NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Enumerator | Functions | Variables
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< stringCOrg_ref_Base::TMod
 
typedef vector< CRef< CDbtag > > COrg_ref_Base::TDb
 
typedef list< stringCOrg_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)
 
CBinomialOrgNameCBinomialOrgName::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 TGenusCBinomialOrgName_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)
 
TGenusCBinomialOrgName_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 TSpeciesCBinomialOrgName_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)
 
TSpeciesCBinomialOrgName_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 TSubspeciesCBinomialOrgName_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)
 
TSubspeciesCBinomialOrgName_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_BaseCBinomialOrgName_Base::operator= (const CBinomialOrgName_Base &)
 
 CMultiOrgName::CMultiOrgName (void)
 
 CMultiOrgName::~CMultiOrgName (void)
 
 CMultiOrgName::CMultiOrgName (const CMultiOrgName &value)
 
CMultiOrgNameCMultiOrgName::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 TdataCMultiOrgName_Base::Get (void) const
 Get the member data. More...
 
TdataCMultiOrgName_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_BaseCMultiOrgName_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 TTaxnameCOrg_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)
 
TTaxnameCOrg_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 TCommonCOrg_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)
 
TCommonCOrg_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 TModCOrg_ref_Base::GetMod (void) const
 Get the Mod member data. More...
 
TModCOrg_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 TDbCOrg_ref_Base::GetDb (void) const
 Get the Db member data. More...
 
TDbCOrg_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 TSynCOrg_ref_Base::GetSyn (void) const
 Get the Syn member data. More...
 
TSynCOrg_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 TOrgnameCOrg_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...
 
TOrgnameCOrg_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_BaseCOrg_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...
 
TSubtypeCOrgMod_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 TSubnameCOrgMod_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)
 
TSubnameCOrgMod_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 TAttribCOrgMod_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)
 
TAttribCOrgMod_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_BaseCOrgMod_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 TBinomialCOrgName_Base::C_Name::GetBinomial (void) const
 Get the variant data. More...
 
TBinomialCOrgName_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 TVirusCOrgName_Base::C_Name::GetVirus (void) const
 Get the variant data. More...
 
TVirusCOrgName_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 THybridCOrgName_Base::C_Name::GetHybrid (void) const
 Get the variant data. More...
 
THybridCOrgName_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 TNamedhybridCOrgName_Base::C_Name::GetNamedhybrid (void) const
 Get the variant data. More...
 
TNamedhybridCOrgName_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 TPartialCOrgName_Base::C_Name::GetPartial (void) const
 Get the variant data. More...
 
TPartialCOrgName_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_NameCOrgName_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 TNameCOrgName_Base::GetName (void) const
 Get the Name member data. More...
 
void COrgName_Base::SetName (TName &value)
 Assign a value to Name data member. More...
 
TNameCOrgName_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 TAttribCOrgName_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)
 
TAttribCOrgName_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 TModCOrgName_Base::GetMod (void) const
 Get the Mod member data. More...
 
TModCOrgName_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 TLineageCOrgName_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)
 
TLineageCOrgName_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...
 
TGcodeCOrgName_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...
 
TMgcodeCOrgName_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 TDivCOrgName_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)
 
TDivCOrgName_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...
 
TPgcodeCOrgName_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_BaseCOrgName_Base::operator= (const COrgName_Base &)
 
 CPartialOrgName::CPartialOrgName (void)
 
 CPartialOrgName::~CPartialOrgName (void)
 
 CPartialOrgName::CPartialOrgName (const CPartialOrgName &value)
 
CPartialOrgNameCPartialOrgName::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 TdataCPartialOrgName_Base::Get (void) const
 Get the member data. More...
 
TdataCPartialOrgName_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_BaseCPartialOrgName_Base::operator= (const CPartialOrgName_Base &)
 
 CTaxElement::CTaxElement (void)
 
 CTaxElement::~CTaxElement (void)
 
 CTaxElement::CTaxElement (const CTaxElement &value)
 
CTaxElementCTaxElement::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_levelCTaxElement_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 TLevelCTaxElement_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)
 
TLevelCTaxElement_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 TNameCTaxElement_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)
 
TNameCTaxElement_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_BaseCTaxElement_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< stringCOrg_ref_Base::m_Mod
 
vector< CRef< CDbtag > > COrg_ref_Base::m_Db
 
list< stringCOrg_ref_Base::m_Syn
 
CRef< TOrgnameCOrg_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< TNameCOrgName_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]

Definition at line 134 of file OrgMod_.hpp.

◆ TAttrib [2/2]

Definition at line 331 of file OrgName_.hpp.

◆ TBinomial

Definition at line 172 of file OrgName_.hpp.

◆ TCommon

Definition at line 99 of file Org_ref_.hpp.

◆ Tdata [1/2]

Definition at line 90 of file MultiOrgName_.hpp.

◆ Tdata [2/2]

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

Definition at line 336 of file OrgName_.hpp.

◆ TFixed_level

Definition at line 95 of file TaxElement_.hpp.

◆ TGcode

Definition at line 334 of file OrgName_.hpp.

◆ TGenus

Definition at line 85 of file BinomialOrgName_.hpp.

◆ THybrid

Definition at line 174 of file OrgName_.hpp.

◆ TLevel

Definition at line 96 of file TaxElement_.hpp.

◆ TLineage

Definition at line 333 of file OrgName_.hpp.

◆ TmemberIndex [1/5]

Definition at line 96 of file BinomialOrgName_.hpp.

◆ TmemberIndex [2/5]

Definition at line 115 of file Org_ref_.hpp.

◆ TmemberIndex [3/5]

Definition at line 143 of file OrgMod_.hpp.

◆ TmemberIndex [4/5]

Definition at line 351 of file OrgName_.hpp.

◆ TmemberIndex [5/5]

Definition at line 106 of file TaxElement_.hpp.

◆ 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]

Definition at line 330 of file OrgName_.hpp.

◆ TName [2/2]

Definition at line 97 of file TaxElement_.hpp.

◆ TNamedhybrid

Definition at line 175 of file OrgName_.hpp.

◆ TOrgname

Definition at line 103 of file Org_ref_.hpp.

◆ Tparent [1/12]

Definition at line 67 of file BinomialOrgName.hpp.

◆ Tparent [2/12]

Definition at line 74 of file BinomialOrgName_.hpp.

◆ Tparent [3/12]

Definition at line 67 of file MultiOrgName.hpp.

◆ Tparent [4/12]

Definition at line 79 of file MultiOrgName_.hpp.

◆ Tparent [5/12]

Definition at line 87 of file Org_ref_.hpp.

◆ Tparent [6/12]

Definition at line 74 of file OrgMod_.hpp.

◆ Tparent [7/12]

Definition at line 82 of file OrgName_.hpp.

◆ Tparent [8/12]

Definition at line 99 of file OrgName_.hpp.

◆ Tparent [9/12]

Definition at line 67 of file PartialOrgName.hpp.

◆ Tparent [10/12]

Definition at line 79 of file PartialOrgName_.hpp.

◆ Tparent [11/12]

Definition at line 67 of file TaxElement.hpp.

◆ Tparent [12/12]

Definition at line 74 of file TaxElement_.hpp.

◆ TPartial

Definition at line 176 of file OrgName_.hpp.

◆ TPgcode

Definition at line 337 of file OrgName_.hpp.

◆ TSpecies

Definition at line 86 of file BinomialOrgName_.hpp.

◆ TSubname

Definition at line 133 of file OrgMod_.hpp.

◆ TSubspecies

Definition at line 87 of file BinomialOrgName_.hpp.

◆ 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

Definition at line 98 of file Org_ref_.hpp.

◆ TVirus

Definition at line 173 of file OrgName_.hpp.

Enumeration Type Documentation

◆ 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

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]

Enumerator
e__allMandatory 
e_genus 
e_species 
e_subspecies 

Definition at line 90 of file BinomialOrgName_.hpp.

◆ E_memberIndex [2/5]

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]

Enumerator
e__allMandatory 
e_subtype 
e_subname 
e_attrib 

Definition at line 137 of file OrgMod_.hpp.

◆ E_memberIndex [4/5]

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]

Enumerator
e__allMandatory 
e_fixed_level 
e_level 
e_name 

Definition at line 100 of file TaxElement_.hpp.

◆ 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

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

◆ 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

◆ 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
indexExpected 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

◆ 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

◆ GetBinomial()

const COrgName_Base::C_Name::TBinomial & COrgName_Base::C_Name::GetBinomial ( void  ) const

◆ GetCommon()

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

◆ GetDb()

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

◆ GetDiv()

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

◆ GetFixed_level()

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

◆ GetGcode()

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

◆ GetGenus()

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

◆ 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

◆ GetLineage()

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

◆ GetMgcode()

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

◆ 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(), 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

◆ 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

◆ 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

◆ GetSubname()

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

◆ 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

◆ 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(), CValidError_imp::HandleTaxonomyError(), 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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() [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() [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() [6/8]

void COrgName_Base::Reset ( void  )
virtual

◆ 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  )

◆ ResetDb()

void COrg_ref_Base::ResetDb ( void  )

◆ 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  )

◆ ResetTaxname()

void COrg_ref_Base::ResetTaxname ( void  )

◆ 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
indexNew selection state.
resetFlag 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
indexOne 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
valueValue 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
valueValue 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

◆ 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
valueReference 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

◆ SetCommon() [2/3]

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

◆ 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

◆ SetDiv() [1/3]

void COrgName_Base::SetDiv ( const TDiv value)
inline

Assign a value to Div data member.

Parameters
valueValue 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
valueValue 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
valueValue 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
valueValue 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

◆ 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
valueReference 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
valueValue 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

◆ 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
valueValue 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

◆ 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
valueValue 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

◆ SetMod() [2/2]

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

◆ SetName() [1/5]

void CTaxElement_Base::SetName ( const TName value)
inline

Assign a value to Name data member.

Parameters
valueValue 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

◆ SetName() [3/5]

void COrgName_Base::SetName ( COrgName_Base::TName value)

◆ 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
valueReference 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
valueReference 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
valueReference 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
valueValue 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
valueValue 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

◆ 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

◆ 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
valueValue 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

◆ 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

◆ 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

◆ SetTaxname() [2/3]

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

◆ 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
valueVariant 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
indexExpected 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

◆ m_Attrib [2/2]

string COrgName_Base::m_Attrib
private

◆ 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

◆ m_data [1/2]

list< CRef< COrgName > > CMultiOrgName_Base::m_data
private

◆ m_data [2/2]

list< CRef< CTaxElement > > CPartialOrgName_Base::m_data
private

◆ m_Db

vector< CRef< CDbtag > > COrg_ref_Base::m_Db
private

◆ m_Div

string COrgName_Base::m_Div
private

◆ m_Fixed_level

int CTaxElement_Base::m_Fixed_level
private

◆ m_Gcode

int COrgName_Base::m_Gcode
private

◆ m_Genus

string CBinomialOrgName_Base::m_Genus
private

◆ m_Level

string CTaxElement_Base::m_Level
private

◆ m_Lineage

string COrgName_Base::m_Lineage
private

◆ m_Mgcode

int COrgName_Base::m_Mgcode
private

◆ m_Mod [1/2]

list< string > COrg_ref_Base::m_Mod
private

◆ m_Mod [2/2]

list< CRef< COrgMod > > COrgName_Base::m_Mod
private

◆ m_Name [1/2]

CRef< TName > COrgName_Base::m_Name
private

◆ m_Name [2/2]

string CTaxElement_Base::m_Name
private

◆ 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

◆ m_Pgcode

int COrgName_Base::m_Pgcode
private

◆ m_set_State [1/7]

Uint4 CBinomialOrgName_Base::m_set_State[1]
private

◆ m_set_State [2/7]

Uint4 CMultiOrgName_Base::m_set_State[1]
private

◆ m_set_State [3/7]

Uint4 COrg_ref_Base::m_set_State[1]
private

◆ m_set_State [4/7]

Uint4 COrgMod_Base::m_set_State[1]
private

◆ m_set_State [5/7]

Uint4 COrgName_Base::m_set_State[1]
private

◆ m_set_State [6/7]

Uint4 CPartialOrgName_Base::m_set_State[1]
private

◆ m_set_State [7/7]

Uint4 CTaxElement_Base::m_set_State[1]
private

◆ m_Species

string CBinomialOrgName_Base::m_Species
private

◆ 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

◆ m_Subspecies

string CBinomialOrgName_Base::m_Subspecies
private

◆ m_Subtype

int COrgMod_Base::m_Subtype
private

◆ m_Syn

list< string > COrg_ref_Base::m_Syn
private

◆ m_Taxname

string COrg_ref_Base::m_Taxname
private

◆ 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.

Modified on Wed Jun 19 17:00:44 2024 by modify_doxy.py rev. 669887