Code generated by DATATOOL from 'seqfeat.asn' (module 'NCBI-Organism')

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

Classes
class	CBinomialOrgName
	CBinomialOrgName –. More...
class	CBinomialOrgName_Base
	CBinomialOrgName_Base –. More...
class	CMultiOrgName
	CMultiOrgName –. More...
class	CMultiOrgName_Base
	the first will be used to assign division More...
class	COrg_ref_Base
	*** Org-ref *********************************************** * * Reference to an organism * defines only the organism. More...
class	COrgMod_Base
	COrgMod_Base –. More...
class	COrgName_Base
	COrgName_Base –. More...
class	COrgName_Base::C_Name
	C_Name –. More...
class	CPartialOrgName
	CPartialOrgName –. More...
class	CPartialOrgName_Base
	when we don't know the genus More...
class	CTaxElement
	CTaxElement –. More...
class	CTaxElement_Base
	CTaxElement_Base –. More...

Typedefs
typedef CBinomialOrgName_Base	CBinomialOrgName::Tparent
typedef CSerialObject	CBinomialOrgName_Base::Tparent
typedef string	CBinomialOrgName_Base::TGenus
typedef string	CBinomialOrgName_Base::TSpecies
typedef string	CBinomialOrgName_Base::TSubspecies
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	CBinomialOrgName_Base::TmemberIndex
typedef CMultiOrgName_Base	CMultiOrgName::Tparent
typedef CSerialObject	CMultiOrgName_Base::Tparent
typedef list< CRef< COrgName > >	CMultiOrgName_Base::Tdata
typedef CSerialObject	COrg_ref_Base::Tparent
typedef string	COrg_ref_Base::TTaxname
typedef string	COrg_ref_Base::TCommon
typedef list< string >	COrg_ref_Base::TMod
typedef vector< CRef< CDbtag > >	COrg_ref_Base::TDb
typedef list< string >	COrg_ref_Base::TSyn
typedef COrgName	COrg_ref_Base::TOrgname
typedef Tparent::CMemberIndex< E_memberIndex, 7 >	COrg_ref_Base::TmemberIndex
typedef CSerialObject	COrgMod_Base::Tparent
typedef int	COrgMod_Base::TSubtype
typedef string	COrgMod_Base::TSubname
typedef string	COrgMod_Base::TAttrib
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	COrgMod_Base::TmemberIndex
typedef CSerialObject	COrgName_Base::Tparent
typedef CSerialObject	COrgName_Base::C_Name::Tparent
typedef CBinomialOrgName	COrgName_Base::C_Name::TBinomial
typedef string	COrgName_Base::C_Name::TVirus
typedef CMultiOrgName	COrgName_Base::C_Name::THybrid
typedef CBinomialOrgName	COrgName_Base::C_Name::TNamedhybrid
typedef CPartialOrgName	COrgName_Base::C_Name::TPartial
typedef C_Name	COrgName_Base::TName
typedef string	COrgName_Base::TAttrib
typedef list< CRef< COrgMod > >	COrgName_Base::TMod
typedef string	COrgName_Base::TLineage
typedef int	COrgName_Base::TGcode
typedef int	COrgName_Base::TMgcode
typedef string	COrgName_Base::TDiv
typedef int	COrgName_Base::TPgcode
typedef Tparent::CMemberIndex< E_memberIndex, 9 >	COrgName_Base::TmemberIndex
typedef CPartialOrgName_Base	CPartialOrgName::Tparent
typedef CSerialObject	CPartialOrgName_Base::Tparent
typedef list< CRef< CTaxElement > >	CPartialOrgName_Base::Tdata
typedef CTaxElement_Base	CTaxElement::Tparent
typedef CSerialObject	CTaxElement_Base::Tparent
typedef int	CTaxElement_Base::TFixed_level
typedef string	CTaxElement_Base::TLevel
typedef string	CTaxElement_Base::TName
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	CTaxElement_Base::TmemberIndex

Enumerations
enum class	CBinomialOrgName_Base::E_memberIndex { CBinomialOrgName_Base::e__allMandatory = 0 , CBinomialOrgName_Base::e_genus , CBinomialOrgName_Base::e_species , CBinomialOrgName_Base::e_subspecies }
enum class	COrg_ref_Base::E_memberIndex {   COrg_ref_Base::e__allMandatory = 0 , COrg_ref_Base::e_taxname , COrg_ref_Base::e_common , COrg_ref_Base::e_mod ,   COrg_ref_Base::e_db , COrg_ref_Base::e_syn , COrg_ref_Base::e_orgname }
enum	COrgMod_Base::ESubtype {   COrgMod_Base::eSubtype_strain = 2 , COrgMod_Base::eSubtype_substrain = 3 , COrgMod_Base::eSubtype_type = 4 , COrgMod_Base::eSubtype_subtype = 5 ,   COrgMod_Base::eSubtype_variety = 6 , COrgMod_Base::eSubtype_serotype = 7 , COrgMod_Base::eSubtype_serogroup = 8 , COrgMod_Base::eSubtype_serovar = 9 ,   COrgMod_Base::eSubtype_cultivar = 10 , COrgMod_Base::eSubtype_pathovar = 11 , COrgMod_Base::eSubtype_chemovar = 12 , COrgMod_Base::eSubtype_biovar = 13 ,   COrgMod_Base::eSubtype_biotype = 14 , COrgMod_Base::eSubtype_group = 15 , COrgMod_Base::eSubtype_subgroup = 16 , COrgMod_Base::eSubtype_isolate = 17 ,   COrgMod_Base::eSubtype_common = 18 , COrgMod_Base::eSubtype_acronym = 19 , COrgMod_Base::eSubtype_dosage = 20 , COrgMod_Base::eSubtype_nat_host = 21 ,   COrgMod_Base::eSubtype_sub_species = 22 , COrgMod_Base::eSubtype_specimen_voucher = 23 , COrgMod_Base::eSubtype_authority = 24 , COrgMod_Base::eSubtype_forma = 25 ,   COrgMod_Base::eSubtype_forma_specialis = 26 , COrgMod_Base::eSubtype_ecotype = 27 , COrgMod_Base::eSubtype_synonym = 28 , COrgMod_Base::eSubtype_anamorph = 29 ,   COrgMod_Base::eSubtype_teleomorph = 30 , COrgMod_Base::eSubtype_breed = 31 , COrgMod_Base::eSubtype_gb_acronym = 32 , COrgMod_Base::eSubtype_gb_anamorph = 33 ,   COrgMod_Base::eSubtype_gb_synonym = 34 , COrgMod_Base::eSubtype_culture_collection = 35 , COrgMod_Base::eSubtype_bio_material = 36 , COrgMod_Base::eSubtype_metagenome_source = 37 ,   COrgMod_Base::eSubtype_type_material = 38 , COrgMod_Base::eSubtype_nomenclature = 39 , COrgMod_Base::eSubtype_old_lineage = 253 , COrgMod_Base::eSubtype_old_name = 254 ,   COrgMod_Base::eSubtype_other = 255 }
enum class	COrgMod_Base::E_memberIndex { COrgMod_Base::e__allMandatory = 0 , COrgMod_Base::e_subtype , COrgMod_Base::e_subname , COrgMod_Base::e_attrib }
enum	COrgName_Base::C_Name::E_Choice {   COrgName_Base::C_Name::e_not_set = 0 , COrgName_Base::C_Name::e_Binomial , COrgName_Base::C_Name::e_Virus , COrgName_Base::C_Name::e_Hybrid ,   COrgName_Base::C_Name::e_Namedhybrid , COrgName_Base::C_Name::e_Partial }
	Choice variants. More...
enum	COrgName_Base::C_Name::E_ChoiceStopper { COrgName_Base::C_Name::e_MaxChoice = 6 }
	Maximum+1 value of the choice variant enumerator. More...
enum class	COrgName_Base::E_memberIndex {   COrgName_Base::e__allMandatory = 0 , COrgName_Base::e_name , COrgName_Base::e_attrib , COrgName_Base::e_mod ,   COrgName_Base::e_lineage , COrgName_Base::e_gcode , COrgName_Base::e_mgcode , COrgName_Base::e_div ,   COrgName_Base::e_pgcode }
enum	CTaxElement_Base::EFixed_level { CTaxElement_Base::eFixed_level_other = 0 , CTaxElement_Base::eFixed_level_family = 1 , CTaxElement_Base::eFixed_level_order = 2 , CTaxElement_Base::eFixed_level_class = 3 }
enum class	CTaxElement_Base::E_memberIndex { CTaxElement_Base::e__allMandatory = 0 , CTaxElement_Base::e_fixed_level , CTaxElement_Base::e_level , CTaxElement_Base::e_name }

Functions
	CBinomialOrgName::CBinomialOrgName (void)
	CBinomialOrgName::~CBinomialOrgName (void)
	CBinomialOrgName::CBinomialOrgName (const CBinomialOrgName &value)
CBinomialOrgName &	CBinomialOrgName::operator= (const CBinomialOrgName &value)
	CBinomialOrgName_Base::CBinomialOrgName_Base (void)
virtual	CBinomialOrgName_Base::~CBinomialOrgName_Base (void)
	CBinomialOrgName_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CBinomialOrgName_Base::IsSetGenus (void) const
	required Check if a value has been assigned to Genus data member. More...
bool	CBinomialOrgName_Base::CanGetGenus (void) const
	Check if it is safe to call GetGenus method. More...
void	CBinomialOrgName_Base::ResetGenus (void)
	Reset Genus data member. More...
const TGenus &	CBinomialOrgName_Base::GetGenus (void) const
	Get the Genus member data. More...
void	CBinomialOrgName_Base::SetGenus (const TGenus &value)
	Assign a value to Genus data member. More...
void	CBinomialOrgName_Base::SetGenus (TGenus &&value)
TGenus &	CBinomialOrgName_Base::SetGenus (void)
	Assign a value to Genus data member. More...
bool	CBinomialOrgName_Base::IsSetSpecies (void) const
	species required if subspecies used Check if a value has been assigned to Species data member. More...
bool	CBinomialOrgName_Base::CanGetSpecies (void) const
	Check if it is safe to call GetSpecies method. More...
void	CBinomialOrgName_Base::ResetSpecies (void)
	Reset Species data member. More...
const TSpecies &	CBinomialOrgName_Base::GetSpecies (void) const
	Get the Species member data. More...
void	CBinomialOrgName_Base::SetSpecies (const TSpecies &value)
	Assign a value to Species data member. More...
void	CBinomialOrgName_Base::SetSpecies (TSpecies &&value)
TSpecies &	CBinomialOrgName_Base::SetSpecies (void)
	Assign a value to Species data member. More...
bool	CBinomialOrgName_Base::IsSetSubspecies (void) const
	Check if a value has been assigned to Subspecies data member. More...
bool	CBinomialOrgName_Base::CanGetSubspecies (void) const
	Check if it is safe to call GetSubspecies method. More...
void	CBinomialOrgName_Base::ResetSubspecies (void)
	Reset Subspecies data member. More...
const TSubspecies &	CBinomialOrgName_Base::GetSubspecies (void) const
	Get the Subspecies member data. More...
void	CBinomialOrgName_Base::SetSubspecies (const TSubspecies &value)
	Assign a value to Subspecies data member. More...
void	CBinomialOrgName_Base::SetSubspecies (TSubspecies &&value)
TSubspecies &	CBinomialOrgName_Base::SetSubspecies (void)
	Assign a value to Subspecies data member. More...
virtual void	CBinomialOrgName_Base::Reset (void)
	Reset the whole object. More...
	CBinomialOrgName_Base::CBinomialOrgName_Base (const CBinomialOrgName_Base &)
CBinomialOrgName_Base &	CBinomialOrgName_Base::operator= (const CBinomialOrgName_Base &)
	CMultiOrgName::CMultiOrgName (void)
	CMultiOrgName::~CMultiOrgName (void)
	CMultiOrgName::CMultiOrgName (const CMultiOrgName &value)
CMultiOrgName &	CMultiOrgName::operator= (const CMultiOrgName &value)
	CMultiOrgName_Base::CMultiOrgName_Base (void)
virtual	CMultiOrgName_Base::~CMultiOrgName_Base (void)
	CMultiOrgName_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CMultiOrgName_Base::IsSet (void) const
	Check if a value has been assigned to data member. More...
bool	CMultiOrgName_Base::CanGet (void) const
	Check if it is safe to call Get method. More...
void	CMultiOrgName_Base::Reset (void)
	Reset data member. More...
const Tdata &	CMultiOrgName_Base::Get (void) const
	Get the member data. More...
Tdata &	CMultiOrgName_Base::Set (void)
	Assign a value to data member. More...
	CMultiOrgName_Base::operator const Tdata & (void) const
	Conversion operator to 'const Tdata' type. More...
	CMultiOrgName_Base::operator Tdata & (void)
	Conversion operator to 'Tdata' type. More...
	CMultiOrgName_Base::CMultiOrgName_Base (const CMultiOrgName_Base &)
CMultiOrgName_Base &	CMultiOrgName_Base::operator= (const CMultiOrgName_Base &)
	COrg_ref_Base::COrg_ref_Base (void)
virtual	COrg_ref_Base::~COrg_ref_Base (void)
	COrg_ref_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	COrg_ref_Base::IsSetTaxname (void) const
	preferred formal name Check if a value has been assigned to Taxname data member. More...
bool	COrg_ref_Base::CanGetTaxname (void) const
	Check if it is safe to call GetTaxname method. More...
void	COrg_ref_Base::ResetTaxname (void)
	Reset Taxname data member. More...
const TTaxname &	COrg_ref_Base::GetTaxname (void) const
	Get the Taxname member data. More...
void	COrg_ref_Base::SetTaxname (const TTaxname &value)
	Assign a value to Taxname data member. More...
void	COrg_ref_Base::SetTaxname (TTaxname &&value)
TTaxname &	COrg_ref_Base::SetTaxname (void)
	Assign a value to Taxname data member. More...
bool	COrg_ref_Base::IsSetCommon (void) const
	common name Check if a value has been assigned to Common data member. More...
bool	COrg_ref_Base::CanGetCommon (void) const
	Check if it is safe to call GetCommon method. More...
void	COrg_ref_Base::ResetCommon (void)
	Reset Common data member. More...
const TCommon &	COrg_ref_Base::GetCommon (void) const
	Get the Common member data. More...
void	COrg_ref_Base::SetCommon (const TCommon &value)
	Assign a value to Common data member. More...
void	COrg_ref_Base::SetCommon (TCommon &&value)
TCommon &	COrg_ref_Base::SetCommon (void)
	Assign a value to Common data member. More...
bool	COrg_ref_Base::IsSetMod (void) const
	unstructured modifiers Check if a value has been assigned to Mod data member. More...
bool	COrg_ref_Base::CanGetMod (void) const
	Check if it is safe to call GetMod method. More...
void	COrg_ref_Base::ResetMod (void)
	Reset Mod data member. More...
const TMod &	COrg_ref_Base::GetMod (void) const
	Get the Mod member data. More...
TMod &	COrg_ref_Base::SetMod (void)
	Assign a value to Mod data member. More...
bool	COrg_ref_Base::IsSetDb (void) const
	ids in taxonomic or culture dbases Check if a value has been assigned to Db data member. More...
bool	COrg_ref_Base::CanGetDb (void) const
	Check if it is safe to call GetDb method. More...
void	COrg_ref_Base::ResetDb (void)
	Reset Db data member. More...
const TDb &	COrg_ref_Base::GetDb (void) const
	Get the Db member data. More...
TDb &	COrg_ref_Base::SetDb (void)
	Assign a value to Db data member. More...
bool	COrg_ref_Base::IsSetSyn (void) const
	synonyms for taxname or common Check if a value has been assigned to Syn data member. More...
bool	COrg_ref_Base::CanGetSyn (void) const
	Check if it is safe to call GetSyn method. More...
void	COrg_ref_Base::ResetSyn (void)
	Reset Syn data member. More...
const TSyn &	COrg_ref_Base::GetSyn (void) const
	Get the Syn member data. More...
TSyn &	COrg_ref_Base::SetSyn (void)
	Assign a value to Syn data member. More...
bool	COrg_ref_Base::IsSetOrgname (void) const
	Check if a value has been assigned to Orgname data member. More...
bool	COrg_ref_Base::CanGetOrgname (void) const
	Check if it is safe to call GetOrgname method. More...
void	COrg_ref_Base::ResetOrgname (void)
	Reset Orgname data member. More...
const TOrgname &	COrg_ref_Base::GetOrgname (void) const
	Get the Orgname member data. More...
void	COrg_ref_Base::SetOrgname (TOrgname &value)
	Assign a value to Orgname data member. More...
TOrgname &	COrg_ref_Base::SetOrgname (void)
	Assign a value to Orgname data member. More...
virtual void	COrg_ref_Base::Reset (void)
	Reset the whole object. More...
	COrg_ref_Base::COrg_ref_Base (const COrg_ref_Base &)
COrg_ref_Base &	COrg_ref_Base::operator= (const COrg_ref_Base &)
	COrgMod_Base::COrgMod_Base (void)
virtual	COrgMod_Base::~COrgMod_Base (void)
	COrgMod_Base::DECLARE_INTERNAL_TYPE_INFO ()
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	COrgMod_Base::ESubtype (void)
	Access to ESubtype's attributes (values, names) as defined in spec. More...
bool	COrgMod_Base::IsSetSubtype (void) const
	Check if a value has been assigned to Subtype data member. More...
bool	COrgMod_Base::CanGetSubtype (void) const
	Check if it is safe to call GetSubtype method. More...
void	COrgMod_Base::ResetSubtype (void)
	Reset Subtype data member. More...
TSubtype	COrgMod_Base::GetSubtype (void) const
	Get the Subtype member data. More...
void	COrgMod_Base::SetSubtype (TSubtype value)
	Assign a value to Subtype data member. More...
TSubtype &	COrgMod_Base::SetSubtype (void)
	Assign a value to Subtype data member. More...
bool	COrgMod_Base::IsSetSubname (void) const
	Check if a value has been assigned to Subname data member. More...
bool	COrgMod_Base::CanGetSubname (void) const
	Check if it is safe to call GetSubname method. More...
void	COrgMod_Base::ResetSubname (void)
	Reset Subname data member. More...
const TSubname &	COrgMod_Base::GetSubname (void) const
	Get the Subname member data. More...
void	COrgMod_Base::SetSubname (const TSubname &value)
	Assign a value to Subname data member. More...
void	COrgMod_Base::SetSubname (TSubname &&value)
TSubname &	COrgMod_Base::SetSubname (void)
	Assign a value to Subname data member. More...
bool	COrgMod_Base::IsSetAttrib (void) const
	attribution/source of name Check if a value has been assigned to Attrib data member. More...
bool	COrgMod_Base::CanGetAttrib (void) const
	Check if it is safe to call GetAttrib method. More...
void	COrgMod_Base::ResetAttrib (void)
	Reset Attrib data member. More...
const TAttrib &	COrgMod_Base::GetAttrib (void) const
	Get the Attrib member data. More...
void	COrgMod_Base::SetAttrib (const TAttrib &value)
	Assign a value to Attrib data member. More...
void	COrgMod_Base::SetAttrib (TAttrib &&value)
TAttrib &	COrgMod_Base::SetAttrib (void)
	Assign a value to Attrib data member. More...
virtual void	COrgMod_Base::Reset (void)
	Reset the whole object. More...
	COrgMod_Base::COrgMod_Base (const COrgMod_Base &)
COrgMod_Base &	COrgMod_Base::operator= (const COrgMod_Base &)
	COrgName_Base::COrgName_Base (void)
virtual	COrgName_Base::~COrgName_Base (void)
	COrgName_Base::DECLARE_INTERNAL_TYPE_INFO ()
	COrgName_Base::C_Name::C_Name (void)
	COrgName_Base::C_Name::~C_Name (void)
	COrgName_Base::C_Name::DECLARE_INTERNAL_TYPE_INFO ()
void	COrgName_Base::C_Name::Reset (void)
	Reset the whole object. More...
void	COrgName_Base::C_Name::ResetSelection (void)
	Reset the selection (set it to e_not_set). More...
E_Choice	COrgName_Base::C_Name::Which (void) const
	Which variant is currently selected. More...
void	COrgName_Base::C_Name::CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...
void	COrgName_Base::C_Name::ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...
static string	COrgName_Base::C_Name::SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). More...
void	COrgName_Base::C_Name::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...
void	COrgName_Base::C_Name::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...
bool	COrgName_Base::C_Name::IsBinomial (void) const
	Check if variant Binomial is selected. More...
const TBinomial &	COrgName_Base::C_Name::GetBinomial (void) const
	Get the variant data. More...
TBinomial &	COrgName_Base::C_Name::SetBinomial (void)
	Select the variant. More...
void	COrgName_Base::C_Name::SetBinomial (TBinomial &value)
	Select the variant and set its data. More...
bool	COrgName_Base::C_Name::IsVirus (void) const
	Check if variant Virus is selected. More...
const TVirus &	COrgName_Base::C_Name::GetVirus (void) const
	Get the variant data. More...
TVirus &	COrgName_Base::C_Name::SetVirus (void)
	Select the variant. More...
void	COrgName_Base::C_Name::SetVirus (const TVirus &value)
	Select the variant and set its data. More...
bool	COrgName_Base::C_Name::IsHybrid (void) const
	Check if variant Hybrid is selected. More...
const THybrid &	COrgName_Base::C_Name::GetHybrid (void) const
	Get the variant data. More...
THybrid &	COrgName_Base::C_Name::SetHybrid (void)
	Select the variant. More...
void	COrgName_Base::C_Name::SetHybrid (THybrid &value)
	Select the variant and set its data. More...
bool	COrgName_Base::C_Name::IsNamedhybrid (void) const
	Check if variant Namedhybrid is selected. More...
const TNamedhybrid &	COrgName_Base::C_Name::GetNamedhybrid (void) const
	Get the variant data. More...
TNamedhybrid &	COrgName_Base::C_Name::SetNamedhybrid (void)
	Select the variant. More...
void	COrgName_Base::C_Name::SetNamedhybrid (TNamedhybrid &value)
	Select the variant and set its data. More...
bool	COrgName_Base::C_Name::IsPartial (void) const
	Check if variant Partial is selected. More...
const TPartial &	COrgName_Base::C_Name::GetPartial (void) const
	Get the variant data. More...
TPartial &	COrgName_Base::C_Name::SetPartial (void)
	Select the variant. More...
void	COrgName_Base::C_Name::SetPartial (TPartial &value)
	Select the variant and set its data. More...
	COrgName_Base::C_Name::C_Name (const C_Name &)
C_Name &	COrgName_Base::C_Name::operator= (const C_Name &)
void	COrgName_Base::C_Name::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
bool	COrgName_Base::IsSetName (void) const
	Check if a value has been assigned to Name data member. More...
bool	COrgName_Base::CanGetName (void) const
	Check if it is safe to call GetName method. More...
void	COrgName_Base::ResetName (void)
	Reset Name data member. More...
const TName &	COrgName_Base::GetName (void) const
	Get the Name member data. More...
void	COrgName_Base::SetName (TName &value)
	Assign a value to Name data member. More...
TName &	COrgName_Base::SetName (void)
	Assign a value to Name data member. More...
bool	COrgName_Base::IsSetAttrib (void) const
	attribution of name Check if a value has been assigned to Attrib data member. More...
bool	COrgName_Base::CanGetAttrib (void) const
	Check if it is safe to call GetAttrib method. More...
void	COrgName_Base::ResetAttrib (void)
	Reset Attrib data member. More...
const TAttrib &	COrgName_Base::GetAttrib (void) const
	Get the Attrib member data. More...
void	COrgName_Base::SetAttrib (const TAttrib &value)
	Assign a value to Attrib data member. More...
void	COrgName_Base::SetAttrib (TAttrib &&value)
TAttrib &	COrgName_Base::SetAttrib (void)
	Assign a value to Attrib data member. More...
bool	COrgName_Base::IsSetMod (void) const
	Check if a value has been assigned to Mod data member. More...
bool	COrgName_Base::CanGetMod (void) const
	Check if it is safe to call GetMod method. More...
void	COrgName_Base::ResetMod (void)
	Reset Mod data member. More...
const TMod &	COrgName_Base::GetMod (void) const
	Get the Mod member data. More...
TMod &	COrgName_Base::SetMod (void)
	Assign a value to Mod data member. More...
bool	COrgName_Base::IsSetLineage (void) const
	lineage with semicolon separators Check if a value has been assigned to Lineage data member. More...
bool	COrgName_Base::CanGetLineage (void) const
	Check if it is safe to call GetLineage method. More...
void	COrgName_Base::ResetLineage (void)
	Reset Lineage data member. More...
const TLineage &	COrgName_Base::GetLineage (void) const
	Get the Lineage member data. More...
void	COrgName_Base::SetLineage (const TLineage &value)
	Assign a value to Lineage data member. More...
void	COrgName_Base::SetLineage (TLineage &&value)
TLineage &	COrgName_Base::SetLineage (void)
	Assign a value to Lineage data member. More...
bool	COrgName_Base::IsSetGcode (void) const
	genetic code (see CdRegion) Check if a value has been assigned to Gcode data member. More...
bool	COrgName_Base::CanGetGcode (void) const
	Check if it is safe to call GetGcode method. More...
void	COrgName_Base::ResetGcode (void)
	Reset Gcode data member. More...
TGcode	COrgName_Base::GetGcode (void) const
	Get the Gcode member data. More...
void	COrgName_Base::SetGcode (TGcode value)
	Assign a value to Gcode data member. More...
TGcode &	COrgName_Base::SetGcode (void)
	Assign a value to Gcode data member. More...
bool	COrgName_Base::IsSetMgcode (void) const
	mitochondrial genetic code Check if a value has been assigned to Mgcode data member. More...
bool	COrgName_Base::CanGetMgcode (void) const
	Check if it is safe to call GetMgcode method. More...
void	COrgName_Base::ResetMgcode (void)
	Reset Mgcode data member. More...
TMgcode	COrgName_Base::GetMgcode (void) const
	Get the Mgcode member data. More...
void	COrgName_Base::SetMgcode (TMgcode value)
	Assign a value to Mgcode data member. More...
TMgcode &	COrgName_Base::SetMgcode (void)
	Assign a value to Mgcode data member. More...
bool	COrgName_Base::IsSetDiv (void) const
	GenBank division code Check if a value has been assigned to Div data member. More...
bool	COrgName_Base::CanGetDiv (void) const
	Check if it is safe to call GetDiv method. More...
void	COrgName_Base::ResetDiv (void)
	Reset Div data member. More...
const TDiv &	COrgName_Base::GetDiv (void) const
	Get the Div member data. More...
void	COrgName_Base::SetDiv (const TDiv &value)
	Assign a value to Div data member. More...
void	COrgName_Base::SetDiv (TDiv &&value)
TDiv &	COrgName_Base::SetDiv (void)
	Assign a value to Div data member. More...
bool	COrgName_Base::IsSetPgcode (void) const
	plastid genetic code Check if a value has been assigned to Pgcode data member. More...
bool	COrgName_Base::CanGetPgcode (void) const
	Check if it is safe to call GetPgcode method. More...
void	COrgName_Base::ResetPgcode (void)
	Reset Pgcode data member. More...
TPgcode	COrgName_Base::GetPgcode (void) const
	Get the Pgcode member data. More...
void	COrgName_Base::SetPgcode (TPgcode value)
	Assign a value to Pgcode data member. More...
TPgcode &	COrgName_Base::SetPgcode (void)
	Assign a value to Pgcode data member. More...
virtual void	COrgName_Base::Reset (void)
	Reset the whole object. More...
	COrgName_Base::COrgName_Base (const COrgName_Base &)
COrgName_Base &	COrgName_Base::operator= (const COrgName_Base &)
	CPartialOrgName::CPartialOrgName (void)
	CPartialOrgName::~CPartialOrgName (void)
	CPartialOrgName::CPartialOrgName (const CPartialOrgName &value)
CPartialOrgName &	CPartialOrgName::operator= (const CPartialOrgName &value)
	CPartialOrgName_Base::CPartialOrgName_Base (void)
virtual	CPartialOrgName_Base::~CPartialOrgName_Base (void)
	CPartialOrgName_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CPartialOrgName_Base::IsSet (void) const
	Check if a value has been assigned to data member. More...
bool	CPartialOrgName_Base::CanGet (void) const
	Check if it is safe to call Get method. More...
void	CPartialOrgName_Base::Reset (void)
	Reset data member. More...
const Tdata &	CPartialOrgName_Base::Get (void) const
	Get the member data. More...
Tdata &	CPartialOrgName_Base::Set (void)
	Assign a value to data member. More...
	CPartialOrgName_Base::operator const Tdata & (void) const
	Conversion operator to 'const Tdata' type. More...
	CPartialOrgName_Base::operator Tdata & (void)
	Conversion operator to 'Tdata' type. More...
	CPartialOrgName_Base::CPartialOrgName_Base (const CPartialOrgName_Base &)
CPartialOrgName_Base &	CPartialOrgName_Base::operator= (const CPartialOrgName_Base &)
	CTaxElement::CTaxElement (void)
	CTaxElement::~CTaxElement (void)
	CTaxElement::CTaxElement (const CTaxElement &value)
CTaxElement &	CTaxElement::operator= (const CTaxElement &value)
	CTaxElement_Base::CTaxElement_Base (void)
virtual	CTaxElement_Base::~CTaxElement_Base (void)
	CTaxElement_Base::DECLARE_INTERNAL_TYPE_INFO ()
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	CTaxElement_Base::EFixed_level (void)
	Access to EFixed_level's attributes (values, names) as defined in spec. More...
bool	CTaxElement_Base::IsSetFixed_level (void) const
	Check if a value has been assigned to Fixed_level data member. More...
bool	CTaxElement_Base::CanGetFixed_level (void) const
	Check if it is safe to call GetFixed_level method. More...
void	CTaxElement_Base::ResetFixed_level (void)
	Reset Fixed_level data member. More...
TFixed_level	CTaxElement_Base::GetFixed_level (void) const
	Get the Fixed_level member data. More...
void	CTaxElement_Base::SetFixed_level (TFixed_level value)
	Assign a value to Fixed_level data member. More...
TFixed_level &	CTaxElement_Base::SetFixed_level (void)
	Assign a value to Fixed_level data member. More...
bool	CTaxElement_Base::IsSetLevel (void) const
	Check if a value has been assigned to Level data member. More...
bool	CTaxElement_Base::CanGetLevel (void) const
	Check if it is safe to call GetLevel method. More...
void	CTaxElement_Base::ResetLevel (void)
	Reset Level data member. More...
const TLevel &	CTaxElement_Base::GetLevel (void) const
	Get the Level member data. More...
void	CTaxElement_Base::SetLevel (const TLevel &value)
	Assign a value to Level data member. More...
void	CTaxElement_Base::SetLevel (TLevel &&value)
TLevel &	CTaxElement_Base::SetLevel (void)
	Assign a value to Level data member. More...
bool	CTaxElement_Base::IsSetName (void) const
	Check if a value has been assigned to Name data member. More...
bool	CTaxElement_Base::CanGetName (void) const
	Check if it is safe to call GetName method. More...
void	CTaxElement_Base::ResetName (void)
	Reset Name data member. More...
const TName &	CTaxElement_Base::GetName (void) const
	Get the Name member data. More...
void	CTaxElement_Base::SetName (const TName &value)
	Assign a value to Name data member. More...
void	CTaxElement_Base::SetName (TName &&value)
TName &	CTaxElement_Base::SetName (void)
	Assign a value to Name data member. More...
virtual void	CTaxElement_Base::Reset (void)
	Reset the whole object. More...
	CTaxElement_Base::CTaxElement_Base (const CTaxElement_Base &)
CTaxElement_Base &	CTaxElement_Base::operator= (const CTaxElement_Base &)

Variables
Uint4	CBinomialOrgName_Base::m_set_State [1]
string	CBinomialOrgName_Base::m_Genus
string	CBinomialOrgName_Base::m_Species
string	CBinomialOrgName_Base::m_Subspecies
Uint4	CMultiOrgName_Base::m_set_State [1]
list< CRef< COrgName > >	CMultiOrgName_Base::m_data
Uint4	COrg_ref_Base::m_set_State [1]
string	COrg_ref_Base::m_Taxname
string	COrg_ref_Base::m_Common
list< string >	COrg_ref_Base::m_Mod
vector< CRef< CDbtag > >	COrg_ref_Base::m_Db
list< string >	COrg_ref_Base::m_Syn
CRef< TOrgname >	COrg_ref_Base::m_Orgname
Uint4	COrgMod_Base::m_set_State [1]
int	COrgMod_Base::m_Subtype
string	COrgMod_Base::m_Subname
string	COrgMod_Base::m_Attrib
E_Choice	COrgName_Base::C_Name::m_choice
static const char *const	COrgName_Base::C_Name::sm_SelectionNames []
NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string >   COrgName_Base::C_Name::m_string
NCBI_NS_NCBI::CSerialObject *   COrgName_Base::C_Name::m_object
union {
NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string >   COrgName_Base::C_Name::m_string
NCBI_NS_NCBI::CSerialObject *   COrgName_Base::C_Name::m_object
};
Uint4	COrgName_Base::m_set_State [1]
CRef< TName >	COrgName_Base::m_Name
string	COrgName_Base::m_Attrib
list< CRef< COrgMod > >	COrgName_Base::m_Mod
string	COrgName_Base::m_Lineage
int	COrgName_Base::m_Gcode
int	COrgName_Base::m_Mgcode
string	COrgName_Base::m_Div
int	COrgName_Base::m_Pgcode
Uint4	CPartialOrgName_Base::m_set_State [1]
list< CRef< CTaxElement > >	CPartialOrgName_Base::m_data
Uint4	CTaxElement_Base::m_set_State [1]
int	CTaxElement_Base::m_Fixed_level
string	CTaxElement_Base::m_Level
string	CTaxElement_Base::m_Name

Detailed Description

Typedef Documentation

TAttrib [1/2]

typedef string COrgMod_Base::TAttrib

Definition at line 134 of file OrgMod_.hpp.

TAttrib [2/2]

typedef string COrgName_Base::TAttrib

Definition at line 331 of file OrgName_.hpp.

TBinomial

typedef CBinomialOrgName COrgName_Base::C_Name::TBinomial

Definition at line 172 of file OrgName_.hpp.

TCommon

typedef string COrg_ref_Base::TCommon

Definition at line 99 of file Org_ref_.hpp.

Tdata [1/2]

typedef list< CRef< COrgName > > CMultiOrgName_Base::Tdata

Definition at line 90 of file MultiOrgName_.hpp.

Tdata [2/2]

typedef list< CRef< CTaxElement > > CPartialOrgName_Base::Tdata

Definition at line 90 of file PartialOrgName_.hpp.

TDb

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

Definition at line 101 of file Org_ref_.hpp.

TDiv

typedef string COrgName_Base::TDiv

Definition at line 336 of file OrgName_.hpp.

TFixed_level

typedef int CTaxElement_Base::TFixed_level

Definition at line 95 of file TaxElement_.hpp.

TGcode

typedef int COrgName_Base::TGcode

Definition at line 334 of file OrgName_.hpp.

TGenus

typedef string CBinomialOrgName_Base::TGenus

Definition at line 85 of file BinomialOrgName_.hpp.

THybrid

typedef CMultiOrgName COrgName_Base::C_Name::THybrid

Definition at line 174 of file OrgName_.hpp.

TLevel

typedef string CTaxElement_Base::TLevel

Definition at line 96 of file TaxElement_.hpp.

TLineage

typedef string COrgName_Base::TLineage

Definition at line 333 of file OrgName_.hpp.

TmemberIndex [1/5]

typedef Tparent::CMemberIndex<E_memberIndex, 4> CBinomialOrgName_Base::TmemberIndex

Definition at line 96 of file BinomialOrgName_.hpp.

TmemberIndex [2/5]

typedef Tparent::CMemberIndex<E_memberIndex, 7> COrg_ref_Base::TmemberIndex

Definition at line 115 of file Org_ref_.hpp.

TmemberIndex [3/5]

typedef Tparent::CMemberIndex<E_memberIndex, 4> COrgMod_Base::TmemberIndex

Definition at line 143 of file OrgMod_.hpp.

TmemberIndex [4/5]

typedef Tparent::CMemberIndex<E_memberIndex, 9> COrgName_Base::TmemberIndex

Definition at line 351 of file OrgName_.hpp.

TmemberIndex [5/5]

typedef Tparent::CMemberIndex<E_memberIndex, 4> CTaxElement_Base::TmemberIndex

Definition at line 106 of file TaxElement_.hpp.

TMgcode

typedef int COrgName_Base::TMgcode

Definition at line 335 of file OrgName_.hpp.

TMod [1/2]

typedef list< string > COrg_ref_Base::TMod

Definition at line 100 of file Org_ref_.hpp.

TMod [2/2]

typedef list< CRef< COrgMod > > COrgName_Base::TMod

Definition at line 332 of file OrgName_.hpp.

TName [1/2]

typedef C_Name COrgName_Base::TName

Definition at line 330 of file OrgName_.hpp.

TName [2/2]

typedef string CTaxElement_Base::TName

Definition at line 97 of file TaxElement_.hpp.

TNamedhybrid

typedef CBinomialOrgName COrgName_Base::C_Name::TNamedhybrid

Definition at line 175 of file OrgName_.hpp.

TOrgname

typedef COrgName COrg_ref_Base::TOrgname

Definition at line 103 of file Org_ref_.hpp.

Tparent [1/12]

typedef CBinomialOrgName_Base CBinomialOrgName::Tparent

private

Definition at line 67 of file BinomialOrgName.hpp.

Tparent [2/12]

typedef CSerialObject CBinomialOrgName_Base::Tparent

private

Definition at line 74 of file BinomialOrgName_.hpp.

Tparent [3/12]

typedef CMultiOrgName_Base CMultiOrgName::Tparent

private

Definition at line 67 of file MultiOrgName.hpp.

Tparent [4/12]

typedef CSerialObject CMultiOrgName_Base::Tparent

private

Definition at line 79 of file MultiOrgName_.hpp.

Tparent [5/12]

typedef CSerialObject COrg_ref_Base::Tparent

private

Definition at line 87 of file Org_ref_.hpp.

Tparent [6/12]

typedef CSerialObject COrgMod_Base::Tparent

private

Definition at line 74 of file OrgMod_.hpp.

Tparent [7/12]

typedef CSerialObject COrgName_Base::Tparent

private

Definition at line 82 of file OrgName_.hpp.

Tparent [8/12]

typedef CSerialObject COrgName_Base::C_Name::Tparent

private

Definition at line 99 of file OrgName_.hpp.

Tparent [9/12]

typedef CPartialOrgName_Base CPartialOrgName::Tparent

private

Definition at line 67 of file PartialOrgName.hpp.

Tparent [10/12]

typedef CSerialObject CPartialOrgName_Base::Tparent

private

Definition at line 79 of file PartialOrgName_.hpp.

Tparent [11/12]

typedef CTaxElement_Base CTaxElement::Tparent

private

Definition at line 67 of file TaxElement.hpp.

Tparent [12/12]

typedef CSerialObject CTaxElement_Base::Tparent

private

Definition at line 74 of file TaxElement_.hpp.

TPartial

typedef CPartialOrgName COrgName_Base::C_Name::TPartial

Definition at line 176 of file OrgName_.hpp.

TPgcode

typedef int COrgName_Base::TPgcode

Definition at line 337 of file OrgName_.hpp.

TSpecies

typedef string CBinomialOrgName_Base::TSpecies

Definition at line 86 of file BinomialOrgName_.hpp.

TSubname

typedef string COrgMod_Base::TSubname

Definition at line 133 of file OrgMod_.hpp.

TSubspecies

typedef string CBinomialOrgName_Base::TSubspecies

Definition at line 87 of file BinomialOrgName_.hpp.

TSubtype

typedef int COrgMod_Base::TSubtype

Definition at line 132 of file OrgMod_.hpp.

TSyn

typedef list< string > COrg_ref_Base::TSyn

Definition at line 102 of file Org_ref_.hpp.

TTaxname

typedef string COrg_ref_Base::TTaxname

Definition at line 98 of file Org_ref_.hpp.

TVirus

typedef string COrgName_Base::C_Name::TVirus

Definition at line 173 of file OrgName_.hpp.

Enumeration Type Documentation

E_Choice

enum COrgName_Base::C_Name::E_Choice

Choice variants.

Enumerator
e_not_set	No variant selected.
e_Binomial	genus/species type name
e_Virus	virus names are different
e_Hybrid	hybrid between organisms
e_Namedhybrid	some hybrids have genus x species name
e_Partial	when genus not known

Definition at line 111 of file OrgName_.hpp.

E_ChoiceStopper

enum COrgName_Base::C_Name::E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice	== e_Partial+1

Definition at line 120 of file OrgName_.hpp.

E_memberIndex [1/5]

enum CBinomialOrgName_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_genus
e_species
e_subspecies

Definition at line 90 of file BinomialOrgName_.hpp.

E_memberIndex [2/5]

enum COrg_ref_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_taxname
e_common
e_mod
e_db
e_syn
e_orgname

Definition at line 106 of file Org_ref_.hpp.

E_memberIndex [3/5]

enum COrgMod_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_subtype
e_subname
e_attrib

Definition at line 137 of file OrgMod_.hpp.

E_memberIndex [4/5]

enum COrgName_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_name
e_attrib
e_mod
e_lineage
e_gcode
e_mgcode
e_div
e_pgcode

Definition at line 340 of file OrgName_.hpp.

E_memberIndex [5/5]

enum CTaxElement_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_fixed_level
e_level
e_name

Definition at line 100 of file TaxElement_.hpp.

EFixed_level

enum CTaxElement_Base::EFixed_level

Enumerator
eFixed_level_other	level must be set in string
eFixed_level_family
eFixed_level_order
eFixed_level_class

Definition at line 84 of file TaxElement_.hpp.

ESubtype

enum COrgMod_Base::ESubtype

Enumerator
eSubtype_strain
eSubtype_substrain
eSubtype_type
eSubtype_subtype
eSubtype_variety
eSubtype_serotype
eSubtype_serogroup
eSubtype_serovar
eSubtype_cultivar
eSubtype_pathovar
eSubtype_chemovar
eSubtype_biovar
eSubtype_biotype
eSubtype_group
eSubtype_subgroup
eSubtype_isolate
eSubtype_common
eSubtype_acronym
eSubtype_dosage	chromosome dosage of hybrid
eSubtype_nat_host	natural host of this specimen
eSubtype_sub_species
eSubtype_specimen_voucher
eSubtype_authority
eSubtype_forma
eSubtype_forma_specialis
eSubtype_ecotype
eSubtype_synonym
eSubtype_anamorph
eSubtype_teleomorph
eSubtype_breed
eSubtype_gb_acronym	used by taxonomy database
eSubtype_gb_anamorph	used by taxonomy database
eSubtype_gb_synonym	used by taxonomy database
eSubtype_culture_collection
eSubtype_bio_material
eSubtype_metagenome_source
eSubtype_type_material
eSubtype_nomenclature	code of nomenclature in subname (B,P,V,Z or combination)
eSubtype_old_lineage
eSubtype_old_name
eSubtype_other	ASN5: old-name (254) will be added to next spec.

Definition at line 84 of file OrgMod_.hpp.

Function Documentation

C_Name() [1/2]

COrgName_Base::C_Name::C_Name ( const C_Name &  )

private

C_Name() [2/2]

END_CHOICE_INFO COrgName_Base::C_Name::C_Name

(

void

)

Definition at line 233 of file OrgName_.cpp.

CanGet() [1/2]

bool CMultiOrgName_Base::CanGet ( void  ) const

inline

Check if it is safe to call Get method.

Returns

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

Definition at line 159 of file MultiOrgName_.hpp.

CanGet() [2/2]

bool CPartialOrgName_Base::CanGet ( void  ) const

inline

Check if it is safe to call Get method.

Returns

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

Definition at line 159 of file PartialOrgName_.hpp.

CanGetAttrib() [1/2]

bool COrgMod_Base::CanGetAttrib ( void  ) const

inline

Check if it is safe to call GetAttrib method.

Returns

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

Definition at line 388 of file OrgMod_.hpp.

References COrgMod_Base::IsSetAttrib().

Referenced by COrgMod_Base::GetAttrib().

CanGetAttrib() [2/2]

bool COrgName_Base::CanGetAttrib ( void  ) const

inline

Check if it is safe to call GetAttrib method.

Returns

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

Definition at line 786 of file OrgName_.hpp.

References COrgName_Base::IsSetAttrib().

Referenced by COrgName_Base::GetAttrib().

CanGetCommon()

bool COrg_ref_Base::CanGetCommon ( void  ) const

inline

Check if it is safe to call GetCommon method.

Returns

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

Definition at line 413 of file Org_ref_.hpp.

References COrg_ref_Base::IsSetCommon().

Referenced by COrg_ref_Base::GetCommon(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), s_GetTaxonomyInfoFromBiosrc(), and CSourceItem::x_SetSource().

CanGetDb()

bool COrg_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 485 of file Org_ref_.hpp.

Referenced by CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), and CWriteDB_Impl::x_BuildDeflinesFromBioseq().

CanGetDiv()

bool COrgName_Base::CanGetDiv ( void  ) const

inline

Check if it is safe to call GetDiv method.

Returns

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

Definition at line 999 of file OrgName_.hpp.

References COrgName_Base::IsSetDiv().

Referenced by COrgName_Base::GetDiv(), CValidError_bioseq::IsSynthetic(), UpdateRawBioSource(), x_GetDivisionProc(), and x_GetDivisionProcIdx().

CanGetFixed_level()

bool CTaxElement_Base::CanGetFixed_level ( void  ) const

inline

Check if it is safe to call GetFixed_level method.

Returns

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

Definition at line 256 of file TaxElement_.hpp.

References CTaxElement_Base::IsSetFixed_level().

Referenced by CTaxElement_Base::GetFixed_level().

CanGetGcode()

bool COrgName_Base::CanGetGcode ( void  ) const

inline

Check if it is safe to call GetGcode method.

Returns

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

Definition at line 905 of file OrgName_.hpp.

References COrgName_Base::IsSetGcode().

Referenced by COrgName_Base::GetGcode().

CanGetGenus()

bool CBinomialOrgName_Base::CanGetGenus ( void  ) const

inline

Check if it is safe to call GetGenus method.

Returns

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

Definition at line 249 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::IsSetGenus().

Referenced by CBinomialOrgName_Base::GetGenus().

CanGetLevel()

bool CTaxElement_Base::CanGetLevel ( void  ) const

inline

Check if it is safe to call GetLevel method.

Returns

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

Definition at line 303 of file TaxElement_.hpp.

References CTaxElement_Base::IsSetLevel().

Referenced by CTaxElement_Base::GetLevel().

CanGetLineage()

bool COrgName_Base::CanGetLineage ( void  ) const

inline

Check if it is safe to call GetLineage method.

Returns

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

Definition at line 858 of file OrgName_.hpp.

References COrgName_Base::IsSetLineage().

Referenced by COrgName_Base::GetLineage(), CBioseqIndex::x_InitSource(), and CSourceItem::x_SetSource().

CanGetMgcode()

bool COrgName_Base::CanGetMgcode ( void  ) const

inline

Check if it is safe to call GetMgcode method.

Returns

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

Definition at line 952 of file OrgName_.hpp.

References COrgName_Base::IsSetMgcode().

Referenced by COrgName_Base::GetMgcode().

CanGetMod() [1/2]

bool COrg_ref_Base::CanGetMod ( void  ) const

inline

Check if it is safe to call GetMod method.

Returns

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

Definition at line 460 of file Org_ref_.hpp.

CanGetMod() [2/2]

bool COrgName_Base::CanGetMod ( void  ) const

inline

Check if it is safe to call GetMod method.

Returns

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

Definition at line 833 of file OrgName_.hpp.

Referenced by CheckQualsInSourceFeat(), GetSrcQual(), s_GetOrgModNatHost(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), and CTreeBuilderJob::x_CreateProjectItems().

CanGetName() [1/2]

bool COrgName_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 765 of file OrgName_.hpp.

References COrgName_Base::IsSetName().

Referenced by COrgName_Base::GetName().

CanGetName() [2/2]

bool CTaxElement_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 350 of file TaxElement_.hpp.

References CTaxElement_Base::IsSetName().

Referenced by CTaxElement_Base::GetName().

CanGetOrgname()

bool COrg_ref_Base::CanGetOrgname ( void  ) const

inline

Check if it is safe to call GetOrgname method.

Returns

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

Definition at line 535 of file Org_ref_.hpp.

References COrg_ref_Base::IsSetOrgname().

Referenced by CheckQualsInSourceFeat(), CAutoDefSourceDescription::GetAvailableModifiers(), COrg_ref_Base::GetOrgname(), GetSrcQual(), CAutoDefSourceDescription::IsTrickyHIV(), UpdateRawBioSource(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), x_GetDivisionProc(), x_GetDivisionProcIdx(), and CSourceItem::x_SetSource().

CanGetPgcode()

bool COrgName_Base::CanGetPgcode ( void  ) const

inline

Check if it is safe to call GetPgcode method.

Returns

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

Definition at line 1046 of file OrgName_.hpp.

References COrgName_Base::IsSetPgcode().

Referenced by COrgName_Base::GetPgcode().

CanGetSpecies()

bool CBinomialOrgName_Base::CanGetSpecies ( void  ) const

inline

Check if it is safe to call GetSpecies method.

Returns

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

Definition at line 296 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::IsSetSpecies().

Referenced by CBinomialOrgName_Base::GetSpecies().

CanGetSubname()

bool COrgMod_Base::CanGetSubname ( void  ) const

inline

Check if it is safe to call GetSubname method.

Returns

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

Definition at line 341 of file OrgMod_.hpp.

References COrgMod_Base::IsSetSubname().

Referenced by COrgMod_Base::GetSubname().

CanGetSubspecies()

bool CBinomialOrgName_Base::CanGetSubspecies ( void  ) const

inline

Check if it is safe to call GetSubspecies method.

Returns

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

Definition at line 343 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::IsSetSubspecies().

Referenced by CBinomialOrgName_Base::GetSubspecies().

CanGetSubtype()

bool COrgMod_Base::CanGetSubtype ( void  ) const

inline

Check if it is safe to call GetSubtype method.

Returns

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

Definition at line 294 of file OrgMod_.hpp.

References COrgMod_Base::IsSetSubtype().

Referenced by COrgMod_Base::GetSubtype().

CanGetSyn()

bool COrg_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 510 of file Org_ref_.hpp.

CanGetTaxname()

bool COrg_ref_Base::CanGetTaxname ( void  ) const

inline

Check if it is safe to call GetTaxname method.

Returns

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

Definition at line 366 of file Org_ref_.hpp.

References COrg_ref_Base::IsSetTaxname().

Referenced by CStrainRequest::ExploreStrainsForTaxonInfo(), CAutoDefSourceGroup::GetDefaultExcludeSp(), COrg_ref_Base::GetTaxname(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), UpdateRawBioSource(), CSrcFeatValidator::Validate(), and CSourceItem::x_SetSource().

CBinomialOrgName() [1/2]

CBinomialOrgName::CBinomialOrgName ( const CBinomialOrgName &  value )

private

CBinomialOrgName() [2/2]

CBinomialOrgName::CBinomialOrgName ( void  )

inline

Definition at line 86 of file BinomialOrgName.hpp.

CBinomialOrgName_Base() [1/2]

CBinomialOrgName_Base::CBinomialOrgName_Base ( const CBinomialOrgName_Base &  )

private

CBinomialOrgName_Base() [2/2]

END_CLASS_INFO CBinomialOrgName_Base::CBinomialOrgName_Base

(

void

)

Definition at line 88 of file BinomialOrgName_.cpp.

References CBinomialOrgName_Base::m_set_State.

CheckSelected()

void COrgName_Base::C_Name::CheckSelected ( E_Choice  index ) const

inline

Verify selection, throw exception if it differs from the expected.

Parameters

index

Expected selection.

Definition at line 692 of file OrgName_.hpp.

CMultiOrgName() [1/2]

CMultiOrgName::CMultiOrgName ( const CMultiOrgName &  value )

private

CMultiOrgName() [2/2]

CMultiOrgName::CMultiOrgName ( void  )

inline

Definition at line 86 of file MultiOrgName.hpp.

CMultiOrgName_Base() [1/2]

CMultiOrgName_Base::CMultiOrgName_Base ( const CMultiOrgName_Base &  )

private

CMultiOrgName_Base() [2/2]

END_CLASS_INFO CMultiOrgName_Base::CMultiOrgName_Base

(

void

)

Definition at line 68 of file MultiOrgName_.cpp.

References CMultiOrgName_Base::m_set_State.

COrg_ref_Base() [1/2]

COrg_ref_Base::COrg_ref_Base ( const COrg_ref_Base &  )

private

COrg_ref_Base() [2/2]

END_CLASS_INFO COrg_ref_Base::COrg_ref_Base

(

void

)

Definition at line 125 of file Org_ref_.cpp.

References COrg_ref_Base::m_set_State.

COrgMod_Base() [1/2]

COrgMod_Base::COrgMod_Base ( const COrgMod_Base &  )

private

COrgMod_Base() [2/2]

END_CLASS_INFO COrgMod_Base::COrgMod_Base

(

void

)

Definition at line 130 of file OrgMod_.cpp.

References COrgMod_Base::m_set_State.

COrgName_Base() [1/2]

COrgName_Base::COrgName_Base ( const COrgName_Base &  )

private

COrgName_Base() [2/2]

END_CLASS_INFO COrgName_Base::COrgName_Base

(

void

)

Definition at line 316 of file OrgName_.cpp.

References COrgName_Base::m_set_State.

CPartialOrgName() [1/2]

CPartialOrgName::CPartialOrgName ( const CPartialOrgName &  value )

private

CPartialOrgName() [2/2]

CPartialOrgName::CPartialOrgName ( void  )

inline

Definition at line 86 of file PartialOrgName.hpp.

CPartialOrgName_Base() [1/2]

CPartialOrgName_Base::CPartialOrgName_Base ( const CPartialOrgName_Base &  )

private

CPartialOrgName_Base() [2/2]

END_CLASS_INFO CPartialOrgName_Base::CPartialOrgName_Base

(

void

)

Definition at line 68 of file PartialOrgName_.cpp.

References CPartialOrgName_Base::m_set_State.

CTaxElement() [1/2]

CTaxElement::CTaxElement ( const CTaxElement &  value )

private

CTaxElement() [2/2]

CTaxElement::CTaxElement ( void  )

inline

Definition at line 86 of file TaxElement.hpp.

CTaxElement_Base() [1/2]

CTaxElement_Base::CTaxElement_Base ( const CTaxElement_Base &  )

private

CTaxElement_Base() [2/2]

END_CLASS_INFO CTaxElement_Base::CTaxElement_Base

(

void

)

Definition at line 93 of file TaxElement_.cpp.

References CTaxElement_Base::m_set_State.

DECLARE_INTERNAL_TYPE_INFO() [1/8]

CBinomialOrgName_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [2/8]

CMultiOrgName_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [3/8]

COrg_ref_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [4/8]

COrgMod_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [5/8]

COrgName_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [6/8]

COrgName_Base::C_Name::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [7/8]

CPartialOrgName_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [8/8]

CTaxElement_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DoSelect()

void COrgName_Base::C_Name::DoSelect ( E_Choice  index, CObjectMemoryPool *  pool = 0  )

private

Definition at line 78 of file OrgName_.cpp.

References CObject::AddReference().

EFixed_level()

static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME() CTaxElement_Base::EFixed_level ( void  )

static

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

ESubtype()

static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME() COrgMod_Base::ESubtype ( void  )

static

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

Get() [1/2]

const CMultiOrgName_Base::Tdata & CMultiOrgName_Base::Get ( void  ) const

inline

Get the member data.

Returns

Reference to the member data.

Definition at line 165 of file MultiOrgName_.hpp.

References CMultiOrgName_Base::m_data.

Referenced by COrgName::GetFlatName(), and s_MatchOrgname().

Get() [2/2]

const CPartialOrgName_Base::Tdata & CPartialOrgName_Base::Get ( void  ) const

inline

Get the member data.

Returns

Reference to the member data.

Definition at line 165 of file PartialOrgName_.hpp.

References CPartialOrgName_Base::m_data.

Referenced by COrgName::GetFlatName(), IsCrossKingdom(), s_MatchOrgname(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

GetAttrib() [1/2]

const COrgMod_Base::TAttrib & COrgMod_Base::GetAttrib ( void  ) const

inline

Get the Attrib member data.

Returns

Reference to the member data.

Definition at line 394 of file OrgMod_.hpp.

References COrgMod_Base::CanGetAttrib(), COrgMod_Base::m_Attrib, and CSerialObject::ThrowUnassigned().

Referenced by GetOrgnameDifferences().

GetAttrib() [2/2]

const COrgName_Base::TAttrib & COrgName_Base::GetAttrib ( void  ) const

inline

Get the Attrib member data.

Returns

Reference to the member data.

Definition at line 792 of file OrgName_.hpp.

References COrgName_Base::CanGetAttrib(), COrgName_Base::m_Attrib, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE(), GetOrgnameDifferences(), CFindASN1Dlg::ReplaceInOrg(), CBioSource::SetDisableStrainForwarding(), COrgName::x_GetAttribFlag(), COrgName::x_GetAttribValue(), COrgName::x_ResetAttribFlag(), and COrgName::x_SetAttribFlag().

GetBinomial()

const COrgName_Base::C_Name::TBinomial & COrgName_Base::C_Name::GetBinomial

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 121 of file OrgName_.cpp.

Referenced by COrgName::GetFlatName(), CTaxon1::GetTypeMaterial(), s_TitleEndsInOrganism(), CValidError_imp::ValidateOrgName(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CBioseqIndex::x_InitSource(), and CDeflineGenerator::x_SetBioSrc().

GetCommon()

const COrg_ref_Base::TCommon & COrg_ref_Base::GetCommon ( void  ) const

inline

Get the Common member data.

Returns

Reference to the member data.

Definition at line 419 of file Org_ref_.hpp.

References COrg_ref_Base::CanGetCommon(), COrg_ref_Base::m_Common, and CSerialObject::ThrowUnassigned().

Referenced by CompareDescrFeatSources(), FindMatchInOrgRef(), CBioSource::GetCommon(), COrg_ref::GetLabel(), GetOrgrefDifferences(), GetTaxnameNameFromDescrs(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CEditingActionBiosourceCommonName::GetValue(), IsCommon(), CFindASN1Dlg::ReplaceInOrg(), s_GetOrgRefContentLabel(), s_GetTaxonomyInfoFromBiosrc(), CSourceOtherPanel::TransferFromOrgRef(), CValidError_imp::ValidateOrgRef(), CSourceFeatureItem::x_AddQuals(), CPhyTreeFormatter::x_InitTreeFeatures(), CNewCleanup_imp::x_RemovePopPhyBioSource(), CSourceItem::x_SetSource(), and CSrcWriter::xGatherOrgCommon().

GetDb()

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

inline

Get the Db member data.

Returns

Reference to the member data.

Definition at line 491 of file Org_ref_.hpp.

References COrg_ref_Base::m_Db.

Referenced by BOOST_AUTO_TEST_CASE(), fta_fix_orgref_div(), fta_sort_biosource(), GetEmblDescr(), CSrcTableDbxrefColumn::GetFromBioSource(), COrg_ref::GetLabel(), GetOrgrefDifferences(), COrgrefProp::GetOrgrefProp(), COrgrefProp::GetOrgrefPropBool(), COrgrefProp::GetOrgrefPropInt(), COrg_ref::GetTaxId(), TaxClient::GetTaxIDFromBioseq(), GetTaxIdInBioseq(), GetTaxonTag(), COrgrefProp::HasOrgrefProp(), COrg_ref::MakeCommon(), CCleanup::MakeIRDFeatsFromSourceXrefs(), CEditingActionBiosourceDbxref::Modify(), CRemoveTaxonBioSource::ModifyBioSource(), RemoveTaxId(), s_GetOrgRefContentLabel(), s_GetTaxid(), s_OrgrefEquivalent(), CMacroFunction_RemoveQual::s_RemoveFields(), CReadInSkipObjectHook< Object >::SkipObject(), CMacroFunction_SwapQual::TheFunction(), CSourceOtherPanel::TransferFromOrgRef(), CValidError_imp::ValidateMultipleTaxIds(), CValidError_imp::ValidateOrgRef(), CSourceFeatureItem::x_AddQuals(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CWriteDB_Impl::x_BuildDeflinesFromBioseq(), CDumpASNIndex::x_GetTaxId(), CCleanup::x_MergeDupOrgRefs(), CDbxrefPanel::x_UpdateXrefs(), CGff3Writer::xAssignSourceAttributeDbxref(), CGff3FlybaseWriter::xAssignTaxid(), CSrcWriter::xGatherDb(), and CSrcWriter::xGatherTaxonId().

GetDiv()

const COrgName_Base::TDiv & COrgName_Base::GetDiv ( void  ) const

inline

Get the Div member data.

Returns

Reference to the member data.

Definition at line 1005 of file OrgName_.hpp.

References COrgName_Base::CanGetDiv(), COrgName_Base::m_Div, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE(), COrg_ref::GetDivision(), GetFlatBiomol(), GetGBBlock(), GetOrgnameDifferences(), CEditingActionBiosourceDivision::GetValue(), CValidError_bioseq::IsSynthetic(), CValidError_imp::IsSyntheticConstruct(), CFindASN1Dlg::ReplaceInOrg(), s_DuplicatesBiosource(), s_GetDiv(), UpdateRawBioSource(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateOrgName(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CSourceFeatureItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CCleanup::x_MergeDupOrgNames(), and XMLGetGBBlock().

GetFixed_level()

CTaxElement_Base::TFixed_level CTaxElement_Base::GetFixed_level ( void  ) const

inline

Get the Fixed_level member data.

Returns

Copy of the member data.

Definition at line 269 of file TaxElement_.hpp.

References CTaxElement_Base::CanGetFixed_level(), CTaxElement_Base::m_Fixed_level, and CSerialObject::ThrowUnassigned().

Referenced by IsCrossKingdom(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

GetGcode()

COrgName_Base::TGcode COrgName_Base::GetGcode ( void  ) const

inline

Get the Gcode member data.

Returns

Copy of the member data.

Definition at line 918 of file OrgName_.hpp.

References COrgName_Base::CanGetGcode(), COrgName_Base::m_Gcode, and CSerialObject::ThrowUnassigned().

Referenced by fta_get_gcode_from_biosource(), COrg_ref::GetGcode(), CBioSource::GetGenCode(), GetOrgnameDifferences(), s_GetSplicedSegIdentityMismatch(), s_GetStrictGenCode(), CDeflineGenerator::x_GetModifiers(), and CCleanup::x_MergeDupOrgNames().

GetGenus()

const CBinomialOrgName_Base::TGenus & CBinomialOrgName_Base::GetGenus ( void  ) const

inline

Get the Genus member data.

Returns

Reference to the member data.

Definition at line 255 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::CanGetGenus(), CBinomialOrgName_Base::m_Genus, and CSerialObject::ThrowUnassigned().

Referenced by COrgName::GetFlatName(), s_TitleEndsInOrganism(), CValidError_imp::ValidateOrgName(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CBioseqIndex::x_InitSource(), and CDeflineGenerator::x_SetBioSrc().

GetHybrid()

const COrgName_Base::C_Name::THybrid & COrgName_Base::C_Name::GetHybrid

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 149 of file OrgName_.cpp.

Referenced by COrgName::GetFlatName(), and s_MatchOrgname().

GetLevel()

const CTaxElement_Base::TLevel & CTaxElement_Base::GetLevel ( void  ) const

inline

Get the Level member data.

Returns

Reference to the member data.

Definition at line 309 of file TaxElement_.hpp.

References CTaxElement_Base::CanGetLevel(), CTaxElement_Base::m_Level, and CSerialObject::ThrowUnassigned().

Referenced by IsCrossKingdom(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

GetLineage()

const COrgName_Base::TLineage & COrgName_Base::GetLineage ( void  ) const

inline

Get the Lineage member data.

Returns

Reference to the member data.

Definition at line 864 of file OrgName_.hpp.

References COrgName_Base::CanGetLineage(), COrgName_Base::m_Lineage, and CSerialObject::ThrowUnassigned().

Referenced by CheckMetagenome(), CheckSourceLineage(), CUnculTaxTool::CompareOrgnameLineage(), GetFlatBiomol(), COrgName::GetFlatName(), COrg_ref::GetLineage(), GetOrgnameDifferences(), CEditingActionBiosourceLineage::GetValue(), PropogateSuppliedLineage(), CFindASN1Dlg::ReplaceInOrg(), CUnculturedTool::s_CompareOrgnameLineage(), s_SuppressMultipleEquivBioSources(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_imp::ValidateOrgName(), CValidError_imp::ValidateOrgRef(), CBioseqIndex::x_InitSource(), CCleanup::x_MergeDupOrgNames(), CSourceItem::x_SetSource(), and CSrcWriter::xGatherOrgnameLineage().

GetMgcode()

COrgName_Base::TMgcode COrgName_Base::GetMgcode ( void  ) const

inline

Get the Mgcode member data.

Returns

Copy of the member data.

Definition at line 965 of file OrgName_.hpp.

References COrgName_Base::CanGetMgcode(), COrgName_Base::m_Mgcode, and CSerialObject::ThrowUnassigned().

Referenced by fta_get_gcode_from_biosource(), CBioSource::GetGenCode(), COrg_ref::GetMgcode(), GetOrgnameDifferences(), s_GetStrictGenCode(), CDeflineGenerator::x_GetModifiers(), and CCleanup::x_MergeDupOrgNames().

GetMod() [1/2]

const COrg_ref_Base::TMod & COrg_ref_Base::GetMod ( void  ) const

inline

Get the Mod member data.

Returns

Reference to the member data.

Definition at line 466 of file Org_ref_.hpp.

References COrg_ref_Base::m_Mod.

Referenced by HasMod(), COrg_ref::HasValidVariety(), COrg_ref::MakeCommon(), CSourceFeatureItem::x_AddQuals(), CCleanup::x_MergeDupOrgRefs(), and CSourceItem::x_SetSource().

GetMod() [2/2]

const COrgName_Base::TMod & COrgName_Base::GetMod ( void  ) const

inline

Get the Mod member data.

Returns

Reference to the member data.

Definition at line 839 of file OrgName_.hpp.

References COrgName_Base::m_Mod.

Referenced by AddBioSourceToAttributes(), CQualLookupMap::AddDesc(), CQualLookupMap::AddFeat(), AddMissingCommonOrgMods(), CQualLookupMap::AddOrg(), BOOST_AUTO_TEST_CASE(), CStrainRequest::Check(), CheckQualsInSourceFeat(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CompareOrgModValue(), CreateRawBioSources(), FindMatchInOrgRef(), FixHumanHost(), CAutoDefSourceDescription::GetAvailableModifiers(), COrgName::GetFlatName(), GetGBBlock(), CInfluenzaSet::GetKey(), COrgName::GetNomenclature(), GetOrgnameDifferences(), GetSeqTableFromSeqEntry(), CAutoDefModifierCombo::GetSourceDescriptionString(), GetSourceFields(), GetSrcQual(), GetTaxnameNameFromDescrs(), CSrcTableOrgModColumn::GetValsFromBioSource(), COrgModQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), IsCommon(), IsMissingRequiredClone(), CAutoDefSourceDescription::IsTrickyHIV(), CTaxValidationAndCleanup::ListTaxLookupErrors(), COrgName::MakeCommon(), RemoveMod(), s_GetInstCodeFromBioSource(), s_GetOrgModNatHost(), s_GetSpecificHostFromBioSource(), s_HasMatchingGBMod(), s_HasMetagenomeSource(), s_HasOrgMod(), s_OrgrefEquivalent(), s_ResetModSubsrcQuals(), s_TitleEndsInOrganism(), s_TitleFromBioSource(), s_TitleFromSegment(), SetCultureCollectionFromStrain(), SetOrgMod(), CStrainRequest::StrainContainsTaxonInfo(), CMacroFunction_ApplyStrucVoucherPart::TheFunction(), UpdateBiosourceFromBiosample(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_bioseqset::ValidateNucProtSet(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddMinicircle(), CStrainRequest::x_AddOneStrain(), CAutoDefModifierCombo::x_AddOrgModString(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CStrainRequest::x_CheckOneStrain(), CTreeBuilderJob::x_CreateProjectItems(), CKeywordsItem::x_GatherInfo(), CDeflineGenerator::x_GetModifiers(), CAgpconvertApplication::x_HandleTaxArgs(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CCleanup::x_MergeDupOrgNames(), CNewCleanup_imp::x_MovedNamedValuesInStrain(), CBioSource::x_RemoveStopWords(), CDeflineGenerator::x_SetFlags(), CSourceItem::x_SetSource(), CGff3Writer::xAssignSourceAttributesOrgMod(), and CSrcWriter::xGatherOrgModFeat().

GetName() [1/2]

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

inline

Get the Name member data.

Returns

Reference to the member data.

Definition at line 771 of file OrgName_.hpp.

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

Referenced by COrgName::GetFlatName(), GetOrgnameDifferences(), IsCrossKingdom(), COrgName::MakeCommon(), s_MatchOrgname(), s_TitleEndsInOrganism(), CValidError_imp::ValidateOrgName(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

GetName() [2/2]

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

inline

Get the Name member data.

Returns

Reference to the member data.

Definition at line 356 of file TaxElement_.hpp.

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

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

GetNamedhybrid()

const COrgName_Base::C_Name::TNamedhybrid & COrgName_Base::C_Name::GetNamedhybrid

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 171 of file OrgName_.cpp.

Referenced by COrgName::GetFlatName().

GetOrgname()

const COrg_ref_Base::TOrgname & COrg_ref_Base::GetOrgname ( void  ) const

inline

Get the Orgname member data.

Returns

Reference to the member data.

Definition at line 541 of file Org_ref_.hpp.

References COrg_ref_Base::CanGetOrgname(), COrg_ref_Base::m_Orgname, and CSerialObject::ThrowUnassigned().

Referenced by AddBioSourceToAttributes(), CQualLookupMap::AddDesc(), CQualLookupMap::AddFeat(), AddMissingCommonOrgMods(), CQualLookupMap::AddOrg(), CSrcStructuredVoucherPartColumn::AddToBioSource(), CSpecificHostMapForFix::ApplyToOrg(), CNewCleanup_imp::BiosourceFeatBC(), BOOST_AUTO_TEST_CASE(), CStrainRequest::Check(), CheckQualsInSourceFeat(), CheckSourceLineage(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CUnculTaxTool::CompareOrgnameLineage(), CreateRawBioSources(), FindMatchInOrgRef(), FixHumanHost(), fta_fix_orgref_div(), fta_get_gcode_from_biosource(), fta_sort_biosource(), CAutoDefSourceDescription::GetAvailableModifiers(), COrg_ref::GetDivision(), GetEmblDescr(), GetFlatBiomol(), GetGBBlock(), COrg_ref::GetGcode(), CBioSource::GetGenCode(), CInfluenzaSet::GetKey(), COrg_ref::GetLineage(), COrg_ref::GetMgcode(), CBioSource::GetOrgname(), GetOrgrefDifferences(), COrg_ref::GetPgcode(), CAutoDefModifierCombo::GetSourceDescriptionString(), GetSourceFields(), GetSrcQual(), GetTaxnameNameFromDescrs(), CSrcTableOrgModColumn::GetValsFromBioSource(), COrgModQual::GetValue(), CEditingActionBiosourceDivision::GetValue(), CEditingActionBiosourceLineage::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), COrg_ref::HasValidVariety(), IsCommon(), IsCrossKingdom(), IsMissingRequiredClone(), COrg_ref::IsSetDivision(), COrg_ref::IsSetGcode(), COrg_ref::IsSetLineage(), COrg_ref::IsSetMgcode(), COrg_ref::IsSetOrgMod(), COrg_ref::IsSetPgcode(), CEditingActionBiosourceDivision::IsSetValue(), CEditingActionBiosourceLineage::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), CAutoDefSourceDescription::IsTrickyHIV(), CTaxValidationAndCleanup::ListTaxLookupErrors(), COrg_ref::MakeCommon(), CCompareWithBiosample::OnClickOk(), SRemovableOrgModNote::operator()(), PropogateSuppliedLineage(), RemoveMod(), RemoveStrain(), CFindASN1Dlg::ReplaceInOrg(), CUnculturedTool::s_CompareOrgnameLineage(), s_DuplicatesBiosource(), s_GetDiv(), s_GetInstCodeFromBioSource(), s_GetSpecificHostFromBioSource(), s_GetSplicedSegIdentityMismatch(), s_GetStrictGenCode(), s_HasMetagenomeSource(), s_HasOrgMod(), s_OrgrefEquivalent(), s_ResetModSubsrcQuals(), s_SuppressMultipleEquivBioSources(), s_TitleEndsInOrganism(), s_TitleFromBioSource(), s_TitleFromSegment(), SeqEntryCheckTaxonDiv(), SetCultureCollectionFromStrain(), CBioSource::SetDisableStrainForwarding(), CCleanup::SetGeneticCodes(), SetOrgMod(), CStrainRequest::StrainContainsTaxonInfo(), CMacroFunction_ApplyStrucVoucherPart::TheFunction(), UpdateBiosourceFromBiosample(), UpdateRawBioSource(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_imp::ValidateOrgRef(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddMinicircle(), CStrainRequest::x_AddOneStrain(), CAutoDefModifierCombo::x_AddOrgModString(), CSourceFeatureItem::x_AddQuals(), CTaxValidationAndCleanup::x_ApplySpecificHostMap(), CAppendModToOrg::x_ApplyToBioSource(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CNewCleanup_imp::x_CanRemoveGenbankBlockSource(), CStrainRequest::x_CheckOneStrain(), CNewCleanup_imp::x_CleanupOldName(), CNewCleanup_imp::x_CleanupOrgModNoteEC(), CSourceFeatureItem::x_GatherInfo(), CKeywordsItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CDeflineGenerator::x_GetModifiers(), CStrainSerotypeInfluenza::x_GetStrainSerotypeConflicts(), CAgpconvertApplication::x_HandleTaxArgs(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CCleanup::x_MergeDupOrgRefs(), CBioSource::x_RemoveStopWords(), CSourceItem::x_SetSource(), CGff3Writer::xAssignSourceAttributesOrgMod(), CSrcWriter::xGatherOrgnameLineage(), and XMLGetGBBlock().

GetPartial()

const COrgName_Base::C_Name::TPartial & COrgName_Base::C_Name::GetPartial

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 193 of file OrgName_.cpp.

Referenced by COrgName::GetFlatName(), IsCrossKingdom(), s_MatchOrgname(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

GetPgcode()

COrgName_Base::TPgcode COrgName_Base::GetPgcode ( void  ) const

inline

Get the Pgcode member data.

Returns

Copy of the member data.

Definition at line 1059 of file OrgName_.hpp.

References COrgName_Base::CanGetPgcode(), COrgName_Base::m_Pgcode, and CSerialObject::ThrowUnassigned().

Referenced by CBioSource::GetGenCode(), COrg_ref::GetPgcode(), s_GetStrictGenCode(), and CDeflineGenerator::x_GetModifiers().

GetSpecies()

const CBinomialOrgName_Base::TSpecies & CBinomialOrgName_Base::GetSpecies ( void  ) const

inline

Get the Species member data.

Returns

Reference to the member data.

Definition at line 302 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::CanGetSpecies(), CBinomialOrgName_Base::m_Species, and CSerialObject::ThrowUnassigned().

Referenced by COrgName::GetFlatName(), CTaxon1::GetTypeMaterial(), s_TitleEndsInOrganism(), CValidError_imp::ValidateOrgName(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CBioseqIndex::x_InitSource(), and CDeflineGenerator::x_SetBioSrc().

GetSubname()

const COrgMod_Base::TSubname & COrgMod_Base::GetSubname ( void  ) const

inline

Get the Subname member data.

Returns

Reference to the member data.

Definition at line 347 of file OrgMod_.hpp.

References COrgMod_Base::CanGetSubname(), COrgMod_Base::m_Subname, and CSerialObject::ThrowUnassigned().

Referenced by COrgMod::AutoFix(), BOOST_AUTO_TEST_CASE(), COrgMod::FixCapitalization(), CFlatOrgModQVal::Format(), GetOrgnameDifferences(), CEditingActionBiosourceOrgMod::GetValue(), CEditingActionBiosourceAllNotes::GetValue(), CEditingActionBiosourceStructuredVoucher::GetValue(), CEditingActionBiosourceStructuredVoucher::IsSetValue(), SRemoveNamedStrain::operator()(), CNewCleanup_imp::OrgnameBC(), CBioSource::RemoveLineageSourceNotes(), CEditingActionBiosourceStructuredVoucher::ResetValue(), s_OrgModEqual(), SetOrgMod(), CEditingActionBiosourceStructuredVoucher::SetValue(), CValidError_imp::ValidateOrgModVoucher(), CValidError_imp::ValidateOrgName(), CMacroFunction_ApplyStrucVoucherPart::x_ApplyPart(), CBioseqIndex::x_InitSource(), CNewCleanup_imp::x_OrgModBC(), CMacroFunction_ApplyStrucVoucherPart::x_RemovePart(), CDeflineGenerator::x_SetBioSrc(), and CSrcWriter::xGatherOrgModFeat().

GetSubspecies()

const CBinomialOrgName_Base::TSubspecies & CBinomialOrgName_Base::GetSubspecies ( void  ) const

inline

Get the Subspecies member data.

Returns

Reference to the member data.

Definition at line 349 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::CanGetSubspecies(), CBinomialOrgName_Base::m_Subspecies, and CSerialObject::ThrowUnassigned().

Referenced by COrgName::GetFlatName(), and CTaxon1::GetTypeMaterial().

GetSubtype()

COrgMod_Base::TSubtype COrgMod_Base::GetSubtype ( void  ) const

inline

Get the Subtype member data.

Returns

Copy of the member data.

Definition at line 307 of file OrgMod_.hpp.

References COrgMod_Base::CanGetSubtype(), COrgMod_Base::m_Subtype, and CSerialObject::ThrowUnassigned().

Referenced by COrgMod::AutoFix(), COrgMod::FixCapitalization(), GetOrgModName(), GetOrgnameDifferences(), COrgMod::IsUnexpectedViralOrgModQualifier(), SRemoveNamedStrain::operator()(), CNewCleanup_imp::OrgnameBC(), COrgMod::RemoveAbbreviation(), CBioSource::RemoveLineageSourceNotes(), s_OrgModEqual(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_imp::ValidateOrgModVoucher(), CValidError_imp::ValidateOrgName(), and CSrcWriter::xGatherOrgModFeat().

GetSyn()

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

inline

Get the Syn member data.

Returns

Reference to the member data.

Definition at line 516 of file Org_ref_.hpp.

References COrg_ref_Base::m_Syn.

Referenced by fill_orgref(), fta_fix_orgref(), fta_get_orgref_byid(), GetOrgrefDifferences(), COrg_ref::MakeCommon(), and CCleanup::x_MergeDupOrgRefs().

GetTaxname()

const COrg_ref_Base::TTaxname & COrg_ref_Base::GetTaxname ( void  ) const

inline

Get the Taxname member data.

Returns

Reference to the member data.

Definition at line 372 of file Org_ref_.hpp.

References COrg_ref_Base::CanGetTaxname(), COrg_ref_Base::m_Taxname, and CSerialObject::ThrowUnassigned().

Referenced by AddBioSourceToAttributes(), AddNode(), CSpecificHostRequest::AddReply(), CStrainRequest::AddReply(), CCleanup::AreBioSourcesMergeable(), BOOST_AUTO_TEST_CASE(), CStrainRequest::Check(), CheckMetagenome(), CheckStrainReply(), CompareDescrFeatSources(), CreateRawBioSources(), CStrainRequest::CStrainRequest(), CStrainRequest::ExploreStrainsForTaxonInfo(), FakeGenBankBioSources(), FindMatchInOrgRef(), fta_fix_orgref(), fta_replace_org(), IEditingAction::GetActionCommand(), CAutoDefSourceDescription::GetComboDescription(), CAutoDefSourceGroup::GetDefaultExcludeSp(), CInfluenzaSet::GetKey(), CStrainMap::GetKey(), COrg_ref::GetLabel(), GetOrgrefDifferences(), CCachedTaxon3_impl::GetOrgReply(), CAutoDefModifierCombo::GetSourceDescriptionString(), GetSprotDescr(), CCommentItem::GetStringForTLS(), CCommentItem::GetStringForTSA(), CCommentItem::GetStringForWGS(), CUnculTaxTool::GetSuggestion(), CPriorityTaxNodes::getTaxName(), CBioSource::GetTaxname(), GetTaxnameNameFromDescrs(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CTaxnameQual::GetValue(), CEditingActionBiosourceTaxname::GetValue(), CEditingActionBiosourceTaxnameAfterBinomial::GetValue(), InterpretSpecificHostResult(), IsMissingRequiredClone(), CEditingActionBiosourceTaxnameAfterBinomial::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), CNewCleanup_imp::IsSyntheticConstruct(), CAutoDefSourceDescription::IsTrickyHIV(), CTaxValidationAndCleanup::ListTaxLookupErrors(), CUnculTaxTool::LookupSuggestions(), MakeCommonBioSource(), MakeMailReportPostReport(), MakeMailReportPreReport(), SRemovableOrgModNote::operator()(), OrgDiffers(), PropogateSuppliedLineage(), CFindASN1Dlg::ReplaceInOrg(), CGenusSpeciesFixup::s_GetNameFromTaxonServer(), s_GetOrgRefContentLabel(), CUnculturedTool::s_GetSuggestion(), s_OrgrefEquivalent(), s_SuppressMultipleEquivBioSources(), s_TitleEndsInOrganism(), s_TitleFromBioSource(), s_TitleFromSegment(), CReadInSkipObjectHook< Object >::SkipObject(), CStrainRequest::StrainContainsTaxonInfo(), COrg_ref::UpdateFromTable(), UpdateRawBioSource(), CSrcDescEditorPanel::UpdateSeqdesc(), CSrcFeatValidator::Validate(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_bioseq::ValidateOrgContext(), CValidError_imp::ValidateOrgRef(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_imp::ValidateSubSource(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddHIVModifiers(), CStrainRequest::x_AddOneStrain(), CAutoDefModifierCombo::x_AddOrgModString(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers(), CStrainSerotypeInfluenza::x_AddToInfluenzaNames(), COrgGeneralPanel::x_ApplyChangesToSource(), CAppendModToOrg::x_ApplyToBioSource(), CNewCleanup_imp::x_ChangePopToPhy(), CStrainRequest::x_CheckOneStrain(), CNewCleanup_imp::x_CleanupOldName(), CFeatureGenerator::SImplementation::x_ConstructRnaName(), CStrainSerotypeInfluenza::x_FixupOrganismNames(), CSourceFeatureItem::x_GatherInfo(), CUnculturedTool::x_GetCorrection(), CDeflineGenerator::x_GetModifiers(), CCachedTaxon3::x_GetReplyForOrgRef(), COrg_ref::x_GetTaxnameAfterFirstTwoWords(), CAgpconvertApplication::x_HandleTaxArgs(), CPhyTreeFormatter::x_InitTreeFeatures(), CTaxValidationAndCleanup::x_InterpretTaxonomyError(), CStrainSerotypeInfluenza::x_IsParsableInfluenzaVirusName(), CBioSource::x_RemoveNameElementDiffs(), CNewCleanup_imp::x_RemovePopPhyBioSource(), CBioSource::x_RemoveStopWords(), CSourceItem::x_SetSource(), CStrainSerotypeInfluenza::x_TrimmingOrganismNames(), and XMLFakeBioSources().

GetVirus()

const COrgName_Base::C_Name::TVirus & COrgName_Base::C_Name::GetVirus ( void  ) const

inline

Get the variant data.

Returns

Reference to the data.

Definition at line 727 of file OrgName_.hpp.

Referenced by COrgName::GetFlatName().

IsBinomial()

bool COrgName_Base::C_Name::IsBinomial ( void  ) const

inline

Check if variant Binomial is selected.

Binomial type is defined as 'typedef CBinomialOrgName TBinomial'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 715 of file OrgName_.hpp.

Referenced by CTaxon1::GetTypeMaterial(), s_TitleEndsInOrganism(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CBioseqIndex::x_InitSource(), and CDeflineGenerator::x_SetBioSrc().

IsHybrid()

bool COrgName_Base::C_Name::IsHybrid ( void  ) const

inline

Check if variant Hybrid is selected.

Hybrid type is defined as 'typedef CMultiOrgName THybrid'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 741 of file OrgName_.hpp.

IsNamedhybrid()

bool COrgName_Base::C_Name::IsNamedhybrid ( void  ) const

inline

Check if variant Namedhybrid is selected.

Namedhybrid type is defined as 'typedef CBinomialOrgName TNamedhybrid'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 747 of file OrgName_.hpp.

IsPartial()

bool COrgName_Base::C_Name::IsPartial ( void  ) const

inline

Check if variant Partial is selected.

Partial type is defined as 'typedef CPartialOrgName TPartial'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 753 of file OrgName_.hpp.

Referenced by IsCrossKingdom(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

IsSet() [1/2]

bool CMultiOrgName_Base::IsSet ( void  ) const

inline

Check if a value has been assigned to data member.

Data member is mandatory; its type is defined as 'typedef list< CRef< COrgName > > Tdata'

Returns

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

Definition at line 153 of file MultiOrgName_.hpp.

References CMultiOrgName_Base::m_set_State.

Referenced by CAutogeneratedCleanup::x_BasicCleanupOrgNameName_hybrid().

IsSet() [2/2]

bool CPartialOrgName_Base::IsSet ( void  ) const

inline

Check if a value has been assigned to data member.

Data member is mandatory; its type is defined as 'typedef list< CRef< CTaxElement > > Tdata'

Returns

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

Definition at line 153 of file PartialOrgName_.hpp.

References CPartialOrgName_Base::m_set_State.

Referenced by IsCrossKingdom(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

IsSetAttrib() [1/2]

bool COrgMod_Base::IsSetAttrib ( void  ) const

inline

attribution/source of name Check if a value has been assigned to Attrib data member.

Data member Attrib is optional; its type is defined as 'typedef string TAttrib'

Returns

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

Definition at line 382 of file OrgMod_.hpp.

References COrgMod_Base::m_set_State.

Referenced by COrgMod_Base::CanGetAttrib(), GetOrgnameDifferences(), and COrgMod_Base::SetAttrib().

IsSetAttrib() [2/2]

bool COrgName_Base::IsSetAttrib ( void  ) const

inline

attribution of name Check if a value has been assigned to Attrib data member.

Data member Attrib is optional; its type is defined as 'typedef string TAttrib'

Returns

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

Definition at line 780 of file OrgName_.hpp.

References COrgName_Base::m_set_State.

Referenced by COrgName_Base::CanGetAttrib(), COrg_ref::FilterOutParts(), GetOrgnameDifferences(), COrgName::MakeCommon(), CFindASN1Dlg::ReplaceInOrg(), COrgName_Base::SetAttrib(), COrgName::x_GetAttribFlag(), COrgName::x_GetAttribValue(), COrgName::x_ResetAttribFlag(), and COrgName::x_SetAttribFlag().

IsSetCommon()

bool COrg_ref_Base::IsSetCommon ( void  ) const

inline

common name Check if a value has been assigned to Common data member.

Data member Common is optional; its type is defined as 'typedef string TCommon'

Returns

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

Definition at line 407 of file Org_ref_.hpp.

References COrg_ref_Base::m_set_State.

Referenced by COrg_ref_Base::CanGetCommon(), CompareDescrFeatSources(), fill_orgref(), COrg_ref::FilterOutParts(), FindMatchInOrgRef(), COrg_ref::GetLabel(), GetOrgrefDifferences(), GetTaxnameNameFromDescrs(), IsCommon(), CBioSource::IsSetCommon(), CEditingActionBiosourceCommonName::IsSetValue(), CFindASN1Dlg::ReplaceInOrg(), s_GetOrgRefContentLabel(), COrg_ref_Base::SetCommon(), CSourceOtherPanel::TransferFromOrgRef(), CValidError_imp::ValidateOrgRef(), CSourceFeatureItem::x_AddQuals(), CAutogeneratedCleanup::x_BasicCleanupOrgRef(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC(), CNewCleanup_imp::x_RemovePopPhyBioSource(), and CSrcWriter::xGatherOrgCommon().

IsSetDb()

bool COrg_ref_Base::IsSetDb ( void  ) const

inline

ids in taxonomic or culture 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 479 of file Org_ref_.hpp.

References COrg_ref_Base::m_set_State.

Referenced by CUnculTaxTool::AddBioSource(), COrg_ref::FilterOutParts(), GetEmblDescr(), CSrcTableDbxrefColumn::GetFromBioSource(), COrg_ref::GetLabel(), GetOrgrefDifferences(), COrgrefProp::GetOrgrefProp(), COrgrefProp::GetOrgrefPropBool(), COrgrefProp::GetOrgrefPropInt(), GetSeqTableFromSeqEntry(), COrg_ref::GetTaxId(), CLocalTaxon::GetTaxIdByOrgRef(), GetTaxonTag(), CSrcTableDbxrefColumn::GetValsFromBioSource(), COrgrefProp::HasOrgrefProp(), COrg_ref::MakeCommon(), CCleanup::MakeIRDFeatsFromSourceXrefs(), CEditingActionBiosourceDbxref::Modify(), RemoveDbxref(), COrgrefProp::RemoveOrgrefProp(), RemoveTaxId(), CFindASN1Dlg::ReplaceInOrg(), s_GetOrgRefContentLabel(), s_OrgrefEquivalent(), CMacroFunction_RemoveQual::s_RemoveFields(), CMacroFunction_SwapQual::TheFunction(), CSourceOtherPanel::TransferFromOrgRef(), CValidError_imp::ValidateMultipleTaxIds(), CValidError_imp::ValidateOrgRef(), CSourceFeatureItem::x_AddQuals(), CAppendModToOrg::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupOrgRef(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC(), CDumpASNIndex::x_GetTaxId(), CCleanup::x_MergeDupOrgRefs(), CDbxrefPanel::x_UpdateXrefs(), CGff3Writer::xAssignSourceAttributeDbxref(), CGff3FlybaseWriter::xAssignTaxid(), CSrcWriter::xGatherDb(), and CSrcWriter::xGatherTaxonId().

IsSetDiv()

bool COrgName_Base::IsSetDiv ( void  ) const

inline

GenBank division code Check if a value has been assigned to Div data member.

Data member Div is optional; its type is defined as 'typedef string TDiv'

Returns

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

Definition at line 993 of file OrgName_.hpp.

References COrgName_Base::m_set_State.

Referenced by COrgName_Base::CanGetDiv(), COrg_ref::FilterOutParts(), fta_fix_orgref_div(), GetEmblDescr(), GetFlatBiomol(), GetGBBlock(), GetOrgnameDifferences(), COrg_ref::IsSetDivision(), CEditingActionBiosourceDivision::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), COrgName::MakeCommon(), CFindASN1Dlg::ReplaceInOrg(), s_DuplicatesBiosource(), SeqEntryCheckTaxonDiv(), COrgName_Base::SetDiv(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateOrgName(), CSourceFeatureItem::x_GatherInfo(), CCleanup::x_MergeDupOrgNames(), and XMLGetGBBlock().

IsSetFixed_level()

bool CTaxElement_Base::IsSetFixed_level ( void  ) const

inline

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

Data member Fixed_level is mandatory; its type is defined as 'typedef int TFixed_level'

Returns

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

Definition at line 250 of file TaxElement_.hpp.

References CTaxElement_Base::m_set_State.

Referenced by CTaxElement_Base::CanGetFixed_level(), IsCrossKingdom(), CTaxElement_Base::SetFixed_level(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

IsSetGcode()

bool COrgName_Base::IsSetGcode ( void  ) const

inline

genetic code (see CdRegion) Check if a value has been assigned to Gcode data member.

Data member Gcode is optional; its type is defined as 'typedef int TGcode'

Returns

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

Definition at line 899 of file OrgName_.hpp.

References COrgName_Base::m_set_State.

Referenced by COrgName_Base::CanGetGcode(), COrg_ref::FilterOutParts(), fta_get_gcode_from_biosource(), CBioSource::GetGenCode(), GetOrgnameDifferences(), COrg_ref::IsSetGcode(), COrgName::MakeCommon(), s_GetStrictGenCode(), COrgName_Base::SetGcode(), CDeflineGenerator::x_GetModifiers(), and CCleanup::x_MergeDupOrgNames().

IsSetGenus()

bool CBinomialOrgName_Base::IsSetGenus ( void  ) const

inline

required Check if a value has been assigned to Genus data member.

Data member Genus is mandatory; its type is defined as 'typedef string TGenus'

Returns

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

Definition at line 243 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_set_State.

Referenced by CBinomialOrgName_Base::CanGetGenus(), s_TitleEndsInOrganism(), CBinomialOrgName_Base::SetGenus(), CValidError_imp::ValidateOrgName(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CBioseqIndex::x_InitSource(), and CDeflineGenerator::x_SetBioSrc().

IsSetLevel()

bool CTaxElement_Base::IsSetLevel ( void  ) const

inline

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

Data member Level is optional; its type is defined as 'typedef string TLevel'

Returns

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

Definition at line 297 of file TaxElement_.hpp.

References CTaxElement_Base::m_set_State.

Referenced by CTaxElement_Base::CanGetLevel(), IsCrossKingdom(), CTaxElement_Base::SetLevel(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

IsSetLineage()

bool COrgName_Base::IsSetLineage ( void  ) const

inline

lineage with semicolon separators Check if a value has been assigned to Lineage data member.

Data member Lineage is optional; its type is defined as 'typedef string TLineage'

Returns

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

Definition at line 852 of file OrgName_.hpp.

References COrgName_Base::m_set_State.

Referenced by COrgName_Base::CanGetLineage(), CheckMetagenome(), CheckSourceLineage(), CUnculTaxTool::CompareOrgnameLineage(), COrg_ref::FilterOutParts(), GetFlatBiomol(), COrgName::GetFlatName(), GetOrgnameDifferences(), COrg_ref::IsSetLineage(), CEditingActionBiosourceLineage::IsSetValue(), COrgName::MakeCommon(), PropogateSuppliedLineage(), CFindASN1Dlg::ReplaceInOrg(), CUnculturedTool::s_CompareOrgnameLineage(), s_SuppressMultipleEquivBioSources(), COrgName_Base::SetLineage(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_imp::ValidateOrgName(), CValidError_imp::ValidateOrgRef(), CCleanup::x_MergeDupOrgNames(), and CSrcWriter::xGatherOrgnameLineage().

IsSetMgcode()

bool COrgName_Base::IsSetMgcode ( void  ) const

inline

mitochondrial genetic code Check if a value has been assigned to Mgcode data member.

Data member Mgcode is optional; its type is defined as 'typedef int TMgcode'

Returns

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

Definition at line 946 of file OrgName_.hpp.

References COrgName_Base::m_set_State.

Referenced by COrgName_Base::CanGetMgcode(), COrg_ref::FilterOutParts(), fta_get_gcode_from_biosource(), CBioSource::GetGenCode(), GetOrgnameDifferences(), COrg_ref::IsSetMgcode(), COrgName::MakeCommon(), s_GetStrictGenCode(), COrgName_Base::SetMgcode(), CDeflineGenerator::x_GetModifiers(), and CCleanup::x_MergeDupOrgNames().

IsSetMod() [1/2]

bool COrg_ref_Base::IsSetMod ( void  ) const

inline

unstructured modifiers Check if a value has been assigned to Mod data member.

Data member Mod is optional; its type is defined as 'typedef list< string > TMod'

Returns

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

Definition at line 454 of file Org_ref_.hpp.

References COrg_ref_Base::m_set_State.

Referenced by CNewCleanup_imp::BiosourceFeatBC(), COrg_ref::FilterOutParts(), HasMod(), COrg_ref::HasValidVariety(), COrg_ref::MakeCommon(), CFindASN1Dlg::ReplaceInOrg(), CSourceFeatureItem::x_AddQuals(), CAutogeneratedCleanup::x_BasicCleanupOrgRef(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC(), and CCleanup::x_MergeDupOrgRefs().

IsSetMod() [2/2]

bool COrgName_Base::IsSetMod ( void  ) const

inline

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

Data member Mod is optional; its type is defined as 'typedef list< CRef< COrgMod > > TMod'

Returns

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

Definition at line 827 of file OrgName_.hpp.

References COrgName_Base::m_set_State.

Referenced by CSrcStructuredVoucherPartColumn::AddToBioSource(), CSpecificHostMapForFix::ApplyToOrg(), CNewCleanup_imp::BiosourceFeatBC(), BOOST_AUTO_TEST_CASE(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), COrg_ref::FilterOutParts(), FindMatchInOrgRef(), fta_sort_biosource(), CAutoDefSourceDescription::GetAvailableModifiers(), COrgName::GetFlatName(), GetGBBlock(), CInfluenzaSet::GetKey(), COrgName::GetNomenclature(), GetOrgnameDifferences(), GetSourceFields(), GetTaxnameNameFromDescrs(), CSrcTableOrgModColumn::GetValsFromBioSource(), COrgModQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), IsMissingRequiredClone(), COrg_ref::IsSetOrgMod(), CAutoDefSourceDescription::IsTrickyHIV(), COrgName::MakeCommon(), RemoveMod(), COrgName::RemoveModBySubtype(), CFindASN1Dlg::ReplaceInOrg(), s_GetInstCodeFromBioSource(), s_GetSpecificHostFromBioSource(), s_HasMatchingGBMod(), s_HasOrgMod(), s_OrgrefEquivalent(), s_TitleFromBioSource(), s_TitleFromSegment(), SetCultureCollectionFromStrain(), SetOrgMod(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_imp::ValidateOrgName(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDefModifierCombo::x_AddOrgModString(), CTaxValidationAndCleanup::x_ApplySpecificHostMap(), CAppendModToOrg::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeatDataOrgName(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CNewCleanup_imp::x_CleanupOldName(), CNewCleanup_imp::x_CleanupOrgModNoteEC(), CDeflineGenerator::x_GetModifiers(), CStrainSerotypeInfluenza::x_GetStrainSerotypeConflicts(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CCleanup::x_MergeDupOrgNames(), CNewCleanup_imp::x_MovedNamedValuesInStrain(), CDeflineGenerator::x_SetFlags(), and CGff3Writer::xAssignSourceAttributesOrgMod().

IsSetName() [1/2]

bool COrgName_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 C_Name TName'

Returns

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

Definition at line 759 of file OrgName_.hpp.

References COrgName_Base::m_Name.

Referenced by COrgName_Base::CanGetName(), COrg_ref::FilterOutParts(), COrgName::GetFlatName(), GetOrgnameDifferences(), IsCrossKingdom(), COrgName::MakeCommon(), CCompareWithBiosample::OnClickOk(), s_MatchOrgname(), s_MoreCleanupForTaxnameChange(), s_TitleEndsInOrganism(), CValidError_imp::ValidateOrgName(), CValidError_imp::ValidateOrgRef(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeatDataOrgName(), CBioseqIndex::x_InitDescs(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), and CBioseqContext::x_SetTaxname().

IsSetName() [2/2]

bool CTaxElement_Base::IsSetName ( void  ) const

inline

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

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

Returns

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

Definition at line 344 of file TaxElement_.hpp.

References CTaxElement_Base::m_set_State.

Referenced by CTaxElement_Base::CanGetName(), IsCrossKingdom(), CTaxElement_Base::SetName(), CBioseqIndex::x_InitDescs(), CDeflineGenerator::x_SetFlags(), and CBioseqContext::x_SetTaxname().

IsSetOrgname()

bool COrg_ref_Base::IsSetOrgname ( void  ) const

inline

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

Data member Orgname is optional; its type is defined as 'typedef COrgName TOrgname'

Returns

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

Definition at line 529 of file Org_ref_.hpp.

References COrg_ref_Base::m_Orgname.

Referenced by CSrcStructuredVoucherPartColumn::AddToBioSource(), CSpecificHostMapForFix::ApplyToOrg(), CNewCleanup_imp::BiosourceBC(), CNewCleanup_imp::BiosourceFeatBC(), BOOST_AUTO_TEST_CASE(), COrg_ref_Base::CanGetOrgname(), CheckSourceLineage(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CUnculTaxTool::CompareOrgnameLineage(), CreateRawBioSources(), FakeEmblBioSources(), COrg_ref::FilterOutParts(), FindMatchInOrgRef(), fta_fix_orgref_div(), fta_get_gcode_from_biosource(), fta_sort_biosource(), GetEmblDescr(), GetFlatBiomol(), GetGBBlock(), GetGeneticCodeForBioseq(), CInfluenzaSet::GetKey(), GetOrgrefDifferences(), GetSourceFields(), GetTaxnameNameFromDescrs(), CSrcTableOrgModColumn::GetValsFromBioSource(), COrgModQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), COrg_ref::HasValidVariety(), IsCrossKingdom(), IsMissingRequiredClone(), COrg_ref::IsSetDivision(), COrg_ref::IsSetGcode(), COrg_ref::IsSetLineage(), COrg_ref::IsSetMgcode(), COrg_ref::IsSetOrgMod(), CBioSource::IsSetOrgname(), COrg_ref::IsSetPgcode(), CEditingActionBiosourceDivision::IsSetValue(), CEditingActionBiosourceLineage::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), COrg_ref::MakeCommon(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PropogateSuppliedLineage(), RemoveMod(), CFindASN1Dlg::ReplaceInOrg(), CUnculturedTool::s_CompareOrgnameLineage(), s_DuplicatesBiosource(), s_GetInstCodeFromBioSource(), s_GetSpecificHostFromBioSource(), s_GetStrictGenCode(), s_HasOrgMod(), s_OrgrefEquivalent(), s_SuppressMultipleEquivBioSources(), s_TitleEndsInOrganism(), s_TitleFromBioSource(), s_TitleFromSegment(), SeqEntryCheckTaxonDiv(), SetOrgMod(), UpdateBiosourceFromBiosample(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_imp::ValidateOrgRef(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDefModifierCombo::x_AddOrgModString(), CSourceFeatureItem::x_AddQuals(), CTaxValidationAndCleanup::x_ApplySpecificHostMap(), CAppendModToOrg::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupOrgRef(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CNewCleanup_imp::x_CleanupOldName(), CNewCleanup_imp::x_CleanupOrgModNoteEC(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupOrgRef(), CSourceFeatureItem::x_GatherInfo(), CKeywordsItem::x_GatherInfo(), CDeflineGenerator::x_GetModifiers(), CStrainSerotypeInfluenza::x_GetStrainSerotypeConflicts(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CCleanup::x_MergeDupOrgRefs(), CGff3Writer::xAssignSourceAttributesOrgMod(), CSrcWriter::xGatherOrgnameLineage(), and XMLGetGBBlock().

IsSetPgcode()

bool COrgName_Base::IsSetPgcode ( void  ) const

inline

plastid genetic code Check if a value has been assigned to Pgcode data member.

Data member Pgcode is optional; its type is defined as 'typedef int TPgcode'

Returns

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

Definition at line 1040 of file OrgName_.hpp.

References COrgName_Base::m_set_State.

Referenced by COrgName_Base::CanGetPgcode(), COrg_ref::FilterOutParts(), CBioSource::GetGenCode(), COrg_ref::IsSetPgcode(), COrgName::MakeCommon(), s_GetStrictGenCode(), COrgName_Base::SetPgcode(), and CDeflineGenerator::x_GetModifiers().

IsSetSpecies()

bool CBinomialOrgName_Base::IsSetSpecies ( void  ) const

inline

species required if subspecies used Check if a value has been assigned to Species data member.

Data member Species is optional; its type is defined as 'typedef string TSpecies'

Returns

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

Definition at line 290 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_set_State.

Referenced by CBinomialOrgName_Base::CanGetSpecies(), COrgName::GetFlatName(), CTaxon1::GetTypeMaterial(), s_TitleEndsInOrganism(), CBinomialOrgName_Base::SetSpecies(), CValidError_imp::ValidateOrgName(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CBioseqIndex::x_InitSource(), and CDeflineGenerator::x_SetBioSrc().

IsSetSubname()

bool COrgMod_Base::IsSetSubname ( void  ) const

inline

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

Data member Subname is mandatory; its type is defined as 'typedef string TSubname'

Returns

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

Definition at line 335 of file OrgMod_.hpp.

References COrgMod_Base::m_set_State.

Referenced by COrgMod::AutoFix(), COrgMod_Base::CanGetSubname(), COrgMod::FixCapitalization(), GetOrgnameDifferences(), CEditingActionBiosourceOrgMod::IsSetValue(), CEditingActionBiosourceAllNotes::IsSetValue(), CEditingActionBiosourceStructuredVoucher::IsSetValue(), SRemoveNamedStrain::operator()(), COrgMod::RemoveAbbreviation(), CBioSource::RemoveLineageSourceNotes(), CEditingActionBiosourceStructuredVoucher::ResetValue(), COrgMod_Base::SetSubname(), CEditingActionBiosourceStructuredVoucher::SetValue(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_imp::ValidateOrgModVoucher(), CValidError_imp::ValidateOrgName(), CMacroFunction_ApplyStrucVoucherPart::x_ApplyPart(), CBioseqIndex::x_InitSource(), CNewCleanup_imp::x_OrgModBC(), CMacroFunction_ApplyStrucVoucherPart::x_RemovePart(), and CDeflineGenerator::x_SetBioSrc().

IsSetSubspecies()

bool CBinomialOrgName_Base::IsSetSubspecies ( void  ) const

inline

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

Data member Subspecies is optional; its type is defined as 'typedef string TSubspecies'

Returns

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

Definition at line 337 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_set_State.

Referenced by CBinomialOrgName_Base::CanGetSubspecies(), COrgName::GetFlatName(), CTaxon1::GetTypeMaterial(), and CBinomialOrgName_Base::SetSubspecies().

IsSetSubtype()

bool COrgMod_Base::IsSetSubtype ( void  ) const

inline

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

Data member Subtype is mandatory; its type is defined as 'typedef int TSubtype'

Returns

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

Definition at line 288 of file OrgMod_.hpp.

References COrgMod_Base::m_set_State.

Referenced by COrgMod::AutoFix(), COrgMod_Base::CanGetSubtype(), COrgMod::FixCapitalization(), GetOrgnameDifferences(), COrgMod::IsUnexpectedViralOrgModQualifier(), SRemoveNamedStrain::operator()(), COrgMod::RemoveAbbreviation(), CBioSource::RemoveLineageSourceNotes(), COrgMod_Base::SetSubtype(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_imp::ValidateOrgModVoucher(), and CNewCleanup_imp::x_OrgModBC().

IsSetSyn()

bool COrg_ref_Base::IsSetSyn ( void  ) const

inline

synonyms for taxname or common 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 504 of file Org_ref_.hpp.

References COrg_ref_Base::m_set_State.

Referenced by BOOST_AUTO_TEST_CASE(), fill_orgref(), COrg_ref::FilterOutParts(), fta_fix_orgref(), fta_get_orgref_byid(), GetOrgrefDifferences(), COrg_ref::MakeCommon(), CFindASN1Dlg::ReplaceInOrg(), and CCleanup::x_MergeDupOrgRefs().

IsSetTaxname()

bool COrg_ref_Base::IsSetTaxname ( void  ) const

inline

preferred formal name Check if a value has been assigned to Taxname data member.

Data member Taxname is optional; its type is defined as 'typedef string TTaxname'

Returns

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

Definition at line 360 of file Org_ref_.hpp.

References COrg_ref_Base::m_set_State.

Referenced by AddBioSourceToAttributes(), AddNode(), CCleanup::AreBioSourcesMergeable(), BOOST_AUTO_TEST_CASE(), COrg_ref_Base::CanGetTaxname(), CStrainRequest::Check(), CheckMetagenome(), CheckStrainReply(), CompareDescrFeatSources(), CStrainRequest::CStrainRequest(), fill_orgref(), COrg_ref::FilterOutParts(), FindMatchInOrgRef(), fix_taxname_dot(), fta_fix_orgref(), fta_replace_org(), IEditingAction::GetActionCommand(), CInfluenzaSet::GetKey(), CStrainMap::GetKey(), COrg_ref::GetLabel(), GetOrgrefDifferences(), CCachedTaxon3_impl::GetOrgReply(), GetSourceFields(), GetSprotDescr(), CCommentItem::GetStringForTLS(), CCommentItem::GetStringForTSA(), CCommentItem::GetStringForWGS(), CPriorityTaxNodes::getTaxName(), CTaxnameQual::GetValue(), IsMissingRequiredClone(), CBioSource::IsSetTaxname(), CEditingActionBiosourceTaxname::IsSetValue(), CEditingActionBiosourceTaxnameAfterBinomial::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), CNewCleanup_imp::IsSyntheticConstruct(), CTaxValidationAndCleanup::ListTaxLookupErrors(), MakeCommonBioSource(), MakeMailReportPostReport(), MakeMailReportPreReport(), SRemovableOrgModNote::operator()(), OrgDiffers(), PropogateSuppliedLineage(), CFindASN1Dlg::ReplaceInOrg(), s_GetOrgRefContentLabel(), s_OrgrefEquivalent(), s_SuppressMultipleEquivBioSources(), s_TitleEndsInOrganism(), s_TitleFromBioSource(), s_TitleFromSegment(), COrg_ref_Base::SetTaxname(), CStrainRequest::StrainContainsTaxonInfo(), COrg_ref::UpdateFromTable(), CSrcDescEditorPanel::UpdateSeqdesc(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_bioseq::ValidateOrgContext(), CValidError_imp::ValidateOrgRef(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateSeqDescContext(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddHIVModifiers(), CStrainRequest::x_AddOneStrain(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers(), COrgGeneralPanel::x_ApplyChangesToSource(), CAppendModToOrg::x_ApplyToBioSource(), CNewCleanup_imp::x_ChangePopToPhy(), CStrainRequest::x_CheckOneStrain(), CNewCleanup_imp::x_CleanupOldName(), CFeatureGenerator::SImplementation::x_ConstructRnaName(), CSourceFeatureItem::x_GatherInfo(), CDeflineGenerator::x_GetModifiers(), CCachedTaxon3::x_GetReplyForOrgRef(), COrg_ref::x_GetTaxnameAfterFirstTwoWords(), CTaxValidationAndCleanup::x_InterpretTaxonomyError(), CBioSource::x_RemoveNameElementDiffs(), CNewCleanup_imp::x_RemovePopPhyBioSource(), CBioSource::x_RemoveStopWords(), and CRemoteUpdater::xUpdateOrgTaxname().

IsVirus()

bool COrgName_Base::C_Name::IsVirus ( void  ) const

inline

Check if variant Virus is selected.

Virus type is defined as 'typedef string TVirus'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 721 of file OrgName_.hpp.

operator const Tdata &() [1/2]

CMultiOrgName_Base::operator const CMultiOrgName_Base::Tdata & ( void  ) const

inline

Conversion operator to 'const Tdata' type.

Definition at line 178 of file MultiOrgName_.hpp.

operator const Tdata &() [2/2]

CPartialOrgName_Base::operator const CPartialOrgName_Base::Tdata & ( void  ) const

inline

Conversion operator to 'const Tdata' type.

Definition at line 178 of file PartialOrgName_.hpp.

operator Tdata &() [1/2]

CMultiOrgName_Base::operator CMultiOrgName_Base::Tdata & ( void  )

inline

Conversion operator to 'Tdata' type.

Definition at line 184 of file MultiOrgName_.hpp.

operator Tdata &() [2/2]

CPartialOrgName_Base::operator CPartialOrgName_Base::Tdata & ( void  )

inline

Conversion operator to 'Tdata' type.

Definition at line 184 of file PartialOrgName_.hpp.

operator=() [1/12]

C_Name& COrgName_Base::C_Name::operator= ( const C_Name &  )

private

operator=() [2/12]

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

private

operator=() [3/12]

CBinomialOrgName_Base& CBinomialOrgName_Base::operator= ( const CBinomialOrgName_Base &  )

private

operator=() [4/12]

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

private

operator=() [5/12]

CMultiOrgName_Base& CMultiOrgName_Base::operator= ( const CMultiOrgName_Base &  )

private

operator=() [6/12]

COrg_ref_Base& COrg_ref_Base::operator= ( const COrg_ref_Base &  )

private

operator=() [7/12]

COrgMod_Base& COrgMod_Base::operator= ( const COrgMod_Base &  )

private

operator=() [8/12]

COrgName_Base& COrgName_Base::operator= ( const COrgName_Base &  )

private

operator=() [9/12]

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

private

operator=() [10/12]

CPartialOrgName_Base& CPartialOrgName_Base::operator= ( const CPartialOrgName_Base &  )

private

operator=() [11/12]

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

private

operator=() [12/12]

CTaxElement_Base& CTaxElement_Base::operator= ( const CTaxElement_Base &  )

private

Reset() [1/8]

void CBinomialOrgName_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 68 of file BinomialOrgName_.cpp.

References CBinomialOrgName_Base::ResetGenus(), CBinomialOrgName_Base::ResetSpecies(), and CBinomialOrgName_Base::ResetSubspecies().

Reset() [2/8]

void CMultiOrgName_Base::Reset

(

void

)

Reset data member.

Definition at line 51 of file MultiOrgName_.cpp.

References CMultiOrgName_Base::m_data, and CMultiOrgName_Base::m_set_State.

Reset() [3/8]

void COrg_ref_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 99 of file Org_ref_.cpp.

References COrg_ref_Base::ResetCommon(), COrg_ref_Base::ResetDb(), COrg_ref_Base::ResetMod(), COrg_ref_Base::ResetOrgname(), COrg_ref_Base::ResetSyn(), and COrg_ref_Base::ResetTaxname().

Referenced by BOOST_AUTO_TEST_CASE(), COrg_ref::FilterOutParts(), and TaxClient::GetOrgRef().

Reset() [4/8]

void COrgMod_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 110 of file OrgMod_.cpp.

References COrgMod_Base::ResetAttrib(), COrgMod_Base::ResetSubname(), and COrgMod_Base::ResetSubtype().

Reset() [5/8]

void COrgName_Base::C_Name::Reset

(

void

)

Reset the whole object.

Definition at line 54 of file OrgName_.cpp.

References COrgName_Base::C_Name::e_not_set, COrgName_Base::C_Name::m_choice, and COrgName_Base::C_Name::ResetSelection().

Reset() [6/8]

void COrgName_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 286 of file OrgName_.cpp.

References COrgName_Base::ResetAttrib(), COrgName_Base::ResetDiv(), COrgName_Base::ResetGcode(), COrgName_Base::ResetLineage(), COrgName_Base::ResetMgcode(), COrgName_Base::ResetMod(), COrgName_Base::ResetName(), and COrgName_Base::ResetPgcode().

Referenced by COrgName_Base::C_Name::~C_Name().

Reset() [7/8]

void CPartialOrgName_Base::Reset

(

void

)

Reset data member.

Definition at line 51 of file PartialOrgName_.cpp.

References CPartialOrgName_Base::m_data, and CPartialOrgName_Base::m_set_State.

Reset() [8/8]

void CTaxElement_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 73 of file TaxElement_.cpp.

References CTaxElement_Base::ResetFixed_level(), CTaxElement_Base::ResetLevel(), and CTaxElement_Base::ResetName().

ResetAttrib() [1/2]

void COrgMod_Base::ResetAttrib

(

void

)

Reset Attrib data member.

Definition at line 104 of file OrgMod_.cpp.

References COrgMod_Base::m_Attrib, and COrgMod_Base::m_set_State.

Referenced by COrgMod_Base::Reset().

ResetAttrib() [2/2]

void COrgName_Base::ResetAttrib

(

void

)

Reset Attrib data member.

Definition at line 262 of file OrgName_.cpp.

References COrgName_Base::m_Attrib, and COrgName_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), COrgName_Base::Reset(), and COrgName::x_ResetAttribFlag().

ResetCommon()

void COrg_ref_Base::ResetCommon

(

void

)

Reset Common data member.

Definition at line 58 of file Org_ref_.cpp.

References COrg_ref_Base::m_Common, and COrg_ref_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), CFindASN1Dlg::ReplaceInOrg(), COrg_ref_Base::Reset(), and CSourceOtherPanel::TransferToOrgRef().

ResetDb()

void COrg_ref_Base::ResetDb

(

void

)

Reset Db data member.

Definition at line 70 of file Org_ref_.cpp.

References COrg_ref_Base::m_Db, and COrg_ref_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), CCleanup::MakeIRDFeatsFromSourceXrefs(), and COrg_ref_Base::Reset().

ResetDiv()

void COrgName_Base::ResetDiv

(

void

)

Reset Div data member.

Definition at line 280 of file OrgName_.cpp.

References COrgName_Base::m_Div, and COrgName_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), and COrgName_Base::Reset().

ResetFixed_level()

void CTaxElement_Base::ResetFixed_level ( void  )

inline

Reset Fixed_level data member.

Definition at line 262 of file TaxElement_.hpp.

References CTaxElement_Base::m_Fixed_level, and CTaxElement_Base::m_set_State.

Referenced by CTaxElement_Base::Reset().

ResetGcode()

void COrgName_Base::ResetGcode ( void  )

inline

Reset Gcode data member.

Definition at line 911 of file OrgName_.hpp.

References COrgName_Base::m_Gcode, and COrgName_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), and COrgName_Base::Reset().

ResetGenus()

void CBinomialOrgName_Base::ResetGenus

(

void

)

Reset Genus data member.

Definition at line 50 of file BinomialOrgName_.cpp.

References CBinomialOrgName_Base::m_Genus, and CBinomialOrgName_Base::m_set_State.

Referenced by CBinomialOrgName_Base::Reset().

ResetLevel()

END_ENUM_INFO void CTaxElement_Base::ResetLevel

(

void

)

Reset Level data member.

Definition at line 61 of file TaxElement_.cpp.

References CTaxElement_Base::m_Level, and CTaxElement_Base::m_set_State.

Referenced by CTaxElement_Base::Reset().

ResetLineage()

void COrgName_Base::ResetLineage

(

void

)

Reset Lineage data member.

Definition at line 274 of file OrgName_.cpp.

References COrgName_Base::m_Lineage, and COrgName_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), PropogateSuppliedLineage(), and COrgName_Base::Reset().

ResetMgcode()

void COrgName_Base::ResetMgcode ( void  )

inline

Reset Mgcode data member.

Definition at line 958 of file OrgName_.hpp.

References COrgName_Base::m_Mgcode, and COrgName_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), and COrgName_Base::Reset().

ResetMod() [1/2]

void COrg_ref_Base::ResetMod

(

void

)

Reset Mod data member.

Definition at line 64 of file Org_ref_.cpp.

References COrg_ref_Base::m_Mod, and COrg_ref_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), COrg_ref::MakeCommon(), and COrg_ref_Base::Reset().

ResetMod() [2/2]

void COrgName_Base::ResetMod

(

void

)

Reset Mod data member.

Definition at line 268 of file OrgName_.cpp.

References COrgName_Base::m_Mod, and COrgName_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), and COrgName_Base::Reset().

ResetName() [1/2]

void COrgName_Base::ResetName

(

void

)

Reset Name data member.

Definition at line 245 of file OrgName_.cpp.

References COrgName_Base::m_Name.

Referenced by COrg_ref::FilterOutParts(), COrgName_Base::Reset(), and s_MoreCleanupForTaxnameChange().

ResetName() [2/2]

void CTaxElement_Base::ResetName

(

void

)

Reset Name data member.

Definition at line 67 of file TaxElement_.cpp.

References CTaxElement_Base::m_Name, and CTaxElement_Base::m_set_State.

Referenced by CTaxElement_Base::Reset().

ResetOrgname()

void COrg_ref_Base::ResetOrgname

(

void

)

Reset Orgname data member.

Definition at line 82 of file Org_ref_.cpp.

References COrg_ref_Base::m_Orgname.

Referenced by COrg_ref::FilterOutParts(), and COrg_ref_Base::Reset().

ResetPgcode()

void COrgName_Base::ResetPgcode ( void  )

inline

Reset Pgcode data member.

Definition at line 1052 of file OrgName_.hpp.

References COrgName_Base::m_Pgcode, and COrgName_Base::m_set_State.

Referenced by COrg_ref::FilterOutParts(), and COrgName_Base::Reset().

ResetSelection()

void COrgName_Base::C_Name::ResetSelection

(

void

)

Reset the selection (set it to e_not_set).

Definition at line 60 of file OrgName_.cpp.

References e_not_set.

Referenced by COrgName_Base::C_Name::Reset().

ResetSpecies()

void CBinomialOrgName_Base::ResetSpecies

(

void

)

Reset Species data member.

Definition at line 56 of file BinomialOrgName_.cpp.

References CBinomialOrgName_Base::m_set_State, and CBinomialOrgName_Base::m_Species.

Referenced by CBinomialOrgName_Base::Reset().

ResetSubname()

END_ENUM_INFO void COrgMod_Base::ResetSubname

(

void

)

Reset Subname data member.

Definition at line 98 of file OrgMod_.cpp.

References COrgMod_Base::m_set_State, and COrgMod_Base::m_Subname.

Referenced by COrgMod_Base::Reset().

ResetSubspecies()

void CBinomialOrgName_Base::ResetSubspecies

(

void

)

Reset Subspecies data member.

Definition at line 62 of file BinomialOrgName_.cpp.

References CBinomialOrgName_Base::m_set_State, and CBinomialOrgName_Base::m_Subspecies.

Referenced by CBinomialOrgName_Base::Reset().

ResetSubtype()

void COrgMod_Base::ResetSubtype ( void  )

inline

Reset Subtype data member.

Definition at line 300 of file OrgMod_.hpp.

References COrgMod_Base::m_set_State, and COrgMod_Base::m_Subtype.

Referenced by COrgMod_Base::Reset().

ResetSyn()

void COrg_ref_Base::ResetSyn

(

void

)

Reset Syn data member.

Definition at line 76 of file Org_ref_.cpp.

References COrg_ref_Base::m_set_State, and COrg_ref_Base::m_Syn.

Referenced by COrg_ref::CleanForGenBank(), fill_orgref(), COrg_ref::FilterOutParts(), fta_fix_orgref(), fta_get_orgref_byid(), COrg_ref::MakeCommon(), and COrg_ref_Base::Reset().

ResetTaxname()

void COrg_ref_Base::ResetTaxname

(

void

)

Reset Taxname data member.

Definition at line 52 of file Org_ref_.cpp.

References COrg_ref_Base::m_set_State, and COrg_ref_Base::m_Taxname.

Referenced by COrg_ref::FilterOutParts(), COrg_ref_Base::Reset(), COrgGeneralPanel::x_ApplyChangesToSource(), and CBioSource::x_RemoveStopWords().

Select() [1/2]

void COrgName_Base::C_Name::Select	(	E_Choice	index,
		EResetVariant	reset,
		CObjectMemoryPool *	pool
	)

Select the requested variant if needed, allocating CObject variants from memory pool.

Select() [2/2]

void COrgName_Base::C_Name::Select	(	E_Choice	index,
		EResetVariant	reset = eDoResetVariant
	)

Select the requested variant if needed.

Parameters

index	New selection state.
reset	Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant.

SelectionName()

NCBI_NS_STD::string COrgName_Base::C_Name::SelectionName ( E_Choice  index )

static

Retrieve selection name (for diagnostic purposes).

Parameters

index

One of possible selection states.

Returns

Name string.

Definition at line 111 of file OrgName_.cpp.

Set() [1/2]

CMultiOrgName_Base::Tdata & CMultiOrgName_Base::Set ( void  )

inline

Assign a value to data member.

Returns

Reference to the data value.

Definition at line 171 of file MultiOrgName_.hpp.

References CMultiOrgName_Base::m_data, and CMultiOrgName_Base::m_set_State.

Referenced by CAutogeneratedCleanup::x_BasicCleanupOrgNameName_hybrid().

Set() [2/2]

CPartialOrgName_Base::Tdata & CPartialOrgName_Base::Set ( void  )

inline

Assign a value to data member.

Returns

Reference to the data value.

Definition at line 171 of file PartialOrgName_.hpp.

References CPartialOrgName_Base::m_data, and CPartialOrgName_Base::m_set_State.

SetAttrib() [1/6]

void COrgMod_Base::SetAttrib ( const TAttrib &  value )

inline

Assign a value to Attrib data member.

Parameters

value

Value to assign

Definition at line 403 of file OrgMod_.hpp.

References COrgMod_Base::m_Attrib, COrgMod_Base::m_set_State, and rapidjson::value.

SetAttrib() [2/6]

void COrgName_Base::SetAttrib ( const TAttrib &  value )

inline

Assign a value to Attrib data member.

Parameters

value

Value to assign

Definition at line 801 of file OrgName_.hpp.

References COrgName_Base::m_Attrib, COrgName_Base::m_set_State, and rapidjson::value.

SetAttrib() [3/6]

void COrgMod_Base::SetAttrib ( COrgMod_Base::TAttrib &&  value )

inline

Definition at line 410 of file OrgMod_.hpp.

References COrgMod_Base::m_Attrib, COrgMod_Base::m_set_State, and rapidjson::value.

SetAttrib() [4/6]

void COrgName_Base::SetAttrib ( COrgName_Base::TAttrib &&  value )

inline

Definition at line 808 of file OrgName_.hpp.

References COrgName_Base::m_Attrib, COrgName_Base::m_set_State, and rapidjson::value.

SetAttrib() [5/6]

COrgMod_Base::TAttrib & COrgMod_Base::SetAttrib ( void  )

inline

Assign a value to Attrib data member.

Returns

Reference to the data value.

Definition at line 417 of file OrgMod_.hpp.

References COrgMod_Base::IsSetAttrib(), COrgMod_Base::m_Attrib, COrgMod_Base::m_set_State, and CSerialObject::UnassignedString().

SetAttrib() [6/6]

COrgName_Base::TAttrib & COrgName_Base::SetAttrib ( void  )

inline

Assign a value to Attrib data member.

Returns

Reference to the data value.

Definition at line 815 of file OrgName_.hpp.

References COrgName_Base::IsSetAttrib(), COrgName_Base::m_Attrib, COrgName_Base::m_set_State, and CSerialObject::UnassignedString().

Referenced by COrgName::x_ResetAttribFlag(), and COrgName::x_SetAttribFlag().

SetBinomial() [1/2]

void COrgName_Base::C_Name::SetBinomial

(

TBinomial &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 133 of file OrgName_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetBinomial() [2/2]

COrgName_Base::C_Name::TBinomial & COrgName_Base::C_Name::SetBinomial

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 127 of file OrgName_.cpp.

References eDoNotResetVariant.

SetCommon() [1/3]

void COrg_ref_Base::SetCommon ( const TCommon &  value )

inline

Assign a value to Common data member.

Parameters

value

Value to assign

Definition at line 428 of file Org_ref_.hpp.

References COrg_ref_Base::m_Common, COrg_ref_Base::m_set_State, and rapidjson::value.

Referenced by fill_orgref(), GetEmblOrgRef(), CFindASN1Dlg::ReplaceInOrg(), s_ProcessOrgRefMapLine(), CSourceOtherPanel::TransferToOrgRef(), CAutogeneratedCleanup::x_BasicCleanupOrgRef(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC(), CSeqDBVol::x_GetTaxonomy(), and XMLFakeBioSources().

SetCommon() [2/3]

void COrg_ref_Base::SetCommon ( COrg_ref_Base::TCommon &&  value )

inline

Definition at line 435 of file Org_ref_.hpp.

References COrg_ref_Base::m_Common, COrg_ref_Base::m_set_State, and rapidjson::value.

SetCommon() [3/3]

COrg_ref_Base::TCommon & COrg_ref_Base::SetCommon ( void  )

inline

Assign a value to Common data member.

Returns

Reference to the data value.

Definition at line 442 of file Org_ref_.hpp.

References COrg_ref_Base::IsSetCommon(), COrg_ref_Base::m_Common, COrg_ref_Base::m_set_State, and CSerialObject::UnassignedString().

Referenced by COrg_ref::UpdateFromTable().

SetDb()

COrg_ref_Base::TDb & COrg_ref_Base::SetDb ( void  )

inline

Assign a value to Db data member.

Returns

Reference to the data value.

Definition at line 497 of file Org_ref_.hpp.

References COrg_ref_Base::m_Db, and COrg_ref_Base::m_set_State.

Referenced by BOOST_AUTO_TEST_CASE(), COrg_ref::FilterOutParts(), COrg_ref::MakeCommon(), CCleanup::MakeIRDFeatsFromSourceXrefs(), CNewCleanup_imp::OrgrefBC(), COrgrefProp::RemoveOrgrefProp(), s_ProcessOrgRefMapLine(), COrg_ref::SetTaxId(), CAutogeneratedCleanup::x_BasicCleanupOrgRef(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC(), CTaxon1::x_ConvertOrgrefProps(), CSeqDBVol::x_GetTaxonomy(), and CCleanup::x_MergeDupOrgRefs().

SetDiv() [1/3]

void COrgName_Base::SetDiv ( const TDiv &  value )

inline

Assign a value to Div data member.

Parameters

value

Value to assign

Definition at line 1014 of file OrgName_.hpp.

References COrgName_Base::m_Div, COrgName_Base::m_set_State, and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), COrg_ref::UpdateFromTable(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), and CCleanup::x_MergeDupOrgNames().

SetDiv() [2/3]

void COrgName_Base::SetDiv ( COrgName_Base::TDiv &&  value )

inline

Definition at line 1021 of file OrgName_.hpp.

References COrgName_Base::m_Div, COrgName_Base::m_set_State, and rapidjson::value.

SetDiv() [3/3]

COrgName_Base::TDiv & COrgName_Base::SetDiv ( void  )

inline

Assign a value to Div data member.

Returns

Reference to the data value.

Definition at line 1028 of file OrgName_.hpp.

References COrgName_Base::IsSetDiv(), COrgName_Base::m_Div, COrgName_Base::m_set_State, and CSerialObject::UnassignedString().

SetFixed_level() [1/2]

void CTaxElement_Base::SetFixed_level ( CTaxElement_Base::TFixed_level  value )

inline

Assign a value to Fixed_level data member.

Parameters

value

Value to assign

Definition at line 278 of file TaxElement_.hpp.

References CTaxElement_Base::m_Fixed_level, CTaxElement_Base::m_set_State, and rapidjson::value.

SetFixed_level() [2/2]

CTaxElement_Base::TFixed_level & CTaxElement_Base::SetFixed_level ( void  )

inline

Assign a value to Fixed_level data member.

Returns

Reference to the data value.

Definition at line 285 of file TaxElement_.hpp.

References CTaxElement_Base::IsSetFixed_level(), CTaxElement_Base::m_Fixed_level, CTaxElement_Base::m_set_State, and CSerialObject::UnassignedByte().

SetGcode() [1/2]

void COrgName_Base::SetGcode ( COrgName_Base::TGcode  value )

inline

Assign a value to Gcode data member.

Parameters

value

Value to assign

Definition at line 927 of file OrgName_.hpp.

References COrgName_Base::m_Gcode, COrgName_Base::m_set_State, and rapidjson::value.

Referenced by COrg_ref::UpdateFromTable(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), and CCleanup::x_MergeDupOrgNames().

SetGcode() [2/2]

COrgName_Base::TGcode & COrgName_Base::SetGcode ( void  )

inline

Assign a value to Gcode data member.

Returns

Reference to the data value.

Definition at line 934 of file OrgName_.hpp.

References COrgName_Base::IsSetGcode(), COrgName_Base::m_Gcode, COrgName_Base::m_set_State, and CSerialObject::UnassignedByte().

Referenced by CDescrModApply::x_TryOrgNameMod().

SetGenus() [1/3]

void CBinomialOrgName_Base::SetGenus ( const TGenus &  value )

inline

Assign a value to Genus data member.

Parameters

value

Value to assign

Definition at line 264 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_Genus, CBinomialOrgName_Base::m_set_State, and rapidjson::value.

SetGenus() [2/3]

void CBinomialOrgName_Base::SetGenus ( CBinomialOrgName_Base::TGenus &&  value )

inline

Definition at line 271 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_Genus, CBinomialOrgName_Base::m_set_State, and rapidjson::value.

SetGenus() [3/3]

CBinomialOrgName_Base::TGenus & CBinomialOrgName_Base::SetGenus ( void  )

inline

Assign a value to Genus data member.

Returns

Reference to the data value.

Definition at line 278 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::IsSetGenus(), CBinomialOrgName_Base::m_Genus, CBinomialOrgName_Base::m_set_State, and CSerialObject::UnassignedString().

SetHybrid() [1/2]

void COrgName_Base::C_Name::SetHybrid

(

THybrid &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 161 of file OrgName_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetHybrid() [2/2]

COrgName_Base::C_Name::THybrid & COrgName_Base::C_Name::SetHybrid

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 155 of file OrgName_.cpp.

References eDoNotResetVariant.

Referenced by CAutogeneratedCleanup::x_BasicCleanupOrgNameName().

SetLevel() [1/3]

void CTaxElement_Base::SetLevel ( const TLevel &  value )

inline

Assign a value to Level data member.

Parameters

value

Value to assign

Definition at line 318 of file TaxElement_.hpp.

References CTaxElement_Base::m_Level, CTaxElement_Base::m_set_State, and rapidjson::value.

SetLevel() [2/3]

void CTaxElement_Base::SetLevel ( CTaxElement_Base::TLevel &&  value )

inline

Definition at line 325 of file TaxElement_.hpp.

References CTaxElement_Base::m_Level, CTaxElement_Base::m_set_State, and rapidjson::value.

SetLevel() [3/3]

CTaxElement_Base::TLevel & CTaxElement_Base::SetLevel ( void  )

inline

Assign a value to Level data member.

Returns

Reference to the data value.

Definition at line 332 of file TaxElement_.hpp.

References CTaxElement_Base::IsSetLevel(), CTaxElement_Base::m_Level, CTaxElement_Base::m_set_State, and CSerialObject::UnassignedString().

SetLineage() [1/3]

void COrgName_Base::SetLineage ( const TLineage &  value )

inline

Assign a value to Lineage data member.

Parameters

value

Value to assign

Definition at line 873 of file OrgName_.hpp.

References COrgName_Base::m_Lineage, COrgName_Base::m_set_State, and rapidjson::value.

Referenced by PropogateSuppliedLineage(), COrg_ref::UpdateFromTable(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), and CCleanup::x_MergeDupOrgNames().

SetLineage() [2/3]

void COrgName_Base::SetLineage ( COrgName_Base::TLineage &&  value )

inline

Definition at line 880 of file OrgName_.hpp.

References COrgName_Base::m_Lineage, COrgName_Base::m_set_State, and rapidjson::value.

SetLineage() [3/3]

COrgName_Base::TLineage & COrgName_Base::SetLineage ( void  )

inline

Assign a value to Lineage data member.

Returns

Reference to the data value.

Definition at line 887 of file OrgName_.hpp.

References COrgName_Base::IsSetLineage(), COrgName_Base::m_Lineage, COrgName_Base::m_set_State, and CSerialObject::UnassignedString().

SetMgcode() [1/2]

void COrgName_Base::SetMgcode ( COrgName_Base::TMgcode  value )

inline

Assign a value to Mgcode data member.

Parameters

value

Value to assign

Definition at line 974 of file OrgName_.hpp.

References COrgName_Base::m_Mgcode, COrgName_Base::m_set_State, and rapidjson::value.

Referenced by COrg_ref::UpdateFromTable(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), and CCleanup::x_MergeDupOrgNames().

SetMgcode() [2/2]

COrgName_Base::TMgcode & COrgName_Base::SetMgcode ( void  )

inline

Assign a value to Mgcode data member.

Returns

Reference to the data value.

Definition at line 981 of file OrgName_.hpp.

References COrgName_Base::IsSetMgcode(), COrgName_Base::m_Mgcode, COrgName_Base::m_set_State, and CSerialObject::UnassignedByte().

Referenced by CDescrModApply::x_TryOrgNameMod().

SetMod() [1/2]

COrg_ref_Base::TMod & COrg_ref_Base::SetMod ( void  )

inline

Assign a value to Mod data member.

Returns

Reference to the data value.

Definition at line 472 of file Org_ref_.hpp.

References COrg_ref_Base::m_Mod, and COrg_ref_Base::m_set_State.

Referenced by COrg_ref::MakeCommon(), CFindASN1Dlg::ReplaceInOrg(), CAutogeneratedCleanup::x_BasicCleanupOrgRef(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC(), CNewCleanup_imp::x_GBQualToOrgRef(), and CCleanup::x_MergeDupOrgRefs().

SetMod() [2/2]

COrgName_Base::TMod & COrgName_Base::SetMod ( void  )

inline

Assign a value to Mod data member.

Returns

Reference to the data value.

Definition at line 845 of file OrgName_.hpp.

References COrgName_Base::m_Mod, and COrgName_Base::m_set_State.

Referenced by AddOrgMod(), BOOST_AUTO_TEST_CASE(), CollectSubNames(), GetSprotDescr(), COrgName::MakeCommon(), COrgName::RemoveModBySubtype(), CMacroFunction_AddorSetContElement::s_AddSrcOrgMod(), s_SetBioSourceField(), COrgName::SetNomenclature(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeatDataOrgName(), CCleanup::x_MergeDupOrgNames(), CNewCleanup_imp::x_MovedNamedValuesInStrain(), and CStrainSerotypeInfluenza::x_UpdateStrainSerotype().

SetName() [1/5]

void CTaxElement_Base::SetName ( const TName &  value )

inline

Assign a value to Name data member.

Parameters

value

Value to assign

Definition at line 365 of file TaxElement_.hpp.

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

SetName() [2/5]

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

inline

Definition at line 372 of file TaxElement_.hpp.

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

SetName() [3/5]

void COrgName_Base::SetName

(

COrgName_Base::TName &

value

)

Assign a value to Name data member.

Parameters

value

Reference to value.

Definition at line 250 of file OrgName_.cpp.

References COrgName_Base::m_Name, and rapidjson::value.

Referenced by COrgName::MakeCommon(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeatDataOrgName().

SetName() [4/5]

COrgName_Base::TName & COrgName_Base::SetName

(

void

)

Assign a value to Name data member.

Returns

Reference to the data value.

Definition at line 255 of file OrgName_.cpp.

References COrgName_Base::m_Name.

SetName() [5/5]

CTaxElement_Base::TName & CTaxElement_Base::SetName ( void  )

inline

Assign a value to Name data member.

Returns

Reference to the data value.

Definition at line 379 of file TaxElement_.hpp.

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

SetNamedhybrid() [1/2]

void COrgName_Base::C_Name::SetNamedhybrid

(

TNamedhybrid &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 183 of file OrgName_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetNamedhybrid() [2/2]

COrgName_Base::C_Name::TNamedhybrid & COrgName_Base::C_Name::SetNamedhybrid

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 177 of file OrgName_.cpp.

References eDoNotResetVariant.

SetOrgname() [1/2]

void COrg_ref_Base::SetOrgname

(

COrg_ref_Base::TOrgname &

value

)

Assign a value to Orgname data member.

Parameters

value

Reference to value.

Definition at line 87 of file Org_ref_.cpp.

References COrg_ref_Base::m_Orgname, and rapidjson::value.

Referenced by AddMissingCommonOrgMods(), AddOrgmod(), AddOrgMod(), CSpecificHostMapForFix::ApplyToOrg(), CBioSource::AutoFix(), BOOST_AUTO_TEST_CASE(), CreateRawBioSources(), FakeEmblBioSources(), FakeGenBankBioSources(), fta_fix_orgref_div(), GetEmblDescr(), GetOrganismFrom_OS_OC(), CLocalTaxon::LookupMerge(), COrg_ref::MakeCommon(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveOrgMod(), CBioSource::RemoveUnexpectedViralQualifiers(), CFindASN1Dlg::ReplaceInOrg(), s_ProcessOrgRefMapLine(), CBioSource::SetDisableStrainForwarding(), TestBulkSpecificHostFixList(), CSourceOtherPanel::TransferToOrgRef(), CBioSource::UpdateWithBioSample(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), COrgGeneralPanel::x_ApplyChangesToSource(), CTaxValidationAndCleanup::x_ApplySpecificHostMap(), CAutogeneratedCleanup::x_BasicCleanupOrgRef(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC(), CNewCleanup_imp::x_CleanupOldName(), CNewCleanup_imp::x_CleanupOrgModNoteEC(), CNewCleanup_imp::x_CopyGBBlockDivToOrgnameDiv(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupOrgRef(), CAgpconvertApplication::x_HandleTaxArgs(), CCleanup::x_MergeDupOrgRefs(), CBioSource::x_RemoveStopWords(), and XMLFakeBioSources().

SetOrgname() [2/2]

COrg_ref_Base::TOrgname & COrg_ref_Base::SetOrgname

(

void

)

Assign a value to Orgname data member.

Returns

Reference to the data value.

Definition at line 92 of file Org_ref_.cpp.

References COrg_ref_Base::m_Orgname.

Referenced by COrg_ref::FilterOutParts(), and COrg_ref::UpdateFromTable().

SetPartial() [1/2]

void COrgName_Base::C_Name::SetPartial

(

TPartial &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 205 of file OrgName_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetPartial() [2/2]

COrgName_Base::C_Name::TPartial & COrgName_Base::C_Name::SetPartial

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 199 of file OrgName_.cpp.

References eDoNotResetVariant.

SetPgcode() [1/2]

void COrgName_Base::SetPgcode ( COrgName_Base::TPgcode  value )

inline

Assign a value to Pgcode data member.

Parameters

value

Value to assign

Definition at line 1068 of file OrgName_.hpp.

References COrgName_Base::m_Pgcode, COrgName_Base::m_set_State, and rapidjson::value.

SetPgcode() [2/2]

COrgName_Base::TPgcode & COrgName_Base::SetPgcode ( void  )

inline

Assign a value to Pgcode data member.

Returns

Reference to the data value.

Definition at line 1075 of file OrgName_.hpp.

References COrgName_Base::IsSetPgcode(), COrgName_Base::m_Pgcode, COrgName_Base::m_set_State, and CSerialObject::UnassignedByte().

Referenced by CDescrModApply::x_TryOrgNameMod().

SetSpecies() [1/3]

void CBinomialOrgName_Base::SetSpecies ( const TSpecies &  value )

inline

Assign a value to Species data member.

Parameters

value

Value to assign

Definition at line 311 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_set_State, CBinomialOrgName_Base::m_Species, and rapidjson::value.

SetSpecies() [2/3]

void CBinomialOrgName_Base::SetSpecies ( CBinomialOrgName_Base::TSpecies &&  value )

inline

Definition at line 318 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_set_State, CBinomialOrgName_Base::m_Species, and rapidjson::value.

SetSpecies() [3/3]

CBinomialOrgName_Base::TSpecies & CBinomialOrgName_Base::SetSpecies ( void  )

inline

Assign a value to Species data member.

Returns

Reference to the data value.

Definition at line 325 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::IsSetSpecies(), CBinomialOrgName_Base::m_set_State, CBinomialOrgName_Base::m_Species, and CSerialObject::UnassignedString().

SetSubname() [1/3]

void COrgMod_Base::SetSubname ( const TSubname &  value )

inline

Assign a value to Subname data member.

Parameters

value

Value to assign

Definition at line 356 of file OrgMod_.hpp.

References COrgMod_Base::m_set_State, COrgMod_Base::m_Subname, and rapidjson::value.

Referenced by CSrcStructuredVoucherPartColumn::AddToBioSource(), CPrefixAuthority::apply_to(), BioSourceFromImpFeat(), BOOST_AUTO_TEST_CASE(), CSrcModListPanel::PopulateModifiers(), CEditingActionBiosourceStructuredVoucher::ResetValue(), CMacroFunction_AddorSetContElement::s_AddSrcOrgMod(), s_SetBioSourceField(), SetOrgMod(), CEditingActionBiosourceOrgMod::SetValue(), CEditingActionBiosourceAllNotes::SetValue(), CEditingActionBiosourceStructuredVoucher::SetValue(), CMacroFunction_ApplyStrucVoucherPart::x_AddNewQual(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CSourceModParser::x_ApplyMods(), CMacroFunction_ApplyStrucVoucherPart::x_ApplyPart(), CMacroFunction_ApplyStrucVoucherPart::x_RemovePart(), and CGff2Record::xMigrateAttributesOrgName().

SetSubname() [2/3]

void COrgMod_Base::SetSubname ( COrgMod_Base::TSubname &&  value )

inline

Definition at line 363 of file OrgMod_.hpp.

References COrgMod_Base::m_set_State, COrgMod_Base::m_Subname, and rapidjson::value.

SetSubname() [3/3]

COrgMod_Base::TSubname & COrgMod_Base::SetSubname ( void  )

inline

Assign a value to Subname data member.

Returns

Reference to the data value.

Definition at line 370 of file OrgMod_.hpp.

References COrgMod_Base::IsSetSubname(), COrgMod_Base::m_set_State, COrgMod_Base::m_Subname, and CSerialObject::UnassignedString().

Referenced by COrgMod::AutoFix(), COrgMod::COrgMod(), COrgMod::FixCapitalization(), and COrgMod::RemoveAbbreviation().

SetSubspecies() [1/3]

void CBinomialOrgName_Base::SetSubspecies ( const TSubspecies &  value )

inline

Assign a value to Subspecies data member.

Parameters

value

Value to assign

Definition at line 358 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_set_State, CBinomialOrgName_Base::m_Subspecies, and rapidjson::value.

SetSubspecies() [2/3]

void CBinomialOrgName_Base::SetSubspecies ( CBinomialOrgName_Base::TSubspecies &&  value )

inline

Definition at line 365 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::m_set_State, CBinomialOrgName_Base::m_Subspecies, and rapidjson::value.

SetSubspecies() [3/3]

CBinomialOrgName_Base::TSubspecies & CBinomialOrgName_Base::SetSubspecies ( void  )

inline

Assign a value to Subspecies data member.

Returns

Reference to the data value.

Definition at line 372 of file BinomialOrgName_.hpp.

References CBinomialOrgName_Base::IsSetSubspecies(), CBinomialOrgName_Base::m_set_State, CBinomialOrgName_Base::m_Subspecies, and CSerialObject::UnassignedString().

SetSubtype() [1/2]

void COrgMod_Base::SetSubtype ( COrgMod_Base::TSubtype  value )

inline

Assign a value to Subtype data member.

Parameters

value

Value to assign

Definition at line 316 of file OrgMod_.hpp.

References COrgMod_Base::m_set_State, COrgMod_Base::m_Subtype, and rapidjson::value.

Referenced by CSrcStructuredVoucherPartColumn::AddToBioSource(), BioSourceFromImpFeat(), BOOST_AUTO_TEST_CASE(), CSrcModListPanel::PopulateModifiers(), CMacroFunction_AddorSetContElement::s_AddSrcOrgMod(), s_SetBioSourceField(), CEditingActionBiosourceOrgMod::SetValue(), CEditingActionBiosourceStructuredVoucher::SetValue(), CMacroFunction_ApplyStrucVoucherPart::x_AddNewQual(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CSourceModParser::x_ApplyMods(), and CGff2Record::xMigrateAttributesOrgName().

SetSubtype() [2/2]

COrgMod_Base::TSubtype & COrgMod_Base::SetSubtype ( void  )

inline

Assign a value to Subtype data member.

Returns

Reference to the data value.

Definition at line 323 of file OrgMod_.hpp.

References COrgMod_Base::IsSetSubtype(), COrgMod_Base::m_set_State, COrgMod_Base::m_Subtype, and CSerialObject::UnassignedByte().

Referenced by COrgMod::COrgMod().

SetSyn()

COrg_ref_Base::TSyn & COrg_ref_Base::SetSyn ( void  )

inline

Assign a value to Syn data member.

Returns

Reference to the data value.

Definition at line 522 of file Org_ref_.hpp.

References COrg_ref_Base::m_set_State, and COrg_ref_Base::m_Syn.

Referenced by fill_orgref(), fix_synonyms(), COrg_ref::MakeCommon(), CFindASN1Dlg::ReplaceInOrg(), and CCleanup::x_MergeDupOrgRefs().

SetTaxname() [1/3]

void COrg_ref_Base::SetTaxname ( const TTaxname &  value )

inline

Assign a value to Taxname data member.

Parameters

value

Value to assign

Definition at line 381 of file Org_ref_.hpp.

References COrg_ref_Base::m_set_State, COrg_ref_Base::m_Taxname, and rapidjson::value.

Referenced by CQualifierRequest::AddRequests(), TaxTreeData::addTaxToBioseq(), BOOST_AUTO_TEST_CASE(), CreateRawBioSources(), CStrainRequest::ExploreStrainsForTaxonInfo(), FakeEmblBioSources(), FakeGenBankBioSources(), fill_orgref(), fix_taxname_dot(), fta_fix_orgref(), GetEmblOrgRef(), CUnculTaxTool::GetReply(), CUnculturedTool::GetSuggestedCorrection(), MakeMailReportPostReport(), CUnculTaxTool::PreloadCache(), CDUpdater::reformatBioseq(), CFindASN1Dlg::ReplaceInOrg(), s_CreateOrgRef(), CGenusSpeciesFixup::s_GetNameFromTaxonServer(), s_ProcessOrgRefMapLine(), CStrainRequest::StrainContainsTaxonInfo(), TestBulkSpecificHostFixList(), CBioSource::UpdateWithBioSample(), CValidError_imp::ValidateTentativeName(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), COrgGeneralPanel::x_ApplyChangesToSource(), CUnculturedTool::x_GetReply(), CSeqDBVol::x_GetTaxonomy(), CAgpconvertApplication::x_HandleTaxArgs(), and XMLFakeBioSources().

SetTaxname() [2/3]

void COrg_ref_Base::SetTaxname ( COrg_ref_Base::TTaxname &&  value )

inline

Definition at line 388 of file Org_ref_.hpp.

References COrg_ref_Base::m_set_State, COrg_ref_Base::m_Taxname, and rapidjson::value.

SetTaxname() [3/3]

COrg_ref_Base::TTaxname & COrg_ref_Base::SetTaxname ( void  )

inline

Assign a value to Taxname data member.

Returns

Reference to the data value.

Definition at line 395 of file Org_ref_.hpp.

References COrg_ref_Base::IsSetTaxname(), COrg_ref_Base::m_set_State, COrg_ref_Base::m_Taxname, and CSerialObject::UnassignedString().

SetVirus() [1/2]

void COrgName_Base::C_Name::SetVirus

(

const TVirus &

value

)

Select the variant and set its data.

Parameters

value

Variant data.

Definition at line 143 of file OrgName_.cpp.

References eDoNotResetVariant, and rapidjson::value.

SetVirus() [2/2]

COrgName_Base::C_Name::TVirus & COrgName_Base::C_Name::SetVirus ( void  )

inline

Select the variant.

Returns

Reference to the variant data.

Definition at line 734 of file OrgName_.hpp.

References eDoNotResetVariant.

ThrowInvalidSelection()

void COrgName_Base::C_Name::ThrowInvalidSelection

(

E_Choice

index

)

const

Throw 'InvalidSelection' exception.

Parameters

index

Expected selection.

Definition at line 116 of file OrgName_.cpp.

References DIAG_COMPILE_INFO.

Which()

COrgName_Base::C_Name::E_Choice COrgName_Base::C_Name::Which ( void  ) const

inline

Which variant is currently selected.

Returns

Choice state enumerator.

Definition at line 686 of file OrgName_.hpp.

References COrgName_Base::C_Name::m_choice.

Referenced by COrgName::GetFlatName(), GetOrgnameDifferences(), s_MatchOrgname(), CValidError_imp::ValidateOrgName(), and CAutogeneratedCleanup::x_BasicCleanupOrgNameName().

~C_Name()

COrgName_Base::C_Name::~C_Name

(

void

)

Definition at line 239 of file OrgName_.cpp.

References COrgName_Base::Reset().

~CBinomialOrgName()

CBinomialOrgName::~CBinomialOrgName

(

void

)

Definition at line 50 of file BinomialOrgName.cpp.

~CBinomialOrgName_Base()

CBinomialOrgName_Base::~CBinomialOrgName_Base ( void  )

virtual

Definition at line 94 of file BinomialOrgName_.cpp.

~CMultiOrgName()

CMultiOrgName::~CMultiOrgName

(

void

)

Definition at line 50 of file MultiOrgName.cpp.

~CMultiOrgName_Base()

CMultiOrgName_Base::~CMultiOrgName_Base ( void  )

virtual

Definition at line 74 of file MultiOrgName_.cpp.

~COrg_ref_Base()

COrg_ref_Base::~COrg_ref_Base ( void  )

virtual

Definition at line 131 of file Org_ref_.cpp.

~COrgMod_Base()

COrgMod_Base::~COrgMod_Base ( void  )

virtual

Definition at line 137 of file OrgMod_.cpp.

~COrgName_Base()

COrgName_Base::~COrgName_Base ( void  )

virtual

Definition at line 323 of file OrgName_.cpp.

~CPartialOrgName()

CPartialOrgName::~CPartialOrgName

(

void

)

Definition at line 50 of file PartialOrgName.cpp.

~CPartialOrgName_Base()

CPartialOrgName_Base::~CPartialOrgName_Base ( void  )

virtual

Definition at line 74 of file PartialOrgName_.cpp.

~CTaxElement()

CTaxElement::~CTaxElement

(

void

)

Definition at line 50 of file TaxElement.cpp.

~CTaxElement_Base()

CTaxElement_Base::~CTaxElement_Base ( void  )

virtual

Definition at line 100 of file TaxElement_.cpp.

Variable Documentation

union { ... }

m_Attrib [1/2]

string COrgMod_Base::m_Attrib

private

Definition at line 275 of file OrgMod_.hpp.

Referenced by COrgMod_Base::GetAttrib(), COrgMod_Base::ResetAttrib(), and COrgMod_Base::SetAttrib().

m_Attrib [2/2]

string COrgName_Base::m_Attrib

private

Definition at line 667 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::GetAttrib(), COrgName_Base::ResetAttrib(), and COrgName_Base::SetAttrib().

m_choice

E_Choice COrgName_Base::C_Name::m_choice

private

Definition at line 318 of file OrgName_.hpp.

Referenced by COrgName_Base::C_Name::Reset(), and COrgName_Base::C_Name::Which().

m_Common

string COrg_ref_Base::m_Common

private

Definition at line 343 of file Org_ref_.hpp.

Referenced by COrg_ref_Base::GetCommon(), COrg_ref_Base::ResetCommon(), and COrg_ref_Base::SetCommon().

m_data [1/2]

list< CRef< COrgName > > CMultiOrgName_Base::m_data

private

Definition at line 140 of file MultiOrgName_.hpp.

Referenced by CMultiOrgName_Base::Get(), CMultiOrgName_Base::Reset(), and CMultiOrgName_Base::Set().

m_data [2/2]

list< CRef< CTaxElement > > CPartialOrgName_Base::m_data

private

Definition at line 140 of file PartialOrgName_.hpp.

Referenced by CPartialOrgName_Base::Get(), CPartialOrgName_Base::Reset(), and CPartialOrgName_Base::Set().

m_Db

vector< CRef< CDbtag > > COrg_ref_Base::m_Db

private

Definition at line 345 of file Org_ref_.hpp.

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

m_Div

string COrgName_Base::m_Div

private

Definition at line 672 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::GetDiv(), COrgName_Base::ResetDiv(), and COrgName_Base::SetDiv().

m_Fixed_level

int CTaxElement_Base::m_Fixed_level

private

Definition at line 235 of file TaxElement_.hpp.

Referenced by CTaxElement_Base::GetFixed_level(), CTaxElement_Base::ResetFixed_level(), and CTaxElement_Base::SetFixed_level().

m_Gcode

int COrgName_Base::m_Gcode

private

Definition at line 670 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::GetGcode(), COrgName_Base::ResetGcode(), and COrgName_Base::SetGcode().

m_Genus

string CBinomialOrgName_Base::m_Genus

private

Definition at line 228 of file BinomialOrgName_.hpp.

Referenced by CBinomialOrgName_Base::GetGenus(), CBinomialOrgName_Base::ResetGenus(), and CBinomialOrgName_Base::SetGenus().

m_Level

string CTaxElement_Base::m_Level

private

Definition at line 236 of file TaxElement_.hpp.

Referenced by CTaxElement_Base::GetLevel(), CTaxElement_Base::ResetLevel(), and CTaxElement_Base::SetLevel().

m_Lineage

string COrgName_Base::m_Lineage

private

Definition at line 669 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::GetLineage(), COrgName_Base::ResetLineage(), and COrgName_Base::SetLineage().

m_Mgcode

int COrgName_Base::m_Mgcode

private

Definition at line 671 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::GetMgcode(), COrgName_Base::ResetMgcode(), and COrgName_Base::SetMgcode().

m_Mod [1/2]

list< string > COrg_ref_Base::m_Mod

private

Definition at line 344 of file Org_ref_.hpp.

Referenced by COrg_ref_Base::GetMod(), COrg_ref_Base::ResetMod(), and COrg_ref_Base::SetMod().

m_Mod [2/2]

list< CRef< COrgMod > > COrgName_Base::m_Mod

private

Definition at line 668 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::GetMod(), COrgName_Base::ResetMod(), and COrgName_Base::SetMod().

m_Name [1/2]

CRef< TName > COrgName_Base::m_Name

private

Definition at line 666 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::GetName(), COrgName_Base::IsSetName(), COrgName_Base::ResetName(), and COrgName_Base::SetName().

m_Name [2/2]

string CTaxElement_Base::m_Name

private

Definition at line 237 of file TaxElement_.hpp.

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

m_object [1/2]

NCBI_NS_NCBI::CSerialObject* COrgName_Base::C_Name::m_object

Definition at line 326 of file OrgName_.hpp.

[2/2]

NCBI_NS_NCBI::CSerialObject* { ... } ::m_object

Definition at line 326 of file OrgName_.hpp.

m_Orgname

CRef< TOrgname > COrg_ref_Base::m_Orgname

private

Definition at line 347 of file Org_ref_.hpp.

Referenced by COrg_ref_Base::GetOrgname(), COrg_ref_Base::IsSetOrgname(), COrg_ref_Base::ResetOrgname(), and COrg_ref_Base::SetOrgname().

m_Pgcode

int COrgName_Base::m_Pgcode

private

Definition at line 673 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::GetPgcode(), COrgName_Base::ResetPgcode(), and COrgName_Base::SetPgcode().

m_set_State [1/7]

Uint4 CBinomialOrgName_Base::m_set_State[1]

private

Definition at line 227 of file BinomialOrgName_.hpp.

Referenced by CBinomialOrgName_Base::CBinomialOrgName_Base(), CBinomialOrgName_Base::IsSetGenus(), CBinomialOrgName_Base::IsSetSpecies(), CBinomialOrgName_Base::IsSetSubspecies(), CBinomialOrgName_Base::ResetGenus(), CBinomialOrgName_Base::ResetSpecies(), CBinomialOrgName_Base::ResetSubspecies(), CBinomialOrgName_Base::SetGenus(), CBinomialOrgName_Base::SetSpecies(), and CBinomialOrgName_Base::SetSubspecies().

m_set_State [2/7]

Uint4 CMultiOrgName_Base::m_set_State[1]

private

Definition at line 139 of file MultiOrgName_.hpp.

Referenced by CMultiOrgName_Base::CMultiOrgName_Base(), CMultiOrgName_Base::IsSet(), CMultiOrgName_Base::Reset(), and CMultiOrgName_Base::Set().

m_set_State [3/7]

Uint4 COrg_ref_Base::m_set_State[1]

private

Definition at line 341 of file Org_ref_.hpp.

Referenced by COrg_ref_Base::COrg_ref_Base(), COrg_ref_Base::IsSetCommon(), COrg_ref_Base::IsSetDb(), COrg_ref_Base::IsSetMod(), COrg_ref_Base::IsSetSyn(), COrg_ref_Base::IsSetTaxname(), COrg_ref_Base::ResetCommon(), COrg_ref_Base::ResetDb(), COrg_ref_Base::ResetMod(), COrg_ref_Base::ResetSyn(), COrg_ref_Base::ResetTaxname(), COrg_ref_Base::SetCommon(), COrg_ref_Base::SetDb(), COrg_ref_Base::SetMod(), COrg_ref_Base::SetSyn(), and COrg_ref_Base::SetTaxname().

m_set_State [4/7]

Uint4 COrgMod_Base::m_set_State[1]

private

Definition at line 272 of file OrgMod_.hpp.

Referenced by COrgMod_Base::COrgMod_Base(), COrgMod_Base::IsSetAttrib(), COrgMod_Base::IsSetSubname(), COrgMod_Base::IsSetSubtype(), COrgMod_Base::ResetAttrib(), COrgMod_Base::ResetSubname(), COrgMod_Base::ResetSubtype(), COrgMod_Base::SetAttrib(), COrgMod_Base::SetSubname(), and COrgMod_Base::SetSubtype().

m_set_State [5/7]

Uint4 COrgName_Base::m_set_State[1]

private

Definition at line 665 of file OrgName_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), COrgName_Base::COrgName_Base(), COrgName_Base::IsSetAttrib(), COrgName_Base::IsSetDiv(), COrgName_Base::IsSetGcode(), COrgName_Base::IsSetLineage(), COrgName_Base::IsSetMgcode(), COrgName_Base::IsSetMod(), COrgName_Base::IsSetPgcode(), COrgName_Base::ResetAttrib(), COrgName_Base::ResetDiv(), COrgName_Base::ResetGcode(), COrgName_Base::ResetLineage(), COrgName_Base::ResetMgcode(), COrgName_Base::ResetMod(), COrgName_Base::ResetPgcode(), COrgName_Base::SetAttrib(), COrgName_Base::SetDiv(), COrgName_Base::SetGcode(), COrgName_Base::SetLineage(), COrgName_Base::SetMgcode(), COrgName_Base::SetMod(), and COrgName_Base::SetPgcode().

m_set_State [6/7]

Uint4 CPartialOrgName_Base::m_set_State[1]

private

Definition at line 139 of file PartialOrgName_.hpp.

Referenced by CPartialOrgName_Base::CPartialOrgName_Base(), CPartialOrgName_Base::IsSet(), CPartialOrgName_Base::Reset(), and CPartialOrgName_Base::Set().

m_set_State [7/7]

Uint4 CTaxElement_Base::m_set_State[1]

private

Definition at line 234 of file TaxElement_.hpp.

Referenced by CTaxElement_Base::CTaxElement_Base(), CTaxElement_Base::IsSetFixed_level(), CTaxElement_Base::IsSetLevel(), CTaxElement_Base::IsSetName(), CTaxElement_Base::ResetFixed_level(), CTaxElement_Base::ResetLevel(), CTaxElement_Base::ResetName(), CTaxElement_Base::SetFixed_level(), CTaxElement_Base::SetLevel(), and CTaxElement_Base::SetName().

m_Species

string CBinomialOrgName_Base::m_Species

private

Definition at line 229 of file BinomialOrgName_.hpp.

Referenced by CBinomialOrgName_Base::GetSpecies(), CBinomialOrgName_Base::ResetSpecies(), and CBinomialOrgName_Base::SetSpecies().

m_string [1/2]

NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> COrgName_Base::C_Name::m_string

Definition at line 325 of file OrgName_.hpp.

[2/2]

NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> { ... } ::m_string

Definition at line 325 of file OrgName_.hpp.

m_Subname

string COrgMod_Base::m_Subname

private

Definition at line 274 of file OrgMod_.hpp.

Referenced by COrgMod_Base::GetSubname(), COrgMod_Base::ResetSubname(), and COrgMod_Base::SetSubname().

m_Subspecies

string CBinomialOrgName_Base::m_Subspecies

private

Definition at line 230 of file BinomialOrgName_.hpp.

Referenced by CBinomialOrgName_Base::GetSubspecies(), CBinomialOrgName_Base::ResetSubspecies(), and CBinomialOrgName_Base::SetSubspecies().

m_Subtype

int COrgMod_Base::m_Subtype

private

Definition at line 273 of file OrgMod_.hpp.

Referenced by COrgMod_Base::GetSubtype(), COrgMod_Base::ResetSubtype(), and COrgMod_Base::SetSubtype().

m_Syn

list< string > COrg_ref_Base::m_Syn

private

Definition at line 346 of file Org_ref_.hpp.

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

m_Taxname

string COrg_ref_Base::m_Taxname

private

Definition at line 342 of file Org_ref_.hpp.

Referenced by COrg_ref_Base::GetTaxname(), COrg_ref_Base::ResetTaxname(), and COrg_ref_Base::SetTaxname().

sm_SelectionNames

const char *const COrgName_Base::C_Name::sm_SelectionNames

staticprivate

Initial value:

= {
    "not set",
    "binomial",
    "virus",
    "hybrid",
    "namedhybrid",
    "partial"
}

Definition at line 322 of file OrgName_.hpp.