#include <objects/general/User_object.hpp>

Inheritance diagram for CUser_object:

Collaboration diagram for CUser_object:

Classes
class	CRefGeneTrackingAccession

class	CRefGeneTrackingException

Public Types
enum	EParseField { eParse_String , eParse_Number }
	how to interpret the value in the AddField() conversion functions below. More...

enum	ELabelContent { eType , eContent , eBoth }
	enum controlling what to return for a label this mirrors a request inside of feature::GetLabel() More...

enum	ECategory { eCategory_Unknown = -1 , eCategory_Experiment }
	enums for implicit typing of user objects More...

enum	EExperiment { eExperiment_Unknown = -1 , eExperiment_Sage }
	sub-category experiment More...

enum	EObjectType { eObjectType_Unknown = -1 , eObjectType_DBLink , eObjectType_StructuredComment , eObjectType_OriginalId , eObjectType_Unverified , eObjectType_ValidationSuppression , eObjectType_Cleanup , eObjectType_AutodefOptions , eObjectType_FileTrack , eObjectType_RefGeneTracking , eObjectType_Unreviewed }
	Object Type. More...

enum	ERefGeneTrackingStatus { eRefGeneTrackingStatus_Error = -1 , eRefGeneTrackingStatus_NotSet , eRefGeneTrackingStatus_PREDICTED , eRefGeneTrackingStatus_PROVISIONAL , eRefGeneTrackingStatus_INFERRED , eRefGeneTrackingStatus_VALIDATED , eRefGeneTrackingStatus_REVIEWED , eRefGeneTrackingStatus_PIPELINE , eRefGeneTrackingStatus_WGS }

typedef vector< CConstRef< CRefGeneTrackingAccession > >	TRefGeneTrackingAccessions

Public Types inherited from CUser_object_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_class , e_type , e_data }

typedef string	TClass

typedef CObject_id	TType

typedef vector< CRef< CUser_field > >	TData

typedef Tparent::CMemberIndex< E_memberIndex, 4 >	TmemberIndex

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CUser_object (void)
	constructor More...

	~CUser_object (void)
	destructor More...

CUser_object &	AddField (const string &label, const string &value, EParseField parse=eParse_String)
	add a data field to the user object that holds a given value More...

CUser_object &	AddField (const string &label, const char *value, EParseField parse=eParse_String)

CUser_object &	AddField (const string &label, int value)

CUser_object &	AddField (const string &label, Int8 value)

CUser_object &	AddField (const string &label, double value)

CUser_object &	AddField (const string &label, bool value)

CUser_object &	AddField (const string &label, TGi value)

CUser_object &	AddField (const string &label, const vector< string > &value)

CUser_object &	AddField (const string &label, const vector< int > &value)

CUser_object &	AddField (const string &label, const vector< double > &value)

CUser_object &	AddField (const string &label, CUser_object &value)

CUser_object &	AddField (const string &label, const vector< CRef< CUser_object > > &value)

CUser_object &	AddField (const string &label, const vector< CRef< CUser_field > > &value)

const CUser_field &	GetField (const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const
	Access a named field in this user object. More...

CConstRef< CUser_field >	GetFieldRef (const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

CUser_field &	SetField (const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)
	Access a named field in this user object. More...

CRef< CUser_field >	SetFieldRef (const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

bool	HasField (const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const
	Verify that a named field exists. More...

void	GetLabel (string *label, ELabelContent mode=eContent) const
	Append a label to label. More...

ECategory	GetCategory (void) const
	accessors: classify a given user object More...

EExperiment	GetExperimentType (void) const
	sub-category accessors: More...

const CUser_object &	GetExperiment (void) const

CUser_object &	SetCategory (ECategory category)
	format a user object as a given type. More...

CUser_object &	SetExperiment (EExperiment category)
	format a user object as a given type. More...

EObjectType	GetObjectType () const

void	SetObjectType (EObjectType obj_type)

bool	IsDBLink () const

bool	IsStructuredComment () const

bool	IsOriginalId () const

bool	IsUnverified () const

bool	IsValidationSuppression () const

bool	IsCleanup () const

bool	IsAutodefOptions () const

bool	IsFileTrack () const

bool	IsRefGeneTracking () const

bool	IsUnreviewed () const

bool	IsUnverifiedOrganism () const

void	AddUnverifiedOrganism ()

void	RemoveUnverifiedOrganism ()

bool	IsUnverifiedFeature () const

void	AddUnverifiedFeature ()

void	RemoveUnverifiedFeature ()

bool	IsUnverifiedMisassembled () const

void	AddUnverifiedMisassembled ()

void	RemoveUnverifiedMisassembled ()

bool	IsUnverifiedContaminant () const

void	AddUnverifiedContaminant ()

void	RemoveUnverifiedContaminant ()

bool	IsUnreviewedUnannotated () const

void	AddUnreviewedUnannotated ()

void	RemoveUnreviewedUnannotated ()

void	UpdateNcbiCleanup (int version)

bool	RemoveNamedField (const string &field_name, NStr::ECase ecase=NStr::eCase)

void	SetFileTrackURL (const string &url)

void	SetFileTrackUploadId (const string &upload_id)

void	SetRefGeneTrackingStatus (ERefGeneTrackingStatus status)

ERefGeneTrackingStatus	GetRefGeneTrackingStatus () const

void	ResetRefGeneTrackingStatus ()

bool	IsSetRefGeneTrackingStatus () const

void	SetRefGeneTrackingGenomicSource (const string &genomic_source)

const string &	GetRefGeneTrackingGenomicSource () const

void	ResetRefGeneTrackingGenomicSource ()

bool	IsSetRefGeneTrackingGenomicSource () const

void	SetRefGeneTrackingGenerated (bool val=true)

bool	GetRefGeneTrackingGenerated () const

void	ResetRefGeneTrackingGenerated ()

void	SetRefGeneTrackingCollaborator (const string &collaborator)

const string &	GetRefGeneTrackingCollaborator () const

void	ResetRefGeneTrackingCollaborator ()

bool	IsSetRefGeneTrackingCollaborator () const

void	SetRefGeneTrackingCollaboratorURL (const string &collaborator_url)

const string &	GetRefGeneTrackingCollaboratorURL () const

void	ResetRefGeneTrackingCollaboratorURL ()

bool	IsSetRefGeneTrackingCollaboratorURL () const

void	SetRefGeneTrackingIdenticalTo (const CRefGeneTrackingAccession &accession)

CConstRef< CRefGeneTrackingAccession >	GetRefGeneTrackingIdenticalTo () const

void	ResetRefGeneTrackingIdenticalTo ()

bool	IsSetRefGeneTrackingIdenticalTo () const

void	SetRefGeneTrackingAssembly (const TRefGeneTrackingAccessions &acc_list)

TRefGeneTrackingAccessions	GetRefGeneTrackingAssembly () const

void	ResetRefGeneTrackingAssembly ()

bool	IsSetRefGeneTrackingAssembly () const

Public Member Functions inherited from CUser_object_Base
	CUser_object_Base (void)

virtual	~CUser_object_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetClass (void) const
	endeavor which designed this object Check if a value has been assigned to Class data member. More...

bool	CanGetClass (void) const
	Check if it is safe to call GetClass method. More...

void	ResetClass (void)
	Reset Class data member. More...

const TClass &	GetClass (void) const
	Get the Class member data. More...

void	SetClass (const TClass &value)
	Assign a value to Class data member. More...

void	SetClass (TClass &&value)

TClass &	SetClass (void)
	Assign a value to Class data member. More...

bool	IsSetType (void) const
	type of object within class Check if a value has been assigned to Type data member. More...

bool	CanGetType (void) const
	Check if it is safe to call GetType method. More...

void	ResetType (void)
	Reset Type data member. More...

const TType &	GetType (void) const
	Get the Type member data. More...

void	SetType (TType &value)
	Assign a value to Type data member. More...

TType &	SetType (void)
	Assign a value to Type data member. More...

bool	IsSetData (void) const
	the object itself Check if a value has been assigned to Data data member. More...

bool	CanGetData (void) const
	Check if it is safe to call GetData method. More...

void	ResetData (void)
	Reset Data data member. More...

const TData &	GetData (void) const
	Get the Data member data. More...

TData &	SetData (void)
	Assign a value to Data data member. More...

virtual void	Reset (void)
	Reset the whole object. More...

Public Member Functions inherited from CSerialObject
	CSerialObject (void)

virtual	~CSerialObject (void)

virtual const CTypeInfo *	GetThisTypeInfo (void) const =0

virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...

virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

void	ThrowUnassigned (TMemberIndex index) const

void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const

bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...

const string &	GetNamespaceName (void) const
	Get namespace name. More...

bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...

const string &	GetNamespacePrefix (void) const
	Get namespace prefix. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Private Types
typedef CUser_object_Base	Tparent

Private Member Functions
	CUser_object (const CUser_object &value)
	Prohibit copy constructor and assignment operator. More...

CUser_object &	operator= (const CUser_object &value)

bool	x_IsUnverifiedType (const string &val) const

bool	x_IsUnverifiedType (const string &val, const CUser_field &field) const

void	x_AddUnverifiedType (const string &val)

void	x_RemoveUnverifiedType (const string &val)

bool	x_IsUnreviewedType (const string &val) const

bool	x_IsUnreviewedType (const string &val, const CUser_field &field) const

void	x_AddUnreviewedType (const string &val)

void	x_RemoveUnreviewedType (const string &val)

void	x_SetRefGeneTrackingField (const string &field_name, const string &value)

const string &	x_GetRefGeneTrackingField (const string &field_name) const

Additional Inherited Members
Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 50 of file User_object.hpp.

Member Typedef Documentation

◆ Tparent

typedef CUser_object_Base CUser_object::Tparent

private

Definition at line 52 of file User_object.hpp.

◆ TRefGeneTrackingAccessions

typedef vector<CConstRef<CRefGeneTrackingAccession> > CUser_object::TRefGeneTrackingAccessions

Definition at line 334 of file User_object.hpp.

Member Enumeration Documentation

◆ ECategory

enum CUser_object::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

enum CUser_object::EExperiment

sub-category experiment

Enumerator
eExperiment_Unknown
eExperiment_Sage

Definition at line 140 of file User_object.hpp.

◆ ELabelContent

enum CUser_object::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

enum CUser_object::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

enum CUser_object::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

enum CUser_object::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.

Constructor & Destructor Documentation

◆ CUser_object() [1/2]

CUser_object::CUser_object ( void )

inline

constructor

Definition at line 374 of file User_object.hpp.

Referenced by SetCategory().

◆ ~CUser_object()

CUser_object::~CUser_object ( void )

destructor

Definition at line 62 of file User_object.cpp.

◆ CUser_object() [2/2]

CUser_object::CUser_object ( const CUser_object & value )

private

Prohibit copy constructor and assignment operator.

Member Function Documentation

◆ AddField() [1/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		bool	value
	)

Definition at line 269 of file User_object.cpp.

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

◆ AddField() [2/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		const char *	value,
		EParseField	parse = `eParse_String`
	)

Definition at line 211 of file User_object.cpp.

References AddField(), label, and rapidjson::value.

◆ AddField() [3/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		const string &	value,
		EParseField	parse = `eParse_String`
	)

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 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]

CUser_object & CUser_object::AddField	(	const string &	label,
		const vector< CRef< CUser_field > > &	value
	)

Definition at line 343 of file User_object.cpp.

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

◆ AddField() [5/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		const vector< CRef< CUser_object > > &	value
	)

Definition at line 331 of file User_object.cpp.

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

◆ AddField() [6/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		const vector< double > &	value
	)

Definition at line 318 of file User_object.cpp.

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

◆ AddField() [7/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		const vector< int > &	value
	)

Definition at line 306 of file User_object.cpp.

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

◆ AddField() [8/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		const vector< string > &	value
	)

Definition at line 294 of file User_object.cpp.

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

◆ AddField() [9/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		CUser_object &	value
	)

Definition at line 282 of file User_object.cpp.

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

◆ AddField() [10/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		double	value
	)

Definition at line 257 of file User_object.cpp.

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

◆ AddField() [11/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		int	value
	)

Definition at line 231 of file User_object.cpp.

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

◆ AddField() [12/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		Int8	value
	)

Definition at line 219 of file User_object.cpp.

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

◆ AddField() [13/13]

CUser_object & CUser_object::AddField	(	const string &	label,
		TGi	value
	)

Definition at line 244 of file User_object.cpp.

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

◆ AddUnreviewedUnannotated()

void CUser_object::AddUnreviewedUnannotated ( )

Definition at line 869 of file User_object.cpp.

References x_AddUnreviewedType().

Referenced by CUnreviewedPanel::GetUser_object(), and CApplyIndexerComments::GetUserObjectComment().

◆ AddUnverifiedContaminant()

void CUser_object::AddUnverifiedContaminant ( )

Definition at line 851 of file User_object.cpp.

References x_AddUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), CUnverifiedPanel::GetUser_object(), CApplyIndexerComments::GetUserObjectComment(), and s_AddUnverifiedType().

◆ AddUnverifiedFeature()

void CUser_object::AddUnverifiedFeature ( )

Definition at line 815 of file User_object.cpp.

References x_AddUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), CConvertCdsToMiscFeat::GetCommand(), CUnverifiedPanel::GetUser_object(), CApplyIndexerComments::GetUserObjectComment(), s_AddUnverifiedType(), and CConvertFeatDlg::x_AddUnverified().

◆ AddUnverifiedMisassembled()

void CUser_object::AddUnverifiedMisassembled ( )

Definition at line 833 of file User_object.cpp.

References x_AddUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), CUnverifiedPanel::GetUser_object(), CApplyIndexerComments::GetUserObjectComment(), and s_AddUnverifiedType().

◆ AddUnverifiedOrganism()

void CUser_object::AddUnverifiedOrganism ( )

Definition at line 797 of file User_object.cpp.

References x_AddUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), CUnverifiedPanel::GetUser_object(), CApplyIndexerComments::GetUserObjectComment(), and s_AddUnverifiedType().

◆ GetCategory()

CUser_object::ECategory CUser_object::GetCategory ( void ) const

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()

const CUser_object & CUser_object::GetExperiment ( void ) const

Definition at line 429 of file User_object.cpp.

References eExperiment_Sage, eExperiment_Unknown, CUser_object_Base::GetData(), and GetExperimentType().

◆ GetExperimentType()

CUser_object::EExperiment CUser_object::GetExperimentType ( void ) const

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()

const CUser_field & CUser_object::GetField	(	const string &	str,
		const string &	delim = `"."`,
		NStr::ECase	use_case = `NStr::eCase`
	)		const

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()

CConstRef< CUser_field > CUser_object::GetFieldRef	(	const string &	str,
		const string &	delim = `"."`,
		NStr::ECase	use_case = `NStr::eCase`
	)		const

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()

void CUser_object::GetLabel	(	string *	label,
		ELabelContent	mode = `eContent`
	)		const

Append a label to label.

The type defaults to content for backward compatibility

Definition at line 533 of file User_object.cpp.

References eBoth, eContent, eType, label, s_GetUserObjectContent(), and s_GetUserObjectType().

Referenced by s_GetContentLabel().

◆ GetObjectType()

CUser_object::EObjectType CUser_object::GetObjectType ( void ) const

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_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()

CUser_object::TRefGeneTrackingAccessions CUser_object::GetRefGeneTrackingAssembly ( ) const

Definition at line 1285 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(), kRefGeneTrackingAssembly, and CUser_object::CRefGeneTrackingAccession::MakeAccessionFromUserField().

Referenced by BOOST_AUTO_TEST_CASE(), and IsSetRefGeneTrackingAssembly().

◆ GetRefGeneTrackingCollaborator()

const string & CUser_object::GetRefGeneTrackingCollaborator ( ) const

Definition at line 1055 of file User_object.cpp.

References kRefGeneTrackingCollaborator, and x_GetRefGeneTrackingField().

Referenced by BOOST_AUTO_TEST_CASE(), and IsSetRefGeneTrackingCollaborator().

◆ GetRefGeneTrackingCollaboratorURL()

const string & CUser_object::GetRefGeneTrackingCollaboratorURL ( ) const

Definition at line 1074 of file User_object.cpp.

References kRefGeneTrackingCollaboratorURL, and x_GetRefGeneTrackingField().

Referenced by BOOST_AUTO_TEST_CASE(), and IsSetRefGeneTrackingCollaboratorURL().

◆ GetRefGeneTrackingGenerated()

bool CUser_object::GetRefGeneTrackingGenerated ( ) const

Definition at line 1096 of file User_object.cpp.

References eObjectType_RefGeneTracking, CUser_field_Base::C_Data::GetBool(), CUser_field_Base::GetData(), GetFieldRef(), GetObjectType(), CUser_field_Base::C_Data::IsBool(), CUser_field_Base::IsSetData(), and kRefGeneTrackingGenerated.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetRefGeneTrackingGenomicSource()

const string & CUser_object::GetRefGeneTrackingGenomicSource ( ) const

Definition at line 1036 of file User_object.cpp.

References kRefGeneTrackingGenomicSource, and x_GetRefGeneTrackingField().

Referenced by BOOST_AUTO_TEST_CASE(), and IsSetRefGeneTrackingGenomicSource().

◆ GetRefGeneTrackingIdenticalTo()

CConstRef< CUser_object::CRefGeneTrackingAccession > CUser_object::GetRefGeneTrackingIdenticalTo ( ) const

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()

CUser_object::ERefGeneTrackingStatus CUser_object::GetRefGeneTrackingStatus ( ) const

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()

bool CUser_object::HasField	(	const string &	str,
		const string &	delim = `"."`,
		NStr::ECase	use_case = `NStr::eCase`
	)		const

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

Definition at line 183 of file User_object.hpp.

References eObjectType_AutodefOptions, and GetObjectType().

◆ IsCleanup()

bool CUser_object::IsCleanup ( ) const

inline

Definition at line 182 of file User_object.hpp.

References eObjectType_Cleanup, and GetObjectType().

◆ IsDBLink()

bool CUser_object::IsDBLink ( ) const

inline

Definition at line 177 of file User_object.hpp.

References eObjectType_DBLink, and GetObjectType().

Referenced by CMultiReader::LoadTemplate(), s_IsDBLink(), CDescrCache::SetDBLink(), and CValidError_desc::ValidateUser().

◆ IsFileTrack()

bool CUser_object::IsFileTrack ( ) const

inline

Definition at line 184 of file User_object.hpp.

References eObjectType_FileTrack, and GetObjectType().

◆ IsOriginalId()

bool CUser_object::IsOriginalId ( ) const

inline

Definition at line 179 of file User_object.hpp.

References eObjectType_OriginalId, and GetObjectType().

◆ IsRefGeneTracking()

bool CUser_object::IsRefGeneTracking ( ) const

inline

Definition at line 185 of file User_object.hpp.

References eObjectType_RefGeneTracking, and GetObjectType().

Referenced by BOOST_AUTO_TEST_CASE(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateSeqDescContext(), and CValidError_desc::ValidateUser().

◆ IsSetRefGeneTrackingAssembly()

bool CUser_object::IsSetRefGeneTrackingAssembly ( ) const

inline

Definition at line 346 of file User_object.hpp.

References GetRefGeneTrackingAssembly().

◆ IsSetRefGeneTrackingCollaborator()

bool CUser_object::IsSetRefGeneTrackingCollaborator ( ) const

inline

Definition at line 252 of file User_object.hpp.

References GetRefGeneTrackingCollaborator().

Referenced by BOOST_AUTO_TEST_CASE().

◆ IsSetRefGeneTrackingCollaboratorURL()

bool CUser_object::IsSetRefGeneTrackingCollaboratorURL ( ) const

inline

Definition at line 259 of file User_object.hpp.

References GetRefGeneTrackingCollaboratorURL().

Referenced by BOOST_AUTO_TEST_CASE().

◆ IsSetRefGeneTrackingGenomicSource()

bool CUser_object::IsSetRefGeneTrackingGenomicSource ( ) const

inline

Definition at line 242 of file User_object.hpp.

References GetRefGeneTrackingGenomicSource().

Referenced by BOOST_AUTO_TEST_CASE().

◆ IsSetRefGeneTrackingIdenticalTo()

bool CUser_object::IsSetRefGeneTrackingIdenticalTo ( ) const

inline

Definition at line 340 of file User_object.hpp.

References GetRefGeneTrackingIdenticalTo(), and NULL.

Referenced by BOOST_AUTO_TEST_CASE().

◆ IsSetRefGeneTrackingStatus()

bool CUser_object::IsSetRefGeneTrackingStatus ( ) const

inline

Definition at line 233 of file User_object.hpp.

References eRefGeneTrackingStatus_Error, eRefGeneTrackingStatus_NotSet, GetRefGeneTrackingStatus(), and val.

Referenced by BOOST_AUTO_TEST_CASE().

◆ IsStructuredComment()

bool CUser_object::IsStructuredComment ( ) const

inline

Definition at line 178 of file User_object.hpp.

References eObjectType_StructuredComment, and GetObjectType().

Referenced by CValidError_bioseq::ValidateSeqDescContext(), and CValidError_desc::ValidateUser().

◆ IsUnreviewed()

bool CUser_object::IsUnreviewed ( ) const

inline

Definition at line 186 of file User_object.hpp.

References eObjectType_Unreviewed, and GetObjectType().

Referenced by CDeflineGenerator::x_SetFlags().

◆ IsUnreviewedUnannotated()

bool CUser_object::IsUnreviewedUnannotated ( ) const

Definition at line 863 of file User_object.cpp.

References x_IsUnreviewedType().

Referenced by CBioseqIndex::x_InitDescs(), CBioseqContext::x_SetDataFromUserObjects(), and CDeflineGenerator::x_SetFlags().

◆ IsUnverified()

bool CUser_object::IsUnverified ( ) const

inline

Definition at line 180 of file User_object.hpp.

References eObjectType_Unverified, and GetObjectType().

Referenced by BOOST_AUTO_TEST_CASE(), and CDeflineGenerator::x_SetFlags().

◆ IsUnverifiedContaminant()

bool CUser_object::IsUnverifiedContaminant ( ) const

Definition at line 845 of file User_object.cpp.

References x_IsUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), CBioseqIndex::x_InitDescs(), CBioseqContext::x_SetDataFromUserObjects(), and CDeflineGenerator::x_SetFlags().

◆ IsUnverifiedFeature()

bool CUser_object::IsUnverifiedFeature ( ) const

Definition at line 809 of file User_object.cpp.

References x_IsUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), CBioseqIndex::x_InitDescs(), CBioseqContext::x_SetDataFromUserObjects(), and CDeflineGenerator::x_SetFlags().

◆ IsUnverifiedMisassembled()

bool CUser_object::IsUnverifiedMisassembled ( ) const

Definition at line 827 of file User_object.cpp.

References x_IsUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), CBioseqIndex::x_InitDescs(), CBioseqContext::x_SetDataFromUserObjects(), and CDeflineGenerator::x_SetFlags().

◆ IsUnverifiedOrganism()

bool CUser_object::IsUnverifiedOrganism ( ) const

Definition at line 791 of file User_object.cpp.

References x_IsUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), CBioseqIndex::x_InitDescs(), CBioseqContext::x_SetDataFromUserObjects(), and CDeflineGenerator::x_SetFlags().

◆ IsValidationSuppression()

bool CUser_object::IsValidationSuppression ( ) const

inline

Definition at line 181 of file User_object.hpp.

References eObjectType_ValidationSuppression, and GetObjectType().

◆ operator=()

CUser_object& CUser_object::operator= ( const CUser_object & value )

private

◆ RemoveNamedField()

bool CUser_object::RemoveNamedField	(	const string &	field_name,
		NStr::ECase	ecase = `NStr::eCase`
	)

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 ( )

Definition at line 875 of file User_object.cpp.

References x_RemoveUnreviewedType().

Referenced by CUnreviewedPanel::GetUser_object().

◆ RemoveUnverifiedContaminant()

void CUser_object::RemoveUnverifiedContaminant ( )

Definition at line 857 of file User_object.cpp.

References x_RemoveUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), and CUnverifiedPanel::GetUser_object().

◆ RemoveUnverifiedFeature()

void CUser_object::RemoveUnverifiedFeature ( )

Definition at line 821 of file User_object.cpp.

References x_RemoveUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), and CUnverifiedPanel::GetUser_object().

◆ RemoveUnverifiedMisassembled()

void CUser_object::RemoveUnverifiedMisassembled ( )

Definition at line 839 of file User_object.cpp.

References x_RemoveUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), and CUnverifiedPanel::GetUser_object().

◆ RemoveUnverifiedOrganism()

void CUser_object::RemoveUnverifiedOrganism ( )

Definition at line 803 of file User_object.cpp.

References x_RemoveUnverifiedType().

Referenced by BOOST_AUTO_TEST_CASE(), and CUnverifiedPanel::GetUser_object().

◆ ResetRefGeneTrackingAssembly()

void CUser_object::ResetRefGeneTrackingAssembly ( )

Definition at line 1306 of file User_object.cpp.

References kRefGeneTrackingAssembly, and RemoveNamedField().

Referenced by BOOST_AUTO_TEST_CASE().

◆ ResetRefGeneTrackingCollaborator()

void CUser_object::ResetRefGeneTrackingCollaborator ( )

Definition at line 1061 of file User_object.cpp.

References kRefGeneTrackingCollaborator, and RemoveNamedField().

Referenced by BOOST_AUTO_TEST_CASE().

◆ ResetRefGeneTrackingCollaboratorURL()

void CUser_object::ResetRefGeneTrackingCollaboratorURL ( )

Definition at line 1080 of file User_object.cpp.

References kRefGeneTrackingCollaboratorURL, and RemoveNamedField().

Referenced by BOOST_AUTO_TEST_CASE().

◆ ResetRefGeneTrackingGenerated()

void CUser_object::ResetRefGeneTrackingGenerated ( )

Definition at line 1111 of file User_object.cpp.

References kRefGeneTrackingGenerated, and RemoveNamedField().

Referenced by BOOST_AUTO_TEST_CASE().

◆ ResetRefGeneTrackingGenomicSource()

void CUser_object::ResetRefGeneTrackingGenomicSource ( )

Definition at line 1042 of file User_object.cpp.

References kRefGeneTrackingGenomicSource, and RemoveNamedField().

Referenced by BOOST_AUTO_TEST_CASE().

◆ ResetRefGeneTrackingIdenticalTo()

void CUser_object::ResetRefGeneTrackingIdenticalTo ( )

Definition at line 1263 of file User_object.cpp.

References kRefGeneTrackingIdenticalTo, and RemoveNamedField().

Referenced by BOOST_AUTO_TEST_CASE().

◆ ResetRefGeneTrackingStatus()

void CUser_object::ResetRefGeneTrackingStatus ( )

Definition at line 1022 of file User_object.cpp.

References kRefGeneTrackingStatus, and RemoveNamedField().

Referenced by BOOST_AUTO_TEST_CASE().

◆ SetCategory()

CUser_object & CUser_object::SetCategory ( ECategory category )

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()

CUser_object & CUser_object::SetExperiment ( EExperiment category )

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 578 of file User_object.cpp.

References eExperiment_Sage, eExperiment_Unknown, CUser_object_Base::Reset(), s_ncbi, s_sage, CUser_object_Base::SetClass(), CObject_id_Base::SetStr(), and CUser_object_Base::SetType().

◆ SetField()

CUser_field & CUser_object::SetField	(	const string &	str,
		const string &	delim = `"."`,
		const string &	obj_subtype = `kEmptyStr`,
		NStr::ECase	use_case = `NStr::eCase`
	)

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()

CRef< CUser_field > CUser_object::SetFieldRef	(	const string &	str,
		const string &	delim = `"."`,
		const string &	obj_subtype = `kEmptyStr`,
		NStr::ECase	use_case = `NStr::eCase`
	)