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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/groupdataspecNCBI__RNA.html below:

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

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 } 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 &) ◆ TAa ◆ TAnticodon ◆ TClass ◆ TCodon ◆ Tdata ◆ TExt ◆ TGen ◆ TIupacaa ◆ TmemberIndex [1/4] ◆ TmemberIndex [2/4] ◆ TmemberIndex [3/4] ◆ TmemberIndex [4/4] ◆ TName ◆ TNcbi8aa ◆ TNcbieaa ◆ TNcbistdaa ◆ Tparent [1/9] ◆ Tparent [2/9] ◆ Tparent [3/9] ◆ Tparent [4/9] ◆ Tparent [5/9] ◆ Tparent [6/9] ◆ Tparent [7/9] ◆ Tparent [8/9] ◆ Tparent [9/9] ◆ TProduct ◆ TPseudo ◆ TQual ◆ TQuals ◆ TTRNA ◆ TType ◆ TVal ◆ E_Choice [1/2]

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]

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]

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]

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] Enumerator e__allMandatory e_class e_product e_quals

Definition at line 94 of file RNA_gen_.hpp.

◆ E_memberIndex [2/4] Enumerator e__allMandatory e_qual e_val

Definition at line 90 of file RNA_qual_.hpp.

◆ E_memberIndex [3/4] Enumerator e__allMandatory e_type e_pseudo e_ext

Definition at line 300 of file RNA_ref_.hpp.

◆ E_memberIndex [4/4] Enumerator e__allMandatory e_aa e_codon e_anticodon

Definition at line 310 of file Trna_ext_.hpp.

◆ EType

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.

◆ C_Aa() [1/2] ◆ C_Aa() [2/2] ◆ C_Ext() [1/2] ◆ C_Ext() [2/2] ◆ 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 ◆ CanGetAnticodon() bool CTrna_ext_Base::CanGetAnticodon ( void ) const inline ◆ CanGetClass() bool CRNA_gen_Base::CanGetClass ( void ) const inline ◆ CanGetCodon() bool CTrna_ext_Base::CanGetCodon ( void ) const inline ◆ 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 ◆ CanGetPseudo() bool CRNA_ref_Base::CanGetPseudo ( void ) const inline ◆ CanGetQual() bool CRNA_qual_Base::CanGetQual ( void ) const inline ◆ CanGetQuals() bool CRNA_gen_Base::CanGetQuals ( void ) const inline ◆ CanGetType() bool CRNA_ref_Base::CanGetType ( void ) const inline ◆ CanGetVal() bool CRNA_qual_Base::CanGetVal ( void ) const inline ◆ 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() [2/2] ◆ CRNA_qual() [1/2] ◆ 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() [2/2] ◆ CRNA_qual_set() [1/2] ◆ 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() [2/2] ◆ CRNA_ref_Base() [1/2] ◆ CRNA_ref_Base() [2/2] ◆ CTrna_ext_Base() [1/2] ◆ CTrna_ext_Base() [2/2] ◆ 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] ◆ DoSelect() [2/2] ◆ EType()

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

◆ Get() ◆ GetAa()

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(), CFlatFileGenerator::GetFTableAnticodonText(), 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()

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(), CFlatFileGenerator::GetFTableAnticodonText(), 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()

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() ◆ GetExt()

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().

◆ GetGen()

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() ◆ GetName()

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() ◆ GetNcbieaa()

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(), CFlatFileGenerator::GetFTableAnticodonText(), CWriteUtil::GetTrnaProductName(), s_ConvertTrnaAaToLetter(), s_GetAaAsChar(), s_GetTrnaProduct(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddQualsRna(), CNewCleanup_imp::x_HandleTrnaProductGBQual(), and CRNAValidator::x_ValidateTrnaCodons().

◆ GetNcbistdaa() ◆ GetProduct() ◆ GetPseudo() ◆ GetQual() ◆ GetQuals() ◆ GetTRNA()

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(), CFlatFileGenerator::GetFTableAnticodonText(), 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()

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().

◆ GetVal() ◆ 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 ◆ 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 ◆ 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 ◆ 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(), CFlatFileGenerator::GetFTableAnticodonText(), 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.

◆ IsSetProduct() bool CRNA_gen_Base::IsSetProduct ( void ) const inline ◆ IsSetPseudo() bool CRNA_ref_Base::IsSetPseudo ( void ) const inline ◆ IsSetQual() bool CRNA_qual_Base::IsSetQual ( void ) const inline ◆ IsSetQuals() bool CRNA_gen_Base::IsSetQuals ( void ) const inline ◆ 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 ◆ 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 &() ◆ operator Tdata &() ◆ operator=() [1/9] ◆ operator=() [2/9] ◆ operator=() [3/9] ◆ operator=() [4/9] ◆ operator=() [5/9] ◆ operator=() [6/9] ◆ operator=() [7/9] ◆ operator=() [8/9] ◆ operator=() [9/9] ◆ Reset() [1/7] void CRNA_gen_Base::Reset ( void ) virtual ◆ Reset() [2/7] void CRNA_qual_Base::Reset ( void ) virtual ◆ Reset() [3/7] void CRNA_qual_set_Base::Reset ( void ) ◆ Reset() [4/7] ◆ Reset() [5/7] void CRNA_ref_Base::Reset ( void ) virtual ◆ Reset() [6/7] void CTrna_ext_Base::C_Aa::Reset ( void ) ◆ Reset() [7/7] void CTrna_ext_Base::Reset ( void ) virtual ◆ ResetAa() void CTrna_ext_Base::ResetAa ( void ) ◆ ResetAnticodon() void CTrna_ext_Base::ResetAnticodon ( void ) ◆ ResetClass() void CRNA_gen_Base::ResetClass ( void ) ◆ ResetCodon() void CTrna_ext_Base::ResetCodon ( void ) ◆ ResetExt() void CRNA_ref_Base::ResetExt ( void ) ◆ ResetProduct() void CRNA_gen_Base::ResetProduct ( void ) ◆ ResetPseudo() void CRNA_ref_Base::ResetPseudo ( void ) inline ◆ ResetQual() void CRNA_qual_Base::ResetQual ( void ) ◆ ResetQuals() void CRNA_gen_Base::ResetQuals ( void ) ◆ ResetSelection() [1/2] void CRNA_ref_Base::C_Ext::ResetSelection ( void ) ◆ ResetSelection() [2/2] void CTrna_ext_Base::C_Aa::ResetSelection ( void ) ◆ ResetType() void CRNA_ref_Base::ResetType ( void ) inline ◆ ResetVal() void CRNA_qual_Base::ResetVal ( void ) ◆ Select() [1/4]

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

◆ Select() [2/4]

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

◆ Select() [3/4]

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]

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]

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]

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() ◆ SetAa() [1/2] ◆ SetAa() [2/2] ◆ SetAnticodon() [1/2]

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(), CFeatureTableReader_Imp::ParseTrnaExtString(), 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(), and CFeatTrim::x_TrimTrnaExt().

◆ SetAnticodon() [2/2] ◆ SetClass() [1/3] ◆ SetClass() [2/3] ◆ SetClass() [3/3] ◆ SetCodon() ◆ SetExt() [1/2]

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] ◆ SetGen() [1/2] void CRNA_ref_Base::C_Ext::SetGen ( TGen & value ) ◆ SetGen() [2/2] ◆ SetIupacaa() [1/2] void CTrna_ext_Base::C_Aa::SetIupacaa ( TIupacaa value ) inline ◆ SetIupacaa() [2/2] ◆ SetName() [1/2] void CRNA_ref_Base::C_Ext::SetName ( const TName & value ) ◆ SetName() [2/2] ◆ SetNcbi8aa() [1/2] void CTrna_ext_Base::C_Aa::SetNcbi8aa ( TNcbi8aa value ) inline ◆ SetNcbi8aa() [2/2] ◆ SetNcbieaa() [1/2] void CTrna_ext_Base::C_Aa::SetNcbieaa ( TNcbieaa value ) inline ◆ SetNcbieaa() [2/2] ◆ SetNcbistdaa() [1/2] void CTrna_ext_Base::C_Aa::SetNcbistdaa ( TNcbistdaa value ) inline ◆ SetNcbistdaa() [2/2] ◆ SetProduct() [1/3] ◆ SetProduct() [2/3] ◆ SetProduct() [3/3] ◆ SetPseudo() [1/2] ◆ SetPseudo() [2/2] ◆ SetQual() [1/3] void CRNA_qual_Base::SetQual ( const TQual & value ) inline ◆ SetQual() [2/3] ◆ SetQual() [3/3] ◆ SetQuals() [1/2] ◆ SetQuals() [2/2] ◆ SetTRNA() [1/2] void CRNA_ref_Base::C_Ext::SetTRNA ( TTRNA & value ) ◆ SetTRNA() [2/2] ◆ SetType() [1/2]

Assign a value to Type data member.

Parameters

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(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

◆ SetType() [2/2] ◆ SetVal() [1/3] void CRNA_qual_Base::SetVal ( const TVal & value ) inline ◆ SetVal() [2/3] ◆ SetVal() [3/3] ◆ ThrowInvalidSelection() [1/2] void CRNA_ref_Base::C_Ext::ThrowInvalidSelection ( E_Choice index ) const ◆ ThrowInvalidSelection() [2/2] void CTrna_ext_Base::C_Aa::ThrowInvalidSelection ( E_Choice index ) const ◆ Which() [1/2] ◆ Which() [2/2] ◆ ~C_Aa() CTrna_ext_Base::C_Aa::~C_Aa ( void ) ◆ ~C_Ext() CRNA_ref_Base::C_Ext::~C_Ext ( void ) ◆ ~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_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.

◆ ◆ ◆ m_Aa ◆ m_Anticodon ◆ m_choice [1/2] ◆ m_choice [2/2] ◆ m_Class ◆ m_Codon list< int > CTrna_ext_Base::m_Codon private ◆ m_data ◆ m_Ext ◆ m_Iupacaa [1/2] ◆ [2/2] ◆ m_Ncbi8aa [1/2] ◆ [2/2] ◆ [1/2] ◆ m_Ncbieaa [2/2] ◆ [1/2] ◆ m_Ncbistdaa [2/2] ◆ 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 ◆ m_Pseudo bool CRNA_ref_Base::m_Pseudo private ◆ m_Qual ◆ m_Quals ◆ m_set_State [1/5] Uint4 CRNA_gen_Base::m_set_State[1] private ◆ m_set_State [2/5] Uint4 CRNA_qual_Base::m_set_State[1] private ◆ m_set_State [3/5] Uint4 CRNA_qual_set_Base::m_set_State[1] private ◆ m_set_State [4/5] Uint4 CRNA_ref_Base::m_set_State[1] private ◆ m_set_State [5/5] Uint4 CTrna_ext_Base::m_set_State[1] private ◆ [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] ◆ m_Type EType CRNA_ref_Base::m_Type private ◆ m_Val ◆ 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.

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