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

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

Classes
class	CRNA_gen_Base
	CRNA_gen_Base –. More...
class	CRNA_qual
	CRNA_qual –. More...
class	CRNA_qual_Base
	Additional data values for RNA-gen,. More...
class	CRNA_qual_set
	CRNA_qual_set –. More...
class	CRNA_qual_set_Base
	CRNA_qual_set_Base –. More...
class	CRNA_ref_Base
	*** rnas *********************************************** * * various rnas * minimal RNA sequence More...
class	CRNA_ref_Base::C_Ext
	C_Ext –. More...
class	CTrna_ext_Base
	tRNA feature extensions More...
class	CTrna_ext_Base::C_Aa
	aa this carries More...

Typedefs
typedef CSerialObject	CRNA_gen_Base::Tparent
typedef string	CRNA_gen_Base::TClass
typedef string	CRNA_gen_Base::TProduct
typedef CRNA_qual_set	CRNA_gen_Base::TQuals
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	CRNA_gen_Base::TmemberIndex
typedef CRNA_qual_Base	CRNA_qual::Tparent
typedef CSerialObject	CRNA_qual_Base::Tparent
typedef string	CRNA_qual_Base::TQual
typedef string	CRNA_qual_Base::TVal
typedef Tparent::CMemberIndex< E_memberIndex, 3 >	CRNA_qual_Base::TmemberIndex
typedef CRNA_qual_set_Base	CRNA_qual_set::Tparent
typedef CSerialObject	CRNA_qual_set_Base::Tparent
typedef list< CRef< CRNA_qual > >	CRNA_qual_set_Base::Tdata
typedef CSerialObject	CRNA_ref_Base::Tparent
typedef CSerialObject	CRNA_ref_Base::C_Ext::Tparent
typedef string	CRNA_ref_Base::C_Ext::TName
typedef CTrna_ext	CRNA_ref_Base::C_Ext::TTRNA
typedef CRNA_gen	CRNA_ref_Base::C_Ext::TGen
typedef EType	CRNA_ref_Base::TType
typedef bool	CRNA_ref_Base::TPseudo
typedef C_Ext	CRNA_ref_Base::TExt
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	CRNA_ref_Base::TmemberIndex
typedef CSerialObject	CTrna_ext_Base::Tparent
typedef CSerialObject	CTrna_ext_Base::C_Aa::Tparent
typedef int	CTrna_ext_Base::C_Aa::TIupacaa
typedef int	CTrna_ext_Base::C_Aa::TNcbieaa
typedef int	CTrna_ext_Base::C_Aa::TNcbi8aa
typedef int	CTrna_ext_Base::C_Aa::TNcbistdaa
typedef C_Aa	CTrna_ext_Base::TAa
typedef list< int >	CTrna_ext_Base::TCodon
typedef CSeq_loc	CTrna_ext_Base::TAnticodon
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	CTrna_ext_Base::TmemberIndex

Enumerations
enum class	CRNA_gen_Base::E_memberIndex { CRNA_gen_Base::e__allMandatory = 0 , CRNA_gen_Base::e_class , CRNA_gen_Base::e_product , CRNA_gen_Base::e_quals }
enum class	CRNA_qual_Base::E_memberIndex { CRNA_qual_Base::e__allMandatory = 0 , CRNA_qual_Base::e_qual , CRNA_qual_Base::e_val }
enum	CRNA_ref_Base::EType {   CRNA_ref_Base::eType_unknown = 0 , CRNA_ref_Base::eType_premsg = 1 , CRNA_ref_Base::eType_mRNA = 2 , CRNA_ref_Base::eType_tRNA = 3 ,   CRNA_ref_Base::eType_rRNA = 4 , CRNA_ref_Base::eType_snRNA = 5 , CRNA_ref_Base::eType_scRNA = 6 , CRNA_ref_Base::eType_snoRNA = 7 ,   CRNA_ref_Base::eType_ncRNA = 8 , CRNA_ref_Base::eType_tmRNA = 9 , CRNA_ref_Base::eType_miscRNA = 10 , CRNA_ref_Base::eType_other = 255 }
	type of RNA feature More...
enum	CRNA_ref_Base::C_Ext::E_Choice { CRNA_ref_Base::C_Ext::e_not_set = 0 , CRNA_ref_Base::C_Ext::e_Name , CRNA_ref_Base::C_Ext::e_TRNA , CRNA_ref_Base::C_Ext::e_Gen }
	Choice variants. More...
enum	CRNA_ref_Base::C_Ext::E_ChoiceStopper { CRNA_ref_Base::C_Ext::e_MaxChoice = 4 }
	Maximum+1 value of the choice variant enumerator. More...
enum class	CRNA_ref_Base::E_memberIndex { CRNA_ref_Base::e__allMandatory = 0 , CRNA_ref_Base::e_type , CRNA_ref_Base::e_pseudo , CRNA_ref_Base::e_ext }
enum	CTrna_ext_Base::C_Aa::E_Choice {   CTrna_ext_Base::C_Aa::e_not_set = 0 , CTrna_ext_Base::C_Aa::e_Iupacaa , CTrna_ext_Base::C_Aa::e_Ncbieaa , CTrna_ext_Base::C_Aa::e_Ncbi8aa ,   CTrna_ext_Base::C_Aa::e_Ncbistdaa }
	Choice variants. More...
enum	CTrna_ext_Base::C_Aa::E_ChoiceStopper { CTrna_ext_Base::C_Aa::e_MaxChoice = 5 }
	Maximum+1 value of the choice variant enumerator. More...
enum class	CTrna_ext_Base::E_memberIndex { CTrna_ext_Base::e__allMandatory = 0 , CTrna_ext_Base::e_aa , CTrna_ext_Base::e_codon , CTrna_ext_Base::e_anticodon }

Functions
	CRNA_gen_Base::CRNA_gen_Base (void)
virtual	CRNA_gen_Base::~CRNA_gen_Base (void)
	CRNA_gen_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CRNA_gen_Base::IsSetClass (void) const
	for ncRNAs, the class of non-coding RNA: examples: antisense_RNA, guide_RNA, snRNA Check if a value has been assigned to Class data member. More...
bool	CRNA_gen_Base::CanGetClass (void) const
	Check if it is safe to call GetClass method. More...
void	CRNA_gen_Base::ResetClass (void)
	Reset Class data member. More...
const TClass &	CRNA_gen_Base::GetClass (void) const
	Get the Class member data. More...
void	CRNA_gen_Base::SetClass (const TClass &value)
	Assign a value to Class data member. More...
void	CRNA_gen_Base::SetClass (TClass &&value)
TClass &	CRNA_gen_Base::SetClass (void)
	Assign a value to Class data member. More...
bool	CRNA_gen_Base::IsSetProduct (void) const
	Check if a value has been assigned to Product data member. More...
bool	CRNA_gen_Base::CanGetProduct (void) const
	Check if it is safe to call GetProduct method. More...
void	CRNA_gen_Base::ResetProduct (void)
	Reset Product data member. More...
const TProduct &	CRNA_gen_Base::GetProduct (void) const
	Get the Product member data. More...
void	CRNA_gen_Base::SetProduct (const TProduct &value)
	Assign a value to Product data member. More...
void	CRNA_gen_Base::SetProduct (TProduct &&value)
TProduct &	CRNA_gen_Base::SetProduct (void)
	Assign a value to Product data member. More...
bool	CRNA_gen_Base::IsSetQuals (void) const
	e.g., tag_peptide qualifier for tmRNAs Check if a value has been assigned to Quals data member. More...
bool	CRNA_gen_Base::CanGetQuals (void) const
	Check if it is safe to call GetQuals method. More...
void	CRNA_gen_Base::ResetQuals (void)
	Reset Quals data member. More...
const TQuals &	CRNA_gen_Base::GetQuals (void) const
	Get the Quals member data. More...
void	CRNA_gen_Base::SetQuals (TQuals &value)
	Assign a value to Quals data member. More...
TQuals &	CRNA_gen_Base::SetQuals (void)
	Assign a value to Quals data member. More...
virtual void	CRNA_gen_Base::Reset (void)
	Reset the whole object. More...
	CRNA_gen_Base::CRNA_gen_Base (const CRNA_gen_Base &)
CRNA_gen_Base &	CRNA_gen_Base::operator= (const CRNA_gen_Base &)
	CRNA_qual::CRNA_qual (void)
	CRNA_qual::~CRNA_qual (void)
	CRNA_qual::CRNA_qual (const CRNA_qual &value)
CRNA_qual &	CRNA_qual::operator= (const CRNA_qual &value)
	CRNA_qual_Base::CRNA_qual_Base (void)
virtual	CRNA_qual_Base::~CRNA_qual_Base (void)
	CRNA_qual_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CRNA_qual_Base::IsSetQual (void) const
	in a tag (qual), value (val) format Check if a value has been assigned to Qual data member. More...
bool	CRNA_qual_Base::CanGetQual (void) const
	Check if it is safe to call GetQual method. More...
void	CRNA_qual_Base::ResetQual (void)
	Reset Qual data member. More...
const TQual &	CRNA_qual_Base::GetQual (void) const
	Get the Qual member data. More...
void	CRNA_qual_Base::SetQual (const TQual &value)
	Assign a value to Qual data member. More...
void	CRNA_qual_Base::SetQual (TQual &&value)
TQual &	CRNA_qual_Base::SetQual (void)
	Assign a value to Qual data member. More...
bool	CRNA_qual_Base::IsSetVal (void) const
	Check if a value has been assigned to Val data member. More...
bool	CRNA_qual_Base::CanGetVal (void) const
	Check if it is safe to call GetVal method. More...
void	CRNA_qual_Base::ResetVal (void)
	Reset Val data member. More...
const TVal &	CRNA_qual_Base::GetVal (void) const
	Get the Val member data. More...
void	CRNA_qual_Base::SetVal (const TVal &value)
	Assign a value to Val data member. More...
void	CRNA_qual_Base::SetVal (TVal &&value)
TVal &	CRNA_qual_Base::SetVal (void)
	Assign a value to Val data member. More...
virtual void	CRNA_qual_Base::Reset (void)
	Reset the whole object. More...
	CRNA_qual_Base::CRNA_qual_Base (const CRNA_qual_Base &)
CRNA_qual_Base &	CRNA_qual_Base::operator= (const CRNA_qual_Base &)
	CRNA_qual_set::CRNA_qual_set (void)
	CRNA_qual_set::~CRNA_qual_set (void)
	CRNA_qual_set::CRNA_qual_set (const CRNA_qual_set &value)
CRNA_qual_set &	CRNA_qual_set::operator= (const CRNA_qual_set &value)
	CRNA_qual_set_Base::CRNA_qual_set_Base (void)
virtual	CRNA_qual_set_Base::~CRNA_qual_set_Base (void)
	CRNA_qual_set_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CRNA_qual_set_Base::IsSet (void) const
	Check if a value has been assigned to data member. More...
bool	CRNA_qual_set_Base::CanGet (void) const
	Check if it is safe to call Get method. More...
void	CRNA_qual_set_Base::Reset (void)
	Reset data member. More...
const Tdata &	CRNA_qual_set_Base::Get (void) const
	Get the member data. More...
Tdata &	CRNA_qual_set_Base::Set (void)
	Assign a value to data member. More...
	CRNA_qual_set_Base::operator const Tdata & (void) const
	Conversion operator to 'const Tdata' type. More...
	CRNA_qual_set_Base::operator Tdata & (void)
	Conversion operator to 'Tdata' type. More...
	CRNA_qual_set_Base::CRNA_qual_set_Base (const CRNA_qual_set_Base &)
CRNA_qual_set_Base &	CRNA_qual_set_Base::operator= (const CRNA_qual_set_Base &)
	CRNA_ref_Base::CRNA_ref_Base (void)
virtual	CRNA_ref_Base::~CRNA_ref_Base (void)
	CRNA_ref_Base::DECLARE_INTERNAL_TYPE_INFO ()
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	CRNA_ref_Base::EType (void)
	Access to EType's attributes (values, names) as defined in spec. More...
	CRNA_ref_Base::C_Ext::C_Ext (void)
	CRNA_ref_Base::C_Ext::~C_Ext (void)
	CRNA_ref_Base::C_Ext::DECLARE_INTERNAL_TYPE_INFO ()
void	CRNA_ref_Base::C_Ext::Reset (void)
	Reset the whole object. More...
void	CRNA_ref_Base::C_Ext::ResetSelection (void)
	Reset the selection (set it to e_not_set). More...
E_Choice	CRNA_ref_Base::C_Ext::Which (void) const
	Which variant is currently selected. More...
void	CRNA_ref_Base::C_Ext::CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...
void	CRNA_ref_Base::C_Ext::ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...
static string	CRNA_ref_Base::C_Ext::SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). More...
void	CRNA_ref_Base::C_Ext::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...
void	CRNA_ref_Base::C_Ext::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...
bool	CRNA_ref_Base::C_Ext::IsName (void) const
	Check if variant Name is selected. More...
const TName &	CRNA_ref_Base::C_Ext::GetName (void) const
	Get the variant data. More...
TName &	CRNA_ref_Base::C_Ext::SetName (void)
	Select the variant. More...
void	CRNA_ref_Base::C_Ext::SetName (const TName &value)
	Select the variant and set its data. More...
bool	CRNA_ref_Base::C_Ext::IsTRNA (void) const
	Check if variant TRNA is selected. More...
const TTRNA &	CRNA_ref_Base::C_Ext::GetTRNA (void) const
	Get the variant data. More...
TTRNA &	CRNA_ref_Base::C_Ext::SetTRNA (void)
	Select the variant. More...
void	CRNA_ref_Base::C_Ext::SetTRNA (TTRNA &value)
	Select the variant and set its data. More...
bool	CRNA_ref_Base::C_Ext::IsGen (void) const
	Check if variant Gen is selected. More...
const TGen &	CRNA_ref_Base::C_Ext::GetGen (void) const
	Get the variant data. More...
TGen &	CRNA_ref_Base::C_Ext::SetGen (void)
	Select the variant. More...
void	CRNA_ref_Base::C_Ext::SetGen (TGen &value)
	Select the variant and set its data. More...
	CRNA_ref_Base::C_Ext::C_Ext (const C_Ext &)
C_Ext &	CRNA_ref_Base::C_Ext::operator= (const C_Ext &)
void	CRNA_ref_Base::C_Ext::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
bool	CRNA_ref_Base::IsSetType (void) const
	Check if a value has been assigned to Type data member. More...
bool	CRNA_ref_Base::CanGetType (void) const
	Check if it is safe to call GetType method. More...
void	CRNA_ref_Base::ResetType (void)
	Reset Type data member. More...
TType	CRNA_ref_Base::GetType (void) const
	Get the Type member data. More...
void	CRNA_ref_Base::SetType (TType value)
	Assign a value to Type data member. More...
TType &	CRNA_ref_Base::SetType (void)
	Assign a value to Type data member. More...
bool	CRNA_ref_Base::IsSetPseudo (void) const
	Check if a value has been assigned to Pseudo data member. More...
bool	CRNA_ref_Base::CanGetPseudo (void) const
	Check if it is safe to call GetPseudo method. More...
void	CRNA_ref_Base::ResetPseudo (void)
	Reset Pseudo data member. More...
TPseudo	CRNA_ref_Base::GetPseudo (void) const
	Get the Pseudo member data. More...
void	CRNA_ref_Base::SetPseudo (TPseudo value)
	Assign a value to Pseudo data member. More...
TPseudo &	CRNA_ref_Base::SetPseudo (void)
	Assign a value to Pseudo data member. More...
bool	CRNA_ref_Base::IsSetExt (void) const
	generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member. More...
bool	CRNA_ref_Base::CanGetExt (void) const
	Check if it is safe to call GetExt method. More...
void	CRNA_ref_Base::ResetExt (void)
	Reset Ext data member. More...
const TExt &	CRNA_ref_Base::GetExt (void) const
	Get the Ext member data. More...
void	CRNA_ref_Base::SetExt (TExt &value)
	Assign a value to Ext data member. More...
TExt &	CRNA_ref_Base::SetExt (void)
	Assign a value to Ext data member. More...
virtual void	CRNA_ref_Base::Reset (void)
	Reset the whole object. More...
	CRNA_ref_Base::CRNA_ref_Base (const CRNA_ref_Base &)
CRNA_ref_Base &	CRNA_ref_Base::operator= (const CRNA_ref_Base &)
	CTrna_ext_Base::CTrna_ext_Base (void)
virtual	CTrna_ext_Base::~CTrna_ext_Base (void)
	CTrna_ext_Base::DECLARE_INTERNAL_TYPE_INFO ()
	CTrna_ext_Base::C_Aa::C_Aa (void)
	CTrna_ext_Base::C_Aa::~C_Aa (void)
	CTrna_ext_Base::C_Aa::DECLARE_INTERNAL_TYPE_INFO ()
void	CTrna_ext_Base::C_Aa::Reset (void)
	Reset the whole object. More...
void	CTrna_ext_Base::C_Aa::ResetSelection (void)
	Reset the selection (set it to e_not_set). More...
E_Choice	CTrna_ext_Base::C_Aa::Which (void) const
	Which variant is currently selected. More...
void	CTrna_ext_Base::C_Aa::CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...
void	CTrna_ext_Base::C_Aa::ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...
static string	CTrna_ext_Base::C_Aa::SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). More...
void	CTrna_ext_Base::C_Aa::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...
void	CTrna_ext_Base::C_Aa::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...
bool	CTrna_ext_Base::C_Aa::IsIupacaa (void) const
	Check if variant Iupacaa is selected. More...
TIupacaa	CTrna_ext_Base::C_Aa::GetIupacaa (void) const
	Get the variant data. More...
TIupacaa &	CTrna_ext_Base::C_Aa::SetIupacaa (void)
	Select the variant. More...
void	CTrna_ext_Base::C_Aa::SetIupacaa (TIupacaa value)
	Select the variant and set its data. More...
bool	CTrna_ext_Base::C_Aa::IsNcbieaa (void) const
	Check if variant Ncbieaa is selected. More...
TNcbieaa	CTrna_ext_Base::C_Aa::GetNcbieaa (void) const
	Get the variant data. More...
TNcbieaa &	CTrna_ext_Base::C_Aa::SetNcbieaa (void)
	Select the variant. More...
void	CTrna_ext_Base::C_Aa::SetNcbieaa (TNcbieaa value)
	Select the variant and set its data. More...
bool	CTrna_ext_Base::C_Aa::IsNcbi8aa (void) const
	Check if variant Ncbi8aa is selected. More...
TNcbi8aa	CTrna_ext_Base::C_Aa::GetNcbi8aa (void) const
	Get the variant data. More...
TNcbi8aa &	CTrna_ext_Base::C_Aa::SetNcbi8aa (void)
	Select the variant. More...
void	CTrna_ext_Base::C_Aa::SetNcbi8aa (TNcbi8aa value)
	Select the variant and set its data. More...
bool	CTrna_ext_Base::C_Aa::IsNcbistdaa (void) const
	Check if variant Ncbistdaa is selected. More...
TNcbistdaa	CTrna_ext_Base::C_Aa::GetNcbistdaa (void) const
	Get the variant data. More...
TNcbistdaa &	CTrna_ext_Base::C_Aa::SetNcbistdaa (void)
	Select the variant. More...
void	CTrna_ext_Base::C_Aa::SetNcbistdaa (TNcbistdaa value)
	Select the variant and set its data. More...
	CTrna_ext_Base::C_Aa::C_Aa (const C_Aa &)
C_Aa &	CTrna_ext_Base::C_Aa::operator= (const C_Aa &)
void	CTrna_ext_Base::C_Aa::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
bool	CTrna_ext_Base::IsSetAa (void) const
	Check if a value has been assigned to Aa data member. More...
bool	CTrna_ext_Base::CanGetAa (void) const
	Check if it is safe to call GetAa method. More...
void	CTrna_ext_Base::ResetAa (void)
	Reset Aa data member. More...
const TAa &	CTrna_ext_Base::GetAa (void) const
	Get the Aa member data. More...
void	CTrna_ext_Base::SetAa (TAa &value)
	Assign a value to Aa data member. More...
TAa &	CTrna_ext_Base::SetAa (void)
	Assign a value to Aa data member. More...
bool	CTrna_ext_Base::IsSetCodon (void) const
	codon(s) as in Genetic-code Check if a value has been assigned to Codon data member. More...
bool	CTrna_ext_Base::CanGetCodon (void) const
	Check if it is safe to call GetCodon method. More...
void	CTrna_ext_Base::ResetCodon (void)
	Reset Codon data member. More...
const TCodon &	CTrna_ext_Base::GetCodon (void) const
	Get the Codon member data. More...
TCodon &	CTrna_ext_Base::SetCodon (void)
	Assign a value to Codon data member. More...
bool	CTrna_ext_Base::IsSetAnticodon (void) const
	location of anticodon Check if a value has been assigned to Anticodon data member. More...
bool	CTrna_ext_Base::CanGetAnticodon (void) const
	Check if it is safe to call GetAnticodon method. More...
void	CTrna_ext_Base::ResetAnticodon (void)
	Reset Anticodon data member. More...
const TAnticodon &	CTrna_ext_Base::GetAnticodon (void) const
	Get the Anticodon member data. More...
void	CTrna_ext_Base::SetAnticodon (TAnticodon &value)
	Assign a value to Anticodon data member. More...
TAnticodon &	CTrna_ext_Base::SetAnticodon (void)
	Assign a value to Anticodon data member. More...
virtual void	CTrna_ext_Base::Reset (void)
	Reset the whole object. More...
	CTrna_ext_Base::CTrna_ext_Base (const CTrna_ext_Base &)
CTrna_ext_Base &	CTrna_ext_Base::operator= (const CTrna_ext_Base &)

Variables
Uint4	CRNA_gen_Base::m_set_State [1]
string	CRNA_gen_Base::m_Class
string	CRNA_gen_Base::m_Product
CRef< TQuals >	CRNA_gen_Base::m_Quals
Uint4	CRNA_qual_Base::m_set_State [1]
string	CRNA_qual_Base::m_Qual
string	CRNA_qual_Base::m_Val
Uint4	CRNA_qual_set_Base::m_set_State [1]
list< CRef< CRNA_qual > >	CRNA_qual_set_Base::m_data
E_Choice	CRNA_ref_Base::C_Ext::m_choice
static const char *const	CRNA_ref_Base::C_Ext::sm_SelectionNames []
NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string >   CRNA_ref_Base::C_Ext::m_string
NCBI_NS_NCBI::CSerialObject *   CRNA_ref_Base::C_Ext::m_object
union {
NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string >   CRNA_ref_Base::C_Ext::m_string
NCBI_NS_NCBI::CSerialObject *   CRNA_ref_Base::C_Ext::m_object
};
Uint4	CRNA_ref_Base::m_set_State [1]
EType	CRNA_ref_Base::m_Type
bool	CRNA_ref_Base::m_Pseudo
CRef< TExt >	CRNA_ref_Base::m_Ext
E_Choice	CTrna_ext_Base::C_Aa::m_choice
static const char *const	CTrna_ext_Base::C_Aa::sm_SelectionNames []
TIupacaa   CTrna_ext_Base::C_Aa::m_Iupacaa
TNcbieaa   CTrna_ext_Base::C_Aa::m_Ncbieaa
TNcbi8aa   CTrna_ext_Base::C_Aa::m_Ncbi8aa
TNcbistdaa   CTrna_ext_Base::C_Aa::m_Ncbistdaa
union {
TIupacaa   CTrna_ext_Base::C_Aa::m_Iupacaa
TNcbieaa   CTrna_ext_Base::C_Aa::m_Ncbieaa
TNcbi8aa   CTrna_ext_Base::C_Aa::m_Ncbi8aa
TNcbistdaa   CTrna_ext_Base::C_Aa::m_Ncbistdaa
};
Uint4	CTrna_ext_Base::m_set_State [1]
CRef< TAa >	CTrna_ext_Base::m_Aa
list< int >	CTrna_ext_Base::m_Codon
CRef< TAnticodon >	CTrna_ext_Base::m_Anticodon

Detailed Description

Typedef Documentation

TAa

typedef C_Aa CTrna_ext_Base::TAa

Definition at line 305 of file Trna_ext_.hpp.

TAnticodon

typedef CSeq_loc CTrna_ext_Base::TAnticodon

Definition at line 307 of file Trna_ext_.hpp.

TClass

typedef string CRNA_gen_Base::TClass

Definition at line 89 of file RNA_gen_.hpp.

TCodon

typedef list< int > CTrna_ext_Base::TCodon

Definition at line 306 of file Trna_ext_.hpp.

Tdata

typedef list< CRef< CRNA_qual > > CRNA_qual_set_Base::Tdata

Definition at line 89 of file RNA_qual_set_.hpp.

TExt

typedef C_Ext CRNA_ref_Base::TExt

Definition at line 297 of file RNA_ref_.hpp.

TGen

typedef CRNA_gen CRNA_ref_Base::C_Ext::TGen

Definition at line 193 of file RNA_ref_.hpp.

TIupacaa

typedef int CTrna_ext_Base::C_Aa::TIupacaa

Definition at line 169 of file Trna_ext_.hpp.

TmemberIndex [1/4]

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

Definition at line 100 of file RNA_gen_.hpp.

TmemberIndex [2/4]

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

Definition at line 95 of file RNA_qual_.hpp.

TmemberIndex [3/4]

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

Definition at line 306 of file RNA_ref_.hpp.

TmemberIndex [4/4]

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

Definition at line 316 of file Trna_ext_.hpp.

TName

typedef string CRNA_ref_Base::C_Ext::TName

Definition at line 191 of file RNA_ref_.hpp.

TNcbi8aa

typedef int CTrna_ext_Base::C_Aa::TNcbi8aa

Definition at line 171 of file Trna_ext_.hpp.

TNcbieaa

typedef int CTrna_ext_Base::C_Aa::TNcbieaa

Definition at line 170 of file Trna_ext_.hpp.

TNcbistdaa

typedef int CTrna_ext_Base::C_Aa::TNcbistdaa

Definition at line 172 of file Trna_ext_.hpp.

Tparent [1/9]

typedef CSerialObject CRNA_gen_Base::Tparent

private

Definition at line 78 of file RNA_gen_.hpp.

Tparent [2/9]

typedef CRNA_qual_Base CRNA_qual::Tparent

private

Definition at line 67 of file RNA_qual.hpp.

Tparent [3/9]

typedef CSerialObject CRNA_qual_Base::Tparent

private

Definition at line 75 of file RNA_qual_.hpp.

Tparent [4/9]

typedef CRNA_qual_set_Base CRNA_qual_set::Tparent

private

Definition at line 67 of file RNA_qual_set.hpp.

Tparent [5/9]

typedef CSerialObject CRNA_qual_set_Base::Tparent

private

Definition at line 78 of file RNA_qual_set_.hpp.

Tparent [6/9]

typedef CSerialObject CRNA_ref_Base::Tparent

private

Definition at line 84 of file RNA_ref_.hpp.

Tparent [7/9]

typedef CSerialObject CRNA_ref_Base::C_Ext::Tparent

private

Definition at line 120 of file RNA_ref_.hpp.

Tparent [8/9]

typedef CSerialObject CTrna_ext_Base::Tparent

private

Definition at line 79 of file Trna_ext_.hpp.

Tparent [9/9]

typedef CSerialObject CTrna_ext_Base::C_Aa::Tparent

private

Definition at line 97 of file Trna_ext_.hpp.

TProduct

typedef string CRNA_gen_Base::TProduct

Definition at line 90 of file RNA_gen_.hpp.

TPseudo

typedef bool CRNA_ref_Base::TPseudo

Definition at line 296 of file RNA_ref_.hpp.

TQual

typedef string CRNA_qual_Base::TQual

Definition at line 86 of file RNA_qual_.hpp.

TQuals

typedef CRNA_qual_set CRNA_gen_Base::TQuals

Definition at line 91 of file RNA_gen_.hpp.

TTRNA

typedef CTrna_ext CRNA_ref_Base::C_Ext::TTRNA

Definition at line 192 of file RNA_ref_.hpp.

TType

typedef EType CRNA_ref_Base::TType

Definition at line 295 of file RNA_ref_.hpp.

TVal

typedef string CRNA_qual_Base::TVal

Definition at line 87 of file RNA_qual_.hpp.

Enumeration Type Documentation

E_Choice [1/2]

enum CRNA_ref_Base::C_Ext::E_Choice

Choice variants.

Enumerator
e_not_set	No variant selected.
e_Name	for naming "other" type
e_TRNA	for tRNAs
e_Gen

Definition at line 132 of file RNA_ref_.hpp.

E_Choice [2/2]

enum CTrna_ext_Base::C_Aa::E_Choice

Choice variants.

Enumerator
e_not_set	No variant selected.
e_Iupacaa
e_Ncbieaa
e_Ncbi8aa
e_Ncbistdaa

Definition at line 109 of file Trna_ext_.hpp.

E_ChoiceStopper [1/2]

enum CRNA_ref_Base::C_Ext::E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice	== e_Gen+1

Definition at line 139 of file RNA_ref_.hpp.

E_ChoiceStopper [2/2]

enum CTrna_ext_Base::C_Aa::E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice	== e_Ncbistdaa+1

Definition at line 117 of file Trna_ext_.hpp.

E_memberIndex [1/4]

enum CRNA_gen_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_class
e_product
e_quals

Definition at line 94 of file RNA_gen_.hpp.

E_memberIndex [2/4]

enum CRNA_qual_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_qual
e_val

Definition at line 90 of file RNA_qual_.hpp.

E_memberIndex [3/4]

enum CRNA_ref_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_type
e_pseudo
e_ext

Definition at line 300 of file RNA_ref_.hpp.

E_memberIndex [4/4]

enum CTrna_ext_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_aa
e_codon
e_anticodon

Definition at line 310 of file Trna_ext_.hpp.

EType

enum CRNA_ref_Base::EType

(

void

)

type of RNA feature

Enumerator
eType_unknown
eType_premsg
eType_mRNA
eType_tRNA
eType_rRNA
eType_snRNA	will become ncRNA, with RNA-gen.class = snRNA
eType_scRNA	will become ncRNA, with RNA-gen.class = scRNA
eType_snoRNA	will become ncRNA, with RNA-gen.class = snoRNA
eType_ncRNA	non-coding RNA; subsumes snRNA, scRNA, snoRNA
eType_tmRNA
eType_miscRNA
eType_other

Definition at line 95 of file RNA_ref_.hpp.

Function Documentation

C_Aa() [1/2]

CTrna_ext_Base::C_Aa::C_Aa ( const C_Aa &  )

private

C_Aa() [2/2]

END_CHOICE_INFO CTrna_ext_Base::C_Aa::C_Aa

(

void

)

Definition at line 118 of file Trna_ext_.cpp.

C_Ext() [1/2]

CRNA_ref_Base::C_Ext::C_Ext ( const C_Ext &  )

private

C_Ext() [2/2]

END_CHOICE_INFO CRNA_ref_Base::C_Ext::C_Ext

(

void

)

Definition at line 194 of file RNA_ref_.cpp.

CanGet()

bool CRNA_qual_set_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 RNA_qual_set_.hpp.

CanGetAa()

bool CTrna_ext_Base::CanGetAa ( void  ) const

inline

Check if it is safe to call GetAa method.

Returns

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

Definition at line 597 of file Trna_ext_.hpp.

References CTrna_ext_Base::IsSetAa().

Referenced by get_my_feat_type(), get_trna_string(), and CTrna_ext_Base::GetAa().

CanGetAnticodon()

bool CTrna_ext_Base::CanGetAnticodon ( void  ) const

inline

Check if it is safe to call GetAnticodon method.

Returns

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

Definition at line 643 of file Trna_ext_.hpp.

References CTrna_ext_Base::IsSetAnticodon().

Referenced by CTrna_ext_Base::GetAnticodon(), CAntiCodonColumn::GetFromFeat(), and CRNAValidator::x_ValidateTrnaData().

CanGetClass()

bool CRNA_gen_Base::CanGetClass ( void  ) const

inline

Check if it is safe to call GetClass method.

Returns

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

Definition at line 253 of file RNA_gen_.hpp.

References CRNA_gen_Base::IsSetClass().

Referenced by CRNA_gen_Base::GetClass(), and CRna_feat_type::Match().

CanGetCodon()

bool CTrna_ext_Base::CanGetCodon ( void  ) const

inline

Check if it is safe to call GetCodon method.

Returns

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

Definition at line 618 of file Trna_ext_.hpp.

Referenced by CCodonsRecColumn::GetFromFeat().

CanGetExt()

bool CRNA_ref_Base::CanGetExt ( void  ) const

inline

Check if it is safe to call GetExt method.

Returns

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

Definition at line 610 of file RNA_ref_.hpp.

References CRNA_ref_Base::IsSetExt().

Referenced by get_my_feat_type(), get_trna_string(), CRNA_ref_Base::GetExt(), CCodonsRecColumn::GetFromFeat(), CAntiCodonColumn::GetFromFeat(), CTagPeptideColumn::GetFromFeat(), GetRNAname(), CRna_feat_type::Match(), CValidError_bioseq::ValidateSeqFeatContext(), and CSeqFeatData::x_InitFeatDataInfo().

CanGetProduct()

bool CRNA_gen_Base::CanGetProduct ( void  ) const

inline

Check if it is safe to call GetProduct method.

Returns

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

Definition at line 300 of file RNA_gen_.hpp.

References CRNA_gen_Base::IsSetProduct().

Referenced by CRNA_gen_Base::GetProduct(), and GetRNAProductString().

CanGetPseudo()

bool CRNA_ref_Base::CanGetPseudo ( void  ) const

inline

Check if it is safe to call GetPseudo method.

Returns

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

Definition at line 563 of file RNA_ref_.hpp.

References CRNA_ref_Base::IsSetPseudo().

Referenced by get_my_feat_type(), get_trna_string(), and CRNA_ref_Base::GetPseudo().

CanGetQual()

bool CRNA_qual_Base::CanGetQual ( void  ) const

inline

Check if it is safe to call GetQual method.

Returns

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

Definition at line 208 of file RNA_qual_.hpp.

References CRNA_qual_Base::IsSetQual().

Referenced by CRNA_qual_Base::GetQual().

CanGetQuals()

bool CRNA_gen_Base::CanGetQuals ( void  ) const

inline

Check if it is safe to call GetQuals method.

Returns

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

Definition at line 347 of file RNA_gen_.hpp.

References CRNA_gen_Base::IsSetQuals().

Referenced by CTagPeptideColumn::GetFromFeat(), and CRNA_gen_Base::GetQuals().

CanGetType()

bool CRNA_ref_Base::CanGetType ( void  ) const

inline

Check if it is safe to call GetType method.

Returns

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

Definition at line 516 of file RNA_ref_.hpp.

References CRNA_ref_Base::IsSetType().

Referenced by get_my_feat_type(), get_trna_string(), GetRNAname(), CRNA_ref_Base::GetType(), and CFeatureGenerator::SImplementation::x_SetExceptText().

CanGetVal()

bool CRNA_qual_Base::CanGetVal ( void  ) const

inline

Check if it is safe to call GetVal method.

Returns

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

Definition at line 255 of file RNA_qual_.hpp.

References CRNA_qual_Base::IsSetVal().

Referenced by CRNA_qual_Base::GetVal().

CheckSelected() [1/2]

void CRNA_ref_Base::C_Ext::CheckSelected ( E_Choice  index ) const

inline

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

Parameters

index

Expected selection.

Definition at line 455 of file RNA_ref_.hpp.

CheckSelected() [2/2]

void CTrna_ext_Base::C_Aa::CheckSelected ( E_Choice  index ) const

inline

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

Parameters

index

Expected selection.

Definition at line 460 of file Trna_ext_.hpp.

CRNA_gen_Base() [1/2]

CRNA_gen_Base::CRNA_gen_Base ( const CRNA_gen_Base &  )

private

CRNA_gen_Base() [2/2]

END_CLASS_INFO CRNA_gen_Base::CRNA_gen_Base

(

void

)

Definition at line 100 of file RNA_gen_.cpp.

References CRNA_gen_Base::m_set_State.

CRNA_qual() [1/2]

CRNA_qual::CRNA_qual ( const CRNA_qual &  value )

private

CRNA_qual() [2/2]

CRNA_qual::CRNA_qual ( void  )

inline

Definition at line 86 of file RNA_qual.hpp.

CRNA_qual_Base() [1/2]

CRNA_qual_Base::CRNA_qual_Base ( const CRNA_qual_Base &  )

private

CRNA_qual_Base() [2/2]

END_CLASS_INFO CRNA_qual_Base::CRNA_qual_Base

(

void

)

Definition at line 80 of file RNA_qual_.cpp.

References CRNA_qual_Base::m_set_State.

CRNA_qual_set() [1/2]

CRNA_qual_set::CRNA_qual_set ( const CRNA_qual_set &  value )

private

CRNA_qual_set() [2/2]

CRNA_qual_set::CRNA_qual_set ( void  )

inline

Definition at line 86 of file RNA_qual_set.hpp.

CRNA_qual_set_Base() [1/2]

CRNA_qual_set_Base::CRNA_qual_set_Base ( const CRNA_qual_set_Base &  )

private

CRNA_qual_set_Base() [2/2]

END_CLASS_INFO CRNA_qual_set_Base::CRNA_qual_set_Base

(

void

)

Definition at line 68 of file RNA_qual_set_.cpp.

References CRNA_qual_set_Base::m_set_State.

CRNA_ref_Base() [1/2]

CRNA_ref_Base::CRNA_ref_Base ( const CRNA_ref_Base &  )

private

CRNA_ref_Base() [2/2]

END_CLASS_INFO CRNA_ref_Base::CRNA_ref_Base

(

void

)

Definition at line 243 of file RNA_ref_.cpp.

References CRNA_ref_Base::m_set_State.

CTrna_ext_Base() [1/2]

CTrna_ext_Base::CTrna_ext_Base ( const CTrna_ext_Base &  )

private

CTrna_ext_Base() [2/2]

END_CLASS_INFO CTrna_ext_Base::CTrna_ext_Base

(

void

)

Definition at line 190 of file Trna_ext_.cpp.

References CTrna_ext_Base::m_set_State.

DECLARE_INTERNAL_TYPE_INFO() [1/7]

CRNA_gen_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [2/7]

CRNA_qual_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [3/7]

CRNA_qual_set_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [4/7]

CRNA_ref_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [5/7]

CRNA_ref_Base::C_Ext::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [6/7]

CTrna_ext_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [7/7]

CTrna_ext_Base::C_Aa::DECLARE_INTERNAL_TYPE_INFO

(

)

DoSelect() [1/2]

void CRNA_ref_Base::C_Ext::DoSelect ( E_Choice  index, CObjectMemoryPool *  pool = 0  )

private

Definition at line 93 of file RNA_ref_.cpp.

References CObject::AddReference().

DoSelect() [2/2]

void CTrna_ext_Base::C_Aa::DoSelect ( E_Choice  index, CObjectMemoryPool *  pool = 0  )

private

Definition at line 62 of file Trna_ext_.cpp.

EType()

static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME() CRNA_ref_Base::EType ( void  )

static

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

Get()

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

inline

Get the member data.

Returns

Reference to the member data.

Definition at line 164 of file RNA_qual_set_.hpp.

References CRNA_qual_set_Base::m_data.

Referenced by CTagPeptideColumn::GetFromFeat().

GetAa()

const CTrna_ext_Base::TAa & CTrna_ext_Base::GetAa ( void  ) const

inline

Get the Aa member data.

Returns

Reference to the member data.

Definition at line 603 of file Trna_ext_.hpp.

References CTrna_ext_Base::CanGetAa(), CTrna_ext_Base::m_Aa, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), get_aa_from_trna(), get_my_feat_type(), get_trna_string(), CWriteUtil::GetTrnaProductName(), s_GetAaAsChar(), s_GetTrnaProduct(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddQualsRna(), CNewCleanup_imp::x_HandleTrnaProductGBQual(), CNewCleanup_imp::x_SeqFeatTRNABC(), and CRNAValidator::x_ValidateTrnaCodons().

GetAnticodon()

const CTrna_ext_Base::TAnticodon & CTrna_ext_Base::GetAnticodon ( void  ) const

inline

Get the Anticodon member data.

Returns

Reference to the member data.

Definition at line 649 of file Trna_ext_.hpp.

References CTrna_ext_Base::CanGetAnticodon(), CTrna_ext_Base::m_Anticodon, and CSerialObject::ThrowUnassigned().

Referenced by CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), CFeatTrim::Apply(), BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), CAntiCodonColumn::GetFromFeat(), CWriteUtil::GetTrnaAntiCodon(), CEditingActionFeatAnticodon::GetValue(), CNewCleanup_imp::RnaFeatBC(), CSequenceUpdater::s_Shift_tRNAAntiCodon(), s_UpdateCodeBreaksAndAnticodons(), TestTrnaAnticodon(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddQualsRna(), CFeatGapInfo::x_AdjustAnticodons(), CFeaturePropagator::x_PropagatetRNA(), CFeatTrim::x_TrimTrnaExt(), CRNAValidator::x_ValidateTrnaCodons(), and CRNAValidator::x_ValidateTrnaData().

GetClass()

const CRNA_gen_Base::TClass & CRNA_gen_Base::GetClass ( void  ) const

inline

Get the Class member data.

Returns

Reference to the member data.

Definition at line 259 of file RNA_gen_.hpp.

References CRNA_gen_Base::CanGetClass(), CRNA_gen_Base::m_Class, and CSerialObject::ThrowUnassigned().

Referenced by CEditObjectSeq_feat::CanClose(), CNcrnaClassColumn::GetFromFeat(), CRNA_gen::IsLegalClass(), CRna_feat_type::Match(), CFindASN1Dlg::ReplaceInFeature(), s_CheckQuals_ncRNA(), IEditingActionFeat::s_GetncRNAClass(), sGetFeatureGeneBiotypeWrapper(), CFastaOstreamEx::x_AddncRNAClassAttribute(), CAutoDefNcRNAClause::x_GetProductName(), CSingleFeatValidator::x_ValidateNonImpFeat(), CGff3Writer::xAssignFeatureAttributeNcrnaClass(), and CGff3Writer::xAssignFeatureAttributeNote().

GetCodon()

const CTrna_ext_Base::TCodon & CTrna_ext_Base::GetCodon ( void  ) const

inline

Get the Codon member data.

Returns

Reference to the member data.

Definition at line 624 of file Trna_ext_.hpp.

References CTrna_ext_Base::m_Codon.

Referenced by CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), get_first_codon_from_trna(), CCodonsRecColumn::GetFromFeat(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), s_ComposeCodonRecognizedStr(), s_IsEmpty(), CCodonsStringListValidator::TransferToWindow(), and CRNAValidator::x_ValidateTrnaCodons().

GetExt()

const CRNA_ref_Base::TExt & CRNA_ref_Base::GetExt ( void  ) const

inline

Get the Ext member data.

Returns

Reference to the member data.

Definition at line 616 of file RNA_ref_.hpp.

References CRNA_ref_Base::CanGetExt(), CRNA_ref_Base::m_Ext, and CSerialObject::ThrowUnassigned().

Referenced by AddMiscRNAFeatures(), CReportTrim::AdjustAndTranslate(), CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), CFixProductNames::apply(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CEditObjectSeq_feat::CanClose(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), get_my_feat_type(), get_trna_string(), CEntrezgene::GetDescription(), CNcrnaClassColumn::GetFromFeat(), CCodonsRecColumn::GetFromFeat(), CAntiCodonColumn::GetFromFeat(), CTagPeptideColumn::GetFromFeat(), CCdsFromGeneMrnaExon::GetNameFromMRNA(), GetRNAname(), CRNA_ref::GetRnaProductName(), GetRnaRef(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), CEditingActionFeatAnticodon::IsSetValue(), CRna_feat_type::Match(), CEditingActionFeatRnaQual::Modify(), CSuspectProductRulesEditor::OnApplyFixes(), CSuspectProductRulesEditor::OnListMatches(), CFindASN1Dlg::ReplaceInFeature(), CEditingActionFeatCodonsRecognized::ResetValue(), CEditingActionFeatAnticodon::ResetValue(), CEditingActionFeatNcRnaClass::ResetValue(), s_CheckQuals_ncRNA(), s_GetmRNAName(), IEditingActionFeat::s_GetncRNAClass(), IEditingActionFeat::s_IsSetncRNAClass(), s_SetProtRef(), s_UpdateCodeBreaksAndAnticodons(), CRNA_ref::SetRnaProductName(), CEditingActionFeatRnaQual::SetValue(), TestTrnaAnticodon(), TestTrnaAnticodonFromLastBioseq(), CValidError_bioseq::ValidateSeqFeatContext(), WeDontNeedToJoinThis(), CFastaOstreamEx::x_AddncRNAClassAttribute(), CFeatureTableReader_Imp::x_AddQualifierToRna(), CFeatGapInfo::x_AdjustAnticodons(), CSequenceUpdater::x_FuseFeatures(), CAutoDefNcRNAClause::x_GetProductName(), CSeqFeatData::x_InitFeatDataInfo(), CAutoDef::x_Is5SList(), CValidError_bioseq::x_IsMicroRNA(), CFeaturePropagator::x_PropagatetRNA(), CModifySeqId::x_UpdateFeat(), CEditObjectSeq_feat::x_UpdatemRNA(), CSingleFeatValidator::x_ValidateNonImpFeat(), CRNAValidator::x_ValidateTrnaCodons(), CRNAValidator::x_ValidateTrnaData(), and CGff3Writer::xAssignFeatureAttributeNote().

GetGen()

const CRNA_ref_Base::C_Ext::TGen & CRNA_ref_Base::C_Ext::GetGen

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 156 of file RNA_ref_.cpp.

Referenced by AddMiscRNAFeatures(), CFixProductNames::apply(), CEditObjectSeq_feat::CanClose(), CRNAPanel::CreateControls(), CNcrnaClassColumn::GetFromFeat(), CTagPeptideColumn::GetFromFeat(), CRNA_ref::GetRnaProductName(), GetRNAProductString(), CRna_feat_type::Match(), CEditingActionFeatRnaQual::Modify(), CFindASN1Dlg::ReplaceInFeature(), s_CheckQuals_ncRNA(), IEditingActionFeat::s_GetncRNAClass(), IEditingActionFeat::s_IsSetncRNAClass(), sGetFeatureGeneBiotypeWrapper(), CFeatureItem::x_AddFTableRnaQuals(), CFastaOstreamEx::x_AddncRNAClassAttribute(), CFeatureItem::x_AddQualsRna(), CAutoDefNcRNAClause::x_GetProductName(), CSingleFeatValidator::x_ValidateNonImpFeat(), CGff3Writer::xAssignFeatureAttributeNcrnaClass(), and CGff3Writer::xAssignFeatureAttributeNote().

GetIupacaa()

CTrna_ext_Base::C_Aa::TIupacaa CTrna_ext_Base::C_Aa::GetIupacaa ( void  ) const

inline

Get the variant data.

Returns

Copy of the variant data.

Definition at line 489 of file Trna_ext_.hpp.

Referenced by s_ConvertTrnaAaToLetter(), s_GetAaAsChar(), s_GetTrnaProduct(), CFeatureItem::x_AddFTableAnticodon(), CNewCleanup_imp::x_SeqFeatTRNABC(), and CRNAValidator::x_ValidateTrnaCodons().

GetName()

const CRNA_ref_Base::C_Ext::TName & CRNA_ref_Base::C_Ext::GetName ( void  ) const

inline

Get the variant data.

Returns

Reference to the data.

Definition at line 484 of file RNA_ref_.hpp.

Referenced by AddMiscRNAFeatures(), CFixProductNames::apply(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CRNAPanel::CreateControls(), CEntrezgene::GetDescription(), CCdsFromGeneMrnaExon::GetNameFromMRNA(), GetRNAname(), CRNA_ref::GetRnaProductName(), GetRNAProductString(), CSuspectProductRulesEditor::OnApplyFixes(), CSuspectProductRulesEditor::OnListMatches(), CFindASN1Dlg::ReplaceInFeature(), s_GetmRNAName(), s_SetProtRef(), CValidError_bioseq::ValidateSeqFeatContext(), WeDontNeedToJoinThis(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddQualsRna(), CSequenceUpdater::x_FuseFeatures(), CAutoDefNcRNAClause::x_GetProductName(), CSeqFeatData::x_InitFeatDataInfo(), CAutoDef::x_Is5SList(), CValidError_bioseq::x_IsMicroRNA(), and CEditObjectSeq_feat::x_UpdatemRNA().

GetNcbi8aa()

CTrna_ext_Base::C_Aa::TNcbi8aa CTrna_ext_Base::C_Aa::GetNcbi8aa ( void  ) const

inline

Get the variant data.

Returns

Copy of the variant data.

Definition at line 543 of file Trna_ext_.hpp.

Referenced by s_ConvertTrnaAaToLetter(), s_GetAaAsChar(), CFeatureItem::x_AddFTableAnticodon(), and CRNAValidator::x_ValidateTrnaCodons().

GetNcbieaa()

CTrna_ext_Base::C_Aa::TNcbieaa CTrna_ext_Base::C_Aa::GetNcbieaa ( void  ) const

inline

Get the variant data.

Returns

Copy of the variant data.

Definition at line 516 of file Trna_ext_.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), get_aa_from_trna(), get_my_feat_type(), get_trna_string(), CWriteUtil::GetTrnaProductName(), s_ConvertTrnaAaToLetter(), s_GetAaAsChar(), s_GetTrnaProduct(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddQualsRna(), CNewCleanup_imp::x_HandleTrnaProductGBQual(), and CRNAValidator::x_ValidateTrnaCodons().

GetNcbistdaa()

CTrna_ext_Base::C_Aa::TNcbistdaa CTrna_ext_Base::C_Aa::GetNcbistdaa ( void  ) const

inline

Get the variant data.

Returns

Copy of the variant data.

Definition at line 570 of file Trna_ext_.hpp.

Referenced by s_ConvertTrnaAaToLetter(), and CFeatureItem::x_AddFTableAnticodon().

GetProduct()

const CRNA_gen_Base::TProduct & CRNA_gen_Base::GetProduct ( void  ) const

inline

Get the Product member data.

Returns

Reference to the member data.

Definition at line 306 of file RNA_gen_.hpp.

References CRNA_gen_Base::CanGetProduct(), CRNA_gen_Base::m_Product, and CSerialObject::ThrowUnassigned().

Referenced by AddMiscRNAFeatures(), CFixProductNames::apply(), CRNAPanel::CreateControls(), CRNA_ref::GetRnaProductName(), GetRNAProductString(), CFindASN1Dlg::ReplaceInFeature(), and CAutoDefNcRNAClause::x_GetProductName().

GetPseudo()

CRNA_ref_Base::TPseudo CRNA_ref_Base::GetPseudo ( void  ) const

inline

Get the Pseudo member data.

Returns

Copy of the member data.

Definition at line 576 of file RNA_ref_.hpp.

References CRNA_ref_Base::CanGetPseudo(), CRNA_ref_Base::m_Pseudo, and CSerialObject::ThrowUnassigned().

Referenced by CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), get_my_feat_type(), and get_trna_string().

GetQual()

const CRNA_qual_Base::TQual & CRNA_qual_Base::GetQual ( void  ) const

inline

Get the Qual member data.

Returns

Reference to the member data.

Definition at line 214 of file RNA_qual_.hpp.

References CRNA_qual_Base::CanGetQual(), CRNA_qual_Base::m_Qual, and CSerialObject::ThrowUnassigned().

GetQuals()

const CRNA_gen_Base::TQuals & CRNA_gen_Base::GetQuals ( void  ) const

inline

Get the Quals member data.

Returns

Reference to the member data.

Definition at line 353 of file RNA_gen_.hpp.

References CRNA_gen_Base::CanGetQuals(), CRNA_gen_Base::m_Quals, and CSerialObject::ThrowUnassigned().

Referenced by CTagPeptideColumn::GetFromFeat(), CFindASN1Dlg::ReplaceInFeature(), and CFeatureItem::x_AddQualsRna().

GetTRNA()

const CRNA_ref_Base::C_Ext::TTRNA & CRNA_ref_Base::C_Ext::GetTRNA

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 134 of file RNA_ref_.cpp.

Referenced by CReportTrim::AdjustAndTranslate(), CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), CRNAPanel::CreateControls(), get_my_feat_type(), get_trna_string(), CCodonsRecColumn::GetFromFeat(), CAntiCodonColumn::GetFromFeat(), GetRnaRef(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), CEditingActionFeatAnticodon::IsSetValue(), CSequenceUpdater::s_Shift_tRNAAntiCodon(), TestTrnaAnticodon(), TestTrnaAnticodonFromLastBioseq(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddQualsRna(), CFeaturePropagator::x_PropagatetRNA(), CModifySeqId::x_UpdateFeat(), CRNAValidator::x_ValidateTrnaCodons(), and CRNAValidator::x_ValidateTrnaData().

GetType()

CRNA_ref_Base::TType CRNA_ref_Base::GetType ( void  ) const

inline

Get the Type member data.

Returns

Copy of the member data.

Definition at line 529 of file RNA_ref_.hpp.

References CRNA_ref_Base::CanGetType(), CRNA_ref_Base::m_Type, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), fta_parse_rrna_feat(), fta_rnas_cds_feat(), get_my_feat_type(), get_trna_string(), GetFeatNameAndLoc(), CCdsFromGeneMrnaExon::GetSuggestedName(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), CEditingActionFeatAnticodon::IsSetValue(), CRna_feat_type::Match(), CSuspectProductRulesEditor::OnApplyFixes(), CSuspectProductRulesEditor::OnListMatches(), CNewCleanup_imp::RnarefBC(), CRNA_ref::SetRnaProductName(), CEditingActionFeatCodonsRecognized::SetValue(), CEditingActionFeatAnticodon::SetValue(), CEditingActionFeatNcRnaClass::SetValue(), CEditingActionFeatProduct::SetValue(), UpdatemRNAProduct(), CValidError_bioseq::ValidateSeqFeatContext(), WeDontNeedToJoinThis(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CFeatureTableReader_Imp::x_AddQualifierToRna(), CSeqFeatData::x_InitFeatDataInfo(), CFeatureGenerator::SImplementation::x_SetExceptText(), CValidError_bioseq::x_ValidateOverlappingRNAFeatures(), CRNAValidator::x_ValidateRnaProductType(), CRNAValidator::x_ValidateTrnaCodons(), CRNAValidator::x_ValidateTrnaData(), CRNAValidator::x_ValidateTrnaOverlap(), CRNAValidator::x_ValidateTrnaType(), and CGff3Writer::xAssignFeatureAttributeNote().

GetVal()

const CRNA_qual_Base::TVal & CRNA_qual_Base::GetVal ( void  ) const

inline

Get the Val member data.

Returns

Reference to the member data.

Definition at line 261 of file RNA_qual_.hpp.

References CRNA_qual_Base::CanGetVal(), CRNA_qual_Base::m_Val, and CSerialObject::ThrowUnassigned().

Referenced by CEditingActionFeatRnaQual::GetValue().

IsGen()

bool CRNA_ref_Base::C_Ext::IsGen ( void  ) const

inline

Check if variant Gen is selected.

Gen type is defined as 'typedef CRNA_gen TGen'.

Returns

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

Definition at line 504 of file RNA_ref_.hpp.

Referenced by AddMiscRNAFeatures(), CFixProductNames::apply(), CEditObjectSeq_feat::CanClose(), CRNAPanel::CreateControls(), CNcrnaClassColumn::GetFromFeat(), CTagPeptideColumn::GetFromFeat(), CRna_feat_type::Match(), CEditingActionFeatRnaQual::Modify(), CFindASN1Dlg::ReplaceInFeature(), CEditingActionFeatNcRnaClass::ResetValue(), s_CheckQuals_ncRNA(), IEditingActionFeat::s_IsSetncRNAClass(), CEditingActionFeatRnaQual::SetValue(), sGetFeatureGeneBiotypeWrapper(), CFeatureItem::x_AddFTableRnaQuals(), CFastaOstreamEx::x_AddncRNAClassAttribute(), CFeatureItem::x_AddQualsRna(), CAutoDefNcRNAClause::x_GetProductName(), CSingleFeatValidator::x_ValidateNonImpFeat(), CGff3Writer::xAssignFeatureAttributeNcrnaClass(), and CGff3Writer::xAssignFeatureAttributeNote().

IsIupacaa()

bool CTrna_ext_Base::C_Aa::IsIupacaa ( void  ) const

inline

Check if variant Iupacaa is selected.

Iupacaa type is defined as 'typedef int TIupacaa'.

Returns

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

Definition at line 483 of file Trna_ext_.hpp.

Referenced by s_GetTrnaProduct(), and CNewCleanup_imp::x_SeqFeatTRNABC().

IsName()

bool CRNA_ref_Base::C_Ext::IsName ( void  ) const

inline

Check if variant Name is selected.

Name type is defined as 'typedef string TName'.

Returns

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

Definition at line 478 of file RNA_ref_.hpp.

Referenced by AddMiscRNAFeatures(), CFixProductNames::apply(), CRNAPanel::CreateControls(), CEntrezgene::GetDescription(), CCdsFromGeneMrnaExon::GetNameFromMRNA(), GetRNAname(), CSuspectProductRulesEditor::OnApplyFixes(), CSuspectProductRulesEditor::OnListMatches(), CFindASN1Dlg::ReplaceInFeature(), s_GetmRNAName(), s_SetProtRef(), CValidError_bioseq::ValidateSeqFeatContext(), WeDontNeedToJoinThis(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddQualsRna(), CSequenceUpdater::x_FuseFeatures(), CAutoDefNcRNAClause::x_GetProductName(), CSeqFeatData::x_InitFeatDataInfo(), CAutoDef::x_Is5SList(), CValidError_bioseq::x_IsMicroRNA(), and CEditObjectSeq_feat::x_UpdatemRNA().

IsNcbi8aa()

bool CTrna_ext_Base::C_Aa::IsNcbi8aa ( void  ) const

inline

Check if variant Ncbi8aa is selected.

Ncbi8aa type is defined as 'typedef int TNcbi8aa'.

Returns

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

Definition at line 537 of file Trna_ext_.hpp.

IsNcbieaa()

bool CTrna_ext_Base::C_Aa::IsNcbieaa ( void  ) const

inline

Check if variant Ncbieaa is selected.

Ncbieaa type is defined as 'typedef int TNcbieaa'.

Returns

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

Definition at line 510 of file Trna_ext_.hpp.

Referenced by get_aa_from_trna(), get_my_feat_type(), get_trna_string(), CWriteUtil::GetTrnaProductName(), s_GetTrnaProduct(), CFeatureItem::x_AddQualsRna(), and CNewCleanup_imp::x_HandleTrnaProductGBQual().

IsNcbistdaa()

bool CTrna_ext_Base::C_Aa::IsNcbistdaa ( void  ) const

inline

Check if variant Ncbistdaa is selected.

Ncbistdaa type is defined as 'typedef int TNcbistdaa'.

Returns

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

Definition at line 564 of file Trna_ext_.hpp.

IsSet()

bool CRNA_qual_set_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< CRNA_qual > > Tdata'

Returns

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

Definition at line 152 of file RNA_qual_set_.hpp.

References CRNA_qual_set_Base::m_set_State.

Referenced by CFindASN1Dlg::ReplaceInFeature(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_ETC().

IsSetAa()

bool CTrna_ext_Base::IsSetAa ( void  ) const

inline

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

Data member Aa is optional; its type is defined as 'typedef C_Aa TAa'

Returns

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

Definition at line 591 of file Trna_ext_.hpp.

References CTrna_ext_Base::m_Aa.

Referenced by BOOST_AUTO_TEST_CASE(), CTrna_ext_Base::CanGetAa(), get_aa_from_trna(), CWriteUtil::GetTrnaProductName(), s_GetTrnaProduct(), s_IsEmpty(), CFeatureItem::x_AddQualsRna(), CNewCleanup_imp::x_HandleTrnaProductGBQual(), CNewCleanup_imp::x_SeqFeatTRNABC(), CNewCleanup_imp::x_tRNACodonEC(), and CRNAValidator::x_ValidateTrnaCodons().

IsSetAnticodon()

bool CTrna_ext_Base::IsSetAnticodon ( void  ) const

inline

location of anticodon Check if a value has been assigned to Anticodon data member.

Data member Anticodon is optional; its type is defined as 'typedef CSeq_loc TAnticodon'

Returns

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

Definition at line 637 of file Trna_ext_.hpp.

References CTrna_ext_Base::m_Anticodon.

Referenced by CReportTrim::AdjustAndTranslate(), CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), BOOST_AUTO_TEST_CASE(), CTrna_ext_Base::CanGetAnticodon(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), GetRnaRef(), CWriteUtil::GetTrnaAntiCodon(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatAnticodon::IsSetValue(), ReverseComplementTrna(), CNewCleanup_imp::RnaFeatBC(), s_IsEmpty(), CSequenceUpdater::s_Shift_tRNAAntiCodon(), s_UpdateCodeBreaksAndAnticodons(), TestTrnaAnticodon(), TestTrnaAnticodonFromLastBioseq(), TrnaAdjustForInsert(), TrnaAdjustForTrim(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddQualsRna(), CFeatGapInfo::x_AdjustAnticodons(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_tRNA_tRNA_ETC(), CFeaturePropagator::x_PropagatetRNA(), CFeatTrim::x_TrimTrnaExt(), CModifySeqId::x_UpdateFeat(), and CRNAValidator::x_ValidateTrnaCodons().

IsSetClass()

bool CRNA_gen_Base::IsSetClass ( void  ) const

inline

for ncRNAs, the class of non-coding RNA: examples: antisense_RNA, guide_RNA, snRNA Check if a value has been assigned to Class data member.

Data member Class is optional; its type is defined as 'typedef string TClass'

Returns

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

Definition at line 247 of file RNA_gen_.hpp.

References CRNA_gen_Base::m_set_State.

Referenced by CEditObjectSeq_feat::CanClose(), CRNA_gen_Base::CanGetClass(), CNcrnaClassColumn::GetFromFeat(), CRNA_gen::IsLegalClass(), CFindASN1Dlg::ReplaceInFeature(), s_CheckQuals_ncRNA(), IEditingActionFeat::s_IsSetncRNAClass(), CRNA_gen_Base::SetClass(), sGetFeatureGeneBiotypeWrapper(), CFastaOstreamEx::x_AddncRNAClassAttribute(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_ETC(), CAutoDefNcRNAClause::x_GetProductName(), CSingleFeatValidator::x_ValidateNonImpFeat(), CGff3Writer::xAssignFeatureAttributeNcrnaClass(), and CGff3Writer::xAssignFeatureAttributeNote().

IsSetCodon()

bool CTrna_ext_Base::IsSetCodon ( void  ) const

inline

codon(s) as in Genetic-code Check if a value has been assigned to Codon data member.

Data member Codon is optional; its type is defined as 'typedef list< int > TCodon'

Returns

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

Definition at line 612 of file Trna_ext_.hpp.

References CTrna_ext_Base::m_set_State.

Referenced by CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), CFlatTrnaCodonsQVal::Format(), get_first_codon_from_trna(), CWriteUtil::GetTrnaCodons(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), s_ComposeCodonRecognizedStr(), s_IsEmpty(), CCodonsStringListValidator::TransferToWindow(), CFeatureItem::x_AddQualsRna(), and CNewCleanup_imp::x_tRNACodonEC().

IsSetExt()

bool CRNA_ref_Base::IsSetExt ( void  ) const

inline

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

Data member Ext is optional; its type is defined as 'typedef C_Ext TExt'

Returns

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

Definition at line 604 of file RNA_ref_.hpp.

References CRNA_ref_Base::m_Ext.

Referenced by AddMiscRNAFeatures(), CReportTrim::AdjustAndTranslate(), CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), CFixProductNames::apply(), CEditObjectSeq_feat::CanClose(), CRNA_ref_Base::CanGetExt(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), CEntrezgene::GetDescription(), CNcrnaClassColumn::GetFromFeat(), CCdsFromGeneMrnaExon::GetNameFromMRNA(), CRNA_ref::GetRnaProductName(), GetRnaRef(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), CEditingActionFeatAnticodon::IsSetValue(), CEditingActionFeatRnaQual::Modify(), CSuspectProductRulesEditor::OnApplyFixes(), CSuspectProductRulesEditor::OnListMatches(), CFindASN1Dlg::ReplaceInFeature(), CEditingActionFeatCodonsRecognized::ResetValue(), CEditingActionFeatAnticodon::ResetValue(), CEditingActionFeatNcRnaClass::ResetValue(), s_CheckQuals_ncRNA(), s_GetmRNAName(), IEditingActionFeat::s_IsSetncRNAClass(), s_SetProtRef(), CSequenceUpdater::s_Shift_tRNAAntiCodon(), s_UpdateCodeBreaksAndAnticodons(), CCleanup::SetMrnaName(), CEditingActionFeatRnaQual::SetValue(), WeDontNeedToJoinThis(), CFastaOstreamEx::x_AddncRNAClassAttribute(), CFeatureTableReader_Imp::x_AddQualifierToRna(), CFeatGapInfo::x_AdjustAnticodons(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_rna(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_ETC(), CSequenceUpdater::x_FuseFeatures(), CAutoDefNcRNAClause::x_GetProductName(), CAutoDef::x_Is5SList(), CValidError_bioseq::x_IsMicroRNA(), CFeaturePropagator::x_PropagatetRNA(), CModifySeqId::x_UpdateFeat(), CEditObjectSeq_feat::x_UpdatemRNA(), CSingleFeatValidator::x_ValidateNonImpFeat(), CRNAValidator::x_ValidateTrnaCodons(), CRNAValidator::x_ValidateTrnaData(), and CGff3Writer::xAssignFeatureAttributeNote().

IsSetProduct()

bool CRNA_gen_Base::IsSetProduct ( void  ) const

inline

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

Data member Product is optional; its type is defined as 'typedef string TProduct'

Returns

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

Definition at line 294 of file RNA_gen_.hpp.

References CRNA_gen_Base::m_set_State.

Referenced by AddMiscRNAFeatures(), CFixProductNames::apply(), CRNA_gen_Base::CanGetProduct(), CRNAPanel::CreateControls(), CFindASN1Dlg::ReplaceInFeature(), CRNA_gen_Base::SetProduct(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_ETC(), and CAutoDefNcRNAClause::x_GetProductName().

IsSetPseudo()

bool CRNA_ref_Base::IsSetPseudo ( void  ) const

inline

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

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

Returns

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

Definition at line 557 of file RNA_ref_.hpp.

References CRNA_ref_Base::m_set_State.

Referenced by CRNA_ref_Base::CanGetPseudo(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), and CRNA_ref_Base::SetPseudo().

IsSetQual()

bool CRNA_qual_Base::IsSetQual ( void  ) const

inline

in a tag (qual), value (val) format Check if a value has been assigned to Qual data member.

Data member Qual is mandatory; its type is defined as 'typedef string TQual'

Returns

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

Definition at line 202 of file RNA_qual_.hpp.

References CRNA_qual_Base::m_set_State.

Referenced by CRNA_qual_Base::CanGetQual(), CRNA_qual_Base::SetQual(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_E_ETC().

IsSetQuals()

bool CRNA_gen_Base::IsSetQuals ( void  ) const

inline

e.g., tag_peptide qualifier for tmRNAs Check if a value has been assigned to Quals data member.

Data member Quals is optional; its type is defined as 'typedef CRNA_qual_set TQuals'

Returns

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

Definition at line 341 of file RNA_gen_.hpp.

References CRNA_gen_Base::m_Quals.

Referenced by CRNA_gen_Base::CanGetQuals(), CEditingActionFeatRnaQual::Modify(), CFindASN1Dlg::ReplaceInFeature(), CFeatureItem::x_AddQualsRna(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_ETC().

IsSetType()

bool CRNA_ref_Base::IsSetType ( void  ) const

inline

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

Data member Type is mandatory; its type is defined as 'typedef EType TType'

Returns

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

Definition at line 510 of file RNA_ref_.hpp.

References CRNA_ref_Base::m_set_State.

Referenced by CRNA_ref_Base::CanGetType(), fta_rnas_cds_feat(), GetFeatNameAndLoc(), CCdsFromGeneMrnaExon::GetSuggestedName(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), CEditingActionFeatAnticodon::IsSetValue(), CSuspectProductRulesEditor::OnApplyFixes(), CSuspectProductRulesEditor::OnListMatches(), CNewCleanup_imp::RnarefBC(), s_FindKeyFromFeatDefType(), CRNA_ref_Base::SetType(), CEditingActionFeatCodonsRecognized::SetValue(), CEditingActionFeatAnticodon::SetValue(), CEditingActionFeatNcRnaClass::SetValue(), CEditingActionFeatProduct::SetValue(), WeDontNeedToJoinThis(), CValidError_bioseq::x_ValidateOverlappingRNAFeatures(), CRNAValidator::x_ValidateRnaProductType(), CRNAValidator::x_ValidateTrnaCodons(), CRNAValidator::x_ValidateTrnaData(), CRNAValidator::x_ValidateTrnaOverlap(), CRNAValidator::x_ValidateTrnaType(), and CGff3Writer::xAssignFeatureAttributeNote().

IsSetVal()

bool CRNA_qual_Base::IsSetVal ( void  ) const

inline

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

Data member Val is mandatory; its type is defined as 'typedef string TVal'

Returns

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

Definition at line 249 of file RNA_qual_.hpp.

References CRNA_qual_Base::m_set_State.

Referenced by CRNA_qual_Base::CanGetVal(), CEditingActionFeatRnaQual::IsSetValue(), CRNA_qual_Base::SetVal(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_E_ETC().

IsTRNA()

bool CRNA_ref_Base::C_Ext::IsTRNA ( void  ) const

inline

Check if variant TRNA is selected.

TRNA type is defined as 'typedef CTrna_ext TTRNA'.

Returns

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

Definition at line 498 of file RNA_ref_.hpp.

Referenced by CReportTrim::AdjustAndTranslate(), CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), CRNAPanel::CreateControls(), get_my_feat_type(), get_trna_string(), CCodonsRecColumn::GetFromFeat(), CAntiCodonColumn::GetFromFeat(), GetRnaRef(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), CEditingActionFeatAnticodon::IsSetValue(), CEditingActionFeatCodonsRecognized::ResetValue(), CEditingActionFeatAnticodon::ResetValue(), CSequenceUpdater::s_Shift_tRNAAntiCodon(), s_UpdateCodeBreaksAndAnticodons(), CFeatureItem::x_AddFTableRnaQuals(), CFeatGapInfo::x_AdjustAnticodons(), CFeaturePropagator::x_PropagatetRNA(), CModifySeqId::x_UpdateFeat(), CRNAValidator::x_ValidateTrnaCodons(), and CRNAValidator::x_ValidateTrnaData().

operator const Tdata &()

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

inline

Conversion operator to 'const Tdata' type.

Definition at line 177 of file RNA_qual_set_.hpp.

operator Tdata &()

CRNA_qual_set_Base::operator CRNA_qual_set_Base::Tdata & ( void  )

inline

Conversion operator to 'Tdata' type.

Definition at line 183 of file RNA_qual_set_.hpp.

operator=() [1/9]

C_Aa& CTrna_ext_Base::C_Aa::operator= ( const C_Aa &  )

private

operator=() [2/9]

C_Ext& CRNA_ref_Base::C_Ext::operator= ( const C_Ext &  )

private

operator=() [3/9]

CRNA_gen_Base& CRNA_gen_Base::operator= ( const CRNA_gen_Base &  )

private

operator=() [4/9]

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

private

operator=() [5/9]

CRNA_qual_Base& CRNA_qual_Base::operator= ( const CRNA_qual_Base &  )

private

operator=() [6/9]

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

private

operator=() [7/9]

CRNA_qual_set_Base& CRNA_qual_set_Base::operator= ( const CRNA_qual_set_Base &  )

private

operator=() [8/9]

CRNA_ref_Base& CRNA_ref_Base::operator= ( const CRNA_ref_Base &  )

private

operator=() [9/9]

CTrna_ext_Base& CTrna_ext_Base::operator= ( const CTrna_ext_Base &  )

private

Reset() [1/7]

void CRNA_gen_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 80 of file RNA_gen_.cpp.

References CRNA_gen_Base::ResetClass(), CRNA_gen_Base::ResetProduct(), and CRNA_gen_Base::ResetQuals().

Reset() [2/7]

void CRNA_qual_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 62 of file RNA_qual_.cpp.

References CRNA_qual_Base::ResetQual(), and CRNA_qual_Base::ResetVal().

Reset() [3/7]

void CRNA_qual_set_Base::Reset

(

void

)

Reset data member.

Definition at line 51 of file RNA_qual_set_.cpp.

References CRNA_qual_set_Base::m_data, and CRNA_qual_set_Base::m_set_State.

Reset() [4/7]

END_ENUM_INFO void CRNA_ref_Base::C_Ext::Reset

(

void

)

Reset the whole object.

Definition at line 71 of file RNA_ref_.cpp.

References CRNA_ref_Base::C_Ext::e_not_set, CRNA_ref_Base::C_Ext::m_choice, and CRNA_ref_Base::C_Ext::ResetSelection().

Reset() [5/7]

void CRNA_ref_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 223 of file RNA_ref_.cpp.

References CRNA_ref_Base::ResetExt(), CRNA_ref_Base::ResetPseudo(), and CRNA_ref_Base::ResetType().

Referenced by CRNA_ref_Base::C_Ext::~C_Ext().

Reset() [6/7]

void CTrna_ext_Base::C_Aa::Reset

(

void

)

Reset the whole object.

Definition at line 51 of file Trna_ext_.cpp.

References CTrna_ext_Base::C_Aa::e_not_set, CTrna_ext_Base::C_Aa::m_choice, and CTrna_ext_Base::C_Aa::ResetSelection().

Reset() [7/7]

void CTrna_ext_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 170 of file Trna_ext_.cpp.

References CTrna_ext_Base::ResetAa(), CTrna_ext_Base::ResetAnticodon(), and CTrna_ext_Base::ResetCodon().

Referenced by CTrna_ext_Base::C_Aa::~C_Aa().

ResetAa()

void CTrna_ext_Base::ResetAa

(

void

)

Reset Aa data member.

Definition at line 130 of file Trna_ext_.cpp.

References CTrna_ext_Base::m_Aa.

Referenced by CTrna_ext_Base::Reset(), s_SetTrnaProduct(), and CFeatureTableReader_Imp::x_ParseTrnaExtString().

ResetAnticodon()

void CTrna_ext_Base::ResetAnticodon

(

void

)

Reset Anticodon data member.

Definition at line 153 of file Trna_ext_.cpp.

References CTrna_ext_Base::m_Anticodon.

Referenced by CTrna_ext_Base::Reset(), s_UpdateCodeBreaksAndAnticodons(), TrnaAdjustForTrim(), CFeatGapInfo::x_AdjustAnticodons(), and CFeatTrim::x_TrimTrnaExt().

ResetClass()

void CRNA_gen_Base::ResetClass

(

void

)

Reset Class data member.

Definition at line 51 of file RNA_gen_.cpp.

References CRNA_gen_Base::m_Class, and CRNA_gen_Base::m_set_State.

Referenced by CRNA_gen_Base::Reset().

ResetCodon()

void CTrna_ext_Base::ResetCodon

(

void

)

Reset Codon data member.

Definition at line 147 of file Trna_ext_.cpp.

References CTrna_ext_Base::m_Codon, and CTrna_ext_Base::m_set_State.

Referenced by CTrna_ext_Base::Reset(), s_SetTrnaProduct(), and CCodonsStringListValidator::TransferFromWindow().

ResetExt()

void CRNA_ref_Base::ResetExt

(

void

)

Reset Ext data member.

Definition at line 206 of file RNA_ref_.cpp.

References CRNA_ref_Base::m_Ext.

Referenced by GetRnaRef(), CRNA_ref_Base::Reset(), and CRNA_ref::SetRnaProductName().

ResetProduct()

void CRNA_gen_Base::ResetProduct

(

void

)

Reset Product data member.

Definition at line 57 of file RNA_gen_.cpp.

References CRNA_gen_Base::m_Product, and CRNA_gen_Base::m_set_State.

Referenced by CRNA_gen_Base::Reset(), and CRNA_ref::SetRnaProductName().

ResetPseudo()

void CRNA_ref_Base::ResetPseudo ( void  )

inline

Reset Pseudo data member.

Definition at line 569 of file RNA_ref_.hpp.

References CRNA_ref_Base::m_Pseudo, and CRNA_ref_Base::m_set_State.

Referenced by CRNA_ref_Base::Reset().

ResetQual()

void CRNA_qual_Base::ResetQual

(

void

)

Reset Qual data member.

Definition at line 50 of file RNA_qual_.cpp.

References CRNA_qual_Base::m_Qual, and CRNA_qual_Base::m_set_State.

Referenced by CRNA_qual_Base::Reset().

ResetQuals()

void CRNA_gen_Base::ResetQuals

(

void

)

Reset Quals data member.

Definition at line 63 of file RNA_gen_.cpp.

References CRNA_gen_Base::m_Quals.

Referenced by CRNA_gen_Base::Reset().

ResetSelection() [1/2]

void CRNA_ref_Base::C_Ext::ResetSelection

(

void

)

Reset the selection (set it to e_not_set).

Definition at line 77 of file RNA_ref_.cpp.

References e_not_set.

Referenced by CRNA_ref_Base::C_Ext::Reset().

ResetSelection() [2/2]

void CTrna_ext_Base::C_Aa::ResetSelection

(

void

)

Reset the selection (set it to e_not_set).

Definition at line 57 of file Trna_ext_.cpp.

References e_not_set.

Referenced by CTrna_ext_Base::C_Aa::Reset().

ResetType()

void CRNA_ref_Base::ResetType ( void  )

inline

Reset Type data member.

Definition at line 522 of file RNA_ref_.hpp.

References CRNA_ref_Base::m_set_State, and CRNA_ref_Base::m_Type.

Referenced by CRNA_ref_Base::Reset().

ResetVal()

void CRNA_qual_Base::ResetVal

(

void

)

Reset Val data member.

Definition at line 56 of file RNA_qual_.cpp.

References CRNA_qual_Base::m_set_State, and CRNA_qual_Base::m_Val.

Referenced by CRNA_qual_Base::Reset().

Select() [1/4]

void CRNA_ref_Base::C_Ext::Select	(	E_Choice	index,
		EResetVariant	reset,
		CObjectMemoryPool *	pool
	)

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

Select() [2/4]

void CTrna_ext_Base::C_Aa::Select	(	E_Choice	index,
		EResetVariant	reset,
		CObjectMemoryPool *	pool
	)

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

Select() [3/4]

void CRNA_ref_Base::C_Ext::Select	(	E_Choice	index,
		EResetVariant	reset = eDoResetVariant
	)

Select the requested variant if needed.

Parameters

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

Select() [4/4]

void CTrna_ext_Base::C_Aa::Select	(	E_Choice	index,
		EResetVariant	reset = eDoResetVariant
	)

Select the requested variant if needed.

Parameters

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

SelectionName() [1/2]

NCBI_NS_STD::string CRNA_ref_Base::C_Ext::SelectionName ( E_Choice  index )

static

Retrieve selection name (for diagnostic purposes).

Parameters

index

One of possible selection states.

Returns

Name string.

Definition at line 118 of file RNA_ref_.cpp.

SelectionName() [2/2]

NCBI_NS_STD::string CTrna_ext_Base::C_Aa::SelectionName ( E_Choice  index )

static

Retrieve selection name (for diagnostic purposes).

Parameters

index

One of possible selection states.

Returns

Name string.

Definition at line 91 of file Trna_ext_.cpp.

Set()

CRNA_qual_set_Base::Tdata & CRNA_qual_set_Base::Set ( void  )

inline

Assign a value to data member.

Returns

Reference to the data value.

Definition at line 170 of file RNA_qual_set_.hpp.

References CRNA_qual_set_Base::m_data, and CRNA_qual_set_Base::m_set_State.

Referenced by GetRnaRef(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_ETC().

SetAa() [1/2]

void CTrna_ext_Base::SetAa

(

CTrna_ext_Base::TAa &

value

)

Assign a value to Aa data member.

Parameters

value

Reference to value.

Definition at line 135 of file Trna_ext_.cpp.

References CTrna_ext_Base::m_Aa, and rapidjson::value.

Referenced by s_SetTrnaProduct(), CFeatureTableReader_Imp::x_AddCodons(), CFeatureTableReader_Imp::x_AddQualifierToRna(), CNewCleanup_imp::x_HandleTrnaProductGBQual(), CFeatureTableReader_Imp::x_ParseTrnaExtString(), and CNewCleanup_imp::x_SeqFeatTRNABC().

SetAa() [2/2]

CTrna_ext_Base::TAa & CTrna_ext_Base::SetAa

(

void

)

Assign a value to Aa data member.

Returns

Reference to the data value.

Definition at line 140 of file Trna_ext_.cpp.

References CTrna_ext_Base::m_Aa.

SetAnticodon() [1/2]

void CTrna_ext_Base::SetAnticodon

(

CTrna_ext_Base::TAnticodon &

value

)

Assign a value to Anticodon data member.

Parameters

value

Reference to value.

Definition at line 158 of file Trna_ext_.cpp.

References CTrna_ext_Base::m_Anticodon, and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), ReverseComplementTrna(), CNewCleanup_imp::RnaFeatBC(), CSequenceUpdater::s_Shift_tRNAAntiCodon(), s_UpdateCodeBreaksAndAnticodons(), TrnaAdjustForInsert(), TrnaAdjustForTrim(), CFeatGapInfo::x_AdjustAnticodons(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_tRNA_tRNA_ETC(), CFeatureTableReader_Imp::x_ParseTrnaExtString(), and CFeatTrim::x_TrimTrnaExt().

SetAnticodon() [2/2]

CTrna_ext_Base::TAnticodon & CTrna_ext_Base::SetAnticodon

(

void

)

Assign a value to Anticodon data member.

Returns

Reference to the data value.

Definition at line 163 of file Trna_ext_.cpp.

References CTrna_ext_Base::m_Anticodon.

SetClass() [1/3]

void CRNA_gen_Base::SetClass ( const TClass &  value )

inline

Assign a value to Class data member.

Parameters

value

Value to assign

Definition at line 268 of file RNA_gen_.hpp.

References CRNA_gen_Base::m_Class, CRNA_gen_Base::m_set_State, and rapidjson::value.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_ETC().

SetClass() [2/3]

void CRNA_gen_Base::SetClass ( CRNA_gen_Base::TClass &&  value )

inline

Definition at line 275 of file RNA_gen_.hpp.

References CRNA_gen_Base::m_Class, CRNA_gen_Base::m_set_State, and rapidjson::value.

SetClass() [3/3]

CRNA_gen_Base::TClass & CRNA_gen_Base::SetClass ( void  )

inline

Assign a value to Class data member.

Returns

Reference to the data value.

Definition at line 282 of file RNA_gen_.hpp.

References CRNA_gen_Base::IsSetClass(), CRNA_gen_Base::m_Class, CRNA_gen_Base::m_set_State, and CSerialObject::UnassignedString().

SetCodon()

CTrna_ext_Base::TCodon & CTrna_ext_Base::SetCodon ( void  )

inline

Assign a value to Codon data member.

Returns

Reference to the data value.

Definition at line 630 of file Trna_ext_.hpp.

References CTrna_ext_Base::m_Codon, and CTrna_ext_Base::m_set_State.

Referenced by CTrna_ext::ParseDegenerateCodon(), s_SetTrnaProduct(), CCodonsStringListValidator::TransferFromWindow(), CFeatureTableReader_Imp::x_AddCodons(), and CNewCleanup_imp::x_tRNACodonEC().

SetExt() [1/2]

void CRNA_ref_Base::SetExt

(

CRNA_ref_Base::TExt &

value

)

Assign a value to Ext data member.

Parameters

value

Reference to value.

Definition at line 211 of file RNA_ref_.cpp.

References CRNA_ref_Base::m_Ext, and rapidjson::value.

Referenced by AddMiscRNA(), CBulkRNAAddPanel::AddOneCommand(), CAlignRNAAddPanel::AddOneCommand(), AddRibosomalRNA(), fta_parse_rrna_feat(), GetRnaRef(), CNewCleanup_imp::RnarefBC(), CFeatureTableReader_Imp::x_AddQualifierToRna(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_rna(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_ETC(), CSequenceUpdater::x_FuseFeatures(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

SetExt() [2/2]

CRNA_ref_Base::TExt & CRNA_ref_Base::SetExt

(

void

)

Assign a value to Ext data member.

Returns

Reference to the data value.

Definition at line 216 of file RNA_ref_.cpp.

References CRNA_ref_Base::m_Ext.

Referenced by CRNA_ref::SetRnaProductName().

SetGen() [1/2]

void CRNA_ref_Base::C_Ext::SetGen

(

TGen &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 168 of file RNA_ref_.cpp.

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

SetGen() [2/2]

CRNA_ref_Base::C_Ext::TGen & CRNA_ref_Base::C_Ext::SetGen

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 162 of file RNA_ref_.cpp.

References eDoNotResetVariant.

Referenced by CNewCleanup_imp::RnarefBC(), CRNA_ref::SetRnaProductName(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_ETC().

SetIupacaa() [1/2]

void CTrna_ext_Base::C_Aa::SetIupacaa ( TIupacaa  value )

inline

Select the variant and set its data.

Parameters

value

Variant data.

Definition at line 503 of file Trna_ext_.hpp.

References eDoNotResetVariant, and rapidjson::value.

SetIupacaa() [2/2]

CTrna_ext_Base::C_Aa::TIupacaa & CTrna_ext_Base::C_Aa::SetIupacaa ( void  )

inline

Select the variant.

Returns

Reference to the variant data.

Definition at line 496 of file Trna_ext_.hpp.

References eDoNotResetVariant.

SetName() [1/2]

void CRNA_ref_Base::C_Ext::SetName

(

const TName &

value

)

Select the variant and set its data.

Parameters

value

Variant data.

Definition at line 128 of file RNA_ref_.cpp.

References eDoNotResetVariant, and rapidjson::value.

SetName() [2/2]

CRNA_ref_Base::C_Ext::TName & CRNA_ref_Base::C_Ext::SetName ( void  )

inline

Select the variant.

Returns

Reference to the variant data.

Definition at line 491 of file RNA_ref_.hpp.

References eDoNotResetVariant.

Referenced by CRNA_ref::SetRnaProductName(), CFeatureTableReader_Imp::x_AddQualifierToRna(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_ETC().

SetNcbi8aa() [1/2]

void CTrna_ext_Base::C_Aa::SetNcbi8aa ( TNcbi8aa  value )

inline

Select the variant and set its data.

Parameters

value

Variant data.

Definition at line 557 of file Trna_ext_.hpp.

References eDoNotResetVariant, and rapidjson::value.

SetNcbi8aa() [2/2]

CTrna_ext_Base::C_Aa::TNcbi8aa & CTrna_ext_Base::C_Aa::SetNcbi8aa ( void  )

inline

Select the variant.

Returns

Reference to the variant data.

Definition at line 550 of file Trna_ext_.hpp.

References eDoNotResetVariant.

SetNcbieaa() [1/2]

void CTrna_ext_Base::C_Aa::SetNcbieaa ( TNcbieaa  value )

inline

Select the variant and set its data.

Parameters

value

Variant data.

Definition at line 530 of file Trna_ext_.hpp.

References eDoNotResetVariant, and rapidjson::value.

SetNcbieaa() [2/2]

CTrna_ext_Base::C_Aa::TNcbieaa & CTrna_ext_Base::C_Aa::SetNcbieaa ( void  )

inline

Select the variant.

Returns

Reference to the variant data.

Definition at line 523 of file Trna_ext_.hpp.

References eDoNotResetVariant.

SetNcbistdaa() [1/2]

void CTrna_ext_Base::C_Aa::SetNcbistdaa ( TNcbistdaa  value )

inline

Select the variant and set its data.

Parameters

value

Variant data.

Definition at line 584 of file Trna_ext_.hpp.

References eDoNotResetVariant, and rapidjson::value.

SetNcbistdaa() [2/2]

CTrna_ext_Base::C_Aa::TNcbistdaa & CTrna_ext_Base::C_Aa::SetNcbistdaa ( void  )

inline

Select the variant.

Returns

Reference to the variant data.

Definition at line 577 of file Trna_ext_.hpp.

References eDoNotResetVariant.

SetProduct() [1/3]

void CRNA_gen_Base::SetProduct ( const TProduct &  value )

inline

Assign a value to Product data member.

Parameters

value

Value to assign

Definition at line 315 of file RNA_gen_.hpp.

References CRNA_gen_Base::m_Product, CRNA_gen_Base::m_set_State, and rapidjson::value.

Referenced by CNewCleanup_imp::RnarefBC(), CRNA_ref::SetRnaProductName(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_ETC(), and CNewCleanup_imp::x_SeqFeatRnaGBQualBC().

SetProduct() [2/3]

void CRNA_gen_Base::SetProduct ( CRNA_gen_Base::TProduct &&  value )

inline

Definition at line 322 of file RNA_gen_.hpp.

References CRNA_gen_Base::m_Product, CRNA_gen_Base::m_set_State, and rapidjson::value.

SetProduct() [3/3]

CRNA_gen_Base::TProduct & CRNA_gen_Base::SetProduct ( void  )

inline

Assign a value to Product data member.

Returns

Reference to the data value.

Definition at line 329 of file RNA_gen_.hpp.

References CRNA_gen_Base::IsSetProduct(), CRNA_gen_Base::m_Product, CRNA_gen_Base::m_set_State, and CSerialObject::UnassignedString().

SetPseudo() [1/2]

void CRNA_ref_Base::SetPseudo ( CRNA_ref_Base::TPseudo  value )

inline

Assign a value to Pseudo data member.

Parameters

value

Value to assign

Definition at line 585 of file RNA_ref_.hpp.

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

SetPseudo() [2/2]

CRNA_ref_Base::TPseudo & CRNA_ref_Base::SetPseudo ( void  )

inline

Assign a value to Pseudo data member.

Returns

Reference to the data value.

Definition at line 592 of file RNA_ref_.hpp.

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

SetQual() [1/3]

void CRNA_qual_Base::SetQual ( const TQual &  value )

inline

Assign a value to Qual data member.

Parameters

value

Value to assign

Definition at line 223 of file RNA_qual_.hpp.

References CRNA_qual_Base::m_Qual, CRNA_qual_Base::m_set_State, and rapidjson::value.

Referenced by GetRnaRef(), s_FixtmRNA(), CEditingActionFeatRnaQual::SetValue(), CtmRNASubPanel::TransferDataFromWindow(), CFeatureTableReader_Imp::x_AddQualifierToRna(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_E_ETC().

SetQual() [2/3]

void CRNA_qual_Base::SetQual ( CRNA_qual_Base::TQual &&  value )

inline

Definition at line 230 of file RNA_qual_.hpp.

References CRNA_qual_Base::m_Qual, CRNA_qual_Base::m_set_State, and rapidjson::value.

SetQual() [3/3]

CRNA_qual_Base::TQual & CRNA_qual_Base::SetQual ( void  )

inline

Assign a value to Qual data member.

Returns

Reference to the data value.

Definition at line 237 of file RNA_qual_.hpp.

References CRNA_qual_Base::IsSetQual(), CRNA_qual_Base::m_Qual, CRNA_qual_Base::m_set_State, and CSerialObject::UnassignedString().

SetQuals() [1/2]

void CRNA_gen_Base::SetQuals

(

CRNA_gen_Base::TQuals &

value

)

Assign a value to Quals data member.

Parameters

value

Reference to value.

Definition at line 68 of file RNA_gen_.cpp.

References CRNA_gen_Base::m_Quals, and rapidjson::value.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_ETC().

SetQuals() [2/2]

CRNA_gen_Base::TQuals & CRNA_gen_Base::SetQuals

(

void

)

Assign a value to Quals data member.

Returns

Reference to the data value.

Definition at line 73 of file RNA_gen_.cpp.

References CRNA_gen_Base::m_Quals.

SetTRNA() [1/2]

void CRNA_ref_Base::C_Ext::SetTRNA

(

TTRNA &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 146 of file RNA_ref_.cpp.

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

SetTRNA() [2/2]

CRNA_ref_Base::C_Ext::TTRNA & CRNA_ref_Base::C_Ext::SetTRNA

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 140 of file RNA_ref_.cpp.

References eDoNotResetVariant.

Referenced by BOOST_AUTO_TEST_CASE(), CSequenceUpdater::s_Shift_tRNAAntiCodon(), CFeatureTableReader_Imp::x_AddQualifierToRna(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_ETC().

SetType() [1/2]

void CRNA_ref_Base::SetType ( CRNA_ref_Base::TType  value )

inline

Assign a value to Type data member.

Parameters

value

Value to assign

Definition at line 538 of file RNA_ref_.hpp.

References CRNA_ref_Base::m_set_State, CRNA_ref_Base::m_Type, and rapidjson::value.

Referenced by AddMiscRNA(), CBulkRNAAddPanel::AddOneCommand(), CAlignRNAAddPanel::AddOneCommand(), AddRibosomalRNA(), AddSpanningSentinelFeat(), GetRnaRef(), CNewCleanup_imp::ImpFeatBC(), CMacroFunction_ApplyRNA::TheFunction(), CFeatureTableReader_Imp::x_SetupSeqFeat(), and CGtfReader::xFeatureSetDataRna().

SetType() [2/2]

CRNA_ref_Base::TType & CRNA_ref_Base::SetType ( void  )

inline

Assign a value to Type data member.

Returns

Reference to the data value.

Definition at line 545 of file RNA_ref_.hpp.

References CRNA_ref_Base::IsSetType(), CRNA_ref_Base::m_set_State, CRNA_ref_Base::m_Type, and CSerialObject::UnassignedByte().

SetVal() [1/3]

void CRNA_qual_Base::SetVal ( const TVal &  value )

inline

Assign a value to Val data member.

Parameters

value

Value to assign

Definition at line 270 of file RNA_qual_.hpp.

References CRNA_qual_Base::m_set_State, CRNA_qual_Base::m_Val, and rapidjson::value.

Referenced by GetRnaRef(), s_FixtmRNA(), CEditingActionFeatRnaQual::SetValue(), CtmRNASubPanel::TransferDataFromWindow(), CFeatureTableReader_Imp::x_AddQualifierToRna(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_E_ETC().

SetVal() [2/3]

void CRNA_qual_Base::SetVal ( CRNA_qual_Base::TVal &&  value )

inline

Definition at line 277 of file RNA_qual_.hpp.

References CRNA_qual_Base::m_set_State, CRNA_qual_Base::m_Val, and rapidjson::value.

SetVal() [3/3]

CRNA_qual_Base::TVal & CRNA_qual_Base::SetVal ( void  )

inline

Assign a value to Val data member.

Returns

Reference to the data value.

Definition at line 284 of file RNA_qual_.hpp.

References CRNA_qual_Base::IsSetVal(), CRNA_qual_Base::m_set_State, CRNA_qual_Base::m_Val, and CSerialObject::UnassignedString().

ThrowInvalidSelection() [1/2]

void CRNA_ref_Base::C_Ext::ThrowInvalidSelection

(

E_Choice

index

)

const

Throw 'InvalidSelection' exception.

Parameters

index

Expected selection.

Definition at line 123 of file RNA_ref_.cpp.

References DIAG_COMPILE_INFO.

ThrowInvalidSelection() [2/2]

void CTrna_ext_Base::C_Aa::ThrowInvalidSelection

(

E_Choice

index

)

const

Throw 'InvalidSelection' exception.

Parameters

index

Expected selection.

Definition at line 96 of file Trna_ext_.cpp.

References DIAG_COMPILE_INFO.

Which() [1/2]

CRNA_ref_Base::C_Ext::E_Choice CRNA_ref_Base::C_Ext::Which ( void  ) const

inline

Which variant is currently selected.

Returns

Choice state enumerator.

Definition at line 449 of file RNA_ref_.hpp.

References CRNA_ref_Base::C_Ext::m_choice.

Referenced by GetRNAProductString(), CNewCleanup_imp::RnarefBC(), CFeatureTableReader_Imp::x_AddQualifierToRna(), CFeatureItem::x_AddQualsRna(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_ETC().

Which() [2/2]

CTrna_ext_Base::C_Aa::E_Choice CTrna_ext_Base::C_Aa::Which ( void  ) const

inline

Which variant is currently selected.

Returns

Choice state enumerator.

Definition at line 454 of file Trna_ext_.hpp.

References CTrna_ext_Base::C_Aa::m_choice.

Referenced by CNewCleanup_imp::RnarefBC(), s_ConvertTrnaAaToLetter(), s_GetAaAsChar(), CFeatureItem::x_AddFTableAnticodon(), and CRNAValidator::x_ValidateTrnaCodons().

~C_Aa()

CTrna_ext_Base::C_Aa::~C_Aa

(

void

)

Definition at line 124 of file Trna_ext_.cpp.

References CTrna_ext_Base::Reset().

~C_Ext()

CRNA_ref_Base::C_Ext::~C_Ext

(

void

)

Definition at line 200 of file RNA_ref_.cpp.

References CRNA_ref_Base::Reset().

~CRNA_gen_Base()

CRNA_gen_Base::~CRNA_gen_Base ( void  )

virtual

Definition at line 106 of file RNA_gen_.cpp.

~CRNA_qual()

CRNA_qual::~CRNA_qual

(

void

)

Definition at line 50 of file RNA_qual.cpp.

~CRNA_qual_Base()

CRNA_qual_Base::~CRNA_qual_Base ( void  )

virtual

Definition at line 86 of file RNA_qual_.cpp.

~CRNA_qual_set()

CRNA_qual_set::~CRNA_qual_set

(

void

)

Definition at line 50 of file RNA_qual_set.cpp.

~CRNA_qual_set_Base()

CRNA_qual_set_Base::~CRNA_qual_set_Base ( void  )

virtual

Definition at line 74 of file RNA_qual_set_.cpp.

~CRNA_ref_Base()

CRNA_ref_Base::~CRNA_ref_Base ( void  )

virtual

Definition at line 250 of file RNA_ref_.cpp.

~CTrna_ext_Base()

CTrna_ext_Base::~CTrna_ext_Base ( void  )

virtual

Definition at line 196 of file Trna_ext_.cpp.

Variable Documentation

union { ... }

union { ... }

m_Aa

CRef< TAa > CTrna_ext_Base::m_Aa

private

Definition at line 439 of file Trna_ext_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CTrna_ext_Base::GetAa(), CTrna_ext_Base::IsSetAa(), CTrna_ext_Base::ResetAa(), and CTrna_ext_Base::SetAa().

m_Anticodon

CRef< TAnticodon > CTrna_ext_Base::m_Anticodon

private

Definition at line 441 of file Trna_ext_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CTrna_ext_Base::GetAnticodon(), CTrna_ext_Base::IsSetAnticodon(), CTrna_ext_Base::ResetAnticodon(), and CTrna_ext_Base::SetAnticodon().

m_choice [1/2]

E_Choice CRNA_ref_Base::C_Ext::m_choice

private

Definition at line 283 of file RNA_ref_.hpp.

Referenced by CRNA_ref_Base::C_Ext::Reset(), and CRNA_ref_Base::C_Ext::Which().

m_choice [2/2]

E_Choice CTrna_ext_Base::C_Aa::m_choice

private

Definition at line 291 of file Trna_ext_.hpp.

Referenced by CTrna_ext_Base::C_Aa::Reset(), and CTrna_ext_Base::C_Aa::Which().

m_Class

string CRNA_gen_Base::m_Class

private

Definition at line 232 of file RNA_gen_.hpp.

Referenced by CRNA_gen_Base::GetClass(), CRNA_gen_Base::ResetClass(), and CRNA_gen_Base::SetClass().

m_Codon

list< int > CTrna_ext_Base::m_Codon

private

Definition at line 440 of file Trna_ext_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CTrna_ext_Base::GetCodon(), CTrna_ext_Base::ResetCodon(), and CTrna_ext_Base::SetCodon().

m_data

list< CRef< CRNA_qual > > CRNA_qual_set_Base::m_data

private

Definition at line 139 of file RNA_qual_set_.hpp.

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

m_Ext

CRef< TExt > CRNA_ref_Base::m_Ext

private

Definition at line 436 of file RNA_ref_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CRNA_ref_Base::GetExt(), CRNA_ref_Base::IsSetExt(), CRNA_ref_Base::ResetExt(), and CRNA_ref_Base::SetExt().

m_Iupacaa [1/2]

TIupacaa CTrna_ext_Base::C_Aa::m_Iupacaa

Definition at line 298 of file Trna_ext_.hpp.

[2/2]

TIupacaa { ... } ::m_Iupacaa

Definition at line 298 of file Trna_ext_.hpp.

m_Ncbi8aa [1/2]

TNcbi8aa CTrna_ext_Base::C_Aa::m_Ncbi8aa

Definition at line 300 of file Trna_ext_.hpp.

[2/2]

TNcbi8aa { ... } ::m_Ncbi8aa

Definition at line 300 of file Trna_ext_.hpp.

[1/2]

TNcbieaa { ... } ::m_Ncbieaa

Definition at line 299 of file Trna_ext_.hpp.

m_Ncbieaa [2/2]

TNcbieaa CTrna_ext_Base::C_Aa::m_Ncbieaa

Definition at line 299 of file Trna_ext_.hpp.

[1/2]

TNcbistdaa { ... } ::m_Ncbistdaa

Definition at line 301 of file Trna_ext_.hpp.

m_Ncbistdaa [2/2]

TNcbistdaa CTrna_ext_Base::C_Aa::m_Ncbistdaa

Definition at line 301 of file Trna_ext_.hpp.

m_object [1/2]

NCBI_NS_NCBI::CSerialObject* CRNA_ref_Base::C_Ext::m_object

Definition at line 291 of file RNA_ref_.hpp.

[2/2]

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

Definition at line 291 of file RNA_ref_.hpp.

m_Product

string CRNA_gen_Base::m_Product

private

Definition at line 233 of file RNA_gen_.hpp.

Referenced by CRNA_gen_Base::GetProduct(), CRNA_gen_Base::ResetProduct(), and CRNA_gen_Base::SetProduct().

m_Pseudo

bool CRNA_ref_Base::m_Pseudo

private

Definition at line 435 of file RNA_ref_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CRNA_ref_Base::GetPseudo(), CRNA_ref_Base::ResetPseudo(), and CRNA_ref_Base::SetPseudo().

m_Qual

string CRNA_qual_Base::m_Qual

private

Definition at line 188 of file RNA_qual_.hpp.

Referenced by CRNA_qual_Base::GetQual(), CRNA_qual_Base::ResetQual(), and CRNA_qual_Base::SetQual().

m_Quals

CRef< TQuals > CRNA_gen_Base::m_Quals

private

Definition at line 234 of file RNA_gen_.hpp.

Referenced by CRNA_gen_Base::GetQuals(), CRNA_gen_Base::IsSetQuals(), CRNA_gen_Base::ResetQuals(), and CRNA_gen_Base::SetQuals().

m_set_State [1/5]

Uint4 CRNA_gen_Base::m_set_State[1]

private

Definition at line 231 of file RNA_gen_.hpp.

Referenced by CRNA_gen_Base::CRNA_gen_Base(), CRNA_gen_Base::IsSetClass(), CRNA_gen_Base::IsSetProduct(), CRNA_gen_Base::ResetClass(), CRNA_gen_Base::ResetProduct(), CRNA_gen_Base::SetClass(), and CRNA_gen_Base::SetProduct().

m_set_State [2/5]

Uint4 CRNA_qual_Base::m_set_State[1]

private

Definition at line 187 of file RNA_qual_.hpp.

Referenced by CRNA_qual_Base::CRNA_qual_Base(), CRNA_qual_Base::IsSetQual(), CRNA_qual_Base::IsSetVal(), CRNA_qual_Base::ResetQual(), CRNA_qual_Base::ResetVal(), CRNA_qual_Base::SetQual(), and CRNA_qual_Base::SetVal().

m_set_State [3/5]

Uint4 CRNA_qual_set_Base::m_set_State[1]

private

Definition at line 138 of file RNA_qual_set_.hpp.

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

m_set_State [4/5]

Uint4 CRNA_ref_Base::m_set_State[1]

private

Definition at line 433 of file RNA_ref_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CRNA_ref_Base::CRNA_ref_Base(), CRNA_ref_Base::IsSetPseudo(), CRNA_ref_Base::IsSetType(), CRNA_ref_Base::ResetPseudo(), CRNA_ref_Base::ResetType(), CRNA_ref_Base::SetPseudo(), and CRNA_ref_Base::SetType().

m_set_State [5/5]

Uint4 CTrna_ext_Base::m_set_State[1]

private

Definition at line 438 of file Trna_ext_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CTrna_ext_Base::CTrna_ext_Base(), CTrna_ext_Base::IsSetCodon(), CTrna_ext_Base::ResetCodon(), and CTrna_ext_Base::SetCodon().

[1/2]

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

Definition at line 290 of file RNA_ref_.hpp.

m_string [2/2]

NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> CRNA_ref_Base::C_Ext::m_string

Definition at line 290 of file RNA_ref_.hpp.

m_Type

EType CRNA_ref_Base::m_Type

private

Definition at line 434 of file RNA_ref_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CRNA_ref_Base::GetType(), CRNA_ref_Base::ResetType(), and CRNA_ref_Base::SetType().

m_Val

string CRNA_qual_Base::m_Val

private

Definition at line 189 of file RNA_qual_.hpp.

Referenced by CRNA_qual_Base::GetVal(), CRNA_qual_Base::ResetVal(), and CRNA_qual_Base::SetVal().

sm_SelectionNames [1/2]

const char *const CRNA_ref_Base::C_Ext::sm_SelectionNames

staticprivate

Initial value:

= {
    "not set",
    "name",
    "tRNA",
    "gen"
}

Definition at line 287 of file RNA_ref_.hpp.

sm_SelectionNames [2/2]

const char *const CTrna_ext_Base::C_Aa::sm_SelectionNames

staticprivate

Initial value:

= {
    "not set",
    "iupacaa",
    "ncbieaa",
    "ncbi8aa",
    "ncbistdaa"
}

Definition at line 295 of file Trna_ext_.hpp.