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CTSE_Chunk_Info Class Reference

Search Toolkit Book for CTSE_Chunk_Info

#include <objmgr/impl/tse_chunk_info.hpp>

+ Inheritance diagram for CTSE_Chunk_Info:
+ Collaboration diagram for CTSE_Chunk_Info:

Classes

struct  SFeatIds
 

Public Types

enum  { kMain_ChunkId = -1 , kMasterWGS_ChunkId = kMax_Int-1 , kDelayedMain_ChunkId = kMax_Int }
 
typedef CBlobIdKey TBlobId
 
typedef int TBlobVersion
 
typedef int TChunkId
 
typedef int TBioseq_setId
 
typedef CSeq_id_Handle TBioseqId
 
typedef pair< TBioseqId, TBioseq_setIdTPlace
 
typedef unsigned TDescTypeMask
 
typedef pair< TDescTypeMask, TPlaceTDescInfo
 
typedef vector< TPlaceTPlaces
 
typedef vector< TDescInfoTDescInfos
 
typedef vector< TBioseq_setIdTBioseqPlaces
 
typedef vector< TBioseqIdTBioseqIds
 
typedef TBioseqId TAssemblyInfo
 
typedef vector< TAssemblyInfoTAssemblyInfos
 
typedef CSeq_id_Handle TLocationId
 
typedef CRange< TSeqPosTLocationRange
 
typedef pair< TLocationId, TLocationRangeTLocation
 
typedef vector< TLocationTLocationSet
 
typedef map< SAnnotTypeSelector, TLocationSetTAnnotTypes
 
typedef map< CAnnotName, TAnnotTypesTAnnotContents
 
typedef SAnnotObjectsIndex TObjectIndex
 
typedef list< TObjectIndexTObjectIndexList
 
typedef list< CRef< CSeq_literal > > TSequence
 
typedef list< CRef< CSeq_align > > TAssembly
 
typedef int TFeatIdInt
 
typedef string TFeatIdStr
 
typedef vector< TFeatIdIntTFeatIdIntList
 
typedef list< TFeatIdStrTFeatIdStrList
 
typedef map< SAnnotTypeSelector, SFeatIdsTFeatIdsMap
 
- 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

 CTSE_Chunk_Info (TChunkId id)
 
virtual ~CTSE_Chunk_Info (void)
 
TBlobId GetBlobId (void) const
 
TBlobVersion GetBlobVersion (void) const
 
TChunkId GetChunkId (void) const
 
const CTSE_Split_InfoGetSplitInfo (void) const
 
bool NotLoaded (void) const
 
bool IsLoaded (void) const
 
void Load (void) const
 
CInitGuardGetLoadInitGuard (void)
 
void x_AddDescInfo (TDescTypeMask type_mask, const TBioseqId &id)
 
void x_AddDescInfo (TDescTypeMask type_mask, TBioseq_setId id)
 
void x_AddDescInfo (const TDescInfo &info)
 
void x_AddAssemblyInfo (const TBioseqId &id)
 
void x_AddAnnotPlace (const TBioseqId &id)
 
void x_AddAnnotPlace (TBioseq_setId id)
 
void x_AddAnnotPlace (const TPlace &place)
 
void x_AddBioseqPlace (TBioseq_setId id)
 
void x_AddBioseqId (const TBioseqId &id)
 
void x_AddAnnotType (const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)
 
void x_AddAnnotType (const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id, const TLocationRange &location_range)
 
void x_AddAnnotType (const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationSet &location)
 
void x_AddFeat_ids (void)
 
void x_AddFeat_ids (const SAnnotTypeSelector &type, const TFeatIdIntList &ids)
 
void x_AddXref_ids (const SAnnotTypeSelector &type, const TFeatIdIntList &ids)
 
void x_AddFeat_ids (const SAnnotTypeSelector &type, const TFeatIdStrList &ids)
 
void x_AddXref_ids (const SAnnotTypeSelector &type, const TFeatIdStrList &ids)
 
void x_AddSeq_data (const TLocationSet &location)
 
 operator CInitMutex_Base & (void)
 
void SetLoaded (CObject *obj=0)
 
void SetLoadListener (CRef< CTSEChunkLoadListener > listener)
 
void x_LoadDescr (const TPlace &place, const CSeq_descr &descr)
 
void x_LoadAnnot (const TPlace &place, const CSeq_annot &annot)
 
void x_LoadBioseq (const TPlace &place, const CBioseq &bioseq)
 
void x_LoadBioseqs (const TPlace &place, const list< CRef< CBioseq > > &bioseqs)
 
void x_LoadSequence (const TPlace &place, TSeqPos pos, const TSequence &seq)
 
void x_LoadAssembly (const TBioseqId &seq_id, const TAssembly &assembly)
 
void x_LoadSeq_entry (CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)
 
void x_AddUsedMemory (size_t size)
 
const TDescInfosGetDescInfos (void) const
 
const TPlacesGetAnnotPlaces (void) const
 
const TBioseqPlacesGetBioseqPlaces (void) const
 
const TBioseqIdsGetBioseqIds (void) const
 
const TAnnotContentsGetAnnotContents (void) const
 
const TLocationSetGetSeq_dataInfos (void) const
 
const TAssemblyInfosGetAssemblyInfos (void) const
 
Uint4 GetLoadBytes () const
 
double GetLoadSeconds () const
 
pair< Uint4, double > GetLoadCost () const
 
void x_SetLoadBytes (Uint4 bytes)
 
void x_SetLoadSeconds (double seconds)
 
- 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_SplitAttach (CTSE_Split_Info &split_info)
 
void x_TSEAttach (CTSE_Info &tse, ITSE_Assigner &tse_info)
 
bool x_Attached (void) const
 
bool x_GetRecords (const CSeq_id_Handle &id, bool bioseq) const
 
void GetBioseqsIds (TBioseqIds &ids) const
 
bool ContainsBioseq (const CSeq_id_Handle &id) const
 
bool x_AnnotIndexNeedsUpdate () const
 
void x_UpdateAnnotIndex (CTSE_Info &tse)
 
void x_UpdateAnnotIndexContents (CTSE_Info &tse)
 
bool x_ContainsFeatType (CSeqFeatData::E_Choice type) const
 
bool x_ContainsFeatType (CSeqFeatData::ESubtype subtype) const
 
bool x_ContainsFeatIds (CSeqFeatData::E_Choice type, EFeatIdType id_type) const
 
bool x_ContainsFeatIds (CSeqFeatData::ESubtype subtype, EFeatIdType id_type) const
 
void x_DropAnnotObjects (void)
 
void x_InitObjectIndexList (void)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Member Functions

 CTSE_Chunk_Info (const CTSE_Chunk_Info &)
 
CTSE_Chunk_Infooperator= (const CTSE_Chunk_Info &)
 

Private Attributes

CTSE_Split_Infom_SplitInfo
 
TChunkId m_ChunkId
 
Uint4 m_LoadBytes
 
float m_LoadSeconds
 
bool m_ExplicitFeatIds
 
TDescInfos m_DescInfos
 
TPlaces m_AnnotPlaces
 
TBioseqPlaces m_BioseqPlaces
 
TBioseqIds m_BioseqIds
 
TAnnotContents m_AnnotContents
 
TLocationSet m_Seq_data
 
TAssemblyInfos m_AssemblyInfos
 
TFeatIdsMap m_FeatIds
 
TFeatIdsMap m_XrefIds
 
CInitMutex< CObjectm_LoadLock
 
TObjectIndexList m_ObjectIndexList
 
CMutex m_ListenerMutex
 
CRef< CTSEChunkLoadListenerm_LoadListener
 

Friends

class CTSE_Info
 
class CTSE_Split_Info
 
class CTSE_Default_Assigner
 

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 74 of file tse_chunk_info.hpp.

Member Typedef Documentation

◆ TAnnotContents

Definition at line 111 of file tse_chunk_info.hpp.

◆ TAnnotTypes

Definition at line 110 of file tse_chunk_info.hpp.

◆ TAssembly

Definition at line 119 of file tse_chunk_info.hpp.

◆ TAssemblyInfo

Definition at line 102 of file tse_chunk_info.hpp.

◆ TAssemblyInfos

Definition at line 103 of file tse_chunk_info.hpp.

◆ TBioseq_setId

Definition at line 93 of file tse_chunk_info.hpp.

◆ TBioseqId

Definition at line 94 of file tse_chunk_info.hpp.

◆ TBioseqIds

Definition at line 101 of file tse_chunk_info.hpp.

◆ TBioseqPlaces

Definition at line 100 of file tse_chunk_info.hpp.

◆ TBlobId

Definition at line 82 of file tse_chunk_info.hpp.

◆ TBlobVersion

Definition at line 83 of file tse_chunk_info.hpp.

◆ TChunkId

Definition at line 84 of file tse_chunk_info.hpp.

◆ TDescInfo

Definition at line 97 of file tse_chunk_info.hpp.

◆ TDescInfos

Definition at line 99 of file tse_chunk_info.hpp.

◆ TDescTypeMask

Definition at line 96 of file tse_chunk_info.hpp.

◆ TFeatIdInt

Definition at line 176 of file tse_chunk_info.hpp.

◆ TFeatIdIntList

Definition at line 178 of file tse_chunk_info.hpp.

◆ TFeatIdsMap

Definition at line 184 of file tse_chunk_info.hpp.

◆ TFeatIdStr

Definition at line 177 of file tse_chunk_info.hpp.

◆ TFeatIdStrList

Definition at line 179 of file tse_chunk_info.hpp.

◆ TLocation

Definition at line 108 of file tse_chunk_info.hpp.

◆ TLocationId

Definition at line 106 of file tse_chunk_info.hpp.

◆ TLocationRange

Definition at line 107 of file tse_chunk_info.hpp.

◆ TLocationSet

Definition at line 109 of file tse_chunk_info.hpp.

◆ TObjectIndex

Definition at line 114 of file tse_chunk_info.hpp.

◆ TObjectIndexList

Definition at line 115 of file tse_chunk_info.hpp.

◆ TPlace

Definition at line 95 of file tse_chunk_info.hpp.

◆ TPlaces

Definition at line 98 of file tse_chunk_info.hpp.

◆ TSequence

Definition at line 118 of file tse_chunk_info.hpp.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
Enumerator
kMain_ChunkId 
kMasterWGS_ChunkId 
kDelayedMain_ChunkId 

Definition at line 86 of file tse_chunk_info.hpp.

Constructor & Destructor Documentation

◆ CTSE_Chunk_Info() [1/2]

CTSE_Chunk_Info::CTSE_Chunk_Info ( TChunkId  id)

Definition at line 66 of file tse_chunk_info.cpp.

◆ ~CTSE_Chunk_Info()

CTSE_Chunk_Info::~CTSE_Chunk_Info ( void  )
virtual

Definition at line 76 of file tse_chunk_info.cpp.

◆ CTSE_Chunk_Info() [2/2]

CTSE_Chunk_Info::CTSE_Chunk_Info ( const CTSE_Chunk_Info )
private

Member Function Documentation

◆ ContainsBioseq()

bool CTSE_Chunk_Info::ContainsBioseq ( const CSeq_id_Handle id) const
protected

◆ GetAnnotContents()

const TAnnotContents& CTSE_Chunk_Info::GetAnnotContents ( void  ) const
inline

Definition at line 246 of file tse_chunk_info.hpp.

References m_AnnotContents.

◆ GetAnnotPlaces()

const TPlaces& CTSE_Chunk_Info::GetAnnotPlaces ( void  ) const
inline

Definition at line 234 of file tse_chunk_info.hpp.

References m_AnnotPlaces.

◆ GetAssemblyInfos()

const TAssemblyInfos& CTSE_Chunk_Info::GetAssemblyInfos ( void  ) const
inline

Definition at line 254 of file tse_chunk_info.hpp.

References m_AssemblyInfos.

◆ GetBioseqIds()

const TBioseqIds& CTSE_Chunk_Info::GetBioseqIds ( void  ) const
inline

Definition at line 242 of file tse_chunk_info.hpp.

References m_BioseqIds.

◆ GetBioseqPlaces()

const TBioseqPlaces& CTSE_Chunk_Info::GetBioseqPlaces ( void  ) const
inline

Definition at line 238 of file tse_chunk_info.hpp.

References m_BioseqPlaces.

◆ GetBioseqsIds()

void CTSE_Chunk_Info::GetBioseqsIds ( TBioseqIds ids) const
protected

Definition at line 234 of file tse_chunk_info.cpp.

References m_BioseqIds.

◆ GetBlobId()

CTSE_Chunk_Info::TBlobId CTSE_Chunk_Info::GetBlobId ( void  ) const

◆ GetBlobVersion()

CTSE_Chunk_Info::TBlobVersion CTSE_Chunk_Info::GetBlobVersion ( void  ) const

◆ GetChunkId()

CTSE_Chunk_Info::TChunkId CTSE_Chunk_Info::GetChunkId ( void  ) const
inline

◆ GetDescInfos()

const TDescInfos& CTSE_Chunk_Info::GetDescInfos ( void  ) const
inline

Definition at line 230 of file tse_chunk_info.hpp.

References m_DescInfos.

◆ GetLoadBytes()

Uint4 CTSE_Chunk_Info::GetLoadBytes ( ) const
inline

Definition at line 375 of file tse_chunk_info.hpp.

References m_LoadBytes.

Referenced by GetLoadCost().

◆ GetLoadCost()

pair< Uint4, double > CTSE_Chunk_Info::GetLoadCost ( ) const

◆ GetLoadInitGuard()

CInitGuard * CTSE_Chunk_Info::GetLoadInitGuard ( void  )

◆ GetLoadSeconds()

double CTSE_Chunk_Info::GetLoadSeconds ( ) const
inline

Definition at line 382 of file tse_chunk_info.hpp.

References m_LoadSeconds.

Referenced by GetLoadCost().

◆ GetSeq_dataInfos()

const TLocationSet& CTSE_Chunk_Info::GetSeq_dataInfos ( void  ) const
inline

Definition at line 250 of file tse_chunk_info.hpp.

References m_Seq_data.

Referenced by CBlastDbDataLoader::GetChunk(), and CRemoteBlastDbDataLoader::GetChunks().

◆ GetSplitInfo()

const CTSE_Split_Info & CTSE_Chunk_Info::GetSplitInfo ( void  ) const
inline

◆ IsLoaded()

bool CTSE_Chunk_Info::IsLoaded ( void  ) const
inline

◆ Load()

void CTSE_Chunk_Info::Load ( void  ) const

◆ NotLoaded()

bool CTSE_Chunk_Info::NotLoaded ( void  ) const
inline

◆ operator CInitMutex_Base &()

CTSE_Chunk_Info::operator CInitMutex_Base & ( void  )
inline

Definition at line 205 of file tse_chunk_info.hpp.

References m_LoadLock.

◆ operator=()

CTSE_Chunk_Info& CTSE_Chunk_Info::operator= ( const CTSE_Chunk_Info )
private

◆ SetLoaded()

void CTSE_Chunk_Info::SetLoaded ( CObject obj = 0)

◆ SetLoadListener()

void CTSE_Chunk_Info::SetLoadListener ( CRef< CTSEChunkLoadListener listener)

◆ x_AddAnnotPlace() [1/3]

void CTSE_Chunk_Info::x_AddAnnotPlace ( const TBioseqId id)

◆ x_AddAnnotPlace() [2/3]

void CTSE_Chunk_Info::x_AddAnnotPlace ( const TPlace place)

◆ x_AddAnnotPlace() [3/3]

void CTSE_Chunk_Info::x_AddAnnotPlace ( TBioseq_setId  id)

Definition at line 354 of file tse_chunk_info.cpp.

References x_AddAnnotPlace().

◆ x_AddAnnotType() [1/3]

void CTSE_Chunk_Info::x_AddAnnotType ( const CAnnotName annot_name,
const SAnnotTypeSelector annot_type,
const TLocationId location_id 
)

◆ x_AddAnnotType() [2/3]

void CTSE_Chunk_Info::x_AddAnnotType ( const CAnnotName annot_name,
const SAnnotTypeSelector annot_type,
const TLocationId location_id,
const TLocationRange location_range 
)

Definition at line 394 of file tse_chunk_info.cpp.

References _ASSERT, m_AnnotContents, and x_Attached().

◆ x_AddAnnotType() [3/3]

void CTSE_Chunk_Info::x_AddAnnotType ( const CAnnotName annot_name,
const SAnnotTypeSelector annot_type,
const TLocationSet location 
)

◆ x_AddAssemblyInfo()

void CTSE_Chunk_Info::x_AddAssemblyInfo ( const TBioseqId id)

◆ x_AddBioseqId()

void CTSE_Chunk_Info::x_AddBioseqId ( const TBioseqId id)

◆ x_AddBioseqPlace()

void CTSE_Chunk_Info::x_AddBioseqPlace ( TBioseq_setId  id)

◆ x_AddDescInfo() [1/3]

void CTSE_Chunk_Info::x_AddDescInfo ( const TDescInfo info)

◆ x_AddDescInfo() [2/3]

void CTSE_Chunk_Info::x_AddDescInfo ( TDescTypeMask  type_mask,
const TBioseqId id 
)

◆ x_AddDescInfo() [3/3]

void CTSE_Chunk_Info::x_AddDescInfo ( TDescTypeMask  type_mask,
TBioseq_setId  id 
)

Definition at line 323 of file tse_chunk_info.cpp.

References x_AddDescInfo().

◆ x_AddFeat_ids() [1/3]

void CTSE_Chunk_Info::x_AddFeat_ids ( const SAnnotTypeSelector type,
const TFeatIdIntList ids 
)

◆ x_AddFeat_ids() [2/3]

void CTSE_Chunk_Info::x_AddFeat_ids ( const SAnnotTypeSelector type,
const TFeatIdStrList ids 
)

◆ x_AddFeat_ids() [3/3]

void CTSE_Chunk_Info::x_AddFeat_ids ( void  )

Definition at line 426 of file tse_chunk_info.cpp.

References m_ExplicitFeatIds.

Referenced by CSplitParser::x_Attach().

◆ x_AddSeq_data()

void CTSE_Chunk_Info::x_AddSeq_data ( const TLocationSet location)

◆ x_AddUsedMemory()

void CTSE_Chunk_Info::x_AddUsedMemory ( size_t  size)

◆ x_AddXref_ids() [1/2]

void CTSE_Chunk_Info::x_AddXref_ids ( const SAnnotTypeSelector type,
const TFeatIdIntList ids 
)

◆ x_AddXref_ids() [2/2]

void CTSE_Chunk_Info::x_AddXref_ids ( const SAnnotTypeSelector type,
const TFeatIdStrList ids 
)

◆ x_AnnotIndexNeedsUpdate()

bool CTSE_Chunk_Info::x_AnnotIndexNeedsUpdate ( ) const
inlineprotected

Definition at line 360 of file tse_chunk_info.hpp.

◆ x_Attached()

bool CTSE_Chunk_Info::x_Attached ( void  ) const
protected

◆ x_ContainsFeatIds() [1/2]

bool CTSE_Chunk_Info::x_ContainsFeatIds ( CSeqFeatData::E_Choice  type,
EFeatIdType  id_type 
) const
protected

◆ x_ContainsFeatIds() [2/2]

bool CTSE_Chunk_Info::x_ContainsFeatIds ( CSeqFeatData::ESubtype  subtype,
EFeatIdType  id_type 
) const
protected

◆ x_ContainsFeatType() [1/2]

bool CTSE_Chunk_Info::x_ContainsFeatType ( CSeqFeatData::E_Choice  type) const
protected

Definition at line 615 of file tse_chunk_info.cpp.

References ITERATE, m_AnnotContents, and x_HasFeatType().

Referenced by x_ContainsFeatIds().

◆ x_ContainsFeatType() [2/2]

bool CTSE_Chunk_Info::x_ContainsFeatType ( CSeqFeatData::ESubtype  subtype) const
protected

Definition at line 626 of file tse_chunk_info.cpp.

References ITERATE, m_AnnotContents, and x_HasFeatType().

◆ x_DropAnnotObjects()

void CTSE_Chunk_Info::x_DropAnnotObjects ( void  )
protected

Definition at line 715 of file tse_chunk_info.cpp.

References m_ObjectIndexList.

◆ x_GetRecords()

bool CTSE_Chunk_Info::x_GetRecords ( const CSeq_id_Handle id,
bool  bioseq 
) const
protected

Definition at line 246 of file tse_chunk_info.cpp.

References ContainsBioseq(), IsLoaded(), and Load().

Referenced by CTSE_Split_Info::x_GetRecords().

◆ x_InitObjectIndexList()

void CTSE_Chunk_Info::x_InitObjectIndexList ( void  )
protected

◆ x_LoadAnnot()

void CTSE_Chunk_Info::x_LoadAnnot ( const TPlace place,
const CSeq_annot annot 
)

◆ x_LoadAssembly()

void CTSE_Chunk_Info::x_LoadAssembly ( const TBioseqId seq_id,
const TAssembly assembly 
)

◆ x_LoadBioseq()

void CTSE_Chunk_Info::x_LoadBioseq ( const TPlace place,
const CBioseq bioseq 
)

Definition at line 741 of file tse_chunk_info.cpp.

References _ASSERT, IsLoaded(), Ref(), x_Attached(), and x_LoadBioseqs().

◆ x_LoadBioseqs()

void CTSE_Chunk_Info::x_LoadBioseqs ( const TPlace place,
const list< CRef< CBioseq > > &  bioseqs 
)

◆ x_LoadDescr()

void CTSE_Chunk_Info::x_LoadDescr ( const TPlace place,
const CSeq_descr descr 
)

◆ x_LoadSeq_entry()

void CTSE_Chunk_Info::x_LoadSeq_entry ( CSeq_entry entry,
CTSE_SetObjectInfo set_info = 0 
)

◆ x_LoadSequence()

void CTSE_Chunk_Info::x_LoadSequence ( const TPlace place,
TSeqPos  pos,
const TSequence seq 
)

◆ x_SetLoadBytes()

void CTSE_Chunk_Info::x_SetLoadBytes ( Uint4  bytes)

◆ x_SetLoadSeconds()

void CTSE_Chunk_Info::x_SetLoadSeconds ( double  seconds)

Definition at line 801 of file tse_chunk_info.cpp.

References m_LoadSeconds.

Referenced by CCSRARefSeqInfo::LoadAnnotMainChunk().

◆ x_SplitAttach()

void CTSE_Chunk_Info::x_SplitAttach ( CTSE_Split_Info split_info)
protected

◆ x_TSEAttach()

void CTSE_Chunk_Info::x_TSEAttach ( CTSE_Info tse,
ITSE_Assigner tse_info 
)
protected

◆ x_UpdateAnnotIndex()

void CTSE_Chunk_Info::x_UpdateAnnotIndex ( CTSE_Info tse)
protected

◆ x_UpdateAnnotIndexContents()

void CTSE_Chunk_Info::x_UpdateAnnotIndexContents ( CTSE_Info tse)
protected

Friends And Related Function Documentation

◆ CTSE_Default_Assigner

friend class CTSE_Default_Assigner
friend

Definition at line 306 of file tse_chunk_info.hpp.

◆ CTSE_Info

friend class CTSE_Info ( void  )
friend

Definition at line 303 of file tse_chunk_info.hpp.

◆ CTSE_Split_Info

friend class CTSE_Split_Info
friend

Definition at line 304 of file tse_chunk_info.hpp.

Member Data Documentation

◆ m_AnnotContents

TAnnotContents CTSE_Chunk_Info::m_AnnotContents
private

◆ m_AnnotPlaces

TPlaces CTSE_Chunk_Info::m_AnnotPlaces
private

Definition at line 321 of file tse_chunk_info.hpp.

Referenced by GetAnnotPlaces(), x_AddAnnotPlace(), x_SplitAttach(), and x_TSEAttach().

◆ m_AssemblyInfos

TAssemblyInfos CTSE_Chunk_Info::m_AssemblyInfos
private

◆ m_BioseqIds

TBioseqIds CTSE_Chunk_Info::m_BioseqIds
private

◆ m_BioseqPlaces

TBioseqPlaces CTSE_Chunk_Info::m_BioseqPlaces
private

Definition at line 322 of file tse_chunk_info.hpp.

Referenced by GetBioseqPlaces(), x_AddBioseqPlace(), x_SplitAttach(), and x_TSEAttach().

◆ m_ChunkId

TChunkId CTSE_Chunk_Info::m_ChunkId
private

Definition at line 313 of file tse_chunk_info.hpp.

Referenced by GetChunkId().

◆ m_DescInfos

TDescInfos CTSE_Chunk_Info::m_DescInfos
private

Definition at line 320 of file tse_chunk_info.hpp.

Referenced by GetDescInfos(), x_AddDescInfo(), x_SplitAttach(), and x_TSEAttach().

◆ m_ExplicitFeatIds

bool CTSE_Chunk_Info::m_ExplicitFeatIds
private

◆ m_FeatIds

TFeatIdsMap CTSE_Chunk_Info::m_FeatIds
private

◆ m_ListenerMutex

CMutex CTSE_Chunk_Info::m_ListenerMutex
private

Definition at line 333 of file tse_chunk_info.hpp.

Referenced by SetLoaded(), and SetLoadListener().

◆ m_LoadBytes

Uint4 CTSE_Chunk_Info::m_LoadBytes
private

Definition at line 315 of file tse_chunk_info.hpp.

Referenced by GetLoadBytes(), and x_SetLoadBytes().

◆ m_LoadListener

CRef<CTSEChunkLoadListener> CTSE_Chunk_Info::m_LoadListener
private

Definition at line 334 of file tse_chunk_info.hpp.

Referenced by SetLoaded(), and SetLoadListener().

◆ m_LoadLock

CInitMutex<CObject> CTSE_Chunk_Info::m_LoadLock
private

◆ m_LoadSeconds

float CTSE_Chunk_Info::m_LoadSeconds
private

Definition at line 316 of file tse_chunk_info.hpp.

Referenced by GetLoadSeconds(), and x_SetLoadSeconds().

◆ m_ObjectIndexList

TObjectIndexList CTSE_Chunk_Info::m_ObjectIndexList
private

◆ m_Seq_data

TLocationSet CTSE_Chunk_Info::m_Seq_data
private

Definition at line 325 of file tse_chunk_info.hpp.

Referenced by GetSeq_dataInfos(), x_AddSeq_data(), x_SplitAttach(), and x_TSEAttach().

◆ m_SplitInfo

CTSE_Split_Info* CTSE_Chunk_Info::m_SplitInfo
private

◆ m_XrefIds

TFeatIdsMap CTSE_Chunk_Info::m_XrefIds
private

The documentation for this class was generated from the following files:
Modified on Tue May 28 05:52:06 2024 by modify_doxy.py rev. 669887