConstRef< CBioseq_set >	GetBioseq_setCore (void) const
	Return core data for the bioseq-set. More...

CConstRef< TObject >	GetCompleteObject (void) const

CConstRef< TObject >	GetObjectCore (void) const

const CBioObjectId &	GetBioObjectId (void) const
	Get unique object id. More...

bool	IsEmptySeq_set (void) const
	Check if the bioseq set is empty. More...

bool	IsSetId (void) const

bool	CanGetId (void) const

const TId &	GetId (void) const

bool	IsSetColl (void) const

bool	CanGetColl (void) const

const TColl &	GetColl (void) const

bool	IsSetLevel (void) const

bool	CanGetLevel (void) const

TLevel	GetLevel (void) const

bool	IsSetClass (void) const

bool	CanGetClass (void) const

TClass	GetClass (void) const

bool	IsSetRelease (void) const

bool	CanGetRelease (void) const

const TRelease &	GetRelease (void) const

bool	IsSetDate (void) const

bool	CanGetDate (void) const

const TDate &	GetDate (void) const

bool	IsSetDescr (void) const

bool	CanGetDescr (void) const

const TDescr &	GetDescr (void) const

bool	HasAnnots (void) const

	DECLARE_OPERATOR_BOOL (m_Info.IsValid())
	Check if handle points to a bioseq-set. More...

bool	IsRemoved (void) const

const CTSE_Handle &	GetTSE_Handle (void) const

void	Reset (void)

bool	operator== (const CBioseq_set_Handle &handle) const
	Check if handles point to the same bioseq. More...

bool	operator!= (const CBioseq_set_Handle &handle) const

bool	operator< (const CBioseq_set_Handle &handle) const
	For usage in containers. More...

CSeq_entry_Handle	GetComplexityLevel (CBioseq_set::EClass cls) const
	Go up to a certain complexity level (or the nearest level of the same priority if the required class is not found). More...

CSeq_entry_Handle	GetExactComplexityLevel (CBioseq_set::EClass cls) const
	Return level with exact complexity, or empty handle if not found. More...

int	GetSeq_entry_Index (const CSeq_entry_Handle &handle) const

const TScopeInfo &	x_GetScopeInfo (void) const

const CBioseq_set_Info &	x_GetInfo (void) const

Protected Member Functions
	CBioseq_set_EditHandle (CBioseq_set_Info &info, const CTSE_Handle &tse)

void	x_Detach (void) const

Protected Member Functions inherited from CBioseq_set_Handle
	CBioseq_set_Handle (const CBioseq_set_Info &info, const CTSE_Handle &tse)

	CBioseq_set_Handle (const TLock &lock)

CScope_Impl &	x_GetScopeImpl (void) const

Friends
class	CScope_Impl

class	CBioseq_EditHandle

class	CSeq_entry_EditHandle

Additional Inherited Members
Protected Types inherited from CBioseq_set_Handle
typedef CBioseq_set_ScopeInfo	TScopeInfo

typedef CScopeInfo_Ref< TScopeInfo >	TLock

typedef int	TComplexityTable[25]

Static Protected Member Functions inherited from CBioseq_set_Handle
static const TComplexityTable &	sx_GetComplexityTable (void)

Protected Attributes inherited from CBioseq_set_Handle
TLock	m_Info

Static Protected Attributes inherited from CBioseq_set_Handle
static TComplexityTable	sm_ComplexityTable

Detailed Description

CBioseq_set_EditHandle –.

Proxy to access and edit the bioseq_set objects

Definition at line 265 of file bioseq_set_handle.hpp.

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

include/objmgr/bioseq_set_handle.hpp
src/objmgr/bioseq_set_handle.cpp

Public Types

Public Member Functions

Protected Member Functions

Friends

Additional Inherited Members

Detailed Description