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

vector<CSeq_id_Handle>

;

AddDataLoader(

& loader_name,

fUserFlagMask = 0xff,

ResetScope(

);

ResetHistory(

action);

ResetDataAndHistory(

);

RemoveFromHistory(

& tse,

action);

RemoveDataLoader(

& loader_name,

RemoveTopLevelSeqEntry(

& entry);

IsTransactionActive()

;

x_DetachFromOM(

);

x_ReportNewDataConflict(

* conflict_id = 0);

x_ClearCacheOnNewDS(

);

x_ClearCacheOnNewData(

& seq_ids,

& annot_ids);

x_ClearCacheOnNewData(

& new_tse);

x_ClearCacheOnNewData(

& new_tse,

x_ClearCacheOnNewData(

& new_tse,

x_ClearCacheOnRemoveData(

* old_tse = 0);

x_ClearAnnotCache(

);

x_ClearCacheOnNewAnnot(

& new_tse);

x_ClearCacheOnRemoveAnnot(

& old_tse);

x_GetBioseqHandlesFromTSE(

& ids,

x_IsDummyTSE(

& tse,

x_IsDummyTSE(

& tse,

x_IsDummyTSE(

& tse,

x_GetBioseqHandlesSorted(

& ids,

m_KeepExternalAnnotsForEdit;

SetKeepExternalAnnotsForEdit(

keep =

);

unique_ptr<SAnnotSelector>& sel_copy,

CTSE_CI;

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

vector< pair< TTSE_ScopeInfo, CSeq_id_Handle > > TTSE_MatchSet

CBioseq_set_EditHandle –.

vector< pair< TTSE_Lock, CSeq_id_Handle > > TTSE_LockMatchSet

CFastMutex TSeq_idMapLock

CDataSource::TTSE_LockMatchSet TTSE_LockMatchSet_DS

TConfLock::TWriteLockGuard TConfWriteLockGuard

CBioseq_ScopeInfo::TTSE_MatchSet TTSE_MatchSet

CPriorityTree m_setDataSrc

CRef< CObjectManager > m_ObjMgr

map< CRef< CDataSource >, CRef< CDataSource_ScopeInfo > > TDSMap

vector< CBioseq_Handle > TBioseqHandles

Bulk retrieval methods.

TSeq_idMapValue & x_GetSeq_id_Info(const CBioseq_Handle &bh)

CTSE_ScopeUserLock TTSE_Lock

vector< CTSE_Handle > TCDD_Entries

IScopeTransaction_Impl * m_Transaction

TSeq_idMap::value_type TSeq_idMapValue

bool GetKeepExternalAnnotsForEdit() const

set< CSeq_id_Handle > TSeq_idSet

bool m_KeepExternalAnnotsForEdit

vector< TSeqPos > TSequenceLengths

pair< CConstRef< CSeq_entry_Info >, TTSE_Lock > TSeq_entry_Lock

vector< pair< CTSE_Handle, CSeq_id_Handle > > TTSE_LockMatchSet

CScope_Impl(const CScope_Impl &)

vector< CBioseq_Handle > TBioseq_HandleSet

CDataSource_ScopeInfo::TBioseq_Lock TBioseq_Lock

CInitMutexPool m_MutexPool

vector< int > TSequenceStates

map< CSeq_id_Handle, SSeq_id_ScopeInfo > TSeq_idMap

atomic< int > m_AnnotChangeCounter

map< CConstRef< CObject >, CRef< CObject > > TEditInfoMap

vector< CSeq_entry_Handle > TTSE_Handles

atomic< int > m_BioseqChangeCounter

vector< CSeq_inst::TMol > TSequenceTypes

TConfLock::TReadLockGuard TConfReadLockGuard

TSeq_idMapLock m_Seq_idMapLock

vector< int > TSequenceHashes

vector< CSeq_id_Handle > TIds

CObjectManager & GetObjectManager(void)

pair< CConstRef< CSeq_annot_Info >, TTSE_Lock > TSeq_annot_Lock

pair< CConstRef< CBioseq_set_Info >, TTSE_Lock > TBioseq_set_Lock

CScope_Impl & operator=(const CScope_Impl &)

namespace ncbi::objects::

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

string GetLabel(const CSeq_id &id)

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

#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

double value_type

The numeric datatype used by the parser.

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

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

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

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.

TBlobStateFlags m_BlobState

CTSE_ScopeUserLock m_TSE_Lock

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