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CBioseq_ScopeInfo Class Reference

Search Toolkit Book for CBioseq_ScopeInfo

#include <objmgr/impl/scope_info.hpp>

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

Public Types

typedef CRef< CTSE_ScopeInfoTTSE_ScopeInfo
 
typedef set< CSeq_id_HandleTSeq_idSet
 
typedef vector< pair< TTSE_ScopeInfo, CSeq_id_Handle > > TTSE_MatchSet
 
typedef CObjectFor< TTSE_MatchSetTTSE_MatchSetObject
 
typedef CInitMutex< TTSE_MatchSetObjectTAnnotRefInfo
 
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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CBioseq_ScopeInfo (TBlobStateFlags flag)
 
 CBioseq_ScopeInfo (CTSE_ScopeInfo &tse)
 
 CBioseq_ScopeInfo (CTSE_ScopeInfo &tse, const TIds &ids)
 
 ~CBioseq_ScopeInfo (void)
 
const CBioseq_InfoGetObjectInfo (void) const
 
CBioseq_InfoGetNCObjectInfo (void)
 
const TIdsGetIds (void) const
 
const TIndexIdsGetIndexIds (void) const
 
bool HasBioseq (void) 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 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_ForgetTSE (CTSE_ScopeInfo *tse)
 
- Protected Member Functions inherited from CScopeInfo_Base
virtual void x_SetLock (const CTSE_ScopeUserLock &tse, const CTSE_Info_Object &info)
 
virtual void x_ResetLock (void)
 
bool x_Check (TCheckFlags zero_counter_mode) const
 
void x_RemoveLastInfoLock (void)
 
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
 
CInitMutex< CSynonymsSetm_SynCache
 
CInitMutex< TTSE_MatchSetObjectm_BioseqAnnotRef_Info
 

Friends

class CScope_Impl
 
class CTSE_ScopeInfo
 
class CSeq_id_ScopeInfo
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 500 of file scope_info.hpp.

Member Typedef Documentation

Definition at line 507 of file scope_info.hpp.

Definition at line 510 of file scope_info.hpp.

Definition at line 509 of file scope_info.hpp.

Definition at line 508 of file scope_info.hpp.

Definition at line 504 of file scope_info.hpp.

Definition at line 505 of file scope_info.hpp.

Definition at line 506 of file scope_info.hpp.

Definition at line 503 of file scope_info.hpp.

Constructor & Destructor Documentation

CBioseq_ScopeInfo::CBioseq_ScopeInfo ( TBlobStateFlags  flag)
explicit

Definition at line 1765 of file scope_info.cpp.

References BIOSEQ_TRACE.

CBioseq_ScopeInfo::CBioseq_ScopeInfo ( CTSE_ScopeInfo tse)
explicit

Definition at line 1772 of file scope_info.cpp.

References BIOSEQ_TRACE, and x_AttachTSE().

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

Definition at line 1780 of file scope_info.cpp.

References BIOSEQ_TRACE, and x_AttachTSE().

CBioseq_ScopeInfo::~CBioseq_ScopeInfo ( void  )
CBioseq_ScopeInfo::CBioseq_ScopeInfo ( const CBioseq_ScopeInfo info)
private

Member Function Documentation

bool CBioseq_ScopeInfo::AddId ( const CSeq_id_Handle id)
TBlobStateFlags CBioseq_ScopeInfo::GetBlobState ( void  ) const
inline
const TIds& CBioseq_ScopeInfo::GetIds ( void  ) const
inline
const CBioseq_ScopeInfo::TIndexIds * CBioseq_ScopeInfo::GetIndexIds ( void  ) const
virtual

Reimplemented from CScopeInfo_Base.

Definition at line 1803 of file scope_info.cpp.

References GetIds().

CBioseq_ScopeInfo::TBioseq_Lock CBioseq_ScopeInfo::GetLock ( CConstRef< CBioseq_Info bioseq)
CBioseq_Info& CBioseq_ScopeInfo::GetNCObjectInfo ( void  )
inline

Definition at line 521 of file scope_info.hpp.

References GetObjectInfo().

Referenced by CTSE_ScopeInfo::SelectSeq().

const CBioseq_Info& CBioseq_ScopeInfo::GetObjectInfo ( void  ) const
inline
bool CBioseq_ScopeInfo::HasBioseq ( void  ) const
string CBioseq_ScopeInfo::IdString ( void  ) const

Definition at line 1856 of file scope_info.cpp.

References GetIds(), and ITERATE.

Referenced by CScope_Impl::x_AddSynonym().

const CBioseq_ScopeInfo& CBioseq_ScopeInfo::operator= ( const CBioseq_ScopeInfo info)
private
bool CBioseq_ScopeInfo::RemoveId ( const CSeq_id_Handle id)
void CBioseq_ScopeInfo::ResetId ( void  )
void CBioseq_ScopeInfo::x_AttachTSE ( CTSE_ScopeInfo tse)
protectedvirtual
void CBioseq_ScopeInfo::x_DetachTSE ( CTSE_ScopeInfo tse)
protectedvirtual
void CBioseq_ScopeInfo::x_ForgetTSE ( CTSE_ScopeInfo tse)
protectedvirtual

Friends And Related Function Documentation

friend class CScope_Impl
friend

Definition at line 550 of file scope_info.hpp.

friend class CSeq_id_ScopeInfo
friend

Definition at line 552 of file scope_info.hpp.

friend class CTSE_ScopeInfo
friend

Definition at line 551 of file scope_info.hpp.

Member Data Documentation

CInitMutex<TTSE_MatchSetObject> CBioseq_ScopeInfo::m_BioseqAnnotRef_Info
private
TBlobStateFlags CBioseq_ScopeInfo::m_BlobState
private

Definition at line 563 of file scope_info.hpp.

Referenced by GetBlobState(), and x_AttachTSE().

TIds CBioseq_ScopeInfo::m_Ids
private

Definition at line 561 of file scope_info.hpp.

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

CInitMutex<CSynonymsSet> CBioseq_ScopeInfo::m_SynCache
private

The documentation for this class was generated from the following files:
Modified on Sun Mar 26 18:29:17 2017 by modify_doxy.py rev. 506947