NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Enumerator | Functions | Variables
Code generated by DATATOOL from 'seqfeat.asn' (module 'NCBI-BioSource')
+ Collaboration diagram for Code generated by DATATOOL from 'seqfeat.asn' (module 'NCBI-BioSource'):

Classes

class  CBioSource_Base
 ******************************************************************** More...
 
class  CPCRPrimer
 CPCRPrimer –. More...
 
class  CPCRPrimer_Base
 CPCRPrimer_Base –. More...
 
class  CPCRPrimerName
 CPCRPrimerName –. More...
 
class  CPCRPrimerName_Base
 CPCRPrimerName_Base –. More...
 
class  CPCRPrimerSeq_Base
 CPCRPrimerSeq_Base –. More...
 
class  CPCRPrimerSet
 CPCRPrimerSet –. More...
 
class  CPCRPrimerSet_Base
 CPCRPrimerSet_Base –. More...
 
class  CPCRReaction
 CPCRReaction –. More...
 
class  CPCRReaction_Base
 CPCRReaction_Base –. More...
 
class  CPCRReactionSet
 CPCRReactionSet –. More...
 
class  CPCRReactionSet_Base
 CPCRReactionSet_Base –. More...
 
class  CSubSource_Base
 CSubSource_Base –. More...
 

Typedefs

typedef CSerialObject CBioSource_Base::Tparent
 
typedef int CBioSource_Base::TGenome
 
typedef int CBioSource_Base::TOrigin
 
typedef COrg_ref CBioSource_Base::TOrg
 
typedef list< CRef< CSubSource > > CBioSource_Base::TSubtype
 
typedef CPCRReactionSet CBioSource_Base::TPcr_primers
 
typedef Tparent::CMemberIndex< E_memberIndex, 7 > CBioSource_Base::TmemberIndex
 
typedef CPCRPrimer_Base CPCRPrimer::Tparent
 
typedef CSerialObject CPCRPrimer_Base::Tparent
 
typedef CPCRPrimerSeq CPCRPrimer_Base::TSeq
 
typedef CPCRPrimerName CPCRPrimer_Base::TName
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CPCRPrimer_Base::TmemberIndex
 
typedef CPCRPrimerName_Base CPCRPrimerName::Tparent
 
typedef CStringAliasBase< stringCPCRPrimerName_Base::Tparent
 
typedef CStringAliasBase< stringCPCRPrimerSeq_Base::Tparent
 
typedef CPCRPrimerSet_Base CPCRPrimerSet::Tparent
 
typedef CSerialObject CPCRPrimerSet_Base::Tparent
 
typedef list< CRef< CPCRPrimer > > CPCRPrimerSet_Base::Tdata
 
typedef CPCRReaction_Base CPCRReaction::Tparent
 
typedef CSerialObject CPCRReaction_Base::Tparent
 
typedef CPCRPrimerSet CPCRReaction_Base::TForward
 
typedef CPCRPrimerSet CPCRReaction_Base::TReverse
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CPCRReaction_Base::TmemberIndex
 
typedef CPCRReactionSet_Base CPCRReactionSet::Tparent
 
typedef CSerialObject CPCRReactionSet_Base::Tparent
 
typedef list< CRef< CPCRReaction > > CPCRReactionSet_Base::Tdata
 
typedef CSerialObject CSubSource_Base::Tparent
 
typedef int CSubSource_Base::TSubtype
 
typedef string CSubSource_Base::TName
 
typedef string CSubSource_Base::TAttrib
 
typedef Tparent::CMemberIndex< E_memberIndex, 4 > CSubSource_Base::TmemberIndex
 

Enumerations

enum  CBioSource_Base::EGenome {
  CBioSource_Base::eGenome_unknown = 0 , CBioSource_Base::eGenome_genomic = 1 , CBioSource_Base::eGenome_chloroplast = 2 , CBioSource_Base::eGenome_chromoplast = 3 ,
  CBioSource_Base::eGenome_kinetoplast = 4 , CBioSource_Base::eGenome_mitochondrion = 5 , CBioSource_Base::eGenome_plastid = 6 , CBioSource_Base::eGenome_macronuclear = 7 ,
  CBioSource_Base::eGenome_extrachrom = 8 , CBioSource_Base::eGenome_plasmid = 9 , CBioSource_Base::eGenome_transposon = 10 , CBioSource_Base::eGenome_insertion_seq = 11 ,
  CBioSource_Base::eGenome_cyanelle = 12 , CBioSource_Base::eGenome_proviral = 13 , CBioSource_Base::eGenome_virion = 14 , CBioSource_Base::eGenome_nucleomorph = 15 ,
  CBioSource_Base::eGenome_apicoplast = 16 , CBioSource_Base::eGenome_leucoplast = 17 , CBioSource_Base::eGenome_proplastid = 18 , CBioSource_Base::eGenome_endogenous_virus = 19 ,
  CBioSource_Base::eGenome_hydrogenosome = 20 , CBioSource_Base::eGenome_chromosome = 21 , CBioSource_Base::eGenome_chromatophore = 22 , CBioSource_Base::eGenome_plasmid_in_mitochondrion = 23 ,
  CBioSource_Base::eGenome_plasmid_in_plastid = 24
}
 biological context More...
 
enum  CBioSource_Base::EOrigin {
  CBioSource_Base::eOrigin_unknown = 0 , CBioSource_Base::eOrigin_natural = 1 , CBioSource_Base::eOrigin_natmut = 2 , CBioSource_Base::eOrigin_mut = 3 ,
  CBioSource_Base::eOrigin_artificial = 4 , CBioSource_Base::eOrigin_synthetic = 5 , CBioSource_Base::eOrigin_other = 255
}
 
enum class  CBioSource_Base::E_memberIndex {
  CBioSource_Base::e__allMandatory = 0 , CBioSource_Base::e_genome , CBioSource_Base::e_origin , CBioSource_Base::e_org ,
  CBioSource_Base::e_subtype , CBioSource_Base::e_is_focus , CBioSource_Base::e_pcr_primers
}
 
enum class  CPCRPrimer_Base::E_memberIndex { CPCRPrimer_Base::e__allMandatory = 0 , CPCRPrimer_Base::e_seq , CPCRPrimer_Base::e_name }
 
enum class  CPCRReaction_Base::E_memberIndex { CPCRReaction_Base::e__allMandatory = 0 , CPCRReaction_Base::e_forward , CPCRReaction_Base::e_reverse }
 
enum  CSubSource_Base::ESubtype {
  CSubSource_Base::eSubtype_chromosome = 1 , CSubSource_Base::eSubtype_map = 2 , CSubSource_Base::eSubtype_clone = 3 , CSubSource_Base::eSubtype_subclone = 4 ,
  CSubSource_Base::eSubtype_haplotype = 5 , CSubSource_Base::eSubtype_genotype = 6 , CSubSource_Base::eSubtype_sex = 7 , CSubSource_Base::eSubtype_cell_line = 8 ,
  CSubSource_Base::eSubtype_cell_type = 9 , CSubSource_Base::eSubtype_tissue_type = 10 , CSubSource_Base::eSubtype_clone_lib = 11 , CSubSource_Base::eSubtype_dev_stage = 12 ,
  CSubSource_Base::eSubtype_frequency = 13 , CSubSource_Base::eSubtype_germline = 14 , CSubSource_Base::eSubtype_rearranged = 15 , CSubSource_Base::eSubtype_lab_host = 16 ,
  CSubSource_Base::eSubtype_pop_variant = 17 , CSubSource_Base::eSubtype_tissue_lib = 18 , CSubSource_Base::eSubtype_plasmid_name = 19 , CSubSource_Base::eSubtype_transposon_name = 20 ,
  CSubSource_Base::eSubtype_insertion_seq_name = 21 , CSubSource_Base::eSubtype_plastid_name = 22 , CSubSource_Base::eSubtype_country = 23 , CSubSource_Base::eSubtype_segment = 24 ,
  CSubSource_Base::eSubtype_endogenous_virus_name = 25 , CSubSource_Base::eSubtype_transgenic = 26 , CSubSource_Base::eSubtype_environmental_sample = 27 , CSubSource_Base::eSubtype_isolation_source = 28 ,
  CSubSource_Base::eSubtype_lat_lon = 29 , CSubSource_Base::eSubtype_collection_date = 30 , CSubSource_Base::eSubtype_collected_by = 31 , CSubSource_Base::eSubtype_identified_by = 32 ,
  CSubSource_Base::eSubtype_fwd_primer_seq = 33 , CSubSource_Base::eSubtype_rev_primer_seq = 34 , CSubSource_Base::eSubtype_fwd_primer_name = 35 , CSubSource_Base::eSubtype_rev_primer_name = 36 ,
  CSubSource_Base::eSubtype_metagenomic = 37 , CSubSource_Base::eSubtype_mating_type = 38 , CSubSource_Base::eSubtype_linkage_group = 39 , CSubSource_Base::eSubtype_haplogroup = 40 ,
  CSubSource_Base::eSubtype_whole_replicon = 41 , CSubSource_Base::eSubtype_phenotype = 42 , CSubSource_Base::eSubtype_altitude = 43 , CSubSource_Base::eSubtype_other = 255
}
 
enum class  CSubSource_Base::E_memberIndex { CSubSource_Base::e__allMandatory = 0 , CSubSource_Base::e_subtype , CSubSource_Base::e_name , CSubSource_Base::e_attrib }
 

Functions

 CBioSource_Base::CBioSource_Base (void)
 
virtual CBioSource_Base::~CBioSource_Base (void)
 
 CBioSource_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() CBioSource_Base::EGenome (void)
 Access to EGenome's attributes (values, names) as defined in spec. More...
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() CBioSource_Base::EOrigin (void)
 Access to EOrigin's attributes (values, names) as defined in spec. More...
 
bool CBioSource_Base::IsSetGenome (void) const
 Check if a value has been assigned to Genome data member. More...
 
bool CBioSource_Base::CanGetGenome (void) const
 Check if it is safe to call GetGenome method. More...
 
void CBioSource_Base::ResetGenome (void)
 Reset Genome data member. More...
 
void CBioSource_Base::SetDefaultGenome (void)
 Assign default value to Genome data member. More...
 
TGenome CBioSource_Base::GetGenome (void) const
 Get the Genome member data. More...
 
void CBioSource_Base::SetGenome (TGenome value)
 Assign a value to Genome data member. More...
 
TGenomeCBioSource_Base::SetGenome (void)
 Assign a value to Genome data member. More...
 
bool CBioSource_Base::IsSetOrigin (void) const
 Check if a value has been assigned to Origin data member. More...
 
bool CBioSource_Base::CanGetOrigin (void) const
 Check if it is safe to call GetOrigin method. More...
 
void CBioSource_Base::ResetOrigin (void)
 Reset Origin data member. More...
 
void CBioSource_Base::SetDefaultOrigin (void)
 Assign default value to Origin data member. More...
 
TOrigin CBioSource_Base::GetOrigin (void) const
 Get the Origin member data. More...
 
void CBioSource_Base::SetOrigin (TOrigin value)
 Assign a value to Origin data member. More...
 
TOriginCBioSource_Base::SetOrigin (void)
 Assign a value to Origin data member. More...
 
bool CBioSource_Base::IsSetOrg (void) const
 Check if a value has been assigned to Org data member. More...
 
bool CBioSource_Base::CanGetOrg (void) const
 Check if it is safe to call GetOrg method. More...
 
void CBioSource_Base::ResetOrg (void)
 Reset Org data member. More...
 
const TOrgCBioSource_Base::GetOrg (void) const
 Get the Org member data. More...
 
void CBioSource_Base::SetOrg (TOrg &value)
 Assign a value to Org data member. More...
 
TOrgCBioSource_Base::SetOrg (void)
 Assign a value to Org data member. More...
 
bool CBioSource_Base::IsSetSubtype (void) const
 Check if a value has been assigned to Subtype data member. More...
 
bool CBioSource_Base::CanGetSubtype (void) const
 Check if it is safe to call GetSubtype method. More...
 
void CBioSource_Base::ResetSubtype (void)
 Reset Subtype data member. More...
 
const TSubtypeCBioSource_Base::GetSubtype (void) const
 Get the Subtype member data. More...
 
TSubtypeCBioSource_Base::SetSubtype (void)
 Assign a value to Subtype data member. More...
 
bool CBioSource_Base::IsSetIs_focus (void) const
 to distinguish biological focus Check if a value has been assigned to Is_focus data member. More...
 
bool CBioSource_Base::CanGetIs_focus (void) const
 Check if value of Is_focus member is getatable. More...
 
void CBioSource_Base::ResetIs_focus (void)
 Reset Is_focus data member. More...
 
void CBioSource_Base::SetIs_focus (void)
 Set NULL data member (assign 'NULL' value to Is_focus data member). More...
 
bool CBioSource_Base::IsSetPcr_primers (void) const
 Check if a value has been assigned to Pcr_primers data member. More...
 
bool CBioSource_Base::CanGetPcr_primers (void) const
 Check if it is safe to call GetPcr_primers method. More...
 
void CBioSource_Base::ResetPcr_primers (void)
 Reset Pcr_primers data member. More...
 
const TPcr_primersCBioSource_Base::GetPcr_primers (void) const
 Get the Pcr_primers member data. More...
 
void CBioSource_Base::SetPcr_primers (TPcr_primers &value)
 Assign a value to Pcr_primers data member. More...
 
TPcr_primersCBioSource_Base::SetPcr_primers (void)
 Assign a value to Pcr_primers data member. More...
 
virtual void CBioSource_Base::Reset (void)
 Reset the whole object. More...
 
 CBioSource_Base::CBioSource_Base (const CBioSource_Base &)
 
CBioSource_BaseCBioSource_Base::operator= (const CBioSource_Base &)
 
 CPCRPrimer::CPCRPrimer (void)
 
 CPCRPrimer::~CPCRPrimer (void)
 
 CPCRPrimer::CPCRPrimer (const CPCRPrimer &value)
 
CPCRPrimerCPCRPrimer::operator= (const CPCRPrimer &value)
 
 CPCRPrimer_Base::CPCRPrimer_Base (void)
 
virtual CPCRPrimer_Base::~CPCRPrimer_Base (void)
 
 CPCRPrimer_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPCRPrimer_Base::IsSetSeq (void) const
 Check if a value has been assigned to Seq data member. More...
 
bool CPCRPrimer_Base::CanGetSeq (void) const
 Check if it is safe to call GetSeq method. More...
 
void CPCRPrimer_Base::ResetSeq (void)
 Reset Seq data member. More...
 
const TSeqCPCRPrimer_Base::GetSeq (void) const
 Get the Seq member data. More...
 
void CPCRPrimer_Base::SetSeq (const TSeq &value)
 Assign a value to Seq data member. More...
 
TSeqCPCRPrimer_Base::SetSeq (void)
 Assign a value to Seq data member. More...
 
bool CPCRPrimer_Base::IsSetName (void) const
 Check if a value has been assigned to Name data member. More...
 
bool CPCRPrimer_Base::CanGetName (void) const
 Check if it is safe to call GetName method. More...
 
void CPCRPrimer_Base::ResetName (void)
 Reset Name data member. More...
 
const TNameCPCRPrimer_Base::GetName (void) const
 Get the Name member data. More...
 
void CPCRPrimer_Base::SetName (const TName &value)
 Assign a value to Name data member. More...
 
TNameCPCRPrimer_Base::SetName (void)
 Assign a value to Name data member. More...
 
virtual void CPCRPrimer_Base::Reset (void)
 Reset the whole object. More...
 
 CPCRPrimer_Base::CPCRPrimer_Base (const CPCRPrimer_Base &)
 
CPCRPrimer_BaseCPCRPrimer_Base::operator= (const CPCRPrimer_Base &)
 
 CPCRPrimerName::CPCRPrimerName (void)
 
 CPCRPrimerName::CPCRPrimerName (const std::string &value)
 Explicit constructor from the primitive type. More...
 
 CPCRPrimerName_Base::CPCRPrimerName_Base (void)
 
 CPCRPrimerName_Base::DECLARE_STD_ALIAS_TYPE_INFO ()
 
 CPCRPrimerName_Base::CPCRPrimerName_Base (const string &data)
 
NCBI_NS_NCBI::CNcbiOstreamoperator<< (NCBI_NS_NCBI::CNcbiOstream &str, const CPCRPrimerName_Base &obj)
 
NCBI_NS_NCBI::CNcbiIstreamoperator>> (NCBI_NS_NCBI::CNcbiIstream &str, CPCRPrimerName_Base &obj)
 
 CPCRPrimerSeq_Base::CPCRPrimerSeq_Base (void)
 
 CPCRPrimerSeq_Base::DECLARE_STD_ALIAS_TYPE_INFO ()
 
 CPCRPrimerSeq_Base::CPCRPrimerSeq_Base (const string &data)
 
NCBI_NS_NCBI::CNcbiOstreamoperator<< (NCBI_NS_NCBI::CNcbiOstream &str, const CPCRPrimerSeq_Base &obj)
 
NCBI_NS_NCBI::CNcbiIstreamoperator>> (NCBI_NS_NCBI::CNcbiIstream &str, CPCRPrimerSeq_Base &obj)
 
 CPCRPrimerSet::CPCRPrimerSet (void)
 
 CPCRPrimerSet::~CPCRPrimerSet (void)
 
 CPCRPrimerSet::CPCRPrimerSet (const CPCRPrimerSet &value)
 
CPCRPrimerSetCPCRPrimerSet::operator= (const CPCRPrimerSet &value)
 
 CPCRPrimerSet_Base::CPCRPrimerSet_Base (void)
 
virtual CPCRPrimerSet_Base::~CPCRPrimerSet_Base (void)
 
 CPCRPrimerSet_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPCRPrimerSet_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CPCRPrimerSet_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CPCRPrimerSet_Base::Reset (void)
 Reset data member. More...
 
const TdataCPCRPrimerSet_Base::Get (void) const
 Get the member data. More...
 
TdataCPCRPrimerSet_Base::Set (void)
 Assign a value to data member. More...
 
 CPCRPrimerSet_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CPCRPrimerSet_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CPCRPrimerSet_Base::CPCRPrimerSet_Base (const CPCRPrimerSet_Base &)
 
CPCRPrimerSet_BaseCPCRPrimerSet_Base::operator= (const CPCRPrimerSet_Base &)
 
 CPCRReaction::CPCRReaction (void)
 
 CPCRReaction::~CPCRReaction (void)
 
 CPCRReaction::CPCRReaction (const CPCRReaction &value)
 
CPCRReactionCPCRReaction::operator= (const CPCRReaction &value)
 
 CPCRReaction_Base::CPCRReaction_Base (void)
 
virtual CPCRReaction_Base::~CPCRReaction_Base (void)
 
 CPCRReaction_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPCRReaction_Base::IsSetForward (void) const
 Check if a value has been assigned to Forward data member. More...
 
bool CPCRReaction_Base::CanGetForward (void) const
 Check if it is safe to call GetForward method. More...
 
void CPCRReaction_Base::ResetForward (void)
 Reset Forward data member. More...
 
const TForwardCPCRReaction_Base::GetForward (void) const
 Get the Forward member data. More...
 
void CPCRReaction_Base::SetForward (TForward &value)
 Assign a value to Forward data member. More...
 
TForwardCPCRReaction_Base::SetForward (void)
 Assign a value to Forward data member. More...
 
bool CPCRReaction_Base::IsSetReverse (void) const
 Check if a value has been assigned to Reverse data member. More...
 
bool CPCRReaction_Base::CanGetReverse (void) const
 Check if it is safe to call GetReverse method. More...
 
void CPCRReaction_Base::ResetReverse (void)
 Reset Reverse data member. More...
 
const TReverseCPCRReaction_Base::GetReverse (void) const
 Get the Reverse member data. More...
 
void CPCRReaction_Base::SetReverse (TReverse &value)
 Assign a value to Reverse data member. More...
 
TReverseCPCRReaction_Base::SetReverse (void)
 Assign a value to Reverse data member. More...
 
virtual void CPCRReaction_Base::Reset (void)
 Reset the whole object. More...
 
 CPCRReaction_Base::CPCRReaction_Base (const CPCRReaction_Base &)
 
CPCRReaction_BaseCPCRReaction_Base::operator= (const CPCRReaction_Base &)
 
 CPCRReactionSet::CPCRReactionSet (void)
 
 CPCRReactionSet::~CPCRReactionSet (void)
 
 CPCRReactionSet::CPCRReactionSet (const CPCRReactionSet &value)
 
CPCRReactionSetCPCRReactionSet::operator= (const CPCRReactionSet &value)
 
 CPCRReactionSet_Base::CPCRReactionSet_Base (void)
 
virtual CPCRReactionSet_Base::~CPCRReactionSet_Base (void)
 
 CPCRReactionSet_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPCRReactionSet_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CPCRReactionSet_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CPCRReactionSet_Base::Reset (void)
 Reset data member. More...
 
const TdataCPCRReactionSet_Base::Get (void) const
 Get the member data. More...
 
TdataCPCRReactionSet_Base::Set (void)
 Assign a value to data member. More...
 
 CPCRReactionSet_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CPCRReactionSet_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CPCRReactionSet_Base::CPCRReactionSet_Base (const CPCRReactionSet_Base &)
 
CPCRReactionSet_BaseCPCRReactionSet_Base::operator= (const CPCRReactionSet_Base &)
 
 CSubSource_Base::CSubSource_Base (void)
 
virtual CSubSource_Base::~CSubSource_Base (void)
 
 CSubSource_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() CSubSource_Base::ESubtype (void)
 Access to ESubtype's attributes (values, names) as defined in spec. More...
 
bool CSubSource_Base::IsSetSubtype (void) const
 Check if a value has been assigned to Subtype data member. More...
 
bool CSubSource_Base::CanGetSubtype (void) const
 Check if it is safe to call GetSubtype method. More...
 
void CSubSource_Base::ResetSubtype (void)
 Reset Subtype data member. More...
 
TSubtype CSubSource_Base::GetSubtype (void) const
 Get the Subtype member data. More...
 
void CSubSource_Base::SetSubtype (TSubtype value)
 Assign a value to Subtype data member. More...
 
TSubtypeCSubSource_Base::SetSubtype (void)
 Assign a value to Subtype data member. More...
 
bool CSubSource_Base::IsSetName (void) const
 Check if a value has been assigned to Name data member. More...
 
bool CSubSource_Base::CanGetName (void) const
 Check if it is safe to call GetName method. More...
 
void CSubSource_Base::ResetName (void)
 Reset Name data member. More...
 
const TNameCSubSource_Base::GetName (void) const
 Get the Name member data. More...
 
void CSubSource_Base::SetName (const TName &value)
 Assign a value to Name data member. More...
 
void CSubSource_Base::SetName (TName &&value)
 
TNameCSubSource_Base::SetName (void)
 Assign a value to Name data member. More...
 
bool CSubSource_Base::IsSetAttrib (void) const
 attribution/source of this name Check if a value has been assigned to Attrib data member. More...
 
bool CSubSource_Base::CanGetAttrib (void) const
 Check if it is safe to call GetAttrib method. More...
 
void CSubSource_Base::ResetAttrib (void)
 Reset Attrib data member. More...
 
const TAttribCSubSource_Base::GetAttrib (void) const
 Get the Attrib member data. More...
 
void CSubSource_Base::SetAttrib (const TAttrib &value)
 Assign a value to Attrib data member. More...
 
void CSubSource_Base::SetAttrib (TAttrib &&value)
 
TAttribCSubSource_Base::SetAttrib (void)
 Assign a value to Attrib data member. More...
 
virtual void CSubSource_Base::Reset (void)
 Reset the whole object. More...
 
 CSubSource_Base::CSubSource_Base (const CSubSource_Base &)
 
CSubSource_BaseCSubSource_Base::operator= (const CSubSource_Base &)
 

Variables

Uint4 CBioSource_Base::m_set_State [1]
 
int CBioSource_Base::m_Genome
 
int CBioSource_Base::m_Origin
 
CRef< TOrgCBioSource_Base::m_Org
 
list< CRef< CSubSource > > CBioSource_Base::m_Subtype
 
CRef< TPcr_primersCBioSource_Base::m_Pcr_primers
 
Uint4 CPCRPrimer_Base::m_set_State [1]
 
CPCRPrimerSeq CPCRPrimer_Base::m_Seq
 
CPCRPrimerName CPCRPrimer_Base::m_Name
 
Uint4 CPCRPrimerSet_Base::m_set_State [1]
 
list< CRef< CPCRPrimer > > CPCRPrimerSet_Base::m_data
 
Uint4 CPCRReaction_Base::m_set_State [1]
 
CRef< TForwardCPCRReaction_Base::m_Forward
 
CRef< TReverseCPCRReaction_Base::m_Reverse
 
Uint4 CPCRReactionSet_Base::m_set_State [1]
 
list< CRef< CPCRReaction > > CPCRReactionSet_Base::m_data
 
Uint4 CSubSource_Base::m_set_State [1]
 
int CSubSource_Base::m_Subtype
 
string CSubSource_Base::m_Name
 
string CSubSource_Base::m_Attrib
 

Detailed Description

Typedef Documentation

◆ TAttrib

Definition at line 137 of file SubSource_.hpp.

◆ Tdata [1/2]

Definition at line 89 of file PCRPrimerSet_.hpp.

◆ Tdata [2/2]

Definition at line 89 of file PCRReactionSet_.hpp.

◆ TForward

Definition at line 85 of file PCRReaction_.hpp.

◆ TGenome

Definition at line 142 of file BioSource_.hpp.

◆ TmemberIndex [1/4]

Definition at line 158 of file BioSource_.hpp.

◆ TmemberIndex [2/4]

Definition at line 95 of file PCRPrimer_.hpp.

◆ TmemberIndex [3/4]

Definition at line 94 of file PCRReaction_.hpp.

◆ TmemberIndex [4/4]

Definition at line 146 of file SubSource_.hpp.

◆ TName [1/2]

Definition at line 87 of file PCRPrimer_.hpp.

◆ TName [2/2]

Definition at line 136 of file SubSource_.hpp.

◆ TOrg

Definition at line 144 of file BioSource_.hpp.

◆ TOrigin

Definition at line 143 of file BioSource_.hpp.

◆ Tparent [1/13]

Definition at line 86 of file BioSource_.hpp.

◆ Tparent [2/13]

Definition at line 67 of file PCRPrimer.hpp.

◆ Tparent [3/13]

Definition at line 75 of file PCRPrimer_.hpp.

◆ Tparent [4/13]

Definition at line 67 of file PCRPrimerName.hpp.

◆ Tparent [5/13]

Definition at line 74 of file PCRPrimerName_.hpp.

◆ Tparent [6/13]

Definition at line 74 of file PCRPrimerSeq_.hpp.

◆ Tparent [7/13]

Definition at line 67 of file PCRPrimerSet.hpp.

◆ Tparent [8/13]

Definition at line 78 of file PCRPrimerSet_.hpp.

◆ Tparent [9/13]

Definition at line 67 of file PCRReaction.hpp.

◆ Tparent [10/13]

Definition at line 74 of file PCRReaction_.hpp.

◆ Tparent [11/13]

Definition at line 67 of file PCRReactionSet.hpp.

◆ Tparent [12/13]

Definition at line 78 of file PCRReactionSet_.hpp.

◆ Tparent [13/13]

Definition at line 74 of file SubSource_.hpp.

◆ TPcr_primers

Definition at line 146 of file BioSource_.hpp.

◆ TReverse

Definition at line 86 of file PCRReaction_.hpp.

◆ TSeq

Definition at line 86 of file PCRPrimer_.hpp.

◆ TSubtype [1/2]

Definition at line 145 of file BioSource_.hpp.

◆ TSubtype [2/2]

Definition at line 135 of file SubSource_.hpp.

Enumeration Type Documentation

◆ E_memberIndex [1/4]

Enumerator
e__allMandatory 
e_genome 
e_origin 
e_org 
e_subtype 
e_is_focus 
e_pcr_primers 

Definition at line 149 of file BioSource_.hpp.

◆ E_memberIndex [2/4]

Enumerator
e__allMandatory 
e_seq 
e_name 

Definition at line 90 of file PCRPrimer_.hpp.

◆ E_memberIndex [3/4]

Enumerator
e__allMandatory 
e_forward 
e_reverse 

Definition at line 89 of file PCRReaction_.hpp.

◆ E_memberIndex [4/4]

Enumerator
e__allMandatory 
e_subtype 
e_name 
e_attrib 

Definition at line 140 of file SubSource_.hpp.

◆ EGenome

biological context

Enumerator
eGenome_unknown 
eGenome_genomic 
eGenome_chloroplast 
eGenome_chromoplast 
eGenome_kinetoplast 
eGenome_mitochondrion 
eGenome_plastid 
eGenome_macronuclear 
eGenome_extrachrom 
eGenome_plasmid 
eGenome_transposon 
eGenome_insertion_seq 
eGenome_cyanelle 
eGenome_proviral 
eGenome_virion 
eGenome_nucleomorph 
eGenome_apicoplast 
eGenome_leucoplast 
eGenome_proplastid 
eGenome_endogenous_virus 
eGenome_hydrogenosome 
eGenome_chromosome 
eGenome_chromatophore 
eGenome_plasmid_in_mitochondrion 
eGenome_plasmid_in_plastid 

Definition at line 97 of file BioSource_.hpp.

◆ EOrigin

Enumerator
eOrigin_unknown 
eOrigin_natural 

normal biological entity

eOrigin_natmut 

naturally occurring mutant

eOrigin_mut 

artificially mutagenized

eOrigin_artificial 

artificially engineered

eOrigin_synthetic 

purely synthetic

eOrigin_other 

Definition at line 128 of file BioSource_.hpp.

◆ ESubtype

Enumerator
eSubtype_chromosome 
eSubtype_map 
eSubtype_clone 
eSubtype_subclone 
eSubtype_haplotype 
eSubtype_genotype 
eSubtype_sex 
eSubtype_cell_line 
eSubtype_cell_type 
eSubtype_tissue_type 
eSubtype_clone_lib 
eSubtype_dev_stage 
eSubtype_frequency 
eSubtype_germline 
eSubtype_rearranged 
eSubtype_lab_host 
eSubtype_pop_variant 
eSubtype_tissue_lib 
eSubtype_plasmid_name 
eSubtype_transposon_name 
eSubtype_insertion_seq_name 
eSubtype_plastid_name 
eSubtype_country 
eSubtype_segment 
eSubtype_endogenous_virus_name 
eSubtype_transgenic 
eSubtype_environmental_sample 
eSubtype_isolation_source 
eSubtype_lat_lon 

+/- decimal degrees

eSubtype_collection_date 

DD-MMM-YYYY format.

eSubtype_collected_by 

name of person who collected the sample

eSubtype_identified_by 

name of person who identified the sample

eSubtype_fwd_primer_seq 

sequence (possibly more than one; semicolon-separated)

eSubtype_rev_primer_seq 

sequence (possibly more than one; semicolon-separated)

eSubtype_fwd_primer_name 
eSubtype_rev_primer_name 
eSubtype_metagenomic 
eSubtype_mating_type 
eSubtype_linkage_group 
eSubtype_haplogroup 
eSubtype_whole_replicon 
eSubtype_phenotype 
eSubtype_altitude 
eSubtype_other 

Definition at line 84 of file SubSource_.hpp.

Function Documentation

◆ CanGet() [1/2]

bool CPCRPrimerSet_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 158 of file PCRPrimerSet_.hpp.

Referenced by CSourceFeatureItem::x_AddPcrPrimersQuals(), and CDeflineGenerator::x_GetModifiers().

◆ CanGet() [2/2]

bool CPCRReactionSet_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 158 of file PCRReactionSet_.hpp.

Referenced by CSourceFeatureItem::x_AddPcrPrimersQuals(), and CDeflineGenerator::x_GetModifiers().

◆ CanGetAttrib()

bool CSubSource_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 391 of file SubSource_.hpp.

References CSubSource_Base::IsSetAttrib().

Referenced by CSubSource_Base::GetAttrib().

◆ CanGetForward()

bool CPCRReaction_Base::CanGetForward ( void  ) const
inline

Check if it is safe to call GetForward method.

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

Definition at line 204 of file PCRReaction_.hpp.

References CPCRReaction_Base::IsSetForward().

Referenced by CPCRReaction_Base::GetForward().

◆ CanGetGenome()

bool CBioSource_Base::CanGetGenome ( void  ) const
inline

Check if it is safe to call GetGenome method.

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

Definition at line 403 of file BioSource_.hpp.

Referenced by CBioSource::GetGenCode(), CAutoDef::GetOneDefLine(), CAutoDef::x_GetFeatureClauseProductEnding(), CDeflineGenerator::x_GetModifiers(), CSourceItem::x_SetSource(), and CCdregionValidator::x_ValidateGeneticCode().

◆ CanGetIs_focus()

bool CBioSource_Base::CanGetIs_focus ( void  ) const
inline

Check if value of Is_focus member is getatable.

Returns
  • false; the data member of type 'NULL' has no value.

Definition at line 558 of file BioSource_.hpp.

Referenced by CSrcFocusSet::apply_to().

◆ CanGetName() [1/2]

bool CPCRPrimer_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 240 of file PCRPrimer_.hpp.

References CPCRPrimer_Base::IsSetName().

Referenced by CPCRPrimer_Base::GetName().

◆ CanGetName() [2/2]

bool CSubSource_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 344 of file SubSource_.hpp.

References CSubSource_Base::IsSetName().

Referenced by CFlatSubSourceQVal::Format(), CSubSource_Base::GetName(), and CSubtypeEquals::operator()().

◆ CanGetOrg()

bool CBioSource_Base::CanGetOrg ( void  ) const
inline

◆ CanGetOrigin()

bool CBioSource_Base::CanGetOrigin ( void  ) const
inline

Check if it is safe to call GetOrigin method.

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

Definition at line 453 of file BioSource_.hpp.

Referenced by CAutoDefModifierCombo::GetSourceDescriptionString().

◆ CanGetPcr_primers()

bool CBioSource_Base::CanGetPcr_primers ( void  ) const
inline

Check if it is safe to call GetPcr_primers method.

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

Definition at line 582 of file BioSource_.hpp.

References CBioSource_Base::IsSetPcr_primers().

Referenced by CBioSource_Base::GetPcr_primers().

◆ CanGetReverse()

bool CPCRReaction_Base::CanGetReverse ( void  ) const
inline

Check if it is safe to call GetReverse method.

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

Definition at line 225 of file PCRReaction_.hpp.

References CPCRReaction_Base::IsSetReverse().

Referenced by CPCRReaction_Base::GetReverse().

◆ CanGetSeq()

bool CPCRPrimer_Base::CanGetSeq ( void  ) const
inline

Check if it is safe to call GetSeq method.

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

Definition at line 205 of file PCRPrimer_.hpp.

References CPCRPrimer_Base::IsSetSeq().

Referenced by CPCRPrimer_Base::GetSeq().

◆ CanGetSubtype() [1/2]

bool CBioSource_Base::CanGetSubtype ( void  ) const
inline

◆ CanGetSubtype() [2/2]

bool CSubSource_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 297 of file SubSource_.hpp.

References CSubSource_Base::IsSetSubtype().

Referenced by CSubSource_Base::GetSubtype(), and CSubtypeEquals::operator()().

◆ CBioSource_Base() [1/2]

CBioSource_Base::CBioSource_Base ( const CBioSource_Base )
private

◆ CBioSource_Base() [2/2]

END_CLASS_INFO CBioSource_Base::CBioSource_Base ( void  )

◆ CPCRPrimer() [1/2]

CPCRPrimer::CPCRPrimer ( const CPCRPrimer value)
private

◆ CPCRPrimer() [2/2]

CPCRPrimer::CPCRPrimer ( void  )
inline

Definition at line 86 of file PCRPrimer.hpp.

◆ CPCRPrimer_Base() [1/2]

CPCRPrimer_Base::CPCRPrimer_Base ( const CPCRPrimer_Base )
private

◆ CPCRPrimer_Base() [2/2]

END_CLASS_INFO CPCRPrimer_Base::CPCRPrimer_Base ( void  )

Definition at line 80 of file PCRPrimer_.cpp.

References CPCRPrimer_Base::m_set_State.

◆ CPCRPrimerName() [1/2]

CPCRPrimerName::CPCRPrimerName ( const std::string value)
inlineexplicit

Explicit constructor from the primitive type.

Definition at line 72 of file PCRPrimerName.hpp.

◆ CPCRPrimerName() [2/2]

CPCRPrimerName::CPCRPrimerName ( void  )
inline

Definition at line 69 of file PCRPrimerName.hpp.

◆ CPCRPrimerName_Base() [1/2]

CPCRPrimerName_Base::CPCRPrimerName_Base ( const string data)
inlineexplicit

Definition at line 100 of file PCRPrimerName_.hpp.

◆ CPCRPrimerName_Base() [2/2]

CPCRPrimerName_Base::CPCRPrimerName_Base ( void  )
inline

Definition at line 95 of file PCRPrimerName_.hpp.

◆ CPCRPrimerSeq_Base() [1/2]

CPCRPrimerSeq_Base::CPCRPrimerSeq_Base ( const string data)
inlineexplicit

Definition at line 100 of file PCRPrimerSeq_.hpp.

◆ CPCRPrimerSeq_Base() [2/2]

CPCRPrimerSeq_Base::CPCRPrimerSeq_Base ( void  )
inline

Definition at line 95 of file PCRPrimerSeq_.hpp.

◆ CPCRPrimerSet() [1/2]

CPCRPrimerSet::CPCRPrimerSet ( const CPCRPrimerSet value)
private

◆ CPCRPrimerSet() [2/2]

CPCRPrimerSet::CPCRPrimerSet ( void  )
inline

Definition at line 86 of file PCRPrimerSet.hpp.

◆ CPCRPrimerSet_Base() [1/2]

CPCRPrimerSet_Base::CPCRPrimerSet_Base ( const CPCRPrimerSet_Base )
private

◆ CPCRPrimerSet_Base() [2/2]

END_CLASS_INFO CPCRPrimerSet_Base::CPCRPrimerSet_Base ( void  )

Definition at line 68 of file PCRPrimerSet_.cpp.

References CPCRPrimerSet_Base::m_set_State.

◆ CPCRReaction() [1/2]

CPCRReaction::CPCRReaction ( const CPCRReaction value)
private

◆ CPCRReaction() [2/2]

CPCRReaction::CPCRReaction ( void  )
inline

Definition at line 86 of file PCRReaction.hpp.

◆ CPCRReaction_Base() [1/2]

CPCRReaction_Base::CPCRReaction_Base ( const CPCRReaction_Base )
private

◆ CPCRReaction_Base() [2/2]

END_CLASS_INFO CPCRReaction_Base::CPCRReaction_Base ( void  )

Definition at line 103 of file PCRReaction_.cpp.

References CPCRReaction_Base::m_set_State.

◆ CPCRReactionSet() [1/2]

CPCRReactionSet::CPCRReactionSet ( const CPCRReactionSet value)
private

◆ CPCRReactionSet() [2/2]

CPCRReactionSet::CPCRReactionSet ( void  )
inline

Definition at line 86 of file PCRReactionSet.hpp.

◆ CPCRReactionSet_Base() [1/2]

CPCRReactionSet_Base::CPCRReactionSet_Base ( const CPCRReactionSet_Base )
private

◆ CPCRReactionSet_Base() [2/2]

END_CLASS_INFO CPCRReactionSet_Base::CPCRReactionSet_Base ( void  )

Definition at line 68 of file PCRReactionSet_.cpp.

References CPCRReactionSet_Base::m_set_State.

◆ CSubSource_Base() [1/2]

CSubSource_Base::CSubSource_Base ( const CSubSource_Base )
private

◆ CSubSource_Base() [2/2]

END_CLASS_INFO CSubSource_Base::CSubSource_Base ( void  )

Definition at line 133 of file SubSource_.cpp.

References CSubSource_Base::m_set_State.

◆ DECLARE_INTERNAL_TYPE_INFO() [1/6]

CBioSource_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [2/6]

CPCRPrimer_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [3/6]

CPCRPrimerSet_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [4/6]

CPCRReaction_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [5/6]

CPCRReactionSet_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [6/6]

CSubSource_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_STD_ALIAS_TYPE_INFO() [1/2]

CPCRPrimerName_Base::DECLARE_STD_ALIAS_TYPE_INFO ( )

◆ DECLARE_STD_ALIAS_TYPE_INFO() [2/2]

CPCRPrimerSeq_Base::DECLARE_STD_ALIAS_TYPE_INFO ( )

◆ EGenome()

static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME() CBioSource_Base::EGenome ( void  )
static

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

◆ EOrigin()

static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME() CBioSource_Base::EOrigin ( void  )
static

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

◆ ESubtype()

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

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

◆ Get() [1/2]

const CPCRPrimerSet_Base::Tdata & CPCRPrimerSet_Base::Get ( void  ) const
inline

◆ Get() [2/2]

const CPCRReactionSet_Base::Tdata & CPCRReactionSet_Base::Get ( void  ) const
inline

◆ GetAttrib()

const CSubSource_Base::TAttrib & CSubSource_Base::GetAttrib ( void  ) const
inline

Get the Attrib member data.

Returns
Reference to the member data.

Definition at line 397 of file SubSource_.hpp.

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

Referenced by CSubSource::GetLabel(), CGuiObjectInfoComponent::GetToolTip(), and IsSameSubtype().

◆ GetForward()

const CPCRReaction_Base::TForward & CPCRReaction_Base::GetForward ( void  ) const
inline

◆ GetGenome()

CBioSource_Base::TGenome CBioSource_Base::GetGenome ( void  ) const
inline

Get the Genome member data.

Returns
Copy of the member data.

Definition at line 422 of file BioSource_.hpp.

References CBioSource_Base::m_Genome.

Referenced by CCleanup::AddPartialToProteinTitle(), BioSourceFromImpFeat(), BOOST_AUTO_TEST_CASE(), CValidError_bioseq::CheckSourceDescriptor(), FakeEmblBioSources(), FakeGenBankBioSources(), CBioSource::FixGenomeForQualifiers(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), CConvertBadCdsAndRnaToMiscFeat::getCdsOverlap(), CAutoDefWithTaxonomy::GetDocsumDefLine(), CBioSource::GetGenCode(), CWriteUtil::GetGenomeString(), CSource_qual_choice::GetLimitedSourceQualFromBioSource(), variation::CVariationUtil::GetMolType(), CAutoDef::GetOneDefLine(), CBioSource::GetRepliconName(), CConvertBadCdsAndRnaToMiscFeat::getRnaOverlap(), GetSeqTableFromSeqEntry(), CGenomeQual::GetValue(), CEditingActionBiosourceLocation::GetValue(), CSGUtils::IsChromosome(), CDiscrepancyContext::IsEukaryotic(), IsInOrganelleSmallGenomeSet(), variation::IsMitochondrion(), CSGUtils::IsMitochondrion(), IsOrganelle(), CDiscrepancyContext::IsOrganelle(), CMRnaForCDS::IsOrganelle(), CSGUtils::IsPlastid(), CCleanup::MergeDupBioSources(), CBioSourceKind::operator=(), s_GetStrictGenCode(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_Relaxed(), s_IsChromosome(), CValidError_imp::Validate(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateSeqFeatContext(), CSourceFeatureItem::x_AddQuals(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CApplyGCode::x_ApplyToBioSource(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CAutoDef::x_GetFeatureClauseProductEnding(), CDeflineGenerator::x_GetModifiers(), CValidError_bioseq::x_IgnoreEndGap(), CBioseqIndex::x_InitSource(), CValidError_bioseq::x_ParentAndComponentLocationsDiffer(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CDeflineGenerator::x_SetBioSrc(), CSourceItem::x_SetSource(), CValidError_bioseq::x_ValidateCompletness(), CCdregionValidator::x_ValidateGeneticCode(), CSrcWriter::xGatherGenome(), and XMLFakeBioSources().

◆ GetName() [1/2]

const CPCRPrimer_Base::TName & CPCRPrimer_Base::GetName ( void  ) const
inline

Get the Name member data.

Returns
Reference to the member data.

Definition at line 246 of file PCRPrimer_.hpp.

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

Referenced by s_PcrPrimerCompare(), s_PCRPrimerLess(), CValidError_imp::x_CheckPCRPrimer(), and CSrcWriter::xPrimerSetNames().

◆ GetName() [2/2]

const CSubSource_Base::TName & CSubSource_Base::GetName ( void  ) const
inline

◆ GetOrg()

const CBioSource_Base::TOrg & CBioSource_Base::GetOrg ( void  ) const
inline

Get the Org member data.

Returns
Reference to the member data.

Definition at line 509 of file BioSource_.hpp.

References CBioSource_Base::m_Org, and CBioSource_Base::ResetOrg().

Referenced by CUnculTaxTool::AddBioSource(), AddBioSourceToAttributes(), CQualLookupMap::AddDesc(), CQualLookupMap::AddFeat(), CCleanup::AddPartialToProteinTitle(), CSrcStructuredVoucherPartColumn::AddToBioSource(), CBioSource::AllowMatingTypeQualifier(), CBioSource::AllowSexQualifier(), CCleanup::AreBioSourcesMergeable(), CBioSource::AutoFix(), CNewCleanup_imp::BiosourceBC(), CNewCleanup_imp::BiosourceFeatBC(), BOOST_AUTO_TEST_CASE(), CheckMetagenome(), CheckQualsInSourceFeat(), CheckSourceLineage(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CompareDescrFeatSources(), CopyOrg(), CBioSource::FixEnvironmentalSample(), FixHumanHost(), fta_fix_orgref_div(), fta_get_gcode_from_biosource(), fta_sort_biosource(), IEditingAction::GetActionCommand(), CAutoDefSourceDescription::GetAvailableModifiers(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), CAutoDefSourceDescription::GetComboDescription(), CBioSource::GetCommon(), CAutoDefSourceGroup::GetDefaultExcludeSp(), CBioSource::GetDisableStrainForwarding(), CBioSource::GetDivision(), CAutoDefWithTaxonomy::GetDocsumOrgDescription(), CSrcTableDbxrefColumn::GetFromBioSource(), GetGBBlock(), CBioSource::GetGcode(), CBioSource::GetGenCode(), GetGeneticCodeForBioseq(), CEntrezgeneHandler::GetLabel(), CBioSource::GetLineage(), CBioSource::GetMgcode(), CBioSource::GetNameValPairs(), GetOrg_refOrNull(), IAlignRowHandle::GetOrgLabel(), CBioSource::GetOrgname(), CBioSource::GetPgcode(), CUnculTaxTool::GetReply(), GetRmCultureNotesCommand(), GetSeqTableFromSeqEntry(), CAutoDefModifierCombo::GetSourceDescriptionString(), GetSourceFields(), GetSprotDescr(), GetSrcQual(), CCommentItem::GetStringForTLS(), CCommentItem::GetStringForTSA(), CCommentItem::GetStringForWGS(), CBioseq::GetTaxId(), CBioSource::GetTaxname(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CSrcTableDbxrefColumn::GetValsFromBioSource(), CSrcTableOrgModColumn::GetValsFromBioSource(), CTaxnameQual::GetValue(), COrgModQual::GetValue(), CEditingActionBiosourceTaxname::GetValue(), CEditingActionBiosourceTaxnameAfterBinomial::GetValue(), CEditingActionBiosourceCommonName::GetValue(), CEditingActionBiosourceDivision::GetValue(), CEditingActionBiosourceLineage::GetValue(), CValidError_imp::HandleTaxonomyError(), HasAmplifiedWithSpeciesSpecificPrimerNote(), IsMissingRequiredClone(), CBioSource::IsSetCommon(), CBioSource::IsSetDivision(), CBioSource::IsSetGcode(), CBioSource::IsSetLineage(), CBioSource::IsSetMgcode(), CBioSource::IsSetOrgMod(), CBioSource::IsSetOrgname(), CBioSource::IsSetPgcode(), CBioSource::IsSetTaxname(), CEditingActionBiosourceTaxname::IsSetValue(), CEditingActionBiosourceTaxnameAfterBinomial::IsSetValue(), CEditingActionBiosourceCommonName::IsSetValue(), CEditingActionBiosourceDivision::IsSetValue(), CEditingActionBiosourceLineage::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), CNewCleanup_imp::IsSyntheticConstruct(), CAutoDefSourceDescription::IsTrickyHIV(), CBioSource::IsViral(), CBioSource::MakeCommon(), MakeCommonBioSource(), CCleanup::MakeIRDFeatsFromSourceXrefs(), MakeMailReportPostReport(), MakeMailReportPreReport(), CCleanup::MakeSmallGenomeSet(), CCleanup::MergeDupBioSources(), CEditingActionBiosourceDbxref::Modify(), CRemoveTaxonBioSource::ModifyBioSource(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PropogateSuppliedLineage(), RemoveDbxref(), CBioSource::RemoveLineageSourceNotes(), RemoveMod(), CBioSource::RemoveNullTerms(), CBioSource::RemoveOrgMod(), RemoveStrain(), RemoveTaxId(), CBioSource::RemoveUnexpectedViralQualifiers(), CPrimeCacheApplication::Run(), s_DuplicatesBiosource(), s_GetBioSourceContentLabel(), s_GetContentLabel(), s_GetDiv(), s_GetInstCodeFromBioSource(), s_GetSpecificHostFromBioSource(), s_GetStrictGenCode(), s_GetTaxId(), s_GetTaxid(), CMacroFunction_MakeBoldXrefs::s_HasBarcodeDbXref(), CGenusSpeciesFixup::s_HasTaxId(), CUnculturedTool::s_HasTaxId(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_AdjustEnds(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_Strict(), CMacroFunction_RemoveQual::s_RemoveFields(), s_ResetModSubsrcQuals(), s_SuppressMultipleEquivBioSources(), s_TitleFromSegment(), SeqEntryCheckTaxonDiv(), SetCultureCollectionFromStrain(), CBioSource::SetDisableStrainForwarding(), CCleanup::SetGeneticCodes(), SetOrgMod(), CCleanup::TaxonomyLookup(), CMacroFunction_SwapQual::TheFunction(), CMacroFunction_ApplyStrucVoucherPart::TheFunction(), UpdateBiosourceFromBiosample(), UpdateRawBioSource(), CBioSource::UpdateWithBioSample(), CSrcFeatValidator::Validate(), CValidError_imp::Validate(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_imp::ValidateSubSource(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddHIVModifiers(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDefModifierCombo::x_AddOrgModString(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers(), CStrainSerotypeInfluenza::x_AddToInfluenzaNames(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CAppendModToOrg::x_ApplyToBioSource(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CWriteDB_Impl::x_BuildDeflinesFromBioseq(), CNewCleanup_imp::x_CanRemoveGenbankBlockSource(), CNewCleanup_imp::x_ChangePopToPhy(), CNewCleanup_imp::x_CopyGBBlockDivToOrgnameDiv(), CStrainSerotypeInfluenza::x_FixupOrganismNames(), CSourceFeatureItem::x_GatherInfo(), CKeywordsItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CAutoDef::x_GetFeatureClauses(), CDeflineGenerator::x_GetModifiers(), CBioSource::x_GetOrgModNameValPairs(), CStrainSerotypeInfluenza::x_GetStrainSerotypeConflicts(), CDumpASNIndex::x_GetTaxId(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CBioseqIndex::x_InitSource(), CStrainSerotypeInfluenza::x_IsParsableInfluenzaVirusName(), CBioSource::x_RemoveNameElementDiffs(), CSourceItem::x_SetSource(), CBlastTabularInfo::x_SetTaxInfoAll(), CBioSource::x_ShouldIgnoreNoteForBiosample(), CStrainSerotypeInfluenza::x_TrimmingOrganismNames(), CValidError_bioseq::x_ValidateMolInfoForBioSource(), CValidError_bioseq::x_ValidateSourceFeatures(), CGff3Writer::xAssignSourceAttributeDbxref(), CGff3Writer::xAssignSourceAttributesOrgMod(), CGff3FlybaseWriter::xAssignTaxid(), CSrcWriter::xGatherDb(), CSrcWriter::xGatherDivision(), CSrcWriter::xGatherOrgCommon(), CSrcWriter::xGatherOrgnameLineage(), CSrcWriter::xGatherTaxonId(), XMLGetGBBlock(), and CGff3Writer::xWriteSequenceHeader().

◆ GetOrigin()

CBioSource_Base::TOrigin CBioSource_Base::GetOrigin ( void  ) const
inline

◆ GetPcr_primers()

const CBioSource_Base::TPcr_primers & CBioSource_Base::GetPcr_primers ( void  ) const
inline

◆ GetReverse()

const CPCRReaction_Base::TReverse & CPCRReaction_Base::GetReverse ( void  ) const
inline

◆ GetSeq()

const CPCRPrimer_Base::TSeq & CPCRPrimer_Base::GetSeq ( void  ) const
inline

Get the Seq member data.

Returns
Reference to the member data.

Definition at line 211 of file PCRPrimer_.hpp.

References CPCRPrimer_Base::CanGetSeq(), CPCRPrimer_Base::m_Seq, and CSerialObject::ThrowUnassigned().

Referenced by s_PcrPrimerCompare(), s_PCRPrimerLess(), CValidError_imp::x_CheckPCRPrimer(), and CSrcWriter::xPrimerSetSequences().

◆ GetSubtype() [1/2]

const CBioSource_Base::TSubtype & CBioSource_Base::GetSubtype ( void  ) const
inline

Get the Subtype member data.

Returns
Reference to the member data.

Definition at line 539 of file BioSource_.hpp.

References CBioSource_Base::m_Subtype.

Referenced by AddBioSourceToAttributes(), CBioSource::AutoFix(), BOOST_AUTO_TEST_CASE(), ChangeCountryColonToComma(), CBioSource::FixEnvironmentalSample(), CBioSource::FixSexMatingTypeInconsistencies(), FTASubSourceAdd(), g_FindSegs(), CAutoDefSourceDescription::GetAvailableModifiers(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), GetDescrEmblBlock(), GetEmblGBBlock(), GetGBBlock(), CBioSource::GetRepliconName(), GetSeqTableFromSeqEntry(), GetSourceFields(), CGuiObjectInfoComponent::GetToolTip(), CSrcTableSubSourceColumn::GetValsFromBioSource(), CSubSrcQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), CBioSource::HasSubtype(), CAutoDefFeatureClause::IsEndogenousVirusSourceFeature(), IsMissingRequiredClone(), IsSegmentSubtype(), CUnculTaxTool::IsSpeciesSpecific(), CAutoDefSourceDescription::IsTrickyHIV(), CBioSource::MakeCommonExceptOrg(), CCleanup::MergeDupBioSources(), CTabularFormatter_SeqChrom::Print(), CTabularFormatter_SeqClone::Print(), RemoveCountryColon(), CBioSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveSubSource(), s_GetContentLabel(), s_GetEncodeValues(), s_GetSourceSubtype(), s_HasSubSourceNote(), s_ResetModSubsrcQuals(), s_SubSourceListUniqued(), s_TitleFromSegment(), SetSubsource(), CNewCleanup_imp::SubSourceListBC(), UpdateBiosourceFromBiosample(), CValidError_imp::ValidateBioSource(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddMinicircle(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_AddSubsourceString(), CAutoDefModifierCombo::x_BioSourceHasSubSrc(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CUnculturedTool::x_ConvertNote(), CKeywordsItem::x_GatherInfo(), CAutoDefFeatureClause::x_GetDescription(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CAutoDef::x_GetFeatureClauseProductEnding(), CDeflineGenerator::x_GetModifiers(), CBioSource::x_GetSubtypeNameValPairs(), CSetTransgSrcDesc::x_HasTransgenicSubtype(), CCulturedTool::x_RemoveIfFoundSubSourceNote(), CSubmissionWizard::x_TransferImportedSubSources(), CValidError_bioseq::x_ValidateSourceFeatures(), CGff3Writer::xAssignSourceAttributesSubSource(), CSrcWriter::xGatherSubtypeFeat(), and XMLGetGBBlock().

◆ GetSubtype() [2/2]

CSubSource_Base::TSubtype CSubSource_Base::GetSubtype ( void  ) const
inline

◆ IsSet() [1/2]

bool CPCRPrimerSet_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< CPCRPrimer > > Tdata'

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

Definition at line 152 of file PCRPrimerSet_.hpp.

References CPCRPrimerSet_Base::m_set_State.

Referenced by s_PcrPrimerSetCompare(), s_PCRPrimerSetLess(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().

◆ IsSet() [2/2]

bool CPCRReactionSet_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< CPCRReaction > > Tdata'

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

Definition at line 152 of file PCRReactionSet_.hpp.

References CPCRReactionSet_Base::m_set_State.

Referenced by CPCRSetList::AreSetsUnique(), CEditingActionBiosourcePrimers::Modify(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().

◆ IsSetAttrib()

bool CSubSource_Base::IsSetAttrib ( void  ) const
inline

attribution/source of this 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 385 of file SubSource_.hpp.

References CSubSource_Base::m_set_State.

Referenced by CSubSource_Base::CanGetAttrib(), CSubSource::GetLabel(), CGuiObjectInfoComponent::GetToolTip(), IsSameSubtype(), and CSubSource_Base::SetAttrib().

◆ IsSetForward()

bool CPCRReaction_Base::IsSetForward ( void  ) const
inline

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

Data member Forward is optional; its type is defined as 'typedef CPCRPrimerSet TForward'

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

Definition at line 198 of file PCRReaction_.hpp.

References CPCRReaction_Base::m_Forward.

Referenced by CPCRReaction_Base::CanGetForward(), CPcrReactionLessThan::operator()(), s_PCRReactionLess(), CSrcTablePrimerColumn::x_DoesReactionHaveSpace(), CSrcTablePrimerColumn::x_GetValues(), CSrcTablePrimerColumn::x_RemoveEmptyValues(), and CSrcWriter::xGatherPcrPrimers().

◆ IsSetGenome()

bool CBioSource_Base::IsSetGenome ( void  ) const
inline

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

Data member Genome is optional with default eGenome_unknown; its type is defined as 'typedef int TGenome'

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

Definition at line 397 of file BioSource_.hpp.

References CBioSource_Base::m_set_State.

Referenced by CCleanup::AddPartialToProteinTitle(), BioSourceFromImpFeat(), BOOST_AUTO_TEST_CASE(), CValidError_bioseq::CheckSourceDescriptor(), CBioSource::FixGenomeForQualifiers(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), CAutoDefWithTaxonomy::GetDocsumDefLine(), CWriteUtil::GetGenomeString(), variation::CVariationUtil::GetMolType(), CBioSource::GetRepliconName(), GetSeqTableFromSeqEntry(), CGenomeQual::GetValue(), IsInOrganelleSmallGenomeSet(), IsOrganelle(), CDiscrepancyContext::IsOrganelle(), CMRnaForCDS::IsOrganelle(), CEditingActionBiosourceLocation::IsSetValue(), CCleanup::MergeDupBioSources(), CBioSourceKind::operator=(), s_GetStrictGenCode(), s_IsChromosome(), s_IsEmptyBioSource(), CBioSource_Base::SetGenome(), CValidError_imp::Validate(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateSeqFeatContext(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CApplyGCode::x_ApplyToBioSource(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CValidError_bioseq::x_IgnoreEndGap(), CBioseqIndex::x_InitSource(), CValidError_bioseq::x_ParentAndComponentLocationsDiffer(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CDeflineGenerator::x_SetBioSrc(), CValidError_bioseq::x_ValidateCompletness(), and CSrcWriter::xGatherGenome().

◆ IsSetIs_focus()

bool CBioSource_Base::IsSetIs_focus ( void  ) const
inline

to distinguish biological focus Check if a value has been assigned to Is_focus data member.

Data member Is_focus is optional

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

Definition at line 552 of file BioSource_.hpp.

References CBioSource_Base::m_set_State.

Referenced by CCleanup::ConvertSrcFeatsToSrcDescs(), GetBiosourceDifferences(), CCleanup::MergeDupBioSources(), s_BiosrcFullLengthIsOk(), CSrcFeatValidator::Validate(), CSourceFeatureItem::x_AddQuals(), CSourceFeatureItem::x_GatherInfo(), and CValidError_bioseq::x_ValidateSourceFeatures().

◆ IsSetName() [1/2]

bool CPCRPrimer_Base::IsSetName ( void  ) const
inline

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

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

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

Definition at line 234 of file PCRPrimer_.hpp.

References CPCRPrimer_Base::m_set_State.

Referenced by CPCRPrimer_Base::CanGetName(), s_PcrPrimerCompare(), s_PCRPrimerLess(), CValidError_imp::x_CheckPCRPrimer(), and CSrcWriter::xPrimerSetNames().

◆ IsSetName() [2/2]

bool CSubSource_Base::IsSetName ( void  ) const
inline

◆ IsSetOrg()

bool CBioSource_Base::IsSetOrg ( void  ) const
inline

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

Data member Org is mandatory; its type is defined as 'typedef COrg_ref TOrg'

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

Definition at line 497 of file BioSource_.hpp.

References CBioSource_Base::m_Org.

Referenced by CUnculTaxTool::AddBioSource(), AddBioSourceToAttributes(), CQualLookupMap::AddDesc(), CQualLookupMap::AddFeat(), CCleanup::AddPartialToProteinTitle(), CSrcStructuredVoucherPartColumn::AddToBioSource(), CBioSource::AllowMatingTypeQualifier(), CBioSource::AllowSexQualifier(), CCleanup::AreBioSourcesMergeable(), CBioSource::AutoFix(), CNewCleanup_imp::BiosourceBC(), CNewCleanup_imp::BioSourceEC(), CNewCleanup_imp::BiosourceFeatBC(), CheckMetagenome(), CheckSourceLineage(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CompareDescrFeatSources(), CSourceFeatureItem::CSourceFeatureItem(), CBioSource::FixEnvironmentalSample(), FixHumanHost(), fta_fix_orgref_div(), fta_get_gcode_from_biosource(), IEditingAction::GetActionCommand(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), CLowerQuals::GetCommand(), CBioSource::GetDisableStrainForwarding(), CAutoDefWithTaxonomy::GetDocsumOrgDescription(), GetEmblDescr(), GetGBBlock(), GetGenBankDescr(), GetGeneticCodeForBioseq(), CBioSource::GetNameValPairs(), GetSeqTableFromSeqEntry(), GetSourceFields(), GetSprotDescr(), CCommentItem::GetStringForTLS(), CCommentItem::GetStringForTSA(), CCommentItem::GetStringForWGS(), CBioseq::GetTaxId(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CSrcTableOrgModColumn::GetValsFromBioSource(), CTaxnameQual::GetValue(), COrgModQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), IsMissingRequiredClone(), CBioSource::IsSetCommon(), CBioSource::IsSetDivision(), CBioSource::IsSetGcode(), CBioSource::IsSetLineage(), CBioSource::IsSetMgcode(), CBioSource::IsSetOrgMod(), CBioSource::IsSetOrgname(), CBioSource::IsSetPgcode(), CBioSource::IsSetTaxname(), CEditingActionBiosourceTaxname::IsSetValue(), CEditingActionBiosourceTaxnameAfterBinomial::IsSetValue(), CEditingActionBiosourceCommonName::IsSetValue(), CEditingActionBiosourceDivision::IsSetValue(), CEditingActionBiosourceLineage::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), CNewCleanup_imp::IsSyntheticConstruct(), CBioSource::IsViral(), CBioSource::MakeCommon(), MakeCommonBioSource(), CCleanup::MakeIRDFeatsFromSourceXrefs(), MakeMailReportPostReport(), MakeMailReportPreReport(), CCleanup::MakeSmallGenomeSet(), CEditingActionBiosourceDbxref::Modify(), CSrcModListPanel::PopulateModifiers(), PropogateSuppliedLineage(), RemoveDbxref(), CBioSource::RemoveLineageSourceNotes(), RemoveMod(), CBioSource::RemoveNullTerms(), CBioSource::RemoveOrgMod(), RemoveStrain(), RemoveTaxId(), CBioSource::RemoveUnexpectedViralQualifiers(), CFindASN1Dlg::ReplaceInBiosource(), s_DuplicatesBiosource(), s_GetBioSourceContentLabel(), s_GetDiv(), s_GetInstCodeFromBioSource(), s_GetSpecificHostFromBioSource(), s_GetStrictGenCode(), CMacroFunction_MakeBoldXrefs::s_HasBarcodeDbXref(), CGenusSpeciesFixup::s_HasTaxId(), CUnculturedTool::s_HasTaxId(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_AdjustEnds(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_Strict(), s_IsEmptyBioSource(), CMacroFunction_RemoveQual::s_RemoveFields(), s_SuppressMultipleEquivBioSources(), SeqEntryCheckTaxonDiv(), SetCultureCollectionFromStrain(), CBioSource::SetDisableStrainForwarding(), SetOrgMod(), CCleanup::TaxonomyLookup(), CMacroFunction_SwapQual::TheFunction(), UpdateBiosourceFromBiosample(), CRemoteUpdater::UpdateOrgFromTaxon(), CValidError_imp::Validate(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateSeqDescContext(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddHIVModifiers(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDefModifierCombo::x_AddOrgModString(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CAppendModToOrg::x_ApplyToBioSource(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CNewCleanup_imp::x_CanRemoveGenbankBlockSource(), CNewCleanup_imp::x_ChangePopToPhy(), CFlatGatherer::x_CollectSourceDescriptors(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioSource(), CSourceFeatureItem::x_GatherInfo(), CKeywordsItem::x_GatherInfo(), CFlatGatherer::x_GatherSourceOrganism(), CAutoDef::x_GetFeatureClauses(), CDeflineGenerator::x_GetModifiers(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CBioSource::x_RemoveNameElementDiffs(), CBioSource::x_ShouldIgnoreNoteForBiosample(), CValidError_bioseq::x_ValidateMolInfoForBioSource(), CValidError_bioseq::x_ValidateSourceFeatures(), CGff3Writer::xAssignSourceAttributeDbxref(), CGff3Writer::xAssignSourceAttributesOrgMod(), CGff3FlybaseWriter::xAssignTaxid(), CSrcWriter::xGatherDb(), CSrcWriter::xGatherDivision(), CSrcWriter::xGatherOrgCommon(), CSrcWriter::xGatherOrgnameLineage(), CSrcWriter::xGatherTaxonId(), XMLGetDescr(), XMLGetGBBlock(), and CGff3Writer::xWriteSequenceHeader().

◆ IsSetOrigin()

bool CBioSource_Base::IsSetOrigin ( void  ) const
inline

◆ IsSetPcr_primers()

bool CBioSource_Base::IsSetPcr_primers ( void  ) const
inline

◆ IsSetReverse()

bool CPCRReaction_Base::IsSetReverse ( void  ) const
inline

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

Data member Reverse is optional; its type is defined as 'typedef CPCRPrimerSet TReverse'

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

Definition at line 219 of file PCRReaction_.hpp.

References CPCRReaction_Base::m_Reverse.

Referenced by CPCRReaction_Base::CanGetReverse(), CPcrReactionLessThan::operator()(), s_PCRReactionLess(), CSrcTablePrimerColumn::x_DoesReactionHaveSpace(), CSrcTablePrimerColumn::x_GetValues(), CSrcTablePrimerColumn::x_RemoveEmptyValues(), and CSrcWriter::xGatherPcrPrimers().

◆ IsSetSeq()

bool CPCRPrimer_Base::IsSetSeq ( void  ) const
inline

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

Data member Seq is optional; its type is defined as 'typedef CPCRPrimerSeq TSeq'

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

Definition at line 199 of file PCRPrimer_.hpp.

References CPCRPrimer_Base::m_set_State.

Referenced by CPCRPrimer_Base::CanGetSeq(), s_PcrPrimerCompare(), s_PCRPrimerLess(), CValidError_imp::x_CheckPCRPrimer(), and CSrcWriter::xPrimerSetSequences().

◆ IsSetSubtype() [1/2]

bool CBioSource_Base::IsSetSubtype ( void  ) const
inline

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

Data member Subtype is optional; its type is defined as 'typedef list< CRef< CSubSource > > TSubtype'

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

Definition at line 527 of file BioSource_.hpp.

References CBioSource_Base::m_set_State.

Referenced by AddBioSourceToAttributes(), CBioSource::AutoFix(), BOOST_AUTO_TEST_CASE(), ChangeCountryColonToComma(), CCleanup::CleanupCollectionDates(), CUnculTaxTool::ConvertSpeciesSpecificNote(), CBioSource::FixEnvironmentalSample(), CBioSource::FixSexMatingTypeInconsistencies(), fta_sort_biosource(), g_FindSegs(), GetBiosourceDifferences(), GetDescrEmblBlock(), GetEmblGBBlock(), GetGBBlock(), GetSeqTableFromSeqEntry(), GetSourceFields(), CGuiObjectInfoComponent::GetToolTip(), CSrcTableSubSourceColumn::GetValsFromBioSource(), CSubSrcQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), CBioSource::HasSubtype(), IsMissingRequiredClone(), IsSegmentSubtype(), CUnculTaxTool::IsSpeciesSpecific(), CBioSource::MakeCommonExceptOrg(), CCleanup::MergeDupBioSources(), RemoveCountryColon(), CBioSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveSubSource(), CFindASN1Dlg::ReplaceInBiosource(), s_GetContentLabel(), s_GetSourceSubtype(), s_HasSubSourceNote(), s_IsEmptyBioSource(), s_ResetModSubsrcQuals(), s_SubSourceListUniqued(), s_TitleFromSegment(), SetChromosome(), SetSubSource(), SetTransgenic(), CNewCleanup_imp::SubSourceListBC(), UpdateBiosourceFromBiosample(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDefModifierCombo::x_AddSubsourceString(), CAppendModToOrg::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC(), CAutoDefModifierCombo::x_BioSourceHasSubSrc(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CBioSource::x_ClearCoordinatedBioSampleSubSources(), CUnculturedTool::x_ConvertNote(), CDeflineGenerator::x_GetModifiers(), CBioSource::x_GetSubtypeNameValPairs(), CCulturedTool::x_RemoveIfFoundSubSourceNote(), CSubmissionWizard::x_TransferImportedSubSources(), CValidError_bioseq::x_ValidateSourceFeatures(), CGff3Writer::xAssignSourceAttributesSubSource(), CSrcWriter::xGatherSubtypeFeat(), and XMLGetGBBlock().

◆ IsSetSubtype() [2/2]

bool CSubSource_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 291 of file SubSource_.hpp.

References CSubSource_Base::m_set_State.

Referenced by CSubSource::AutoFix(), CSubSource_Base::CanGetSubtype(), CSubSource::FixCapitalization(), CWriteUtil::GetSubSourceSubType(), CGuiObjectInfoComponent::GetToolTip(), IsSameSubtype(), CBioSource::RemoveLineageSourceNotes(), s_SameSubtype(), s_SameSubtypeC(), CSubSource_Base::SetSubtype(), CValidError_imp::ValidateSubSource(), CDeflineGenerator::x_GetModifiers(), and CNewCleanup_imp::x_SubSourceBC().

◆ operator const Tdata &() [1/2]

CPCRPrimerSet_Base::operator const CPCRPrimerSet_Base::Tdata & ( void  ) const
inline

Conversion operator to 'const Tdata' type.

Definition at line 177 of file PCRPrimerSet_.hpp.

◆ operator const Tdata &() [2/2]

CPCRReactionSet_Base::operator const CPCRReactionSet_Base::Tdata & ( void  ) const
inline

Conversion operator to 'const Tdata' type.

Definition at line 177 of file PCRReactionSet_.hpp.

◆ operator Tdata &() [1/2]

CPCRPrimerSet_Base::operator CPCRPrimerSet_Base::Tdata & ( void  )
inline

Conversion operator to 'Tdata' type.

Definition at line 183 of file PCRPrimerSet_.hpp.

◆ operator Tdata &() [2/2]

CPCRReactionSet_Base::operator CPCRReactionSet_Base::Tdata & ( void  )
inline

Conversion operator to 'Tdata' type.

Definition at line 183 of file PCRReactionSet_.hpp.

◆ operator<<() [1/2]

Definition at line 106 of file PCRPrimerName_.hpp.

References str(), and WriteObject().

◆ operator<<() [2/2]

Definition at line 106 of file PCRPrimerSeq_.hpp.

References str(), and WriteObject().

◆ operator=() [1/10]

CBioSource_Base& CBioSource_Base::operator= ( const CBioSource_Base )
private

◆ operator=() [2/10]

CPCRPrimer& CPCRPrimer::operator= ( const CPCRPrimer value)
private

◆ operator=() [3/10]

CPCRPrimer_Base& CPCRPrimer_Base::operator= ( const CPCRPrimer_Base )
private

◆ operator=() [4/10]

CPCRPrimerSet& CPCRPrimerSet::operator= ( const CPCRPrimerSet value)
private

◆ operator=() [5/10]

CPCRPrimerSet_Base& CPCRPrimerSet_Base::operator= ( const CPCRPrimerSet_Base )
private

◆ operator=() [6/10]

CPCRReaction& CPCRReaction::operator= ( const CPCRReaction value)
private

◆ operator=() [7/10]

CPCRReaction_Base& CPCRReaction_Base::operator= ( const CPCRReaction_Base )
private

◆ operator=() [8/10]

CPCRReactionSet& CPCRReactionSet::operator= ( const CPCRReactionSet value)
private

◆ operator=() [9/10]

CPCRReactionSet_Base& CPCRReactionSet_Base::operator= ( const CPCRReactionSet_Base )
private

◆ operator=() [10/10]

CSubSource_Base& CSubSource_Base::operator= ( const CSubSource_Base )
private

◆ operator>>() [1/2]

Definition at line 117 of file PCRPrimerName_.hpp.

References ReadObject(), and str().

◆ operator>>() [2/2]

Definition at line 117 of file PCRPrimerSeq_.hpp.

References ReadObject(), and str().

◆ Reset() [1/6]

void CBioSource_Base::Reset ( void  )
virtual

◆ Reset() [2/6]

void CPCRPrimer_Base::Reset ( void  )
virtual

Reset the whole object.

Definition at line 62 of file PCRPrimer_.cpp.

References CPCRPrimer_Base::ResetName(), and CPCRPrimer_Base::ResetSeq().

◆ Reset() [3/6]

void CPCRPrimerSet_Base::Reset ( void  )

Reset data member.

Definition at line 51 of file PCRPrimerSet_.cpp.

References CPCRPrimerSet_Base::m_data, and CPCRPrimerSet_Base::m_set_State.

◆ Reset() [4/6]

void CPCRReaction_Base::Reset ( void  )
virtual

Reset the whole object.

Definition at line 85 of file PCRReaction_.cpp.

References CPCRReaction_Base::ResetForward(), and CPCRReaction_Base::ResetReverse().

◆ Reset() [5/6]

void CPCRReactionSet_Base::Reset ( void  )

Reset data member.

Definition at line 51 of file PCRReactionSet_.cpp.

References CPCRReactionSet_Base::m_data, and CPCRReactionSet_Base::m_set_State.

◆ Reset() [6/6]

void CSubSource_Base::Reset ( void  )
virtual

◆ ResetAttrib()

void CSubSource_Base::ResetAttrib ( void  )

Reset Attrib data member.

Definition at line 107 of file SubSource_.cpp.

References CSubSource_Base::m_Attrib, and CSubSource_Base::m_set_State.

Referenced by CSubSource_Base::Reset().

◆ ResetForward()

void CPCRReaction_Base::ResetForward ( void  )

Reset Forward data member.

Definition at line 51 of file PCRReaction_.cpp.

References CPCRReaction_Base::m_Forward.

Referenced by CPCRReaction_Base::Reset(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().

◆ ResetGenome()

void CBioSource_Base::ResetGenome ( void  )
inline

◆ ResetIs_focus()

void CBioSource_Base::ResetIs_focus ( void  )
inline

Reset Is_focus data member.

Definition at line 564 of file BioSource_.hpp.

References CBioSource_Base::m_set_State.

Referenced by CSrcFocusClear::apply_to(), ParseSourceFeat(), and CBioSource_Base::Reset().

◆ ResetName() [1/2]

void CPCRPrimer_Base::ResetName ( void  )

Reset Name data member.

Definition at line 56 of file PCRPrimer_.cpp.

References CPCRPrimer_Base::m_Name, CPCRPrimer_Base::m_set_State, and CAliasBase< TPrim >::Set().

Referenced by CPCRPrimer_Base::Reset().

◆ ResetName() [2/2]

END_ENUM_INFO void CSubSource_Base::ResetName ( void  )

Reset Name data member.

Definition at line 101 of file SubSource_.cpp.

References CSubSource_Base::m_Name, and CSubSource_Base::m_set_State.

Referenced by CSubSource::RemoveCultureNotes(), and CSubSource_Base::Reset().

◆ ResetOrg()

END_ENUM_INFO void CBioSource_Base::ResetOrg ( void  )

◆ ResetOrigin()

void CBioSource_Base::ResetOrigin ( void  )
inline

◆ ResetPcr_primers()

void CBioSource_Base::ResetPcr_primers ( void  )

◆ ResetReverse()

void CPCRReaction_Base::ResetReverse ( void  )

Reset Reverse data member.

Definition at line 68 of file PCRReaction_.cpp.

References CPCRReaction_Base::m_Reverse.

Referenced by CPCRReaction_Base::Reset(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().

◆ ResetSeq()

void CPCRPrimer_Base::ResetSeq ( void  )

Reset Seq data member.

Definition at line 50 of file PCRPrimer_.cpp.

References CPCRPrimer_Base::m_Seq, CPCRPrimer_Base::m_set_State, and CAliasBase< TPrim >::Set().

Referenced by CPCRPrimer_Base::Reset().

◆ ResetSubtype() [1/2]

void CBioSource_Base::ResetSubtype ( void  )

◆ ResetSubtype() [2/2]

void CSubSource_Base::ResetSubtype ( void  )
inline

Reset Subtype data member.

Definition at line 303 of file SubSource_.hpp.

References CSubSource_Base::m_set_State, and CSubSource_Base::m_Subtype.

Referenced by CSubSource_Base::Reset().

◆ Set() [1/2]

CPCRPrimerSet_Base::Tdata & CPCRPrimerSet_Base::Set ( void  )
inline

Assign a value to data member.

Returns
Reference to the data value.

Definition at line 170 of file PCRPrimerSet_.hpp.

References CPCRPrimerSet_Base::m_data, and CPCRPrimerSet_Base::m_set_State.

Referenced by s_AddPrimers(), s_SetPrimerNames(), and s_SetPrimerSeqs().

◆ Set() [2/2]

CPCRReactionSet_Base::Tdata & CPCRReactionSet_Base::Set ( void  )
inline

Assign a value to data member.

Returns
Reference to the data value.

Definition at line 170 of file PCRReactionSet_.hpp.

References CPCRReactionSet_Base::m_data, and CPCRReactionSet_Base::m_set_State.

Referenced by BOOST_AUTO_TEST_CASE(), CDescrCache::SetPCR_primers(), and CNewCleanup_imp::x_ModernizePCRPrimers().

◆ SetAttrib() [1/3]

void CSubSource_Base::SetAttrib ( const TAttrib value)
inline

Assign a value to Attrib data member.

Parameters
valueValue to assign

Definition at line 406 of file SubSource_.hpp.

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

◆ SetAttrib() [2/3]

void CSubSource_Base::SetAttrib ( CSubSource_Base::TAttrib &&  value)
inline

◆ SetAttrib() [3/3]

CSubSource_Base::TAttrib & CSubSource_Base::SetAttrib ( void  )
inline

Assign a value to Attrib data member.

Returns
Reference to the data value.

Definition at line 420 of file SubSource_.hpp.

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

◆ SetDefaultGenome()

void CBioSource_Base::SetDefaultGenome ( void  )
inline

Assign default value to Genome data member.

Definition at line 416 of file BioSource_.hpp.

References CBioSource_Base::ResetGenome().

◆ SetDefaultOrigin()

void CBioSource_Base::SetDefaultOrigin ( void  )
inline

Assign default value to Origin data member.

Definition at line 466 of file BioSource_.hpp.

References CBioSource_Base::ResetOrigin().

◆ SetForward() [1/2]

void CPCRReaction_Base::SetForward ( CPCRReaction_Base::TForward value)

◆ SetForward() [2/2]

CPCRReaction_Base::TForward & CPCRReaction_Base::SetForward ( void  )

Assign a value to Forward data member.

Returns
Reference to the data value.

Definition at line 61 of file PCRReaction_.cpp.

References CPCRReaction_Base::m_Forward.

◆ SetGenome() [1/2]

void CBioSource_Base::SetGenome ( CBioSource_Base::TGenome  value)
inline

◆ SetGenome() [2/2]

CBioSource_Base::TGenome & CBioSource_Base::SetGenome ( void  )
inline

Assign a value to Genome data member.

Returns
Reference to the data value.

Definition at line 435 of file BioSource_.hpp.

References CBioSource_Base::IsSetGenome(), CBioSource_Base::m_Genome, CBioSource_Base::m_set_State, and CSerialObject::UnassignedByte().

Referenced by CBioSource::FixGenomeForQualifiers().

◆ SetIs_focus()

void CBioSource_Base::SetIs_focus ( void  )
inline

Set NULL data member (assign 'NULL' value to Is_focus data member).

Definition at line 570 of file BioSource_.hpp.

References CBioSource_Base::m_set_State.

Referenced by CSrcFocusSet::apply_to(), CCleanup::MergeDupBioSources(), and ParseSourceFeat().

◆ SetName() [1/5]

void CPCRPrimer_Base::SetName ( const TName value)
inline

◆ SetName() [2/5]

void CSubSource_Base::SetName ( const TName value)
inline

◆ SetName() [3/5]

void CSubSource_Base::SetName ( CSubSource_Base::TName &&  value)
inline

◆ SetName() [4/5]

CPCRPrimer_Base::TName & CPCRPrimer_Base::SetName ( void  )
inline

Assign a value to Name data member.

Returns
Reference to the data value.

Definition at line 262 of file PCRPrimer_.hpp.

References CPCRPrimer_Base::m_Name, and CPCRPrimer_Base::m_set_State.

◆ SetName() [5/5]

CSubSource_Base::TName & CSubSource_Base::SetName ( void  )
inline

◆ SetOrg() [1/2]

void CBioSource_Base::SetOrg ( CBioSource_Base::TOrg value)

Assign a value to Org data member.

Parameters
valueReference to value.

Definition at line 108 of file BioSource_.cpp.

References CBioSource_Base::m_Org, and rapidjson::value.

Referenced by AddGoodSource(), AddOrgmodDescriptor(), AddSource(), AddStrainDescriptor(), CSrcTableDbxrefColumn::AddToBioSource(), CSrcTaxnameAfterBinomialColumn::AddToBioSource(), CSrcStructuredVoucherPartColumn::AddToBioSource(), CApplyFBOL::apply(), COrgGeneralPanel::ApplyCommand(), CBarcodeTool::ApplyDbxrefs(), ApplySrcTableToSeqEntry(), CProSplign::AssignGeneticCode(), CNewCleanup_imp::BiosourceBC(), CNewCleanup_imp::BioSourceEC(), CNewCleanup_imp::BiosourceFeatBC(), BioSourceFromImpFeat(), CCleanup::BioSrcFromFeat(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGoodSegSet(), CachedTaxonomyLookupCommand(), CheckQualsInSourceFeat(), CheckViruses(), CSrcTaxnameAfterBinomialColumn::ClearInBioSource(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CUnculturedTool::CorrectBioSource(), CCulturedTool::CorrectBioSource(), CreateRawBioSources(), FakeEmblBioSources(), FakeGenBankBioSources(), fta_sort_biosource(), CUnculTaxTool::GetCommandFromValuesTable(), GetEmblDescr(), GetGenBankDescr(), GetSprotDescr(), CBioSource::MakeCommon(), MakeCommonBioSource(), CCleanup::MergeDupBioSources(), CEditingActionBiosourceDbxref::Modify(), CRemoveDbXrefsBioSource::ModifyBioSource(), CRemoveTaxonBioSource::ModifyBioSource(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PropogateSuppliedLineage(), RemoveDbxref(), RemoveMod(), RemoveTaxId(), CFindASN1Dlg::ReplaceInBiosource(), CEditingActionBiosourceTaxname::ResetValue(), CEditingActionBiosourceTaxnameAfterBinomial::ResetValue(), CEditingActionBiosourceCommonName::ResetValue(), CEditingActionBiosourceDivision::ResetValue(), CEditingActionBiosourceLineage::ResetValue(), CMacroFunction_AddorSetContElement::s_AddSrcOrgMod(), CMacroFunction_RemoveQual::s_RemoveFields(), s_ResetModSubsrcQuals(), s_SetBioSourceField(), SetCultureCollectionFromStrain(), SetDbxref(), SetOrgMod(), CDescrCache::SetOrgMods(), CEditingActionBiosourceTaxname::SetValue(), CEditingActionBiosourceTaxnameAfterBinomial::SetValue(), CEditingActionBiosourceCommonName::SetValue(), CEditingActionBiosourceDivision::SetValue(), CEditingActionBiosourceLineage::SetValue(), CEditingActionBiosourceOrgMod::SetValue(), CEditingActionBiosourceStructuredVoucher::SetValue(), CEditingActionBiosourceDbxref::SetValue(), SpecificHostCleanupCommand(), CCleanup::TaxonomyLookup(), TaxonomyLookupCommand(), CMacroFunction_SwapQual::TheFunction(), CMacroFunction_ApplyStrucVoucherPart::TheFunction(), CMacroFunction_MakeBoldXrefs::TheFunction(), UpdateBiosourceFromBiosample(), CRemoteUpdater::UpdateOrgFromTaxon(), UpdateRawBioSource(), CSrcDescEditorPanel::UpdateSeqdesc(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CStrainSerotypeInfluenza::x_AddToInfluenzaNames(), COrgGeneralPanel::x_ApplyChangesToSource(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CAppendModToOrg::x_ApplyToBioSource(), CApplyGCode::x_ApplyToBioSource(), CGenusSpeciesFixup::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC(), CFlatGatherer::x_CollectBioSources(), CNewCleanup_imp::x_CopyGBBlockDivToOrgnameDiv(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioSource(), CStrainSerotypeInfluenza::x_FixupOrganismNames(), CFlatGatherer::x_GatherSourceOrganism(), CAgpconvertApplication::x_HandleTaxArgs(), CNewCleanup_imp::x_MoveSeqdescOrgToSourceOrg(), CCulturedTool::x_RemoveIfFoundOrgModNote(), CNewCleanup_imp::x_RemovePopPhyBioSource(), CStrainSerotypeInfluenza::x_SplittingQualifiersAtCommas(), CStrainSerotypeInfluenza::x_SplittingStructCollections(), CStrainSerotypeInfluenza::x_TrimmingOrganismNames(), CStrainSerotypeInfluenza::x_UpdateStrainSerotype(), XMLFakeBioSources(), and XMLGetDescr().

◆ SetOrg() [2/2]

CBioSource_Base::TOrg & CBioSource_Base::SetOrg ( void  )
inline

◆ SetOrigin() [1/2]

void CBioSource_Base::SetOrigin ( CBioSource_Base::TOrigin  value)
inline

Assign a value to Origin data member.

Parameters
valueValue to assign

Definition at line 478 of file BioSource_.hpp.

References CBioSource_Base::m_Origin, CBioSource_Base::m_set_State, and rapidjson::value.

Referenced by CSrcTableOriginColumn::AddToBioSource(), CCleanup::MergeDupBioSources(), CEditingActionBiosourceOrigin::SetValue(), and UpdateRawBioSource().

◆ SetOrigin() [2/2]

CBioSource_Base::TOrigin & CBioSource_Base::SetOrigin ( void  )
inline

Assign a value to Origin data member.

Returns
Reference to the data value.

Definition at line 485 of file BioSource_.hpp.

References CBioSource_Base::IsSetOrigin(), CBioSource_Base::m_Origin, CBioSource_Base::m_set_State, and CSerialObject::UnassignedByte().

◆ SetPcr_primers() [1/2]

void CBioSource_Base::SetPcr_primers ( CBioSource_Base::TPcr_primers value)

◆ SetPcr_primers() [2/2]

CBioSource_Base::TPcr_primers & CBioSource_Base::SetPcr_primers ( void  )

Assign a value to Pcr_primers data member.

Returns
Reference to the data value.

Definition at line 129 of file BioSource_.cpp.

References CBioSource_Base::m_Pcr_primers.

◆ SetReverse() [1/2]

void CPCRReaction_Base::SetReverse ( CPCRReaction_Base::TReverse value)

◆ SetReverse() [2/2]

CPCRReaction_Base::TReverse & CPCRReaction_Base::SetReverse ( void  )

Assign a value to Reverse data member.

Returns
Reference to the data value.

Definition at line 78 of file PCRReaction_.cpp.

References CPCRReaction_Base::m_Reverse.

◆ SetSeq() [1/2]

void CPCRPrimer_Base::SetSeq ( const TSeq value)
inline

◆ SetSeq() [2/2]

CPCRPrimer_Base::TSeq & CPCRPrimer_Base::SetSeq ( void  )
inline

Assign a value to Seq data member.

Returns
Reference to the data value.

Definition at line 227 of file PCRPrimer_.hpp.

References CPCRPrimer_Base::m_Seq, and CPCRPrimer_Base::m_set_State.

◆ SetSubtype() [1/3]

void CSubSource_Base::SetSubtype ( CSubSource_Base::TSubtype  value)
inline

◆ SetSubtype() [2/3]

CBioSource_Base::TSubtype & CBioSource_Base::SetSubtype ( void  )
inline

Assign a value to Subtype data member.

Returns
Reference to the data value.

Definition at line 545 of file BioSource_.hpp.

References CBioSource_Base::m_set_State, and CBioSource_Base::m_Subtype.

Referenced by AddGoodSource(), CConvertFeatToDescSource::apply(), CSetTransgSrcDesc::apply_to(), CBioSource::AutoFix(), CCleanup::BioSrcFromFeat(), BOOST_AUTO_TEST_CASE(), BuildGoodSegSet(), CheckMetagenome(), CheckPlasmid(), CCleanup::CleanupCollectionDates(), CUnculTaxTool::ConvertSpeciesSpecificNote(), CBioSource::FixEnvironmentalSample(), CBioSource::FixSexMatingTypeInconsistencies(), fta_sort_biosource(), FTASubSourceAdd(), CBioSource::MakeCommonExceptOrg(), CCleanup::MergeDupBioSources(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PopulatePcrPrimers(), CBioSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveSubSource(), CFindASN1Dlg::ReplaceInBiosource(), CAgpconvertApplication::Run(), CMacroFunction_FixFormat::s_AddAltitudeToSubSourceNote(), CUnculturedTool::s_AddEnvironmentalSample(), CMacroFunction_AddorSetContElement::s_AddSrcSubSource(), s_SetBioSourceField(), s_SubSourceListUniqued(), SetChromosome(), SetEnvSampleFixAmplifiedPrimers(), SetSubSource(), SetSubsource(), CDescrCache::SetSubtype(), SetTransgenic(), CEditingActionBiosourceSubSource::SetValue(), CNewCleanup_imp::SubSourceListBC(), UpdateBiosourceFromBiosample(), CBioSource::UpdateWithBioSample(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CGenusSpeciesFixup::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC(), CBioSource::x_ClearCoordinatedBioSampleSubSources(), CUnculturedTool::x_ConvertNote(), CCulturedTool::x_RemoveIfFoundSubSourceNote(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), and CSubmissionWizard::x_TransferImportedSubSources().

◆ SetSubtype() [3/3]

CSubSource_Base::TSubtype & CSubSource_Base::SetSubtype ( void  )
inline

Assign a value to Subtype data member.

Returns
Reference to the data value.

Definition at line 326 of file SubSource_.hpp.

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

Referenced by CSubSource::CSubSource().

◆ ~CBioSource_Base()

CBioSource_Base::~CBioSource_Base ( void  )
virtual

Definition at line 172 of file BioSource_.cpp.

◆ ~CPCRPrimer()

CPCRPrimer::~CPCRPrimer ( void  )

Definition at line 50 of file PCRPrimer.cpp.

◆ ~CPCRPrimer_Base()

CPCRPrimer_Base::~CPCRPrimer_Base ( void  )
virtual

Definition at line 86 of file PCRPrimer_.cpp.

◆ ~CPCRPrimerSet()

CPCRPrimerSet::~CPCRPrimerSet ( void  )

Definition at line 50 of file PCRPrimerSet.cpp.

◆ ~CPCRPrimerSet_Base()

CPCRPrimerSet_Base::~CPCRPrimerSet_Base ( void  )
virtual

Definition at line 74 of file PCRPrimerSet_.cpp.

◆ ~CPCRReaction()

CPCRReaction::~CPCRReaction ( void  )

Definition at line 50 of file PCRReaction.cpp.

◆ ~CPCRReaction_Base()

CPCRReaction_Base::~CPCRReaction_Base ( void  )
virtual

Definition at line 109 of file PCRReaction_.cpp.

◆ ~CPCRReactionSet()

CPCRReactionSet::~CPCRReactionSet ( void  )

Definition at line 50 of file PCRReactionSet.cpp.

◆ ~CPCRReactionSet_Base()

CPCRReactionSet_Base::~CPCRReactionSet_Base ( void  )
virtual

Definition at line 74 of file PCRReactionSet_.cpp.

◆ ~CSubSource_Base()

CSubSource_Base::~CSubSource_Base ( void  )
virtual

Definition at line 140 of file SubSource_.cpp.

Variable Documentation

◆ m_Attrib

string CSubSource_Base::m_Attrib
private

◆ m_data [1/2]

list< CRef< CPCRPrimer > > CPCRPrimerSet_Base::m_data
private

◆ m_data [2/2]

list< CRef< CPCRReaction > > CPCRReactionSet_Base::m_data
private

◆ m_Forward

CRef< TForward > CPCRReaction_Base::m_Forward
private

◆ m_Genome

int CBioSource_Base::m_Genome
private

◆ m_Name [1/2]

CPCRPrimerName CPCRPrimer_Base::m_Name
private

◆ m_Name [2/2]

string CSubSource_Base::m_Name
private

◆ m_Org

CRef< TOrg > CBioSource_Base::m_Org
private

◆ m_Origin

int CBioSource_Base::m_Origin
private

◆ m_Pcr_primers

CRef< TPcr_primers > CBioSource_Base::m_Pcr_primers
private

◆ m_Reverse

CRef< TReverse > CPCRReaction_Base::m_Reverse
private

◆ m_Seq

CPCRPrimerSeq CPCRPrimer_Base::m_Seq
private

◆ m_set_State [1/6]

Uint4 CBioSource_Base::m_set_State[1]
private

◆ m_set_State [2/6]

Uint4 CPCRPrimer_Base::m_set_State[1]
private

◆ m_set_State [3/6]

Uint4 CPCRPrimerSet_Base::m_set_State[1]
private

◆ m_set_State [4/6]

Uint4 CPCRReaction_Base::m_set_State[1]
private

Definition at line 183 of file PCRReaction_.hpp.

Referenced by CPCRReaction_Base::CPCRReaction_Base().

◆ m_set_State [5/6]

Uint4 CPCRReactionSet_Base::m_set_State[1]
private

◆ m_set_State [6/6]

Uint4 CSubSource_Base::m_set_State[1]
private

◆ m_Subtype [1/2]

list< CRef< CSubSource > > CBioSource_Base::m_Subtype
private

◆ m_Subtype [2/2]

int CSubSource_Base::m_Subtype
private
Modified on Mon Apr 22 04:01:17 2024 by modify_doxy.py rev. 669887