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CBioseq_ScopeInfo Class Reference

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#include <objmgr/impl/scope_info.hpp>

+ Inheritance diagram for CBioseq_ScopeInfo:
+ Collaboration diagram for CBioseq_ScopeInfo:

Classes

struct  SAnnotSetCache
 
struct  SNASetKey
 

Public Types

typedef CRef< CTSE_ScopeInfoTTSE_ScopeInfo
 
typedef set< CSeq_id_HandleTSeq_idSet
 
typedef vector< pair< TTSE_ScopeInfo, CSeq_id_Handle > > TTSE_MatchSet
 
typedef SNASetKey TNASetKey
 
typedef CInitMutex< SAnnotSetCacheTAnnotRefInfo
 
typedef map< TNASetKey, TAnnotRefInfoTNAAnnotRefInfo
 
typedef TIndexIds TIds
 
typedef int TBlobStateFlags
 
typedef CScopeInfo_Ref< CBioseq_ScopeInfoTBioseq_Lock
 
- Public Types inherited from CScopeInfo_Base
typedef CSeq_id_Handle TIndexId
 
typedef vector< TIndexIdTIndexIds
 
- 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_ScopeInfo (TBlobStateFlags flag, int timestamp)
 
 CBioseq_ScopeInfo (CTSE_ScopeInfo &tse)
 
 CBioseq_ScopeInfo (CTSE_ScopeInfo &tse, const TIds &ids)
 
 ~CBioseq_ScopeInfo (void)
 
void SetUnresolved (TBlobStateFlags flag, int timestamp)
 
void SetResolved (CTSE_ScopeInfo &tse, const TIds &ids)
 
const CBioseq_InfoGetObjectInfo (void) const
 
CBioseq_InfoGetNCObjectInfo (void)
 
const TIdsGetIds (void) const
 
const TIndexIdsGetIndexIds (void) const
 
bool HasBioseq (void) const
 
bool NeedsReResolve (int timestamp) const
 
string IdString (void) const
 
TBlobStateFlags GetBlobState (void) const
 
TBioseq_Lock GetLock (CConstRef< CBioseq_Info > bioseq)
 
void ResetId (void)
 
bool AddId (const CSeq_id_Handle &id)
 
bool RemoveId (const CSeq_id_Handle &id)
 
- Public Member Functions inherited from CScopeInfo_Base
 CScopeInfo_Base (void)
 
 CScopeInfo_Base (const CTSE_ScopeUserLock &tse, const CTSE_Info_Object &info)
 
 CScopeInfo_Base (const CTSE_Handle &tse, const CTSE_Info_Object &info)
 
 ~CScopeInfo_Base (void)
 
bool IsDetached (void) const
 
bool IsAttached (void) const
 
bool HasObject (void) const
 
bool HasObject (const CTSE_Info_Object &info) const
 
bool IsTemporary (void) const
 
CTSE_ScopeInfox_GetTSE_ScopeInfo (void) const
 
const CTSE_HandleGetTSE_Handle (void) const
 
CScope_Implx_GetScopeImpl (void) const
 
const CTSE_Info_ObjectGetObjectInfo_Base (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_AttachTSE (CTSE_ScopeInfo *tse)
 
void x_DetachTSE (CTSE_ScopeInfo *tse)
 
void x_ResetAnnotRef_Info ()
 
- Protected Member Functions inherited from CScopeInfo_Base
void x_ResetTSE_Lock (void)
 
void x_SetTSE_Lock (const CTSE_ScopeUserLock &tse, const CTSE_Info_Object &info)
 
void x_SetTSE_Handle (const CTSE_Handle &tse)
 
void AddInfoLock (void)
 
void RemoveInfoLock (void)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Member Functions

 CBioseq_ScopeInfo (const CBioseq_ScopeInfo &info)
 
const CBioseq_ScopeInfooperator= (const CBioseq_ScopeInfo &info)
 

Private Attributes

TIds m_Ids
 
TBlobStateFlags m_BlobState
 
atomic< intm_UnresolvedTimestamp
 
CInitMutex< CSynonymsSetm_SynCache
 
TAnnotRefInfo m_BioseqAnnotRef_Info
 
TNAAnnotRefInfo m_NABioseqAnnotRef_Info
 

Friends

class CScope_Impl
 
class CTSE_ScopeInfo
 
class CSeq_id_ScopeInfo
 

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 Types inherited from CScopeInfo_Base
enum  ECheckFlags {
  fAllowZero = 0x00 , fForceZero = 0x01 , fForbidZero = 0x02 , fAllowInfo = 0x00 ,
  fForceInfo = 0x10 , fForbidInfo = 0x20
}
 
typedef int TCheckFlags
 

Detailed Description

Definition at line 519 of file scope_info.hpp.

Member Typedef Documentation

◆ TAnnotRefInfo

Definition at line 538 of file scope_info.hpp.

◆ TBioseq_Lock

Definition at line 542 of file scope_info.hpp.

◆ TBlobStateFlags

Definition at line 541 of file scope_info.hpp.

◆ TIds

Definition at line 540 of file scope_info.hpp.

◆ TNAAnnotRefInfo

Definition at line 539 of file scope_info.hpp.

◆ TNASetKey

Definition at line 537 of file scope_info.hpp.

◆ TSeq_idSet

Definition at line 523 of file scope_info.hpp.

◆ TTSE_MatchSet

Definition at line 524 of file scope_info.hpp.

◆ TTSE_ScopeInfo

Definition at line 522 of file scope_info.hpp.

Constructor & Destructor Documentation

◆ CBioseq_ScopeInfo() [1/4]

CBioseq_ScopeInfo::CBioseq_ScopeInfo ( TBlobStateFlags  flag,
int  timestamp 
)

Definition at line 2050 of file scope_info.cpp.

References BIOSEQ_TRACE.

◆ CBioseq_ScopeInfo() [2/4]

CBioseq_ScopeInfo::CBioseq_ScopeInfo ( CTSE_ScopeInfo tse)
explicit

Definition at line 2058 of file scope_info.cpp.

References BIOSEQ_TRACE, and x_AttachTSE().

◆ CBioseq_ScopeInfo() [3/4]

CBioseq_ScopeInfo::CBioseq_ScopeInfo ( CTSE_ScopeInfo tse,
const TIds ids 
)

Definition at line 2067 of file scope_info.cpp.

References BIOSEQ_TRACE, and x_AttachTSE().

◆ ~CBioseq_ScopeInfo()

CBioseq_ScopeInfo::~CBioseq_ScopeInfo ( void  )

◆ CBioseq_ScopeInfo() [4/4]

CBioseq_ScopeInfo::CBioseq_ScopeInfo ( const CBioseq_ScopeInfo info)
private

Member Function Documentation

◆ AddId()

bool CBioseq_ScopeInfo::AddId ( const CSeq_id_Handle id)

◆ GetBlobState()

TBlobStateFlags CBioseq_ScopeInfo::GetBlobState ( void  ) const
inline

Definition at line 576 of file scope_info.hpp.

References m_BlobState.

Referenced by CBioseq_Handle::GetState(), and HasBioseq().

◆ GetIds()

const TIds& CBioseq_ScopeInfo::GetIds ( void  ) const
inline

◆ GetIndexIds()

const CBioseq_ScopeInfo::TIndexIds * CBioseq_ScopeInfo::GetIndexIds ( void  ) const
virtual

Reimplemented from CScopeInfo_Base.

Definition at line 2110 of file scope_info.cpp.

References GetIds().

◆ GetLock()

CBioseq_ScopeInfo::TBioseq_Lock CBioseq_ScopeInfo::GetLock ( CConstRef< CBioseq_Info bioseq)

◆ GetNCObjectInfo()

CBioseq_Info& CBioseq_ScopeInfo::GetNCObjectInfo ( void  )
inline

Definition at line 557 of file scope_info.hpp.

References GetObjectInfo().

Referenced by CTSE_ScopeInfo::SelectSeq().

◆ GetObjectInfo()

const CBioseq_Info& CBioseq_ScopeInfo::GetObjectInfo ( void  ) const
inline

◆ HasBioseq()

bool CBioseq_ScopeInfo::HasBioseq ( void  ) const

◆ IdString()

string CBioseq_ScopeInfo::IdString ( void  ) const

Definition at line 2153 of file scope_info.cpp.

References GetIds(), and ITERATE.

Referenced by CScope_Impl::x_AddSynonym().

◆ NeedsReResolve()

bool CBioseq_ScopeInfo::NeedsReResolve ( int  timestamp) const
inline

Definition at line 569 of file scope_info.hpp.

References HasBioseq(), and m_UnresolvedTimestamp.

◆ operator=()

const CBioseq_ScopeInfo& CBioseq_ScopeInfo::operator= ( const CBioseq_ScopeInfo info)
private

◆ RemoveId()

bool CBioseq_ScopeInfo::RemoveId ( const CSeq_id_Handle id)

◆ ResetId()

void CBioseq_ScopeInfo::ResetId ( void  )

◆ SetResolved()

void CBioseq_ScopeInfo::SetResolved ( CTSE_ScopeInfo tse,
const TIds ids 
)

◆ SetUnresolved()

void CBioseq_ScopeInfo::SetUnresolved ( TBlobStateFlags  flag,
int  timestamp 
)

◆ x_AttachTSE()

void CBioseq_ScopeInfo::x_AttachTSE ( CTSE_ScopeInfo tse)
protectedvirtual

◆ x_DetachTSE()

void CBioseq_ScopeInfo::x_DetachTSE ( CTSE_ScopeInfo tse)
protectedvirtual

◆ x_ResetAnnotRef_Info()

void CBioseq_ScopeInfo::x_ResetAnnotRef_Info ( )
inlineprotected

Friends And Related Function Documentation

◆ CScope_Impl

friend class CScope_Impl
friend

Definition at line 590 of file scope_info.hpp.

◆ CSeq_id_ScopeInfo

friend class CSeq_id_ScopeInfo
friend

Definition at line 592 of file scope_info.hpp.

◆ CTSE_ScopeInfo

friend class CTSE_ScopeInfo
friend

Definition at line 591 of file scope_info.hpp.

Member Data Documentation

◆ m_BioseqAnnotRef_Info

TAnnotRefInfo CBioseq_ScopeInfo::m_BioseqAnnotRef_Info
private

Definition at line 615 of file scope_info.hpp.

Referenced by CScope_Impl::x_GetTSESetWithAnnots(), and x_ResetAnnotRef_Info().

◆ m_BlobState

TBlobStateFlags CBioseq_ScopeInfo::m_BlobState
private

Definition at line 607 of file scope_info.hpp.

Referenced by GetBlobState(), SetResolved(), SetUnresolved(), and x_AttachTSE().

◆ m_Ids

TIds CBioseq_ScopeInfo::m_Ids
private

Definition at line 605 of file scope_info.hpp.

Referenced by AddId(), GetIds(), RemoveId(), ResetId(), and SetResolved().

◆ m_NABioseqAnnotRef_Info

TNAAnnotRefInfo CBioseq_ScopeInfo::m_NABioseqAnnotRef_Info
private

Definition at line 616 of file scope_info.hpp.

Referenced by CScope_Impl::x_GetTSESetWithAnnots(), and x_ResetAnnotRef_Info().

◆ m_SynCache

CInitMutex<CSynonymsSet> CBioseq_ScopeInfo::m_SynCache
private

◆ m_UnresolvedTimestamp

atomic<int> CBioseq_ScopeInfo::m_UnresolvedTimestamp
private

The documentation for this class was generated from the following files:
Modified on Tue Feb 27 05:51:33 2024 by modify_doxy.py rev. 669887