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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< 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

 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< TObjectGetCompleteBioseq_set (void) const
 
CConstRef< TObjectGetBioseq_setCore (void) const
 
bool IsEmptySeq_set (void) const
 
bool IsSetId (void) const
 
bool CanGetId (void) const
 
const TIdGetId (void) const
 
void SetId (TId &v)
 
void ResetId (void)
 
bool x_IsSetDescr (void) const
 
bool x_CanGetDescr (void) const
 
const TDescrx_GetDescr (void) const
 
TDescrx_SetDescr (void)
 
void x_SetDescr (TDescr &v)
 
void x_ResetDescr (void)
 
bool IsSetColl (void) const
 
bool CanGetColl (void) const
 
const TCollGetColl (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 TReleaseGetRelease (void) const
 
void SetRelease (TRelease &v)
 
void ResetRelease (void)
 
bool IsSetDate (void) const
 
bool CanGetDate (void) const
 
const TDateGetDate (void) const
 
void SetDate (TDate &v)
 
void ResetDate (void)
 
bool IsSetSeq_set (void) const
 
bool CanGetSeq_set (void) const
 
const TSeq_setGetSeq_set (void) const
 
TSeq_setSetSeq_set (void)
 
CConstRef< CSeq_entry_InfoGetFirstEntry (void) const
 
CRef< CSeq_entry_InfoAddEntry (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 TChunkIdsx_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_InfoGetParentSeq_entry_Info (void) const
 
CSeq_entry_InfoGetParentSeq_entry_Info (void)
 
bool IsSetDescr (void) const
 
bool CanGetDescr (void) const
 
const TDescrGetDescr (void) const
 
TDescrSetDescr (void)
 
void SetDescr (TDescr &v)
 
void ResetDescr (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 TDescListx_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 CSeqdescx_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 TAnnotGetAnnot (void) const
 
const TAnnotGetLoadedAnnot (void) const
 
void ResetAnnot (void)
 
CRef< CSeq_annot_InfoAddAnnot (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 TChunkIdsx_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 CBioObjectIdGetBioObjectId (void) const
 
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)
 
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 Types

typedef pair< int, TChunkIdTChunkSeqSetsKey
 
- Protected Types inherited from CBioseq_Base_Info
typedef CFastMutex TDescrMutex
 
typedef CFastMutexGuard TDescrMutexGuard
 
typedef vector< TDescTypeMaskTDescTypeMasks
 

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)
 
TObjectx_GetObject (void)
 
const TObjectx_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)
 
TObjAnnotx_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< TObjectsx_ShallowCopy (const TObject &obj)
 

Private Types

typedef CBioseq_Base_Info TParent
 
typedef map< TChunkSeqSetsKey, SChunkSeqSetTChunkSeqSets
 

Private Attributes

CRef< TObjectm_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
 
TObjAnnotm_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

Definition at line 221 of file bioseq_set_info.hpp.

◆ TChunkSeqSetsKey

Definition at line 205 of file bioseq_set_info.hpp.

◆ TClass

Definition at line 106 of file bioseq_set_info.hpp.

◆ TColl

Definition at line 92 of file bioseq_set_info.hpp.

◆ TDate

Definition at line 120 of file bioseq_set_info.hpp.

◆ TId

Definition at line 78 of file bioseq_set_info.hpp.

◆ TLevel

Definition at line 99 of file bioseq_set_info.hpp.

◆ TObject

Definition at line 70 of file bioseq_set_info.hpp.

◆ TParent

Definition at line 61 of file bioseq_set_info.hpp.

◆ TRelease

Definition at line 113 of file bioseq_set_info.hpp.

◆ 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

◆ 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 
)

◆ AddEntry() [2/2]

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

◆ 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

◆ GetBioseq_setCore()

CConstRef< CBioseq_set > CBioseq_set_Info::GetBioseq_setCore ( void  ) const

◆ GetClass()

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

◆ 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

◆ 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

◆ 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

◆ IsEmptySeq_set()

bool CBioseq_set_Info::IsEmptySeq_set ( void  ) const
inline

◆ 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

◆ 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

◆ RemoveEntry()

void CBioseq_set_Info::RemoveEntry ( CRef< CSeq_entry_Info entry)

◆ 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

◆ sx_ShallowCopy()

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

◆ UpdateAnnotIndex()

void CBioseq_set_Info::UpdateAnnotIndex ( void  ) const

◆ x_AddBioseqChunkId()

void CBioseq_set_Info::x_AddBioseqChunkId ( TChunkId  chunk_id)

◆ 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

◆ x_DSAttachContents() [1/2]

void CBioseq_set_Info::x_DSAttachContents ( CDataSource ds)
virtual

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ x_SetObject() [2/2]

void CBioseq_set_Info::x_SetObject ( TObject obj)
protected

◆ x_TSEAttachContents()

void CBioseq_set_Info::x_TSEAttachContents ( CTSE_Info tse)
virtual

◆ x_TSEDetachContents()

void CBioseq_set_Info::x_TSEDetachContents ( CTSE_Info tse)
virtual

◆ 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

◆ 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

◆ m_Seq_set

TSeq_set CBioseq_set_Info::m_Seq_set
private

The documentation for this class was generated from the following files:
Modified on Sun May 19 04:43:44 2024 by modify_doxy.py rev. 669887