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

DropAllTSEs(

);

IsEmpty(

)

;

RevokeDataLoader(

);

CanBeEdited(

)

;

UpdateAnnotIndex(

);

GetTSESetWithOrphanAnnots(

& ids,

GetTSESetWithBioseqAnnots(

& bioseq,

external_only =

);

GetTSESetWithBioseqAnnots(bioseq, tse, tse_set, sel, processed_nas,

);

vector<CSeq_id_Handle>

;

GetSequenceLengths(

& ids,

& loaded,

GetSequenceTypes(

& ids,

& loaded,

GetSequenceStates(

& ids,

& loaded,

GetSequenceHashes(

& ids,

& loaded,

GetName(

)

;

GetDefaultPriority(

)

;

SetDefaultPriority(

priority);

GetDefaultBlobCacheSizeLimit();

fLockNoHistory = 1<<0,

fLockNoManual = 1<<1,

IsLoaded(

& tse)

;

fLoaded_bioseqs = 1<<0,

fLoaded_bioseq_annots = 1<<1,

fLoaded_orphan_annots = 1<<2,

fLoaded_annots = fLoaded_bioseq_annots | fLoaded_orphan_annots,

fLoaded_all = fLoaded_bioseqs | fLoaded_annots,

fSplit_bioseqs = 1<<3,

fKnown_bioseqs = fLoaded_bioseqs | fSplit_bioseqs

debug::set<TTSE_Ref>

;

x_ReleaseLastLock(

& lock);

x_FindTSE_Info(

& tse)

;

x_FindSeq_entry_Info(

& entry)

;

x_FindBioseq_Info(

& seq)

;

x_FindSeq_annot_Info(

& annot)

;

x_FindBioseq_set_Info(

& seqset)

;

x_SetDirtyAnnotIndex(

& tse);

x_ResetDirtyAnnotIndex(

& tse);

x_IndexSeqTSE(

vector<CSeq_id_Handle>& ids,

* tse_info);

x_IndexSplitInfo(

vector<CSeq_id_Handle>& ids,

x_UnindexSplitInfo(

vector<CSeq_id_Handle>& ids,

x_IndexAnnotTSEs(

* tse_info);

x_UnindexAnnotTSEs(

* tse_info);

x_CleanupUnusedEntries(

);

pair< string, int > GetAccVer(const CAlignModel &a, CScope &scope)

CDataSource::TMainLock::TReadLockGuard m_MainGuard

CDataSource::TAnnotLock::TReadLockGuard m_AnnotGuard

CDataSource::TAnnotLock::TWriteLockGuard m_AnnotGuard

CDataSource::TMainLock::TReadLockGuard m_MainGuard

pair< CConstRef< CSeq_annot_Info >, TTSE_Lock > TSeq_annot_Lock

vector< TSeqPos > TSequenceLengths

TSeq_id2TSE_Set m_TSE_seq_annot

TPriority m_DefaultPriority

vector< int > TSequenceStates

CRef< CTSE_Info > TTSE_Ref

CDataSource & operator=(const CDataSource &)

CRef< CTSE_Split_Info > TSplitInfoRef

CDataSource(const CDataSource &)

bool x_IsTrackingSplitSeq() const

bool CanBeEdited(void) const

TTSE_LockSet m_StaticBlobs

set< CSeq_id_Handle > TSeq_idSet

CRef< CDataLoader > m_Loader

CRef< CPrefetchThreadOld > m_PrefetchThread

CDataLoader::STypeFound STypeFound

map< CSeq_id_Handle, SSeqMatch_DS > TSeqMatchMap

vector< pair< TTSE_Lock, CSeq_id_Handle > > TTSE_LockMatchSet

unsigned m_StaticBlobCounter

CConstRef< CObject > m_SharedObject

TPriority GetDefaultPriority(void) const

TMainLock & GetMainLock() const

set< TBlobId > TLoadedBlob_ids_Set

CDSAnnotLockWriteGuard TAnnotLockWriteGuard

map< const CObject *, const CTSE_Info_Object * > TInfoMap

CDataLoader * GetDataLoader(void) const

pair< CConstRef< CSeq_entry_Info >, TTSE_Lock > TSeq_entry_Lock

vector< CSeq_inst::TMol > TSequenceTypes

CFastMutex m_PrefetchLock

CTSE_LockSet TTSE_LockSet

unsigned m_Blob_Cache_Size

TSeq_id2TSE_Set m_TSE_orphan_annot

vector< CSeq_id_Handle > TIds

CDSAnnotLockReadGuard TAnnotLockReadGuard

const CConstRef< CObject > & GetSharedObject(void) const

CDataLoader::SGiFound SGiFound

list< TTSE_Ref > TBlob_Cache

map< CSeq_id_Handle, TTSE_Set > TSeq_id2TSE_Set

vector< bool > THashKnown

vector< CConstRef< CBioseq_Info > > TBioseq_InfoSet

const CTSE_LockSet & GetStaticBlobs(void) const

vector< CTSE_Lock > TCDD_Locks

unsigned m_Blob_Cache_Size_Limit

TTSE_Set m_DirtyAnnot_TSEs

vector< int > TSequenceHashes

CDataLoader::SHashFound SHashFound

vector< SSeqMatch_DS > TSeqMatches

vector< TBlobId > TLoadedBlob_ids

pair< CConstRef< CBioseq_set_Info >, TTSE_Lock > TBioseq_set_Lock

TSeq_id2SplitInfoSet m_TSE_split_seq

map< TBlobId, TTSE_Ref > TBlob_Map

pair< TSeq_annot_Lock, int > TSeq_feat_Lock

vector< vector< CSeq_id_Handle > > TSeqIdSets

set< TSplitInfoRef > TSplitInfoSet

void GetTSESetWithExternalAnnots(const CBioseq_Info &bioseq, const TTSE_Lock &tse, TTSE_LockMatchSet &tse_set, const SAnnotSelector *sel, CDataLoader::TProcessedNAs *processed_nas=0)

map< CSeq_id_Handle, TSplitInfoSet > TSeq_id2SplitInfoSet

bool IsLive(const CTSE_Info &tse)

pair< CConstRef< CBioseq_Info >, TTSE_Lock > TBioseq_Lock

CDataLoader::SAccVerFound SAccVerFound

TSeq_id2TSE_Set m_TSE_seq

void SetDefaultPriority(TPriority priority)

namespace ncbi::objects::

CBioseq_Handle::TBioseqStateFlags TBlobState

CTimeout – Timeout interval.

static const struct type types[]

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

string GetLabel(const CSeq_id &id)

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

TObjectType * GetNCPointerOrNull(void) const THROWS_NONE

Get pointer value.

#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

EMol

molecule class in living organism

EEmptyGuard

class CGuard<> implements a templatized "resource acquisition is initialization" (RAII) locking guard...

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

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

Return a (corrected) set of flags identifying the sequence type.

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

SSeqMatch_DS(const CTSE_Lock &tse_lock, const CSeq_id_Handle &id)

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