Collaboration diagram for Code generated by DATATOOL from 'seqfeat.asn' (module 'NCBI-Gene'):

Classes
class	CGene_nomenclature
	CGene_nomenclature –. More...

class	CGene_nomenclature_Base
	CGene_nomenclature_Base –. More...

class	CGene_ref_Base
	* Gene ********************************************* * * reference to a gene * More...

Typedefs
typedef CGene_nomenclature_Base	CGene_nomenclature::Tparent

typedef CSerialObject	CGene_nomenclature_Base::Tparent

typedef EStatus	CGene_nomenclature_Base::TStatus

typedef string	CGene_nomenclature_Base::TSymbol

typedef string	CGene_nomenclature_Base::TName

typedef CDbtag	CGene_nomenclature_Base::TSource

typedef Tparent::CMemberIndex< E_memberIndex, 5 >	CGene_nomenclature_Base::TmemberIndex

typedef CSerialObject	CGene_ref_Base::Tparent

typedef string	CGene_ref_Base::TLocus

typedef string	CGene_ref_Base::TAllele

typedef string	CGene_ref_Base::TDesc

typedef string	CGene_ref_Base::TMaploc

typedef bool	CGene_ref_Base::TPseudo

typedef vector< CRef< CDbtag > >	CGene_ref_Base::TDb

typedef list< string >	CGene_ref_Base::TSyn

typedef string	CGene_ref_Base::TLocus_tag

typedef CGene_nomenclature	CGene_ref_Base::TFormal_name

typedef Tparent::CMemberIndex< E_memberIndex, 10 >	CGene_ref_Base::TmemberIndex

Functions
	CGene_nomenclature::CGene_nomenclature (void)

	CGene_nomenclature::~CGene_nomenclature (void)

	CGene_nomenclature::CGene_nomenclature (const CGene_nomenclature &value)

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

	CGene_nomenclature_Base::CGene_nomenclature_Base (void)

virtual	CGene_nomenclature_Base::~CGene_nomenclature_Base (void)

	CGene_nomenclature_Base::DECLARE_INTERNAL_TYPE_INFO ()

static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	CGene_nomenclature_Base::EStatus (void)
	Access to EStatus's attributes (values, names) as defined in spec. More...

bool	CGene_nomenclature_Base::IsSetStatus (void) const
	Check if a value has been assigned to Status data member. More...

bool	CGene_nomenclature_Base::CanGetStatus (void) const
	Check if it is safe to call GetStatus method. More...

void	CGene_nomenclature_Base::ResetStatus (void)
	Reset Status data member. More...

TStatus	CGene_nomenclature_Base::GetStatus (void) const
	Get the Status member data. More...

void	CGene_nomenclature_Base::SetStatus (TStatus value)
	Assign a value to Status data member. More...

TStatus &	CGene_nomenclature_Base::SetStatus (void)
	Assign a value to Status data member. More...

bool	CGene_nomenclature_Base::IsSetSymbol (void) const
	Check if a value has been assigned to Symbol data member. More...

bool	CGene_nomenclature_Base::CanGetSymbol (void) const
	Check if it is safe to call GetSymbol method. More...

void	CGene_nomenclature_Base::ResetSymbol (void)
	Reset Symbol data member. More...

const TSymbol &	CGene_nomenclature_Base::GetSymbol (void) const
	Get the Symbol member data. More...

void	CGene_nomenclature_Base::SetSymbol (const TSymbol &value)
	Assign a value to Symbol data member. More...

void	CGene_nomenclature_Base::SetSymbol (TSymbol &&value)

TSymbol &	CGene_nomenclature_Base::SetSymbol (void)
	Assign a value to Symbol data member. More...

bool	CGene_nomenclature_Base::IsSetName (void) const
	Check if a value has been assigned to Name data member. More...

bool	CGene_nomenclature_Base::CanGetName (void) const
	Check if it is safe to call GetName method. More...

void	CGene_nomenclature_Base::ResetName (void)
	Reset Name data member. More...

const TName &	CGene_nomenclature_Base::GetName (void) const
	Get the Name member data. More...

void	CGene_nomenclature_Base::SetName (const TName &value)
	Assign a value to Name data member. More...

void	CGene_nomenclature_Base::SetName (TName &&value)

TName &	CGene_nomenclature_Base::SetName (void)
	Assign a value to Name data member. More...

bool	CGene_nomenclature_Base::IsSetSource (void) const
	Check if a value has been assigned to Source data member. More...

bool	CGene_nomenclature_Base::CanGetSource (void) const
	Check if it is safe to call GetSource method. More...

void	CGene_nomenclature_Base::ResetSource (void)
	Reset Source data member. More...

const TSource &	CGene_nomenclature_Base::GetSource (void) const
	Get the Source member data. More...

void	CGene_nomenclature_Base::SetSource (TSource &value)
	Assign a value to Source data member. More...

TSource &	CGene_nomenclature_Base::SetSource (void)
	Assign a value to Source data member. More...

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

	CGene_nomenclature_Base::CGene_nomenclature_Base (const CGene_nomenclature_Base &)

CGene_nomenclature_Base &	CGene_nomenclature_Base::operator= (const CGene_nomenclature_Base &)

	CGene_ref_Base::CGene_ref_Base (void)

virtual	CGene_ref_Base::~CGene_ref_Base (void)

	CGene_ref_Base::DECLARE_INTERNAL_TYPE_INFO ()

bool	CGene_ref_Base::IsSetLocus (void) const
	Official gene symbol Check if a value has been assigned to Locus data member. More...

bool	CGene_ref_Base::CanGetLocus (void) const
	Check if it is safe to call GetLocus method. More...

void	CGene_ref_Base::ResetLocus (void)
	Reset Locus data member. More...

const TLocus &	CGene_ref_Base::GetLocus (void) const
	Get the Locus member data. More...

void	CGene_ref_Base::SetLocus (const TLocus &value)
	Assign a value to Locus data member. More...

void	CGene_ref_Base::SetLocus (TLocus &&value)

TLocus &	CGene_ref_Base::SetLocus (void)
	Assign a value to Locus data member. More...

bool	CGene_ref_Base::IsSetAllele (void) const
	Official allele designation Check if a value has been assigned to Allele data member. More...

bool	CGene_ref_Base::CanGetAllele (void) const
	Check if it is safe to call GetAllele method. More...

void	CGene_ref_Base::ResetAllele (void)
	Reset Allele data member. More...

const TAllele &	CGene_ref_Base::GetAllele (void) const
	Get the Allele member data. More...

void	CGene_ref_Base::SetAllele (const TAllele &value)
	Assign a value to Allele data member. More...

void	CGene_ref_Base::SetAllele (TAllele &&value)

TAllele &	CGene_ref_Base::SetAllele (void)
	Assign a value to Allele data member. More...

bool	CGene_ref_Base::IsSetDesc (void) const
	descriptive name Check if a value has been assigned to Desc data member. More...

bool	CGene_ref_Base::CanGetDesc (void) const
	Check if it is safe to call GetDesc method. More...

void	CGene_ref_Base::ResetDesc (void)
	Reset Desc data member. More...

const TDesc &	CGene_ref_Base::GetDesc (void) const
	Get the Desc member data. More...

void	CGene_ref_Base::SetDesc (const TDesc &value)
	Assign a value to Desc data member. More...

void	CGene_ref_Base::SetDesc (TDesc &&value)

TDesc &	CGene_ref_Base::SetDesc (void)
	Assign a value to Desc data member. More...

bool	CGene_ref_Base::IsSetMaploc (void) const
	descriptive map location Check if a value has been assigned to Maploc data member. More...

bool	CGene_ref_Base::CanGetMaploc (void) const
	Check if it is safe to call GetMaploc method. More...

void	CGene_ref_Base::ResetMaploc (void)
	Reset Maploc data member. More...

const TMaploc &	CGene_ref_Base::GetMaploc (void) const
	Get the Maploc member data. More...

void	CGene_ref_Base::SetMaploc (const TMaploc &value)
	Assign a value to Maploc data member. More...

void	CGene_ref_Base::SetMaploc (TMaploc &&value)

TMaploc &	CGene_ref_Base::SetMaploc (void)
	Assign a value to Maploc data member. More...

bool	CGene_ref_Base::IsSetPseudo (void) const
	pseudogene Check if a value has been assigned to Pseudo data member. More...

bool	CGene_ref_Base::CanGetPseudo (void) const
	Check if it is safe to call GetPseudo method. More...

void	CGene_ref_Base::ResetPseudo (void)
	Reset Pseudo data member. More...

void	CGene_ref_Base::SetDefaultPseudo (void)
	Assign default value to Pseudo data member. More...

TPseudo	CGene_ref_Base::GetPseudo (void) const
	Get the Pseudo member data. More...

void	CGene_ref_Base::SetPseudo (TPseudo value)
	Assign a value to Pseudo data member. More...

TPseudo &	CGene_ref_Base::SetPseudo (void)
	Assign a value to Pseudo data member. More...

bool	CGene_ref_Base::IsSetDb (void) const
	ids in other dbases Check if a value has been assigned to Db data member. More...

bool	CGene_ref_Base::CanGetDb (void) const
	Check if it is safe to call GetDb method. More...

void	CGene_ref_Base::ResetDb (void)
	Reset Db data member. More...

const TDb &	CGene_ref_Base::GetDb (void) const
	Get the Db member data. More...

TDb &	CGene_ref_Base::SetDb (void)
	Assign a value to Db data member. More...

bool	CGene_ref_Base::IsSetSyn (void) const
	synonyms for locus Check if a value has been assigned to Syn data member. More...

bool	CGene_ref_Base::CanGetSyn (void) const
	Check if it is safe to call GetSyn method. More...

void	CGene_ref_Base::ResetSyn (void)
	Reset Syn data member. More...

const TSyn &	CGene_ref_Base::GetSyn (void) const
	Get the Syn member data. More...

TSyn &	CGene_ref_Base::SetSyn (void)
	Assign a value to Syn data member. More...

bool	CGene_ref_Base::IsSetLocus_tag (void) const
	systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data member. More...

bool	CGene_ref_Base::CanGetLocus_tag (void) const
	Check if it is safe to call GetLocus_tag method. More...

void	CGene_ref_Base::ResetLocus_tag (void)
	Reset Locus_tag data member. More...

const TLocus_tag &	CGene_ref_Base::GetLocus_tag (void) const
	Get the Locus_tag member data. More...

void	CGene_ref_Base::SetLocus_tag (const TLocus_tag &value)
	Assign a value to Locus_tag data member. More...

void	CGene_ref_Base::SetLocus_tag (TLocus_tag &&value)

TLocus_tag &	CGene_ref_Base::SetLocus_tag (void)
	Assign a value to Locus_tag data member. More...

bool	CGene_ref_Base::IsSetFormal_name (void) const
	Check if a value has been assigned to Formal_name data member. More...

bool	CGene_ref_Base::CanGetFormal_name (void) const
	Check if it is safe to call GetFormal_name method. More...

void	CGene_ref_Base::ResetFormal_name (void)
	Reset Formal_name data member. More...

const TFormal_name &	CGene_ref_Base::GetFormal_name (void) const
	Get the Formal_name member data. More...

void	CGene_ref_Base::SetFormal_name (TFormal_name &value)
	Assign a value to Formal_name data member. More...

TFormal_name &	CGene_ref_Base::SetFormal_name (void)
	Assign a value to Formal_name data member. More...

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

	CGene_ref_Base::CGene_ref_Base (const CGene_ref_Base &)

CGene_ref_Base &	CGene_ref_Base::operator= (const CGene_ref_Base &)

Detailed Description

Typedef Documentation

◆ TAllele

typedef string CGene_ref_Base::TAllele

Definition at line 97 of file Gene_ref_.hpp.

◆ TDb

typedef vector< CRef< CDbtag > > CGene_ref_Base::TDb

Definition at line 101 of file Gene_ref_.hpp.

◆ TDesc

typedef string CGene_ref_Base::TDesc

Definition at line 98 of file Gene_ref_.hpp.

◆ TFormal_name

typedef CGene_nomenclature CGene_ref_Base::TFormal_name

Definition at line 104 of file Gene_ref_.hpp.

◆ TLocus

typedef string CGene_ref_Base::TLocus

Definition at line 96 of file Gene_ref_.hpp.

◆ TLocus_tag

typedef string CGene_ref_Base::TLocus_tag

Definition at line 103 of file Gene_ref_.hpp.

◆ TMaploc

typedef string CGene_ref_Base::TMaploc

Definition at line 99 of file Gene_ref_.hpp.

◆ TmemberIndex [1/2]

typedef Tparent::CMemberIndex<E_memberIndex, 5> CGene_nomenclature_Base::TmemberIndex

Definition at line 111 of file Gene_nomenclature_.hpp.

◆ TmemberIndex [2/2]

typedef Tparent::CMemberIndex<E_memberIndex, 10> CGene_ref_Base::TmemberIndex

Definition at line 119 of file Gene_ref_.hpp.

◆ TName

typedef string CGene_nomenclature_Base::TName

Definition at line 100 of file Gene_nomenclature_.hpp.

◆ Tparent [1/3]

typedef CGene_nomenclature_Base CGene_nomenclature::Tparent

private

Definition at line 67 of file Gene_nomenclature.hpp.

◆ Tparent [2/3]

typedef CSerialObject CGene_nomenclature_Base::Tparent

private

Definition at line 78 of file Gene_nomenclature_.hpp.

◆ Tparent [3/3]

typedef CSerialObject CGene_ref_Base::Tparent

private

Definition at line 85 of file Gene_ref_.hpp.

◆ TPseudo

typedef bool CGene_ref_Base::TPseudo

Definition at line 100 of file Gene_ref_.hpp.

◆ TSource

typedef CDbtag CGene_nomenclature_Base::TSource

Definition at line 101 of file Gene_nomenclature_.hpp.

◆ TStatus

typedef EStatus CGene_nomenclature_Base::TStatus

Definition at line 98 of file Gene_nomenclature_.hpp.

◆ TSymbol

typedef string CGene_nomenclature_Base::TSymbol

Definition at line 99 of file Gene_nomenclature_.hpp.

◆ TSyn

typedef list< string > CGene_ref_Base::TSyn

Definition at line 102 of file Gene_ref_.hpp.

Enumeration Type Documentation

◆ E_memberIndex [1/2]

enum CGene_nomenclature_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_status
e_symbol
e_name
e_source

Definition at line 104 of file Gene_nomenclature_.hpp.

◆ E_memberIndex [2/2]

enum CGene_ref_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_locus
e_allele
e_desc
e_maploc
e_pseudo
e_db
e_syn
e_locus_tag
e_formal_name

Definition at line 107 of file Gene_ref_.hpp.

◆ EStatus

enum CGene_nomenclature_Base::EStatus

Enumerator
eStatus_unknown
eStatus_official
eStatus_interim

Definition at line 88 of file Gene_nomenclature_.hpp.

Function Documentation

◆ CanGetAllele()

bool CGene_ref_Base::CanGetAllele ( void ) const

inline

Check if it is safe to call GetAllele method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 546 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetAllele().

Referenced by CAutoDefGeneClause::CAutoDefGeneClause(), CGene_ref_Base::GetAllele(), s_EquivGenes(), and s_GetGeneRefFields().

◆ CanGetDb()

bool CGene_ref_Base::CanGetDb ( void ) const

inline

Check if it is safe to call GetDb method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 737 of file Gene_ref_.hpp.

Referenced by CFeatureItem::x_AddQualDb().

◆ CanGetDesc()

bool CGene_ref_Base::CanGetDesc ( void ) const

inline

Check if it is safe to call GetDesc method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 593 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetDesc().

Referenced by CGene_ref_Base::GetDesc(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), s_GetGeneRefFields(), and CAutoDefGeneClause::x_GetProductName().

◆ CanGetFormal_name()

bool CGene_ref_Base::CanGetFormal_name ( void ) const

inline

Check if it is safe to call GetFormal_name method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 834 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetFormal_name().

Referenced by CGene_ref_Base::GetFormal_name().

◆ CanGetLocus()

bool CGene_ref_Base::CanGetLocus ( void ) const

inline

Check if it is safe to call GetLocus method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 499 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetLocus().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), GetGeneForFeature(), CGene_ref_Base::GetLocus(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), s_EquivGenes(), s_GetGeneRefFields(), and CAutoDefFeatureClause::x_GetGeneName().

◆ CanGetLocus_tag()

bool CGene_ref_Base::CanGetLocus_tag ( void ) const

inline

Check if it is safe to call GetLocus_tag method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 787 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetLocus_tag().

Referenced by GetGeneForFeature(), CGene_ref_Base::GetLocus_tag(), GetLocusTagForFeature(), s_EquivGenes(), and s_GetGeneRefFields().

◆ CanGetMaploc()

bool CGene_ref_Base::CanGetMaploc ( void ) const

inline

Check if it is safe to call GetMaploc method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 640 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetMaploc().

Referenced by CGene_ref_Base::GetMaploc().

◆ CanGetName()

bool CGene_nomenclature_Base::CanGetName ( void ) const

inline

Check if it is safe to call GetName method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 393 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::IsSetName().

Referenced by CGene_nomenclature_Base::GetName().

◆ CanGetPseudo()

bool CGene_ref_Base::CanGetPseudo ( void ) const

inline

Check if it is safe to call GetPseudo method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 687 of file Gene_ref_.hpp.

Referenced by CAutoDefGeneClause::x_IsPseudo().

◆ CanGetSource()

bool CGene_nomenclature_Base::CanGetSource ( void ) const

inline

Check if it is safe to call GetSource method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 440 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::IsSetSource().

Referenced by CGene_nomenclature_Base::GetSource().

◆ CanGetStatus()

bool CGene_nomenclature_Base::CanGetStatus ( void ) const

inline

Check if it is safe to call GetStatus method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 299 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::IsSetStatus().

Referenced by CGene_nomenclature_Base::GetStatus().

◆ CanGetSymbol()

bool CGene_nomenclature_Base::CanGetSymbol ( void ) const

inline

Check if it is safe to call GetSymbol method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 346 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::IsSetSymbol().

Referenced by CGene_nomenclature_Base::GetSymbol().

◆ CanGetSyn()

bool CGene_ref_Base::CanGetSyn ( void ) const

inline

Check if it is safe to call GetSyn method.

Returns

true, if the data member is getatable.
false, otherwise.

Definition at line 762 of file Gene_ref_.hpp.

◆ CGene_nomenclature() [1/2]

CGene_nomenclature::CGene_nomenclature ( const CGene_nomenclature & value )

private

◆ CGene_nomenclature() [2/2]

CGene_nomenclature::CGene_nomenclature ( void )

inline

Definition at line 86 of file Gene_nomenclature.hpp.

◆ CGene_nomenclature_Base() [1/2]

CGene_nomenclature_Base::CGene_nomenclature_Base ( const CGene_nomenclature_Base & )

private

◆ CGene_nomenclature_Base() [2/2]

END_CLASS_INFO CGene_nomenclature_Base::CGene_nomenclature_Base ( void )

Definition at line 112 of file Gene_nomenclature_.cpp.

References CGene_nomenclature_Base::m_set_State.

◆ CGene_ref_Base() [1/2]

CGene_ref_Base::CGene_ref_Base ( const CGene_ref_Base & )

private

◆ CGene_ref_Base() [2/2]

END_CLASS_INFO CGene_ref_Base::CGene_ref_Base ( void )

Definition at line 143 of file Gene_ref_.cpp.

References CGene_ref_Base::m_set_State.

◆ DECLARE_INTERNAL_TYPE_INFO() [1/2]

CGene_nomenclature_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [2/2]

CGene_ref_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ EStatus()

static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME() CGene_nomenclature_Base::EStatus ( void )

static

Access to EStatus's attributes (values, names) as defined in spec.

◆ GetAllele()

const CGene_ref_Base::TAllele & CGene_ref_Base::GetAllele ( void ) const

inline

Get the Allele member data.

Returns: Reference to the member data.

Definition at line 552 of file Gene_ref_.hpp.

References CGene_ref_Base::CanGetAllele(), CGene_ref_Base::m_Allele, and CSerialObject::ThrowUnassigned().

Referenced by CGeneRefColumn::AddToFeature(), CAutoDefGeneClause::CAutoDefGeneClause(), GeneRefMatch(), CBulkGene::GetCommandFromValuesTable(), CGeneRefColumn::GetFromFeat(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CEditingActionFeatAllele::GetValue(), CBulkGene::GetValuesTableFromSeqEntry(), CGene_ref::IsSuppressed(), CFindASN1Dlg::ReplaceInFeature(), s_EquivGenes(), s_GetGeneRefFields(), CGeneValidator::Validate(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CNewCleanup_imp::x_CleanEmptyGene(), CNewCleanup_imp::x_GeneGBQualBC(), and CSingleFeatValidator::x_ValidateGeneXRef().

◆ GetDb()

const CGene_ref_Base::TDb & CGene_ref_Base::GetDb ( void ) const

inline

Get the Db member data.

Returns: Reference to the member data.

Definition at line 743 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Db.

Referenced by CScoreLookup::GetGeneId(), CGene_ref::GetLabel(), CGene_ref::IsSuppressed(), s_CopyDbToFeat(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneID(), CCompareSeqRegions::s_GetGeneId(), CGeneValidator::Validate(), CFeatureItem::x_AddQualDb(), CFeatureItem::x_AddQualGeneXref(), CFeatureItem::x_AddQualsGene(), and CNewCleanup_imp::x_CleanEmptyGene().

◆ GetDesc()

const CGene_ref_Base::TDesc & CGene_ref_Base::GetDesc ( void ) const

inline

Get the Desc member data.

Returns: Reference to the member data.

Definition at line 599 of file Gene_ref_.hpp.

References CGene_ref_Base::CanGetDesc(), CGene_ref_Base::m_Desc, and CSerialObject::ThrowUnassigned().

Referenced by CDescriptionColumn::AddToFeature(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CConvertGeneToImp::Convert(), GeneRefMatch(), CBulkGene::GetCommandFromValuesTable(), CEntrezgene::GetDescription(), CDescriptionColumn::GetFromFeat(), CEntrezgeneHandler::GetLabel(), CGene_ref::GetLabel(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CEditingActionFeatDesc::GetValue(), CBulkGene::GetValuesTableFromSeqEntry(), CGene_ref::IsSuppressed(), CAnnotObjectType_Less::operator()(), CFindASN1Dlg::ReplaceInFeature(), s_CheckQuals_gene(), s_CompareFtables(), s_GetGeneTextLabel(), s_GetProteinName(), s_ReportableCollision(), CGeneValidator::Validate(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CConvertCDSToPseudoGene::x_AddToGeneDescr(), CNewCleanup_imp::x_CleanEmptyGene(), CAutoDefFeatureClause::x_GetGeneName(), CAutoDefGeneClause::x_GetProductName(), CSeq_annot_Info::x_MapFeatByGene(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), and CSeq_annot_Info::x_UnmapFeatByGene().

◆ GetFormal_name()

const CGene_ref_Base::TFormal_name & CGene_ref_Base::GetFormal_name ( void ) const

inline

Get the Formal_name member data.

Returns: Reference to the member data.

Definition at line 840 of file Gene_ref_.hpp.

References CGene_ref_Base::CanGetFormal_name(), CGene_ref_Base::m_Formal_name, and CSerialObject::ThrowUnassigned().

Referenced by CEntrezgene::GetNomenclature(), and CFeatureItem::x_AddQualsGene().

◆ GetLocus()

const CGene_ref_Base::TLocus & CGene_ref_Base::GetLocus ( void ) const

inline

Get the Locus member data.

Returns: Reference to the member data.

Definition at line 505 of file Gene_ref_.hpp.

References CGene_ref_Base::CanGetLocus(), CGene_ref_Base::m_Locus, and CSerialObject::ThrowUnassigned().

Referenced by CLinkUtils::AddDbxrefLinksForSNP(), CGeneRefColumn::AddToFeature(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CConvertMiscFeatToGene::Convert(), CConvertGeneToImp::Convert(), CExploreProcess::DoOneBioseq(), EndAdded(), CCleanup::FindMatchingLocusGene(), fta_cmp_gene_refs(), GeneLocusCheck(), CGeneFinder::GeneMatchesXref(), CNewCleanup_imp::GenerefBC(), GeneRefMatch(), CEditSequenceEnds::GetCommand(), CBulkGene::GetCommandFromValuesTable(), CGeneRefColumn::GetFromFeat(), CTSE_Handle::GetGeneByRef(), GetGeneForFeature(), CTSE_Handle::GetGenesByRef(), GetIsLength(), CGene_ref::GetLabel(), CGuiObjectInfoVariation::GetLinks(), GetLocalGeneByXref(), NMacroUtil::GetLocusTagFromGene(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CEntrezgene::GetSymbol(), GetTargetedLocusName(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CEditingActionFeatGeneLocus::GetValue(), CBulkGene::GetValuesTableFromSeqEntry(), IsGeneInXref(), CGene_ref::IsSuppressed(), CAnnotObjectType_Less::operator()(), operator<<(), CTabularFormatter_GeneSymbol::Print(), CGFFReader::Read(), CGene_ref::RefersToSameGene(), CFindASN1Dlg::ReplaceInFeature(), CGeneFinder::ResolveGeneXref(), s_CheckQuals_gene(), s_CompareFtables(), s_EquivGenes(), CSingleFeatValidator::s_GeneRefsAreEquivalent(), CCompareSeqRegions::s_GetGeneId(), s_GetGeneRefFields(), s_GetGeneTextLabel(), s_GetProteinName(), s_ReportableCollision(), s_TitleFromSegment(), CReportEntry::SetGene(), CGeneOverlapProcess::TestFeatureGeneOverlap(), CGeneFeatTreeProcess::TestFeatureGeneTree(), CGeneValidator::Validate(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_bioseq::ValidateSeqFeatContext(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CFeatureItem::x_AddQualsIdx(), CConvertCDSToPseudoGene::x_AddToGeneLocus(), CNewCleanup_imp::x_CleanEmptyGene(), CFeatureGenerator::SImplementation::x_ConstructRnaName(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CAutoDefFeatureClause::x_GetGeneName(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), CSeq_annot_Info::x_MapFeatByGene(), CGFFReader::x_RemapGeneRefs(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CSeq_annot_Info::x_UnmapFeatByGene(), CCdregionValidator::x_ValidateCDSPeptides(), CSingleFeatValidator::x_ValidateGeneXRef(), and CCdregionValidator::x_ValidateParentPartialness().

◆ GetLocus_tag()

const CGene_ref_Base::TLocus_tag & CGene_ref_Base::GetLocus_tag ( void ) const

inline

Get the Locus_tag member data.

Returns: Reference to the member data.

Definition at line 793 of file Gene_ref_.hpp.

References CGene_ref_Base::CanGetLocus_tag(), CGene_ref_Base::m_Locus_tag, and CSerialObject::ThrowUnassigned().

Referenced by CGeneRefColumn::AddToFeature(), CCreateProteinId::apply(), CExploreProcess::DoOneBioseq(), CCleanup::FindMatchingLocus_tagGene(), fta_cmp_gene_refs(), GeneLocusCheck(), CGeneFinder::GeneMatchesXref(), GeneRefMatch(), CBulkGene::GetCommandFromValuesTable(), CValidator::CCacheImpl::GetFeatStrKeyToFeats(), CGeneRefColumn::GetFromFeat(), CTSE_Handle::GetGeneByRef(), GetGeneForFeature(), CTSE_Handle::GetGenesByRef(), CGene_ref::GetLabel(), GetLocalGeneByXref(), GetLocusTag(), GetLocusTagForFeature(), NMacroUtil::GetLocusTagFromGene(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CEntrezgene::GetSymbol(), CEditingActionFeatLocus_tag::GetValue(), CBulkGene::GetValuesTableFromSeqEntry(), IsGeneInXref(), CGene_ref::IsSuppressed(), CFeatComparatorByLabel::Less(), CCleanup::NormalizeGeneQuals(), operator<<(), CValidError_imp::PostErr(), CGene_ref::RefersToSameGene(), CFindASN1Dlg::ReplaceInFeature(), CGeneFinder::ResolveGeneXref(), s_CheckQuals_gene(), s_EquivGenes(), CSingleFeatValidator::s_GeneRefsAreEquivalent(), NSearchFeatPanel::s_GetFeatureLabel(), s_GetGeneRefFields(), s_GetGeneTextLabel(), s_GetProteinName(), s_ReportableCollision(), CReportEntry::SetGene(), CGeneOverlapProcess::TestFeatureGeneOverlap(), CGeneFeatTreeProcess::TestFeatureGeneTree(), CGeneValidator::Validate(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_bioseq::ValidateSeqFeatContext(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CFeatureItem::x_AddQualsIdx(), CNewCleanup_imp::x_CleanEmptyGene(), CImportFeatTable::x_CreateCommand(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CValidErrorFormat::x_FormatECNumberForSubmitterReport(), CAutoDefFeatureClause::x_GetGeneName(), CValidErrorFormat::x_GetLocusTag(), CSeq_annot_Info::x_MapFeatByGene(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CSeq_annot_Info::x_UnmapFeatByGene(), CCdregionValidator::x_ValidateCDSPeptides(), CSingleFeatValidator::x_ValidateGeneXRef(), CSingleFeatValidator::x_ValidateLocusTagGeneralMatch(), CSingleFeatValidator::x_ValidateOldLocusTag(), CFeatTableEdit::xGenerate_mRNA_Product(), CFeatTableEdit::xGetCurrentLocusTagPrefix(), CFeatTableEdit::xNextProteinId(), CFeatTableEdit::xNextTranscriptId(), and CFeatureTableReader::xTranslateProtein().

◆ GetMaploc()

const CGene_ref_Base::TMaploc & CGene_ref_Base::GetMaploc ( void ) const

inline

Get the Maploc member data.

Returns: Reference to the member data.

Definition at line 646 of file Gene_ref_.hpp.

References CGene_ref_Base::CanGetMaploc(), CGene_ref_Base::m_Maploc, and CSerialObject::ThrowUnassigned().

Referenced by CGeneRefColumn::AddToFeature(), GeneRefMatch(), CGeneRefColumn::GetFromFeat(), CGene_ref::GetLabel(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CEditingActionFeatMaploc::GetValue(), CGene_ref::IsSuppressed(), CFindASN1Dlg::ReplaceInFeature(), CGeneValidator::Validate(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CNewCleanup_imp::x_CleanEmptyGene(), and CGff2Writer::xAssignFeatureAttributeMapLoc().

◆ GetName()

const CGene_nomenclature_Base::TName & CGene_nomenclature_Base::GetName ( void ) const

inline

Get the Name member data.

Returns: Reference to the member data.

Definition at line 399 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::CanGetName(), CGene_nomenclature_Base::m_Name, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetPseudo()

CGene_ref_Base::TPseudo CGene_ref_Base::GetPseudo ( void ) const

inline

Get the Pseudo member data.

Returns: Copy of the member data.

Definition at line 706 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Pseudo.

Referenced by CDiscrepancyContext::IsPseudo(), IsPseudo(), s_CheckQuals_cdregion(), CSingleFeatValidator::s_IsPseudo(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_GetPseudo(), CGeneCache::x_IsPseudo(), x_IsPseudo(), and CRNAValidator::x_ValidateTrnaType().

◆ GetSource()

const CGene_nomenclature_Base::TSource & CGene_nomenclature_Base::GetSource ( void ) const

inline

Get the Source member data.

Returns: Reference to the member data.

Definition at line 446 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::CanGetSource(), CGene_nomenclature_Base::m_Source, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetStatus()

CGene_nomenclature_Base::TStatus CGene_nomenclature_Base::GetStatus ( void ) const

inline

Get the Status member data.

Returns: Copy of the member data.

Definition at line 312 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::CanGetStatus(), CGene_nomenclature_Base::m_Status, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetSymbol()

const CGene_nomenclature_Base::TSymbol & CGene_nomenclature_Base::GetSymbol ( void ) const

inline

Get the Symbol member data.

Returns: Reference to the member data.

Definition at line 352 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::CanGetSymbol(), CGene_nomenclature_Base::m_Symbol, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetSyn()

const CGene_ref_Base::TSyn & CGene_ref_Base::GetSyn ( void ) const

inline

Get the Syn member data.

Returns: Reference to the member data.

Definition at line 768 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Syn.

Referenced by EndAdded(), fta_cmp_gene_refs(), CGeneFinder::GeneMatchesXref(), CBulkGene::GetCommandFromValuesTable(), CGeneRefColumn::GetFromFeat(), CGene_ref::GetLabel(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CBulkGene::GetValuesTableFromSeqEntry(), CGene_ref::IsSuppressed(), CGene_ref::RefersToSameGene(), s_CheckQuals_gene(), s_CompareFtables(), CSingleFeatValidator::s_GeneRefsAreEquivalent(), s_GetProteinName(), s_TitleFromSegment(), CGeneValidator::Validate(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CNewCleanup_imp::x_CleanEmptyGene(), and CFeatureItem::x_CleanQuals().

◆ IsSetAllele()

bool CGene_ref_Base::IsSetAllele ( void ) const

inline

Official allele designation Check if a value has been assigned to Allele data member.

Data member Allele is optional; its type is defined as 'typedef string TAllele'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 540 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State.

Referenced by CGeneRefColumn::AddToFeature(), CGene_ref_Base::CanGetAllele(), GeneRefMatch(), CBulkGene::GetCommandFromValuesTable(), CGeneRefColumn::GetFromFeat(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CEditingActionFeatAllele::GetValue(), CBulkGene::GetValuesTableFromSeqEntry(), CEditingActionFeatAllele::IsSetValue(), CGene_ref::IsSuppressed(), CFindASN1Dlg::ReplaceInFeature(), CGene_ref_Base::SetAllele(), CGeneValidator::Validate(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CNewCleanup_imp::x_CleanEmptyGene(), CNewCleanup_imp::x_GeneGBQualBC(), CNewCleanup_imp::x_RemoveRedundantComment(), CNewCleanup_imp::x_ShouldRemoveEmptyGene(), and CSingleFeatValidator::x_ValidateGeneXRef().

◆ IsSetDb()

bool CGene_ref_Base::IsSetDb ( void ) const

inline

ids in other dbases Check if a value has been assigned to Db data member.

Data member Db is optional; its type is defined as 'typedef vector< CRef< CDbtag > > TDb'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 731 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State.

Referenced by CScoreLookup::GetGeneId(), CGene_ref::GetLabel(), CGene_ref::IsSuppressed(), CFindASN1Dlg::ReplaceInFeature(), s_CopyDbToFeat(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneID(), CGeneValidator::Validate(), CFeatureItem::x_AddQualGeneXref(), CFeatureItem::x_AddQualsGene(), CNewCleanup_imp::x_CleanEmptyGene(), CNewCleanup_imp::x_RemoveRedundantComment(), and CNewCleanup_imp::x_ShouldRemoveEmptyGene().

◆ IsSetDesc()

bool CGene_ref_Base::IsSetDesc ( void ) const

inline

descriptive name Check if a value has been assigned to Desc data member.

Data member Desc is optional; its type is defined as 'typedef string TDesc'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 587 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State.

Referenced by CDescriptionColumn::AddToFeature(), CGene_ref_Base::CanGetDesc(), CConvertGeneToImp::Convert(), CConvertCDSToPseudoGene::Convert(), GeneRefMatch(), CBulkGene::GetCommandFromValuesTable(), CDescriptionColumn::GetFromFeat(), CEntrezgeneHandler::GetLabel(), CGene_ref::GetLabel(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CEditingActionFeatDesc::GetValue(), CBulkGene::GetValuesTableFromSeqEntry(), CEditingActionFeatDesc::IsSetValue(), CGene_ref::IsSuppressed(), CAnnotObjectType_Less::operator()(), CFindASN1Dlg::ReplaceInFeature(), s_CheckQuals_gene(), s_CompareFtables(), s_GetGeneTextLabel(), s_GetProteinName(), s_ReportableCollision(), CGene_ref_Base::SetDesc(), CGeneValidator::Validate(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CConvertCDSToPseudoGene::x_AddToGeneDescr(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CNewCleanup_imp::x_CleanEmptyGene(), CAutoDefFeatureClause::x_GetGeneName(), CSeq_annot_Info::x_MapFeatByGene(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CNewCleanup_imp::x_ShouldRemoveEmptyGene(), and CSeq_annot_Info::x_UnmapFeatByGene().

◆ IsSetFormal_name()

bool CGene_ref_Base::IsSetFormal_name ( void ) const

inline

Check if a value has been assigned to Formal_name data member.

Data member Formal_name is optional; its type is defined as 'typedef CGene_nomenclature TFormal_name'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 828 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Formal_name.

Referenced by CClearNomenclature::apply(), BOOST_AUTO_TEST_CASE(), CGene_ref_Base::CanGetFormal_name(), CEntrezgene::GetNomenclature(), and CFeatureItem::x_AddQualsGene().

◆ IsSetLocus()

bool CGene_ref_Base::IsSetLocus ( void ) const

inline

Official gene symbol Check if a value has been assigned to Locus data member.

Data member Locus is optional; its type is defined as 'typedef string TLocus'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 493 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State.

Referenced by CLinkUtils::AddDbxrefLinksForSNP(), CGeneRefColumn::AddToFeature(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CGene_ref_Base::CanGetLocus(), CConvertGeneToImp::Convert(), CExploreProcess::DoOneBioseq(), CCleanup::FindMatchingLocusGene(), CCleanup::FixGeneXrefSkew(), fta_cmp_gene_refs(), GeneLocusCheck(), CGeneFinder::GeneMatchesXref(), CNewCleanup_imp::GenerefBC(), GeneRefMatch(), CEditSequenceEnds::GetCommand(), CBulkGene::GetCommandFromValuesTable(), CGeneRefColumn::GetFromFeat(), CTSE_Handle::GetGeneByRef(), CTSE_Handle::GetGenesByRef(), GetIsLength(), CGene_ref::GetLabel(), CGuiObjectInfoVariation::GetLinks(), GetLocalGeneByXref(), NMacroUtil::GetLocusTagFromGene(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), GetTargetedLocusName(), CEditingActionFeatGeneLocus::GetValue(), CBulkGene::GetValuesTableFromSeqEntry(), IsGeneInXref(), CEditingActionFeatGeneLocus::IsSetValue(), CGene_ref::IsSuppressed(), CCleanup::NormalizeGeneQuals(), CAnnotObjectType_Less::operator()(), operator<<(), CTabularFormatter_GeneSymbol::Print(), CGFFReader::Read(), CGene_ref::RefersToSameGene(), CFindASN1Dlg::ReplaceInFeature(), CGeneFinder::ResolveGeneXref(), s_CheckQuals_gene(), s_CompareFtables(), CSingleFeatValidator::s_GeneRefsAreEquivalent(), s_GetGeneTextLabel(), s_GetProteinName(), s_ReportableCollision(), s_TitleFromSegment(), CReportEntry::SetGene(), CGene_ref_Base::SetLocus(), sx_GeneIsSuppressed(), CGeneOverlapProcess::TestFeatureGeneOverlap(), CGeneFeatTreeProcess::TestFeatureGeneTree(), CGeneValidator::Validate(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_bioseq::ValidateSeqFeatContext(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CFeatureItem::x_AddQualsIdx(), CConvertCDSToPseudoGene::x_AddToGeneLocus(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CNewCleanup_imp::x_CleanEmptyGene(), CFeatureGenerator::SImplementation::x_ConstructRnaName(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CNewCleanup_imp::x_GeneGBQualBC(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), CSeq_annot_Info::x_MapFeatByGene(), CGFFReader::x_RemapGeneRefs(), CNewCleanup_imp::x_RemoveRedundantComment(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CNewCleanup_imp::x_ShouldRemoveEmptyGene(), CSeq_annot_Info::x_UnmapFeatByGene(), CCdregionValidator::x_ValidateCDSPeptides(), CValidError_bioseq::x_ValidateCDSVDJCmatch(), CSingleFeatValidator::x_ValidateGeneXRef(), and CCdregionValidator::x_ValidateParentPartialness().

◆ IsSetLocus_tag()

bool CGene_ref_Base::IsSetLocus_tag ( void ) const

inline

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data member.

Data member Locus_tag is optional; its type is defined as 'typedef string TLocus_tag'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 781 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State.

Referenced by CGeneRefColumn::AddToFeature(), CFeatTableEdit::AnnotHasAllLocusTags(), CCreateProteinId::apply(), CCreateLocusTagGene::apply(), CGene_ref_Base::CanGetLocus_tag(), CExploreProcess::DoOneBioseq(), CCleanup::FindMatchingLocus_tagGene(), CCleanup::FixGeneXrefSkew(), fta_cmp_gene_refs(), GeneLocusCheck(), CGeneFinder::GeneMatchesXref(), GeneRefMatch(), CBulkGene::GetCommandFromValuesTable(), CValidator::CCacheImpl::GetFeatStrKeyToFeats(), CGeneRefColumn::GetFromFeat(), CTSE_Handle::GetGeneByRef(), CTSE_Handle::GetGenesByRef(), CGene_ref::GetLabel(), GetLocalGeneByXref(), GetLocusTag(), NMacroUtil::GetLocusTagFromGene(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CEditingActionFeatLocus_tag::GetValue(), CBulkGene::GetValuesTableFromSeqEntry(), IsGeneInXref(), CEditingActionFeatLocus_tag::IsSetValue(), CGene_ref::IsSuppressed(), CFeatComparatorByLabel::Less(), CCleanup::NormalizeGeneQuals(), operator<<(), CValidError_imp::PostErr(), CGene_ref::RefersToSameGene(), CFindASN1Dlg::ReplaceInFeature(), CGeneFinder::ResolveGeneXref(), s_CheckQuals_gene(), CSingleFeatValidator::s_GeneRefsAreEquivalent(), NSearchFeatPanel::s_GetFeatureLabel(), s_GetGeneTextLabel(), s_GetProteinName(), s_ReportableCollision(), CReportEntry::SetGene(), CGene_ref_Base::SetLocus_tag(), SPParseGeneRefTag(), sx_GeneIsSuppressed(), CGeneOverlapProcess::TestFeatureGeneOverlap(), CGeneFeatTreeProcess::TestFeatureGeneTree(), CGeneValidator::Validate(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_bioseq::ValidateSeqFeatContext(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CFeatureItem::x_AddQualsIdx(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CNewCleanup_imp::x_CleanEmptyGene(), CImportFeatTable::x_CreateCommand(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupGeneRef(), CValidErrorFormat::x_FormatECNumberForSubmitterReport(), CNewCleanup_imp::x_GeneGBQualBC(), CAutoDefFeatureClause::x_GetGeneName(), CValidErrorFormat::x_GetLocusTag(), CSeq_annot_Info::x_MapFeatByGene(), CNewCleanup_imp::x_RemoveRedundantComment(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CNewCleanup_imp::x_ShouldRemoveEmptyGene(), CSeq_annot_Info::x_UnmapFeatByGene(), CCdregionValidator::x_ValidateCDSPeptides(), CValidError_bioseq::x_ValidateCDSVDJCmatch(), CSingleFeatValidator::x_ValidateGeneXRef(), CSingleFeatValidator::x_ValidateLocusTagGeneralMatch(), CSingleFeatValidator::x_ValidateOldLocusTag(), CFeatTableEdit::xGenerate_mRNA_Product(), CFeatTableEdit::xGenerateLocusIdsUseExisting(), CFeatTableEdit::xNextProteinId(), CFeatTableEdit::xNextTranscriptId(), and CFeatureTableReader::xTranslateProtein().

◆ IsSetMaploc()

bool CGene_ref_Base::IsSetMaploc ( void ) const

inline

descriptive map location Check if a value has been assigned to Maploc data member.

Data member Maploc is optional; its type is defined as 'typedef string TMaploc'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 634 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State.

Referenced by CGeneRefColumn::AddToFeature(), CGene_ref_Base::CanGetMaploc(), GeneRefMatch(), CGeneRefColumn::GetFromFeat(), CGene_ref::GetLabel(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CEditingActionFeatMaploc::GetValue(), CEditingActionFeatMaploc::IsSetValue(), CGene_ref::IsSuppressed(), CFindASN1Dlg::ReplaceInFeature(), CGene_ref_Base::SetMaploc(), CGeneValidator::Validate(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddQualsGene(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CNewCleanup_imp::x_CleanEmptyGene(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupGeneRef(), CNewCleanup_imp::x_GeneGBQualBC(), CNewCleanup_imp::x_RemoveRedundantComment(), CNewCleanup_imp::x_ShouldRemoveEmptyGene(), and CGff2Writer::xAssignFeatureAttributeMapLoc().

◆ IsSetName()

bool CGene_nomenclature_Base::IsSetName ( void ) const

inline

Check if a value has been assigned to Name data member.

Data member Name is optional; its type is defined as 'typedef string TName'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 387 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_set_State.

Referenced by CGene_nomenclature_Base::CanGetName(), and CGene_nomenclature_Base::SetName().

◆ IsSetPseudo()

bool CGene_ref_Base::IsSetPseudo ( void ) const

inline

pseudogene Check if a value has been assigned to Pseudo data member.

Data member Pseudo is optional with default false; its type is defined as 'typedef bool TPseudo'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 681 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State.

Referenced by GeneRefMatch(), CDiscrepancyContext::IsPseudo(), IsPseudo(), CSingleFeatValidator::s_IsPseudo(), CGene_ref_Base::SetPseudo(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_GetPseudo(), CAutoDefGeneClause::x_IsPseudo(), CGeneCache::x_IsPseudo(), x_IsPseudo(), and CNewCleanup_imp::x_ShouldRemoveEmptyGene().

◆ IsSetSource()

bool CGene_nomenclature_Base::IsSetSource ( void ) const

inline

Check if a value has been assigned to Source data member.

Data member Source is optional; its type is defined as 'typedef CDbtag TSource'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 434 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_Source.

Referenced by CGene_nomenclature_Base::CanGetSource().

◆ IsSetStatus()

bool CGene_nomenclature_Base::IsSetStatus ( void ) const

inline

Check if a value has been assigned to Status data member.

Data member Status is mandatory; its type is defined as 'typedef EStatus TStatus'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 293 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_set_State.

Referenced by CGene_nomenclature_Base::CanGetStatus(), and CGene_nomenclature_Base::SetStatus().

◆ IsSetSymbol()

bool CGene_nomenclature_Base::IsSetSymbol ( void ) const

inline

Check if a value has been assigned to Symbol data member.

Data member Symbol is optional; its type is defined as 'typedef string TSymbol'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 340 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_set_State.

Referenced by CGene_nomenclature_Base::CanGetSymbol(), CEntrezgene::GetNomenclature(), and CGene_nomenclature_Base::SetSymbol().

◆ IsSetSyn()

bool CGene_ref_Base::IsSetSyn ( void ) const

inline

synonyms for locus Check if a value has been assigned to Syn data member.

Data member Syn is optional; its type is defined as 'typedef list< string > TSyn'

Returns

true, if a value has been assigned.
false, otherwise.

Definition at line 756 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State.

Referenced by CGeneRefColumn::AddToFeature(), EndAdded(), fta_cmp_gene_refs(), CGeneFinder::GeneMatchesXref(), CBulkGene::GetCommandFromValuesTable(), CGeneRefColumn::GetFromFeat(), CGene_ref::GetLabel(), CCdsFromGeneMrnaExon::GetNameFromGene(), CmRNAFromGeneCdsExon::GetNameFromGene(), CtRNAFromGene::GetNameFromGene(), CBulkGene::GetValuesTableFromSeqEntry(), CGene_ref::IsSuppressed(), CGene_ref::RefersToSameGene(), CFindASN1Dlg::ReplaceInFeature(), s_CompareFtables(), CSingleFeatValidator::s_GeneRefsAreEquivalent(), s_GetProteinName(), s_TitleFromSegment(), CGeneValidator::Validate(), CFeatureItem::x_AddQualsGene(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CNewCleanup_imp::x_CleanEmptyGene(), CFeatureItem::x_CleanQuals(), CNewCleanup_imp::x_RemoveRedundantComment(), and CNewCleanup_imp::x_ShouldRemoveEmptyGene().

◆ operator=() [1/3]

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

private

◆ operator=() [2/3]

CGene_nomenclature_Base& CGene_nomenclature_Base::operator= ( const CGene_nomenclature_Base & )

private

◆ operator=() [3/3]

CGene_ref_Base& CGene_ref_Base::operator= ( const CGene_ref_Base & )

private

◆ Reset() [1/2]

void CGene_nomenclature_Base::Reset ( void )

virtual

Reset the whole object.

Definition at line 90 of file Gene_nomenclature_.cpp.

References CGene_nomenclature_Base::ResetName(), CGene_nomenclature_Base::ResetSource(), CGene_nomenclature_Base::ResetStatus(), and CGene_nomenclature_Base::ResetSymbol().

◆ Reset() [2/2]

void CGene_ref_Base::Reset ( void )

virtual

Reset the whole object.

Definition at line 111 of file Gene_ref_.cpp.

References CGene_ref_Base::ResetAllele(), CGene_ref_Base::ResetDb(), CGene_ref_Base::ResetDesc(), CGene_ref_Base::ResetFormal_name(), CGene_ref_Base::ResetLocus(), CGene_ref_Base::ResetLocus_tag(), CGene_ref_Base::ResetMaploc(), CGene_ref_Base::ResetPseudo(), and CGene_ref_Base::ResetSyn().

Referenced by CFeatureGenePanel::TransferDataFromWindow().

◆ ResetAllele()

void CGene_ref_Base::ResetAllele ( void )

Reset Allele data member.

Definition at line 58 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Allele, and CGene_ref_Base::m_set_State.

Referenced by CGene_ref_Base::Reset(), and CNewCleanup_imp::x_CleanEmptyGene().

◆ ResetDb()

void CGene_ref_Base::ResetDb ( void )

Reset Db data member.

Definition at line 76 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Db, and CGene_ref_Base::m_set_State.

Referenced by CGene_ref_Base::Reset(), s_CopyDbToFeat(), and CNewCleanup_imp::x_CleanEmptyGene().

◆ ResetDesc()

void CGene_ref_Base::ResetDesc ( void )

Reset Desc data member.

Definition at line 64 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Desc, and CGene_ref_Base::m_set_State.

Referenced by CGene_ref_Base::Reset(), CNewCleanup_imp::x_CleanEmptyGene(), and CNewCleanup_imp::x_RemoveRedundantComment().

◆ ResetFormal_name()

void CGene_ref_Base::ResetFormal_name ( void )

Reset Formal_name data member.

Definition at line 94 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Formal_name.

Referenced by CGene_ref_Base::Reset().

◆ ResetLocus()

void CGene_ref_Base::ResetLocus ( void )

Reset Locus data member.

Definition at line 52 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Locus, and CGene_ref_Base::m_set_State.

Referenced by CGene_ref_Base::Reset(), and CNewCleanup_imp::x_CleanEmptyGene().

◆ ResetLocus_tag()

void CGene_ref_Base::ResetLocus_tag ( void )

Reset Locus_tag data member.

Definition at line 88 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Locus_tag, and CGene_ref_Base::m_set_State.

Referenced by CGene_ref_Base::Reset(), and CNewCleanup_imp::x_CleanEmptyGene().

◆ ResetMaploc()

void CGene_ref_Base::ResetMaploc ( void )

Reset Maploc data member.

Definition at line 70 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Maploc, and CGene_ref_Base::m_set_State.

Referenced by CGene_ref_Base::Reset(), and CNewCleanup_imp::x_CleanEmptyGene().

◆ ResetName()

void CGene_nomenclature_Base::ResetName ( void )

Reset Name data member.

Definition at line 67 of file Gene_nomenclature_.cpp.

References CGene_nomenclature_Base::m_Name, and CGene_nomenclature_Base::m_set_State.

Referenced by CGene_nomenclature_Base::Reset().

◆ ResetPseudo()

void CGene_ref_Base::ResetPseudo ( void )

inline

Reset Pseudo data member.

Definition at line 693 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Pseudo, and CGene_ref_Base::m_set_State.

Referenced by CGene_ref_Base::Reset(), and CGene_ref_Base::SetDefaultPseudo().

◆ ResetSource()

void CGene_nomenclature_Base::ResetSource ( void )

Reset Source data member.

Definition at line 73 of file Gene_nomenclature_.cpp.

References CGene_nomenclature_Base::m_Source.

Referenced by CGene_nomenclature_Base::Reset().

◆ ResetStatus()

void CGene_nomenclature_Base::ResetStatus ( void )

inline

Reset Status data member.

Definition at line 305 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_set_State, and CGene_nomenclature_Base::m_Status.

Referenced by CGene_nomenclature_Base::Reset().

◆ ResetSymbol()

END_ENUM_INFO void CGene_nomenclature_Base::ResetSymbol ( void )

Reset Symbol data member.

Definition at line 61 of file Gene_nomenclature_.cpp.

References CGene_nomenclature_Base::m_set_State, and CGene_nomenclature_Base::m_Symbol.

Referenced by CGene_nomenclature_Base::Reset().

◆ ResetSyn()

void CGene_ref_Base::ResetSyn ( void )

Reset Syn data member.

Definition at line 82 of file Gene_ref_.cpp.

References CGene_ref_Base::m_set_State, and CGene_ref_Base::m_Syn.

Referenced by CGene_ref_Base::Reset(), and CNewCleanup_imp::x_CleanEmptyGene().

◆ SetAllele() [1/3]

void CGene_ref_Base::SetAllele ( const TAllele & value )

inline

Assign a value to Allele data member.

Parameters

value Value to assign

Definition at line 561 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Allele, CGene_ref_Base::m_set_State, and rapidjson::value.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToGene(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), and CNewCleanup_imp::x_GeneGBQualBC().

◆ SetAllele() [2/3]

void CGene_ref_Base::SetAllele ( CGene_ref_Base::TAllele && value )

inline

Definition at line 568 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Allele, CGene_ref_Base::m_set_State, and rapidjson::value.

◆ SetAllele() [3/3]

CGene_ref_Base::TAllele & CGene_ref_Base::SetAllele ( void )

inline

Assign a value to Allele data member.

Returns: Reference to the data value.

Definition at line 575 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetAllele(), CGene_ref_Base::m_Allele, CGene_ref_Base::m_set_State, and CSerialObject::UnassignedString().

◆ SetDb()

CGene_ref_Base::TDb & CGene_ref_Base::SetDb ( void )

inline

Assign a value to Db data member.

Returns: Reference to the data value.

Definition at line 749 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Db, and CGene_ref_Base::m_set_State.

◆ SetDefaultPseudo()

void CGene_ref_Base::SetDefaultPseudo ( void )

inline

Assign default value to Pseudo data member.

Definition at line 700 of file Gene_ref_.hpp.

References CGene_ref_Base::ResetPseudo().

◆ SetDesc() [1/3]

void CGene_ref_Base::SetDesc ( const TDesc & value )

inline

Assign a value to Desc data member.

Parameters

value Value to assign

Definition at line 608 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Desc, CGene_ref_Base::m_set_State, and rapidjson::value.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToFeature(), CFeatureTableReader_Imp::x_AddQualifierToGene(), CConvertCDSToPseudoGene::x_AddToGeneDescr(), and CAutogeneratedCleanup::x_BasicCleanupGeneRef().

◆ SetDesc() [2/3]

void CGene_ref_Base::SetDesc ( CGene_ref_Base::TDesc && value )

inline

Definition at line 615 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Desc, CGene_ref_Base::m_set_State, and rapidjson::value.

◆ SetDesc() [3/3]

CGene_ref_Base::TDesc & CGene_ref_Base::SetDesc ( void )

inline

Assign a value to Desc data member.

Returns: Reference to the data value.

Definition at line 622 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetDesc(), CGene_ref_Base::m_Desc, CGene_ref_Base::m_set_State, and CSerialObject::UnassignedString().

◆ SetFormal_name() [1/2]

void CGene_ref_Base::SetFormal_name ( CGene_ref_Base::TFormal_name & value )

Assign a value to Formal_name data member.

Parameters

value Reference to value.

Definition at line 99 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Formal_name, and rapidjson::value.

◆ SetFormal_name() [2/2]

CGene_ref_Base::TFormal_name & CGene_ref_Base::SetFormal_name ( void )

Assign a value to Formal_name data member.

Returns: Reference to the data value.

Definition at line 104 of file Gene_ref_.cpp.

References CGene_ref_Base::m_Formal_name.

◆ SetLocus() [1/3]

void CGene_ref_Base::SetLocus ( const TLocus & value )

inline

Assign a value to Locus data member.

Parameters

value Value to assign

Definition at line 514 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Locus, CGene_ref_Base::m_set_State, and rapidjson::value.

Referenced by AddGeneFeat(), FixAnnot(), CNewCleanup_imp::GenerefBC(), ParseGeneNameSP(), SPGetOneGeneRefNew(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CFeatureTableReader_Imp::x_AddQualifierToGene(), CConvertCDSToPseudoGene::x_AddToGeneLocus(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CNewCleanup_imp::x_GeneGBQualBC(), and CGtfReader::xFeatureSetDataGene().

◆ SetLocus() [2/3]

void CGene_ref_Base::SetLocus ( CGene_ref_Base::TLocus && value )

inline

Definition at line 521 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Locus, CGene_ref_Base::m_set_State, and rapidjson::value.

◆ SetLocus() [3/3]

CGene_ref_Base::TLocus & CGene_ref_Base::SetLocus ( void )

inline

Assign a value to Locus data member.

Returns: Reference to the data value.

Definition at line 528 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetLocus(), CGene_ref_Base::m_Locus, CGene_ref_Base::m_set_State, and CSerialObject::UnassignedString().

◆ SetLocus_tag() [1/3]

void CGene_ref_Base::SetLocus_tag ( const TLocus_tag & value )

inline

Assign a value to Locus_tag data member.

Parameters

value Value to assign

Definition at line 802 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Locus_tag, CGene_ref_Base::m_set_State, and rapidjson::value.

Referenced by AddGeneFeat(), FixAnnot(), SPParseGeneRefTag(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CFeatureTableReader_Imp::x_AddQualifierToGene(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupGeneRef(), CNewCleanup_imp::x_GeneGBQualBC(), and CGtfReader::xFeatureSetDataGene().

◆ SetLocus_tag() [2/3]

void CGene_ref_Base::SetLocus_tag ( CGene_ref_Base::TLocus_tag && value )

inline

Definition at line 809 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Locus_tag, CGene_ref_Base::m_set_State, and rapidjson::value.

◆ SetLocus_tag() [3/3]

CGene_ref_Base::TLocus_tag & CGene_ref_Base::SetLocus_tag ( void )

inline

Assign a value to Locus_tag data member.

Returns: Reference to the data value.

Definition at line 816 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetLocus_tag(), CGene_ref_Base::m_Locus_tag, CGene_ref_Base::m_set_State, and CSerialObject::UnassignedString().

◆ SetMaploc() [1/3]

void CGene_ref_Base::SetMaploc ( const TMaploc & value )

inline

Assign a value to Maploc data member.

Parameters

value Value to assign

Definition at line 655 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Maploc, CGene_ref_Base::m_set_State, and rapidjson::value.

Referenced by AddGeneFeat(), CFeatureTableReader_Imp::x_AddQualifierToGene(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupGeneRef(), and CNewCleanup_imp::x_GeneGBQualBC().

◆ SetMaploc() [2/3]

void CGene_ref_Base::SetMaploc ( CGene_ref_Base::TMaploc && value )

inline

Definition at line 662 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Maploc, CGene_ref_Base::m_set_State, and rapidjson::value.

◆ SetMaploc() [3/3]

CGene_ref_Base::TMaploc & CGene_ref_Base::SetMaploc ( void )

inline

Assign a value to Maploc data member.

Returns: Reference to the data value.

Definition at line 669 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetMaploc(), CGene_ref_Base::m_Maploc, CGene_ref_Base::m_set_State, and CSerialObject::UnassignedString().

◆ SetName() [1/3]

void CGene_nomenclature_Base::SetName ( const TName & value )

inline

Assign a value to Name data member.

Parameters

value Value to assign

Definition at line 408 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_Name, CGene_nomenclature_Base::m_set_State, and rapidjson::value.

Referenced by CNewCleanup_imp::GeneFeatBC(), and CEntrezgene::GetNomenclature().

◆ SetName() [2/3]

void CGene_nomenclature_Base::SetName ( CGene_nomenclature_Base::TName && value )

inline

Definition at line 415 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_Name, CGene_nomenclature_Base::m_set_State, and rapidjson::value.

◆ SetName() [3/3]

CGene_nomenclature_Base::TName & CGene_nomenclature_Base::SetName ( void )

inline

Assign a value to Name data member.

Returns: Reference to the data value.

Definition at line 422 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::IsSetName(), CGene_nomenclature_Base::m_Name, CGene_nomenclature_Base::m_set_State, and CSerialObject::UnassignedString().

◆ SetPseudo() [1/2]

void CGene_ref_Base::SetPseudo ( CGene_ref_Base::TPseudo value )

inline

Assign a value to Pseudo data member.

Parameters

value Value to assign

Definition at line 712 of file Gene_ref_.hpp.

References CGene_ref_Base::m_Pseudo, CGene_ref_Base::m_set_State, and rapidjson::value.

◆ SetPseudo() [2/2]

CGene_ref_Base::TPseudo & CGene_ref_Base::SetPseudo ( void )

inline

Assign a value to Pseudo data member.

Returns: Reference to the data value.

Definition at line 719 of file Gene_ref_.hpp.

References CGene_ref_Base::IsSetPseudo(), CGene_ref_Base::m_Pseudo, CGene_ref_Base::m_set_State, and CSerialObject::UnassignedByte().

◆ SetSource() [1/2]

void CGene_nomenclature_Base::SetSource ( CGene_nomenclature_Base::TSource & value )

Assign a value to Source data member.

Parameters

value Reference to value.

Definition at line 78 of file Gene_nomenclature_.cpp.

References CGene_nomenclature_Base::m_Source, and rapidjson::value.

Referenced by CNewCleanup_imp::GeneFeatBC().

◆ SetSource() [2/2]

CGene_nomenclature_Base::TSource & CGene_nomenclature_Base::SetSource ( void )

Assign a value to Source data member.

Returns: Reference to the data value.

Definition at line 83 of file Gene_nomenclature_.cpp.

References CGene_nomenclature_Base::m_Source.

◆ SetStatus() [1/2]

void CGene_nomenclature_Base::SetStatus ( CGene_nomenclature_Base::TStatus value )

inline

Assign a value to Status data member.

Parameters

value Value to assign

Definition at line 321 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_set_State, CGene_nomenclature_Base::m_Status, and rapidjson::value.

Referenced by CNewCleanup_imp::GeneFeatBC(), and CEntrezgene::GetNomenclature().

◆ SetStatus() [2/2]

CGene_nomenclature_Base::TStatus & CGene_nomenclature_Base::SetStatus ( void )

inline

Assign a value to Status data member.

Returns: Reference to the data value.

Definition at line 328 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::IsSetStatus(), CGene_nomenclature_Base::m_set_State, CGene_nomenclature_Base::m_Status, and CSerialObject::UnassignedByte().

◆ SetSymbol() [1/3]

void CGene_nomenclature_Base::SetSymbol ( const TSymbol & value )

inline

Assign a value to Symbol data member.

Parameters

value Value to assign

Definition at line 361 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_set_State, CGene_nomenclature_Base::m_Symbol, and rapidjson::value.

Referenced by CNewCleanup_imp::GeneFeatBC(), and CEntrezgene::GetNomenclature().

◆ SetSymbol() [2/3]

void CGene_nomenclature_Base::SetSymbol ( CGene_nomenclature_Base::TSymbol && value )

inline

Definition at line 368 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::m_set_State, CGene_nomenclature_Base::m_Symbol, and rapidjson::value.

◆ SetSymbol() [3/3]

CGene_nomenclature_Base::TSymbol & CGene_nomenclature_Base::SetSymbol ( void )

inline

Assign a value to Symbol data member.

Returns: Reference to the data value.

Definition at line 375 of file Gene_nomenclature_.hpp.

References CGene_nomenclature_Base::IsSetSymbol(), CGene_nomenclature_Base::m_set_State, CGene_nomenclature_Base::m_Symbol, and CSerialObject::UnassignedString().

◆ SetSyn()

CGene_ref_Base::TSyn & CGene_ref_Base::SetSyn ( void )

inline

Assign a value to Syn data member.

Returns: Reference to the data value.

Definition at line 774 of file Gene_ref_.hpp.

References CGene_ref_Base::m_set_State, and CGene_ref_Base::m_Syn.

Referenced by AddGeneFeat(), FixAnnot(), CNewCleanup_imp::GenerefBC(), ParseGeneNameSP(), SPParseGeneRefTag(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CFeatureTableReader_Imp::x_AddQualifierToGene(), CAutogeneratedCleanup::x_BasicCleanupGeneRef(), CNewCleanup_imp::x_GeneGBQualBC(), and CGtfReader::xFeatureSetDataGene().

◆ ~CGene_nomenclature()

CGene_nomenclature::~CGene_nomenclature ( void )

Definition at line 50 of file Gene_nomenclature.cpp.

◆ ~CGene_nomenclature_Base()

CGene_nomenclature_Base::~CGene_nomenclature_Base ( void )

virtual

Definition at line 119 of file Gene_nomenclature_.cpp.

◆ ~CGene_ref_Base()

CGene_ref_Base::~CGene_ref_Base ( void )

virtual

Definition at line 150 of file Gene_ref_.cpp.

Variable Documentation

◆ m_Allele

string CGene_ref_Base::m_Allele

private

Definition at line 473 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetAllele(), CGene_ref_Base::ResetAllele(), and CGene_ref_Base::SetAllele().

◆ m_Db

vector< CRef< CDbtag > > CGene_ref_Base::m_Db

private

Definition at line 477 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetDb(), CGene_ref_Base::ResetDb(), and CGene_ref_Base::SetDb().

◆ m_Desc

string CGene_ref_Base::m_Desc

private

Definition at line 474 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetDesc(), CGene_ref_Base::ResetDesc(), and CGene_ref_Base::SetDesc().

◆ m_Formal_name

CRef< TFormal_name > CGene_ref_Base::m_Formal_name

private

Definition at line 480 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetFormal_name(), CGene_ref_Base::IsSetFormal_name(), CGene_ref_Base::ResetFormal_name(), and CGene_ref_Base::SetFormal_name().

◆ m_Locus

string CGene_ref_Base::m_Locus

private

Definition at line 472 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetLocus(), CGene_ref_Base::ResetLocus(), and CGene_ref_Base::SetLocus().

◆ m_Locus_tag

string CGene_ref_Base::m_Locus_tag

private

Definition at line 479 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::ResetLocus_tag(), and CGene_ref_Base::SetLocus_tag().

◆ m_Maploc

string CGene_ref_Base::m_Maploc

private

Definition at line 475 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetMaploc(), CGene_ref_Base::ResetMaploc(), and CGene_ref_Base::SetMaploc().

◆ m_Name

string CGene_nomenclature_Base::m_Name

private

Definition at line 279 of file Gene_nomenclature_.hpp.

Referenced by CGene_nomenclature_Base::GetName(), CGene_nomenclature_Base::ResetName(), and CGene_nomenclature_Base::SetName().

◆ m_Pseudo

bool CGene_ref_Base::m_Pseudo

private

Definition at line 476 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetPseudo(), CGene_ref_Base::ResetPseudo(), and CGene_ref_Base::SetPseudo().

◆ m_set_State [1/2]

Uint4 CGene_nomenclature_Base::m_set_State[1]

private

Definition at line 276 of file Gene_nomenclature_.hpp.

Referenced by CGene_nomenclature_Base::CGene_nomenclature_Base(), CGene_nomenclature_Base::IsSetName(), CGene_nomenclature_Base::IsSetStatus(), CGene_nomenclature_Base::IsSetSymbol(), CGene_nomenclature_Base::ResetName(), CGene_nomenclature_Base::ResetStatus(), CGene_nomenclature_Base::ResetSymbol(), CGene_nomenclature_Base::SetName(), CGene_nomenclature_Base::SetStatus(), and CGene_nomenclature_Base::SetSymbol().

◆ m_set_State [2/2]

Uint4 CGene_ref_Base::m_set_State[1]

private

◆ m_Source

CRef< TSource > CGene_nomenclature_Base::m_Source

private

Definition at line 280 of file Gene_nomenclature_.hpp.

Referenced by CGene_nomenclature_Base::GetSource(), CGene_nomenclature_Base::IsSetSource(), CGene_nomenclature_Base::ResetSource(), and CGene_nomenclature_Base::SetSource().

◆ m_Status

EStatus CGene_nomenclature_Base::m_Status

private

Definition at line 277 of file Gene_nomenclature_.hpp.

Referenced by CGene_nomenclature_Base::GetStatus(), CGene_nomenclature_Base::ResetStatus(), and CGene_nomenclature_Base::SetStatus().

◆ m_Symbol

string CGene_nomenclature_Base::m_Symbol

private

Definition at line 278 of file Gene_nomenclature_.hpp.

Referenced by CGene_nomenclature_Base::GetSymbol(), CGene_nomenclature_Base::ResetSymbol(), and CGene_nomenclature_Base::SetSymbol().

◆ m_Syn

list< string > CGene_ref_Base::m_Syn

private

Definition at line 478 of file Gene_ref_.hpp.

Referenced by CGene_ref_Base::GetSyn(), CGene_ref_Base::ResetSyn(), and CGene_ref_Base::SetSyn().

Enumerations
enum	CGene_nomenclature_Base::EStatus { CGene_nomenclature_Base::eStatus_unknown = 0 , CGene_nomenclature_Base::eStatus_official = 1 , CGene_nomenclature_Base::eStatus_interim = 2 }

enum class	CGene_nomenclature_Base::E_memberIndex { CGene_nomenclature_Base::e__allMandatory = 0 , CGene_nomenclature_Base::e_status , CGene_nomenclature_Base::e_symbol , CGene_nomenclature_Base::e_name , CGene_nomenclature_Base::e_source }

enum class	CGene_ref_Base::E_memberIndex { CGene_ref_Base::e__allMandatory = 0 , CGene_ref_Base::e_locus , CGene_ref_Base::e_allele , CGene_ref_Base::e_desc , CGene_ref_Base::e_maploc , CGene_ref_Base::e_pseudo , CGene_ref_Base::e_db , CGene_ref_Base::e_syn , CGene_ref_Base::e_locus_tag , CGene_ref_Base::e_formal_name }

Variables
Uint4	CGene_nomenclature_Base::m_set_State [1]

EStatus	CGene_nomenclature_Base::m_Status

string	CGene_nomenclature_Base::m_Symbol

string	CGene_nomenclature_Base::m_Name

CRef< TSource >	CGene_nomenclature_Base::m_Source

Uint4	CGene_ref_Base::m_set_State [1]

string	CGene_ref_Base::m_Locus

string	CGene_ref_Base::m_Allele

string	CGene_ref_Base::m_Desc

string	CGene_ref_Base::m_Maploc

bool	CGene_ref_Base::m_Pseudo

vector< CRef< CDbtag > >	CGene_ref_Base::m_Db

list< string >	CGene_ref_Base::m_Syn

string	CGene_ref_Base::m_Locus_tag

CRef< TFormal_name >	CGene_ref_Base::m_Formal_name

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ TAllele

◆ TDb

◆ TDesc

◆ TFormal_name

◆ TLocus

◆ TLocus_tag

◆ TMaploc

◆ TmemberIndex [1/2]

◆ TmemberIndex [2/2]

◆ TName

◆ Tparent [1/3]

◆ Tparent [2/3]

◆ Tparent [3/3]

◆ TPseudo

◆ TSource

◆ TStatus

◆ TSymbol

◆ TSyn

Enumeration Type Documentation

◆ E_memberIndex [1/2]

◆ E_memberIndex [2/2]

◆ EStatus

Function Documentation

◆ CanGetAllele()

◆ CanGetDb()

◆ CanGetDesc()

◆ CanGetFormal_name()

◆ CanGetLocus()

◆ CanGetLocus_tag()

◆ CanGetMaploc()

◆ CanGetName()

◆ CanGetPseudo()

◆ CanGetSource()

◆ CanGetStatus()

◆ CanGetSymbol()

◆ CanGetSyn()

◆ CGene_nomenclature() [1/2]

◆ CGene_nomenclature() [2/2]

◆ CGene_nomenclature_Base() [1/2]

◆ CGene_nomenclature_Base() [2/2]

◆ CGene_ref_Base() [1/2]

◆ CGene_ref_Base() [2/2]

◆ DECLARE_INTERNAL_TYPE_INFO() [1/2]

◆ DECLARE_INTERNAL_TYPE_INFO() [2/2]

◆ EStatus()

◆ GetAllele()

◆ GetDb()

◆ GetDesc()

◆ GetFormal_name()

◆ GetLocus()

◆ GetLocus_tag()

◆ GetMaploc()

◆ GetName()

◆ GetPseudo()

◆ GetSource()

◆ GetStatus()

◆ GetSymbol()

◆ GetSyn()

◆ IsSetAllele()

◆ IsSetDb()

◆ IsSetDesc()

◆ IsSetFormal_name()

◆ IsSetLocus()

◆ IsSetLocus_tag()

◆ IsSetMaploc()

◆ IsSetName()

◆ IsSetPseudo()

◆ IsSetSource()

◆ IsSetStatus()

◆ IsSetSymbol()

◆ IsSetSyn()

◆ operator=() [1/3]

◆ operator=() [2/3]