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

Classes

class  CGiimport_id
 CGiimport_id –. More...
 
class  CGiimport_id_Base
 CGiimport_id_Base –. More...
 
class  CPacked_seqint_Base
 CPacked_seqint_Base –. More...
 
class  CPacked_seqpnt_Base
 CPacked_seqpnt_Base –. More...
 
class  CPatent_seq_id_Base
 CPatent_seq_id_Base –. More...
 
class  CPDB_mol_id
 CPDB_mol_id –. More...
 
class  CPDB_mol_id_Base
 NB: unlike 'chain', 'chain-id' has no default name of mol, 4 chars. More...
 
class  CPDB_seq_id_Base
 CPDB_seq_id_Base –. More...
 
class  CSeq_bond_Base
 bond between residues More...
 
class  CSeq_id_Base
 *** Sequence identifiers ******************************** * More...
 
class  CSeq_id_set
 CSeq_id_set –. More...
 
class  CSeq_id_set_Base
 CSeq_id_set_Base –. More...
 
class  CSeq_interval_Base
 CSeq_interval_Base –. More...
 
class  CSeq_loc_Base
 *** Sequence locations ********************************** * More...
 
class  CSeq_loc_equiv_Base
 for a set of equivalent locations More...
 
class  CSeq_loc_mix_Base
 this will hold anything More...
 
class  CSeq_point_Base
 CSeq_point_Base –. More...
 
class  CTextseq_id_Base
 CTextseq_id_Base –. More...
 

Typedefs

typedef CGiimport_id_Base CGiimport_id::Tparent
 
typedef CSerialObject CGiimport_id_Base::Tparent
 
typedef int CGiimport_id_Base::TId
 
typedef string CGiimport_id_Base::TDb
 
typedef string CGiimport_id_Base::TRelease
 
typedef Tparent::CMemberIndex< E_memberIndex, 4 > CGiimport_id_Base::TmemberIndex
 
typedef CSerialObject CPacked_seqint_Base::Tparent
 
typedef list< CRef< CSeq_interval > > CPacked_seqint_Base::Tdata
 
typedef CSerialObject CPacked_seqpnt_Base::Tparent
 
typedef ENa_strand CPacked_seqpnt_Base::TStrand
 
typedef CSeq_id CPacked_seqpnt_Base::TId
 
typedef CInt_fuzz CPacked_seqpnt_Base::TFuzz
 
typedef vector< TSeqPosCPacked_seqpnt_Base::TPoints
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > CPacked_seqpnt_Base::TmemberIndex
 
typedef CSerialObject CPatent_seq_id_Base::Tparent
 
typedef int CPatent_seq_id_Base::TSeqid
 
typedef CId_pat CPatent_seq_id_Base::TCit
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CPatent_seq_id_Base::TmemberIndex
 
typedef CPDB_mol_id_Base CPDB_mol_id::Tparent
 
typedef CStringAliasBase< stringCPDB_mol_id_Base::Tparent
 
typedef CSerialObject CPDB_seq_id_Base::Tparent
 
typedef CPDB_mol_id CPDB_seq_id_Base::TMol
 
typedef int CPDB_seq_id_Base::TChain
 
typedef CDate CPDB_seq_id_Base::TRel
 
typedef string CPDB_seq_id_Base::TChain_id
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > CPDB_seq_id_Base::TmemberIndex
 
typedef CSerialObject CSeq_bond_Base::Tparent
 
typedef CSeq_point CSeq_bond_Base::TA
 
typedef CSeq_point CSeq_bond_Base::TB
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CSeq_bond_Base::TmemberIndex
 
typedef CSerialObject CSeq_id_Base::Tparent
 
typedef CObject_id CSeq_id_Base::TLocal
 
typedef int CSeq_id_Base::TGibbsq
 
typedef int CSeq_id_Base::TGibbmt
 
typedef CGiimport_id CSeq_id_Base::TGiim
 
typedef CTextseq_id CSeq_id_Base::TGenbank
 
typedef CTextseq_id CSeq_id_Base::TEmbl
 
typedef CTextseq_id CSeq_id_Base::TPir
 
typedef CTextseq_id CSeq_id_Base::TSwissprot
 
typedef CPatent_seq_id CSeq_id_Base::TPatent
 
typedef CTextseq_id CSeq_id_Base::TOther
 
typedef CDbtag CSeq_id_Base::TGeneral
 
typedef NCBI_NS_NCBI::TGi CSeq_id_Base::TGi
 
typedef CTextseq_id CSeq_id_Base::TDdbj
 
typedef CTextseq_id CSeq_id_Base::TPrf
 
typedef CPDB_seq_id CSeq_id_Base::TPdb
 
typedef CTextseq_id CSeq_id_Base::TTpg
 
typedef CTextseq_id CSeq_id_Base::TTpe
 
typedef CTextseq_id CSeq_id_Base::TTpd
 
typedef CTextseq_id CSeq_id_Base::TGpipe
 
typedef CTextseq_id CSeq_id_Base::TNamed_annot_track
 
typedef CSeq_id_set_Base CSeq_id_set::Tparent
 
typedef CSerialObject CSeq_id_set_Base::Tparent
 
typedef list< CRef< CSeq_id > > CSeq_id_set_Base::Tdata
 
typedef CSerialObject CSeq_interval_Base::Tparent
 
typedef TSeqPos CSeq_interval_Base::TFrom
 
typedef TSeqPos CSeq_interval_Base::TTo
 
typedef ENa_strand CSeq_interval_Base::TStrand
 
typedef CSeq_id CSeq_interval_Base::TId
 
typedef CInt_fuzz CSeq_interval_Base::TFuzz_from
 
typedef CInt_fuzz CSeq_interval_Base::TFuzz_to
 
typedef Tparent::CMemberIndex< E_memberIndex, 7 > CSeq_interval_Base::TmemberIndex
 
typedef CSerialObject CSeq_loc_Base::Tparent
 
typedef CSeq_id CSeq_loc_Base::TEmpty
 
typedef CSeq_id CSeq_loc_Base::TWhole
 
typedef CSeq_interval CSeq_loc_Base::TInt
 
typedef CPacked_seqint CSeq_loc_Base::TPacked_int
 
typedef CSeq_point CSeq_loc_Base::TPnt
 
typedef CPacked_seqpnt CSeq_loc_Base::TPacked_pnt
 
typedef CSeq_loc_mix CSeq_loc_Base::TMix
 
typedef CSeq_loc_equiv CSeq_loc_Base::TEquiv
 
typedef CSeq_bond CSeq_loc_Base::TBond
 
typedef CFeat_id CSeq_loc_Base::TFeat
 
typedef CSerialObject CSeq_loc_equiv_Base::Tparent
 
typedef list< CRef< CSeq_loc > > CSeq_loc_equiv_Base::Tdata
 
typedef CSerialObject CSeq_loc_mix_Base::Tparent
 
typedef list< CRef< CSeq_loc > > CSeq_loc_mix_Base::Tdata
 
typedef CSerialObject CSeq_point_Base::Tparent
 
typedef TSeqPos CSeq_point_Base::TPoint
 
typedef ENa_strand CSeq_point_Base::TStrand
 
typedef CSeq_id CSeq_point_Base::TId
 
typedef CInt_fuzz CSeq_point_Base::TFuzz
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > CSeq_point_Base::TmemberIndex
 
typedef CSerialObject CTextseq_id_Base::Tparent
 
typedef string CTextseq_id_Base::TName
 
typedef string CTextseq_id_Base::TAccession
 
typedef string CTextseq_id_Base::TRelease
 
typedef int CTextseq_id_Base::TVersion
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > CTextseq_id_Base::TmemberIndex
 

Enumerations

enum class  CGiimport_id_Base::E_memberIndex { CGiimport_id_Base::e__allMandatory = 0 , CGiimport_id_Base::e_id , CGiimport_id_Base::e_db , CGiimport_id_Base::e_release }
 
enum  ENa_strand {
  eNa_strand_unknown = 0 , eNa_strand_plus = 1 , eNa_strand_minus = 2 , eNa_strand_both = 3 ,
  eNa_strand_both_rev = 4 , eNa_strand_other = 255
}
 strand of nucleic acid More...
 
enum class  CPacked_seqpnt_Base::E_memberIndex {
  CPacked_seqpnt_Base::e__allMandatory = 0 , CPacked_seqpnt_Base::e_strand , CPacked_seqpnt_Base::e_id , CPacked_seqpnt_Base::e_fuzz ,
  CPacked_seqpnt_Base::e_points
}
 
enum class  CPatent_seq_id_Base::E_memberIndex { CPatent_seq_id_Base::e__allMandatory = 0 , CPatent_seq_id_Base::e_seqid , CPatent_seq_id_Base::e_cit }
 
enum class  CPDB_seq_id_Base::E_memberIndex {
  CPDB_seq_id_Base::e__allMandatory = 0 , CPDB_seq_id_Base::e_mol , CPDB_seq_id_Base::e_chain , CPDB_seq_id_Base::e_rel ,
  CPDB_seq_id_Base::e_chain_id
}
 
enum class  CSeq_bond_Base::E_memberIndex { CSeq_bond_Base::e__allMandatory = 0 , CSeq_bond_Base::e_a , CSeq_bond_Base::e_b }
 
enum  CSeq_id_Base::E_Choice {
  CSeq_id_Base::e_not_set = 0 , CSeq_id_Base::e_Local , CSeq_id_Base::e_Gibbsq , CSeq_id_Base::e_Gibbmt ,
  CSeq_id_Base::e_Giim , CSeq_id_Base::e_Genbank , CSeq_id_Base::e_Embl , CSeq_id_Base::e_Pir ,
  CSeq_id_Base::e_Swissprot , CSeq_id_Base::e_Patent , CSeq_id_Base::e_Other , CSeq_id_Base::e_General ,
  CSeq_id_Base::e_Gi , CSeq_id_Base::e_Ddbj , CSeq_id_Base::e_Prf , CSeq_id_Base::e_Pdb ,
  CSeq_id_Base::e_Tpg , CSeq_id_Base::e_Tpe , CSeq_id_Base::e_Tpd , CSeq_id_Base::e_Gpipe ,
  CSeq_id_Base::e_Named_annot_track
}
 Choice variants. More...
 
enum  CSeq_id_Base::E_ChoiceStopper { CSeq_id_Base::e_MaxChoice = 21 }
 Maximum+1 value of the choice variant enumerator. More...
 
enum class  CSeq_interval_Base::E_memberIndex {
  CSeq_interval_Base::e__allMandatory = 0 , CSeq_interval_Base::e_from , CSeq_interval_Base::e_to , CSeq_interval_Base::e_strand ,
  CSeq_interval_Base::e_id , CSeq_interval_Base::e_fuzz_from , CSeq_interval_Base::e_fuzz_to
}
 
enum  CSeq_loc_Base::E_Choice {
  CSeq_loc_Base::e_not_set = 0 , CSeq_loc_Base::e_Null , CSeq_loc_Base::e_Empty , CSeq_loc_Base::e_Whole ,
  CSeq_loc_Base::e_Int , CSeq_loc_Base::e_Packed_int , CSeq_loc_Base::e_Pnt , CSeq_loc_Base::e_Packed_pnt ,
  CSeq_loc_Base::e_Mix , CSeq_loc_Base::e_Equiv , CSeq_loc_Base::e_Bond , CSeq_loc_Base::e_Feat
}
 Choice variants. More...
 
enum  CSeq_loc_Base::E_ChoiceStopper { CSeq_loc_Base::e_MaxChoice = 12 }
 Maximum+1 value of the choice variant enumerator. More...
 
enum class  CSeq_point_Base::E_memberIndex {
  CSeq_point_Base::e__allMandatory = 0 , CSeq_point_Base::e_point , CSeq_point_Base::e_strand , CSeq_point_Base::e_id ,
  CSeq_point_Base::e_fuzz
}
 
enum class  CTextseq_id_Base::E_memberIndex {
  CTextseq_id_Base::e__allMandatory = 0 , CTextseq_id_Base::e_name , CTextseq_id_Base::e_accession , CTextseq_id_Base::e_release ,
  CTextseq_id_Base::e_version
}
 

Functions

 CGiimport_id::CGiimport_id (void)
 
 CGiimport_id::~CGiimport_id (void)
 
 CGiimport_id::CGiimport_id (const CGiimport_id &value)
 
CGiimport_idCGiimport_id::operator= (const CGiimport_id &value)
 
 CGiimport_id_Base::CGiimport_id_Base (void)
 
virtual CGiimport_id_Base::~CGiimport_id_Base (void)
 
 CGiimport_id_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CGiimport_id_Base::IsSetId (void) const
 the id to use here Check if a value has been assigned to Id data member. More...
 
bool CGiimport_id_Base::CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void CGiimport_id_Base::ResetId (void)
 Reset Id data member. More...
 
TId CGiimport_id_Base::GetId (void) const
 Get the Id member data. More...
 
void CGiimport_id_Base::SetId (TId value)
 Assign a value to Id data member. More...
 
TIdCGiimport_id_Base::SetId (void)
 Assign a value to Id data member. More...
 
bool CGiimport_id_Base::IsSetDb (void) const
 dbase used in Check if a value has been assigned to Db data member. More...
 
bool CGiimport_id_Base::CanGetDb (void) const
 Check if it is safe to call GetDb method. More...
 
void CGiimport_id_Base::ResetDb (void)
 Reset Db data member. More...
 
const TDbCGiimport_id_Base::GetDb (void) const
 Get the Db member data. More...
 
void CGiimport_id_Base::SetDb (const TDb &value)
 Assign a value to Db data member. More...
 
void CGiimport_id_Base::SetDb (TDb &&value)
 
TDbCGiimport_id_Base::SetDb (void)
 Assign a value to Db data member. More...
 
bool CGiimport_id_Base::IsSetRelease (void) const
 the release Check if a value has been assigned to Release data member. More...
 
bool CGiimport_id_Base::CanGetRelease (void) const
 Check if it is safe to call GetRelease method. More...
 
void CGiimport_id_Base::ResetRelease (void)
 Reset Release data member. More...
 
const TReleaseCGiimport_id_Base::GetRelease (void) const
 Get the Release member data. More...
 
void CGiimport_id_Base::SetRelease (const TRelease &value)
 Assign a value to Release data member. More...
 
void CGiimport_id_Base::SetRelease (TRelease &&value)
 
TReleaseCGiimport_id_Base::SetRelease (void)
 Assign a value to Release data member. More...
 
virtual void CGiimport_id_Base::Reset (void)
 Reset the whole object. More...
 
 CGiimport_id_Base::CGiimport_id_Base (const CGiimport_id_Base &)
 
CGiimport_id_BaseCGiimport_id_Base::operator= (const CGiimport_id_Base &)
 
 CPacked_seqint_Base::CPacked_seqint_Base (void)
 
virtual CPacked_seqint_Base::~CPacked_seqint_Base (void)
 
 CPacked_seqint_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPacked_seqint_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CPacked_seqint_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CPacked_seqint_Base::Reset (void)
 Reset data member. More...
 
const TdataCPacked_seqint_Base::Get (void) const
 Get the member data. More...
 
TdataCPacked_seqint_Base::Set (void)
 Assign a value to data member. More...
 
 CPacked_seqint_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CPacked_seqint_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CPacked_seqint_Base::CPacked_seqint_Base (const CPacked_seqint_Base &)
 
CPacked_seqint_BaseCPacked_seqint_Base::operator= (const CPacked_seqint_Base &)
 
 CPacked_seqpnt_Base::CPacked_seqpnt_Base (void)
 
virtual CPacked_seqpnt_Base::~CPacked_seqpnt_Base (void)
 
 CPacked_seqpnt_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPacked_seqpnt_Base::IsSetStrand (void) const
 Check if a value has been assigned to Strand data member. More...
 
bool CPacked_seqpnt_Base::CanGetStrand (void) const
 Check if it is safe to call GetStrand method. More...
 
void CPacked_seqpnt_Base::ResetStrand (void)
 Reset Strand data member. More...
 
TStrand CPacked_seqpnt_Base::GetStrand (void) const
 Get the Strand member data. More...
 
void CPacked_seqpnt_Base::SetStrand (TStrand value)
 Assign a value to Strand data member. More...
 
TStrandCPacked_seqpnt_Base::SetStrand (void)
 Assign a value to Strand data member. More...
 
bool CPacked_seqpnt_Base::IsSetId (void) const
 Check if a value has been assigned to Id data member. More...
 
bool CPacked_seqpnt_Base::CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void CPacked_seqpnt_Base::ResetId (void)
 Reset Id data member. More...
 
const TIdCPacked_seqpnt_Base::GetId (void) const
 Get the Id member data. More...
 
void CPacked_seqpnt_Base::SetId (TId &value)
 Assign a value to Id data member. More...
 
TIdCPacked_seqpnt_Base::SetId (void)
 Assign a value to Id data member. More...
 
bool CPacked_seqpnt_Base::IsSetFuzz (void) const
 Check if a value has been assigned to Fuzz data member. More...
 
bool CPacked_seqpnt_Base::CanGetFuzz (void) const
 Check if it is safe to call GetFuzz method. More...
 
void CPacked_seqpnt_Base::ResetFuzz (void)
 Reset Fuzz data member. More...
 
const TFuzzCPacked_seqpnt_Base::GetFuzz (void) const
 Get the Fuzz member data. More...
 
void CPacked_seqpnt_Base::SetFuzz (TFuzz &value)
 Assign a value to Fuzz data member. More...
 
TFuzzCPacked_seqpnt_Base::SetFuzz (void)
 Assign a value to Fuzz data member. More...
 
bool CPacked_seqpnt_Base::IsSetPoints (void) const
 Check if a value has been assigned to Points data member. More...
 
bool CPacked_seqpnt_Base::CanGetPoints (void) const
 Check if it is safe to call GetPoints method. More...
 
void CPacked_seqpnt_Base::ResetPoints (void)
 Reset Points data member. More...
 
const TPointsCPacked_seqpnt_Base::GetPoints (void) const
 Get the Points member data. More...
 
TPointsCPacked_seqpnt_Base::SetPoints (void)
 Assign a value to Points data member. More...
 
virtual void CPacked_seqpnt_Base::Reset (void)
 Reset the whole object. More...
 
 CPacked_seqpnt_Base::CPacked_seqpnt_Base (const CPacked_seqpnt_Base &)
 
CPacked_seqpnt_BaseCPacked_seqpnt_Base::operator= (const CPacked_seqpnt_Base &)
 
 CPatent_seq_id_Base::CPatent_seq_id_Base (void)
 
virtual CPatent_seq_id_Base::~CPatent_seq_id_Base (void)
 
 CPatent_seq_id_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPatent_seq_id_Base::IsSetSeqid (void) const
 number of sequence in patent Check if a value has been assigned to Seqid data member. More...
 
bool CPatent_seq_id_Base::CanGetSeqid (void) const
 Check if it is safe to call GetSeqid method. More...
 
void CPatent_seq_id_Base::ResetSeqid (void)
 Reset Seqid data member. More...
 
TSeqid CPatent_seq_id_Base::GetSeqid (void) const
 Get the Seqid member data. More...
 
void CPatent_seq_id_Base::SetSeqid (TSeqid value)
 Assign a value to Seqid data member. More...
 
TSeqidCPatent_seq_id_Base::SetSeqid (void)
 Assign a value to Seqid data member. More...
 
bool CPatent_seq_id_Base::IsSetCit (void) const
 patent citation Check if a value has been assigned to Cit data member. More...
 
bool CPatent_seq_id_Base::CanGetCit (void) const
 Check if it is safe to call GetCit method. More...
 
void CPatent_seq_id_Base::ResetCit (void)
 Reset Cit data member. More...
 
const TCitCPatent_seq_id_Base::GetCit (void) const
 Get the Cit member data. More...
 
void CPatent_seq_id_Base::SetCit (TCit &value)
 Assign a value to Cit data member. More...
 
TCitCPatent_seq_id_Base::SetCit (void)
 Assign a value to Cit data member. More...
 
virtual void CPatent_seq_id_Base::Reset (void)
 Reset the whole object. More...
 
 CPatent_seq_id_Base::CPatent_seq_id_Base (const CPatent_seq_id_Base &)
 
CPatent_seq_id_BaseCPatent_seq_id_Base::operator= (const CPatent_seq_id_Base &)
 
 CPDB_mol_id::CPDB_mol_id (void)
 
 CPDB_mol_id::CPDB_mol_id (const std::string &value)
 Explicit constructor from the primitive type. More...
 
 CPDB_mol_id_Base::CPDB_mol_id_Base (void)
 
 CPDB_mol_id_Base::DECLARE_STD_ALIAS_TYPE_INFO ()
 
 CPDB_mol_id_Base::CPDB_mol_id_Base (const string &data)
 
NCBI_NS_NCBI::CNcbiOstreamoperator<< (NCBI_NS_NCBI::CNcbiOstream &str, const CPDB_mol_id_Base &obj)
 
NCBI_NS_NCBI::CNcbiIstreamoperator>> (NCBI_NS_NCBI::CNcbiIstream &str, CPDB_mol_id_Base &obj)
 
 CPDB_seq_id_Base::CPDB_seq_id_Base (void)
 
virtual CPDB_seq_id_Base::~CPDB_seq_id_Base (void)
 
 CPDB_seq_id_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPDB_seq_id_Base::IsSetMol (void) const
 the molecule name Check if a value has been assigned to Mol data member. More...
 
bool CPDB_seq_id_Base::CanGetMol (void) const
 Check if it is safe to call GetMol method. More...
 
void CPDB_seq_id_Base::ResetMol (void)
 Reset Mol data member. More...
 
const TMolCPDB_seq_id_Base::GetMol (void) const
 Get the Mol member data. More...
 
void CPDB_seq_id_Base::SetMol (const TMol &value)
 Assign a value to Mol data member. More...
 
TMolCPDB_seq_id_Base::SetMol (void)
 Assign a value to Mol data member. More...
 
bool CPDB_seq_id_Base::IsSetChain (void) const
 Deprecated: 'chain' can't support multiple character PDB chain identifiers (introduced in 2015). More...
 
bool CPDB_seq_id_Base::CanGetChain (void) const
 Check if it is safe to call GetChain method. More...
 
void CPDB_seq_id_Base::ResetChain (void)
 Reset Chain data member. More...
 
void CPDB_seq_id_Base::SetDefaultChain (void)
 Assign default value to Chain data member. More...
 
TChain CPDB_seq_id_Base::GetChain (void) const
 Get the Chain member data. More...
 
void CPDB_seq_id_Base::SetChain (TChain value)
 Assign a value to Chain data member. More...
 
TChainCPDB_seq_id_Base::SetChain (void)
 Assign a value to Chain data member. More...
 
bool CPDB_seq_id_Base::IsSetRel (void) const
 release date, month and year Check if a value has been assigned to Rel data member. More...
 
bool CPDB_seq_id_Base::CanGetRel (void) const
 Check if it is safe to call GetRel method. More...
 
void CPDB_seq_id_Base::ResetRel (void)
 Reset Rel data member. More...
 
const TRelCPDB_seq_id_Base::GetRel (void) const
 Get the Rel member data. More...
 
void CPDB_seq_id_Base::SetRel (TRel &value)
 Assign a value to Rel data member. More...
 
TRelCPDB_seq_id_Base::SetRel (void)
 Assign a value to Rel data member. More...
 
bool CPDB_seq_id_Base::IsSetChain_id (void) const
 chain identifier; length-independent generalization of 'chain' Check if a value has been assigned to Chain_id data member. More...
 
bool CPDB_seq_id_Base::CanGetChain_id (void) const
 Check if it is safe to call GetChain_id method. More...
 
void CPDB_seq_id_Base::ResetChain_id (void)
 Reset Chain_id data member. More...
 
const TChain_idCPDB_seq_id_Base::GetChain_id (void) const
 Get the Chain_id member data. More...
 
void CPDB_seq_id_Base::SetChain_id (const TChain_id &value)
 Assign a value to Chain_id data member. More...
 
void CPDB_seq_id_Base::SetChain_id (TChain_id &&value)
 
TChain_idCPDB_seq_id_Base::SetChain_id (void)
 Assign a value to Chain_id data member. More...
 
virtual void CPDB_seq_id_Base::Reset (void)
 Reset the whole object. More...
 
 CPDB_seq_id_Base::CPDB_seq_id_Base (const CPDB_seq_id_Base &)
 
CPDB_seq_id_BaseCPDB_seq_id_Base::operator= (const CPDB_seq_id_Base &)
 
 CSeq_bond_Base::CSeq_bond_Base (void)
 
virtual CSeq_bond_Base::~CSeq_bond_Base (void)
 
 CSeq_bond_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSeq_bond_Base::IsSetA (void) const
 connection to a least one residue Check if a value has been assigned to A data member. More...
 
bool CSeq_bond_Base::CanGetA (void) const
 Check if it is safe to call GetA method. More...
 
void CSeq_bond_Base::ResetA (void)
 Reset A data member. More...
 
const TACSeq_bond_Base::GetA (void) const
 Get the A member data. More...
 
void CSeq_bond_Base::SetA (TA &value)
 Assign a value to A data member. More...
 
TACSeq_bond_Base::SetA (void)
 Assign a value to A data member. More...
 
bool CSeq_bond_Base::IsSetB (void) const
 other end may not be available Check if a value has been assigned to B data member. More...
 
bool CSeq_bond_Base::CanGetB (void) const
 Check if it is safe to call GetB method. More...
 
void CSeq_bond_Base::ResetB (void)
 Reset B data member. More...
 
const TBCSeq_bond_Base::GetB (void) const
 Get the B member data. More...
 
void CSeq_bond_Base::SetB (TB &value)
 Assign a value to B data member. More...
 
TBCSeq_bond_Base::SetB (void)
 Assign a value to B data member. More...
 
virtual void CSeq_bond_Base::Reset (void)
 Reset the whole object. More...
 
 CSeq_bond_Base::CSeq_bond_Base (const CSeq_bond_Base &)
 
CSeq_bond_BaseCSeq_bond_Base::operator= (const CSeq_bond_Base &)
 
 CSeq_id_Base::CSeq_id_Base (void)
 
virtual CSeq_id_Base::~CSeq_id_Base (void)
 
 CSeq_id_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
virtual void CSeq_id_Base::Reset (void)
 Reset the whole object. More...
 
virtual void CSeq_id_Base::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CSeq_id_Base::Which (void) const
 Which variant is currently selected. More...
 
void CSeq_id_Base::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CSeq_id_Base::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CSeq_id_Base::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CSeq_id_Base::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CSeq_id_Base::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CSeq_id_Base::IsLocal (void) const
 Check if variant Local is selected. More...
 
const TLocalCSeq_id_Base::GetLocal (void) const
 Get the variant data. More...
 
TLocalCSeq_id_Base::SetLocal (void)
 Select the variant. More...
 
void CSeq_id_Base::SetLocal (TLocal &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsGibbsq (void) const
 Check if variant Gibbsq is selected. More...
 
TGibbsq CSeq_id_Base::GetGibbsq (void) const
 Get the variant data. More...
 
TGibbsqCSeq_id_Base::SetGibbsq (void)
 Select the variant. More...
 
void CSeq_id_Base::SetGibbsq (TGibbsq value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsGibbmt (void) const
 Check if variant Gibbmt is selected. More...
 
TGibbmt CSeq_id_Base::GetGibbmt (void) const
 Get the variant data. More...
 
TGibbmtCSeq_id_Base::SetGibbmt (void)
 Select the variant. More...
 
void CSeq_id_Base::SetGibbmt (TGibbmt value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsGiim (void) const
 Check if variant Giim is selected. More...
 
const TGiimCSeq_id_Base::GetGiim (void) const
 Get the variant data. More...
 
TGiimCSeq_id_Base::SetGiim (void)
 Select the variant. More...
 
void CSeq_id_Base::SetGiim (TGiim &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsGenbank (void) const
 Check if variant Genbank is selected. More...
 
const TGenbankCSeq_id_Base::GetGenbank (void) const
 Get the variant data. More...
 
TGenbankCSeq_id_Base::SetGenbank (void)
 Select the variant. More...
 
void CSeq_id_Base::SetGenbank (TGenbank &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsEmbl (void) const
 Check if variant Embl is selected. More...
 
const TEmblCSeq_id_Base::GetEmbl (void) const
 Get the variant data. More...
 
TEmblCSeq_id_Base::SetEmbl (void)
 Select the variant. More...
 
void CSeq_id_Base::SetEmbl (TEmbl &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsPir (void) const
 Check if variant Pir is selected. More...
 
const TPirCSeq_id_Base::GetPir (void) const
 Get the variant data. More...
 
TPirCSeq_id_Base::SetPir (void)
 Select the variant. More...
 
void CSeq_id_Base::SetPir (TPir &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsSwissprot (void) const
 Check if variant Swissprot is selected. More...
 
const TSwissprotCSeq_id_Base::GetSwissprot (void) const
 Get the variant data. More...
 
TSwissprotCSeq_id_Base::SetSwissprot (void)
 Select the variant. More...
 
void CSeq_id_Base::SetSwissprot (TSwissprot &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsPatent (void) const
 Check if variant Patent is selected. More...
 
const TPatentCSeq_id_Base::GetPatent (void) const
 Get the variant data. More...
 
TPatentCSeq_id_Base::SetPatent (void)
 Select the variant. More...
 
void CSeq_id_Base::SetPatent (TPatent &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsOther (void) const
 Check if variant Other is selected. More...
 
const TOtherCSeq_id_Base::GetOther (void) const
 Get the variant data. More...
 
TOtherCSeq_id_Base::SetOther (void)
 Select the variant. More...
 
void CSeq_id_Base::SetOther (TOther &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsGeneral (void) const
 Check if variant General is selected. More...
 
const TGeneralCSeq_id_Base::GetGeneral (void) const
 Get the variant data. More...
 
TGeneralCSeq_id_Base::SetGeneral (void)
 Select the variant. More...
 
void CSeq_id_Base::SetGeneral (TGeneral &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsGi (void) const
 Check if variant Gi is selected. More...
 
TGi CSeq_id_Base::GetGi (void) const
 Get the variant data. More...
 
TGiCSeq_id_Base::SetGi (void)
 Select the variant. More...
 
void CSeq_id_Base::SetGi (TGi value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsDdbj (void) const
 Check if variant Ddbj is selected. More...
 
const TDdbjCSeq_id_Base::GetDdbj (void) const
 Get the variant data. More...
 
TDdbjCSeq_id_Base::SetDdbj (void)
 Select the variant. More...
 
void CSeq_id_Base::SetDdbj (TDdbj &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsPrf (void) const
 Check if variant Prf is selected. More...
 
const TPrfCSeq_id_Base::GetPrf (void) const
 Get the variant data. More...
 
TPrfCSeq_id_Base::SetPrf (void)
 Select the variant. More...
 
void CSeq_id_Base::SetPrf (TPrf &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsPdb (void) const
 Check if variant Pdb is selected. More...
 
const TPdbCSeq_id_Base::GetPdb (void) const
 Get the variant data. More...
 
TPdbCSeq_id_Base::SetPdb (void)
 Select the variant. More...
 
void CSeq_id_Base::SetPdb (TPdb &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsTpg (void) const
 Check if variant Tpg is selected. More...
 
const TTpgCSeq_id_Base::GetTpg (void) const
 Get the variant data. More...
 
TTpgCSeq_id_Base::SetTpg (void)
 Select the variant. More...
 
void CSeq_id_Base::SetTpg (TTpg &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsTpe (void) const
 Check if variant Tpe is selected. More...
 
const TTpeCSeq_id_Base::GetTpe (void) const
 Get the variant data. More...
 
TTpeCSeq_id_Base::SetTpe (void)
 Select the variant. More...
 
void CSeq_id_Base::SetTpe (TTpe &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsTpd (void) const
 Check if variant Tpd is selected. More...
 
const TTpdCSeq_id_Base::GetTpd (void) const
 Get the variant data. More...
 
TTpdCSeq_id_Base::SetTpd (void)
 Select the variant. More...
 
void CSeq_id_Base::SetTpd (TTpd &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsGpipe (void) const
 Check if variant Gpipe is selected. More...
 
const TGpipeCSeq_id_Base::GetGpipe (void) const
 Get the variant data. More...
 
TGpipeCSeq_id_Base::SetGpipe (void)
 Select the variant. More...
 
void CSeq_id_Base::SetGpipe (TGpipe &value)
 Select the variant and set its data. More...
 
bool CSeq_id_Base::IsNamed_annot_track (void) const
 Check if variant Named_annot_track is selected. More...
 
const TNamed_annot_trackCSeq_id_Base::GetNamed_annot_track (void) const
 Get the variant data. More...
 
TNamed_annot_trackCSeq_id_Base::SetNamed_annot_track (void)
 Select the variant. More...
 
void CSeq_id_Base::SetNamed_annot_track (TNamed_annot_track &value)
 Select the variant and set its data. More...
 
 CSeq_id_Base::CSeq_id_Base (const CSeq_id_Base &)
 
CSeq_id_BaseCSeq_id_Base::operator= (const CSeq_id_Base &)
 
void CSeq_id_Base::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 
 CSeq_id_set::CSeq_id_set (void)
 
 CSeq_id_set::~CSeq_id_set (void)
 
 CSeq_id_set::CSeq_id_set (const CSeq_id_set &value)
 
CSeq_id_setCSeq_id_set::operator= (const CSeq_id_set &value)
 
 CSeq_id_set_Base::CSeq_id_set_Base (void)
 
virtual CSeq_id_set_Base::~CSeq_id_set_Base (void)
 
 CSeq_id_set_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSeq_id_set_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CSeq_id_set_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CSeq_id_set_Base::Reset (void)
 Reset data member. More...
 
const TdataCSeq_id_set_Base::Get (void) const
 Get the member data. More...
 
TdataCSeq_id_set_Base::Set (void)
 Assign a value to data member. More...
 
 CSeq_id_set_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CSeq_id_set_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CSeq_id_set_Base::CSeq_id_set_Base (const CSeq_id_set_Base &)
 
CSeq_id_set_BaseCSeq_id_set_Base::operator= (const CSeq_id_set_Base &)
 
 CSeq_interval_Base::CSeq_interval_Base (void)
 
virtual CSeq_interval_Base::~CSeq_interval_Base (void)
 
 CSeq_interval_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSeq_interval_Base::IsSetFrom (void) const
 Check if a value has been assigned to From data member. More...
 
bool CSeq_interval_Base::CanGetFrom (void) const
 Check if it is safe to call GetFrom method. More...
 
void CSeq_interval_Base::ResetFrom (void)
 Reset From data member. More...
 
TFrom CSeq_interval_Base::GetFrom (void) const
 Get the From member data. More...
 
void CSeq_interval_Base::SetFrom (TFrom value)
 Assign a value to From data member. More...
 
TFromCSeq_interval_Base::SetFrom (void)
 Assign a value to From data member. More...
 
bool CSeq_interval_Base::IsSetTo (void) const
 Check if a value has been assigned to To data member. More...
 
bool CSeq_interval_Base::CanGetTo (void) const
 Check if it is safe to call GetTo method. More...
 
void CSeq_interval_Base::ResetTo (void)
 Reset To data member. More...
 
TTo CSeq_interval_Base::GetTo (void) const
 Get the To member data. More...
 
void CSeq_interval_Base::SetTo (TTo value)
 Assign a value to To data member. More...
 
TToCSeq_interval_Base::SetTo (void)
 Assign a value to To data member. More...
 
bool CSeq_interval_Base::IsSetStrand (void) const
 Check if a value has been assigned to Strand data member. More...
 
bool CSeq_interval_Base::CanGetStrand (void) const
 Check if it is safe to call GetStrand method. More...
 
void CSeq_interval_Base::ResetStrand (void)
 Reset Strand data member. More...
 
TStrand CSeq_interval_Base::GetStrand (void) const
 Get the Strand member data. More...
 
void CSeq_interval_Base::SetStrand (TStrand value)
 Assign a value to Strand data member. More...
 
TStrandCSeq_interval_Base::SetStrand (void)
 Assign a value to Strand data member. More...
 
bool CSeq_interval_Base::IsSetId (void) const
 WARNING: this used to be optional Check if a value has been assigned to Id data member. More...
 
bool CSeq_interval_Base::CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void CSeq_interval_Base::ResetId (void)
 Reset Id data member. More...
 
const TIdCSeq_interval_Base::GetId (void) const
 Get the Id member data. More...
 
void CSeq_interval_Base::SetId (TId &value)
 Assign a value to Id data member. More...
 
TIdCSeq_interval_Base::SetId (void)
 Assign a value to Id data member. More...
 
bool CSeq_interval_Base::IsSetFuzz_from (void) const
 Check if a value has been assigned to Fuzz_from data member. More...
 
bool CSeq_interval_Base::CanGetFuzz_from (void) const
 Check if it is safe to call GetFuzz_from method. More...
 
void CSeq_interval_Base::ResetFuzz_from (void)
 Reset Fuzz_from data member. More...
 
const TFuzz_fromCSeq_interval_Base::GetFuzz_from (void) const
 Get the Fuzz_from member data. More...
 
void CSeq_interval_Base::SetFuzz_from (TFuzz_from &value)
 Assign a value to Fuzz_from data member. More...
 
TFuzz_fromCSeq_interval_Base::SetFuzz_from (void)
 Assign a value to Fuzz_from data member. More...
 
bool CSeq_interval_Base::IsSetFuzz_to (void) const
 Check if a value has been assigned to Fuzz_to data member. More...
 
bool CSeq_interval_Base::CanGetFuzz_to (void) const
 Check if it is safe to call GetFuzz_to method. More...
 
void CSeq_interval_Base::ResetFuzz_to (void)
 Reset Fuzz_to data member. More...
 
const TFuzz_toCSeq_interval_Base::GetFuzz_to (void) const
 Get the Fuzz_to member data. More...
 
void CSeq_interval_Base::SetFuzz_to (TFuzz_to &value)
 Assign a value to Fuzz_to data member. More...
 
TFuzz_toCSeq_interval_Base::SetFuzz_to (void)
 Assign a value to Fuzz_to data member. More...
 
virtual void CSeq_interval_Base::Reset (void)
 Reset the whole object. More...
 
 CSeq_interval_Base::CSeq_interval_Base (const CSeq_interval_Base &)
 
CSeq_interval_BaseCSeq_interval_Base::operator= (const CSeq_interval_Base &)
 
 CSeq_loc_Base::CSeq_loc_Base (void)
 
virtual CSeq_loc_Base::~CSeq_loc_Base (void)
 
 CSeq_loc_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
virtual void CSeq_loc_Base::Reset (void)
 Reset the whole object. More...
 
virtual void CSeq_loc_Base::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CSeq_loc_Base::Which (void) const
 Which variant is currently selected. More...
 
void CSeq_loc_Base::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CSeq_loc_Base::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CSeq_loc_Base::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CSeq_loc_Base::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CSeq_loc_Base::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CSeq_loc_Base::IsNull (void) const
 Check if variant Null is selected. More...
 
void CSeq_loc_Base::SetNull (void)
 Select the variant. More...
 
bool CSeq_loc_Base::IsEmpty (void) const
 Check if variant Empty is selected. More...
 
const TEmptyCSeq_loc_Base::GetEmpty (void) const
 Get the variant data. More...
 
TEmptyCSeq_loc_Base::SetEmpty (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetEmpty (TEmpty &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsWhole (void) const
 Check if variant Whole is selected. More...
 
const TWholeCSeq_loc_Base::GetWhole (void) const
 Get the variant data. More...
 
TWholeCSeq_loc_Base::SetWhole (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetWhole (TWhole &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsInt (void) const
 Check if variant Int is selected. More...
 
const TIntCSeq_loc_Base::GetInt (void) const
 Get the variant data. More...
 
TIntCSeq_loc_Base::SetInt (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetInt (TInt &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsPacked_int (void) const
 Check if variant Packed_int is selected. More...
 
const TPacked_intCSeq_loc_Base::GetPacked_int (void) const
 Get the variant data. More...
 
TPacked_intCSeq_loc_Base::SetPacked_int (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetPacked_int (TPacked_int &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsPnt (void) const
 Check if variant Pnt is selected. More...
 
const TPntCSeq_loc_Base::GetPnt (void) const
 Get the variant data. More...
 
TPntCSeq_loc_Base::SetPnt (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetPnt (TPnt &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsPacked_pnt (void) const
 Check if variant Packed_pnt is selected. More...
 
const TPacked_pntCSeq_loc_Base::GetPacked_pnt (void) const
 Get the variant data. More...
 
TPacked_pntCSeq_loc_Base::SetPacked_pnt (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetPacked_pnt (TPacked_pnt &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsMix (void) const
 Check if variant Mix is selected. More...
 
const TMixCSeq_loc_Base::GetMix (void) const
 Get the variant data. More...
 
TMixCSeq_loc_Base::SetMix (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetMix (TMix &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsEquiv (void) const
 Check if variant Equiv is selected. More...
 
const TEquivCSeq_loc_Base::GetEquiv (void) const
 Get the variant data. More...
 
TEquivCSeq_loc_Base::SetEquiv (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetEquiv (TEquiv &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsBond (void) const
 Check if variant Bond is selected. More...
 
const TBondCSeq_loc_Base::GetBond (void) const
 Get the variant data. More...
 
TBondCSeq_loc_Base::SetBond (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetBond (TBond &value)
 Select the variant and set its data. More...
 
bool CSeq_loc_Base::IsFeat (void) const
 Check if variant Feat is selected. More...
 
const TFeatCSeq_loc_Base::GetFeat (void) const
 Get the variant data. More...
 
TFeatCSeq_loc_Base::SetFeat (void)
 Select the variant. More...
 
void CSeq_loc_Base::SetFeat (TFeat &value)
 Select the variant and set its data. More...
 
 CSeq_loc_Base::CSeq_loc_Base (const CSeq_loc_Base &)
 
CSeq_loc_BaseCSeq_loc_Base::operator= (const CSeq_loc_Base &)
 
void CSeq_loc_Base::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 
 CSeq_loc_equiv_Base::CSeq_loc_equiv_Base (void)
 
virtual CSeq_loc_equiv_Base::~CSeq_loc_equiv_Base (void)
 
 CSeq_loc_equiv_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSeq_loc_equiv_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CSeq_loc_equiv_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CSeq_loc_equiv_Base::Reset (void)
 Reset data member. More...
 
const TdataCSeq_loc_equiv_Base::Get (void) const
 Get the member data. More...
 
TdataCSeq_loc_equiv_Base::Set (void)
 Assign a value to data member. More...
 
 CSeq_loc_equiv_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CSeq_loc_equiv_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CSeq_loc_equiv_Base::CSeq_loc_equiv_Base (const CSeq_loc_equiv_Base &)
 
CSeq_loc_equiv_BaseCSeq_loc_equiv_Base::operator= (const CSeq_loc_equiv_Base &)
 
 CSeq_loc_mix_Base::CSeq_loc_mix_Base (void)
 
virtual CSeq_loc_mix_Base::~CSeq_loc_mix_Base (void)
 
 CSeq_loc_mix_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSeq_loc_mix_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CSeq_loc_mix_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CSeq_loc_mix_Base::Reset (void)
 Reset data member. More...
 
const TdataCSeq_loc_mix_Base::Get (void) const
 Get the member data. More...
 
TdataCSeq_loc_mix_Base::Set (void)
 Assign a value to data member. More...
 
 CSeq_loc_mix_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CSeq_loc_mix_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CSeq_loc_mix_Base::CSeq_loc_mix_Base (const CSeq_loc_mix_Base &)
 
CSeq_loc_mix_BaseCSeq_loc_mix_Base::operator= (const CSeq_loc_mix_Base &)
 
 CSeq_point_Base::CSeq_point_Base (void)
 
virtual CSeq_point_Base::~CSeq_point_Base (void)
 
 CSeq_point_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSeq_point_Base::IsSetPoint (void) const
 Check if a value has been assigned to Point data member. More...
 
bool CSeq_point_Base::CanGetPoint (void) const
 Check if it is safe to call GetPoint method. More...
 
void CSeq_point_Base::ResetPoint (void)
 Reset Point data member. More...
 
TPoint CSeq_point_Base::GetPoint (void) const
 Get the Point member data. More...
 
void CSeq_point_Base::SetPoint (TPoint value)
 Assign a value to Point data member. More...
 
TPointCSeq_point_Base::SetPoint (void)
 Assign a value to Point data member. More...
 
bool CSeq_point_Base::IsSetStrand (void) const
 Check if a value has been assigned to Strand data member. More...
 
bool CSeq_point_Base::CanGetStrand (void) const
 Check if it is safe to call GetStrand method. More...
 
void CSeq_point_Base::ResetStrand (void)
 Reset Strand data member. More...
 
TStrand CSeq_point_Base::GetStrand (void) const
 Get the Strand member data. More...
 
void CSeq_point_Base::SetStrand (TStrand value)
 Assign a value to Strand data member. More...
 
TStrandCSeq_point_Base::SetStrand (void)
 Assign a value to Strand data member. More...
 
bool CSeq_point_Base::IsSetId (void) const
 WARNING: this used to be optional Check if a value has been assigned to Id data member. More...
 
bool CSeq_point_Base::CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void CSeq_point_Base::ResetId (void)
 Reset Id data member. More...
 
const TIdCSeq_point_Base::GetId (void) const
 Get the Id member data. More...
 
void CSeq_point_Base::SetId (TId &value)
 Assign a value to Id data member. More...
 
TIdCSeq_point_Base::SetId (void)
 Assign a value to Id data member. More...
 
bool CSeq_point_Base::IsSetFuzz (void) const
 Check if a value has been assigned to Fuzz data member. More...
 
bool CSeq_point_Base::CanGetFuzz (void) const
 Check if it is safe to call GetFuzz method. More...
 
void CSeq_point_Base::ResetFuzz (void)
 Reset Fuzz data member. More...
 
const TFuzzCSeq_point_Base::GetFuzz (void) const
 Get the Fuzz member data. More...
 
void CSeq_point_Base::SetFuzz (TFuzz &value)
 Assign a value to Fuzz data member. More...
 
TFuzzCSeq_point_Base::SetFuzz (void)
 Assign a value to Fuzz data member. More...
 
virtual void CSeq_point_Base::Reset (void)
 Reset the whole object. More...
 
 CSeq_point_Base::CSeq_point_Base (const CSeq_point_Base &)
 
CSeq_point_BaseCSeq_point_Base::operator= (const CSeq_point_Base &)
 
 CTextseq_id_Base::CTextseq_id_Base (void)
 
virtual CTextseq_id_Base::~CTextseq_id_Base (void)
 
 CTextseq_id_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CTextseq_id_Base::IsSetName (void) const
 Check if a value has been assigned to Name data member. More...
 
bool CTextseq_id_Base::CanGetName (void) const
 Check if it is safe to call GetName method. More...
 
void CTextseq_id_Base::ResetName (void)
 Reset Name data member. More...
 
const TNameCTextseq_id_Base::GetName (void) const
 Get the Name member data. More...
 
void CTextseq_id_Base::SetName (const TName &value)
 Assign a value to Name data member. More...
 
void CTextseq_id_Base::SetName (TName &&value)
 
TNameCTextseq_id_Base::SetName (void)
 Assign a value to Name data member. More...
 
bool CTextseq_id_Base::IsSetAccession (void) const
 Check if a value has been assigned to Accession data member. More...
 
bool CTextseq_id_Base::CanGetAccession (void) const
 Check if it is safe to call GetAccession method. More...
 
void CTextseq_id_Base::ResetAccession (void)
 Reset Accession data member. More...
 
const TAccessionCTextseq_id_Base::GetAccession (void) const
 Get the Accession member data. More...
 
void CTextseq_id_Base::SetAccession (const TAccession &value)
 Assign a value to Accession data member. More...
 
void CTextseq_id_Base::SetAccession (TAccession &&value)
 
TAccessionCTextseq_id_Base::SetAccession (void)
 Assign a value to Accession data member. More...
 
bool CTextseq_id_Base::IsSetRelease (void) const
 Check if a value has been assigned to Release data member. More...
 
bool CTextseq_id_Base::CanGetRelease (void) const
 Check if it is safe to call GetRelease method. More...
 
void CTextseq_id_Base::ResetRelease (void)
 Reset Release data member. More...
 
const TReleaseCTextseq_id_Base::GetRelease (void) const
 Get the Release member data. More...
 
void CTextseq_id_Base::SetRelease (const TRelease &value)
 Assign a value to Release data member. More...
 
void CTextseq_id_Base::SetRelease (TRelease &&value)
 
TReleaseCTextseq_id_Base::SetRelease (void)
 Assign a value to Release data member. More...
 
bool CTextseq_id_Base::IsSetVersion (void) const
 Check if a value has been assigned to Version data member. More...
 
bool CTextseq_id_Base::CanGetVersion (void) const
 Check if it is safe to call GetVersion method. More...
 
void CTextseq_id_Base::ResetVersion (void)
 Reset Version data member. More...
 
TVersion CTextseq_id_Base::GetVersion (void) const
 Get the Version member data. More...
 
void CTextseq_id_Base::SetVersion (TVersion value)
 Assign a value to Version data member. More...
 
TVersionCTextseq_id_Base::SetVersion (void)
 Assign a value to Version data member. More...
 
virtual void CTextseq_id_Base::Reset (void)
 Reset the whole object. More...
 
 CTextseq_id_Base::CTextseq_id_Base (const CTextseq_id_Base &)
 
CTextseq_id_BaseCTextseq_id_Base::operator= (const CTextseq_id_Base &)
 

Variables

Uint4 CGiimport_id_Base::m_set_State [1]
 
int CGiimport_id_Base::m_Id
 
string CGiimport_id_Base::m_Db
 
string CGiimport_id_Base::m_Release
 
Uint4 CPacked_seqint_Base::m_set_State [1]
 
list< CRef< CSeq_interval > > CPacked_seqint_Base::m_data
 
Uint4 CPacked_seqpnt_Base::m_set_State [1]
 
ENa_strand CPacked_seqpnt_Base::m_Strand
 
CRef< TIdCPacked_seqpnt_Base::m_Id
 
CRef< TFuzzCPacked_seqpnt_Base::m_Fuzz
 
vector< TSeqPosCPacked_seqpnt_Base::m_Points
 
Uint4 CPatent_seq_id_Base::m_set_State [1]
 
int CPatent_seq_id_Base::m_Seqid
 
CRef< TCitCPatent_seq_id_Base::m_Cit
 
Uint4 CPDB_seq_id_Base::m_set_State [1]
 
CPDB_mol_id CPDB_seq_id_Base::m_Mol
 
int CPDB_seq_id_Base::m_Chain
 
CRef< TRelCPDB_seq_id_Base::m_Rel
 
string CPDB_seq_id_Base::m_Chain_id
 
Uint4 CSeq_bond_Base::m_set_State [1]
 
CRef< TACSeq_bond_Base::m_A
 
CRef< TBCSeq_bond_Base::m_B
 
E_Choice CSeq_id_Base::m_choice
 
static const char *const CSeq_id_Base::sm_SelectionNames []
 
TGibbsq   CSeq_id_Base::m_Gibbsq
 
TGibbmt   CSeq_id_Base::m_Gibbmt
 
ncbi::TIntId   CSeq_id_Base::m_Gi
 
NCBI_NS_NCBI::CSerialObject *   CSeq_id_Base::m_object
 
union {
   TGibbsq   CSeq_id_Base::m_Gibbsq
 
   TGibbmt   CSeq_id_Base::m_Gibbmt
 
   ncbi::TIntId   CSeq_id_Base::m_Gi
 
   NCBI_NS_NCBI::CSerialObject *   CSeq_id_Base::m_object
 
}; 
 
Uint4 CSeq_id_set_Base::m_set_State [1]
 
list< CRef< CSeq_id > > CSeq_id_set_Base::m_data
 
Uint4 CSeq_interval_Base::m_set_State [1]
 
TSeqPos CSeq_interval_Base::m_From
 
TSeqPos CSeq_interval_Base::m_To
 
ENa_strand CSeq_interval_Base::m_Strand
 
CRef< TIdCSeq_interval_Base::m_Id
 
CRef< TFuzz_fromCSeq_interval_Base::m_Fuzz_from
 
CRef< TFuzz_toCSeq_interval_Base::m_Fuzz_to
 
E_Choice CSeq_loc_Base::m_choice
 
static const char *const CSeq_loc_Base::sm_SelectionNames []
 
NCBI_NS_NCBI::CSerialObject *   CSeq_loc_Base::m_object
 
union {
   NCBI_NS_NCBI::CSerialObject *   CSeq_loc_Base::m_object
 
}; 
 
Uint4 CSeq_loc_equiv_Base::m_set_State [1]
 
list< CRef< CSeq_loc > > CSeq_loc_equiv_Base::m_data
 
Uint4 CSeq_loc_mix_Base::m_set_State [1]
 
list< CRef< CSeq_loc > > CSeq_loc_mix_Base::m_data
 
Uint4 CSeq_point_Base::m_set_State [1]
 
TSeqPos CSeq_point_Base::m_Point
 
ENa_strand CSeq_point_Base::m_Strand
 
CRef< TIdCSeq_point_Base::m_Id
 
CRef< TFuzzCSeq_point_Base::m_Fuzz
 
Uint4 CTextseq_id_Base::m_set_State [1]
 
string CTextseq_id_Base::m_Name
 
string CTextseq_id_Base::m_Accession
 
string CTextseq_id_Base::m_Release
 
int CTextseq_id_Base::m_Version
 

Detailed Description

Typedef Documentation

◆ TA

Definition at line 86 of file Seq_bond_.hpp.

◆ TAccession

Definition at line 86 of file Textseq_id_.hpp.

◆ TB

Definition at line 87 of file Seq_bond_.hpp.

◆ TBond

Definition at line 171 of file Seq_loc_.hpp.

◆ TChain

Definition at line 92 of file PDB_seq_id_.hpp.

◆ TChain_id

Definition at line 94 of file PDB_seq_id_.hpp.

◆ TCit

Definition at line 86 of file Patent_seq_id_.hpp.

◆ Tdata [1/4]

Definition at line 89 of file Packed_seqint_.hpp.

◆ Tdata [2/4]

typedef list< CRef< CSeq_id > > CSeq_id_set_Base::Tdata

Definition at line 89 of file Seq_id_set_.hpp.

◆ Tdata [3/4]

Definition at line 90 of file Seq_loc_equiv_.hpp.

◆ Tdata [4/4]

Definition at line 90 of file Seq_loc_mix_.hpp.

◆ TDb

Definition at line 86 of file Giimport_id_.hpp.

◆ TDdbj

Definition at line 181 of file Seq_id_.hpp.

◆ TEmbl

Definition at line 174 of file Seq_id_.hpp.

◆ TEmpty

Definition at line 163 of file Seq_loc_.hpp.

◆ TEquiv

Definition at line 170 of file Seq_loc_.hpp.

◆ TFeat

Definition at line 172 of file Seq_loc_.hpp.

◆ TFrom

Definition at line 90 of file Seq_interval_.hpp.

◆ TFuzz [1/2]

Definition at line 93 of file Packed_seqpnt_.hpp.

◆ TFuzz [2/2]

Definition at line 93 of file Seq_point_.hpp.

◆ TFuzz_from

Definition at line 94 of file Seq_interval_.hpp.

◆ TFuzz_to

Definition at line 95 of file Seq_interval_.hpp.

◆ TGenbank

Definition at line 173 of file Seq_id_.hpp.

◆ TGeneral

Definition at line 179 of file Seq_id_.hpp.

◆ TGi

typedef NCBI_NS_NCBI::TGi CSeq_id_Base::TGi

Definition at line 180 of file Seq_id_.hpp.

◆ TGibbmt

Definition at line 171 of file Seq_id_.hpp.

◆ TGibbsq

Definition at line 170 of file Seq_id_.hpp.

◆ TGiim

Definition at line 172 of file Seq_id_.hpp.

◆ TGpipe

Definition at line 187 of file Seq_id_.hpp.

◆ TId [1/4]

Definition at line 85 of file Giimport_id_.hpp.

◆ TId [2/4]

Definition at line 92 of file Packed_seqpnt_.hpp.

◆ TId [3/4]

Definition at line 93 of file Seq_interval_.hpp.

◆ TId [4/4]

Definition at line 92 of file Seq_point_.hpp.

◆ TInt

Definition at line 165 of file Seq_loc_.hpp.

◆ TLocal

Definition at line 169 of file Seq_id_.hpp.

◆ TmemberIndex [1/8]

Definition at line 96 of file Giimport_id_.hpp.

◆ TmemberIndex [2/8]

Definition at line 104 of file Packed_seqpnt_.hpp.

◆ TmemberIndex [3/8]

Definition at line 94 of file Patent_seq_id_.hpp.

◆ TmemberIndex [4/8]

Definition at line 104 of file PDB_seq_id_.hpp.

◆ TmemberIndex [5/8]

Definition at line 95 of file Seq_bond_.hpp.

◆ TmemberIndex [6/8]

Definition at line 107 of file Seq_interval_.hpp.

◆ TmemberIndex [7/8]

Definition at line 103 of file Seq_point_.hpp.

◆ TmemberIndex [8/8]

Definition at line 98 of file Textseq_id_.hpp.

◆ TMix

Definition at line 169 of file Seq_loc_.hpp.

◆ TMol

Definition at line 91 of file PDB_seq_id_.hpp.

◆ TName

Definition at line 85 of file Textseq_id_.hpp.

◆ TNamed_annot_track

Definition at line 188 of file Seq_id_.hpp.

◆ TOther

Definition at line 178 of file Seq_id_.hpp.

◆ TPacked_int

Definition at line 166 of file Seq_loc_.hpp.

◆ TPacked_pnt

Definition at line 168 of file Seq_loc_.hpp.

◆ Tparent [1/18]

Definition at line 67 of file Giimport_id.hpp.

◆ Tparent [2/18]

Definition at line 74 of file Giimport_id_.hpp.

◆ Tparent [3/18]

Definition at line 78 of file Packed_seqint_.hpp.

◆ Tparent [4/18]

Definition at line 80 of file Packed_seqpnt_.hpp.

◆ Tparent [5/18]

Definition at line 74 of file Patent_seq_id_.hpp.

◆ Tparent [6/18]

Definition at line 67 of file PDB_mol_id.hpp.

◆ Tparent [7/18]

Definition at line 76 of file PDB_mol_id_.hpp.

◆ Tparent [8/18]

Definition at line 80 of file PDB_seq_id_.hpp.

◆ Tparent [9/18]

Definition at line 75 of file Seq_bond_.hpp.

◆ Tparent [10/18]

Definition at line 81 of file Seq_id_.hpp.

◆ Tparent [11/18]

Definition at line 67 of file Seq_id_set.hpp.

◆ Tparent [12/18]

Definition at line 78 of file Seq_id_set_.hpp.

◆ Tparent [13/18]

Definition at line 79 of file Seq_interval_.hpp.

◆ Tparent [14/18]

Definition at line 84 of file Seq_loc_.hpp.

◆ Tparent [15/18]

Definition at line 79 of file Seq_loc_equiv_.hpp.

◆ Tparent [16/18]

Definition at line 79 of file Seq_loc_mix_.hpp.

◆ Tparent [17/18]

Definition at line 79 of file Seq_point_.hpp.

◆ Tparent [18/18]

Definition at line 74 of file Textseq_id_.hpp.

◆ TPatent

Definition at line 177 of file Seq_id_.hpp.

◆ TPdb

Definition at line 183 of file Seq_id_.hpp.

◆ TPir

Definition at line 175 of file Seq_id_.hpp.

◆ TPnt

Definition at line 167 of file Seq_loc_.hpp.

◆ TPoint

Definition at line 90 of file Seq_point_.hpp.

◆ TPoints

Definition at line 94 of file Packed_seqpnt_.hpp.

◆ TPrf

Definition at line 182 of file Seq_id_.hpp.

◆ TRel

Definition at line 93 of file PDB_seq_id_.hpp.

◆ TRelease [1/2]

Definition at line 87 of file Giimport_id_.hpp.

◆ TRelease [2/2]

Definition at line 87 of file Textseq_id_.hpp.

◆ TSeqid

Definition at line 85 of file Patent_seq_id_.hpp.

◆ TStrand [1/3]

Definition at line 91 of file Packed_seqpnt_.hpp.

◆ TStrand [2/3]

Definition at line 92 of file Seq_interval_.hpp.

◆ TStrand [3/3]

Definition at line 91 of file Seq_point_.hpp.

◆ TSwissprot

Definition at line 176 of file Seq_id_.hpp.

◆ TTo

Definition at line 91 of file Seq_interval_.hpp.

◆ TTpd

Definition at line 186 of file Seq_id_.hpp.

◆ TTpe

Definition at line 185 of file Seq_id_.hpp.

◆ TTpg

Definition at line 184 of file Seq_id_.hpp.

◆ TVersion

Definition at line 88 of file Textseq_id_.hpp.

◆ TWhole

Definition at line 164 of file Seq_loc_.hpp.

Enumeration Type Documentation

◆ E_Choice [1/2]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Local 

local use

e_Gibbsq 

Geninfo backbone seqid.

e_Gibbmt 

Geninfo backbone moltype.

e_Giim 

Geninfo import id.

e_Genbank 
e_Embl 
e_Pir 
e_Swissprot 
e_Patent 
e_Other 

for historical reasons, 'other' = 'refseq'

e_General 

for other databases

e_Gi 

GenInfo Integrated Database.

e_Ddbj 

DDBJ.

e_Prf 

PRF SEQDB.

e_Pdb 

PDB sequence.

e_Tpg 

Third Party Annot/Seq Genbank.

e_Tpe 

Third Party Annot/Seq EMBL.

e_Tpd 

Third Party Annot/Seq DDBJ.

e_Gpipe 

Internal NCBI genome pipeline processing ID.

e_Named_annot_track 

Internal named annotation tracking ID.

Definition at line 93 of file Seq_id_.hpp.

◆ E_Choice [2/2]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Null 

not placed

e_Empty 

to NULL one Seq-id in a collection

e_Whole 

whole sequence

e_Int 

from to

e_Packed_int 
e_Pnt 
e_Packed_pnt 
e_Mix 
e_Equiv 

equivalent sets of locations

e_Bond 
e_Feat 

indirect, through a Seq-feat

Definition at line 96 of file Seq_loc_.hpp.

◆ E_ChoiceStopper [1/2]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Named_annot_track+1

Definition at line 117 of file Seq_id_.hpp.

◆ E_ChoiceStopper [2/2]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Feat+1

Definition at line 111 of file Seq_loc_.hpp.

◆ E_memberIndex [1/8]

Enumerator
e__allMandatory 
e_id 
e_db 
e_release 

Definition at line 90 of file Giimport_id_.hpp.

◆ E_memberIndex [2/8]

Enumerator
e__allMandatory 
e_strand 
e_id 
e_fuzz 
e_points 

Definition at line 97 of file Packed_seqpnt_.hpp.

◆ E_memberIndex [3/8]

Enumerator
e__allMandatory 
e_seqid 
e_cit 

Definition at line 89 of file Patent_seq_id_.hpp.

◆ E_memberIndex [4/8]

Enumerator
e__allMandatory 
e_mol 
e_chain 
e_rel 
e_chain_id 

Definition at line 97 of file PDB_seq_id_.hpp.

◆ E_memberIndex [5/8]

Enumerator
e__allMandatory 
e_a 
e_b 

Definition at line 90 of file Seq_bond_.hpp.

◆ E_memberIndex [6/8]

Enumerator
e__allMandatory 
e_from 
e_to 
e_strand 
e_id 
e_fuzz_from 
e_fuzz_to 

Definition at line 98 of file Seq_interval_.hpp.

◆ E_memberIndex [7/8]

Enumerator
e__allMandatory 
e_point 
e_strand 
e_id 
e_fuzz 

Definition at line 96 of file Seq_point_.hpp.

◆ E_memberIndex [8/8]

Enumerator
e__allMandatory 
e_name 
e_accession 
e_release 
e_version 

Definition at line 91 of file Textseq_id_.hpp.

◆ ENa_strand

enum ENa_strand

strand of nucleic acid

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

Enumerator
eNa_strand_unknown 
eNa_strand_plus 
eNa_strand_minus 
eNa_strand_both 

in forward orientation

eNa_strand_both_rev 

in reverse orientation

eNa_strand_other 

Definition at line 64 of file Na_strand_.hpp.

Function Documentation

◆ CanGet() [1/4]

bool CPacked_seqint_Base::CanGet ( void  ) const
inline

◆ CanGet() [2/4]

bool CSeq_id_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 Seq_id_set_.hpp.

◆ CanGet() [3/4]

bool CSeq_loc_equiv_Base::CanGet ( void  ) const
inline

Check if it is safe to call Get method.

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

Definition at line 159 of file Seq_loc_equiv_.hpp.

◆ CanGet() [4/4]

bool CSeq_loc_mix_Base::CanGet ( void  ) const
inline

Check if it is safe to call Get method.

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

Definition at line 159 of file Seq_loc_mix_.hpp.

◆ CanGetA()

bool CSeq_bond_Base::CanGetA ( void  ) const
inline

Check if it is safe to call GetA method.

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

Definition at line 207 of file Seq_bond_.hpp.

Referenced by FTASeqLocCheck(), s_AddSeqBondString(), CFlatSeqLoc::x_Add(), and CSeq_loc::x_CheckId().

◆ CanGetAccession()

bool CTextseq_id_Base::CanGetAccession ( void  ) const
inline

◆ CanGetB()

bool CSeq_bond_Base::CanGetB ( void  ) const
inline

Check if it is safe to call GetB method.

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

Definition at line 237 of file Seq_bond_.hpp.

References CSeq_bond_Base::IsSetB().

Referenced by CSeq_bond_Base::GetB(), GetReverseComplement(), s_AddSeqBondString(), SeqLocPrintUseBestID(), CFlatSeqLoc::x_Add(), and CSeq_loc::x_CheckId().

◆ CanGetChain()

bool CPDB_seq_id_Base::CanGetChain ( void  ) const
inline

Check if it is safe to call GetChain method.

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

Definition at line 335 of file PDB_seq_id_.hpp.

Referenced by CGencollIdMapper::x_FixImperfectId().

◆ CanGetChain_id()

bool CPDB_seq_id_Base::CanGetChain_id ( void  ) const
inline

Check if it is safe to call GetChain_id method.

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

Definition at line 406 of file PDB_seq_id_.hpp.

References CPDB_seq_id_Base::IsSetChain_id().

Referenced by CPDB_seq_id_Base::GetChain_id().

◆ CanGetCit()

bool CPatent_seq_id_Base::CanGetCit ( void  ) const
inline

Check if it is safe to call GetCit method.

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

Definition at line 253 of file Patent_seq_id_.hpp.

◆ CanGetDb()

bool CGiimport_id_Base::CanGetDb ( void  ) const
inline

Check if it is safe to call GetDb method.

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

Definition at line 296 of file Giimport_id_.hpp.

References CGiimport_id_Base::IsSetDb().

Referenced by GetAccessionAndDatabaseSource(), and CGiimport_id_Base::GetDb().

◆ CanGetFrom()

bool CSeq_interval_Base::CanGetFrom ( void  ) const
inline

◆ CanGetFuzz() [1/2]

bool CPacked_seqpnt_Base::CanGetFuzz ( void  ) const
inline

Check if it is safe to call GetFuzz method.

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

Definition at line 361 of file Packed_seqpnt_.hpp.

References CPacked_seqpnt_Base::IsSetFuzz().

Referenced by CPacked_seqpnt_Base::GetFuzz(), and CFlatSeqLoc::x_Add().

◆ CanGetFuzz() [2/2]

bool CSeq_point_Base::CanGetFuzz ( void  ) const
inline

Check if it is safe to call GetFuzz method.

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

Definition at line 414 of file Seq_point_.hpp.

References CSeq_point_Base::IsSetFuzz().

Referenced by CSeq_point_Base::GetFuzz(), CSGFeatureJob::x_CalcIntervals(), CFeatGlyph::x_DrawFeatureBar(), and CFeatGlyph::x_DrawRSites().

◆ CanGetFuzz_from()

bool CSeq_interval_Base::CanGetFuzz_from ( void  ) const
inline

Check if it is safe to call GetFuzz_from method.

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

Definition at line 541 of file Seq_interval_.hpp.

References CSeq_interval_Base::IsSetFuzz_from().

Referenced by CSeq_interval_Base::GetFuzz_from(), PrintSeqIntUseBestID(), and s_FixIntervalProtToCds().

◆ CanGetFuzz_to()

bool CSeq_interval_Base::CanGetFuzz_to ( void  ) const
inline

Check if it is safe to call GetFuzz_to method.

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

Definition at line 562 of file Seq_interval_.hpp.

References CSeq_interval_Base::IsSetFuzz_to().

Referenced by CSeq_interval_Base::GetFuzz_to(), PrintSeqIntUseBestID(), and s_FixIntervalProtToCds().

◆ CanGetId() [1/4]

bool CGiimport_id_Base::CanGetId ( void  ) const
inline

Check if it is safe to call GetId method.

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

Definition at line 249 of file Giimport_id_.hpp.

References CGiimport_id_Base::IsSetId().

Referenced by CGiimport_id_Base::GetId().

◆ CanGetId() [2/4]

bool CPacked_seqpnt_Base::CanGetId ( void  ) const
inline

Check if it is safe to call GetId method.

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

Definition at line 331 of file Packed_seqpnt_.hpp.

◆ CanGetId() [3/4]

bool CSeq_interval_Base::CanGetId ( void  ) const
inline

Check if it is safe to call GetId method.

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

Definition at line 511 of file Seq_interval_.hpp.

Referenced by CBedFeatureRecord::AssignLocation().

◆ CanGetId() [4/4]

bool CSeq_point_Base::CanGetId ( void  ) const
inline

Check if it is safe to call GetId method.

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

Definition at line 384 of file Seq_point_.hpp.

◆ CanGetMol()

bool CPDB_seq_id_Base::CanGetMol ( void  ) const
inline

Check if it is safe to call GetMol method.

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

Definition at line 300 of file PDB_seq_id_.hpp.

References CPDB_seq_id_Base::IsSetMol().

Referenced by CPDB_seq_id_Base::GetMol(), CWriteDB_IsamIndex::x_AddPdb(), and CGencollIdMapper::x_FixImperfectId().

◆ CanGetName()

bool CTextseq_id_Base::CanGetName ( void  ) const
inline

◆ CanGetPoint()

bool CSeq_point_Base::CanGetPoint ( void  ) const
inline

Check if it is safe to call GetPoint method.

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

Definition at line 290 of file Seq_point_.hpp.

References CSeq_point_Base::IsSetPoint().

Referenced by CSeq_point_Base::GetPoint(), CFlatSeqLoc::x_Add(), and CFeatGlyph::x_DrawRSites().

◆ CanGetPoints()

bool CPacked_seqpnt_Base::CanGetPoints ( void  ) const
inline

Check if it is safe to call GetPoints method.

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

Definition at line 382 of file Packed_seqpnt_.hpp.

◆ CanGetRel()

bool CPDB_seq_id_Base::CanGetRel ( void  ) const
inline

Check if it is safe to call GetRel method.

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

Definition at line 385 of file PDB_seq_id_.hpp.

References CPDB_seq_id_Base::IsSetRel().

Referenced by CPDB_seq_id_Base::GetRel(), and CDBSourceItem::x_FormatDBSourceID().

◆ CanGetRelease() [1/2]

bool CGiimport_id_Base::CanGetRelease ( void  ) const
inline

Check if it is safe to call GetRelease method.

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

Definition at line 343 of file Giimport_id_.hpp.

References CGiimport_id_Base::IsSetRelease().

Referenced by CGiimport_id_Base::GetRelease().

◆ CanGetRelease() [2/2]

bool CTextseq_id_Base::CanGetRelease ( void  ) const
inline

Check if it is safe to call GetRelease method.

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

Definition at line 381 of file Textseq_id_.hpp.

References CTextseq_id_Base::IsSetRelease().

Referenced by CTextseq_id_Base::GetRelease().

◆ CanGetSeqid()

bool CPatent_seq_id_Base::CanGetSeqid ( void  ) const
inline

Check if it is safe to call GetSeqid method.

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

Definition at line 206 of file Patent_seq_id_.hpp.

References CPatent_seq_id_Base::IsSetSeqid().

Referenced by CPatent_seq_id_Base::GetSeqid().

◆ CanGetStrand() [1/3]

bool CPacked_seqpnt_Base::CanGetStrand ( void  ) const
inline

Check if it is safe to call GetStrand method.

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

Definition at line 284 of file Packed_seqpnt_.hpp.

References CPacked_seqpnt_Base::IsSetStrand().

Referenced by CPacked_seqpnt_Base::GetStrand(), and s_AddSeqPackedPointString().

◆ CanGetStrand() [2/3]

bool CSeq_interval_Base::CanGetStrand ( void  ) const
inline

◆ CanGetStrand() [3/3]

bool CSeq_point_Base::CanGetStrand ( void  ) const
inline

Check if it is safe to call GetStrand method.

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

Definition at line 337 of file Seq_point_.hpp.

References CSeq_point_Base::IsSetStrand().

Referenced by CSeq_point_Base::GetStrand(), s_AddSeqPointString(), s_SeqPntRevCmp(), CNewCleanup_imp::x_BothStrandBC(), and CFeatGlyph::x_DrawRSites().

◆ CanGetTo()

bool CSeq_interval_Base::CanGetTo ( void  ) const
inline

◆ CanGetVersion()

bool CTextseq_id_Base::CanGetVersion ( void  ) const
inline

◆ CGiimport_id() [1/2]

CGiimport_id::CGiimport_id ( const CGiimport_id value)
private

◆ CGiimport_id() [2/2]

CGiimport_id::CGiimport_id ( void  )
inline

Definition at line 86 of file Giimport_id.hpp.

◆ CGiimport_id_Base() [1/2]

CGiimport_id_Base::CGiimport_id_Base ( const CGiimport_id_Base )
private

◆ CGiimport_id_Base() [2/2]

END_CLASS_INFO CGiimport_id_Base::CGiimport_id_Base ( void  )

Definition at line 82 of file Giimport_id_.cpp.

References CGiimport_id_Base::m_set_State.

◆ CheckSelected() [1/2]

void CSeq_id_Base::CheckSelected ( E_Choice  index) const
inline

◆ CheckSelected() [2/2]

void CSeq_loc_Base::CheckSelected ( E_Choice  index) const
inline

◆ CPacked_seqint_Base() [1/2]

CPacked_seqint_Base::CPacked_seqint_Base ( const CPacked_seqint_Base )
private

◆ CPacked_seqint_Base() [2/2]

END_CLASS_INFO CPacked_seqint_Base::CPacked_seqint_Base ( void  )

Definition at line 68 of file Packed_seqint_.cpp.

References CPacked_seqint_Base::m_set_State.

◆ CPacked_seqpnt_Base() [1/2]

CPacked_seqpnt_Base::CPacked_seqpnt_Base ( const CPacked_seqpnt_Base )
private

◆ CPacked_seqpnt_Base() [2/2]

END_CLASS_INFO CPacked_seqpnt_Base::CPacked_seqpnt_Base ( void  )

◆ CPatent_seq_id_Base() [1/2]

CPatent_seq_id_Base::CPatent_seq_id_Base ( const CPatent_seq_id_Base )
private

◆ CPatent_seq_id_Base() [2/2]

END_CLASS_INFO CPatent_seq_id_Base::CPatent_seq_id_Base ( void  )

◆ CPDB_mol_id() [1/2]

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

Explicit constructor from the primitive type.

Definition at line 72 of file PDB_mol_id.hpp.

◆ CPDB_mol_id() [2/2]

CPDB_mol_id::CPDB_mol_id ( void  )
inline

Definition at line 69 of file PDB_mol_id.hpp.

◆ CPDB_mol_id_Base() [1/2]

CPDB_mol_id_Base::CPDB_mol_id_Base ( const string data)
inlineexplicit

Definition at line 102 of file PDB_mol_id_.hpp.

◆ CPDB_mol_id_Base() [2/2]

CPDB_mol_id_Base::CPDB_mol_id_Base ( void  )
inline

Definition at line 97 of file PDB_mol_id_.hpp.

◆ CPDB_seq_id_Base() [1/2]

CPDB_seq_id_Base::CPDB_seq_id_Base ( const CPDB_seq_id_Base )
private

◆ CPDB_seq_id_Base() [2/2]

END_CLASS_INFO CPDB_seq_id_Base::CPDB_seq_id_Base ( void  )

Definition at line 102 of file PDB_seq_id_.cpp.

References CPDB_seq_id_Base::m_set_State.

◆ CSeq_bond_Base() [1/2]

CSeq_bond_Base::CSeq_bond_Base ( const CSeq_bond_Base )
private

◆ CSeq_bond_Base() [2/2]

END_CLASS_INFO CSeq_bond_Base::CSeq_bond_Base ( void  )

◆ CSeq_id_Base() [1/2]

CSeq_id_Base::CSeq_id_Base ( const CSeq_id_Base )
private

◆ CSeq_id_Base() [2/2]

END_CHOICE_INFO CSeq_id_Base::CSeq_id_Base ( void  )

Definition at line 599 of file Seq_id_.cpp.

◆ CSeq_id_set() [1/2]

CSeq_id_set::CSeq_id_set ( const CSeq_id_set value)
private

◆ CSeq_id_set() [2/2]

CSeq_id_set::CSeq_id_set ( void  )
inline

Definition at line 86 of file Seq_id_set.hpp.

◆ CSeq_id_set_Base() [1/2]

CSeq_id_set_Base::CSeq_id_set_Base ( const CSeq_id_set_Base )
private

◆ CSeq_id_set_Base() [2/2]

END_CLASS_INFO CSeq_id_set_Base::CSeq_id_set_Base ( void  )

Definition at line 68 of file Seq_id_set_.cpp.

References CSeq_id_set_Base::m_set_State.

◆ CSeq_interval_Base() [1/2]

CSeq_interval_Base::CSeq_interval_Base ( const CSeq_interval_Base )
private

◆ CSeq_interval_Base() [2/2]

END_CLASS_INFO CSeq_interval_Base::CSeq_interval_Base ( void  )

◆ CSeq_loc_Base() [1/2]

CSeq_loc_Base::CSeq_loc_Base ( const CSeq_loc_Base )
private

◆ CSeq_loc_Base() [2/2]

END_CHOICE_INFO CSeq_loc_Base::CSeq_loc_Base ( void  )

Definition at line 393 of file Seq_loc_.cpp.

◆ CSeq_loc_equiv_Base() [1/2]

CSeq_loc_equiv_Base::CSeq_loc_equiv_Base ( const CSeq_loc_equiv_Base )
private

◆ CSeq_loc_equiv_Base() [2/2]

END_CLASS_INFO CSeq_loc_equiv_Base::CSeq_loc_equiv_Base ( void  )

Definition at line 68 of file Seq_loc_equiv_.cpp.

References CSeq_loc_equiv_Base::m_set_State.

◆ CSeq_loc_mix_Base() [1/2]

CSeq_loc_mix_Base::CSeq_loc_mix_Base ( const CSeq_loc_mix_Base )
private

◆ CSeq_loc_mix_Base() [2/2]

END_CLASS_INFO CSeq_loc_mix_Base::CSeq_loc_mix_Base ( void  )

Definition at line 68 of file Seq_loc_mix_.cpp.

References CSeq_loc_mix_Base::m_set_State.

◆ CSeq_point_Base() [1/2]

CSeq_point_Base::CSeq_point_Base ( const CSeq_point_Base )
private

◆ CSeq_point_Base() [2/2]

END_CLASS_INFO CSeq_point_Base::CSeq_point_Base ( void  )

◆ CTextseq_id_Base() [1/2]

CTextseq_id_Base::CTextseq_id_Base ( const CTextseq_id_Base )
private

◆ CTextseq_id_Base() [2/2]

END_CLASS_INFO CTextseq_id_Base::CTextseq_id_Base ( void  )

Definition at line 90 of file Textseq_id_.cpp.

References CTextseq_id_Base::m_set_State.

◆ DECLARE_INTERNAL_TYPE_INFO() [1/14]

CGiimport_id_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [2/14]

CPacked_seqint_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [3/14]

CPacked_seqpnt_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [4/14]

CPatent_seq_id_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [5/14]

CPDB_seq_id_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [6/14]

CSeq_bond_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [7/14]

CSeq_id_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [8/14]

CSeq_id_set_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [9/14]

CSeq_interval_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [10/14]

CSeq_loc_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [11/14]

CSeq_loc_equiv_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [12/14]

CSeq_loc_mix_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [13/14]

CSeq_point_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [14/14]

CTextseq_id_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_STD_ALIAS_TYPE_INFO()

CPDB_mol_id_Base::DECLARE_STD_ALIAS_TYPE_INFO ( )

◆ DoSelect() [1/2]

void CSeq_id_Base::DoSelect ( E_Choice  index,
CObjectMemoryPool pool = 0 
)
private

◆ DoSelect() [2/2]

void CSeq_loc_Base::DoSelect ( E_Choice  index,
CObjectMemoryPool pool = 0 
)
private

◆ Get() [1/4]

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

Get the member data.

Returns
Reference to the member data.

Definition at line 164 of file Packed_seqint_.hpp.

References CPacked_seqint_Base::m_data.

Referenced by CPacked_seqint::AddIntervals(), NTweakExon::AsString(), BOOST_AUTO_TEST_CASE(), Canonicalize(), NTweakExon::CheckIdAndStrand(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSequenceSearchForm::ConstructQuery(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CorrectIntervalOrder(), CSeqUtils::CreateSeq_loc(), CSeqUtils::GetCdsMappingInfoFromRna(), IBISInteraction::GetFootprint(), CReadBlastApp::getFromTo(), IBISInteraction::GetGi(), CPacked_seqint::GetLength(), CRemoteBlast::GetMasks(), GetPositionsForAlignAnnot(), GetReverseComplement(), CPacked_seqint::GetStart(), CPacked_seqint::GetStartInt(), CPacked_seqint::GetStop(), CPacked_seqint::GetStopInt(), CPacked_seqint::GetStrand(), CWriteUtil::GetTranssplicedEndpoints(), CGencollIdMapper::IsLocInAGap(), CPacked_seqint::IsPartialStart(), CPacked_seqint::IsPartialStop(), CPacked_seqint::IsSetStrand(), CPacked_seqint::IsTruncatedStart(), CPacked_seqint::IsTruncatedStop(), CFastaObjectLoader::LoadFromStream(), CGtfLocationMerger::MergeLocationForGene(), CSeqUtils::MixLocToLoc(), NormalizeLoc(), s_AddLocString(), s_CountIntervals(), s_CreateBlastMask(), s_Fingerprint_Packed_seqint(), s_FlattenLoc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), s_Load_Packed_seqint(), s_LocationToStartStopPairs(), s_SeqLoc2MaskedSubjRanges(), SeqLocAdjustForTrim(), SeqLocPartialCheck(), SeqLocPrintUseBestID(), CBedImportData::Serialize(), CCleanup::SetCodeBreakLocation(), CPacked_seqint::SetPartialStart(), CPacked_seqint::SetPartialStop(), SplitLocationForGap(), NTweakExon::Validate(), CUCSCRegionWriter::WriteAnnot(), CSeqMap::x_Add(), CFlatSeqLoc::x_Add(), x_Assign(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CValidError_imp::x_CheckPackedInt(), x_CompareConsecutiveIntervals(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CValidError_imp::x_ReportInvalidFuzz(), CBioseq::x_SeqLoc_To_DeltaExt(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGtfWriter::xWriteFeatureExons(), CGff3Writer::xWriteFeatureRecords(), CGff3Writer::xWriteFeatureRna(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().

◆ Get() [2/4]

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

Get the member data.

Returns
Reference to the member data.

Definition at line 164 of file Seq_id_set_.hpp.

References CSeq_id_set_Base::m_data.

◆ Get() [3/4]

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

◆ Get() [4/4]

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

Get the member data.

Returns
Reference to the member data.

Definition at line 165 of file Seq_loc_mix_.hpp.

References CSeq_loc_mix_Base::m_data.

Referenced by CHandleRangeMap::AddLocation(), CSeq_loc_mix::AddSeqLoc(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CWriteUtil::ChangeToPackedInt(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_loc_mix::GetFirstLoc(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), CSeq_loc_mix::GetLastLoc(), GetLength(), GetReverseComplement(), GetSeqLocation(), CSeq_loc_mix::GetStart(), CSeq_loc_mix::GetStop(), CSeq_loc_mix::GetStrand(), CGuiObjectInfoPrimer::GetToolTip(), CEditingActionFeatAnticodon::GetValue(), CLocationEditPolicy::HasNulls(), CLocationPanel::Init(), CWriteUtil::IsLocationOrdered(), CGencollIdMapper::IsLocInAGap(), CFeaturePropagator::IsOrdered(), CSeq_loc_mix::IsPartialStart(), CSeq_loc_mix::IsPartialStop(), CSeq_loc_mix::IsSetStrand(), CSeq_loc_mix::IsTruncatedStart(), CSeq_loc_mix::IsTruncatedStop(), CSeq_loc_Conversion::MakeDstMix(), CSeq_loc_CI_Impl::MakeLoc(), CFeaturePropagator::MakeOrdered(), NormalizeLoc(), SRelLoc::Resolve(), s_AddLocString(), s_CalcCoverageCount(), s_CountIntervals(), s_Fingerprint_Seq_loc_mix(), s_FlattenLoc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), s_IsOrdered(), s_NeedsFlattening(), s_NormalizeNullsBetween(), s_SeqLoc2MaskedSubjRanges(), SeqLocPrintUseBestID(), CLocationPanel::TransferDataToWindow(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), x_Assign(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSGFeatureJob::x_CreateCloneFeature(), CFeatureTableReader_Imp::x_FinishFeature(), CFeatureTableReader_Imp::x_GetPointStrand(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CGFFReader::x_ResolveLoc(), CBioseq::x_SeqLoc_To_DeltaExt(), and CCDSTranslationPanel::x_SetLocationForProtein().

◆ GetA()

const CSeq_bond_Base::TA & CSeq_bond_Base::GetA ( void  ) const
inline

◆ GetAccession()

const CTextseq_id_Base::TAccession & CTextseq_id_Base::GetAccession ( void  ) const
inline

Get the Accession member data.

Returns
Reference to the member data.

Definition at line 340 of file Textseq_id_.hpp.

References CTextseq_id_Base::CanGetAccession(), CTextseq_id_Base::m_Accession, and CSerialObject::ThrowUnassigned().

Referenced by AllowOrphanedProtein(), CTextseq_id::AsFastaString(), CSeq_id_Descr::Assign(), CGffRecord::AssignSeqId(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CAlnMix::ChooseSeqId(), CTextseq_id::Compare(), CSeq_id::ComposeOSLT(), CpSeqId(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), extractBioseqInfo(), CSeq_id_Textseq_Tree::FindInfo(), CSeq_id_Textseq_Tree::FindMatch(), CSeq_id_Textseq_Tree::FindOrCreate(), CWGSFileInfo::FindProtAcc(), CSeq_id_Textseq_Tree::FindReverseMatch(), flat2asn_range_func(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), fta_fix_seq_id(), FTASeqLocCheck(), get_accession_from_id(), GetAccAndVersion(), GetAccessionAndDatabaseSource(), GetAccVer(), CDefaultSynonymMapper::GetBestSynonym(), GetDirectLabel(), CWGSDataLoader_Impl::GetFileInfoByAcc(), CWGSDataLoader_Impl::GetFileInfoByProtAcc(), GetLabel(), GetProtRefSeqId(), CVDBGraphDb_Impl::GetSeqInfo(), GetWGSMasterSeq_id(), CSeq_id::IdentifyAccession(), CValidError_bioseq::IsTSAAccession(), CValidError_bioseq::IsWGSAccession(), CValidError_bioseq::IsWp(), Make_SeqID_String(), CTextseq_id::Match(), CSeq_id_Textseq_Info::Pack(), CSeq_id_Textseq_PlainInfo::ParseCaseVariant(), CWGSResolver_Ids::ParseWGSPrefix(), s_AssignTextseq_id(), s_DeflineCompare(), s_Fingerprint_Textseq_id(), s_GetBestSynonym(), s_GetIdLabel(), s_GetModelEvidance(), s_ValidateAcc(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CValidError_imp::Setup(), StrippedAccVer(), CWGSFileInfo::SAccFileInfo::ValidateAcc(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateOrgContext(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqIds(), x_Assign(), CFeatureGenerator::SImplementation::x_CheckMatch(), CSeqDBVol::x_CheckVersions(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CGenbankGatherer::x_DoSingleSection(), CSeq_id_Textseq_Tree::x_Equals(), CVectorScreen::x_FindAccession(), CSeq_id_Textseq_Tree::x_FindStrInfo(), CGencollIdMapper::x_FixImperfectId(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), CGencollIdMapper::x_Init(), CTopLevelSeqEntryContext::x_InitSeqs(), CCdregionValidator::x_IsProductMisplaced(), CFlatGatherer::x_MergeEqualBioSources(), CDeflineGenerator::x_SetFlags(), CBioseqContext::x_SetId(), CLocusItem::x_SetName(), CFeatureGenerator::SImplementation::x_SetQualForGapFilledModel(), CValidError_bioseq::x_ShowBioProjectWarning(), CSeq_id_Textseq_Tree::x_Unindex(), and CFastaOstream::x_WriteAsFasta().

◆ GetB()

const CSeq_bond_Base::TB & CSeq_bond_Base::GetB ( void  ) const
inline

◆ GetBond()

const CSeq_loc_Base::TBond & CSeq_loc_Base::GetBond ( void  ) const

◆ GetChain()

CPDB_seq_id_Base::TChain CPDB_seq_id_Base::GetChain ( void  ) const
inline

◆ GetChain_id()

const CPDB_seq_id_Base::TChain_id & CPDB_seq_id_Base::GetChain_id ( void  ) const
inline

◆ GetCit()

const CPatent_seq_id_Base::TCit & CPatent_seq_id_Base::GetCit ( void  ) const
inline

◆ GetDb()

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

Get the Db member data.

Returns
Reference to the member data.

Definition at line 302 of file Giimport_id_.hpp.

References CGiimport_id_Base::CanGetDb(), CGiimport_id_Base::m_Db, and CSerialObject::ThrowUnassigned().

Referenced by GetAccessionAndDatabaseSource(), SChildLess::operator()(), s_Fingerprint_Giimport_id(), and x_Assign().

◆ GetDdbj()

const CSeq_id_Base::TDdbj & CSeq_id_Base::GetDdbj ( void  ) const

◆ GetEmbl()

const CSeq_id_Base::TEmbl & CSeq_id_Base::GetEmbl ( void  ) const

◆ GetEmpty()

const CSeq_loc_Base::TEmpty & CSeq_loc_Base::GetEmpty ( void  ) const

◆ GetEquiv()

const CSeq_loc_Base::TEquiv & CSeq_loc_Base::GetEquiv ( void  ) const

◆ GetFeat()

const CSeq_loc_Base::TFeat & CSeq_loc_Base::GetFeat ( void  ) const

Get the variant data.

Returns
Reference to the data.

Definition at line 348 of file Seq_loc_.cpp.

References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Feat, and CSeq_loc_Base::m_object.

Referenced by CSeq_loc::Assign(), and s_Fingerprint_Seq_loc().

◆ GetFrom()

CSeq_interval_Base::TFrom CSeq_interval_Base::GetFrom ( void  ) const
inline

Get the From member data.

Returns
Copy of the member data.

Definition at line 383 of file Seq_interval_.hpp.

References CSeq_interval_Base::CanGetFrom(), CSeq_interval_Base::m_From, and CSerialObject::ThrowUnassigned().

Referenced by AgpRead(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), check_short_CDS(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_align::CreateDensegFromStdseg(), CRawWiggleRecord::Dump(), CBioseqEditor::EditSelection(), EndAdded(), CGBObjectLoader::Execute(), AlignmentCollection::FindSeqInterval(), variation::FindSSRLoc(), FixMixLoc(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), fta_get_acc_minmax_strand(), CWriteUtil::GetCodeBreak(), CReadBlastApp::getFromTo(), CSeq_interval::GetLength(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CStd_seg::GetSeqRange(), CSeq_interval::GetStart(), CSeq_interval::GetStop(), CWriteUtil::GetTranssplicedEndpoints(), CWriteUtil::GetTrnaAntiCodon(), IsLocFullLength(), IsNotDuplicateInterval(), IsValid(), CSeq_loc_Conversion::MakeDstMix(), CDDAnnotateDialog::NewOrEditMotif(), CStd_seg::OffsetRow(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), PrintSeqIntUseBestID(), CStd_seg::RemapToLoc(), TMaskedQueryRegions::RestrictToSeqInt(), RevComp(), ReverseComplementLocation(), CFeatTreeSampleApp::Run(), s_AddSeqIntString(), s_CheckInterval(), s_ExtendIntervalToEnd(), s_Fingerprint_Seq_interval(), s_FixIntervalProtToCds(), s_GetLabel(), s_GetSeq_intervalLabel(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_LocationToStartStopPairs(), s_LocToRange(), s_OOFBlastHSP2SeqAlign(), s_RemoveBogusFuzzFromIntervals_Helper(), s_SeqIntervalDelete(), s_SeqIntervalToSeqLocInfo(), s_SeqLoc2MaskedSubjRanges(), s_SubLocDeltaSeq(), s_SubsequentIntron(), sConvertIntToPoint(), CClippedScorer::ScoreAlignments(), SeqIntCheckCpp(), SeqIntPartialCheck(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CBedFeatureRecord::SetBlocks(), CGffFeatureRecord::SetLocation(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), SplitLocationForGap(), sx_AddBits(), CBlastTabular::sx_MineSegment(), TestOneCDS(), CdBlaster::truncateBioseq(), CAssemblyGapValidator::Validate(), NTweakExon::Validate(), CUCSCRegionWriter::WriteAnnot(), CSeqMap::x_Add(), CFeatureItem::x_AddQualsCdregionIdx(), CPhrap_Contig::x_AddReadLocFeats(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CMultiAligner::x_AlignFillerBlocks(), x_Assign(), CGvfWriteRecord::x_AssignAttributeStartRange(), CSeq_loc::x_CalculateTotalRangeCheckId(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CCdsGlyph::x_DrawProtSeqWithMapping(), CDisplaySeqalign::x_FillLocList(), CUnorderedSplitter::x_FixAlignment(), CFastaOstreamEx::x_GetCodeBreak(), CMultiAligner::x_GetSeqalign(), CAnnotTypes_CI::x_Init(), CGencollIdMapper::x_IsLoc_Int_InAGap(), x_IsNotAdjacent(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGFFReader::x_ParseAlignRecord(), CGC_Assembly_Parser::x_ParseGCSequence(), CSeq_loc_CI_Impl::x_ProcessInterval(), variation::CVariationUtil::x_Remap(), CValidError_imp::x_ReportInvalidFuzz(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CNewCleanup_imp::x_SeqIntervalBC(), CVectorTrimPanel::x_SeqIntervalDelete(), CLocusItem::x_SetTopology(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CBlastFilterTest::x_TestLowerCaseMaskWith(), CSingleFeatValidator::x_ValidateImpFeatLoc(), CGff3Writer::xAssignFeature(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), XGappedSeqLocsToDeltaSeqs(), CUCSCRegionReader::xParseFeatureUCSCFormat(), CGff3Reader::xVerifyExonLocation(), and CBedGraphWriter::xWriteSingleFeature().

◆ GetFuzz() [1/2]

const CPacked_seqpnt_Base::TFuzz & CPacked_seqpnt_Base::GetFuzz ( void  ) const
inline

◆ GetFuzz() [2/2]

const CSeq_point_Base::TFuzz & CSeq_point_Base::GetFuzz ( void  ) const
inline

◆ GetFuzz_from()

const CSeq_interval_Base::TFuzz_from & CSeq_interval_Base::GetFuzz_from ( void  ) const
inline

◆ GetFuzz_to()

const CSeq_interval_Base::TFuzz_to & CSeq_interval_Base::GetFuzz_to ( void  ) const
inline

◆ GetGenbank()

const CSeq_id_Base::TGenbank & CSeq_id_Base::GetGenbank ( void  ) const

◆ GetGeneral()

const CSeq_id_Base::TGeneral & CSeq_id_Base::GetGeneral ( void  ) const

Get the variant data.

Returns
Reference to the data.

Definition at line 369 of file Seq_id_.cpp.

References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_General, and CSeq_id_Base::m_object.

Referenced by CFeatGapInfo::AdjustProteinSeq(), CSeq_id::AdjustScore(), CSeq_id::Assign(), CSeq_id::BaseBlastScore(), CSeq_id::BaseFastaAAScore(), CSeq_id::BaseFastaNAScore(), BOOST_AUTO_TEST_CASE(), CReadDispatcher::CannotProcess(), CannotProcess(), CGeneralToLocalId::CGeneralToLocalId(), CLocalToGeneralId::CLocalToGeneralId(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), CGuiObjectInfoSeq_id::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractAccession(), ExtractGnomonModelNum(), CBlastDBExtractor::ExtractSeqId(), CSeq_id_General_Tree::FindMatch(), GetAccessionAndDatabaseSource(), GetCDDPssmIdFromSeqId(), CWGSDataLoader_Impl::GetFileInfo(), GetGeneralOrLocal(), CWriteUtil::GetIdType(), CSeq_id::GetMatchingIds(), GetNewGeneralProtId(), CVDBBlastUtil::GetOIDFromVDBSeqId(), CSeq_id_General_PlainInfo::GetPackedSeqId(), GetProteinId(), CCommentItem::GetStringForTPA(), GetTitle(), CGeneralIDField::GetVal(), CEditingActionEntireGeneralId::GetValue(), CEditingActionGeneralIdDb::GetValue(), CEditingActionGeneralIdTag::GetValue(), CTraceDataProxy::HasData(), CSGTraceGraphDS::HasData(), CSeq_id::IdentifyAccession(), CGuiSeqInfoSeq_id::IsDNA(), CEditingActionFileId::IsSetValue(), CEditingActionGeneralIdDb::IsSetValue(), CEditingActionGeneralIdTag::IsSetValue(), CSGSequenceDS::IsTraceAssembly(), CTraceDataProxy::LoadData(), CSGTraceGraphDS::LoadData(), CId1Reader::LoadSeq_idSeq_ids(), CSeq_id_General_PlainInfo::ParseCaseVariant(), CTabularFormatter_SeqId::Print(), s_AssignSeq_id(), s_CheckTraceMateAlign(), s_FindSmartSeqId(), s_Fingerprint_Seq_id(), s_GetAlignmentTooltip(), CMacroFunction_MakeBoldXrefs::s_GetBarcodeId(), s_GetSRASeqMetadata(), s_ShouldUseOriginalID(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CSeqDBImpl::SeqidToOids(), CValidError_imp::Setup(), TestCollidingAccessionFixes(), CValidError_bioseq::ValidateIDSetAgainstDb(), CVDBBlastUtil::VDBIdType(), CFeatureItem::x_AddQualProteinId(), CWriteDB_IsamIndex::x_AddStringIds(), CWriteDB_IsamIndex::x_AddTraceIds(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CVectorScreen::x_FindTypeGeneral(), CDBSourceItem::x_GatherInfo(), CPrimaryItem::x_GetStrForPrimary(), CFileIDField::x_IsNCBIFILEId(), CId2ReaderBase::x_ProcessGetBlobId(), CCdregionValidator::x_ReportTranslationProblems(), CValidError_bioseq::x_TranscriptIDsMatch(), CSingleFeatValidator::x_ValidateLocusTagGeneralMatch(), CSeq_id::x_WriteContentAsFasta(), and XISAGappedSeqLoc().

◆ GetGi()

CSeq_id_Base::TGi CSeq_id_Base::GetGi ( void  ) const
inline

Get the variant data.

Returns
Copy of the variant data.

Definition at line 889 of file Seq_id_.hpp.

References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Gi, and CSeq_id_Base::m_Gi.

Referenced by CReadUtil::AsSeqId(), CSeq_id::Assign(), CGffRecord::AssignSeqId(), BOOST_AUTO_TEST_CASE(), CTestProtProd_EntrezNeighbors::CanTest(), CAlnMix::ChooseSeqId(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), CTableImportDataSource::ConvertToSeqAnnot(), DensegConvert(), ExtractGi(), CBlastDBExtractor::ExtractLinksInteger(), CBlastDBExtractor::ExtractMembershipInteger(), CSeqAlignFilter::FilterByGiList(), CSeqAlignFilter::FilterByGiListFromFile(), g_DoesNotReferencePrimary(), GetAccessionAndDatabaseSource(), CCdCore::GetGI(), AlignmentCollection::GetGI(), IBISInteraction::GetGi(), CLocationListCtrl::GetIdFromForm(), CSeqUtils::GetLocPlacements(), CWGSDb_Impl::GetMasterGi(), GetMasterGIFromSeqAlign(), CSeq_feat_Handle::GetSNPGi(), TaxClient::GetTaxIDForSeqId(), CTaxTreeDS_ObjMgr::GetTaxMap(), GiFootPrint::GiFootPrint(), CId1Reader::LoadGiBlob_ids(), CId1Reader::LoadGiSeq_ids(), Make_GI_or_PDB_String_CN3D(), Make_SeqID_String(), CSeqUtils::MapStringId(), CSeq_annot_SNP_Info::OffsetGi(), PatchTargetSequence(), CTestProtProd_EntrezNeighbors::RunTest(), s_AssignSeq_id(), s_CheckQuals_cdregion(), CPsiBlastTestFixture::s_CountNumberUniqueGIs(), s_DeflineCompare(), s_DupIdsBioseq(), s_FindGi(), s_Fingerprint_Seq_id(), s_GetAlnMapplingLocs(), s_GetRefSeq_id(), s_GetSequencesIntoScope(), s_IdXrefsNotReciprocal(), s_Matches(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), sx_GetRefSeq_id(), CDUpdater::update(), CValidError_bioseq::ValidateDeltaLoc(), CWriteDB_Volume::WriteSequence(), CWriteDB_IsamIndex::x_AddGis(), CFeatureItem::x_AddQualProteinId(), CFeatureItem::x_AddQualsRna(), CSeq_annot_SNP_Info::x_CheckId(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CTaxTreeToolJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CNgAlignApp::x_CreateSequenceSet(), CGencollIdMapper::x_FindChromosomeSequence(), CGencollIdMapper::x_FixImperfectId(), CDBSourceItem::x_FormatDBSourceID(), CDBSourceItem::x_GatherInfo(), CProjectFileWriter::x_GetGi(), CAppHitFilter::x_LoadConstraints(), CGFFReader::x_ResolveNewSeqName(), CPSGS_CDDProcessor::x_SendAnnotInfo(), CSeqAlignFilter::x_UpdateGiInSeqalign(), and CSeq_id::x_WriteContentAsFasta().

◆ GetGibbmt()

CSeq_id_Base::TGibbmt CSeq_id_Base::GetGibbmt ( void  ) const
inline

◆ GetGibbsq()

CSeq_id_Base::TGibbsq CSeq_id_Base::GetGibbsq ( void  ) const
inline

◆ GetGiim()

const CSeq_id_Base::TGiim & CSeq_id_Base::GetGiim ( void  ) const

◆ GetGpipe()

const CSeq_id_Base::TGpipe & CSeq_id_Base::GetGpipe ( void  ) const

◆ GetId() [1/4]

CGiimport_id_Base::TId CGiimport_id_Base::GetId ( void  ) const
inline

◆ GetId() [2/4]

const CPacked_seqpnt_Base::TId & CPacked_seqpnt_Base::GetId ( void  ) const
inline

◆ GetId() [3/4]

const CSeq_interval_Base::TId & CSeq_interval_Base::GetId ( void  ) const
inline

Get the Id member data.

Returns
Reference to the member data.

Definition at line 517 of file Seq_interval_.hpp.

References CSeq_interval_Base::m_Id, and CSeq_interval_Base::ResetId().

Referenced by CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CRawWiggleRecord::Dump(), EndAdded(), SeqTreeAsnizer::fillSeqItem(), AlignmentCollection::FindSeqInterval(), FixMixLoc(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), GetLowHighFromSeqLoc(), CBlastInput::GetNextSeqBatch(), GetOverlappingFeatures(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), HasExcludedAnnotation(), IsNotDuplicateInterval(), IsValid(), OkToAdjustLoc(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), PrintSeqIntUseBestID(), TMaskedQueryRegions::RestrictToSeqInt(), ReverseComplementLocation(), s_CheckIfMatchesBioseq(), s_Fingerprint_Seq_interval(), s_FixIntervalProtToCds(), s_GetLabel(), s_GetSeq_intervalLabel(), s_IsVirtualSeqInt(), SeqIntPartialCheck(), CBedImportData::Serialize(), CGtfImportData::Serialize(), TryOneCaseMixLoc(), UpgradeSeqLocId(), CSeqMap::x_Add(), x_Assign(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CValidError_imp::x_CheckSeqInt(), CNgAlignApp::x_CreateSequenceSet(), CDisplaySeqalign::x_FillLocList(), CUnorderedSplitter::x_FixAlignment(), CCommonComponentScorer::x_GetDeltaExtCompList(), CMultiAligner::x_GetSeqalign(), CPsiBlastInputData::x_GetSubjectSequence(), CAnnotTypes_CI::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), x_IsCorrectlyOrdered(), CGencollIdMapper::x_IsLoc_Int_InAGap(), x_IsNotAdjacent(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGC_Assembly_Parser::x_ParseGCSequence(), CSeq_loc_CI_Impl::x_ProcessInterval(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CValidError_imp::x_ReportInvalidFuzz(), CAnnot_Collector::x_SearchRange(), CNewCleanup_imp::x_SeqIntervalBC(), and CBedGraphWriter::xWriteSingleFeature().

◆ GetId() [4/4]

const CSeq_point_Base::TId & CSeq_point_Base::GetId ( void  ) const
inline

◆ GetInt()

const CSeq_loc_Base::TInt & CSeq_loc_Base::GetInt ( void  ) const

Get the variant data.

Returns
Reference to the data.

Definition at line 194 of file Seq_loc_.cpp.

References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Int, and CSeq_loc_Base::m_object.

Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), AgpRead(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), check_short_CDS(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CSeq_loc_Conversion::ConvertSimpleMix(), CBioseqEditor::EditSelection(), variation::FindSSRLoc(), FixMixLoc(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), GenelocContained(), CWriteUtil::GetCodeBreak(), CAddGlobalCodeBreak::GetCommand(), GetCoverage(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), CBlobSplitterImpl::GetLength(), GetLength(), GetLowHighFromSeqLoc(), CBlastInput::GetNextSeqBatch(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), GetRetranslateCDSCommand(), GetReverseComplement(), CLocationListCtrl::GetSeq_loc(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), GetStrand(), CSeq_loc::GetStrand(), CWriteUtil::GetTrnaAntiCodon(), CEditingActionFeatAnticodon::GetValue(), HasExcludedAnnotation(), IBISAnnotateDialog::HighlightAnnotation(), CDDAnnotateDialog::HighlightAnnotation(), CLocationPanel::Init(), CBedImportData::Initialize(), IsLocFullLength(), CGencollIdMapper::IsLocInAGap(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CDDAnnotateDialog::NewOrEditMotif(), CStd_seg::OffsetRow(), SSNP_Info::ParseSeq_feat(), CStd_seg::RemapToLoc(), RetranslateCdregion(), RetranslateCDS(), CRetranslateCDS::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), RevComp(), CFeatTreeSampleApp::Run(), s_AddLocString(), s_Fingerprint_Seq_loc(), s_FixIntervalProtToCds(), s_GetLabel(), s_GetStrand(), s_GetTrimmedLength(), s_GetUngapLoc(), s_LocationToStartStopPairs(), s_LocIsFuzz(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocDelete(), s_SubsequentIntron(), sConvertIntToPoint(), CClippedScorer::ScoreAlignments(), SeqIntCheckCpp(), SeqLocPartialCheck(), SeqLocPrintUseBestID(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), sx_AddBits(), CBlastTabular::sx_MineSegment(), TestOneCDS(), CSingleCDSExceptionPanel::TransferDataFromWindow(), CLocationPanel::TransferDataToWindow(), TrimStopsFromCompleteCDS(), CdBlaster::truncateBioseq(), TryOneCaseMixLoc(), CAssemblyGapValidator::Validate(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CFeatureItem::x_AddQualsCdregionIdx(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CMultiAligner::x_AlignFillerBlocks(), CGvfWriteRecord::x_AssignAttributeEndRange(), CGvfWriteRecord::x_AssignAttributeStartRange(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedInt(), CSeq_loc::x_CheckId(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CNgAlignApp::x_CreateSequenceSet(), CFeatGlyph::x_DrawFeatureBar_sv(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFastaOstreamEx::x_GetCodeBreak(), CCommonComponentScorer::x_GetDeltaExtCompList(), CMultiAligner::x_GetSeqalign(), CPsiBlastInputData::x_GetSubjectSequence(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CSeq_align_Mapper_Base::x_Init(), CAnnotTypes_CI::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CSeqTableInfo::x_IsSorted(), CLocationPanel::x_LoadSeqLoc(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGFFReader::x_ParseAlignRecord(), CGC_Assembly_Parser::x_ParseGCSequence(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessLocation(), CIdMapperTestApp::x_RecurseMapSeqAligns(), variation::CVariationUtil::x_Remap(), CVectorTrimPanel::x_RetranslateCDS(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CVectorTrimPanel::x_SeqLocDelete(), CLocusItem::x_SetTopology(), CSingleFeatValidator::x_ValidateImpFeatLoc(), CUCSCRegionReader::xParseFeatureUCSCFormat(), CGff3Reader::xUpdateAnnotGeneric(), CGff3Reader::xUpdateAnnotRna(), CGtfAnnotAssembler::xUpdateCds(), CGff2Record::xUpdateFeatureData(), CGtfAnnotAssembler::xUpdateGene(), and CGff3Reader::xVerifyExonLocation().

◆ GetLocal()

const CSeq_id_Base::TLocal & CSeq_id_Base::GetLocal ( void  ) const

◆ GetMix()

const CSeq_loc_Base::TMix & CSeq_loc_Base::GetMix ( void  ) const

Get the variant data.

Returns
Reference to the data.

Definition at line 282 of file Seq_loc_.cpp.

References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Mix, and CSeq_loc_Base::m_object.

Referenced by CHandleRangeMap::AddLocation(), CAlignCDSAddPanel::AddOneCommand(), CAlignRNAAddPanel::AddOneCommand(), CAlignOtherAddPanel::AddOneCommand(), CSeq_loc_mix::AddSeqLoc(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CWriteUtil::ChangeToPackedInt(), CSeq_loc::ChangeToPackedInt(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_loc_Conversion::GetDstMix(), GetEmblInstContig(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), GetGenBankInstContig(), GetLength(), GetReverseComplement(), GetSeqLocation(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CGuiObjectInfoPrimer::GetToolTip(), CEditingActionFeatAnticodon::GetValue(), CLocationEditPolicy::HasNulls(), CLocationPanel::Init(), CWriteUtil::IsLocationOrdered(), CGencollIdMapper::IsLocInAGap(), CFeaturePropagator::IsOrdered(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CSeq_loc_CI_Impl::MakeLoc(), CFeaturePropagator::MakeOrdered(), NormalizeLoc(), s_AddLocString(), s_CalcCoverageCount(), s_CountIntervals(), s_Fingerprint_Seq_loc(), s_FlattenLoc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), s_IsOrdered(), s_NeedsFlattening(), s_NormalizeNullsBetween(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocDelete(), SeqLocPrintUseBestID(), CLocationPanel::TransferDataToWindow(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSGFeatureJob::x_CreateCloneFeature(), CFeatureTableReader_Imp::x_FinishFeature(), CFeatureTableReader_Imp::x_GetPointStrand(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CGFFReader::x_ResolveLoc(), CBioseq::x_SeqLoc_To_DeltaExt(), CVectorTrimPanel::x_SeqLocDelete(), CCDSTranslationPanel::x_SetLocationForProtein(), and XMLGetInstContig().

◆ GetMol()

const CPDB_seq_id_Base::TMol & CPDB_seq_id_Base::GetMol ( void  ) const
inline

◆ GetName()

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

◆ GetNamed_annot_track()

const CSeq_id_Base::TNamed_annot_track & CSeq_id_Base::GetNamed_annot_track ( void  ) const

◆ GetOther()

const CSeq_id_Base::TOther & CSeq_id_Base::GetOther ( void  ) const

◆ GetPacked_int()

const CSeq_loc_Base::TPacked_int & CSeq_loc_Base::GetPacked_int ( void  ) const

Get the variant data.

Returns
Reference to the data.

Definition at line 216 of file Seq_loc_.cpp.

References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Packed_int, and CSeq_loc_Base::m_object.

Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSequenceSearchForm::ConstructQuery(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), ConvertPackedIntToInterval(), CSeqUtils::GetCdsMappingInfoFromRna(), IBISInteraction::GetFootprint(), CReadBlastApp::getFromTo(), IBISInteraction::GetGi(), GetLength(), CRemoteBlast::GetMasks(), GetPositionsForAlignAnnot(), GetReverseComplement(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CWriteUtil::GetTranssplicedEndpoints(), CLocationPanel::Init(), CGencollIdMapper::IsLocInAGap(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CFastaObjectLoader::LoadFromStream(), CGtfLocationMerger::MergeLocationForGene(), NormalizeLoc(), PackedSeqLocToMaskedQueryRegions(), ProjectExon(), s_AddLocString(), s_CountIntervals(), s_Fingerprint_Seq_loc(), s_FlattenLoc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), s_LocationToStartStopPairs(), s_LocIsFuzz(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocDelete(), SeqLocPartialCheck(), SeqLocPrintUseBestID(), CBedImportData::Serialize(), CCleanup::SetCodeBreakLocation(), CLocationPanel::TransferDataToWindow(), NTweakExon::TweakExon(), NTweakExon::Validate(), CUCSCRegionWriter::WriteAnnot(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedInt(), CSeq_loc::x_CheckId(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CLocationPanel::x_LoadSeqLoc(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CBioseq::x_SeqLoc_To_DeltaExt(), CVectorTrimPanel::x_SeqLocDelete(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGtfWriter::xWriteFeatureExons(), CGff3Writer::xWriteFeatureRecords(), CGff3Writer::xWriteFeatureRna(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().

◆ GetPacked_pnt()

const CSeq_loc_Base::TPacked_pnt & CSeq_loc_Base::GetPacked_pnt ( void  ) const

◆ GetPatent()

const CSeq_id_Base::TPatent & CSeq_id_Base::GetPatent ( void  ) const

◆ GetPdb()

const CSeq_id_Base::TPdb & CSeq_id_Base::GetPdb ( void  ) const

◆ GetPir()

const CSeq_id_Base::TPir & CSeq_id_Base::GetPir ( void  ) const

◆ GetPnt()

const CSeq_loc_Base::TPnt & CSeq_loc_Base::GetPnt ( void  ) const

Get the variant data.

Returns
Reference to the data.

Definition at line 238 of file Seq_loc_.cpp.

References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Pnt, and CSeq_loc_Base::m_object.

Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), FixMixLoc(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), GetLowHighFromSeqLoc(), GetReverseComplement(), CSeq_align::GetSeqRange(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), GetStrand(), CSeq_loc::GetStrand(), CLocationPanel::Init(), CGencollIdMapper::IsLocInAGap(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CStd_seg::OffsetRow(), SSNP_Info::ParseSeq_feat(), PrintPntAndPntsUseBestID(), s_AddLocString(), s_CanAdd(), s_Fingerprint_Seq_loc(), s_GetLabel(), s_GetStrand(), s_IsBetween(), s_LocationToStartStopPairs(), s_LocIsFuzz(), s_PrintLocAsJavascriptArray(), s_SubsequentIntron(), SeqLocPartialCheck(), SeqPntCheckCpp(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), SplitLocationForGap(), CLocationPanel::TransferDataToWindow(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CSGFeatureJob::x_CalcIntervals(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedPnt(), CSeq_loc::x_CheckId(), CFeatGlyph::x_DrawRSites(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CSeq_align_Mapper_Base::x_Init(), CLocationPanel::x_LoadSeqLoc(), variation_ref::CHgvsParser::x_location(), variation::CHgvsParser::x_location(), CReportEntry::x_MapPos(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessLocation(), CBioseqContext::x_SetOpticalMapPoints(), and CAdjustForConsensusSpliceSite::x_UpdateMixLocations().

◆ GetPoint()

CSeq_point_Base::TPoint CSeq_point_Base::GetPoint ( void  ) const
inline

Get the Point member data.

Returns
Copy of the member data.

Definition at line 303 of file Seq_point_.hpp.

References CSeq_point_Base::CanGetPoint(), CSeq_point_Base::m_Point, and CSerialObject::ThrowUnassigned().

Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion_Set::ConvertBond(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertPoint(), CSeq_loc_Conversion_Set::ConvertPoint(), FixMixLoc(), fta_get_acc_minmax_strand(), GetLowHighFromSeqLoc(), CSeq_align::GetSeqRange(), CSeq_bond::GetStart(), CSeq_loc::GetStart(), CSeq_bond::GetStop(), CSeq_loc::GetStop(), CGencollIdMapper::IsLocInAGap(), variation::IsPureFuzzPoint(), IsValid(), CStd_seg::OffsetRow(), SSNP_Info::ParseSeq_feat(), ReverseComplementLocation(), s_AddSeqPointString(), s_Fingerprint_Seq_point(), s_GetLabel(), s_Load_Seq_point(), s_LocationToStartStopPairs(), s_PrintLocAsJavascriptArray(), s_SubsequentIntron(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CNewCleanup_imp::SeqLocBC(), SeqPntCheckCpp(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), SplitLocationForGap(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), x_Assign(), CSGFeatureJob::x_CalcIntervals(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedPnt(), CFeatGlyph::x_DrawRSites(), variation_ref::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_general_pos(), variation_ref::CHgvsParser::x_location(), variation::CHgvsParser::x_location(), CReportEntry::x_MapPos(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessPoint(), variation_ref::CHgvsParser::x_range(), variation::CHgvsParser::x_range(), CValidError_imp::x_ReportInvalidFuzz(), variation_ref::CHgvsParser::x_SeqPntToStr(), CBioseqContext::x_SetOpticalMapPoints(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), and xgbint_ver().

◆ GetPoints()

const CPacked_seqpnt_Base::TPoints & CPacked_seqpnt_Base::GetPoints ( void  ) const
inline

◆ GetPrf()

const CSeq_id_Base::TPrf & CSeq_id_Base::GetPrf ( void  ) const

◆ GetRel()

const CPDB_seq_id_Base::TRel & CPDB_seq_id_Base::GetRel ( void  ) const
inline

Get the Rel member data.

Returns
Reference to the member data.

Definition at line 391 of file PDB_seq_id_.hpp.

References CPDB_seq_id_Base::CanGetRel(), CPDB_seq_id_Base::m_Rel, and CSerialObject::ThrowUnassigned().

Referenced by CSeq_id_PDB_Tree::FindMatch(), CSeq_id_PDB_Info::Normalize(), x_Assign(), and CDBSourceItem::x_FormatDBSourceID().

◆ GetRelease() [1/2]

const CGiimport_id_Base::TRelease & CGiimport_id_Base::GetRelease ( void  ) const
inline

Get the Release member data.

Returns
Reference to the member data.

Definition at line 349 of file Giimport_id_.hpp.

References CGiimport_id_Base::CanGetRelease(), CGiimport_id_Base::m_Release, and CSerialObject::ThrowUnassigned().

Referenced by SChildLess::operator()(), s_Fingerprint_Giimport_id(), and x_Assign().

◆ GetRelease() [2/2]

const CTextseq_id_Base::TRelease & CTextseq_id_Base::GetRelease ( void  ) const
inline

◆ GetSeqid()

CPatent_seq_id_Base::TSeqid CPatent_seq_id_Base::GetSeqid ( void  ) const
inline

◆ GetStrand() [1/3]

CPacked_seqpnt_Base::TStrand CPacked_seqpnt_Base::GetStrand ( void  ) const
inline

◆ GetStrand() [2/3]

CSeq_interval_Base::TStrand CSeq_interval_Base::GetStrand ( void  ) const
inline

Get the Strand member data.

Returns
Copy of the member data.

Definition at line 477 of file Seq_interval_.hpp.

References CSeq_interval_Base::CanGetStrand(), CSeq_interval_Base::m_Strand, and CSerialObject::ThrowUnassigned().

Referenced by CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_align::CreateDensegFromStdseg(), EndAdded(), CSeq_interval::FlipStrand(), fta_get_acc_minmax_strand(), CWriteUtil::GetCodeBreak(), CWriteUtil::GetEffectiveStrand(), CReadBlastApp::getFromTo(), CEditingActionFeatAnticodon::GetIntervalString(), GetIntervalString(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), CSeqMap::GetSeqMapForSeq_loc(), GetStrand(), CSeq_loc::GetStrand(), CWriteUtil::GetTrnaAntiCodon(), CBedImportData::Initialize(), CSeq_loc_Conversion::MakeDstMix(), NTweakExon::MinusStrand(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), PrintSeqIntUseBestID(), CStd_seg::RemapToLoc(), TMaskedQueryRegions::RestrictToSeqInt(), RevComp(), s_AddSeqIntString(), s_ExtendIntervalToEnd(), s_FixIntervalProtToCds(), s_GetLabel(), s_GetSeq_intervalLabel(), s_GetStrand(), SeqIntPartialCheck(), SeqLocAdjustForTrim(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CGffFeatureRecord::SetLocation(), CBedFeatureRecord::SetLocation(), CUCSCRegionWriter::WriteAnnot(), CSeqMap::x_Add(), x_Assign(), CNewCleanup_imp::x_BothStrandBC(), CValidError_imp::x_CheckSeqInt(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CAnnotTypes_CI::x_Init(), x_IsCorrectlyOrdered(), CSeq_interval::x_IsMinusStrand(), x_IsNotAdjacent(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGFFReader::x_ParseAlignRecord(), CSeq_loc_CI_Impl::x_ProcessInterval(), x_SameStrand(), CAnnot_Collector::x_SearchRange(), CNewCleanup_imp::x_SeqIntervalBC(), CLocusItem::x_SetTopology(), CGtfWriter::xAssignFeaturesCds(), and CGff2Record::xUpdateFeatureData().

◆ GetStrand() [3/3]

CSeq_point_Base::TStrand CSeq_point_Base::GetStrand ( void  ) const
inline

◆ GetSwissprot()

const CSeq_id_Base::TSwissprot & CSeq_id_Base::GetSwissprot ( void  ) const

◆ GetTo()

CSeq_interval_Base::TTo CSeq_interval_Base::GetTo ( void  ) const
inline

Get the To member data.

Returns
Copy of the member data.

Definition at line 430 of file Seq_interval_.hpp.

References CSeq_interval_Base::CanGetTo(), CSeq_interval_Base::m_To, and CSerialObject::ThrowUnassigned().

Referenced by AgpRead(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), check_short_CDS(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_align::CreateDensegFromStdseg(), CRawWiggleRecord::Dump(), EndAdded(), CGBObjectLoader::Execute(), AlignmentCollection::FindSeqInterval(), variation::FindSSRLoc(), FixMixLoc(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), fta_get_acc_minmax_strand(), CWriteUtil::GetCodeBreak(), CReadBlastApp::getFromTo(), CSeq_interval::GetLength(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CStd_seg::GetSeqRange(), CSeq_interval::GetStart(), CSeq_interval::GetStop(), CWriteUtil::GetTranssplicedEndpoints(), CWriteUtil::GetTrnaAntiCodon(), IsLocFullLength(), IsNotDuplicateInterval(), IsValid(), CSeq_loc_Conversion::MakeDstMix(), CDDAnnotateDialog::NewOrEditMotif(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), PrintSeqIntUseBestID(), CStd_seg::RemapToLoc(), TMaskedQueryRegions::RestrictToSeqInt(), RevComp(), ReverseComplementLocation(), CFeatTreeSampleApp::Run(), s_AddSeqIntString(), s_CheckInterval(), s_ExtendIntervalToEnd(), s_Fingerprint_Seq_interval(), s_FixIntervalProtToCds(), s_GetLabel(), s_GetSeq_intervalLabel(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_LocationToStartStopPairs(), s_LocToRange(), s_OOFBlastHSP2SeqAlign(), s_RemoveBogusFuzzFromIntervals_Helper(), s_SeqIntervalDelete(), s_SeqIntervalToSeqLocInfo(), s_SeqLoc2MaskedSubjRanges(), s_SubsequentIntron(), CClippedScorer::ScoreAlignments(), SeqIntCheckCpp(), SeqIntPartialCheck(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CGffFeatureRecord::SetLocation(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetThick(), SplitLocationForGap(), CBlastTabular::sx_MineSegment(), TestOneCDS(), TrimStopsFromCompleteCDS(), CdBlaster::truncateBioseq(), CAssemblyGapValidator::Validate(), NTweakExon::Validate(), CUCSCRegionWriter::WriteAnnot(), CFeatureItem::x_AddQualsCdregionIdx(), CPhrap_Contig::x_AddReadLocFeats(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CMultiAligner::x_AlignFillerBlocks(), x_Assign(), CGvfWriteRecord::x_AssignAttributeEndRange(), CSeq_loc::x_CalculateTotalRangeCheckId(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CCdsGlyph::x_DrawProtSeqWithMapping(), CDisplaySeqalign::x_FillLocList(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFastaOstreamEx::x_GetCodeBreak(), CAnnotTypes_CI::x_Init(), x_IsCorrectlyOrdered(), CGencollIdMapper::x_IsLoc_Int_InAGap(), x_IsNotAdjacent(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessInterval(), CValidError_imp::x_ReportInvalidFuzz(), CAnnot_Collector::x_SearchRange(), CNewCleanup_imp::x_SeqIntervalBC(), CVectorTrimPanel::x_SeqIntervalDelete(), CLocusItem::x_SetTopology(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CBlastFilterTest::x_TestLowerCaseMaskWith(), CSingleFeatValidator::x_ValidateImpFeatLoc(), CGff3Writer::xAssignFeature(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), XGappedSeqLocsToDeltaSeqs(), CGff3Reader::xVerifyExonLocation(), and CBedGraphWriter::xWriteSingleFeature().

◆ GetTpd()

const CSeq_id_Base::TTpd & CSeq_id_Base::GetTpd ( void  ) const

◆ GetTpe()

const CSeq_id_Base::TTpe & CSeq_id_Base::GetTpe ( void  ) const

◆ GetTpg()

const CSeq_id_Base::TTpg & CSeq_id_Base::GetTpg ( void  ) const

◆ GetVersion()

CTextseq_id_Base::TVersion CTextseq_id_Base::GetVersion ( void  ) const
inline

◆ GetWhole()

const CSeq_loc_Base::TWhole & CSeq_loc_Base::GetWhole ( void  ) const

◆ IsBond()

bool CSeq_loc_Base::IsBond ( void  ) const
inline

Check if variant Bond is selected.

Bond type is defined as 'typedef CSeq_bond TBond'.

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

Definition at line 564 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Bond, and CSeq_loc_Base::m_choice.

Referenced by fta_seqloc_del_far(), CSeq_loc_CI_Impl::GetBondBegin(), CSeq_loc_CI_Impl::GetBondEnd(), SeqLocPrintUseBestID(), and SrchCdRegion().

◆ IsDdbj()

bool CSeq_id_Base::IsDdbj ( void  ) const
inline

Check if variant Ddbj is selected.

Ddbj type is defined as 'typedef CTextseq_id TDdbj'.

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

Definition at line 910 of file Seq_id_.hpp.

References CSeq_id_Base::e_Ddbj, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), s_GetNameForBioseq(), and CValidError_bioseq::ValidateDeltaLoc().

◆ IsEmbl()

bool CSeq_id_Base::IsEmbl ( void  ) const
inline

Check if variant Embl is selected.

Embl type is defined as 'typedef CTextseq_id TEmbl'.

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

Definition at line 847 of file Seq_id_.hpp.

References CSeq_id_Base::e_Embl, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), s_GetNameForBioseq(), and CValidError_bioseq::ValidateDeltaLoc().

◆ IsEmpty()

bool CSeq_loc_Base::IsEmpty ( void  ) const
inline

◆ IsEquiv()

bool CSeq_loc_Base::IsEquiv ( void  ) const
inline

Check if variant Equiv is selected.

Equiv type is defined as 'typedef CSeq_loc_equiv TEquiv'.

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

Definition at line 558 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Equiv, and CSeq_loc_Base::m_choice.

Referenced by CSeq_loc_equiv::Add(), CheckForeignLoc(), SeqLocPrintUseBestID(), SrchCdRegion(), and CFeatureGenerator::SImplementation::x_CreateCdsFeature().

◆ IsFeat()

bool CSeq_loc_Base::IsFeat ( void  ) const
inline

Check if variant Feat is selected.

Feat type is defined as 'typedef CFeat_id TFeat'.

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

Definition at line 570 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Feat, and CSeq_loc_Base::m_choice.

◆ IsGenbank()

bool CSeq_id_Base::IsGenbank ( void  ) const
inline

◆ IsGeneral()

bool CSeq_id_Base::IsGeneral ( void  ) const
inline

Check if variant General is selected.

General type is defined as 'typedef CDbtag TGeneral'.

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

Definition at line 877 of file Seq_id_.hpp.

References CSeq_id_Base::e_General, and CSeq_id_Base::m_choice.

Referenced by CSeq_id::AdjustScore(), BOOST_AUTO_TEST_CASE(), CGeneralToLocalId::CGeneralToLocalId(), seqsubmit_split::SIdCompare::compare_seq(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractAccession(), ExtractGnomonModelNum(), CBlastDBExtractor::ExtractSeqId(), GetAccessionAndDatabaseSource(), GetCDDPssmIdFromSeqId(), GetGeneralOrLocal(), GetId(), CVDBBlastUtil::GetOIDFromVDBSeqId(), GetProteinId(), CCommentItem::GetStringForTPA(), CGeneralIDField::GetVal(), CTraceDataProxy::HasData(), CSGTraceGraphDS::HasData(), CEditingActionFileId::IsSetValue(), CEditingActionEntireGeneralId::IsSetValue(), CEditingActionGeneralIdDb::IsSetValue(), CEditingActionGeneralIdTag::IsSetValue(), CSGSequenceDS::IsTraceAssembly(), CTraceDataProxy::LoadData(), CSGTraceGraphDS::LoadData(), CTabularFormatter_SeqId::Print(), s_CheckTraceMateAlign(), s_GetAlignmentTooltip(), CMacroFunction_MakeBoldXrefs::s_GetBarcodeId(), TestCollidingAccessionFixes(), CFeatureItem::x_AddQualDbXref(), CFeatureItem::x_AddQualProteinId(), CWriteDB_IsamIndex::x_AddTraceIds(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CImportFeatTable::x_DoImportCDS(), CVectorScreen::x_FindTypeGeneral(), CPrimaryItem::x_GetStrForPrimary(), CFileIDField::x_IsNCBIFILEId(), CId2ReaderBase::x_ProcessGetBlobId(), CCdregionValidator::x_ReportTranslationProblems(), CValidError_bioseq::x_TranscriptIDsMatch(), CSeq_id_General_Tree::x_Unindex(), CSingleFeatValidator::x_ValidateLocusTagGeneralMatch(), seqsubmit_split::SIdCompare::xGetGeneralId(), and XISAGappedSeqLoc().

◆ IsGi()

bool CSeq_id_Base::IsGi ( void  ) const
inline

Check if variant Gi is selected.

Gi type is defined as 'typedef NCBI_NS_NCBI::TGi TGi'.

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

Definition at line 883 of file Seq_id_.hpp.

References CSeq_id_Base::e_Gi, and CSeq_id_Base::m_choice.

Referenced by CReadUtil::AsSeqId(), BlastHitList2SeqAlign_OMF(), BLASTPrelminSearchHitListToStdSeg(), BOOST_AUTO_TEST_CASE(), CAlnMix::ChooseSeqId(), CGuiObjectInfoSeq_id::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), DensegConvert(), CBlastDBExtractor::ExtractLinksInteger(), CBlastDBExtractor::ExtractMembershipInteger(), CFlatSeqIdQVal::Format(), CFtableFormatter::FormatFeatHeader(), CGBSeqFormatter::FormatFeature(), AlignmentCollection::Get_GI_or_PDB_String_FromAlignment(), CCdCore::Get_GI_or_PDB_String_FromAlignment(), GetAccessionAndDatabaseSource(), CCdCore::GetGI(), AlignmentCollection::GetGI(), IBISInteraction::GetGi(), CLocationListCtrl::GetIdFromForm(), GetLabel(), CSeqUtils::GetLocPlacements(), GetMasterGIFromSeqAlign(), GetProductLabel(), CShowBlastDefline::GetSeqIdListString(), GetSequenceLengthAndId(), CCommentItem::GetStringForTPA(), TaxClient::GetTaxIDForSeqId(), CTaxTreeDS_ObjMgr::GetTaxMap(), GiFootPrint::GiFootPrint(), CSeq_id::IsAllowedSNPScaleLimit(), CGuiSeqInfoSeq_id::IsDNA(), CGuiSeqInfoSeq_id::IsProtein(), Make_GI_or_PDB_String_CN3D(), Make_SeqID_String(), CSeqUtils::MapStringId(), CSeq_annot_SNP_Info::OffsetGi(), PatchTargetSequence(), CBlast_def_line_set::RemoveGIs(), CGBDocument::ReplaceGiSeqIds(), s_BLAST_OneSubjectResults2CSeqAlign(), s_CheckQuals_cdregion(), s_DeflineCompare(), s_DupIdsBioseq(), s_FindGi(), s_GetAlignedSeqGi(), s_GetAlnMapplingLocs(), s_GetRefSeq_id(), s_GetSeqLabel(), s_GetSequencesIntoScope(), s_IdXrefsNotReciprocal(), s_Matches(), s_ModifySeqAlnWithFilteredSeqIDs(), s_ProcessSeqIDsForV5(), s_UpdateSeqAlnWithFilteredSeqIDs(), sx_GetRefSeq_id(), CCDSTranslationPanel::TransferDataToWindow(), CValidError_bioseq::ValidateDeltaLoc(), CSeq_id::WriteAsFasta(), WriteBlastSeqidlistFile(), CWriteDB_Volume::WriteSequence(), CWriteDB_IsamIndex::x_AddGis(), CFeatureItem::x_AddQualDbXref(), CFeatureItem::x_AddQualProteinId(), CGencollIdMapper::x_ApplyPatternToId(), CSeq_annot_SNP_Info::x_CheckId(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CTaxTreeToolJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CNgAlignApp::x_CreateSequenceSet(), CGencollIdMapper::x_FindChromosomeSequence(), CGencollIdMapper::x_FixImperfectId(), CDBSourceItem::x_GatherInfo(), CCreateGeneModelTask::x_GetCommand(), CPrimaryItem::x_GetStrForPrimary(), CBlastKmerResults::x_InitScoreVec(), CWriteDB_LMDB::x_InsertEntry(), CAppHitFilter::x_LoadConstraints(), CGencollIdMapper::x_RecursiveSeqFix(), CGFFReader::x_ResolveNewSeqName(), CBuildDatabase::x_ResolveRemoteId(), CPSGS_CDDProcessor::x_SendAnnotInfo(), SWGSCreateInfo::x_SetId(), CSeqAlignFilter::x_UpdateGiInSeqalign(), and CFastaOstream::x_WriteAsFasta().

◆ IsGibbmt()

bool CSeq_id_Base::IsGibbmt ( void  ) const
inline

Check if variant Gibbmt is selected.

Gibbmt type is defined as 'typedef int TGibbmt'.

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

Definition at line 808 of file Seq_id_.hpp.

References CSeq_id_Base::e_Gibbmt, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), and GetAccessionAndDatabaseSource().

◆ IsGibbsq()

bool CSeq_id_Base::IsGibbsq ( void  ) const
inline

Check if variant Gibbsq is selected.

Gibbsq type is defined as 'typedef int TGibbsq'.

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

Definition at line 781 of file Seq_id_.hpp.

References CSeq_id_Base::e_Gibbsq, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), and GetAccessionAndDatabaseSource().

◆ IsGiim()

bool CSeq_id_Base::IsGiim ( void  ) const
inline

Check if variant Giim is selected.

Giim type is defined as 'typedef CGiimport_id TGiim'.

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

Definition at line 835 of file Seq_id_.hpp.

References CSeq_id_Base::e_Giim, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), GetAccessionAndDatabaseSource(), and CSeq_id_Giim_Tree::x_Unindex().

◆ IsGpipe()

bool CSeq_id_Base::IsGpipe ( void  ) const
inline

Check if variant Gpipe is selected.

Gpipe type is defined as 'typedef CTextseq_id TGpipe'.

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

Definition at line 946 of file Seq_id_.hpp.

References CSeq_id_Base::e_Gpipe, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), and FTASeqLocCheck().

◆ IsInt()

bool CSeq_loc_Base::IsInt ( void  ) const
inline

Check if variant Int is selected.

Int type is defined as 'typedef CSeq_interval TInt'.

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

Definition at line 528 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Int, and CSeq_loc_Base::m_choice.

Referenced by CSeq_loc::Add(), CAdjustForConsensusSpliceSite::AdjustCDS(), variation_ref::CVariationUtil::AdjustDelinsToInterval(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), BOOST_AUTO_TEST_CASE(), ChangeNucProtSetNucId(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CCdsToMatPeptide::ConvertInner(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CSeq_loc_Conversion::ConvertSimpleMix(), CGBObjectLoader::Execute(), CCleanup::ExpandGeneToIncludeChildren(), FixMixLoc(), CHTMLFormatterEx::FormatLocation(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), GenelocContained(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), CAddGlobalCodeBreak::GetCommand(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), GetLowHighFromSeqLoc(), CBlastInput::GetNextSeqBatch(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), CCleanup::GetProteinLocationFromNucleotideLocation(), GetRetranslateCDSCommand(), CLocationListCtrl::GetSeq_loc(), GetSeqLocation(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CEditingActionFeatAnticodon::GetValue(), HasExcludedAnnotation(), IBISAnnotateDialog::HighlightAnnotation(), CDDAnnotateDialog::HighlightAnnotation(), IsLocFullLength(), CGencollIdMapper::IsLocInAGap(), IsTransSpliced(), MakeDDFromSeqLoc(), CGtfLocationMerger::MergeLocationForGene(), CDDAnnotateDialog::NewOrEditMotif(), variation::SFastLocSubtract::operator()(), CReadBlastApp::overlaps(), CCleanup::ParseCodeBreak(), ProjectAndCollapseCDS(), RetranslateCdregion(), RetranslateCDS(), CRetranslateCDS::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), RevComp(), CNewCleanup_imp::RnaFeatBC(), variation::CVariationUtil::s_AddIntronicOffsets(), s_ConvertToBlastQueries(), s_FixIntervalProtToCds(), s_GetAlignmentSpans_Interval(), s_GetTrimmedLength(), s_GetUngapLoc(), s_LocationToStartStopPairs(), s_RemapToSubjectLoc(), variation::CVariationUtil::s_ResolveIntronicOffsets(), s_SeqLoc2MaskedSubjRanges(), s_SubLocDeltaSeq(), s_SubsequentIntron(), SeqLocPrintUseBestID(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CSeqTableSetLocFuzzFromLim::SetInt(), CSeqTableSetLocFuzzToLim::SetInt(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), CBlastTabular::sx_MineSegment(), CSingleCDSExceptionPanel::TransferDataFromWindow(), TrimStopsFromCompleteCDS(), CdBlaster::truncateBioseq(), CAssemblyGapValidator::Validate(), CFlatSeqLoc::x_Add(), CFeatureItem::x_AddQualsCdregionIdx(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CGvfWriteRecord::x_AssignAttributeEndRange(), CGvfWriteRecord::x_AssignAttributeStartRange(), CSeq_loc::x_ChangeToPackedInt(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CProSplignJob::x_CreateProjectItems(), CFeatGlyph::x_DrawFeatureBar_sv(), CNewCleanup_imp::x_ExtendSingleGeneOnMrna(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CCommonComponentScorer::x_GetDeltaExtCompList(), CGuiObjectInfoSeq_feat::x_GetLocLengthRow(), CMultiAligner::x_GetSeqalign(), CFeatTrim::x_GetStartOffset(), CAlignedFeatureGraph::x_GetTooltip(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), variation::CVariationUtil::x_InferNAfromAA(), CAnnotTypes_CI::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeqTableInfo::x_IsSorted(), CGFFReader::x_ParseAlignRecord(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CIdMapperTestApp::x_RecurseMapSeqAligns(), variation::CVariationUtil::x_Remap(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CVectorTrimPanel::x_RetranslateCDS(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CProSplignTool::x_SelectCompatibleInputObjects(), CSplignTool::x_SelectCompatibleInputObjects(), CBioseqContext::x_SetLocation(), CLocusItem::x_SetTopology(), CAdjustForConsensusSpliceSite::x_UpdateExonFeatures(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), CValidError_graph::x_ValidateGraphLocation(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CSingleFeatValidator::x_ValidateImpFeatLoc(), xgbloc_ver(), and CGtfAnnotAssembler::xUpdateGene().

◆ IsLocal()

bool CSeq_id_Base::IsLocal ( void  ) const
inline

Check if variant Local is selected.

Local type is defined as 'typedef CObject_id TLocal'.

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

Definition at line 775 of file Seq_id_.hpp.

References CSeq_id_Base::e_Local, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), CCreateProteinId::create_protein_ids(), CRemoveSeqId::CRemoveSeqId(), CSeqFormatter::DumpAll(), CCreateCoverageTask::Execute(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractSeqId(), SeqSwapper::findReplacements(), CTextAlnReader::GenerateID(), GetAccessionAndDatabaseSource(), GetGeneralOrLocal(), CBioseq::GetLocalId(), CBioseq::GetNonLocalId(), CTableDataGCAssembly::GetObjectValue(), CShowBlastDefline::GetSeqIdListString(), CTableDataGCAssembly::GetStringValue(), CSeqTextPanel::InitObject(), CVcfTableView::InitView(), IsConsensus(), IsLocalID(), CLoadStructComments::LoadWithAccessions(), Make_SeqID_String(), CSeqIdValidate::operator()(), OverrideLenIfAccession(), CSeqFastaReader::PostProcessIDs(), CBlastFormat::PrintReport(), CBlastInputReader::ReadOneSeq(), RelaxedMatch(), s_BestLocalRank(), s_BestNonLocalRank(), s_CheckTraceMateAlign(), s_FindLocalId(), s_GetIdLabel(), s_GetLabel(), s_MatchSeqIds(), s_ReplaceLocalId(), s_SeqAlignToXMLHit(), s_UseFastaReaderDeflines(), CNewCleanup_imp::SeqIdBC(), CStructuredCommentsReader::SeqIdMatchesCommentId(), SeqIdMatchesMaster(), CEditSeqId::x_CollectChangedIds(), CInversionMergeAligner::x_CreateDiscAlignment(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), CImportFeatTable::x_DoImportCDS(), CSGSegmentSmearJob::x_Execute(), CVectorScreen::x_FindLocalId(), CGencollIdMapper::x_FixImperfectId(), CBlastHitMatrix::x_GetLabels(), CTableColumnTypeGuesser::x_GuessType(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CCSraDb_Impl::x_MakeRefSeq_ids(), CGC_Assembly_Parser::x_ParseGCSequence(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CBlastFormat::x_ReverseQuery(), CFeaturePanel::x_StartAssemblyJob(), and CSeq_id_Local_Tree::x_Unindex().

◆ IsMix()

bool CSeq_loc_Base::IsMix ( void  ) const
inline

Check if variant Mix is selected.

Mix type is defined as 'typedef CSeq_loc_mix TMix'.

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

Definition at line 552 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Mix, and CSeq_loc_Base::m_choice.

Referenced by AddLoc(), CAlignCDSAddPanel::AddOneCommand(), CAlignRNAAddPanel::AddOneCommand(), CAlignOtherAddPanel::AddOneCommand(), CSeq_loc_mix::AddSeqLoc(), CAdjustForConsensusSpliceSite::AdjustCDS(), BOOST_AUTO_TEST_CASE(), Canonicalize(), ChangeNucProtSetNucId(), CheckForeignLoc(), CollapseDiscontinuitiesInUTR(), CSeq_loc::Compare(), CSeq_loc::CompareSubLoc(), CCleanup::ExtendStopPosition(), FinalCleanup(), GetEmblInstContig(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), GetGenBankInstContig(), GetOverlappingFeatures(), GetSeqLocation(), CGuiObjectInfoPrimer::GetToolTip(), CWriteUtil::GetTranssplicedEndpoints(), CEditingActionFeatAnticodon::GetValue(), CGencollIdMapper::IsLocInAGap(), CFeaturePropagator::IsOrdered(), CSeq_loc_CI_Impl::MakeLoc(), CFeaturePropagator::MakeOrdered(), CGencollIdMapper::Map(), CAnnotObjectType_Less::operator()(), CFeatureTableReader_Imp::ReadSequinFeatureTable(), RevComp(), s_AddSeqLocMix(), CSeq_loc_Conversion::s_ConvertToMix(), s_GetTrimmedLength(), s_IsOrdered(), s_NeedsFlattening(), s_NormalizeNullsBetween(), s_SeqLoc2MaskedSubjRanges(), CNewCleanup_imp::SeqLocMixBC(), SeqLocPrintUseBestID(), SrchGene(), CFlatSeqLoc::x_Add(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CSGFeatureJob::x_CalcIntervals(), CSGFeatureJob::x_CreateCloneFeature(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CFeatureTableReader_Imp::x_FinishFeature(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CFeatureTableReader_Imp::x_GetPointStrand(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_PushLocToDstMix(), x_PushRange(), variation::CVariationUtil::x_Remap(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CCDSTranslationPanel::x_SetLocationForProtein(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), CFeatureTableReader_Imp::x_UpdatePointStrand(), xgbloc_ver(), and XMLGetInstContig().

◆ IsNamed_annot_track()

bool CSeq_id_Base::IsNamed_annot_track ( void  ) const
inline

Check if variant Named_annot_track is selected.

Named_annot_track type is defined as 'typedef CTextseq_id TNamed_annot_track'.

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

Definition at line 952 of file Seq_id_.hpp.

References CSeq_id_Base::e_Named_annot_track, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE().

◆ IsNull()

bool CSeq_loc_Base::IsNull ( void  ) const
inline

Check if variant Null is selected.

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

Definition at line 504 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Null, and CSeq_loc_Base::m_choice.

Referenced by FeatUtil::AddLocations(), CEditSequence::AdjustFeatureLocations(), CEditSequence::AdjustProtFeatureLocations(), CFeatTrim::Apply(), CDiscrepancyVisitorImpl< _Name >::Autofix(), Canonicalize(), CBioseqIndex::CBioseqIndex(), CLocationEditPolicy::ConvertToJoin(), variation::CreateUnknownProtConsequenceVariation(), GetDeltaSeqSummary(), CSeq_loc_mix::GetFirstLoc(), CReadBlastApp::getFromTo(), GetIdHandle(), CSeq_loc_mix::GetLastLoc(), CNSeq::Init(), C5ColImportData::Initialize(), CFastaObjectLoader::LoadFromStream(), CIdMapper::Map(), CLocMapper_Default::Map(), CGencollIdMapper::Map(), CSeq_loc_Mapper_Base::Map(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CCompareSeqRegions::NextComparisonGroup(), CBedAnnotAssembler::ProcessRecord(), ProjectAndCollapseCDS(), RemapOtherProtFeats(), CFeatureLoadingJob::Run(), s_AddSeqLocMix(), s_CombineDustMasksWithUserProvidedMasks(), s_FinishLoc(), s_FlattenLoc(), s_GetAlignmentSpans_Interval(), s_GetTrimmedLength(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocAnyNull(), s_UpdateCodeBreaksAndAnticodons(), CNewCleanup_imp::SeqLocMixBC(), CBedImportData::Serialize(), CSeq_loc_mix::SetFirstLoc(), CSeq_loc_mix::SetLastLoc(), variation::CVariationUtil::TranslateNAtoAA(), TruncateToCDS(), CFlatSeqLoc::x_Add(), CFeatGapInfo::x_AdjustAnticodons(), CFeatGapInfo::x_AdjustCodebreaks(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSGAlignmentJob::x_CreateFeatGlyph(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), IEditingActionFeat::x_GetSublocOnBioseq(), CBioseqContext::x_IsDeltaLitOnly(), CGencollIdMapper::x_Map_Down(), CGencollIdMapper::x_Map_Up(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_id_Resolver__ChrNamesFromGC::x_MapLoc(), CFeaturePropagator::x_MapLocation(), variation::CHgvsParser::x_PlacementCoordsToStr(), CXcompareAnnotsApplication::x_ProcessMappingRange(), CXcompareAnnotsApplication::x_ProcessMappingRanges(), CSeq_loc_Mapper_Base::x_PushLocToDstMix(), CSeq_loc_Mapper_Base::x_PushRangesToDstMix(), CIdMapperTestApp::x_RecurseMapSeqAligns(), variation::CVariationUtil::x_Remap(), CReportTrim::x_RetranslateCDS(), CMasterContext::x_SetNumParts(), CFeatTrim::x_TrimLocation(), CCdregionValidator::x_ValidateCodebreak(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CValidError_align::x_ValidateSeqLength(), and xgbloc_ver().

◆ IsOther()

bool CSeq_id_Base::IsOther ( void  ) const
inline

◆ IsPacked_int()

bool CSeq_loc_Base::IsPacked_int ( void  ) const
inline

Check if variant Packed_int is selected.

Packed_int type is defined as 'typedef CPacked_seqint TPacked_int'.

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

Definition at line 534 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Packed_int, and CSeq_loc_Base::m_choice.

Referenced by CSeq_loc::Add(), CAdjustForConsensusSpliceSite::AdjustCDS(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSequenceSearchForm::ConstructQuery(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CFeaturePropagator::CreateRowSeq_loc(), FinalCleanup(), CReadBlastApp::getFromTo(), CRemoteBlast::GetMasks(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), CWriteUtil::GetTranssplicedEndpoints(), IBISAnnotateDialog::HighlightAnnotation(), CDDAnnotateDialog::HighlightAnnotation(), CGencollIdMapper::IsLocInAGap(), CFastaObjectLoader::LoadFromStream(), MakeDDFromSeqLoc(), CSeq_loc_CI_Impl::MakeLoc(), CDDAnnotateDialog::NewOrEditMotif(), CAnnotObjectType_Less::operator()(), PackedSeqLocToMaskedQueryRegions(), s_CombineDustMasksWithUserProvidedMasks(), s_ConvertToBlastQueries(), s_FlattenLoc(), s_GetTrimmedLength(), s_LocationToStartStopPairs(), s_SeqLoc2MaskedSubjRanges(), SeqLocPrintUseBestID(), NTweakExon::TweakExon(), CFlatSeqLoc::x_Add(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CSeq_loc::x_ChangeToPackedInt(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeaturePropagator::x_MapLocation(), IEditingActionFeat::x_MergeFeatureLocation(), variation::CVariationUtil::x_Remap(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteFeatureRecords(), CGff3Writer::xWriteFeatureRna(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().

◆ IsPacked_pnt()

bool CSeq_loc_Base::IsPacked_pnt ( void  ) const
inline

Check if variant Packed_pnt is selected.

Packed_pnt type is defined as 'typedef CPacked_seqpnt TPacked_pnt'.

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

Definition at line 546 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Packed_pnt, and CSeq_loc_Base::m_choice.

Referenced by CSeq_loc::Add(), CSequenceTrack::CSequenceTrack(), fta_check_con_for_wgs(), fta_seqloc_del_far(), GetOverlappingFeatures(), CSeq_loc_CI_Impl::MakeLoc(), PrintPntAndPntsUseBestID(), s_GetTrimmedLength(), SeqLocPrintUseBestID(), CSeq_loc::x_ChangeToPackedPnt(), and CFeaturePropagator::x_MapLocation().

◆ IsPatent()

bool CSeq_id_Base::IsPatent ( void  ) const
inline

Check if variant Patent is selected.

Patent type is defined as 'typedef CPatent_seq_id TPatent'.

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

Definition at line 865 of file Seq_id_.hpp.

References CSeq_id_Base::e_Patent, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), GetAccessionAndDatabaseSource(), CSeq_id::WriteAsFasta(), and CSeq_id_Patent_Tree::x_Unindex().

◆ IsPdb()

bool CSeq_id_Base::IsPdb ( void  ) const
inline

◆ IsPir()

bool CSeq_id_Base::IsPir ( void  ) const
inline

Check if variant Pir is selected.

Pir type is defined as 'typedef CTextseq_id TPir'.

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

Definition at line 853 of file Seq_id_.hpp.

References CSeq_id_Base::e_Pir, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), FTASeqLocCheck(), GetBlastSeqIdString(), s_PreProcessAccessionsForDBv5(), s_ProcessSeqIDsForV5(), s_UseFastaReaderDeflines(), CSeqDBImpl::SeqidToOids(), WriteBlastSeqidlistFile(), and CWriteDB_LMDB::x_InsertEntry().

◆ IsPnt()

bool CSeq_loc_Base::IsPnt ( void  ) const
inline

Check if variant Pnt is selected.

Pnt type is defined as 'typedef CSeq_point TPnt'.

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

Definition at line 540 of file Seq_loc_.hpp.

References CSeq_loc_Base::e_Pnt, and CSeq_loc_Base::m_choice.

Referenced by CSeq_loc::Add(), CAlignCDSAddPanel::AddOneCommand(), CAdjustForConsensusSpliceSite::AdjustCDS(), variation::CVariationUtil::AttachProteinConsequences(), BOOST_AUTO_TEST_CASE(), FixMixLoc(), CHTMLFormatterEx::FormatLocation(), fta_check_con_for_wgs(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), CCleanup::GetProteinLocationFromNucleotideLocation(), CSeq_align::GetSeqRange(), CGencollIdMapper::IsLocInAGap(), variation::SFastLocSubtract::operator()(), CCleanup::ParseCodeBreak(), PrintPntAndPntsUseBestID(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_GetLength(), s_GetTrimmedLength(), s_IsBetween(), s_LocationToStartStopPairs(), s_PrintLocAsJavascriptArray(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), s_SubsequentIntron(), SeqLocPrintUseBestID(), CReportEntry::SetCds(), CSeqTableSetLocFuzzFromLim::SetInt(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), CFlatSeqLoc::x_Add(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CSGFeatureJob::x_CalcIntervals(), CSeq_loc::x_ChangeToPackedPnt(), CFeatGlyph::x_DrawRSites(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CGuiObjectInfoSeq_feat::x_GetLocLengthRow(), CAlignedFeatureGraph::x_GetTooltip(), variation_ref::CHgvsParser::x_location(), variation::CHgvsParser::x_location(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation::CVariationUtil::x_Remap(), CReportEntry::x_SetRnaCds(), variation::CHgvsParser::x_ssr(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), and xgbloc_ver().

◆ IsPrf()

bool CSeq_id_Base::IsPrf ( void  ) const
inline

Check if variant Prf is selected.

Prf type is defined as 'typedef CTextseq_id TPrf'.

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

Definition at line 916 of file Seq_id_.hpp.

References CSeq_id_Base::e_Prf, and CSeq_id_Base::m_choice.

Referenced by BOOST_AUTO_TEST_CASE(), FTASeqLocCheck(), GetBlastSeqIdString(), s_PreProcessAccessionsForDBv5(), s_ProcessSeqIDsForV5(), s_UseFastaReaderDeflines(), CSeqDBImpl::SeqidToOids(), WriteBlastSeqidlistFile(), and CWriteDB_LMDB::x_InsertEntry().

◆ IsSet() [1/4]

bool CPacked_seqint_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< CSeq_interval > > Tdata'

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

Definition at line 152 of file Packed_seqint_.hpp.

References