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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCUser__object.html below:

NCBI C++ ToolKit: CUser_object Class Reference

Represents ASN.1 type User-object defined in file general.asn

#include <objects/general/User_object.hpp>

Definition at line 50 of file User_object.hpp.

◆ Tparent ◆ TRefGeneTrackingAccessions ◆ ECategory

enums for implicit typing of user objects

general category

Enumerator eCategory_Unknown eCategory_Experiment

Definition at line 134 of file User_object.hpp.

◆ EExperiment

sub-category experiment

Enumerator eExperiment_Unknown eExperiment_Sage

Definition at line 140 of file User_object.hpp.

◆ ELabelContent

enum controlling what to return for a label this mirrors a request inside of feature::GetLabel()

Enumerator eType eContent eBoth

Definition at line 119 of file User_object.hpp.

◆ EObjectType

Object Type.

Enumerator eObjectType_Unknown eObjectType_DBLink eObjectType_StructuredComment eObjectType_OriginalId eObjectType_Unverified eObjectType_ValidationSuppression eObjectType_Cleanup eObjectType_AutodefOptions eObjectType_FileTrack eObjectType_RefGeneTracking eObjectType_Unreviewed

Definition at line 161 of file User_object.hpp.

◆ EParseField

how to interpret the value in the AddField() conversion functions below.

Enumerator eParse_String

Add string even if all numbers.

eParse_Number

Parse a real or integer number, otherwise string.

Definition at line 60 of file User_object.hpp.

◆ ERefGeneTrackingStatus Enumerator eRefGeneTrackingStatus_Error eRefGeneTrackingStatus_NotSet eRefGeneTrackingStatus_PREDICTED eRefGeneTrackingStatus_PROVISIONAL eRefGeneTrackingStatus_INFERRED eRefGeneTrackingStatus_VALIDATED eRefGeneTrackingStatus_REVIEWED eRefGeneTrackingStatus_PIPELINE eRefGeneTrackingStatus_WGS

Definition at line 219 of file User_object.hpp.

◆ CUser_object() [1/2] CUser_object::CUser_object ( void ) inline ◆ ~CUser_object() CUser_object::~CUser_object ( void ) ◆ CUser_object() [2/2]

Prohibit copy constructor and assignment operator.

◆ AddField() [1/13] ◆ AddField() [2/13] ◆ AddField() [3/13]

add a data field to the user object that holds a given value

Definition at line 198 of file User_object.cpp.

References label, CUser_object_Base::SetData(), CUser_field_Base::SetLabel(), CUser_field::SetValue(), and rapidjson::value.

Referenced by CStructuredCommentsReader::_AddStructuredComment(), CAutoSqlCustomField::AddDouble(), AddField(), CAutoSqlCustomField::AddInt(), CAutoSqlCustomField::AddIntArray(), CTableAnnotDataSource::AddSeqLoc(), CTableAnnotDataSource::AddSnpSeqLoc(), CAutoSqlCustomField::AddString(), CAutoSqlCustomField::AddUint(), AlignModelToSeqalign(), CConvertComment::ApplyToComment(), CSetGlobalRefGeneStatus::ApplyToCSeq_entry(), variation_ref::AttachAssertedSequence(), BOOST_AUTO_TEST_CASE(), CTableImportDataSource::ConvertToSeqAnnot(), CAnnotationASN1::CImplementationData::create_internal_feature(), CAnnotationASN1::CImplementationData::create_ModelEvidence_user_object(), CTableAnnotDataSource::CreateFeature(), CBlastFormatUtil::CreateSeqAnnotFromSeqAlignSet(), CTableAnnotDataSource::CreateSnpFeature(), CTableAnnotDataSource::CreateSnps(), CWigObjectLoader::Execute(), CTableImportDataSource::ExportTableParms(), CBedAnnotAssembler::FinalizeAnnot(), CVDBGraphSeqIterator::GetAnnot(), CLoadStructComments::LoadSingle(), MakeCompartment(), CCSraAlignIterator::MakeMatchAnnotIndicator(), CBam2Seq_graph::MakeSeq_annot(), CAnnotationASN1::CImplementationData::model2spliced_seq_align(), CStructuredCommentPanel::OnExport(), CTableXformPanel::OnSaveImportParmsClick(), CPhyTreeView::OnSomethingEdited(), CRepeatToFeat::operator()(), CFastaReader::ParseDefLine(), variation_ref::CVariationUtil::PrecursorToProt(), CMicroArrayReader::ReadSeqAnnot(), CDemoSeqQaApp::Run(), s_AddUserObjectToSeqAlign(), s_CreateSeqAlign(), s_ModifySeqAlnWithFilteredSeqIDs(), s_UpdateField(), s_UpdateSeqAlnWithFilteredSeqIDs(), CDockManager::SaveLayout(), CDockContainer::SaveLayout(), CPhyloSelectionSet::SaveToUserObject(), CTreeLabel::SaveToUserObject(), CPhyloSelectionSetMgr::SaveToUserObject(), CGBenchService::SendAppFinish(), CGBenchService::SendAppStart(), CSeqUtils::SetAnnotShown(), SetCategory(), CEditingActionDescGenomeProjectId::SetValue(), CEditingActionDescUserObject::SetValue(), CEditingActionDescStructCommDbName::SetValue(), CEditingActionDescStructCommFieldName::SetValue(), sWindowPosToUserObject(), sx_GetMatchAnnotIndicator(), sx_SetZoomLevel(), CMacroFunction_ParseToStructComm::TheFunction(), CBLASTParams::ToUserObject(), CNetBlastJobDescriptor::ToUserObject(), CDockContainerDescr::ToUserObject(), CComplexRelation::ToUserObject(), CRelation::UserObjectFromRelation(), CTrackData::WriteToAnnot(), CFeatureTableReader_Imp::x_AddQualifierToImp(), CVariationUtilities::x_AddRefAlleleFixFlag(), x_AddUnreviewedType(), x_AddUnverifiedType(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CMacroFunction_SetStructCommDb::x_MakeNewStructuredComment(), CGraphTrack::x_OnJobCompleted(), CShortReadFastaInputSource::x_ReadFastaOrFastq(), CShortReadFastaInputSource::x_ReadFastc(), CShortReadFastaInputSource::x_ReadFastqOneSeq(), CASN1InputSourceOMF::x_ReadFromSingleFile(), CASN1InputSourceOMF::x_ReadFromTwoFiles(), CShortReadFastaInputSource::x_ReadFromTwoFiles(), CSraInputSource::x_ReadPairs(), CNetBLASTUIDataSource::x_SaveJobDescriptors(), CFeatureGenerator::SImplementation::x_SetComment(), CVariationNormalization_base< T >::x_SetShiftFlag(), CAttribTableColumnIdPanel::x_TableReaderMacro(), CBLASTParams::x_ToUserObject(), CReaderBase::xAddConversionInfo(), CBedReader::xAssignBedColumnCount(), CGvfReader::xFeatureSetExt(), CBedImportData::xInitializeRgb(), CBedImportData::xInitializeScore(), CGvfReader::xParseStructuredComment(), CVcfReader::xProcessFilter(), CVcfReader::xProcessFormat(), CVcfReader::xProcessHeaderLine(), CVcfReader::xProcessInfo(), CVcfReader::xProcessMetaLine(), CVcfReader::xProcessScore(), CBedReader::xSetFeatureColorDefault(), CBedReader::xSetFeatureColorFromItemRgb(), CBedReader::xSetFeatureColorFromScore(), CBedReader::xSetFeatureDisplayData(), CMicroArrayReader::xSetFeatureDisplayData(), CBedReader::xSetFeatureLocationBlock(), CBedReader::xSetFeatureLocationCds(), CBedReader::xSetFeatureLocationChrom(), CBedReader::xSetFeatureLocationGene(), CBedReader::xSetFeatureLocationRna(), CBedReader::xSetFeatureLocationThick(), and CBedReader::xSetFeatureScore().

◆ AddField() [4/13] ◆ AddField() [5/13] ◆ AddField() [6/13] ◆ AddField() [7/13] ◆ AddField() [8/13] ◆ AddField() [9/13] ◆ AddField() [10/13] ◆ AddField() [11/13] ◆ AddField() [12/13] ◆ AddField() [13/13] ◆ AddUnreviewedUnannotated() void CUser_object::AddUnreviewedUnannotated ( ) ◆ AddUnverifiedContaminant() void CUser_object::AddUnverifiedContaminant ( ) ◆ AddUnverifiedFeature() void CUser_object::AddUnverifiedFeature ( ) ◆ AddUnverifiedMisassembled() void CUser_object::AddUnverifiedMisassembled ( ) ◆ AddUnverifiedOrganism() void CUser_object::AddUnverifiedOrganism ( ) ◆ GetCategory()

accessors: classify a given user object

Definition at line 366 of file User_object.cpp.

References NStr::CompareNocase(), data, CUser_field_Base::C_Data::e_Object, eCategory_Experiment, eCategory_Unknown, CUser_object_Base::GetClass(), CUser_field_Base::GetData(), CUser_object_Base::GetData(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CUser_object_Base::IsSetClass(), CUser_field_Base::IsSetLabel(), CObject_id_Base::IsStr(), ITERATE, s_exp, s_expres, s_ncbi, and ncbi::grid::netcache::search::fields::size.

Referenced by GetExperimentType(), s_GetUserObjectContent(), and s_GetUserObjectType().

◆ GetExperiment() ◆ GetExperimentType()

sub-category accessors:

Definition at line 405 of file User_object.cpp.

References NStr::CompareNocase(), eCategory_Experiment, eExperiment_Sage, eExperiment_Unknown, GetCategory(), CUser_field_Base::GetData(), CUser_object_Base::GetData(), CUser_field_Base::C_Data::GetObject(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CObject_id_Base::IsStr(), and s_sage.

Referenced by GetExperiment(), s_GetUserObjectContent(), and s_GetUserObjectType().

◆ GetField()

Access a named field in this user object.

This is a little sneaky in that it interprets a delimiter for recursion. This version will throw an exception if the field doesn't exist.

Definition at line 71 of file User_object.cpp.

References CConstRef< C, Locker >::Empty(), GetFieldRef(), NCBI_THROW, and str().

Referenced by CChangeStructuredCommentKeyword::ApplyToCSeq_entry_user(), CReorderStructuredComment::ApplyToCSeq_entry_user(), CGvfWriteRecord::AssignSource(), CGvfWriteRecord::AssignType(), BOOST_AUTO_TEST_CASE(), CLDBlockGlyph::CLDBlockGlyph(), CAnnotationASN1::CImplementationData::create_ModelEvidence_user_object(), CDockContainerDescr::FromUserObject(), CComplexRelation::FromUserObject(), CBLASTParams::FromUserObject(), CConstSageData::GetCount(), GetDBLinkIDs(), CConstSageData::GetField(), CGenomeAnnotComment::GetGenomeBuildNumber(), CClonePlacementGlyph::GetLabel(), CGC_Replicon::GetMoleculeLabel(), CGC_Replicon::GetMoleculeLocation(), CGC_Replicon::GetMoleculeType(), CCommentItem::GetRefTrackStatus(), CCommentItem::GetStringForBankIt(), CCommentItem::GetStringForRefTrack(), CCommentItem::GetStringForTLS(), CCommentItem::GetStringForTSA(), CCommentItem::GetStringForWGS(), CConstSageData::GetTag(), CGuiObjectInfoSeq_align::GetToolTip(), CEditingActionDescGenomeProjectId::GetValue(), CEditingActionDescStructCommDbName::GetValue(), CTableImportDataSource::ImportTableParms(), CPhyloSelectionSetMgr::InitFromUserObject(), CPhyloSelectionSet::InitFromUserObject(), CTreeLabel::InitializeFromUserObject(), CPhyTreeView::InitView(), CTestApplication::LoadTable(), MakeCompartments(), CPhyTreeView::OnBioTreeChanged(), CPhyTreeView::OnSomethingEdited(), CTabularFormatter_AssemblyInfo::Print(), CRelation::RelationFromUserObject(), CReorderStructuredComment::reorder_comment_by_rule(), RestoreModelMethod(), s_GetAssemblyInfo(), s_GetEncodeValues(), s_GetModelEvidance(), s_IsGenomeAnnotationStart(), s_PassesFilter(), CTreeLabel::SaveToUserObject(), CEditingActionDescUserObject::SetValue(), sGetMethodFromModelEvidence(), sWindowPosFromUserObject(), CGvfWriteRecord::x_AssignAttributeID(), CGvfWriteRecord::x_AssignAttributeParent(), CGvfWriteRecord::x_AssignAttributeVarType(), CBLASTParams::x_FromUserObject(), CClonePlacementGlyph::x_GetCloneEnds(), CCommonComponentScorer::x_GetUserCompList(), CValidError_bioseq::x_HasPGAPStructuredComment(), CLDBlockJob::x_LoadFtable(), CNetBLASTUIDataSource::x_LoadJobDescriptors(), CBamRefSeqInfo::x_LoadRangesCov(), CGraphTrack::x_LoadSettings(), CAlignFilter::x_Query_Op(), CVcfWriter::x_WriteFeatureFilter(), CVcfWriter::x_WriteFeatureInfo(), CVcfWriter::x_WriteFeatureQual(), CVcfWriter::x_WriteInit(), and CGtfWriter::xAssignFeatureMethod().

◆ GetFieldRef()

Definition at line 84 of file User_object.cpp.

References NStr::Equal(), first(), NStr::fSplit_Tokenize, CUser_object_Base::GetData(), CUser_field::GetFieldRef(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_field_Base::IsSetLabel(), CObject_id_Base::IsStr(), ITERATE, NStr::Split(), and str().

Referenced by BOOST_AUTO_TEST_CASE(), CSnpBitfieldFactory::CreateBitfield(), CSnpBitfield2::CSnpBitfield2(), CGBDocument::DetachDataLoader(), GetField(), CUserFeatHandler::GetLabel(), NSnp::GetLength(), CSeq_annot_SplitInfo::GetName(), GetRefGeneTrackingAssembly(), GetRefGeneTrackingGenerated(), GetRefGeneTrackingIdenticalTo(), GetRefGeneTrackingStatus(), CCommentItem::GetStringForRefSeqGenome(), CCommentItem::GetStringForRefTrack(), CSequenceTrack::GetTooltip(), HasField(), CSeqTableReader::Init(), CDiscrepancyContext::IsBGPipe(), CVariationNormalization::isFullyShifted(), CComment_rule::IsValid(), CTabularFormatter_BestPlacementGroup::Print(), CDemoApp::Run(), s_GetBoxStyle(), s_GetVcfAttribute(), s_Render_Feat_Evidence(), s_SeqDescCompare(), CBedWriter::WriteAnnot(), CFeatureItem::x_AddQualsRegion(), CClonePlacementGlyph::x_Draw(), CFlatGatherer::x_GetAnnotDescStrucCommentFromBioseqHandle(), x_GetRefGeneTrackingField(), CBamRefSeqInfo::x_LoadRangesCov(), CBioseqContext::x_SetAuthorizedAccess(), CBioseqContext::x_SetFiletrackURL(), CSeq_annot_Info::x_UpdateName(), CValidError_desc::x_ValidateStructuredComment(), CVcfWriter::x_WriteFeatureGenotypeData(), and CVcfWriter::x_WriteMeta().

◆ GetLabel() ◆ GetObjectType()

Definition at line 625 of file User_object.cpp.

References eObjectType_OriginalId, eObjectType_Unknown, NStr::EqualNocase(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CUser_object_Base::IsSetType(), kOrigIdAltSpell, and label.

Referenced by BOOST_AUTO_TEST_CASE(), CheckAutoDefOptions(), CheckLocalId(), CDeflineGenerator::GenerateDefline(), CLocalIDField::GetApplyObjects(), CEditObjectSeq_desc::GetDescriptorType(), GetOptionsForSet(), GetRefGeneTrackingAssembly(), GetRefGeneTrackingGenerated(), GetRefGeneTrackingIdenticalTo(), GetRefGeneTrackingStatus(), CLocalIDField::GetVals(), IsAutodefOptions(), IsCleanup(), IsDBLink(), CLocalIDField::IsEmpty(), IsFileTrack(), IsOriginalId(), IsRefGeneTracking(), IsStructuredComment(), IsUnreviewed(), IsUnverified(), IsValidationSuppression(), CAutoDef::RegenerateDefLine(), CAutoDef::RegenerateSequenceDefLines(), s_AutoDefUserObjectFromBioseq(), CCleanup::s_CleanupDBLink(), CCleanup::s_CleanupStructuredComment(), s_GetOptionsForSet(), s_GetOriginalId(), s_IsCleanupObject(), s_IsGenomeAnnotationStart(), CMacroFunction_RefreshDefline::s_RefreshDeflineCommand(), CCleanup::s_RemoveEmptyFields(), CValidError_bioseqset::ShouldHaveNoDblink(), CPropagateDescriptors::ShouldStayInPlace(), CValidError_bioseq::ValidateWGSMaster(), CSubmissionWizard::x_ApplyDescriptorToRecord(), CSubmissionWizard::x_ApplyUserDescriptorToRecord(), x_GetRefGeneTrackingField(), CMacroFunction_ParsedText::x_GetSpecialField(), CNewCleanup_imp::x_IsDBLinkUserObj(), CAutoDef::x_IsHumanSTR(), x_IsUnreviewedType(), x_IsUnverifiedType(), x_RemoveUnreviewedType(), x_RemoveUnverifiedType(), CBioseqContext::x_SetDataFromUserObjects(), and CValidError_bioseq::x_ShowBioProjectWarning().

◆ GetRefGeneTrackingAssembly() ◆ GetRefGeneTrackingCollaborator() const string & CUser_object::GetRefGeneTrackingCollaborator ( ) const ◆ GetRefGeneTrackingCollaboratorURL() const string & CUser_object::GetRefGeneTrackingCollaboratorURL ( ) const ◆ GetRefGeneTrackingGenerated() bool CUser_object::GetRefGeneTrackingGenerated ( ) const ◆ GetRefGeneTrackingGenomicSource() const string & CUser_object::GetRefGeneTrackingGenomicSource ( ) const ◆ GetRefGeneTrackingIdenticalTo()

Definition at line 1250 of file User_object.cpp.

References eObjectType_RefGeneTracking, CUser_field_Base::GetData(), GetFieldRef(), CUser_field_Base::C_Data::GetFields(), GetObjectType(), CUser_field_Base::C_Data::IsFields(), CUser_field_Base::IsSetData(), kRefGeneTrackingIdenticalTo, CUser_object::CRefGeneTrackingAccession::MakeAccessionFromUserField(), and NULL.

Referenced by BOOST_AUTO_TEST_CASE(), and IsSetRefGeneTrackingIdenticalTo().

◆ GetRefGeneTrackingStatus()

Definition at line 999 of file User_object.cpp.

References eObjectType_RefGeneTracking, eRefGeneTrackingStatus_Error, eRefGeneTrackingStatus_NotSet, CUser_field_Base::GetData(), GetFieldRef(), GetObjectType(), CUser_field_Base::C_Data::GetStr(), CUser_field_Base::IsSetData(), CUser_field_Base::C_Data::IsStr(), kRefGeneTrackingStatus, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE(), and IsSetRefGeneTrackingStatus().

◆ HasField()

Verify that a named field exists.

Definition at line 138 of file User_object.cpp.

References GetFieldRef(), CConstRef< C, Locker >::GetPointer(), str(), and true.

Referenced by CScoreBuilder::AddTracebacks(), CSetGlobalRefGeneStatus::ApplyToCSeq_entry(), CGvfWriteRecord::AssignSource(), CGvfWriteRecord::AssignType(), BOOST_AUTO_TEST_CASE(), CAnnotationASN1::CImplementationData::create_ModelEvidence_user_object(), CGenomeAnnotComment::GetGenomeBuildNumber(), CClonePlacementGlyph::GetLabel(), CCommentItem::GetRefTrackStatus(), CCommentItem::GetStringForBankIt(), CCommentItem::GetStringForRefTrack(), CCommentItem::GetStringForTLS(), CCommentItem::GetStringForTSA(), CCommentItem::GetStringForWGS(), CGuiObjectInfoSeq_align::GetToolTip(), CEditingActionDescStructCommDbName::GetValue(), CTableImportDataSource::ImportTableParms(), CPhyloSelectionSetMgr::InitFromUserObject(), CPhyloSelectionSet::InitFromUserObject(), CTreeLabel::InitializeFromUserObject(), CPhyTreeView::InitView(), CEditingActionDescGenomeProjectId::IsSetValue(), CEditingActionDescStructCommDbName::IsSetValue(), CTestApplication::LoadTable(), CPhyTreeView::OnBioTreeChanged(), CPhyTreeView::OnSomethingEdited(), CTabularFormatter_AssemblyInfo::Print(), CReorderStructuredComment::reorder_comment_by_rule(), RestoreModelMethod(), s_GetAssemblyInfo(), s_GetEncodeValues(), s_GetModelEvidance(), s_UpdateField(), CTreeLabel::SaveToUserObject(), CPhyloSelectionSetMgr::SaveToUserObject(), CEditingActionDescUserObject::SetValue(), sGetMethodFromModelEvidence(), CMacroFunction_ParseToStructComm::TheFunction(), CMacroFunction_SetStructCommDb::TheFunction(), CBedWriter::WriteAnnot(), CGvfWriteRecord::x_AssignAttributeID(), CGvfWriteRecord::x_AssignAttributeParent(), CGvfWriteRecord::x_AssignAttributeVarType(), CBLASTParams::x_FromUserObject(), CClonePlacementGlyph::x_GetCloneEnds(), CCommonComponentScorer::x_GetUserCompList(), CValidError_bioseq::x_HasPGAPStructuredComment(), CGraphTrack::x_LoadSettings(), CValidError_bioseq::x_ShowBioProjectWarning(), CValidError_desc::x_ValidateStructuredComment(), CVcfWriter::x_WriteFeatureFilter(), CVcfWriter::x_WriteFeatureInfo(), CVcfWriter::x_WriteFeatureQual(), CVcfWriter::x_WriteInit(), and CGtfWriter::xAssignFeatureMethod().

◆ IsAutodefOptions() bool CUser_object::IsAutodefOptions ( ) const inline ◆ IsCleanup() bool CUser_object::IsCleanup ( ) const inline ◆ IsDBLink() bool CUser_object::IsDBLink ( ) const inline ◆ IsFileTrack() bool CUser_object::IsFileTrack ( ) const inline ◆ IsOriginalId() bool CUser_object::IsOriginalId ( ) const inline ◆ IsRefGeneTracking() bool CUser_object::IsRefGeneTracking ( ) const inline ◆ IsSetRefGeneTrackingAssembly() bool CUser_object::IsSetRefGeneTrackingAssembly ( ) const inline ◆ IsSetRefGeneTrackingCollaborator() bool CUser_object::IsSetRefGeneTrackingCollaborator ( ) const inline ◆ IsSetRefGeneTrackingCollaboratorURL() bool CUser_object::IsSetRefGeneTrackingCollaboratorURL ( ) const inline ◆ IsSetRefGeneTrackingGenomicSource() bool CUser_object::IsSetRefGeneTrackingGenomicSource ( ) const inline ◆ IsSetRefGeneTrackingIdenticalTo() bool CUser_object::IsSetRefGeneTrackingIdenticalTo ( ) const inline ◆ IsSetRefGeneTrackingStatus() bool CUser_object::IsSetRefGeneTrackingStatus ( ) const inline ◆ IsStructuredComment() bool CUser_object::IsStructuredComment ( ) const inline ◆ IsUnreviewed() bool CUser_object::IsUnreviewed ( ) const inline ◆ IsUnreviewedUnannotated() bool CUser_object::IsUnreviewedUnannotated ( ) const ◆ IsUnverified() bool CUser_object::IsUnverified ( ) const inline ◆ IsUnverifiedContaminant() bool CUser_object::IsUnverifiedContaminant ( ) const ◆ IsUnverifiedFeature() bool CUser_object::IsUnverifiedFeature ( ) const ◆ IsUnverifiedMisassembled() bool CUser_object::IsUnverifiedMisassembled ( ) const ◆ IsUnverifiedOrganism() bool CUser_object::IsUnverifiedOrganism ( ) const ◆ IsValidationSuppression() bool CUser_object::IsValidationSuppression ( ) const inline ◆ operator=() ◆ RemoveNamedField()

Definition at line 900 of file User_object.cpp.

References NStr::Equal(), CUser_object_Base::IsSetData(), label, NStr::NumericToString(), and CUser_object_Base::SetData().

Referenced by ResetRefGeneTrackingAssembly(), ResetRefGeneTrackingCollaborator(), ResetRefGeneTrackingCollaboratorURL(), ResetRefGeneTrackingGenerated(), ResetRefGeneTrackingGenomicSource(), ResetRefGeneTrackingIdenticalTo(), ResetRefGeneTrackingStatus(), CMacroFunction_SetStructCommDb::TheFunction(), and x_SetRefGeneTrackingField().

◆ RemoveUnreviewedUnannotated() void CUser_object::RemoveUnreviewedUnannotated ( ) ◆ RemoveUnverifiedContaminant() void CUser_object::RemoveUnverifiedContaminant ( ) ◆ RemoveUnverifiedFeature() void CUser_object::RemoveUnverifiedFeature ( ) ◆ RemoveUnverifiedMisassembled() void CUser_object::RemoveUnverifiedMisassembled ( ) ◆ RemoveUnverifiedOrganism() void CUser_object::RemoveUnverifiedOrganism ( ) ◆ ResetRefGeneTrackingAssembly() void CUser_object::ResetRefGeneTrackingAssembly ( ) ◆ ResetRefGeneTrackingCollaborator() void CUser_object::ResetRefGeneTrackingCollaborator ( ) ◆ ResetRefGeneTrackingCollaboratorURL() void CUser_object::ResetRefGeneTrackingCollaboratorURL ( ) ◆ ResetRefGeneTrackingGenerated() void CUser_object::ResetRefGeneTrackingGenerated ( ) ◆ ResetRefGeneTrackingGenomicSource() void CUser_object::ResetRefGeneTrackingGenomicSource ( ) ◆ ResetRefGeneTrackingIdenticalTo() void CUser_object::ResetRefGeneTrackingIdenticalTo ( ) ◆ ResetRefGeneTrackingStatus() void CUser_object::ResetRefGeneTrackingStatus ( ) ◆ SetCategory()

format a user object as a given type.

This returns a user-object that is suitable for containing whatever specifics might be needed

Definition at line 555 of file User_object.cpp.

References AddField(), CUser_object(), eCategory_Experiment, eCategory_Unknown, CUser_object_Base::Reset(), s_exp, s_expres, s_ncbi, CUser_object_Base::SetClass(), CObject_id_Base::SetStr(), and CUser_object_Base::SetType().

◆ SetExperiment() ◆ SetField()

Access a named field in this user object.

This is a little sneaky in that it interprets a delimiter for recursion. The 'obj_subtype' parameter is used to set the subtype of a sub-object if a new sub-object needs to be created

Definition at line 150 of file User_object.cpp.

References SetFieldRef(), and str().

Referenced by CScoreBuilder::AddTracebacks(), CSetGlobalRefGeneStatus::ApplyToCSeq_entry(), variation_ref::AttachAssertedSequence(), NSNPVariationHelper::ConvertFeat(), CTableImportDataSource::ImportTableParms(), CPhyTreeView::OnSomethingEdited(), CDemoContigAssemblyApp::Run(), s_UpdateField(), CTreeLabel::SaveToUserObject(), CGBProjectHandle::SaveViewSettings(), CSageData::SetCount(), CSageData::SetField(), CSageData::SetMethod(), SetRefGeneTrackingAssembly(), SetRefGeneTrackingGenerated(), SetRefGeneTrackingIdenticalTo(), CSageData::SetTag(), CEditingActionDescGenomeProjectId::SetValue(), CEditingActionDescUserObject::SetValue(), CEditingActionDescStructCommDbName::SetValue(), CMacroFunction_ParseToStructComm::TheFunction(), and x_SetRefGeneTrackingField().

◆ SetFieldRef()

Definition at line 159 of file User_object.cpp.

References NStr::Equal(), f, NStr::fSplit_Tokenize, CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CObject_id_Base::IsStr(), NStr::Join(), NON_CONST_ITERATE, CRef< C, Locker >::Reset(), CUser_object_Base::SetData(), CUser_field::SetFieldRef(), CUser_field_Base::SetLabel(), NStr::Split(), and str().

Referenced by CSegregateSetsBase::AddUserObject(), CWithdrawSequences::GetCommand(), CBam2Seq_graph::MakeSeq_annot(), SetField(), SetFileTrackURL(), and UpdateNcbiCleanup().

◆ SetFileTrackUploadId() void CUser_object::SetFileTrackUploadId ( const string & upload_id ) ◆ SetFileTrackURL() void CUser_object::SetFileTrackURL ( const string & url ) ◆ SetObjectType() void CUser_object::SetObjectType ( EObjectType obj_type )

Definition at line 647 of file User_object.cpp.

References CUser_object_Base::ResetType(), CObject_id_Base::SetStr(), and CUser_object_Base::SetType().

Referenced by AddLocalIdUserObjects(), AddRefGeneTrackingUserObject(), BOOST_AUTO_TEST_CASE(), CSequenceEditingEventHandler::CreateDescriptor(), CConvertCdsToMiscFeat::GetCommand(), CUnreviewedPanel::GetUser_object(), CUnverifiedPanel::GetUser_object(), CApplyIndexerComments::GetUserObjectComment(), CDBLinkField::MakeUserObject(), CAutoDefOptions::MakeUserObject(), CValidatePanel::OnListItemRightClick(), s_AddUnverifiedType(), SetFileTrackURL(), SetRefGeneTrackingAssembly(), SetRefGeneTrackingGenerated(), SetRefGeneTrackingIdenticalTo(), CMacroFunction_ParseToStructComm::TheFunction(), UpdateNcbiCleanup(), x_AddUnreviewedType(), CConvertFeatDlg::x_AddUnverified(), x_AddUnverifiedType(), CSubmissionWizard::x_InitializeDescriptorList(), CMacroFunction_SetStructCommDb::x_MakeNewStructuredComment(), and x_SetRefGeneTrackingField().

◆ SetRefGeneTrackingAssembly() ◆ SetRefGeneTrackingCollaborator() void CUser_object::SetRefGeneTrackingCollaborator ( const string & collaborator ) ◆ SetRefGeneTrackingCollaboratorURL() void CUser_object::SetRefGeneTrackingCollaboratorURL ( const string & collaborator_url ) ◆ SetRefGeneTrackingGenerated() void CUser_object::SetRefGeneTrackingGenerated ( bool val = true ) ◆ SetRefGeneTrackingGenomicSource() void CUser_object::SetRefGeneTrackingGenomicSource ( const string & genomic_source ) ◆ SetRefGeneTrackingIdenticalTo() ◆ SetRefGeneTrackingStatus() ◆ UpdateNcbiCleanup() void CUser_object::UpdateNcbiCleanup ( int version ) ◆ x_AddUnreviewedType() void CUser_object::x_AddUnreviewedType ( const string & val ) private ◆ x_AddUnverifiedType() void CUser_object::x_AddUnverifiedType ( const string & val ) private ◆ x_GetRefGeneTrackingField() ◆ x_IsUnreviewedType() [1/2] ◆ x_IsUnreviewedType() [2/2] ◆ x_IsUnverifiedType() [1/2]

Definition at line 673 of file User_object.cpp.

References eObjectType_Unverified, CUser_object_Base::GetData(), GetObjectType(), CUser_object_Base::IsSetData(), ITERATE, and val.

Referenced by IsUnverifiedContaminant(), IsUnverifiedFeature(), IsUnverifiedMisassembled(), IsUnverifiedOrganism(), x_AddUnverifiedType(), and x_RemoveUnverifiedType().

◆ x_IsUnverifiedType() [2/2] ◆ x_RemoveUnreviewedType() void CUser_object::x_RemoveUnreviewedType ( const string & val ) private ◆ x_RemoveUnverifiedType() void CUser_object::x_RemoveUnverifiedType ( const string & val ) private

Definition at line 703 of file User_object.cpp.

References ctll::empty(), eObjectType_Unverified, CUser_object_Base::GetData(), GetObjectType(), CUser_object_Base::IsSetData(), CUser_object_Base::ResetData(), CUser_object_Base::SetData(), val, and x_IsUnverifiedType().

Referenced by RemoveUnverifiedContaminant(), RemoveUnverifiedFeature(), RemoveUnverifiedMisassembled(), and RemoveUnverifiedOrganism().

◆ x_SetRefGeneTrackingField()

The documentation for this class was generated from the following files:

include/objects/general/User_object.hpp
src/objects/general/User_object.cpp

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