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< string >	CPCRPrimerName_Base::Tparent
typedef CStringAliasBase< string >	CPCRPrimerSeq_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...
TGenome &	CBioSource_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...
TOrigin &	CBioSource_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 TOrg &	CBioSource_Base::GetOrg (void) const
	Get the Org member data. More...
void	CBioSource_Base::SetOrg (TOrg &value)
	Assign a value to Org data member. More...
TOrg &	CBioSource_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 TSubtype &	CBioSource_Base::GetSubtype (void) const
	Get the Subtype member data. More...
TSubtype &	CBioSource_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_primers &	CBioSource_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_primers &	CBioSource_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_Base &	CBioSource_Base::operator= (const CBioSource_Base &)
	CPCRPrimer::CPCRPrimer (void)
	CPCRPrimer::~CPCRPrimer (void)
	CPCRPrimer::CPCRPrimer (const CPCRPrimer &value)
CPCRPrimer &	CPCRPrimer::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 TSeq &	CPCRPrimer_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...
TSeq &	CPCRPrimer_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 TName &	CPCRPrimer_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...
TName &	CPCRPrimer_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_Base &	CPCRPrimer_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::CNcbiOstream &	operator<< (NCBI_NS_NCBI::CNcbiOstream &str, const CPCRPrimerName_Base &obj)
NCBI_NS_NCBI::CNcbiIstream &	operator>> (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::CNcbiOstream &	operator<< (NCBI_NS_NCBI::CNcbiOstream &str, const CPCRPrimerSeq_Base &obj)
NCBI_NS_NCBI::CNcbiIstream &	operator>> (NCBI_NS_NCBI::CNcbiIstream &str, CPCRPrimerSeq_Base &obj)
	CPCRPrimerSet::CPCRPrimerSet (void)
	CPCRPrimerSet::~CPCRPrimerSet (void)
	CPCRPrimerSet::CPCRPrimerSet (const CPCRPrimerSet &value)
CPCRPrimerSet &	CPCRPrimerSet::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 Tdata &	CPCRPrimerSet_Base::Get (void) const
	Get the member data. More...
Tdata &	CPCRPrimerSet_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_Base &	CPCRPrimerSet_Base::operator= (const CPCRPrimerSet_Base &)
	CPCRReaction::CPCRReaction (void)
	CPCRReaction::~CPCRReaction (void)
	CPCRReaction::CPCRReaction (const CPCRReaction &value)
CPCRReaction &	CPCRReaction::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 TForward &	CPCRReaction_Base::GetForward (void) const
	Get the Forward member data. More...
void	CPCRReaction_Base::SetForward (TForward &value)
	Assign a value to Forward data member. More...
TForward &	CPCRReaction_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 TReverse &	CPCRReaction_Base::GetReverse (void) const
	Get the Reverse member data. More...
void	CPCRReaction_Base::SetReverse (TReverse &value)
	Assign a value to Reverse data member. More...
TReverse &	CPCRReaction_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_Base &	CPCRReaction_Base::operator= (const CPCRReaction_Base &)
	CPCRReactionSet::CPCRReactionSet (void)
	CPCRReactionSet::~CPCRReactionSet (void)
	CPCRReactionSet::CPCRReactionSet (const CPCRReactionSet &value)
CPCRReactionSet &	CPCRReactionSet::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 Tdata &	CPCRReactionSet_Base::Get (void) const
	Get the member data. More...
Tdata &	CPCRReactionSet_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_Base &	CPCRReactionSet_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...
TSubtype &	CSubSource_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 TName &	CSubSource_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)
TName &	CSubSource_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 TAttrib &	CSubSource_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)
TAttrib &	CSubSource_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_Base &	CSubSource_Base::operator= (const CSubSource_Base &)

Variables
Uint4	CBioSource_Base::m_set_State [1]
int	CBioSource_Base::m_Genome
int	CBioSource_Base::m_Origin
CRef< TOrg >	CBioSource_Base::m_Org
list< CRef< CSubSource > >	CBioSource_Base::m_Subtype
CRef< TPcr_primers >	CBioSource_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< TForward >	CPCRReaction_Base::m_Forward
CRef< TReverse >	CPCRReaction_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

typedef string CSubSource_Base::TAttrib

Definition at line 137 of file SubSource_.hpp.

Tdata [1/2]

typedef list< CRef< CPCRPrimer > > CPCRPrimerSet_Base::Tdata

Definition at line 89 of file PCRPrimerSet_.hpp.

Tdata [2/2]

typedef list< CRef< CPCRReaction > > CPCRReactionSet_Base::Tdata

Definition at line 89 of file PCRReactionSet_.hpp.

TForward

typedef CPCRPrimerSet CPCRReaction_Base::TForward

Definition at line 85 of file PCRReaction_.hpp.

TGenome

typedef int CBioSource_Base::TGenome

Definition at line 142 of file BioSource_.hpp.

TmemberIndex [1/4]

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

Definition at line 158 of file BioSource_.hpp.

TmemberIndex [2/4]

typedef Tparent::CMemberIndex<E_memberIndex, 3> CPCRPrimer_Base::TmemberIndex

Definition at line 95 of file PCRPrimer_.hpp.

TmemberIndex [3/4]

typedef Tparent::CMemberIndex<E_memberIndex, 3> CPCRReaction_Base::TmemberIndex

Definition at line 94 of file PCRReaction_.hpp.

TmemberIndex [4/4]

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

Definition at line 146 of file SubSource_.hpp.

TName [1/2]

typedef CPCRPrimerName CPCRPrimer_Base::TName

Definition at line 87 of file PCRPrimer_.hpp.

TName [2/2]

typedef string CSubSource_Base::TName

Definition at line 136 of file SubSource_.hpp.

TOrg

typedef COrg_ref CBioSource_Base::TOrg

Definition at line 144 of file BioSource_.hpp.

TOrigin

typedef int CBioSource_Base::TOrigin

Definition at line 143 of file BioSource_.hpp.

Tparent [1/13]

typedef CSerialObject CBioSource_Base::Tparent

private

Definition at line 86 of file BioSource_.hpp.

Tparent [2/13]

typedef CPCRPrimer_Base CPCRPrimer::Tparent

private

Definition at line 67 of file PCRPrimer.hpp.

Tparent [3/13]

typedef CSerialObject CPCRPrimer_Base::Tparent

private

Definition at line 75 of file PCRPrimer_.hpp.

Tparent [4/13]

typedef CPCRPrimerName_Base CPCRPrimerName::Tparent

private

Definition at line 67 of file PCRPrimerName.hpp.

Tparent [5/13]

typedef CStringAliasBase< string > CPCRPrimerName_Base::Tparent

private

Definition at line 74 of file PCRPrimerName_.hpp.

Tparent [6/13]

typedef CStringAliasBase< string > CPCRPrimerSeq_Base::Tparent

private

Definition at line 74 of file PCRPrimerSeq_.hpp.

Tparent [7/13]

typedef CPCRPrimerSet_Base CPCRPrimerSet::Tparent

private

Definition at line 67 of file PCRPrimerSet.hpp.

Tparent [8/13]

typedef CSerialObject CPCRPrimerSet_Base::Tparent

private

Definition at line 78 of file PCRPrimerSet_.hpp.

Tparent [9/13]

typedef CPCRReaction_Base CPCRReaction::Tparent

private

Definition at line 67 of file PCRReaction.hpp.

Tparent [10/13]

typedef CSerialObject CPCRReaction_Base::Tparent

private

Definition at line 74 of file PCRReaction_.hpp.

Tparent [11/13]

typedef CPCRReactionSet_Base CPCRReactionSet::Tparent

private

Definition at line 67 of file PCRReactionSet.hpp.

Tparent [12/13]

typedef CSerialObject CPCRReactionSet_Base::Tparent

private

Definition at line 78 of file PCRReactionSet_.hpp.

Tparent [13/13]

typedef CSerialObject CSubSource_Base::Tparent

private

Definition at line 74 of file SubSource_.hpp.

TPcr_primers

typedef CPCRReactionSet CBioSource_Base::TPcr_primers

Definition at line 146 of file BioSource_.hpp.

TReverse

typedef CPCRPrimerSet CPCRReaction_Base::TReverse

Definition at line 86 of file PCRReaction_.hpp.

TSeq

typedef CPCRPrimerSeq CPCRPrimer_Base::TSeq

Definition at line 86 of file PCRPrimer_.hpp.

TSubtype [1/2]

typedef list< CRef< CSubSource > > CBioSource_Base::TSubtype

Definition at line 145 of file BioSource_.hpp.

TSubtype [2/2]

typedef int CSubSource_Base::TSubtype

Definition at line 135 of file SubSource_.hpp.

Enumeration Type Documentation

E_memberIndex [1/4]

enum CBioSource_Base::E_memberIndex

strong

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]

enum CPCRPrimer_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_seq
e_name

Definition at line 90 of file PCRPrimer_.hpp.

E_memberIndex [3/4]

enum CPCRReaction_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_forward
e_reverse

Definition at line 89 of file PCRReaction_.hpp.

E_memberIndex [4/4]

enum CSubSource_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_subtype
e_name
e_attrib

Definition at line 140 of file SubSource_.hpp.

EGenome

enum CBioSource_Base::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

enum CBioSource_Base::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

enum CSubSource_Base::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

Check if it is safe to call GetOrg method.

Returns

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

Definition at line 503 of file BioSource_.hpp.

Referenced by CheckQualsInSourceFeat(), CopyOrg(), fta_sort_biosource(), CAutoDefSourceDescription::GetAvailableModifiers(), CAutoDefSourceGroup::GetDefaultExcludeSp(), CBioSource::GetGenCode(), CAutoDefSourceDescription::IsTrickyHIV(), UpdateRawBioSource(), CValidError_imp::ValidateBioSource(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CBioseqIndex::x_InitSource(), and CSourceItem::x_SetSource().

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

Check if it is safe to call GetSubtype method.

Returns

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

Definition at line 533 of file BioSource_.hpp.

Referenced by CAutoDefSourceDescription::GetAvailableModifiers(), CAutoDefFeatureClause::IsEndogenousVirusSourceFeature(), CValidError_imp::IsTransgenic(), CAutoDefSourceDescription::IsTrickyHIV(), CTabularFormatter_SeqChrom::Print(), CTabularFormatter_SeqClone::Print(), CAutoDefFeatureClause::x_GetDescription(), CAutoDef::x_GetFeatureClauseProductEnding(), and CSetTransgSrcDesc::x_HasTransgenicSubtype().

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

)

Definition at line 162 of file BioSource_.cpp.

References CObject::IsAllocatedInPool(), CBioSource_Base::m_set_State, and CBioSource_Base::ResetOrg().

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 the member data.

Returns

Reference to the member data.

Definition at line 164 of file PCRPrimerSet_.hpp.

References CPCRPrimerSet_Base::m_data.

Referenced by GetPrimerSetNameValues(), GetPrimerSetSeqValues(), s_PcrPrimerSetCompare(), s_PCRPrimerSetLess(), s_SetPrimerNames(), s_SetPrimerSeqs(), CSourceFeatureItem::x_AddPcrPrimersQuals(), CDeflineGenerator::x_GetModifiers(), CSrcWriter::xPrimerSetNames(), and CSrcWriter::xPrimerSetSequences().

Get() [2/2]

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

inline

Get the member data.

Returns

Reference to the member data.

Definition at line 164 of file PCRReactionSet_.hpp.

References CPCRReactionSet_Base::m_data.

Referenced by CPCRSetList::AreSetsUnique(), GetSeqTableFromSeqEntry(), CSrcTablePrimerColumn::GetValsFromBioSource(), CEditingActionBiosourcePrimers::Modify(), CValidError_imp::ValidatePCRReactionSet(), CSourceFeatureItem::x_AddPcrPrimersQuals(), CDeflineGenerator::x_GetModifiers(), CSrcTablePrimerColumn::x_GetValues(), CSrcTablePrimerColumn::x_RemoveEmptyValues(), and CSrcWriter::xGatherPcrPrimers().

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

Get the Forward member data.

Returns

Reference to the member data.

Definition at line 210 of file PCRReaction_.hpp.

References CPCRReaction_Base::CanGetForward(), CPCRReaction_Base::m_Forward, and CSerialObject::ThrowUnassigned().

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

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

Get the Name member data.

Returns

Reference to the member data.

Definition at line 350 of file SubSource_.hpp.

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

Referenced by CSubSource::AutoFix(), BOOST_AUTO_TEST_CASE(), CSubSource::FixCapitalization(), CFlatSubSourceQVal::Format(), CSubSource::GetLabel(), CWriteUtil::GetSubSourceSubType(), CGuiObjectInfoComponent::GetToolTip(), CEditingActionBiosourceSubSource::GetValue(), CEditingActionBiosourceAllNotes::GetValue(), IsSameSubtype(), CSubtypeEquals::operator()(), CSubSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), s_NameCloseEnough(), s_NameCloseEnoughC(), s_SubsourceEquivalent(), SetSubsource(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateSubSource(), CDeflineGenerator::x_GetModifiers(), CBioseqIndex::x_InitSource(), CNewCleanup_imp::x_PostBiosource(), CDeflineGenerator::x_SetBioSrc(), CNewCleanup_imp::x_SubSourceBC(), and CSrcWriter::xGatherSubtypeFeat().

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

Get the Origin member data.

Returns

Copy of the member data.

Definition at line 472 of file BioSource_.hpp.

References CBioSource_Base::m_Origin.

Referenced by CSrcTableOriginColumn::AddToBioSource(), GetBiosourceDifferences(), GetDescrEmblBlock(), CSrcTableOriginColumn::GetFromBioSource(), GetGBBlock(), CSource_qual_choice::GetLimitedSourceQualFromBioSource(), CAutoDefModifierCombo::GetSourceDescriptionString(), CEditingActionBiosourceOrigin::GetValue(), CValidError_imp::IsArtificial(), CNewCleanup_imp::IsSyntheticConstruct(), CCleanup::MergeDupBioSources(), CSourceFeatureItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CValidError_bioseq::x_ValidateCompletness(), CSrcWriter::xGatherOrigin(), XMLGetEMBLBlock(), and XMLGetGBBlock().

GetPcr_primers()

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

inline

Get the Pcr_primers member data.

Returns

Reference to the member data.

Definition at line 588 of file BioSource_.hpp.

References CBioSource_Base::CanGetPcr_primers(), CBioSource_Base::m_Pcr_primers, and CSerialObject::ThrowUnassigned().

Referenced by GetSeqTableFromSeqEntry(), CSrcTablePrimerColumn::GetValsFromBioSource(), CBioSource::MakeCommonExceptOrg(), CEditingActionBiosourcePrimers::Modify(), CValidError_imp::ValidateBioSource(), CSourceFeatureItem::x_AddPcrPrimersQuals(), CDeflineGenerator::x_GetModifiers(), CSrcTablePrimerColumn::x_GetValues(), CSrcTablePrimerColumn::x_RemoveEmptyValues(), and CSrcWriter::xGatherPcrPrimers().

GetReverse()

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

inline

Get the Reverse member data.

Returns

Reference to the member data.

Definition at line 231 of file PCRReaction_.hpp.

References CPCRReaction_Base::CanGetReverse(), CPCRReaction_Base::m_Reverse, and CSerialObject::ThrowUnassigned().

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

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

Get the Subtype member data.

Returns

Copy of the member data.

Definition at line 310 of file SubSource_.hpp.

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

Referenced by CSubSource::AutoFix(), CSubSource::FixCapitalization(), CFlatSubSourceQVal::Format(), CSubSource::GetLabel(), CWriteUtil::GetSubSourceSubType(), GetSubtypeName(), CGuiObjectInfoComponent::GetToolTip(), IsSameSubtype(), CValidError_imp::IsTransgenic(), CSubtypeEquals::operator()(), CBioSource::RemoveLineageSourceNotes(), s_SameSubtype(), s_SameSubtypeC(), s_SubsourceEquivalent(), s_SubSourceToSlot(), CValidError_imp::ValidateSubSource(), CDeflineGenerator::x_GetModifiers(), and CSrcWriter::xGatherSubtypeFeat().

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

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 338 of file SubSource_.hpp.

References CSubSource_Base::m_set_State.

Referenced by CSubSource::AutoFix(), BOOST_AUTO_TEST_CASE(), CSubSource_Base::CanGetName(), CSubSource::FixCapitalization(), CWriteUtil::GetSubSourceSubType(), CGuiObjectInfoComponent::GetToolTip(), IsSameSubtype(), CEditingActionBiosourceSubSource::IsSetValue(), CEditingActionBiosourceAllNotes::IsSetValue(), CSubSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), s_NameCloseEnough(), s_NameCloseEnoughC(), s_SubsourceEquivalent(), CSubSource_Base::SetName(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateSubSource(), CDeflineGenerator::x_GetModifiers(), CBioseqIndex::x_InitSource(), CNewCleanup_imp::x_PostBiosource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CNewCleanup_imp::x_SubSourceBC(), and CSrcWriter::xGatherSubtypeFeat().

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

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

Data member Origin is optional with default eOrigin_unknown; its type is defined as 'typedef int TOrigin'

Returns

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

Definition at line 447 of file BioSource_.hpp.

References CBioSource_Base::m_set_State.

Referenced by CSrcTableOriginColumn::AddToBioSource(), GetBiosourceDifferences(), GetDescrEmblBlock(), CSrcTableOriginColumn::GetFromBioSource(), GetGBBlock(), CValidError_imp::IsArtificial(), CEditingActionBiosourceOrigin::IsSetValue(), CNewCleanup_imp::IsSyntheticConstruct(), CCleanup::MergeDupBioSources(), s_IsEmptyBioSource(), CBioSource_Base::SetOrigin(), CValidError_bioseq::x_ValidateCompletness(), CSrcWriter::xGatherOrigin(), XMLGetEMBLBlock(), and XMLGetGBBlock().

IsSetPcr_primers()

bool CBioSource_Base::IsSetPcr_primers ( void  ) const

inline

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

Data member Pcr_primers is optional; its type is defined as 'typedef CPCRReactionSet TPcr_primers'

Returns

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

Definition at line 576 of file BioSource_.hpp.

References CBioSource_Base::m_Pcr_primers.

Referenced by CBioSource_Base::CanGetPcr_primers(), CSrcTableAllPrimersColumn::ClearInBioSource(), GetSeqTableFromSeqEntry(), GetSourceFields(), CSrcTablePrimerColumn::GetValsFromBioSource(), CBioSource::MakeCommonExceptOrg(), CEditingActionBiosourcePrimers::Modify(), CValidError_imp::ValidateBioSource(), CSourceFeatureItem::x_AddPcrPrimersQuals(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC(), CDeflineGenerator::x_GetModifiers(), CSrcTablePrimerColumn::x_GetValues(), CSrcTablePrimerColumn::x_RemoveEmptyValues(), and CSrcWriter::xGatherPcrPrimers().

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]

NCBI_NS_NCBI::CNcbiOstream& operator<< ( NCBI_NS_NCBI::CNcbiOstream &  str, const CPCRPrimerName_Base &  obj  )

inline

Definition at line 106 of file PCRPrimerName_.hpp.

References str(), and WriteObject().

operator<<() [2/2]

NCBI_NS_NCBI::CNcbiOstream& operator<< ( NCBI_NS_NCBI::CNcbiOstream &  str, const CPCRPrimerSeq_Base &  obj  )

inline

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]

NCBI_NS_NCBI::CNcbiIstream& operator>> ( NCBI_NS_NCBI::CNcbiIstream &  str, CPCRPrimerName_Base &  obj  )

inline

Definition at line 117 of file PCRPrimerName_.hpp.

References ReadObject(), and str().

operator>>() [2/2]

NCBI_NS_NCBI::CNcbiIstream& operator>> ( NCBI_NS_NCBI::CNcbiIstream &  str, CPCRPrimerSeq_Base &  obj  )

inline

Definition at line 117 of file PCRPrimerSeq_.hpp.

References ReadObject(), and str().

Reset() [1/6]

void CBioSource_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 136 of file BioSource_.cpp.

References CBioSource_Base::ResetGenome(), CBioSource_Base::ResetIs_focus(), CBioSource_Base::ResetOrg(), CBioSource_Base::ResetOrigin(), CBioSource_Base::ResetPcr_primers(), and CBioSource_Base::ResetSubtype().

Referenced by BOOST_AUTO_TEST_CASE().

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

Reset the whole object.

Definition at line 113 of file SubSource_.cpp.

References CSubSource_Base::ResetAttrib(), CSubSource_Base::ResetName(), and CSubSource_Base::ResetSubtype().

Referenced by CVariation_ref_Base::C_E_Somatic_origin::SetSource(), and CVariation_Base::C_E_Somatic_origin::SetSource().

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

Reset Genome data member.

Definition at line 409 of file BioSource_.hpp.

References CBioSource_Base::eGenome_unknown, CBioSource_Base::m_Genome, and CBioSource_Base::m_set_State.

Referenced by BOOST_AUTO_TEST_CASE(), CBioSource_Base::Reset(), CEditingActionBiosourceLocation::ResetValue(), and CBioSource_Base::SetDefaultGenome().

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

)

Reset Org data member.

Definition at line 99 of file BioSource_.cpp.

References CBioSource_Base::m_Org.

Referenced by BOOST_AUTO_TEST_CASE(), CBioSource_Base::CBioSource_Base(), CBioSource_Base::GetOrg(), CBioSource_Base::Reset(), and CBioSource_Base::SetOrg().

ResetOrigin()

void CBioSource_Base::ResetOrigin ( void  )

inline

Reset Origin data member.

Definition at line 459 of file BioSource_.hpp.

References CBioSource_Base::eOrigin_unknown, CBioSource_Base::m_Origin, and CBioSource_Base::m_set_State.

Referenced by CSrcTableOriginColumn::ClearInBioSource(), CBioSource_Base::Reset(), CEditingActionBiosourceOrigin::ResetValue(), and CBioSource_Base::SetDefaultOrigin().

ResetPcr_primers()

void CBioSource_Base::ResetPcr_primers

(

void

)

Reset Pcr_primers data member.

Definition at line 119 of file BioSource_.cpp.

References CBioSource_Base::m_Pcr_primers.

Referenced by CSrcTableAllPrimersColumn::ClearInBioSource(), CEditingActionBiosourcePrimers::Modify(), CBioSource_Base::Reset(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().

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

)

Reset Subtype data member.

Definition at line 113 of file BioSource_.cpp.

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

Referenced by CBioSource::AutoFix(), BOOST_AUTO_TEST_CASE(), CheckPlasmid(), CBioSource::FixSexMatingTypeInconsistencies(), CSrcModListPanel::PopulateModifiers(), CBioSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveSubSource(), CBioSource_Base::Reset(), s_ResetModSubsrcQuals(), CUnculturedTool::x_ConvertNote(), and CCulturedTool::x_RemoveIfFoundSubSourceNote().

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

value

Value 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

Definition at line 413 of file SubSource_.hpp.

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

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

)

Assign a value to Forward data member.

Parameters

value

Reference to value.

Definition at line 56 of file PCRReaction_.cpp.

References CPCRReaction_Base::m_Forward, and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), CEditingActionBiosourcePrimers::SetValue(), CPCRPrimersPanel::UpdateBioSourcePrimers(), CSourceModParser::x_AddPCRPrimers(), CSrcTablePrimerColumn::x_ApplyStringToReaction(), CSplitPrimerSets::x_ApplyToBioSource(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().

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

Assign a value to Genome data member.

Parameters

value

Value to assign

Definition at line 428 of file BioSource_.hpp.

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

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), BioSourceFromImpFeat(), BOOST_AUTO_TEST_CASE(), CheckBioProjectLocationVals(), GetGenomeInfo(), GetSprotDescr(), CCleanup::MergeDupBioSources(), CEditingActionBiosourceLocation::SetValue(), UpdateRawBioSource(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), and CNewCleanup_imp::x_PostBiosource().

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

Assign a value to Name data member.

Parameters

value

Value to assign

Definition at line 255 of file PCRPrimer_.hpp.

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

Referenced by BOOST_AUTO_TEST_CASE(), s_ModernizePCRPrimerHalf(), CEditingActionBiosourcePrimers::SetValue(), CPCRPrimersPanel::UpdateBioSourcePrimers(), and CSrcTablePrimerColumn::x_AddFieldToPrimerSet().

SetName() [2/5]

void CSubSource_Base::SetName ( const TName &  value )

inline

Assign a value to Name data member.

Parameters

value

Value to assign

Definition at line 359 of file SubSource_.hpp.

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

Referenced by AddGoodSource(), CSetTransgSrcDesc::apply_to(), CCleanup::BioSrcFromFeat(), BOOST_AUTO_TEST_CASE(), BuildGoodSegSet(), ChangeCountryColonToComma(), CheckMetagenome(), FTASubSourceAdd(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PopulatePcrPrimers(), RemoveCountryColon(), CAgpconvertApplication::Run(), CMacroFunction_AddorSetContElement::s_AddSrcSubSource(), s_SetBioSourceField(), SetSubSource(), SetSubsource(), CEditingActionBiosourceSubSource::SetValue(), CEditingActionBiosourceAllNotes::SetValue(), CBioSource::UpdateWithBioSample(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CSourceModParser::x_ApplyMods(), CGenusSpeciesFixup::x_ApplyToBioSource(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), CGff2Record::xMigrateAttributes(), and CGff2Record::xMigrateAttributesSubSource().

SetName() [3/5]

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

inline

Definition at line 366 of file SubSource_.hpp.

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

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

Assign a value to Name data member.

Returns

Reference to the data value.

Definition at line 373 of file SubSource_.hpp.

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

Referenced by CSubSource::AutoFix(), CSubSource::CSubSource(), CSubSource::FixCapitalization(), and CSubSource::RemoveCultureNotes().

SetOrg() [1/2]

void CBioSource_Base::SetOrg

(

CBioSource_Base::TOrg &

value

)

Assign a value to Org data member.

Parameters

value

Reference 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

Assign a value to Org data member.

Returns

Reference to the data value.

Definition at line 518 of file BioSource_.hpp.

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

Referenced by CBioSource::AutoFix(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveOrgMod(), CBioSource::RemoveUnexpectedViralQualifiers(), CBioSource::SetDisableStrainForwarding(), and CBioSource::UpdateWithBioSample().

SetOrigin() [1/2]

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

inline

Assign a value to Origin data member.

Parameters

value

Value 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

)

Assign a value to Pcr_primers data member.

Parameters

value

Reference to value.

Definition at line 124 of file BioSource_.cpp.

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

Referenced by CSrcTablePrimerColumn::AddToBioSource(), BOOST_AUTO_TEST_CASE(), CBioSource::MakeCommonExceptOrg(), CEditingActionBiosourcePrimers::Modify(), s_ArePrimersUnique(), CDescrCache::SetPCR_primers(), CEditingActionBiosourcePrimers::SetValue(), CPCRPrimerTrimJunk::x_ApplyToBioSource(), CPCRPrimerFixI::x_ApplyToBioSource(), CSwapPrimerNameSeq::x_ApplyToBioSource(), CMergePrimerSets::x_ApplyToBioSource(), CSplitPrimerSets::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().

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

)

Assign a value to Reverse data member.

Parameters

value

Reference to value.

Definition at line 73 of file PCRReaction_.cpp.

References CPCRReaction_Base::m_Reverse, and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), CEditingActionBiosourcePrimers::SetValue(), CPCRPrimersPanel::UpdateBioSourcePrimers(), CSourceModParser::x_AddPCRPrimers(), CSrcTablePrimerColumn::x_ApplyStringToReaction(), CSplitPrimerSets::x_ApplyToBioSource(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().

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

Assign a value to Seq data member.

Parameters

value

Value to assign

Definition at line 220 of file PCRPrimer_.hpp.

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

Referenced by BOOST_AUTO_TEST_CASE(), s_ModernizePCRPrimerHalf(), CEditingActionBiosourcePrimers::SetValue(), CPCRPrimersPanel::UpdateBioSourcePrimers(), and CSrcTablePrimerColumn::x_AddFieldToPrimerSet().

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

Assign a value to Subtype data member.

Parameters

value

Value to assign

Definition at line 319 of file SubSource_.hpp.

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

Referenced by AddGoodSource(), CSetTransgSrcDesc::apply_to(), CCleanup::BioSrcFromFeat(), BOOST_AUTO_TEST_CASE(), BuildGoodSegSet(), CheckMetagenome(), FTASubSourceAdd(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PopulatePcrPrimers(), CAgpconvertApplication::Run(), CMacroFunction_AddorSetContElement::s_AddSrcSubSource(), s_SetBioSourceField(), CEditingActionBiosourceSubSource::SetValue(), CBioSource::UpdateWithBioSample(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CSourceModParser::x_ApplyMods(), CGenusSpeciesFixup::x_ApplyToBioSource(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), CGff2Record::xMigrateAttributes(), and CGff2Record::xMigrateAttributesSubSource().

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

Definition at line 278 of file SubSource_.hpp.

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

m_data [1/2]

list< CRef< CPCRPrimer > > CPCRPrimerSet_Base::m_data

private

Definition at line 139 of file PCRPrimerSet_.hpp.

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

m_data [2/2]

list< CRef< CPCRReaction > > CPCRReactionSet_Base::m_data

private

Definition at line 139 of file PCRReactionSet_.hpp.

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

m_Forward

CRef< TForward > CPCRReaction_Base::m_Forward

private

Definition at line 184 of file PCRReaction_.hpp.

Referenced by CPCRReaction_Base::GetForward(), CPCRReaction_Base::IsSetForward(), CPCRReaction_Base::ResetForward(), and CPCRReaction_Base::SetForward().

m_Genome

int CBioSource_Base::m_Genome

private

Definition at line 380 of file BioSource_.hpp.

Referenced by CBioSource_Base::GetGenome(), CBioSource_Base::ResetGenome(), and CBioSource_Base::SetGenome().

m_Name [1/2]

CPCRPrimerName CPCRPrimer_Base::m_Name

private

Definition at line 186 of file PCRPrimer_.hpp.

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

m_Name [2/2]

string CSubSource_Base::m_Name

private

Definition at line 277 of file SubSource_.hpp.

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

m_Org

CRef< TOrg > CBioSource_Base::m_Org

private

Definition at line 382 of file BioSource_.hpp.

Referenced by CBioSource_Base::GetOrg(), CBioSource_Base::IsSetOrg(), CBioSource_Base::ResetOrg(), and CBioSource_Base::SetOrg().

m_Origin

int CBioSource_Base::m_Origin

private

Definition at line 381 of file BioSource_.hpp.

Referenced by CBioSource_Base::GetOrigin(), CBioSource_Base::ResetOrigin(), and CBioSource_Base::SetOrigin().

m_Pcr_primers

CRef< TPcr_primers > CBioSource_Base::m_Pcr_primers

private

Definition at line 384 of file BioSource_.hpp.

Referenced by CBioSource_Base::GetPcr_primers(), CBioSource_Base::IsSetPcr_primers(), CBioSource_Base::ResetPcr_primers(), and CBioSource_Base::SetPcr_primers().

m_Reverse

CRef< TReverse > CPCRReaction_Base::m_Reverse

private

Definition at line 185 of file PCRReaction_.hpp.

Referenced by CPCRReaction_Base::GetReverse(), CPCRReaction_Base::IsSetReverse(), CPCRReaction_Base::ResetReverse(), and CPCRReaction_Base::SetReverse().

m_Seq

CPCRPrimerSeq CPCRPrimer_Base::m_Seq

private

Definition at line 185 of file PCRPrimer_.hpp.

Referenced by CPCRPrimer_Base::GetSeq(), CPCRPrimer_Base::ResetSeq(), and CPCRPrimer_Base::SetSeq().

m_set_State [1/6]

Uint4 CBioSource_Base::m_set_State[1]

private

Definition at line 379 of file BioSource_.hpp.

Referenced by CBioSource_Base::CBioSource_Base(), CBioSource_Base::IsSetGenome(), CBioSource_Base::IsSetIs_focus(), CBioSource_Base::IsSetOrigin(), CBioSource_Base::IsSetSubtype(), CBioSource_Base::ResetGenome(), CBioSource_Base::ResetIs_focus(), CBioSource_Base::ResetOrigin(), CBioSource_Base::ResetSubtype(), CBioSource_Base::SetGenome(), CBioSource_Base::SetIs_focus(), CBioSource_Base::SetOrigin(), and CBioSource_Base::SetSubtype().

m_set_State [2/6]

Uint4 CPCRPrimer_Base::m_set_State[1]

private

Definition at line 184 of file PCRPrimer_.hpp.

Referenced by CPCRPrimer_Base::CPCRPrimer_Base(), CPCRPrimer_Base::IsSetName(), CPCRPrimer_Base::IsSetSeq(), CPCRPrimer_Base::ResetName(), CPCRPrimer_Base::ResetSeq(), CPCRPrimer_Base::SetName(), and CPCRPrimer_Base::SetSeq().

m_set_State [3/6]

Uint4 CPCRPrimerSet_Base::m_set_State[1]

private

Definition at line 138 of file PCRPrimerSet_.hpp.

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

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

Definition at line 138 of file PCRReactionSet_.hpp.

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

m_set_State [6/6]

Uint4 CSubSource_Base::m_set_State[1]

private

Definition at line 275 of file SubSource_.hpp.

Referenced by CSubSource_Base::CSubSource_Base(), CSubSource_Base::IsSetAttrib(), CSubSource_Base::IsSetName(), CSubSource_Base::IsSetSubtype(), CSubSource_Base::ResetAttrib(), CSubSource_Base::ResetName(), CSubSource_Base::ResetSubtype(), CSubSource_Base::SetAttrib(), CSubSource_Base::SetName(), and CSubSource_Base::SetSubtype().

m_Subtype [1/2]

list< CRef< CSubSource > > CBioSource_Base::m_Subtype

private

Definition at line 383 of file BioSource_.hpp.

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

m_Subtype [2/2]

int CSubSource_Base::m_Subtype

private

Definition at line 276 of file SubSource_.hpp.

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