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

kPriority_Default = -1,

kPriority_NotSet = -1

EGetBioseqFlag get_flag);

EGetBioseqFlag get_flag);

EGetBioseqFlag get_flag);

vector<CSeq_id_Handle>

;

eMissing_Default = eMissing_Throw

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

action = eMissing_Default);

AddDefaults(

pri = kPriority_Default);

AddDataLoader(

& loader_name,

AddScope(

& scope,

eExist_Default = eExist_Throw

TPriority pri = kPriority_Default,

EExist action = eExist_Default);

TPriority pri = kPriority_Default,

EExist action = eExist_Throw);

TPriority pri = kPriority_Default,

EExist action = eExist_Throw);

TPriority pri = kPriority_Default,

EExist action = eExist_Throw);

TPriority pri = kPriority_Default,

EExist action = eExist_Throw);

TPriority pri = kPriority_Default,

EExist action = eExist_Throw);

TPriority pri = kPriority_Default,

EExist action = eExist_Throw);

TPriority pri = kPriority_Default);

ResetHistory(EActionIfLocked action = eKeepIfLocked);

ResetDataAndHistory(

);

ResetDataAndHistory(ERemoveDataLoaders remove_data_loaders);

EActionIfLocked action = eKeepIfLocked);

EActionIfLocked action = eKeepIfLocked);

RemoveFromHistory(

& seq_id);

RemoveDataLoader(

& loader_name,

EActionIfLocked action = eThrowIfLocked);

RemoveTopLevelSeqEntry(

& entry);

fForceLoad = (1 << 0),

fThrowOnMissingSequence = (1 << 1),

fThrowOnMissingData = (1 << 2),

fThrowOnMissing = fThrowOnMissingSequence|fThrowOnMissingData,

fDoNotRecalculate = (1 << 3)

eNoForceLabelLoad = eNoForceLoad,

eForceLabelLoad = eForceLoad

Exists(

&

);

x_GetGi(

TIds& ids);

TGetFlags

= 0);

TGetFlags

= 0);

UpdateAnnotIndex(

);

GetDefaultKeepExternalAnnotsForEdit();

SetDefaultKeepExternalAnnotsForEdit(

keep =

);

GetKeepExternalAnnotsForEdit()

;

SetKeepExternalAnnotsForEdit(

keep =

);

User-defined methods of the data storage class.

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

CBioseq_set_EditHandle –.

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.

void GetAccVers(TSeq_id_Handles *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

EForceLabelLoad

obsolete enum

TSequenceHashes GetSequenceHashes(const TSeq_id_Handles &idhs, TGetFlags flags=0)

vector< TTaxId > TTaxIds

Get taxonomy ids of sequences Return -1 for sequences that aren't found Return 0 for sequences that d...

vector< TSeqPos > TSequenceLengths

Get lengths of sequences Return kInvalidSeqPos for sequences that aren't found.

CScope & operator=(const CScope &)

void GetSequenceLengths(TSequenceLengths *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

CScope_Impl & GetImpl(void)

CBioseq_set_EditHandle GetBioseq_setEditHandle(const CBioseq_set &seqset)

TSequenceStates GetSequenceStates(const TSeq_id_Handles &idhs, TGetFlags flags=0)

EExist

AddXxx() control values.

void GetSequenceHashes(TSequenceHashes *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

void GetGis(TGIs *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TSeq_id_Handles GetAccVers(const TSeq_id_Handles &idhs, TGetFlags flags=0)

Get accession.version Seq-id Returns null CSeq_id_Handles for sequences that aren't found or don't ha...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< string > TLabels

Get short descriptions of sequences, usually "accession.version" Returns empty strings for sequences ...

vector< TGi > TGIs

Get GI of a sequence Returns ZERO_GI for sequence that aren't found or don't have GI.

TSequenceTypes GetSequenceTypes(const TSeq_id_Handles &idhs, TGetFlags flags=0)

EGetFlags

Flags to control behavior of various meta-data getters fForceLoad instructs scope to ignore already l...

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

FParserFlags

Parser options.

vector< CBioseq_Handle::TBioseqStateFlags > TSequenceStates

Get GenBank states of sequences Return (fState_not_found|fState_no_data) for sequences that aren't fo...

vector< TSequenceHash > TSequenceHashes

Get data hashes of sequences Return 0 for sequences that aren't found or they don't have hash Note: 0...

vector< CBioseq_Handle > TBioseqHandles

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &seqset, EMissing action=eMissing_Default)

int TSequenceHash

Get sequence data hash value Return 0 if sequence is not found or if its hash is not known Note: 0 ca...

CSeq_annot_Handle GetSeq_annotHandle(const CSeq_annot &annot, EMissing action=eMissing_Default)

TGIs GetGis(const TSeq_id_Handles &idhs, TGetFlags flags=0)

vector< CTSE_Handle > TCDD_Entries

Get CDD annotations for all ids.

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq().

TLabels GetLabels(const TSeq_id_Handles &idhs, TGetFlags flags=0)

void GetTaxIds(TTaxIds *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

CSeq_entry_EditHandle GetSeq_entryEditHandle(const CSeq_entry &entry)

vector< CSeq_inst::TMol > TSequenceTypes

Get molecular types of sequences (protein/dna/rna) Return CSeq_inst::eMol_not_set for sequences that ...

void GetSequenceTypes(TSequenceTypes *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TBulkIds GetBulkIds(const TSeq_id_Handles &idhs, TGetFlags flags=0)

void GetSequenceStates(TSequenceStates *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

ERemoveDataLoaders

Clear all information in the scope including data loaders.

TSequenceLengths GetSequenceLengths(const TSeq_id_Handles &idhs, TGetFlags flags=0)

TTaxIds GetTaxIds(const TSeq_id_Handles &idhs, TGetFlags flags=0)

EForceLoad

EForceLoad flag instruct scope to ignore already loaded information and always request data loader fo...

int TPriority

priority type and special value for added objects

void GetBulkIds(TBulkIds *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

vector< CSeq_id_Handle > TIds

CRef< CScope_Impl > m_Impl

void GetLabels(TLabels *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

vector< TIds > TBulkIds

Get all ids of sequences Returns empty ids if the sequence is not found.

vector< CSeq_entry_Handle > TTSE_Handles

CRef< CScope > m_HeapScope

CBioseq_EditHandle GetObjectEditHandle(const CBioseq &bioseq)

CSeq_annot_EditHandle GetSeq_annotEditHandle(const CSeq_annot &annot)

EMissing

GetXxxHandle control values.

CBioseq_EditHandle GetBioseqEditHandle(const CBioseq &bioseq)

Get edit handle for the specified object Throw an exception if object is not found,...

CBioseq_Handle GetObjectHandle(const CBioseq &bioseq, EMissing action=eMissing_Default)

vector< CSeq_id_Handle > TSeq_id_Handles

Bulk retrieval methods Common argument typedef - vector of requested ids.

@ eGetBioseq_Resolved

Search only in already resolved ids.

@ eGetBioseq_Loaded

Search in all loaded TSEs in the scope.

const CTSE_Handle & GetTSE_Handle(void) const

#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

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

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.

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