CBioseq_set_Info Class Reference

Search Toolkit Book for CBioseq_set_Info

#include <objmgr/impl/bioseq_set_info.hpp>

Inheritance diagram for CBioseq_set_Info:

Collaboration diagram for CBioseq_set_Info:

Classes
struct	SChunkSeqSet

Public Types
typedef CBioseq_set	TObject
typedef TObject::TId	TId
typedef TObject::TColl	TColl
typedef TObject::TLevel	TLevel
typedef TObject::TClass	TClass
typedef TObject::TRelease	TRelease
typedef TObject::TDate	TDate
typedef vector< CRef< CSeq_entry_Info > >	TSeq_set
Public Types inherited from CBioseq_Base_Info
typedef CSeq_descr	TDescr
typedef TDescr::Tdata	TDescList
typedef TDescList::const_iterator	TDesc_CI
typedef unsigned	TDescTypeMask
typedef vector< CRef< CSeq_annot_Info > >	TAnnot
typedef list< CRef< CSeq_annot > >	TObjAnnot
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
	CBioseq_set_Info (void)
	CBioseq_set_Info (const CBioseq_set_Info &info, TObjectCopyMap *copy_map)
	CBioseq_set_Info (CBioseq_set &seqset)
virtual	~CBioseq_set_Info (void)
CConstRef< TObject >	GetCompleteBioseq_set (void) const
CConstRef< TObject >	GetBioseq_setCore (void) const
bool	IsEmptySeq_set (void) const
bool	IsSetId (void) const
bool	CanGetId (void) const
const TId &	GetId (void) const
void	SetId (TId &v)
void	ResetId (void)
bool	x_IsSetDescr (void) const
bool	x_CanGetDescr (void) const
const TDescr &	x_GetDescr (void) const
TDescr &	x_SetDescr (void)
void	x_SetDescr (TDescr &v)
void	x_ResetDescr (void)
bool	IsSetColl (void) const
bool	CanGetColl (void) const
const TColl &	GetColl (void) const
void	SetColl (TColl &v)
void	ResetColl (void)
bool	IsSetLevel (void) const
bool	CanGetLevel (void) const
TLevel	GetLevel (void) const
void	SetLevel (TLevel v)
void	ResetLevel (void)
bool	IsSetClass (void) const
bool	CanGetClass (void) const
TClass	GetClass (void) const
void	SetClass (TClass v)
void	ResetClass (void)
bool	IsSetRelease (void) const
bool	CanGetRelease (void) const
const TRelease &	GetRelease (void) const
void	SetRelease (TRelease &v)
void	ResetRelease (void)
bool	IsSetDate (void) const
bool	CanGetDate (void) const
const TDate &	GetDate (void) const
void	SetDate (TDate &v)
void	ResetDate (void)
bool	IsSetSeq_set (void) const
bool	CanGetSeq_set (void) const
const TSeq_set &	GetSeq_set (void) const
TSeq_set &	SetSeq_set (void)
CConstRef< CSeq_entry_Info >	GetFirstEntry (void) const
CRef< CSeq_entry_Info >	AddEntry (CSeq_entry &entry, int index, bool set_uniqid=false)
void	AddEntry (CRef< CSeq_entry_Info > entry, int index=-1, bool set_uniqid=false)
void	RemoveEntry (CRef< CSeq_entry_Info > entry)
int	GetEntryIndex (const CSeq_entry_Info &entry) const
virtual void	x_DSAttachContents (CDataSource &ds)
virtual void	x_DSDetachContents (CDataSource &ds)
void	x_AddBioseqChunkId (TChunkId chunk_id)
const TChunkIds &	x_GetBioseqChunkIds () const
virtual void	x_TSEAttachContents (CTSE_Info &tse)
virtual void	x_TSEDetachContents (CTSE_Info &tse)
void	UpdateAnnotIndex (void) const
virtual void	x_UpdateAnnotIndexContents (CTSE_Info &tse)
void	x_AttachEntry (CRef< CSeq_entry_Info > info)
void	x_DetachEntry (CRef< CSeq_entry_Info > info)
void	x_SetChunkBioseqs (const list< CRef< CBioseq > > &bioseqs, int chunk_id)
Public Member Functions inherited from CBioseq_Base_Info
	CBioseq_Base_Info (void)
	CBioseq_Base_Info (const CBioseq_Base_Info &src, TObjectCopyMap *copy_map)
virtual	~CBioseq_Base_Info (void)
const CSeq_entry_Info &	GetParentSeq_entry_Info (void) const
CSeq_entry_Info &	GetParentSeq_entry_Info (void)
bool	IsSetDescr (void) const
bool	CanGetDescr (void) const
const TDescr &	GetDescr (void) const
TDescr &	SetDescr (void)
void	SetDescr (TDescr &v)
void	ResetDescr (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 TDescList &	x_GetDescList (void) const
TDesc_CI	x_GetFirstDesc (TDescTypeMask types) const
TDesc_CI	x_GetNextDesc (TDesc_CI iter, TDescTypeMask types) const
bool	x_IsEndDesc (TDesc_CI iter) const
const CSeqdesc *	x_SearchFirstDesc (TDescTypeMask type) const
TDescTypeMask	x_GetExistingDescrMask (void) const
void	x_AddExistingUserObjectTypes (TUserObjectTypesSet &uo_types) const
bool	IsSetAnnot (void) const
bool	HasAnnots (void) const
const TAnnot &	GetAnnot (void) const
const TAnnot &	GetLoadedAnnot (void) const
void	ResetAnnot (void)
CRef< CSeq_annot_Info >	AddAnnot (CSeq_annot &annot, int chunk_id=0)
void	AddAnnot (CRef< CSeq_annot_Info > annot)
void	RemoveAnnot (CRef< CSeq_annot_Info > annot)
void	x_AttachAnnot (CRef< CSeq_annot_Info > info)
void	x_DetachAnnot (CRef< CSeq_annot_Info > info)
void	x_SetAnnot (void)
void	x_SetAnnot (const CBioseq_Base_Info &info, TObjectCopyMap *copy_map)
void	x_AddDescrChunkId (const TDescTypeMask &types, TChunkId chunk_id)
void	x_AddAnnotChunkId (TChunkId chunk_id)
const TChunkIds &	x_GetDescrChunkIds () const
void	x_SetNeedUpdateParent (TNeedUpdateFlags flags)
void	x_RealLoadDescr (const TDescr &v)
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 const CBioObjectId &	GetBioObjectId (void) const
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)
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 Types
typedef pair< int, TChunkId >	TChunkSeqSetsKey
Protected Types inherited from CBioseq_Base_Info
typedef CFastMutex	TDescrMutex
typedef CFastMutexGuard	TDescrMutexGuard
typedef vector< TDescTypeMask >	TDescTypeMasks

Protected Member Functions
void	x_DSAttachContents (void)
void	x_DSDetachContents (void)
void	x_ParentAttach (CSeq_entry_Info &parent)
void	x_ParentDetach (CSeq_entry_Info &parent)
TObject &	x_GetObject (void)
const TObject &	x_GetObject (void) const
void	x_SetObject (TObject &obj)
void	x_SetObject (const CBioseq_set_Info &info, TObjectCopyMap *copy_map)
void	x_DSMapObject (CConstRef< TObject > obj, CDataSource &ds)
void	x_DSUnmapObject (CConstRef< TObject > obj, CDataSource &ds)
int	x_GetBioseq_set_Id (const CObject_id &object_id)
TObjAnnot &	x_SetObjAnnot (void)
void	x_ResetObjAnnot (void)
void	x_DoUpdate (TNeedUpdateFlags flags)
void	x_SetChunkBioseqs2 (const list< CRef< CBioseq > > &bioseqs, TChunkSeqSetsKey key)
Protected Member Functions inherited from CBioseq_Base_Info
bool	x_IsEndNextDesc (TDesc_CI iter) const
TDesc_CI	x_FindDesc (TDescrMutexGuard &guard, TDesc_CI iter, TDescTypeMask types) const
void	x_PrefetchDesc (TDescrMutexGuard &guard, TDesc_CI last, TDescTypeMask types) const
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 (const TObject &obj)

Private Types
typedef CBioseq_Base_Info	TParent
typedef map< TChunkSeqSetsKey, SChunkSeqSet >	TChunkSeqSets

Private Attributes
CRef< TObject >	m_Object
TSeq_set	m_Seq_set
TChunkSeqSets	m_ChunkSeqSets
TChunkIds	m_BioseqChunks
int	m_Bioseq_set_Id

Friends
class	CDataSource
class	CScope_Impl
class	CTSE_Info
class	CSeq_entry_Info
class	CBioseq_Info
class	CSeq_annot_Info
class	CSeq_entry_CI
class	CSeq_entry_I
class	CSeq_annot_CI
class	CSeq_annot_I
class	CAnnotTypes_CI

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...
Protected Attributes inherited from CBioseq_Base_Info
TAnnot	m_Annot
TObjAnnot *	m_ObjAnnot
TChunkIds	m_DescrChunks
TDescTypeMasks	m_DescrTypeMasks
TChunkIds	m_AnnotChunks
TDescrMutex	m_DescrMutex

Detailed Description

Definition at line 59 of file bioseq_set_info.hpp.

Member Typedef Documentation

TChunkSeqSets

typedef map<TChunkSeqSetsKey, SChunkSeqSet> CBioseq_set_Info::TChunkSeqSets

private

Definition at line 221 of file bioseq_set_info.hpp.

TChunkSeqSetsKey

typedef pair<int, TChunkId> CBioseq_set_Info::TChunkSeqSetsKey

protected

Definition at line 205 of file bioseq_set_info.hpp.

TClass

typedef TObject::TClass CBioseq_set_Info::TClass

Definition at line 106 of file bioseq_set_info.hpp.

TColl

typedef TObject::TColl CBioseq_set_Info::TColl

Definition at line 92 of file bioseq_set_info.hpp.

TDate

typedef TObject::TDate CBioseq_set_Info::TDate

Definition at line 120 of file bioseq_set_info.hpp.

TId

typedef TObject::TId CBioseq_set_Info::TId

Definition at line 78 of file bioseq_set_info.hpp.

TLevel

typedef TObject::TLevel CBioseq_set_Info::TLevel

Definition at line 99 of file bioseq_set_info.hpp.

TObject

typedef CBioseq_set CBioseq_set_Info::TObject

Definition at line 70 of file bioseq_set_info.hpp.

TParent

typedef CBioseq_Base_Info CBioseq_set_Info::TParent

private

Definition at line 61 of file bioseq_set_info.hpp.

TRelease

typedef TObject::TRelease CBioseq_set_Info::TRelease

Definition at line 113 of file bioseq_set_info.hpp.

TSeq_set

typedef vector< CRef<CSeq_entry_Info> > CBioseq_set_Info::TSeq_set

Definition at line 127 of file bioseq_set_info.hpp.

Constructor & Destructor Documentation

CBioseq_set_Info() [1/3]

CBioseq_set_Info::CBioseq_set_Info

(

void

)

Definition at line 57 of file bioseq_set_info.cpp.

CBioseq_set_Info() [2/3]

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

explicit

Definition at line 70 of file bioseq_set_info.cpp.

References info, CBioseq_Base_Info::m_AnnotChunks, m_BioseqChunks, CBioseq_Base_Info::m_DescrChunks, and x_SetObject().

CBioseq_set_Info() [3/3]

CBioseq_set_Info::CBioseq_set_Info ( CBioseq_set &  seqset )

explicit

~CBioseq_set_Info()

CBioseq_set_Info::~CBioseq_set_Info ( void  )

virtual

Definition at line 86 of file bioseq_set_info.cpp.

Member Function Documentation

AddEntry() [1/2]

void CBioseq_set_Info::AddEntry	(	CRef< CSeq_entry_Info >	entry,
		int	index = -1,
		bool	set_uniqid = false
	)

Definition at line 389 of file bioseq_set_info.cpp.

References _ASSERT, CTSE_Info_Object::GetTSE_Info(), i, info, m_Object, m_Seq_set, and x_AttachEntry().

AddEntry() [2/2]

CRef< CSeq_entry_Info > CBioseq_set_Info::AddEntry	(	CSeq_entry &	entry,
		int	index,
		bool	set_uniqid = false
	)

Definition at line 379 of file bioseq_set_info.cpp.

References CSeq_entry_Info, and info.

Referenced by CTSE_ScopeInfo::AddEntry(), CSeq_entry_Info::AddEntry(), CDataSource::AttachEntry(), CTSE_Default_Assigner::LoadBioseq(), CScope_Impl::x_AttachEntry(), and x_SetObject().

CanGetClass()

bool CBioseq_set_Info::CanGetClass ( void  ) const

inline

Definition at line 367 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::CanGetClass().

CanGetColl()

bool CBioseq_set_Info::CanGetColl ( void  ) const

inline

Definition at line 297 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::CanGetColl().

CanGetDate()

bool CBioseq_set_Info::CanGetDate ( void  ) const

inline

Definition at line 437 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::CanGetDate().

CanGetId()

bool CBioseq_set_Info::CanGetId ( void  ) const

inline

Definition at line 262 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::CanGetId().

CanGetLevel()

bool CBioseq_set_Info::CanGetLevel ( void  ) const

inline

Definition at line 332 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::CanGetLevel().

CanGetRelease()

bool CBioseq_set_Info::CanGetRelease ( void  ) const

inline

Definition at line 402 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::CanGetRelease().

CanGetSeq_set()

bool CBioseq_set_Info::CanGetSeq_set ( void  ) const

inline

Definition at line 472 of file bioseq_set_info.hpp.

References CTSE_Info_Object::fNeedUpdate_bioseq, m_Object, and CTSE_Info_Object::x_NeedUpdate().

GetBioseq_setCore()

CConstRef< CBioseq_set > CBioseq_set_Info::GetBioseq_setCore

(

void

)

const

Definition at line 98 of file bioseq_set_info.cpp.

References m_Object, and CTSE_Info_Object::x_UpdateCore().

Referenced by CBioseq_set_Handle::GetBioseq_setCore().

GetClass()

CBioseq_set_Info::TClass CBioseq_set_Info::GetClass ( void  ) const

inline

Definition at line 381 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::GetClass(), CTSE_Info::GetSegSetMaster(), CSeq_entry_Info::GetXrefTSE(), CDataSource::x_CollectBioseqs(), and CBioseq_CI::x_PushEntry().

GetColl()

const CBioseq_set_Info::TColl & CBioseq_set_Info::GetColl ( void  ) const

inline

Definition at line 311 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::GetColl().

GetCompleteBioseq_set()

CConstRef< CBioseq_set > CBioseq_set_Info::GetCompleteBioseq_set

(

void

)

const

Definition at line 91 of file bioseq_set_info.cpp.

References m_Object, and CTSE_Info_Object::x_UpdateComplete().

Referenced by CBioseq_set_Handle::GetCompleteBioseq_set().

GetDate()

const CBioseq_set_Info::TDate & CBioseq_set_Info::GetDate ( void  ) const

inline

Definition at line 451 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::GetDate().

GetEntryIndex()

int CBioseq_set_Info::GetEntryIndex

(

const CSeq_entry_Info &

entry

)

const

Definition at line 442 of file bioseq_set_info.cpp.

References info, ITERATE, and m_Seq_set.

Referenced by CBioseq_set_Handle::GetSeq_entry_Index().

GetFirstEntry()

CConstRef< CSeq_entry_Info > CBioseq_set_Info::GetFirstEntry

(

void

)

const

Definition at line 455 of file bioseq_set_info.cpp.

References m_Seq_set.

Referenced by CWGSMasterSupport::AddWGSMaster(), CTSE_Info::GetSegSetMaster(), and CWGSMasterDescrSetter::Loaded().

GetId()

const CBioseq_set_Info::TId & CBioseq_set_Info::GetId ( void  ) const

inline

Definition at line 276 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::GetId(), and x_TSEAttachContents().

GetLevel()

CBioseq_set_Info::TLevel CBioseq_set_Info::GetLevel ( void  ) const

inline

Definition at line 346 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::GetLevel().

GetRelease()

const CBioseq_set_Info::TRelease & CBioseq_set_Info::GetRelease ( void  ) const

inline

Definition at line 416 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::GetRelease().

GetSeq_set()

const CBioseq_set_Info::TSeq_set & CBioseq_set_Info::GetSeq_set ( void  ) const

inline

Definition at line 480 of file bioseq_set_info.hpp.

References CTSE_Info_Object::fNeedUpdate_bioseq, m_Seq_set, and CTSE_Info_Object::x_Update().

Referenced by IsEmptySeq_set(), CSeq_entry_Info::x_GetAnnotIds(), CSeq_entry_Info::x_GetBioseqsIds(), and CSeq_entry_CI::x_SetCurrentEntry().

IsEmptySeq_set()

bool CBioseq_set_Info::IsEmptySeq_set ( void  ) const

inline

Definition at line 496 of file bioseq_set_info.hpp.

References CTSE_Info_Object::fNeedUpdate_bioseq, GetSeq_set(), IsSetSeq_set(), and CTSE_Info_Object::x_NeedUpdate().

Referenced by CBioseq_set_Handle::IsEmptySeq_set(), and CScope_Impl::x_IsDummyTSE().

IsSetClass()

bool CBioseq_set_Info::IsSetClass ( void  ) const

inline

Definition at line 360 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::IsSetClass(), and CScope_Impl::x_IsDummyTSE().

IsSetColl()

bool CBioseq_set_Info::IsSetColl ( void  ) const

inline

Definition at line 290 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::IsSetColl(), and CScope_Impl::x_IsDummyTSE().

IsSetDate()

bool CBioseq_set_Info::IsSetDate ( void  ) const

inline

Definition at line 430 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::IsSetDate(), and CScope_Impl::x_IsDummyTSE().

IsSetId()

bool CBioseq_set_Info::IsSetId ( void  ) const

inline

Definition at line 255 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::IsSetId(), CScope_Impl::x_IsDummyTSE(), and x_TSEAttachContents().

IsSetLevel()

bool CBioseq_set_Info::IsSetLevel ( void  ) const

inline

Definition at line 325 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::IsSetLevel(), and CScope_Impl::x_IsDummyTSE().

IsSetRelease()

bool CBioseq_set_Info::IsSetRelease ( void  ) const

inline

Definition at line 395 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_Handle::IsSetRelease(), and CScope_Impl::x_IsDummyTSE().

IsSetSeq_set()

bool CBioseq_set_Info::IsSetSeq_set ( void  ) const

inline

Definition at line 465 of file bioseq_set_info.hpp.

References CTSE_Info_Object::fNeedUpdate_bioseq, m_Object, and CTSE_Info_Object::x_NeedUpdate().

Referenced by IsEmptySeq_set(), and CScope_Impl::x_IsDummyTSE().

RemoveEntry()

void CBioseq_set_Info::RemoveEntry

(

CRef< CSeq_entry_Info >

entry

)

Definition at line 417 of file bioseq_set_info.cpp.

References _ASSERT, info, m_Object, m_Seq_set, NCBI_THROW, and x_DetachEntry().

Referenced by CSeq_entry_Info::RemoveEntry(), CDataSource::RemoveEntry(), and CTSE_ScopeInfo::RemoveEntry().

ResetClass()

void CBioseq_set_Info::ResetClass ( void  )

inline

Definition at line 374 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealResetClass().

ResetColl()

void CBioseq_set_Info::ResetColl ( void  )

inline

Definition at line 304 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealResetColl().

ResetDate()

void CBioseq_set_Info::ResetDate ( void  )

inline

Definition at line 444 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealResetDate().

ResetId()

void CBioseq_set_Info::ResetId ( void  )

inline

Definition at line 269 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealResetId().

ResetLevel()

void CBioseq_set_Info::ResetLevel ( void  )

inline

Definition at line 339 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealResetLevel().

ResetRelease()

void CBioseq_set_Info::ResetRelease ( void  )

inline

Definition at line 409 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealResetRelease().

SetClass()

void CBioseq_set_Info::SetClass ( TClass  v )

inline

Definition at line 388 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealSetClass().

SetColl()

void CBioseq_set_Info::SetColl ( TColl &  v )

inline

Definition at line 318 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealSetColl().

SetDate()

void CBioseq_set_Info::SetDate ( TDate &  v )

inline

Definition at line 458 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealSetDate().

SetId()

void CBioseq_set_Info::SetId ( TId &  v )

inline

Definition at line 283 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CLDS2_DataLoader::x_LoadTSE(), and CBioseq_set_EditHandle::x_RealSetId().

SetLevel()

void CBioseq_set_Info::SetLevel ( TLevel  v )

inline

Definition at line 353 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealSetLevel().

SetRelease()

void CBioseq_set_Info::SetRelease ( TRelease &  v )

inline

Definition at line 423 of file bioseq_set_info.hpp.

References m_Object.

Referenced by CBioseq_set_EditHandle::x_RealSetRelease().

SetSeq_set()

CBioseq_set_Info::TSeq_set & CBioseq_set_Info::SetSeq_set ( void  )

inline

Definition at line 488 of file bioseq_set_info.hpp.

References CTSE_Info_Object::fNeedUpdate_bioseq, m_Seq_set, and CTSE_Info_Object::x_Update().

sx_ShallowCopy()

CRef< CBioseq_set > CBioseq_set_Info::sx_ShallowCopy ( const TObject &  obj )

staticprotected

Definition at line 287 of file bioseq_set_info.cpp.

References CSeq_descr_Base::Get(), CBioseq_set_Base::GetAnnot(), CBioseq_set_Base::GetClass(), CBioseq_set_Base::GetColl(), CBioseq_set_Base::GetDate(), CBioseq_set_Base::GetDescr(), CBioseq_set_Base::GetId(), CBioseq_set_Base::GetLevel(), CBioseq_set_Base::GetRelease(), CBioseq_set_Base::GetSeq_set(), CBioseq_set_Base::IsSetAnnot(), CBioseq_set_Base::IsSetClass(), CBioseq_set_Base::IsSetColl(), CBioseq_set_Base::IsSetDate(), CBioseq_set_Base::IsSetDescr(), CBioseq_set_Base::IsSetId(), CBioseq_set_Base::IsSetLevel(), CBioseq_set_Base::IsSetRelease(), and CBioseq_set_Base::IsSetSeq_set().

Referenced by x_SetObject().

UpdateAnnotIndex()

void CBioseq_set_Info::UpdateAnnotIndex

(

void

)

const

Definition at line 555 of file bioseq_set_info.cpp.

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

x_AddBioseqChunkId()

void CBioseq_set_Info::x_AddBioseqChunkId

(

TChunkId

chunk_id

)

Definition at line 206 of file bioseq_set_info.cpp.

References CTSE_Info_Object::fNeedUpdate_bioseq, m_BioseqChunks, and CTSE_Info_Object::x_SetNeedUpdate().

Referenced by CTSE_Default_Assigner::AddBioseqPlace().

x_AttachEntry()

void CBioseq_set_Info::x_AttachEntry

(

CRef< CSeq_entry_Info >

info

)

Definition at line 537 of file bioseq_set_info.cpp.

References _ASSERT, and CTSE_Info_Object::x_AttachObject().

Referenced by AddEntry(), x_SetChunkBioseqs2(), and x_SetObject().

x_CanGetDescr()

bool CBioseq_set_Info::x_CanGetDescr ( void  ) const

virtual

Implements CBioseq_Base_Info.

Definition at line 337 of file bioseq_set_info.cpp.

References m_Object.

x_DetachEntry()

void CBioseq_set_Info::x_DetachEntry

(

CRef< CSeq_entry_Info >

info

)

Definition at line 546 of file bioseq_set_info.cpp.

References _ASSERT, and CTSE_Info_Object::x_DetachObject().

Referenced by RemoveEntry().

x_DoUpdate()

void CBioseq_set_Info::x_DoUpdate ( TNeedUpdateFlags  flags )

protectedvirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 219 of file bioseq_set_info.cpp.

References _ASSERT, flags, CTSE_Info_Object::fNeedUpdate_bioseq, CTSE_Info_Object::fNeedUpdate_children, CTSE_Info_Object::fNeedUpdate_core, CTSE_Info_Object::kNeedUpdate_bits, m_BioseqChunks, m_Object, m_Seq_set, NON_CONST_ITERATE, CBioseq_Base_Info::x_DoUpdate(), and CTSE_Info_Object::x_LoadChunks().

x_DSAttachContents() [1/2]

void CBioseq_set_Info::x_DSAttachContents ( CDataSource &  ds )

virtual

Reimplemented from CBioseq_Base_Info.

Definition at line 105 of file bioseq_set_info.cpp.

References m_Object, m_Seq_set, NON_CONST_ITERATE, CBioseq_Base_Info::x_DSAttachContents(), and x_DSMapObject().

x_DSAttachContents() [2/2]

void CBioseq_set_Info::x_DSAttachContents ( void  )

protected

x_DSDetachContents() [1/2]

void CBioseq_set_Info::x_DSDetachContents ( CDataSource &  ds )

virtual

Reimplemented from CBioseq_Base_Info.

Definition at line 116 of file bioseq_set_info.cpp.

References m_Object, m_Seq_set, NON_CONST_ITERATE, CBioseq_Base_Info::x_DSDetachContents(), and x_DSUnmapObject().

x_DSDetachContents() [2/2]

void CBioseq_set_Info::x_DSDetachContents ( void  )

protected

x_DSMapObject()

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

protected

Definition at line 127 of file bioseq_set_info.cpp.

References CDataSource::x_Map().

Referenced by x_DSAttachContents(), and x_SetObject().

x_DSUnmapObject()

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

protected

Definition at line 133 of file bioseq_set_info.cpp.

References CDataSource::x_Unmap().

Referenced by x_DSDetachContents().

x_GetBioseq_set_Id()

int CBioseq_set_Info::x_GetBioseq_set_Id ( const CObject_id &  object_id )

protected

Definition at line 321 of file bioseq_set_info.cpp.

References CObject_id_Base::e_Id, CObject_id_Base::GetId(), and CObject_id_Base::Which().

Referenced by x_TSEAttachContents().

x_GetBioseqChunkIds()

const CBioseq_set_Info::TChunkIds & CBioseq_set_Info::x_GetBioseqChunkIds

(

)

const

Definition at line 213 of file bioseq_set_info.cpp.

References m_BioseqChunks.

Referenced by CWGSMasterSupport::AddWGSMaster().

x_GetDescr()

const CSeq_descr & CBioseq_set_Info::x_GetDescr ( void  ) const

virtual

Implements CBioseq_Base_Info.

Definition at line 343 of file bioseq_set_info.cpp.

References m_Object.

x_GetObject() [1/2]

CBioseq_set & CBioseq_set_Info::x_GetObject ( void  )

inlineprotected

Definition at line 241 of file bioseq_set_info.hpp.

References m_Object.

x_GetObject() [2/2]

const CBioseq_set & CBioseq_set_Info::x_GetObject ( void  ) const

inlineprotected

Definition at line 248 of file bioseq_set_info.hpp.

References m_Object.

x_IsSetDescr()

bool CBioseq_set_Info::x_IsSetDescr ( void  ) const

virtual

Implements CBioseq_Base_Info.

Definition at line 331 of file bioseq_set_info.cpp.

References m_Object.

x_ParentAttach()

void CBioseq_set_Info::x_ParentAttach ( CSeq_entry_Info &  parent )

protectedvirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 171 of file bioseq_set_info.cpp.

References _ASSERT, CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSet(), m_Object, m_Seq_set, NON_CONST_ITERATE, CSeq_entry::ParentizeOneLevel(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CSeq_entry_Info::x_GetObject(), and CBioseq_Base_Info::x_ParentAttach().

x_ParentDetach()

void CBioseq_set_Info::x_ParentDetach ( CSeq_entry_Info &  parent )

protectedvirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 197 of file bioseq_set_info.cpp.

References m_Seq_set, NON_CONST_ITERATE, and CBioseq_Base_Info::x_ParentDetach().

x_ResetDescr()

void CBioseq_set_Info::x_ResetDescr ( void  )

virtual

Implements CBioseq_Base_Info.

Definition at line 361 of file bioseq_set_info.cpp.

References m_Object.

x_ResetObjAnnot()

void CBioseq_set_Info::x_ResetObjAnnot ( void  )

protectedvirtual

Implements CBioseq_Base_Info.

Definition at line 373 of file bioseq_set_info.cpp.

References m_Object.

x_SetChunkBioseqs()

void CBioseq_set_Info::x_SetChunkBioseqs	(	const list< CRef< CBioseq > > &	bioseqs,
		int	chunk_id
	)

Definition at line 502 of file bioseq_set_info.cpp.

References i, and x_SetChunkBioseqs2().

Referenced by CTSE_Default_Assigner::LoadChunkBioseqs().

x_SetChunkBioseqs2()

void CBioseq_set_Info::x_SetChunkBioseqs2 ( const list< CRef< CBioseq > > &  bioseqs, TChunkSeqSetsKey  key  )

protected

Definition at line 464 of file bioseq_set_info.cpp.

References _ASSERT, map_checker< Container >::begin(), CBioseq_set_Info::SChunkSeqSet::count, CSeq_entry_Info, map_checker< Container >::end(), CBioseq_set_Info::SChunkSeqSet::first_iter, i, info, m_ChunkSeqSets, m_Object, m_Seq_set, CSeq_entry_Base::SetSeq(), and x_AttachEntry().

Referenced by x_SetChunkBioseqs().

x_SetDescr() [1/2]

void CBioseq_set_Info::x_SetDescr ( TDescr &  v )

virtual

Implements CBioseq_Base_Info.

Definition at line 355 of file bioseq_set_info.cpp.

References m_Object.

x_SetDescr() [2/2]

CSeq_descr & CBioseq_set_Info::x_SetDescr ( void  )

virtual

Implements CBioseq_Base_Info.

Definition at line 349 of file bioseq_set_info.cpp.

References m_Object.

x_SetObjAnnot()

CBioseq_set::TAnnot & CBioseq_set_Info::x_SetObjAnnot ( void  )

protectedvirtual

Implements CBioseq_Base_Info.

Definition at line 367 of file bioseq_set_info.cpp.

References m_Object.

x_SetObject() [1/2]

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

protected

Definition at line 266 of file bioseq_set_info.cpp.

References _ASSERT, AddEntry(), CSeq_entry_Info, CTSE_Info_Object::GetDataSource(), CTSE_Info_Object::HasDataSource(), info, ITERATE, m_Object, Ref(), sx_ShallowCopy(), x_DSMapObject(), and CBioseq_Base_Info::x_SetAnnot().

x_SetObject() [2/2]

void CBioseq_set_Info::x_SetObject ( TObject &  obj )

protected

Definition at line 246 of file bioseq_set_info.cpp.

References _ASSERT, CSeq_entry_Info, CTSE_Info_Object::GetDataSource(), CTSE_Info_Object::HasDataSource(), info, CBioseq_set_Base::IsSetAnnot(), CBioseq_set_Base::IsSetSeq_set(), m_Object, m_Seq_set, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), CBioseq_set_Base::SetSeq_set(), x_AttachEntry(), x_DSMapObject(), and CBioseq_Base_Info::x_SetAnnot().

Referenced by CBioseq_set_Info().

x_TSEAttachContents()

void CBioseq_set_Info::x_TSEAttachContents ( CTSE_Info &  tse )

virtual

Reimplemented from CBioseq_Base_Info.

Definition at line 139 of file bioseq_set_info.cpp.

References _ASSERT, GetId(), IsSetId(), m_Bioseq_set_Id, m_Seq_set, NON_CONST_ITERATE, CTSE_Info_Object::SetBioObjectId(), x_GetBioseq_set_Id(), CTSE_Info::x_IndexBioseq_set(), CTSE_Info::x_SetBioseq_setId(), and CBioseq_Base_Info::x_TSEAttachContents().

x_TSEDetachContents()

void CBioseq_set_Info::x_TSEDetachContents ( CTSE_Info &  tse )

virtual

Reimplemented from CBioseq_Base_Info.

Definition at line 157 of file bioseq_set_info.cpp.

References m_Bioseq_set_Id, m_Seq_set, NON_CONST_ITERATE, CTSE_Info::x_ResetBioseq_setId(), and CBioseq_Base_Info::x_TSEDetachContents().

x_UpdateAnnotIndexContents()

void CBioseq_set_Info::x_UpdateAnnotIndexContents ( CTSE_Info &  tse )

virtual

Reimplemented from CBioseq_Base_Info.

Definition at line 564 of file bioseq_set_info.cpp.

References i, m_Seq_set, and CBioseq_Base_Info::x_UpdateAnnotIndexContents().

Friends And Related Function Documentation

CAnnotTypes_CI

friend class CAnnotTypes_CI

friend

Definition at line 179 of file bioseq_set_info.hpp.

CBioseq_Info

friend class CBioseq_Info

friend

Definition at line 172 of file bioseq_set_info.hpp.

CDataSource

friend class CDataSource

friend

Definition at line 167 of file bioseq_set_info.hpp.

CScope_Impl

friend class CScope_Impl

friend

Definition at line 168 of file bioseq_set_info.hpp.

CSeq_annot_CI

friend class CSeq_annot_CI

friend

Definition at line 177 of file bioseq_set_info.hpp.

CSeq_annot_I

friend class CSeq_annot_I

friend

Definition at line 178 of file bioseq_set_info.hpp.

CSeq_annot_Info

friend class CSeq_annot_Info

friend

Definition at line 173 of file bioseq_set_info.hpp.

CSeq_entry_CI

friend class CSeq_entry_CI

friend

Definition at line 175 of file bioseq_set_info.hpp.

CSeq_entry_I

friend class CSeq_entry_I

friend

Definition at line 176 of file bioseq_set_info.hpp.

CSeq_entry_Info

friend class CSeq_entry_Info

friend

Definition at line 171 of file bioseq_set_info.hpp.

Referenced by AddEntry(), x_SetChunkBioseqs2(), and x_SetObject().

CTSE_Info

friend class CTSE_Info

friend

Definition at line 170 of file bioseq_set_info.hpp.

Member Data Documentation

m_Bioseq_set_Id

int CBioseq_set_Info::m_Bioseq_set_Id

private

Definition at line 228 of file bioseq_set_info.hpp.

Referenced by x_TSEAttachContents(), and x_TSEDetachContents().

m_BioseqChunks

TChunkIds CBioseq_set_Info::m_BioseqChunks

private

Definition at line 225 of file bioseq_set_info.hpp.

Referenced by CBioseq_set_Info(), x_AddBioseqChunkId(), x_DoUpdate(), and x_GetBioseqChunkIds().

m_ChunkSeqSets

TChunkSeqSets CBioseq_set_Info::m_ChunkSeqSets

private

Definition at line 222 of file bioseq_set_info.hpp.

Referenced by x_SetChunkBioseqs2().

m_Object

CRef<TObject> CBioseq_set_Info::m_Object

private

Definition at line 210 of file bioseq_set_info.hpp.

Referenced by AddEntry(), CanGetClass(), CanGetColl(), CanGetDate(), CanGetId(), CanGetLevel(), CanGetRelease(), CanGetSeq_set(), GetBioseq_setCore(), GetClass(), GetColl(), GetCompleteBioseq_set(), GetDate(), GetId(), GetLevel(), GetRelease(), IsSetClass(), IsSetColl(), IsSetDate(), IsSetId(), IsSetLevel(), IsSetRelease(), IsSetSeq_set(), RemoveEntry(), ResetClass(), ResetColl(), ResetDate(), ResetId(), ResetLevel(), ResetRelease(), SetClass(), SetColl(), SetDate(), SetId(), SetLevel(), SetRelease(), x_CanGetDescr(), x_DoUpdate(), x_DSAttachContents(), x_DSDetachContents(), x_GetDescr(), x_GetObject(), x_IsSetDescr(), x_ParentAttach(), x_ResetDescr(), x_ResetObjAnnot(), x_SetChunkBioseqs2(), x_SetDescr(), x_SetObjAnnot(), and x_SetObject().

m_Seq_set

TSeq_set CBioseq_set_Info::m_Seq_set

private

Definition at line 213 of file bioseq_set_info.hpp.

Referenced by AddEntry(), GetEntryIndex(), GetFirstEntry(), GetSeq_set(), RemoveEntry(), SetSeq_set(), x_DoUpdate(), x_DSAttachContents(), x_DSDetachContents(), x_ParentAttach(), x_ParentDetach(), x_SetChunkBioseqs2(), x_SetObject(), x_TSEAttachContents(), x_TSEDetachContents(), and x_UpdateAnnotIndexContents().

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

• include/objmgr/impl/bioseq_set_info.hpp
• src/objmgr/bioseq_set_info.cpp