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NCBI C++ ToolKit: src/objmgr/scope.cpp Source File

( CanBeDeleted() ) {

(m_HeapScope->CanBeDeleted());

m_Impl = m_HeapScope->m_Impl;

);

);

);

);

( iter->IsGi() ) {

(

seq_id = iter->GetSeqId() ) {

(

text_id = seq_id->GetTextseq_Id() ) {

( text_id->IsSetAccession() && text_id->IsSetVersion() ) {

( iter->IsGi() ) {

iter->GetGi();

iter->GetSeqId()->GetGi();

);

);

TSeq_id_Handles& idhs,

);

TSeq_id_Handles& idhs,

);

TSeq_id_Handles& idhs,

);

TSeq_id_Handles& idhs,

);

TSeq_id_Handles& idhs,

);

TSeq_id_Handles& ids,

);

TSeq_id_Handles& ids,

);

TSeq_id_Handles& ids,

);

TSeq_id_Handles& ids,

);

CBioseq_set_EditHandle –.

Base class for all object manager exceptions.

void x_ClearAnnotCache(void)

TSeqPos GetSequenceLength(const CSeq_id_Handle &id, TGetFlags flags)

string GetLabel(const CSeq_id_Handle &idh, TGetFlags flags)

void ResetDataAndHistory(void)

TBioseqHandles GetBioseqHandles(const TIds &ids)

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri, TExist action)

void GetSequenceStates(TSequenceStates &ret, const TIds &idhs, TGetFlags flags)

bool Exists(const CSeq_id_Handle &id)

void GetTaxIds(TTaxIds &ret, const TIds &idhs, TGetFlags flags)

CSeq_entry_Handle AddSeq_entry(CSeq_entry &entry, TPriority pri, TExist action)

int GetSequenceHash(const CSeq_id_Handle &id, TGetFlags flags)

TCDD_Entries GetCDDAnnots(const TIds &idhs)

TBioseqHandles GetBioseqHandlesFromTSE(const TIds &ids, const CTSE_Handle &tse)

void AddDefaults(TPriority priority)

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const CBlobIdKey &blob_id, TMissing action)

void GetGis(TGIs &ret, const TIds &idhs, TGetFlags flags)

CSeq_annot_Handle AddSharedSeq_annot(const CSeq_annot &annot, TPriority pri, TExist action)

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id_Handle &id, const CTSE_Handle &tse)

void RemoveFromHistory(const CTSE_Handle &tse, int action)

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri, TExist action)

void GetAccVers(TIds &ret, const TIds &idhs, TGetFlags flags)

void AddScope(CScope_Impl &scope, TPriority priority)

void GetAllTSEs(TTSE_Handles &tses, int kind)

void RemoveTopLevelBioseq(const CBioseq_Handle &seq)

void GetBulkIds(TBulkIds &ret, const TIds &idhs, TGetFlags flags)

void AddDataLoader(const string &loader_name, TPriority priority)

void RemoveTopLevelAnnot(const CSeq_annot_Handle &annot)

CSeq_inst::TMol GetSequenceType(const CSeq_id_Handle &id, TGetFlags flags)

CSeq_annot_Handle GetSeq_annotHandle(const CSeq_annot &annot, TMissing action)

bool IsSameBioseq(const CSeq_id_Handle &id1, const CSeq_id_Handle &id2, int get_flag)

void ResetHistory(int action)

CSeq_entry_Handle AddSeq_submit(CSeq_submit &submit, TPriority pri)

CSeq_entry_Handle AddSharedSeq_entry(const CSeq_entry &entry, TPriority pri, TExist action)

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, TMissing action)

void GetSequenceTypes(TSequenceTypes &ret, const TIds &idhs, TGetFlags flags)

CBioseq_Handle AddSharedBioseq(const CBioseq &bioseq, TPriority pri, TExist action)

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id_Handle &id, int get_flag)

void RemoveDataLoader(const string &loader_name, int action)

void GetSequenceLengths(TSequenceLengths &ret, const TIds &idhs, TGetFlags flags)

CObjectManager & GetObjectManager(void)

void GetSequenceHashes(TSequenceHashes &ret, const TIds &idhs, TGetFlags flags)

CSeq_id_Handle GetAccVer(const CSeq_id_Handle &idh, TGetFlags flags)

void GetLabels(TLabels &ret, const TIds &idhs, TGetFlags flags)

CBioseq_Handle GetBioseqHandle(const CSeq_id_Handle &id, int get_flag)

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &seqset, TMissing action)

TIds GetIds(const CSeq_id_Handle &idh, TGetFlags flags=0)

TGi GetGi(const CSeq_id_Handle &idh, TGetFlags flags)

CTSE_Handle GetEditHandle(const CTSE_Handle &src_tse)

TTaxId GetTaxId(const CSeq_id_Handle &idh, TGetFlags flags)

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

int GetSequenceState(const CSeq_id_Handle &id, TGetFlags flags)

namespace ncbi::objects::

bool CanBeEdited(void) const

Return true if this TSE handle is local to scope and can be edited.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

void RemoveSeq_annot(const CSeq_annot_Handle &annot)

Revoke Seq-annot previously added using AddSeq_annot().

void RemoveAnnot(CSeq_entry &parent, CSeq_annot &annot)

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

CScopeTransaction GetTransaction()

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

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.

void RemoveFromHistory(const CTSE_Handle &tse, EActionIfLocked action=eKeepIfLocked)

Remove single TSE from the scope's history.

CSeq_id_Handle GetAccVer(const CSeq_id_Handle &idh, TGetFlags flags=0)

Get accession.version Seq-id Returns null CSeq_id_Handle if the sequence is not found or if it doesn'...

TTaxId GetTaxId(const CSeq_id &id, TGetFlags flags=0)

Get taxonomy id of bioseq Return -1 if sequence is not found Return 0 if sequence doesn't have taxono...

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

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.

CBioseq_set_EditHandle GetBioseq_setEditHandle(const CBioseq_set &seqset)

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

EExist

AddXxx() control values.

friend class CScopeTransaction

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...

CSeq_entry_Handle AddSeq_submit(CSeq_submit &submit, TPriority pri=kPriority_Default)

Add Seq-submit, return its CSeq_entry_Handle.

void RemoveBioseq(const CBioseq_Handle &seq)

Revoke Bioseq previously added using AddBioseq().

TCDD_Entries GetCDDAnnots(const TIds &idhs)

TSeqPos GetSequenceLength(const CSeq_id &id, TGetFlags flags=0)

Get sequence length Return kInvalidSeqPos if sequence is not found.

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 ...

void AttachEntry(CSeq_entry &parent, CSeq_entry &entry)

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CTSE_Handle GetTSE_Handle(const CSeq_entry &tse, EMissing action=eMissing_Default)

Find object in scope If object is not found GetXxxHandle() methods will either throw an exception or ...

string GetLabel(const CSeq_id &id, TGetFlags flags=0)

Get short description of bioseq, usually "accession.version" Returns empty string if the sequence is ...

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)

CRef< CSeq_entry > GetTSE(void) const

Create seq-entry with all parsed sequences, annotations etc.

TBioseqHandles GetBioseqHandles(const TIds &ids)

Get bioseq handles for all ids.

void GetAllTSEs(TTSE_Handles &tses, enum ETSEKind kind=eManualTSEs)

CSeq_inst::TMol GetSequenceType(const CSeq_id &id, TGetFlags flags=0)

Get molecular type of sequence (protein/dna/rna) Return CSeq_inst::eMol_not_set if sequence is not fo...

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...

CBioseq_EditHandle GetEditHandle(const CBioseq_Handle &seq)

Get editable Biosec handle by regular one.

vector< CBioseq_Handle > TBioseqHandles

static CSeq_id_Handle x_GetAccVer(const TIds &ids)

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

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add Seq-annot, return its CSeq_annot_Handle.

void AttachAnnot(CSeq_entry &parent, CSeq_annot &annot)

CObjectManager & GetObjectManager(void)

Get object manager controlling this scope.

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id &id)

Get bioseq synonyms, resolving to the bioseq in this scope.

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)

void UpdateAnnotIndex(void)

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().

void ReplaceAnnot(CSeq_entry &entry, CSeq_annot &old_annot, CSeq_annot &new_annot)

TGi GetGi(const CSeq_id_Handle &idh, TGetFlags flags=0)

Get GI of a sequence Returns ZERO_GI if the sequence is not found or if it doesn't have GI.

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

void AddScope(CScope &scope, TPriority pri=kPriority_Default)

Add the scope's datasources as a single group with the given priority All data sources (data loaders ...

CSeq_entry_EditHandle GetSeq_entryEditHandle(const CSeq_entry &entry)

static TGi x_GetGi(const TIds &ids)

vector< CSeq_inst::TMol > TSequenceTypes

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

TBulkIds GetBulkIds(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)

TSequenceHash GetSequenceHash(const CSeq_id &id, TGetFlags flags=0)

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

TBioseqHandles GetBioseqHandlesFromTSE(const TIds &ids, const CTSE_Handle &tse)

Bulk get bioseq handles for sequence withing one TSE.

CBioseq_Handle::TBioseqStateFlags GetSequenceState(const CSeq_id &id, TGetFlags flags=0)

Get sequence GenBank state Return (fState_not_found|fState_no_data) if sequence is not found.

int TPriority

priority type and special value for added objects

void RemoveDataLoader(const string &loader_name, EActionIfLocked action=eThrowIfLocked)

Revoke data loader from the scope.

vector< CSeq_id_Handle > TIds

CRef< CScope_Impl > m_Impl

void RemoveEntry(CSeq_entry &entry)

CSeq_entry_Handle AddGC_Assembly(const CGC_Assembly &gc_assembly, CGC_Assembly_Parser::FParserFlags flags=CGC_Assembly_Parser::fDefault, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add GC-Assembly.

vector< TIds > TBulkIds

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

vector< CSeq_entry_Handle > TTSE_Handles

bool IsSameBioseq(const CSeq_id_Handle &id1, const CSeq_id_Handle &id2, EGetBioseqFlag get_flag)

Check if two seq-ids are resolved to the same Bioseq.

CRef< CScope > m_HeapScope

CSeq_annot_EditHandle GetSeq_annotEditHandle(const CSeq_annot &annot)

void ResetDataAndHistory(void)

Clear all information in the scope except added data loaders.

EMissing

GetXxxHandle control values.

bool Exists(const CSeq_id &id)

Check existence of sequence with this id.

CBioseq_EditHandle GetBioseqEditHandle(const CBioseq &bioseq)

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

vector< CSeq_id_Handle > TSeq_id_Handles

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

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

const CTSE_Handle & GetTSE_Handle(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

void Remove(void) const

Remove current annot.

const CTSE_Handle & GetTSE_Handle(void) const

void Remove(void) const

Remove this Seq-entry from parent, or scope if it's top level Seq-entry.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

const CTSE_Handle & GetTSE_Handle(void) const

CSeq_entry_EditHandle GetParentEntry(void) const

Navigate object tree.

void Reset(void)

Reset reference object.

#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.

@ e_Gi

GenInfo Integrated Database.

EMol

molecule class in living organism

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

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