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ITSE_Assigner Class Referenceabstract

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#include <objmgr/impl/tse_assigner.hpp>

+ Inheritance diagram for ITSE_Assigner:
+ Collaboration diagram for ITSE_Assigner:

Public Types

typedef CTSE_Chunk_Info::TPlace TPlace
 
typedef CTSE_Chunk_Info::TSequence TSequence
 
typedef CTSE_Chunk_Info::TAssembly TAssembly
 
typedef CTSE_Chunk_Info::TChunkId TChunkId
 
typedef CTSE_Chunk_Info::TLocationSet TLocationSet
 
typedef CTSE_Chunk_Info::TDescInfo TDescInfo
 
typedef CTSE_Chunk_Info::TBioseq_setId TBioseq_setId
 
typedef CTSE_Chunk_Info::TAssemblyInfo TAssemblyInfo
 
typedef CTSE_Chunk_Info::TBioseqId TBioseqId
 
- 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

virtual ~ITSE_Assigner ()
 
virtual void AddDescInfo (CTSE_Info &, const TDescInfo &info, TChunkId chunk_id)=0
 
virtual void AddAnnotPlace (CTSE_Info &, const TPlace &place, TChunkId chunk_id)=0
 
virtual void AddBioseqPlace (CTSE_Info &, TBioseq_setId place_id, TChunkId chunk_id)=0
 
virtual void AddSeq_data (CTSE_Info &, const TLocationSet &location, CTSE_Chunk_Info &chunk)=0
 
virtual void AddAssemblyInfo (CTSE_Info &, const TAssemblyInfo &info, TChunkId chunk_id)=0
 
virtual void UpdateAnnotIndex (CTSE_Info &, CTSE_Chunk_Info &chunk)=0
 
virtual void LoadDescr (CTSE_Info &, const TPlace &place, const CSeq_descr &descr)=0
 
virtual void LoadAnnot (CTSE_Info &, const TPlace &place, CRef< CSeq_annot > annot, int chunk_id)=0
 
virtual void LoadBioseq (CTSE_Info &, const TPlace &place, CRef< CSeq_entry > entry, int chunk_id)=0
 
virtual void LoadChunkBioseqs (CTSE_Info &, const TPlace &place, const list< CRef< CBioseq > > &bioseqs, int chunk_id)=0
 
virtual void LoadSequence (CTSE_Info &, const TPlace &place, TSeqPos pos, const TSequence &sequence)=0
 
virtual void LoadAssembly (CTSE_Info &, const TBioseqId &seq_id, const TAssembly &assembly)=0
 
virtual void LoadSeq_entry (CTSE_Info &, CSeq_entry &entry, CTSE_SetObjectInfo *set_info)=0
 
- 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
 

Static Public Member Functions

static CBioseq_Base_Infox_GetBase (CTSE_Info &tse, const TPlace &place)
 
static CBioseq_Infox_GetBioseq (CTSE_Info &tse, const TPlace &place)
 
static CBioseq_set_Infox_GetBioseq_set (CTSE_Info &tse, const TPlace &place)
 
static CBioseq_Infox_GetBioseq (CTSE_Info &tse, const TBioseqId &id)
 
static CBioseq_set_Infox_GetBioseq_set (CTSE_Info &tse, TBioseq_setId id)
 
- 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)
 

Additional Inherited Members

- 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 Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 42 of file tse_assigner.hpp.

Member Typedef Documentation

◆ TAssembly

Definition at line 47 of file tse_assigner.hpp.

◆ TAssemblyInfo

Definition at line 52 of file tse_assigner.hpp.

◆ TBioseq_setId

Definition at line 51 of file tse_assigner.hpp.

◆ TBioseqId

Definition at line 53 of file tse_assigner.hpp.

◆ TChunkId

Definition at line 48 of file tse_assigner.hpp.

◆ TDescInfo

Definition at line 50 of file tse_assigner.hpp.

◆ TLocationSet

Definition at line 49 of file tse_assigner.hpp.

◆ TPlace

Definition at line 45 of file tse_assigner.hpp.

◆ TSequence

Definition at line 46 of file tse_assigner.hpp.

Constructor & Destructor Documentation

◆ ~ITSE_Assigner()

virtual ITSE_Assigner::~ITSE_Assigner ( )
inlinevirtual

Definition at line 55 of file tse_assigner.hpp.

Member Function Documentation

◆ AddAnnotPlace()

virtual void ITSE_Assigner::AddAnnotPlace ( CTSE_Info ,
const TPlace place,
TChunkId  chunk_id 
)
pure virtual

◆ AddAssemblyInfo()

virtual void ITSE_Assigner::AddAssemblyInfo ( CTSE_Info ,
const TAssemblyInfo info,
TChunkId  chunk_id 
)
pure virtual

◆ AddBioseqPlace()

virtual void ITSE_Assigner::AddBioseqPlace ( CTSE_Info ,
TBioseq_setId  place_id,
TChunkId  chunk_id 
)
pure virtual

◆ AddDescInfo()

virtual void ITSE_Assigner::AddDescInfo ( CTSE_Info ,
const TDescInfo info,
TChunkId  chunk_id 
)
pure virtual

◆ AddSeq_data()

virtual void ITSE_Assigner::AddSeq_data ( CTSE_Info ,
const TLocationSet location,
CTSE_Chunk_Info chunk 
)
pure virtual

◆ LoadAnnot()

virtual void ITSE_Assigner::LoadAnnot ( CTSE_Info ,
const TPlace place,
CRef< CSeq_annot annot,
int  chunk_id 
)
pure virtual

Implemented in CTSE_Default_Assigner.

Referenced by CTSE_Split_Info::x_LoadAnnot().

◆ LoadAssembly()

virtual void ITSE_Assigner::LoadAssembly ( CTSE_Info ,
const TBioseqId seq_id,
const TAssembly assembly 
)
pure virtual

◆ LoadBioseq()

virtual void ITSE_Assigner::LoadBioseq ( CTSE_Info ,
const TPlace place,
CRef< CSeq_entry entry,
int  chunk_id 
)
pure virtual

Implemented in CTSE_Default_Assigner.

◆ LoadChunkBioseqs()

virtual void ITSE_Assigner::LoadChunkBioseqs ( CTSE_Info ,
const TPlace place,
const list< CRef< CBioseq > > &  bioseqs,
int  chunk_id 
)
pure virtual

◆ LoadDescr()

virtual void ITSE_Assigner::LoadDescr ( CTSE_Info ,
const TPlace place,
const CSeq_descr descr 
)
pure virtual

Implemented in CTSE_Default_Assigner.

Referenced by CTSE_Split_Info::x_LoadDescr().

◆ LoadSeq_entry()

virtual void ITSE_Assigner::LoadSeq_entry ( CTSE_Info ,
CSeq_entry entry,
CTSE_SetObjectInfo set_info 
)
pure virtual

◆ LoadSequence()

virtual void ITSE_Assigner::LoadSequence ( CTSE_Info ,
const TPlace place,
TSeqPos  pos,
const TSequence sequence 
)
pure virtual

◆ UpdateAnnotIndex()

virtual void ITSE_Assigner::UpdateAnnotIndex ( CTSE_Info ,
CTSE_Chunk_Info chunk 
)
pure virtual

Implemented in CTSE_Default_Assigner.

◆ x_GetBase()

CBioseq_Base_Info & ITSE_Assigner::x_GetBase ( CTSE_Info tse,
const TPlace place 
)
static

◆ x_GetBioseq() [1/2]

CBioseq_Info & ITSE_Assigner::x_GetBioseq ( CTSE_Info tse,
const TBioseqId id 
)
static

Definition at line 50 of file tse_assigner.cpp.

References x_GetBioseq().

◆ x_GetBioseq() [2/2]

CBioseq_Info & ITSE_Assigner::x_GetBioseq ( CTSE_Info tse,
const TPlace place 
)
static

◆ x_GetBioseq_set() [1/2]

CBioseq_set_Info & ITSE_Assigner::x_GetBioseq_set ( CTSE_Info tse,
const TPlace place 
)
static

◆ x_GetBioseq_set() [2/2]

CBioseq_set_Info & ITSE_Assigner::x_GetBioseq_set ( CTSE_Info tse,
TBioseq_setId  id 
)
static

Definition at line 57 of file tse_assigner.cpp.

References CTSE_Info::x_GetBioseq_set().


The documentation for this class was generated from the following files:
Modified on Mon Jun 24 05:27:20 2024 by modify_doxy.py rev. 669887