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NCBI C++ ToolKit: include/objmgr/impl/tse_info.hpp Source File

vector<CConstRef<CSeq_annot_SNP_Info> >

;

m_AnnotSet.size();

(index < x_GetRangeMapCount());

!slot || slot->

();

(!x_RangeMapIsEmpty(index));

*m_AnnotSet[index];

TRangeMap& x_GetRangeMap(

index);

x_CleanRangeMaps(

);

fState_suppress_temp = 1 << 0,

fState_suppress_perm = 1 << 1,

fState_suppress = fState_suppress_temp | fState_suppress_perm,

fState_dead = 1 << 2,

fState_confidential = 1 << 3,

fState_withdrawn = 1 << 4,

fState_no_data = 1 << 5,

fState_conflict = 1 << 6,

fState_conn_failed = 1 << 7,

fState_other_error = 1 << 8

enum ETopLevelObjectType {

HasDataSource(

)

;

IsLocked(

)

;

& GetTSE_Info(

)

;

& GetBlobId(

)

;

IsDead(

)

;

IsUnavailable(

)

;

IsTopLevelSeq_submit()

;

& GetTopLevelSeq_submit()

;

GetUsedMemory(

)

;

SetUsedMemory(

);

AddUsedMemory(

);

HasAnnot(

& name)

;

HasUnnamedAnnot(

)

;

HasNamedAnnot(

& name)

;

HasMatchingAnnotIds(

)

;

OnlyGiAnnotIds(

)

;

m_ChunkId = chunk_id;

GetBioseqsIds(

& ids)

;

GetAnnotIds(

& ids)

;

UpdateAnnotIndex(

)

;

UpdateAnnotIndex(

);

x_UpdateAnnotIndexContents(

& tse);

x_SetDirtyAnnotIndexNoParent(

);

x_ResetDirtyAnnotIndexNoParent(

);

x_GetRecords(

&

,

bioseq)

;

x_LoadChunk(

chunk_id)

;

x_LoadChunks(

& chunk_ids)

;

HasSplitInfo(

)

;

x_NeedsDelayedMainChunk(

)

;

x_LoadDelayedMainChunk(

)

;

GetDescription(

)

;

CTSE_Guard;

x_Initialize(

);

x_Reset(

);

* x_GetUnnamedAnnotObjs(

)

;

x_RemoveAnnotObjs(

& name);

pair<SIdAnnotObjs*, bool> x_SetIdObjects(

& objs,

pair<SIdAnnotObjs*, bool> x_SetIdObjects(

& name,

x_UnmapSNP_Table(

& name,

x_MapAnnotObject(

& rangeMap,

x_UnmapAnnotObject(

& rangeMap,

x_MapAnnotObject(

& name,

x_UnmapAnnotObject(

& name,

x_MapFeatById(

&

,

x_UnmapFeatById(

&

,

x_MapFeatByLocus(

& locus,

,

x_UnmapFeatByLocus(

& locus,

,

x_MapChunkByFeatId(

&

,

x_MapChunkByFeatId(

&

,

x_MapChunkByFeatId(

&

,

x_MapChunkByFeatId(

&

,

x_MapChunkByFeatId(

&

,

x_MapChunkByFeatId(

&

,

fAnnotIds_NonGi = 1 << 0,

fAnnotIds_Matching = 1 << 1

CAtomicCounter_WithAutoInit –.

virtual void Update(CBioseq_Info &seq)=0

vector< CSeq_id_Handle > TSeqIds

namespace ncbi::objects::

Base class for all serializable objects.

const CAnnotName & m_Name

void Unmap(const SAnnotObject_Key &key, const CAnnotObject_Info &info) const

bool Map(const SAnnotObject_Key &key, const SAnnotObject_Index &index) const

CTSE_Info::TAnnotObjs & m_AnnotObjs

CTSEAnnotObjectMapper(CTSE_Info &tse, const CAnnotName &name)

ETopLevelObjectType

Type of top level object added to scope.

CConditionVariable m_LoadWait

vector< TChunkId > TChunkIds

TBioseq_sets m_Bioseq_sets

TBlobVersion GetBlobVersion(void) const

TNamedAnnotObjs m_NamedAnnotObjs

TTSE_Cache::iterator m_CachePosition

bool IsUnavailable(void) const

CRef< CTSE_Split_Info > m_Split

TBlobOrder GetBlobOrder(void) const

CAtomicCounter_WithAutoInit m_LockCounter

CSeq_id_Handle m_RequestedId

size_t GetUsedMemory(void) const

CDataSource & GetDataSource(void) const

map< CSeq_id_Handle, SIdAnnotInfo > TIdAnnotInfoMap

SIdAnnotObjs::TRange TRange

pair< TBlobState, TBlobVersion > TBlobOrder

TBioseqs m_Removed_Bioseqs

TBlobVersion m_BlobVersion

CBioseq_Info * TBioseqInfo

TBlobState GetBlobState(void) const

bool OnlyGiAnnotIds(void) const

vector< CAnnotObject_Info * > TAnnotObjects

CRef< CSerialObject > m_TopLevelObjectPtr

CTSE_Info(const CTSE_Info &)

void x_RemoveAnnotObjs(const CAnnotName &name)

SIdAnnotObjs::TRangeMap TRangeMap

void SetBlobState(TBlobState state)

multimap< TLocusKey, CAnnotObject_Info * > TLocusIndex

TAnnotLock::TWriteLockGuard TAnnotLockWriteGuard

bool IsLocked(void) const

unique_ptr< SBaseTSE > m_BaseTSE

TBlobState GetBlobStateOrder(void) const

TAnnotLock::TReadLockGuard TAnnotLockReadGuard

pair< CConstRef< CSeq_annot_Info >, CTSE_Lock > TSeq_annot_Lock

CBioseq_Handle::TBioseqStateFlags TBlobState

CRef< CBioseqUpdater > m_BioseqUpdater

map< CBioObjectId, CTSE_Info_Object * > TBioObjects

CRef< CTSE_SetObjectInfo > m_SetObjectInfo

SIdAnnotObjs::TSNPSet TSNPSet

const TBlobId & GetBlobId(void) const

bool m_MasterSeqSegmentsLoaded

ETopLevelObjectType m_TopLevelObjectType

list< CRef< CTSE_Info > > TTSE_Cache

bool HasMatchingAnnotIds(void) const

map< CSeqFeatData::ESubtype, SFeatIdIndex > TFeatIdIndex

TAnnotLock & GetAnnotLock(void) const

map< CSeq_id_Handle, TBioseqInfo > TBioseqs

map< CAnnotName, TAnnotObjs > TNamedAnnotObjs

atomic< ELoadState > m_LoadState

bool HasDataSource(void) const

TBioseq_sets m_Removed_Bioseq_sets

TFeatIdIndex m_FeatIdIndex

int m_InternalBioObjNumber

vector< CSeq_id_Handle > TSeqIds

const CAnnotName & GetName(void) const

CRef< CLoadMutex > m_LoadMutex

TIdAnnotInfoMap m_IdAnnotInfoMap

void ResetBlobState(TBlobState state=CBioseq_Handle::fState_none)

CFastMutex m_BioseqsMutex

CRef< IEditSaver > m_EditSaver

CDataSource * m_DataSource

pair< string, bool > TLocusKey

TAnnotIdsFlags m_AnnotIdsFlags

CRef< IEditSaver > GetEditSaver() const

pair< TSeq_annot_Lock, int > TSeq_feat_Lock

const CTSE_Info & GetTSE_Info(void) const

map< TIntId, CBioseq_set_Info * > TBioseq_sets

CConstRef< CMasterSeqSegments > m_MasterSeqSegments

const CSeq_id_Handle & GetRequestedId(void) const

void x_MapAnnotObject(TRangeMap &rangeMap, const SAnnotObject_Key &key, const SAnnotObject_Index &index)

CTSE_Handle::ETopLevelObjectType ETopLevelObjectType

bool x_UnmapAnnotObject(TRangeMap &rangeMap, const CAnnotObject_Info &info, const SAnnotObject_Key &key)

SIdAnnotObjs::TAnnotSet TAnnotSet

void SetRequestedId(const CSeq_id_Handle &requested_id) const

map< CSeq_id_Handle, SIdAnnotObjs > TAnnotObjs

CTSE_SetObjectInfo(const CTSE_SetObjectInfo &)

TSeq_annot_InfoMap m_Seq_annot_InfoMap

TBioseq_set_InfoMap m_Bioseq_set_InfoMap

map< CConstRef< CBioseq_set >, SBioseq_set_Info > TBioseq_set_InfoMap

map< CConstRef< CSeq_annot >, SSeq_annot_Info > TSeq_annot_InfoMap

void operator=(const CTSE_SetObjectInfo &)

IEditSaver * GetEditSaver(const Handle &handle)

unsigned int TSeqPos

Type for sequence locations and lengths.

TValue Get(void) const THROWS_NONE

Get atomic counter value.

int8_t Int1

1-byte (8-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJMGR_EXPORT

E_Choice

Choice variants.

const string version

version string

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::KEY key

Multi-threading – mutexes; rw-locks; semaphore.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

SBaseTSE(const CTSE_Lock &tse)

TObjectCopyMap m_ObjectCopyMap

multimap< TFeatIdStr, SFeatIdInfo > TIndexStr

AutoPtr< TIndexInt > m_IndexInt

multimap< TFeatIdInt, SFeatIdInfo > TIndexInt

AutoPtr< TIndexStr > m_IndexStr

SFeatIdInfo(EFeatIdType type, CAnnotObject_Info *info)

SFeatIdInfo(EFeatIdType type, TChunkId chunk_id)

CAnnotObject_Info * m_Info

CRef< CSeq_annot_SNP_Info > m_SNP_annot_Info

const TRangeMap & x_GetRangeMap(size_t index) const

vector< CConstRef< CSeq_annot_SNP_Info > > TSNPSet

vector< TRangeMap * > TAnnotSet

bool x_RangeMapIsEmpty(size_t index) const

const SIdAnnotObjs & operator=(const SIdAnnotObjs &objs)

CRangeMultimap< SAnnotObject_Index, TSeqPos > TRangeMap

size_t x_GetRangeMapCount(void) const

DECLARE_OPERATOR_BOOL_REF(m_Bioseq)

CConstRef< CBioseq_Info > m_Bioseq

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