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CSeq_entry_Info Class Reference

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_HandleTSeqIds
 
- 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< TChunkIdTChunkIds
 
- 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< Uint8TCounter
 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_InfoGetParentBioseq_set_Info (void) const
 
CBioseq_set_InfoGetParentBioseq_set_Info (void)
 
const CSeq_entry_InfoGetParentSeq_entry_Info (void) const
 
CSeq_entry_InfoGetParentSeq_entry_Info (void)
 
const CSeq_entry_InfoGetXrefTSE () const
 
virtual const CBioObjectIdGetBioObjectId (void) const
 
bool HasNoSeq_entry (void) const
 
CConstRef< TObjectGetCompleteSeq_entry (void) const
 
CConstRef< TObjectGetSeq_entryCore (void) const
 
CConstRef< TObjectGetSeq_entrySkeleton (void) const
 
E_Choice Which (void) const
 
void x_CheckWhich (E_Choice which) const
 
void Reset (void)
 
bool IsSet (void) const
 
const TSetGetSet (void) const
 
TSetSetSet (void)
 
TSetSelectSet (void)
 
TSetSelectSet (TSet &seqset)
 
TSetSelectSet (CBioseq_set &seqset)
 
bool IsSeq (void) const
 
const TSeqGetSeq (void) const
 
TSeqSetSeq (void)
 
TSeqSelectSeq (TSeq &seq)
 
TSeqSelectSeq (CBioseq &seq)
 
bool IsSetDescr (void) const
 
const TDescrGetDescr (void) const
 
void ResetDescr (void)
 
void SetDescr (TDescr &v)
 
TDescrSetDescr (void)
 
bool AddSeqdesc (CSeqdesc &d)
 
CRef< CSeqdescRemoveSeqdesc (const CSeqdesc &d)
 
CRef< CSeqdescReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc)
 
void AddSeq_descr (const TDescr &v)
 
const CBioseq_Base_Infox_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_InfoAddAnnot (CSeq_annot &annot)
 
void AddAnnot (CRef< CSeq_annot_Info > annot)
 
void RemoveAnnot (CRef< CSeq_annot_Info > annot)
 
const TAnnotGetLoadedAnnot (void) const
 
CRef< CSeq_entry_InfoAddEntry (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
 
CDataSourceGetDataSource (void) const
 
bool HasTSE_Info (void) const
 
bool BelongsToTSE_Info (const CTSE_Info &tse) const
 
const CTSE_InfoGetTSE_Info (void) const
 
CTSE_InfoGetTSE_Info (void)
 
bool HasParent_Info (void) const
 
const CTSE_Info_ObjectGetBaseParent_Info (void) const
 
CTSE_Info_ObjectGetBaseParent_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...
 
CObjectoperator= (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)
 
TObjectx_GetObject (void)
 
const TObjectx_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_Infooperator= (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< TObjectsx_ShallowCopy (TObject &obj)
 

Protected Attributes

CRef< TObjectm_Object
 
E_Choice m_Which
 
CRef< CBioseq_Base_Infom_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

Definition at line 102 of file seq_entry_info.hpp.

◆ 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

Definition at line 126 of file seq_entry_info.hpp.

◆ TDescTypeMask

Definition at line 144 of file seq_entry_info.hpp.

◆ TObject

Definition at line 94 of file seq_entry_info.hpp.

◆ TParent

Definition at line 74 of file seq_entry_info.hpp.

◆ TSeq

Definition at line 117 of file seq_entry_info.hpp.

◆ TSeqIds

Definition at line 176 of file seq_entry_info.hpp.

◆ 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)

◆ AddEntry() [1/2]

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

◆ AddEntry() [2/2]

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

◆ AddSeq_descr()

void CSeq_entry_Info::AddSeq_descr ( const TDescr v)

◆ AddSeqdesc()

bool CSeq_entry_Info::AddSeqdesc ( CSeqdesc d)

◆ 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

◆ GetDescr()

const CSeq_descr & CSeq_entry_Info::GetDescr ( void  ) const

◆ GetLoadedAnnot()

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

◆ 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

◆ GetParentSeq_entry_Info() [1/2]

CSeq_entry_Info & CSeq_entry_Info::GetParentSeq_entry_Info ( void  )

◆ GetParentSeq_entry_Info() [2/2]

const CSeq_entry_Info & CSeq_entry_Info::GetParentSeq_entry_Info ( void  ) const

◆ GetSeq()

const CBioseq_Info & CSeq_entry_Info::GetSeq ( void  ) const

◆ GetSeq_entryCore()

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

◆ 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

◆ GetXrefTSE()

const CSeq_entry_Info & CSeq_entry_Info::GetXrefTSE ( void  ) const

◆ 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

◆ IsSetDescr()

bool CSeq_entry_Info::IsSetDescr ( void  ) const

◆ 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)

◆ RemoveSeqdesc()

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

◆ ReplaceSeqdesc()

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

◆ Reset()

void CSeq_entry_Info::Reset ( void  )

◆ ResetDescr()

void CSeq_entry_Info::ResetDescr ( void  )

◆ 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)

◆ 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)

◆ 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)

◆ SetDescr() [2/2]

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

◆ SetSeq()

CBioseq_Info & CSeq_entry_Info::SetSeq ( void  )

◆ SetSet()

CBioseq_set_Info & CSeq_entry_Info::SetSet ( void  )

◆ sx_ShallowCopy()

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

◆ UpdateAnnotIndex()

void CSeq_entry_Info::UpdateAnnotIndex ( void  ) const

◆ Which()

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

◆ x_AttachContents()

void CSeq_entry_Info::x_AttachContents ( void  )
protected

◆ x_CheckWhich()

void CSeq_entry_Info::x_CheckWhich ( E_Choice  which) const

◆ x_DetachContents()

void CSeq_entry_Info::x_DetachContents ( void  )
protected

◆ x_DoUpdate()

void CSeq_entry_Info::x_DoUpdate ( TNeedUpdateFlags  flags)
protectedvirtual

◆ x_DSAttachContents()

void CSeq_entry_Info::x_DSAttachContents ( CDataSource ds)
virtual

◆ x_DSDetachContents()

void CSeq_entry_Info::x_DSDetachContents ( CDataSource ds)
virtual

◆ 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

◆ x_GetBaseInfo()

const CBioseq_Base_Info & CSeq_entry_Info::x_GetBaseInfo ( void  ) const

◆ x_GetBioseqsIds()

void CSeq_entry_Info::x_GetBioseqsIds ( TSeqIds ids) const

◆ 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

◆ 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)

◆ 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

◆ x_SetBioseqChunkId()

void CSeq_entry_Info::x_SetBioseqChunkId ( TChunkId  chunk_id)

◆ 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

◆ 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

◆ x_TSEDetachContents()

void CSeq_entry_Info::x_TSEDetachContents ( CTSE_Info tse_info)
virtual

◆ x_Update()

void CSeq_entry_Info::x_Update ( TNeedUpdateFlags  flags) const
protected

◆ x_UpdateAnnotIndexContents()

void CSeq_entry_Info::x_UpdateAnnotIndexContents ( CTSE_Info tse)
protectedvirtual

◆ x_UpdateSkeleton()

void CSeq_entry_Info::x_UpdateSkeleton ( ) const
inlineprotected

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

◆ m_Which

E_Choice CSeq_entry_Info::m_Which
protected

The documentation for this class was generated from the following files:
Modified on Tue Apr 23 07:40:55 2024 by modify_doxy.py rev. 669887