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

Classes

class  CDense_diag_Base
 for (multiway) diagonals More...
 
class  CDense_seg_Base
 Dense-seg: the densist packing for sequence alignments only. More...
 
class  CPacked_seg
 CPacked_seg –. More...
 
class  CPacked_seg_Base
 for (multiway) global or partial alignments More...
 
class  CProduct_pos_Base
 CProduct_pos_Base –. More...
 
class  CProt_pos_Base
 position on protein (1/3 of amino-acid resolution) More...
 
class  CScore_Base
 use of Score is discouraged for external ASN.1 specifications More...
 
class  CScore_Base::C_Value
 C_Value –. More...
 
class  CScore_set
 CScore_set –. More...
 
class  CScore_set_Base
 use of Score-set is encouraged for external ASN.1 specifications More...
 
class  CSeq_align_Base
 CSeq_align_Base –. More...
 
class  CSeq_align_Base::C_Segs
 alignment data More...
 
class  CSeq_align_set_Base
 *** Sequence Alignment ******************************** * More...
 
class  CSparse_align_Base
 CSparse_align_Base –. More...
 
class  CSparse_seg_Base
 ========================================================================== More...
 
class  CSparse_seg_ext
 CSparse_seg_ext –. More...
 
class  CSparse_seg_ext_Base
 CSparse_seg_ext_Base –. More...
 
class  CSplice_site
 CSplice_site –. More...
 
class  CSplice_site_Base
 site involved in splice More...
 
class  CSpliced_exon_Base
 complete or partial exon two consecutive Spliced-exons may belong to one exon More...
 
class  CSpliced_exon_chunk
 CSpliced_exon_chunk –. More...
 
class  CSpliced_exon_chunk_Base
 Spliced-exon-chunk: piece of an exon lengths are given in nucleotide bases (1/3 of aminoacid when product is a protein) More...
 
class  CSpliced_seg_Base
 CSpliced_seg_Base –. More...
 
class  CSpliced_seg_modifier
 CSpliced_seg_modifier –. More...
 
class  CSpliced_seg_modifier_Base
 CSpliced_seg_modifier_Base –. More...
 
class  CStd_seg_Base
 CStd_seg_Base –. More...
 

Typedefs

typedef CSerialObject CDense_diag_Base::Tparent
 
typedef int CDense_diag_Base::TDim
 
typedef vector< CRef< CSeq_id > > CDense_diag_Base::TIds
 
typedef vector< TSeqPosCDense_diag_Base::TStarts
 
typedef TSeqPos CDense_diag_Base::TLen
 
typedef vector< ENa_strandCDense_diag_Base::TStrands
 
typedef vector< CRef< CScore > > CDense_diag_Base::TScores
 
typedef Tparent::CMemberIndex< E_memberIndex, 7 > CDense_diag_Base::TmemberIndex
 
typedef CSerialObject CDense_seg_Base::Tparent
 
typedef int CDense_seg_Base::TDim
 
typedef int CDense_seg_Base::TNumseg
 
typedef vector< CRef< CSeq_id > > CDense_seg_Base::TIds
 
typedef vector< TSignedSeqPosCDense_seg_Base::TStarts
 
typedef vector< TSeqPosCDense_seg_Base::TLens
 
typedef vector< ENa_strandCDense_seg_Base::TStrands
 
typedef vector< CRef< CScore > > CDense_seg_Base::TScores
 
typedef Tparent::CMemberIndex< E_memberIndex, 8 > CDense_seg_Base::TmemberIndex
 
typedef CPacked_seg_Base CPacked_seg::Tparent
 
typedef CSerialObject CPacked_seg_Base::Tparent
 
typedef int CPacked_seg_Base::TDim
 
typedef int CPacked_seg_Base::TNumseg
 
typedef vector< CRef< CSeq_id > > CPacked_seg_Base::TIds
 
typedef vector< TSeqPosCPacked_seg_Base::TStarts
 
typedef vector< char > CPacked_seg_Base::TPresent
 
typedef vector< TSeqPosCPacked_seg_Base::TLens
 
typedef vector< ENa_strandCPacked_seg_Base::TStrands
 
typedef vector< CRef< CScore > > CPacked_seg_Base::TScores
 
typedef Tparent::CMemberIndex< E_memberIndex, 9 > CPacked_seg_Base::TmemberIndex
 
typedef CSerialObject CProduct_pos_Base::Tparent
 
typedef TSeqPos CProduct_pos_Base::TNucpos
 
typedef CProt_pos CProduct_pos_Base::TProtpos
 
typedef CSerialObject CProt_pos_Base::Tparent
 
typedef TSeqPos CProt_pos_Base::TAmin
 
typedef TSeqPos CProt_pos_Base::TFrame
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CProt_pos_Base::TmemberIndex
 
typedef CSerialObject CScore_Base::Tparent
 
typedef CSerialObject CScore_Base::C_Value::Tparent
 
typedef double CScore_Base::C_Value::TReal
 
typedef int CScore_Base::C_Value::TInt
 
typedef CObject_id CScore_Base::TId
 
typedef C_Value CScore_Base::TValue
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CScore_Base::TmemberIndex
 
typedef CScore_set_Base CScore_set::Tparent
 
typedef CSerialObject CScore_set_Base::Tparent
 
typedef list< CRef< CScore > > CScore_set_Base::Tdata
 
typedef CSerialObject CSeq_align_Base::Tparent
 
typedef CSerialObject CSeq_align_Base::C_Segs::Tparent
 
typedef list< CRef< CDense_diag > > CSeq_align_Base::C_Segs::TDendiag
 
typedef CDense_seg CSeq_align_Base::C_Segs::TDenseg
 
typedef list< CRef< CStd_seg > > CSeq_align_Base::C_Segs::TStd
 
typedef CPacked_seg CSeq_align_Base::C_Segs::TPacked
 
typedef CSeq_align_set CSeq_align_Base::C_Segs::TDisc
 
typedef CSpliced_seg CSeq_align_Base::C_Segs::TSpliced
 
typedef CSparse_seg CSeq_align_Base::C_Segs::TSparse
 
typedef EType CSeq_align_Base::TType
 
typedef int CSeq_align_Base::TDim
 
typedef vector< CRef< CScore > > CSeq_align_Base::TScore
 
typedef C_Segs CSeq_align_Base::TSegs
 
typedef list< CRef< CSeq_loc > > CSeq_align_Base::TBounds
 
typedef list< CRef< CObject_id > > CSeq_align_Base::TId
 
typedef list< CRef< CUser_object > > CSeq_align_Base::TExt
 
typedef Tparent::CMemberIndex< E_memberIndex, 8 > CSeq_align_Base::TmemberIndex
 
typedef CSerialObject CSeq_align_set_Base::Tparent
 
typedef list< CRef< CSeq_align > > CSeq_align_set_Base::Tdata
 
typedef CSerialObject CSparse_align_Base::Tparent
 
typedef CSeq_id CSparse_align_Base::TFirst_id
 
typedef CSeq_id CSparse_align_Base::TSecond_id
 
typedef int CSparse_align_Base::TNumseg
 
typedef vector< intCSparse_align_Base::TFirst_starts
 
typedef vector< intCSparse_align_Base::TSecond_starts
 
typedef vector< TSeqPosCSparse_align_Base::TLens
 
typedef vector< ENa_strandCSparse_align_Base::TSecond_strands
 
typedef vector< CRef< CScore > > CSparse_align_Base::TSeg_scores
 
typedef Tparent::CMemberIndex< E_memberIndex, 9 > CSparse_align_Base::TmemberIndex
 
typedef CSerialObject CSparse_seg_Base::Tparent
 
typedef CSeq_id CSparse_seg_Base::TMaster_id
 
typedef vector< CRef< CSparse_align > > CSparse_seg_Base::TRows
 
typedef vector< CRef< CScore > > CSparse_seg_Base::TRow_scores
 
typedef vector< CRef< CSparse_seg_ext > > CSparse_seg_Base::TExt
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > CSparse_seg_Base::TmemberIndex
 
typedef CSparse_seg_ext_Base CSparse_seg_ext::Tparent
 
typedef CSerialObject CSparse_seg_ext_Base::Tparent
 
typedef int CSparse_seg_ext_Base::TIndex
 
typedef Tparent::CMemberIndex< E_memberIndex, 2 > CSparse_seg_ext_Base::TmemberIndex
 
typedef CSplice_site_Base CSplice_site::Tparent
 
typedef CSerialObject CSplice_site_Base::Tparent
 
typedef string CSplice_site_Base::TBases
 
typedef Tparent::CMemberIndex< E_memberIndex, 2 > CSplice_site_Base::TmemberIndex
 
typedef CSerialObject CSpliced_exon_Base::Tparent
 
typedef CProduct_pos CSpliced_exon_Base::TProduct_start
 
typedef CProduct_pos CSpliced_exon_Base::TProduct_end
 
typedef TSeqPos CSpliced_exon_Base::TGenomic_start
 
typedef TSeqPos CSpliced_exon_Base::TGenomic_end
 
typedef CSeq_id CSpliced_exon_Base::TProduct_id
 
typedef CSeq_id CSpliced_exon_Base::TGenomic_id
 
typedef ENa_strand CSpliced_exon_Base::TProduct_strand
 
typedef ENa_strand CSpliced_exon_Base::TGenomic_strand
 
typedef list< CRef< CSpliced_exon_chunk > > CSpliced_exon_Base::TParts
 
typedef CScore_set CSpliced_exon_Base::TScores
 
typedef CSplice_site CSpliced_exon_Base::TAcceptor_before_exon
 
typedef CSplice_site CSpliced_exon_Base::TDonor_after_exon
 
typedef bool CSpliced_exon_Base::TPartial
 
typedef list< CRef< CUser_object > > CSpliced_exon_Base::TExt
 
typedef Tparent::CMemberIndex< E_memberIndex, 15 > CSpliced_exon_Base::TmemberIndex
 
typedef CSpliced_exon_chunk_Base CSpliced_exon_chunk::Tparent
 
typedef CSerialObject CSpliced_exon_chunk_Base::Tparent
 
typedef TSeqPos CSpliced_exon_chunk_Base::TMatch
 
typedef TSeqPos CSpliced_exon_chunk_Base::TMismatch
 
typedef TSeqPos CSpliced_exon_chunk_Base::TDiag
 
typedef TSeqPos CSpliced_exon_chunk_Base::TProduct_ins
 
typedef TSeqPos CSpliced_exon_chunk_Base::TGenomic_ins
 
typedef CSerialObject CSpliced_seg_Base::Tparent
 
typedef CSeq_id CSpliced_seg_Base::TProduct_id
 
typedef CSeq_id CSpliced_seg_Base::TGenomic_id
 
typedef ENa_strand CSpliced_seg_Base::TProduct_strand
 
typedef ENa_strand CSpliced_seg_Base::TGenomic_strand
 
typedef EProduct_type CSpliced_seg_Base::TProduct_type
 
typedef list< CRef< CSpliced_exon > > CSpliced_seg_Base::TExons
 
typedef TSeqPos CSpliced_seg_Base::TPoly_a
 
typedef TSeqPos CSpliced_seg_Base::TProduct_length
 
typedef list< CRef< CSpliced_seg_modifier > > CSpliced_seg_Base::TModifiers
 
typedef Tparent::CMemberIndex< E_memberIndex, 10 > CSpliced_seg_Base::TmemberIndex
 
typedef CSpliced_seg_modifier_Base CSpliced_seg_modifier::Tparent
 
typedef CSerialObject CSpliced_seg_modifier_Base::Tparent
 
typedef bool CSpliced_seg_modifier_Base::TStart_codon_found
 
typedef bool CSpliced_seg_modifier_Base::TStop_codon_found
 
typedef CSerialObject CStd_seg_Base::Tparent
 
typedef int CStd_seg_Base::TDim
 
typedef vector< CRef< CSeq_id > > CStd_seg_Base::TIds
 
typedef vector< CRef< CSeq_loc > > CStd_seg_Base::TLoc
 
typedef vector< CRef< CScore > > CStd_seg_Base::TScores
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > CStd_seg_Base::TmemberIndex
 

Enumerations

enum class  CDense_diag_Base::E_memberIndex {
  CDense_diag_Base::e__allMandatory = 0 , CDense_diag_Base::e_dim , CDense_diag_Base::e_ids , CDense_diag_Base::e_starts ,
  CDense_diag_Base::e_len , CDense_diag_Base::e_strands , CDense_diag_Base::e_scores
}
 
enum class  CDense_seg_Base::E_memberIndex {
  CDense_seg_Base::e__allMandatory = 0 , CDense_seg_Base::e_dim , CDense_seg_Base::e_numseg , CDense_seg_Base::e_ids ,
  CDense_seg_Base::e_starts , CDense_seg_Base::e_lens , CDense_seg_Base::e_strands , CDense_seg_Base::e_scores
}
 
enum class  CPacked_seg_Base::E_memberIndex {
  CPacked_seg_Base::e__allMandatory = 0 , CPacked_seg_Base::e_dim , CPacked_seg_Base::e_numseg , CPacked_seg_Base::e_ids ,
  CPacked_seg_Base::e_starts , CPacked_seg_Base::e_present , CPacked_seg_Base::e_lens , CPacked_seg_Base::e_strands ,
  CPacked_seg_Base::e_scores
}
 
enum  CProduct_pos_Base::E_Choice { CProduct_pos_Base::e_not_set = 0 , CProduct_pos_Base::e_Nucpos , CProduct_pos_Base::e_Protpos }
 Choice variants. More...
 
enum  CProduct_pos_Base::E_ChoiceStopper { CProduct_pos_Base::e_MaxChoice = 3 }
 Maximum+1 value of the choice variant enumerator. More...
 
enum class  CProt_pos_Base::E_memberIndex { CProt_pos_Base::e__allMandatory = 0 , CProt_pos_Base::e_amin , CProt_pos_Base::e_frame }
 
enum  CScore_Base::C_Value::E_Choice { CScore_Base::C_Value::e_not_set = 0 , CScore_Base::C_Value::e_Real , CScore_Base::C_Value::e_Int }
 Choice variants. More...
 
enum  CScore_Base::C_Value::E_ChoiceStopper { CScore_Base::C_Value::e_MaxChoice = 3 }
 Maximum+1 value of the choice variant enumerator. More...
 
enum class  CScore_Base::E_memberIndex { CScore_Base::e__allMandatory = 0 , CScore_Base::e_id , CScore_Base::e_value }
 
enum  CSeq_align_Base::EType {
  CSeq_align_Base::eType_not_set = 0 , CSeq_align_Base::eType_global = 1 , CSeq_align_Base::eType_diags = 2 , CSeq_align_Base::eType_partial = 3 ,
  CSeq_align_Base::eType_disc = 4 , CSeq_align_Base::eType_other = 255
}
 
enum  CSeq_align_Base::C_Segs::E_Choice {
  CSeq_align_Base::C_Segs::e_not_set = 0 , CSeq_align_Base::C_Segs::e_Dendiag , CSeq_align_Base::C_Segs::e_Denseg , CSeq_align_Base::C_Segs::e_Std ,
  CSeq_align_Base::C_Segs::e_Packed , CSeq_align_Base::C_Segs::e_Disc , CSeq_align_Base::C_Segs::e_Spliced , CSeq_align_Base::C_Segs::e_Sparse
}
 Choice variants. More...
 
enum  CSeq_align_Base::C_Segs::E_ChoiceStopper { CSeq_align_Base::C_Segs::e_MaxChoice = 8 }
 Maximum+1 value of the choice variant enumerator. More...
 
enum class  CSeq_align_Base::E_memberIndex {
  CSeq_align_Base::e__allMandatory = 0 , CSeq_align_Base::e_type , CSeq_align_Base::e_dim , CSeq_align_Base::e_score ,
  CSeq_align_Base::e_segs , CSeq_align_Base::e_bounds , CSeq_align_Base::e_id , CSeq_align_Base::e_ext
}
 
enum class  CSparse_align_Base::E_memberIndex {
  CSparse_align_Base::e__allMandatory = 0 , CSparse_align_Base::e_first_id , CSparse_align_Base::e_second_id , CSparse_align_Base::e_numseg ,
  CSparse_align_Base::e_first_starts , CSparse_align_Base::e_second_starts , CSparse_align_Base::e_lens , CSparse_align_Base::e_second_strands ,
  CSparse_align_Base::e_seg_scores
}
 
enum class  CSparse_seg_Base::E_memberIndex {
  CSparse_seg_Base::e__allMandatory = 0 , CSparse_seg_Base::e_master_id , CSparse_seg_Base::e_rows , CSparse_seg_Base::e_row_scores ,
  CSparse_seg_Base::e_ext
}
 
enum class  CSparse_seg_ext_Base::E_memberIndex { CSparse_seg_ext_Base::e__allMandatory = 0 , CSparse_seg_ext_Base::e_index }
 
enum class  CSplice_site_Base::E_memberIndex { CSplice_site_Base::e__allMandatory = 0 , CSplice_site_Base::e_bases }
 
enum class  CSpliced_exon_Base::E_memberIndex {
  CSpliced_exon_Base::e__allMandatory = 0 , CSpliced_exon_Base::e_product_start , CSpliced_exon_Base::e_product_end , CSpliced_exon_Base::e_genomic_start ,
  CSpliced_exon_Base::e_genomic_end , CSpliced_exon_Base::e_product_id , CSpliced_exon_Base::e_genomic_id , CSpliced_exon_Base::e_product_strand ,
  CSpliced_exon_Base::e_genomic_strand , CSpliced_exon_Base::e_parts , CSpliced_exon_Base::e_scores , CSpliced_exon_Base::e_acceptor_before_exon ,
  CSpliced_exon_Base::e_donor_after_exon , CSpliced_exon_Base::e_partial , CSpliced_exon_Base::e_ext
}
 
enum  CSpliced_exon_chunk_Base::E_Choice {
  CSpliced_exon_chunk_Base::e_not_set = 0 , CSpliced_exon_chunk_Base::e_Match , CSpliced_exon_chunk_Base::e_Mismatch , CSpliced_exon_chunk_Base::e_Diag ,
  CSpliced_exon_chunk_Base::e_Product_ins , CSpliced_exon_chunk_Base::e_Genomic_ins
}
 Choice variants. More...
 
enum  CSpliced_exon_chunk_Base::E_ChoiceStopper { CSpliced_exon_chunk_Base::e_MaxChoice = 6 }
 Maximum+1 value of the choice variant enumerator. More...
 
enum  CSpliced_seg_Base::EProduct_type { CSpliced_seg_Base::eProduct_type_transcript = 0 , CSpliced_seg_Base::eProduct_type_protein = 1 }
 
enum class  CSpliced_seg_Base::E_memberIndex {
  CSpliced_seg_Base::e__allMandatory = 0 , CSpliced_seg_Base::e_product_id , CSpliced_seg_Base::e_genomic_id , CSpliced_seg_Base::e_product_strand ,
  CSpliced_seg_Base::e_genomic_strand , CSpliced_seg_Base::e_product_type , CSpliced_seg_Base::e_exons , CSpliced_seg_Base::e_poly_a ,
  CSpliced_seg_Base::e_product_length , CSpliced_seg_Base::e_modifiers
}
 
enum  CSpliced_seg_modifier_Base::E_Choice { CSpliced_seg_modifier_Base::e_not_set = 0 , CSpliced_seg_modifier_Base::e_Start_codon_found , CSpliced_seg_modifier_Base::e_Stop_codon_found }
 Choice variants. More...
 
enum  CSpliced_seg_modifier_Base::E_ChoiceStopper { CSpliced_seg_modifier_Base::e_MaxChoice = 3 }
 Maximum+1 value of the choice variant enumerator. More...
 
enum class  CStd_seg_Base::E_memberIndex {
  CStd_seg_Base::e__allMandatory = 0 , CStd_seg_Base::e_dim , CStd_seg_Base::e_ids , CStd_seg_Base::e_loc ,
  CStd_seg_Base::e_scores
}
 

Functions

 CDense_diag_Base::CDense_diag_Base (void)
 
virtual CDense_diag_Base::~CDense_diag_Base (void)
 
 CDense_diag_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CDense_diag_Base::IsSetDim (void) const
 dimensionality Check if a value has been assigned to Dim data member. More...
 
bool CDense_diag_Base::CanGetDim (void) const
 Check if it is safe to call GetDim method. More...
 
void CDense_diag_Base::ResetDim (void)
 Reset Dim data member. More...
 
void CDense_diag_Base::SetDefaultDim (void)
 Assign default value to Dim data member. More...
 
TDim CDense_diag_Base::GetDim (void) const
 Get the Dim member data. More...
 
void CDense_diag_Base::SetDim (TDim value)
 Assign a value to Dim data member. More...
 
TDimCDense_diag_Base::SetDim (void)
 Assign a value to Dim data member. More...
 
bool CDense_diag_Base::IsSetIds (void) const
 sequences in order Check if a value has been assigned to Ids data member. More...
 
bool CDense_diag_Base::CanGetIds (void) const
 Check if it is safe to call GetIds method. More...
 
void CDense_diag_Base::ResetIds (void)
 Reset Ids data member. More...
 
const TIdsCDense_diag_Base::GetIds (void) const
 Get the Ids member data. More...
 
TIdsCDense_diag_Base::SetIds (void)
 Assign a value to Ids data member. More...
 
bool CDense_diag_Base::IsSetStarts (void) const
 start OFFSETS in ids order Check if a value has been assigned to Starts data member. More...
 
bool CDense_diag_Base::CanGetStarts (void) const
 Check if it is safe to call GetStarts method. More...
 
void CDense_diag_Base::ResetStarts (void)
 Reset Starts data member. More...
 
const TStartsCDense_diag_Base::GetStarts (void) const
 Get the Starts member data. More...
 
TStartsCDense_diag_Base::SetStarts (void)
 Assign a value to Starts data member. More...
 
bool CDense_diag_Base::IsSetLen (void) const
 len of aligned segments Check if a value has been assigned to Len data member. More...
 
bool CDense_diag_Base::CanGetLen (void) const
 Check if it is safe to call GetLen method. More...
 
void CDense_diag_Base::ResetLen (void)
 Reset Len data member. More...
 
TLen CDense_diag_Base::GetLen (void) const
 Get the Len member data. More...
 
void CDense_diag_Base::SetLen (TLen value)
 Assign a value to Len data member. More...
 
TLenCDense_diag_Base::SetLen (void)
 Assign a value to Len data member. More...
 
bool CDense_diag_Base::IsSetStrands (void) const
 Check if a value has been assigned to Strands data member. More...
 
bool CDense_diag_Base::CanGetStrands (void) const
 Check if it is safe to call GetStrands method. More...
 
void CDense_diag_Base::ResetStrands (void)
 Reset Strands data member. More...
 
const TStrandsCDense_diag_Base::GetStrands (void) const
 Get the Strands member data. More...
 
TStrandsCDense_diag_Base::SetStrands (void)
 Assign a value to Strands data member. More...
 
bool CDense_diag_Base::IsSetScores (void) const
 Check if a value has been assigned to Scores data member. More...
 
bool CDense_diag_Base::CanGetScores (void) const
 Check if it is safe to call GetScores method. More...
 
void CDense_diag_Base::ResetScores (void)
 Reset Scores data member. More...
 
const TScoresCDense_diag_Base::GetScores (void) const
 Get the Scores member data. More...
 
TScoresCDense_diag_Base::SetScores (void)
 Assign a value to Scores data member. More...
 
virtual void CDense_diag_Base::Reset (void)
 Reset the whole object. More...
 
 CDense_diag_Base::CDense_diag_Base (const CDense_diag_Base &)
 
CDense_diag_BaseCDense_diag_Base::operator= (const CDense_diag_Base &)
 
 CDense_seg_Base::CDense_seg_Base (void)
 
virtual CDense_seg_Base::~CDense_seg_Base (void)
 
 CDense_seg_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CDense_seg_Base::IsSetDim (void) const
 dimensionality Check if a value has been assigned to Dim data member. More...
 
bool CDense_seg_Base::CanGetDim (void) const
 Check if it is safe to call GetDim method. More...
 
void CDense_seg_Base::ResetDim (void)
 Reset Dim data member. More...
 
void CDense_seg_Base::SetDefaultDim (void)
 Assign default value to Dim data member. More...
 
TDim CDense_seg_Base::GetDim (void) const
 Get the Dim member data. More...
 
void CDense_seg_Base::SetDim (TDim value)
 Assign a value to Dim data member. More...
 
TDimCDense_seg_Base::SetDim (void)
 Assign a value to Dim data member. More...
 
bool CDense_seg_Base::IsSetNumseg (void) const
 number of segments here Check if a value has been assigned to Numseg data member. More...
 
bool CDense_seg_Base::CanGetNumseg (void) const
 Check if it is safe to call GetNumseg method. More...
 
void CDense_seg_Base::ResetNumseg (void)
 Reset Numseg data member. More...
 
TNumseg CDense_seg_Base::GetNumseg (void) const
 Get the Numseg member data. More...
 
void CDense_seg_Base::SetNumseg (TNumseg value)
 Assign a value to Numseg data member. More...
 
TNumsegCDense_seg_Base::SetNumseg (void)
 Assign a value to Numseg data member. More...
 
bool CDense_seg_Base::IsSetIds (void) const
 sequences in order Check if a value has been assigned to Ids data member. More...
 
bool CDense_seg_Base::CanGetIds (void) const
 Check if it is safe to call GetIds method. More...
 
void CDense_seg_Base::ResetIds (void)
 Reset Ids data member. More...
 
const TIdsCDense_seg_Base::GetIds (void) const
 Get the Ids member data. More...
 
TIdsCDense_seg_Base::SetIds (void)
 Assign a value to Ids data member. More...
 
bool CDense_seg_Base::IsSetStarts (void) const
 start OFFSETS in ids order within segs Check if a value has been assigned to Starts data member. More...
 
bool CDense_seg_Base::CanGetStarts (void) const
 Check if it is safe to call GetStarts method. More...
 
void CDense_seg_Base::ResetStarts (void)
 Reset Starts data member. More...
 
const TStartsCDense_seg_Base::GetStarts (void) const
 Get the Starts member data. More...
 
TStartsCDense_seg_Base::SetStarts (void)
 Assign a value to Starts data member. More...
 
bool CDense_seg_Base::IsSetLens (void) const
 lengths in ids order within segs Check if a value has been assigned to Lens data member. More...
 
bool CDense_seg_Base::CanGetLens (void) const
 Check if it is safe to call GetLens method. More...
 
void CDense_seg_Base::ResetLens (void)
 Reset Lens data member. More...
 
const TLensCDense_seg_Base::GetLens (void) const
 Get the Lens member data. More...
 
TLensCDense_seg_Base::SetLens (void)
 Assign a value to Lens data member. More...
 
bool CDense_seg_Base::IsSetStrands (void) const
 Check if a value has been assigned to Strands data member. More...
 
bool CDense_seg_Base::CanGetStrands (void) const
 Check if it is safe to call GetStrands method. More...
 
void CDense_seg_Base::ResetStrands (void)
 Reset Strands data member. More...
 
const TStrandsCDense_seg_Base::GetStrands (void) const
 Get the Strands member data. More...
 
TStrandsCDense_seg_Base::SetStrands (void)
 Assign a value to Strands data member. More...
 
bool CDense_seg_Base::IsSetScores (void) const
 score for each seg Check if a value has been assigned to Scores data member. More...
 
bool CDense_seg_Base::CanGetScores (void) const
 Check if it is safe to call GetScores method. More...
 
void CDense_seg_Base::ResetScores (void)
 Reset Scores data member. More...
 
const TScoresCDense_seg_Base::GetScores (void) const
 Get the Scores member data. More...
 
TScoresCDense_seg_Base::SetScores (void)
 Assign a value to Scores data member. More...
 
virtual void CDense_seg_Base::Reset (void)
 Reset the whole object. More...
 
 CDense_seg_Base::CDense_seg_Base (const CDense_seg_Base &)
 
CDense_seg_BaseCDense_seg_Base::operator= (const CDense_seg_Base &)
 
 CPacked_seg::CPacked_seg (void)
 
 CPacked_seg::~CPacked_seg (void)
 
 CPacked_seg::CPacked_seg (const CPacked_seg &value)
 
CPacked_segCPacked_seg::operator= (const CPacked_seg &value)
 
 CPacked_seg_Base::CPacked_seg_Base (void)
 
virtual CPacked_seg_Base::~CPacked_seg_Base (void)
 
 CPacked_seg_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CPacked_seg_Base::IsSetDim (void) const
 dimensionality Check if a value has been assigned to Dim data member. More...
 
bool CPacked_seg_Base::CanGetDim (void) const
 Check if it is safe to call GetDim method. More...
 
void CPacked_seg_Base::ResetDim (void)
 Reset Dim data member. More...
 
void CPacked_seg_Base::SetDefaultDim (void)
 Assign default value to Dim data member. More...
 
TDim CPacked_seg_Base::GetDim (void) const
 Get the Dim member data. More...
 
void CPacked_seg_Base::SetDim (TDim value)
 Assign a value to Dim data member. More...
 
TDimCPacked_seg_Base::SetDim (void)
 Assign a value to Dim data member. More...
 
bool CPacked_seg_Base::IsSetNumseg (void) const
 number of segments here Check if a value has been assigned to Numseg data member. More...
 
bool CPacked_seg_Base::CanGetNumseg (void) const
 Check if it is safe to call GetNumseg method. More...
 
void CPacked_seg_Base::ResetNumseg (void)
 Reset Numseg data member. More...
 
TNumseg CPacked_seg_Base::GetNumseg (void) const
 Get the Numseg member data. More...
 
void CPacked_seg_Base::SetNumseg (TNumseg value)
 Assign a value to Numseg data member. More...
 
TNumsegCPacked_seg_Base::SetNumseg (void)
 Assign a value to Numseg data member. More...
 
bool CPacked_seg_Base::IsSetIds (void) const
 sequences in order Check if a value has been assigned to Ids data member. More...
 
bool CPacked_seg_Base::CanGetIds (void) const
 Check if it is safe to call GetIds method. More...
 
void CPacked_seg_Base::ResetIds (void)
 Reset Ids data member. More...
 
const TIdsCPacked_seg_Base::GetIds (void) const
 Get the Ids member data. More...
 
TIdsCPacked_seg_Base::SetIds (void)
 Assign a value to Ids data member. More...
 
bool CPacked_seg_Base::IsSetStarts (void) const
 start OFFSETS in ids order for whole alignment Check if a value has been assigned to Starts data member. More...
 
bool CPacked_seg_Base::CanGetStarts (void) const
 Check if it is safe to call GetStarts method. More...
 
void CPacked_seg_Base::ResetStarts (void)
 Reset Starts data member. More...
 
const TStartsCPacked_seg_Base::GetStarts (void) const
 Get the Starts member data. More...
 
TStartsCPacked_seg_Base::SetStarts (void)
 Assign a value to Starts data member. More...
 
bool CPacked_seg_Base::IsSetPresent (void) const
 Boolean if each sequence present or absent in each segment Check if a value has been assigned to Present data member. More...
 
bool CPacked_seg_Base::CanGetPresent (void) const
 Check if it is safe to call GetPresent method. More...
 
void CPacked_seg_Base::ResetPresent (void)
 Reset Present data member. More...
 
const TPresentCPacked_seg_Base::GetPresent (void) const
 Get the Present member data. More...
 
TPresentCPacked_seg_Base::SetPresent (void)
 Assign a value to Present data member. More...
 
bool CPacked_seg_Base::IsSetLens (void) const
 length of each segment Check if a value has been assigned to Lens data member. More...
 
bool CPacked_seg_Base::CanGetLens (void) const
 Check if it is safe to call GetLens method. More...
 
void CPacked_seg_Base::ResetLens (void)
 Reset Lens data member. More...
 
const TLensCPacked_seg_Base::GetLens (void) const
 Get the Lens member data. More...
 
TLensCPacked_seg_Base::SetLens (void)
 Assign a value to Lens data member. More...
 
bool CPacked_seg_Base::IsSetStrands (void) const
 Check if a value has been assigned to Strands data member. More...
 
bool CPacked_seg_Base::CanGetStrands (void) const
 Check if it is safe to call GetStrands method. More...
 
void CPacked_seg_Base::ResetStrands (void)
 Reset Strands data member. More...
 
const TStrandsCPacked_seg_Base::GetStrands (void) const
 Get the Strands member data. More...
 
TStrandsCPacked_seg_Base::SetStrands (void)
 Assign a value to Strands data member. More...
 
bool CPacked_seg_Base::IsSetScores (void) const
 score for each segment Check if a value has been assigned to Scores data member. More...
 
bool CPacked_seg_Base::CanGetScores (void) const
 Check if it is safe to call GetScores method. More...
 
void CPacked_seg_Base::ResetScores (void)
 Reset Scores data member. More...
 
const TScoresCPacked_seg_Base::GetScores (void) const
 Get the Scores member data. More...
 
TScoresCPacked_seg_Base::SetScores (void)
 Assign a value to Scores data member. More...
 
virtual void CPacked_seg_Base::Reset (void)
 Reset the whole object. More...
 
 CPacked_seg_Base::CPacked_seg_Base (const CPacked_seg_Base &)
 
CPacked_seg_BaseCPacked_seg_Base::operator= (const CPacked_seg_Base &)
 
 CProduct_pos_Base::CProduct_pos_Base (void)
 
virtual CProduct_pos_Base::~CProduct_pos_Base (void)
 
 CProduct_pos_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
virtual void CProduct_pos_Base::Reset (void)
 Reset the whole object. More...
 
virtual void CProduct_pos_Base::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CProduct_pos_Base::Which (void) const
 Which variant is currently selected. More...
 
void CProduct_pos_Base::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CProduct_pos_Base::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CProduct_pos_Base::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CProduct_pos_Base::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CProduct_pos_Base::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CProduct_pos_Base::IsNucpos (void) const
 Check if variant Nucpos is selected. More...
 
TNucpos CProduct_pos_Base::GetNucpos (void) const
 Get the variant data. More...
 
TNucposCProduct_pos_Base::SetNucpos (void)
 Select the variant. More...
 
void CProduct_pos_Base::SetNucpos (TNucpos value)
 Select the variant and set its data. More...
 
bool CProduct_pos_Base::IsProtpos (void) const
 Check if variant Protpos is selected. More...
 
const TProtposCProduct_pos_Base::GetProtpos (void) const
 Get the variant data. More...
 
TProtposCProduct_pos_Base::SetProtpos (void)
 Select the variant. More...
 
void CProduct_pos_Base::SetProtpos (TProtpos &value)
 Select the variant and set its data. More...
 
 CProduct_pos_Base::CProduct_pos_Base (const CProduct_pos_Base &)
 
CProduct_pos_BaseCProduct_pos_Base::operator= (const CProduct_pos_Base &)
 
void CProduct_pos_Base::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 
 CProt_pos_Base::CProt_pos_Base (void)
 
virtual CProt_pos_Base::~CProt_pos_Base (void)
 
 CProt_pos_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CProt_pos_Base::IsSetAmin (void) const
 amino-acid position (0-based) Check if a value has been assigned to Amin data member. More...
 
bool CProt_pos_Base::CanGetAmin (void) const
 Check if it is safe to call GetAmin method. More...
 
void CProt_pos_Base::ResetAmin (void)
 Reset Amin data member. More...
 
TAmin CProt_pos_Base::GetAmin (void) const
 Get the Amin member data. More...
 
void CProt_pos_Base::SetAmin (TAmin value)
 Assign a value to Amin data member. More...
 
TAminCProt_pos_Base::SetAmin (void)
 Assign a value to Amin data member. More...
 
bool CProt_pos_Base::IsSetFrame (void) const
 position within codon (1-based) 0 = not set (meaning 1) Check if a value has been assigned to Frame data member. More...
 
bool CProt_pos_Base::CanGetFrame (void) const
 Check if it is safe to call GetFrame method. More...
 
void CProt_pos_Base::ResetFrame (void)
 Reset Frame data member. More...
 
void CProt_pos_Base::SetDefaultFrame (void)
 Assign default value to Frame data member. More...
 
TFrame CProt_pos_Base::GetFrame (void) const
 Get the Frame member data. More...
 
void CProt_pos_Base::SetFrame (TFrame value)
 Assign a value to Frame data member. More...
 
TFrameCProt_pos_Base::SetFrame (void)
 Assign a value to Frame data member. More...
 
virtual void CProt_pos_Base::Reset (void)
 Reset the whole object. More...
 
 CProt_pos_Base::CProt_pos_Base (const CProt_pos_Base &)
 
CProt_pos_BaseCProt_pos_Base::operator= (const CProt_pos_Base &)
 
 CScore_Base::CScore_Base (void)
 
virtual CScore_Base::~CScore_Base (void)
 
 CScore_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
 CScore_Base::C_Value::C_Value (void)
 
 CScore_Base::C_Value::~C_Value (void)
 
 CScore_Base::C_Value::DECLARE_INTERNAL_TYPE_INFO ()
 
void CScore_Base::C_Value::Reset (void)
 Reset the whole object. More...
 
void CScore_Base::C_Value::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CScore_Base::C_Value::Which (void) const
 Which variant is currently selected. More...
 
void CScore_Base::C_Value::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CScore_Base::C_Value::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CScore_Base::C_Value::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CScore_Base::C_Value::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CScore_Base::C_Value::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CScore_Base::C_Value::IsReal (void) const
 Check if variant Real is selected. More...
 
TReal CScore_Base::C_Value::GetReal (void) const
 Get the variant data. More...
 
TRealCScore_Base::C_Value::SetReal (void)
 Select the variant. More...
 
void CScore_Base::C_Value::SetReal (TReal value)
 Select the variant and set its data. More...
 
bool CScore_Base::C_Value::IsInt (void) const
 Check if variant Int is selected. More...
 
TInt CScore_Base::C_Value::GetInt (void) const
 Get the variant data. More...
 
TIntCScore_Base::C_Value::SetInt (void)
 Select the variant. More...
 
void CScore_Base::C_Value::SetInt (TInt value)
 Select the variant and set its data. More...
 
 CScore_Base::C_Value::C_Value (const C_Value &)
 
C_ValueCScore_Base::C_Value::operator= (const C_Value &)
 
void CScore_Base::C_Value::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 
bool CScore_Base::IsSetId (void) const
 Check if a value has been assigned to Id data member. More...
 
bool CScore_Base::CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void CScore_Base::ResetId (void)
 Reset Id data member. More...
 
const TIdCScore_Base::GetId (void) const
 Get the Id member data. More...
 
void CScore_Base::SetId (TId &value)
 Assign a value to Id data member. More...
 
TIdCScore_Base::SetId (void)
 Assign a value to Id data member. More...
 
bool CScore_Base::IsSetValue (void) const
 Check if a value has been assigned to Value data member. More...
 
bool CScore_Base::CanGetValue (void) const
 Check if it is safe to call GetValue method. More...
 
void CScore_Base::ResetValue (void)
 Reset Value data member. More...
 
const TValueCScore_Base::GetValue (void) const
 Get the Value member data. More...
 
TValueCScore_Base::SetValue (void)
 Assign a value to Value data member. More...
 
virtual void CScore_Base::Reset (void)
 Reset the whole object. More...
 
virtual void CScore_Base::DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
 CScore_Base::CScore_Base (const CScore_Base &)
 
CScore_BaseCScore_Base::operator= (const CScore_Base &)
 
 CScore_set::CScore_set (void)
 
 CScore_set::~CScore_set (void)
 
 CScore_set::CScore_set (const CScore_set &value)
 
CScore_setCScore_set::operator= (const CScore_set &value)
 
 CScore_set_Base::CScore_set_Base (void)
 
virtual CScore_set_Base::~CScore_set_Base (void)
 
 CScore_set_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CScore_set_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CScore_set_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CScore_set_Base::Reset (void)
 Reset data member. More...
 
const TdataCScore_set_Base::Get (void) const
 Get the member data. More...
 
TdataCScore_set_Base::Set (void)
 Assign a value to data member. More...
 
 CScore_set_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CScore_set_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CScore_set_Base::CScore_set_Base (const CScore_set_Base &)
 
CScore_set_BaseCScore_set_Base::operator= (const CScore_set_Base &)
 
 CSeq_align_Base::CSeq_align_Base (void)
 
virtual CSeq_align_Base::~CSeq_align_Base (void)
 
 CSeq_align_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() CSeq_align_Base::EType (void)
 Access to EType's attributes (values, names) as defined in spec. More...
 
 CSeq_align_Base::C_Segs::C_Segs (void)
 
 CSeq_align_Base::C_Segs::~C_Segs (void)
 
 CSeq_align_Base::C_Segs::DECLARE_INTERNAL_TYPE_INFO ()
 
void CSeq_align_Base::C_Segs::Reset (void)
 Reset the whole object. More...
 
void CSeq_align_Base::C_Segs::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CSeq_align_Base::C_Segs::Which (void) const
 Which variant is currently selected. More...
 
void CSeq_align_Base::C_Segs::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CSeq_align_Base::C_Segs::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CSeq_align_Base::C_Segs::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CSeq_align_Base::C_Segs::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CSeq_align_Base::C_Segs::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CSeq_align_Base::C_Segs::IsDendiag (void) const
 Check if variant Dendiag is selected. More...
 
const TDendiagCSeq_align_Base::C_Segs::GetDendiag (void) const
 Get the variant data. More...
 
TDendiagCSeq_align_Base::C_Segs::SetDendiag (void)
 Select the variant. More...
 
bool CSeq_align_Base::C_Segs::IsDenseg (void) const
 Check if variant Denseg is selected. More...
 
const TDensegCSeq_align_Base::C_Segs::GetDenseg (void) const
 Get the variant data. More...
 
TDensegCSeq_align_Base::C_Segs::SetDenseg (void)
 Select the variant. More...
 
void CSeq_align_Base::C_Segs::SetDenseg (TDenseg &value)
 Select the variant and set its data. More...
 
bool CSeq_align_Base::C_Segs::IsStd (void) const
 Check if variant Std is selected. More...
 
const TStdCSeq_align_Base::C_Segs::GetStd (void) const
 Get the variant data. More...
 
TStdCSeq_align_Base::C_Segs::SetStd (void)
 Select the variant. More...
 
bool CSeq_align_Base::C_Segs::IsPacked (void) const
 Check if variant Packed is selected. More...
 
const TPackedCSeq_align_Base::C_Segs::GetPacked (void) const
 Get the variant data. More...
 
TPackedCSeq_align_Base::C_Segs::SetPacked (void)
 Select the variant. More...
 
void CSeq_align_Base::C_Segs::SetPacked (TPacked &value)
 Select the variant and set its data. More...
 
bool CSeq_align_Base::C_Segs::IsDisc (void) const
 Check if variant Disc is selected. More...
 
const TDiscCSeq_align_Base::C_Segs::GetDisc (void) const
 Get the variant data. More...
 
TDiscCSeq_align_Base::C_Segs::SetDisc (void)
 Select the variant. More...
 
void CSeq_align_Base::C_Segs::SetDisc (TDisc &value)
 Select the variant and set its data. More...
 
bool CSeq_align_Base::C_Segs::IsSpliced (void) const
 Check if variant Spliced is selected. More...
 
const TSplicedCSeq_align_Base::C_Segs::GetSpliced (void) const
 Get the variant data. More...
 
TSplicedCSeq_align_Base::C_Segs::SetSpliced (void)
 Select the variant. More...
 
void CSeq_align_Base::C_Segs::SetSpliced (TSpliced &value)
 Select the variant and set its data. More...
 
bool CSeq_align_Base::C_Segs::IsSparse (void) const
 Check if variant Sparse is selected. More...
 
const TSparseCSeq_align_Base::C_Segs::GetSparse (void) const
 Get the variant data. More...
 
TSparseCSeq_align_Base::C_Segs::SetSparse (void)
 Select the variant. More...
 
void CSeq_align_Base::C_Segs::SetSparse (TSparse &value)
 Select the variant and set its data. More...
 
 CSeq_align_Base::C_Segs::C_Segs (const C_Segs &)
 
C_SegsCSeq_align_Base::C_Segs::operator= (const C_Segs &)
 
void CSeq_align_Base::C_Segs::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 
bool CSeq_align_Base::IsSetType (void) const
 Check if a value has been assigned to Type data member. More...
 
bool CSeq_align_Base::CanGetType (void) const
 Check if it is safe to call GetType method. More...
 
void CSeq_align_Base::ResetType (void)
 Reset Type data member. More...
 
TType CSeq_align_Base::GetType (void) const
 Get the Type member data. More...
 
void CSeq_align_Base::SetType (TType value)
 Assign a value to Type data member. More...
 
TTypeCSeq_align_Base::SetType (void)
 Assign a value to Type data member. More...
 
bool CSeq_align_Base::IsSetDim (void) const
 dimensionality Check if a value has been assigned to Dim data member. More...
 
bool CSeq_align_Base::CanGetDim (void) const
 Check if it is safe to call GetDim method. More...
 
void CSeq_align_Base::ResetDim (void)
 Reset Dim data member. More...
 
TDim CSeq_align_Base::GetDim (void) const
 Get the Dim member data. More...
 
void CSeq_align_Base::SetDim (TDim value)
 Assign a value to Dim data member. More...
 
TDimCSeq_align_Base::SetDim (void)
 Assign a value to Dim data member. More...
 
bool CSeq_align_Base::IsSetScore (void) const
 for whole alignment Check if a value has been assigned to Score data member. More...
 
bool CSeq_align_Base::CanGetScore (void) const
 Check if it is safe to call GetScore method. More...
 
void CSeq_align_Base::ResetScore (void)
 Reset Score data member. More...
 
const TScoreCSeq_align_Base::GetScore (void) const
 Get the Score member data. More...
 
TScoreCSeq_align_Base::SetScore (void)
 Assign a value to Score data member. More...
 
bool CSeq_align_Base::IsSetSegs (void) const
 Check if a value has been assigned to Segs data member. More...
 
bool CSeq_align_Base::CanGetSegs (void) const
 Check if it is safe to call GetSegs method. More...
 
void CSeq_align_Base::ResetSegs (void)
 Reset Segs data member. More...
 
const TSegsCSeq_align_Base::GetSegs (void) const
 Get the Segs member data. More...
 
void CSeq_align_Base::SetSegs (TSegs &value)
 Assign a value to Segs data member. More...
 
TSegsCSeq_align_Base::SetSegs (void)
 Assign a value to Segs data member. More...
 
bool CSeq_align_Base::IsSetBounds (void) const
 regions of sequence over which align was computed Check if a value has been assigned to Bounds data member. More...
 
bool CSeq_align_Base::CanGetBounds (void) const
 Check if it is safe to call GetBounds method. More...
 
void CSeq_align_Base::ResetBounds (void)
 Reset Bounds data member. More...
 
const TBoundsCSeq_align_Base::GetBounds (void) const
 Get the Bounds member data. More...
 
TBoundsCSeq_align_Base::SetBounds (void)
 Assign a value to Bounds data member. More...
 
bool CSeq_align_Base::IsSetId (void) const
 alignment id Check if a value has been assigned to Id data member. More...
 
bool CSeq_align_Base::CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void CSeq_align_Base::ResetId (void)
 Reset Id data member. More...
 
const TIdCSeq_align_Base::GetId (void) const
 Get the Id member data. More...
 
TIdCSeq_align_Base::SetId (void)
 Assign a value to Id data member. More...
 
bool CSeq_align_Base::IsSetExt (void) const
 extra info Check if a value has been assigned to Ext data member. More...
 
bool CSeq_align_Base::CanGetExt (void) const
 Check if it is safe to call GetExt method. More...
 
void CSeq_align_Base::ResetExt (void)
 Reset Ext data member. More...
 
const TExtCSeq_align_Base::GetExt (void) const
 Get the Ext member data. More...
 
TExtCSeq_align_Base::SetExt (void)
 Assign a value to Ext data member. More...
 
virtual void CSeq_align_Base::Reset (void)
 Reset the whole object. More...
 
 CSeq_align_Base::CSeq_align_Base (const CSeq_align_Base &)
 
CSeq_align_BaseCSeq_align_Base::operator= (const CSeq_align_Base &)
 
 CSeq_align_set_Base::CSeq_align_set_Base (void)
 
virtual CSeq_align_set_Base::~CSeq_align_set_Base (void)
 
 CSeq_align_set_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSeq_align_set_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CSeq_align_set_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CSeq_align_set_Base::Reset (void)
 Reset data member. More...
 
const TdataCSeq_align_set_Base::Get (void) const
 Get the member data. More...
 
TdataCSeq_align_set_Base::Set (void)
 Assign a value to data member. More...
 
 CSeq_align_set_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CSeq_align_set_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CSeq_align_set_Base::CSeq_align_set_Base (const CSeq_align_set_Base &)
 
CSeq_align_set_BaseCSeq_align_set_Base::operator= (const CSeq_align_set_Base &)
 
 CSparse_align_Base::CSparse_align_Base (void)
 
virtual CSparse_align_Base::~CSparse_align_Base (void)
 
 CSparse_align_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSparse_align_Base::IsSetFirst_id (void) const
 Check if a value has been assigned to First_id data member. More...
 
bool CSparse_align_Base::CanGetFirst_id (void) const
 Check if it is safe to call GetFirst_id method. More...
 
void CSparse_align_Base::ResetFirst_id (void)
 Reset First_id data member. More...
 
const TFirst_idCSparse_align_Base::GetFirst_id (void) const
 Get the First_id member data. More...
 
void CSparse_align_Base::SetFirst_id (TFirst_id &value)
 Assign a value to First_id data member. More...
 
TFirst_idCSparse_align_Base::SetFirst_id (void)
 Assign a value to First_id data member. More...
 
bool CSparse_align_Base::IsSetSecond_id (void) const
 Check if a value has been assigned to Second_id data member. More...
 
bool CSparse_align_Base::CanGetSecond_id (void) const
 Check if it is safe to call GetSecond_id method. More...
 
void CSparse_align_Base::ResetSecond_id (void)
 Reset Second_id data member. More...
 
const TSecond_idCSparse_align_Base::GetSecond_id (void) const
 Get the Second_id member data. More...
 
void CSparse_align_Base::SetSecond_id (TSecond_id &value)
 Assign a value to Second_id data member. More...
 
TSecond_idCSparse_align_Base::SetSecond_id (void)
 Assign a value to Second_id data member. More...
 
bool CSparse_align_Base::IsSetNumseg (void) const
 number of segments Check if a value has been assigned to Numseg data member. More...
 
bool CSparse_align_Base::CanGetNumseg (void) const
 Check if it is safe to call GetNumseg method. More...
 
void CSparse_align_Base::ResetNumseg (void)
 Reset Numseg data member. More...
 
TNumseg CSparse_align_Base::GetNumseg (void) const
 Get the Numseg member data. More...
 
void CSparse_align_Base::SetNumseg (TNumseg value)
 Assign a value to Numseg data member. More...
 
TNumsegCSparse_align_Base::SetNumseg (void)
 Assign a value to Numseg data member. More...
 
bool CSparse_align_Base::IsSetFirst_starts (void) const
 starts on the first sequence [numseg] Check if a value has been assigned to First_starts data member. More...
 
bool CSparse_align_Base::CanGetFirst_starts (void) const
 Check if it is safe to call GetFirst_starts method. More...
 
void CSparse_align_Base::ResetFirst_starts (void)
 Reset First_starts data member. More...
 
const TFirst_startsCSparse_align_Base::GetFirst_starts (void) const
 Get the First_starts member data. More...
 
TFirst_startsCSparse_align_Base::SetFirst_starts (void)
 Assign a value to First_starts data member. More...
 
bool CSparse_align_Base::IsSetSecond_starts (void) const
 starts on the second sequence [numseg] Check if a value has been assigned to Second_starts data member. More...
 
bool CSparse_align_Base::CanGetSecond_starts (void) const
 Check if it is safe to call GetSecond_starts method. More...
 
void CSparse_align_Base::ResetSecond_starts (void)
 Reset Second_starts data member. More...
 
const TSecond_startsCSparse_align_Base::GetSecond_starts (void) const
 Get the Second_starts member data. More...
 
TSecond_startsCSparse_align_Base::SetSecond_starts (void)
 Assign a value to Second_starts data member. More...
 
bool CSparse_align_Base::IsSetLens (void) const
 lengths of segments [numseg] Check if a value has been assigned to Lens data member. More...
 
bool CSparse_align_Base::CanGetLens (void) const
 Check if it is safe to call GetLens method. More...
 
void CSparse_align_Base::ResetLens (void)
 Reset Lens data member. More...
 
const TLensCSparse_align_Base::GetLens (void) const
 Get the Lens member data. More...
 
TLensCSparse_align_Base::SetLens (void)
 Assign a value to Lens data member. More...
 
bool CSparse_align_Base::IsSetSecond_strands (void) const
 Check if a value has been assigned to Second_strands data member. More...
 
bool CSparse_align_Base::CanGetSecond_strands (void) const
 Check if it is safe to call GetSecond_strands method. More...
 
void CSparse_align_Base::ResetSecond_strands (void)
 Reset Second_strands data member. More...
 
const TSecond_strandsCSparse_align_Base::GetSecond_strands (void) const
 Get the Second_strands member data. More...
 
TSecond_strandsCSparse_align_Base::SetSecond_strands (void)
 Assign a value to Second_strands data member. More...
 
bool CSparse_align_Base::IsSetSeg_scores (void) const
 per-segment scores Check if a value has been assigned to Seg_scores data member. More...
 
bool CSparse_align_Base::CanGetSeg_scores (void) const
 Check if it is safe to call GetSeg_scores method. More...
 
void CSparse_align_Base::ResetSeg_scores (void)
 Reset Seg_scores data member. More...
 
const TSeg_scoresCSparse_align_Base::GetSeg_scores (void) const
 Get the Seg_scores member data. More...
 
TSeg_scoresCSparse_align_Base::SetSeg_scores (void)
 Assign a value to Seg_scores data member. More...
 
virtual void CSparse_align_Base::Reset (void)
 Reset the whole object. More...
 
 CSparse_align_Base::CSparse_align_Base (const CSparse_align_Base &)
 
CSparse_align_BaseCSparse_align_Base::operator= (const CSparse_align_Base &)
 
 CSparse_seg_Base::CSparse_seg_Base (void)
 
virtual CSparse_seg_Base::~CSparse_seg_Base (void)
 
 CSparse_seg_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSparse_seg_Base::IsSetMaster_id (void) const
 Check if a value has been assigned to Master_id data member. More...
 
bool CSparse_seg_Base::CanGetMaster_id (void) const
 Check if it is safe to call GetMaster_id method. More...
 
void CSparse_seg_Base::ResetMaster_id (void)
 Reset Master_id data member. More...
 
const TMaster_idCSparse_seg_Base::GetMaster_id (void) const
 Get the Master_id member data. More...
 
void CSparse_seg_Base::SetMaster_id (TMaster_id &value)
 Assign a value to Master_id data member. More...
 
TMaster_idCSparse_seg_Base::SetMaster_id (void)
 Assign a value to Master_id data member. More...
 
bool CSparse_seg_Base::IsSetRows (void) const
 pairwise alignments constituting this multiple alignment Check if a value has been assigned to Rows data member. More...
 
bool CSparse_seg_Base::CanGetRows (void) const
 Check if it is safe to call GetRows method. More...
 
void CSparse_seg_Base::ResetRows (void)
 Reset Rows data member. More...
 
const TRowsCSparse_seg_Base::GetRows (void) const
 Get the Rows member data. More...
 
TRowsCSparse_seg_Base::SetRows (void)
 Assign a value to Rows data member. More...
 
bool CSparse_seg_Base::IsSetRow_scores (void) const
 per-row scores Check if a value has been assigned to Row_scores data member. More...
 
bool CSparse_seg_Base::CanGetRow_scores (void) const
 Check if it is safe to call GetRow_scores method. More...
 
void CSparse_seg_Base::ResetRow_scores (void)
 Reset Row_scores data member. More...
 
const TRow_scoresCSparse_seg_Base::GetRow_scores (void) const
 Get the Row_scores member data. More...
 
TRow_scoresCSparse_seg_Base::SetRow_scores (void)
 Assign a value to Row_scores data member. More...
 
bool CSparse_seg_Base::IsSetExt (void) const
 index of extra items Check if a value has been assigned to Ext data member. More...
 
bool CSparse_seg_Base::CanGetExt (void) const
 Check if it is safe to call GetExt method. More...
 
void CSparse_seg_Base::ResetExt (void)
 Reset Ext data member. More...
 
const TExtCSparse_seg_Base::GetExt (void) const
 Get the Ext member data. More...
 
TExtCSparse_seg_Base::SetExt (void)
 Assign a value to Ext data member. More...
 
virtual void CSparse_seg_Base::Reset (void)
 Reset the whole object. More...
 
 CSparse_seg_Base::CSparse_seg_Base (const CSparse_seg_Base &)
 
CSparse_seg_BaseCSparse_seg_Base::operator= (const CSparse_seg_Base &)
 
 CSparse_seg_ext::CSparse_seg_ext (void)
 
 CSparse_seg_ext::~CSparse_seg_ext (void)
 
 CSparse_seg_ext::CSparse_seg_ext (const CSparse_seg_ext &value)
 
CSparse_seg_extCSparse_seg_ext::operator= (const CSparse_seg_ext &value)
 
 CSparse_seg_ext_Base::CSparse_seg_ext_Base (void)
 
virtual CSparse_seg_ext_Base::~CSparse_seg_ext_Base (void)
 
 CSparse_seg_ext_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSparse_seg_ext_Base::IsSetIndex (void) const
 seg-ext SET OF { index INTEGER, data User-field } Check if a value has been assigned to Index data member. More...
 
bool CSparse_seg_ext_Base::CanGetIndex (void) const
 Check if it is safe to call GetIndex method. More...
 
void CSparse_seg_ext_Base::ResetIndex (void)
 Reset Index data member. More...
 
TIndex CSparse_seg_ext_Base::GetIndex (void) const
 Get the Index member data. More...
 
void CSparse_seg_ext_Base::SetIndex (TIndex value)
 Assign a value to Index data member. More...
 
TIndexCSparse_seg_ext_Base::SetIndex (void)
 Assign a value to Index data member. More...
 
virtual void CSparse_seg_ext_Base::Reset (void)
 Reset the whole object. More...
 
 CSparse_seg_ext_Base::CSparse_seg_ext_Base (const CSparse_seg_ext_Base &)
 
CSparse_seg_ext_BaseCSparse_seg_ext_Base::operator= (const CSparse_seg_ext_Base &)
 
 CSplice_site::CSplice_site (void)
 
 CSplice_site::~CSplice_site (void)
 
 CSplice_site::CSplice_site (const CSplice_site &value)
 
CSplice_siteCSplice_site::operator= (const CSplice_site &value)
 
 CSplice_site_Base::CSplice_site_Base (void)
 
virtual CSplice_site_Base::~CSplice_site_Base (void)
 
 CSplice_site_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSplice_site_Base::IsSetBases (void) const
 typically two bases in the intronic region, always in IUPAC format Check if a value has been assigned to Bases data member. More...
 
bool CSplice_site_Base::CanGetBases (void) const
 Check if it is safe to call GetBases method. More...
 
void CSplice_site_Base::ResetBases (void)
 Reset Bases data member. More...
 
const TBasesCSplice_site_Base::GetBases (void) const
 Get the Bases member data. More...
 
void CSplice_site_Base::SetBases (const TBases &value)
 Assign a value to Bases data member. More...
 
void CSplice_site_Base::SetBases (TBases &&value)
 
TBasesCSplice_site_Base::SetBases (void)
 Assign a value to Bases data member. More...
 
virtual void CSplice_site_Base::Reset (void)
 Reset the whole object. More...
 
 CSplice_site_Base::CSplice_site_Base (const CSplice_site_Base &)
 
CSplice_site_BaseCSplice_site_Base::operator= (const CSplice_site_Base &)
 
 CSpliced_exon_Base::CSpliced_exon_Base (void)
 
virtual CSpliced_exon_Base::~CSpliced_exon_Base (void)
 
 CSpliced_exon_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSpliced_exon_Base::IsSetProduct_start (void) const
 product-end >= product-start Check if a value has been assigned to Product_start data member. More...
 
bool CSpliced_exon_Base::CanGetProduct_start (void) const
 Check if it is safe to call GetProduct_start method. More...
 
void CSpliced_exon_Base::ResetProduct_start (void)
 Reset Product_start data member. More...
 
const TProduct_startCSpliced_exon_Base::GetProduct_start (void) const
 Get the Product_start member data. More...
 
void CSpliced_exon_Base::SetProduct_start (TProduct_start &value)
 Assign a value to Product_start data member. More...
 
TProduct_startCSpliced_exon_Base::SetProduct_start (void)
 Assign a value to Product_start data member. More...
 
bool CSpliced_exon_Base::IsSetProduct_end (void) const
 Check if a value has been assigned to Product_end data member. More...
 
bool CSpliced_exon_Base::CanGetProduct_end (void) const
 Check if it is safe to call GetProduct_end method. More...
 
void CSpliced_exon_Base::ResetProduct_end (void)
 Reset Product_end data member. More...
 
const TProduct_endCSpliced_exon_Base::GetProduct_end (void) const
 Get the Product_end member data. More...
 
void CSpliced_exon_Base::SetProduct_end (TProduct_end &value)
 Assign a value to Product_end data member. More...
 
TProduct_endCSpliced_exon_Base::SetProduct_end (void)
 Assign a value to Product_end data member. More...
 
bool CSpliced_exon_Base::IsSetGenomic_start (void) const
 genomic-end >= genomic-start Check if a value has been assigned to Genomic_start data member. More...
 
bool CSpliced_exon_Base::CanGetGenomic_start (void) const
 Check if it is safe to call GetGenomic_start method. More...
 
void CSpliced_exon_Base::ResetGenomic_start (void)
 Reset Genomic_start data member. More...
 
TGenomic_start CSpliced_exon_Base::GetGenomic_start (void) const
 Get the Genomic_start member data. More...
 
void CSpliced_exon_Base::SetGenomic_start (TGenomic_start value)
 Assign a value to Genomic_start data member. More...
 
TGenomic_startCSpliced_exon_Base::SetGenomic_start (void)
 Assign a value to Genomic_start data member. More...
 
bool CSpliced_exon_Base::IsSetGenomic_end (void) const
 Check if a value has been assigned to Genomic_end data member. More...
 
bool CSpliced_exon_Base::CanGetGenomic_end (void) const
 Check if it is safe to call GetGenomic_end method. More...
 
void CSpliced_exon_Base::ResetGenomic_end (void)
 Reset Genomic_end data member. More...
 
TGenomic_end CSpliced_exon_Base::GetGenomic_end (void) const
 Get the Genomic_end member data. More...
 
void CSpliced_exon_Base::SetGenomic_end (TGenomic_end value)
 Assign a value to Genomic_end data member. More...
 
TGenomic_endCSpliced_exon_Base::SetGenomic_end (void)
 Assign a value to Genomic_end data member. More...
 
bool CSpliced_exon_Base::IsSetProduct_id (void) const
 product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member. More...
 
bool CSpliced_exon_Base::CanGetProduct_id (void) const
 Check if it is safe to call GetProduct_id method. More...
 
void CSpliced_exon_Base::ResetProduct_id (void)
 Reset Product_id data member. More...
 
const TProduct_idCSpliced_exon_Base::GetProduct_id (void) const
 Get the Product_id member data. More...
 
void CSpliced_exon_Base::SetProduct_id (TProduct_id &value)
 Assign a value to Product_id data member. More...
 
TProduct_idCSpliced_exon_Base::SetProduct_id (void)
 Assign a value to Product_id data member. More...
 
bool CSpliced_exon_Base::IsSetGenomic_id (void) const
 Check if a value has been assigned to Genomic_id data member. More...
 
bool CSpliced_exon_Base::CanGetGenomic_id (void) const
 Check if it is safe to call GetGenomic_id method. More...
 
void CSpliced_exon_Base::ResetGenomic_id (void)
 Reset Genomic_id data member. More...
 
const TGenomic_idCSpliced_exon_Base::GetGenomic_id (void) const
 Get the Genomic_id member data. More...
 
void CSpliced_exon_Base::SetGenomic_id (TGenomic_id &value)
 Assign a value to Genomic_id data member. More...
 
TGenomic_idCSpliced_exon_Base::SetGenomic_id (void)
 Assign a value to Genomic_id data member. More...
 
bool CSpliced_exon_Base::IsSetProduct_strand (void) const
 should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member. More...
 
bool CSpliced_exon_Base::CanGetProduct_strand (void) const
 Check if it is safe to call GetProduct_strand method. More...
 
void CSpliced_exon_Base::ResetProduct_strand (void)
 Reset Product_strand data member. More...
 
TProduct_strand CSpliced_exon_Base::GetProduct_strand (void) const
 Get the Product_strand member data. More...
 
void CSpliced_exon_Base::SetProduct_strand (TProduct_strand value)
 Assign a value to Product_strand data member. More...
 
TProduct_strandCSpliced_exon_Base::SetProduct_strand (void)
 Assign a value to Product_strand data member. More...
 
bool CSpliced_exon_Base::IsSetGenomic_strand (void) const
 genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_strand data member. More...
 
bool CSpliced_exon_Base::CanGetGenomic_strand (void) const
 Check if it is safe to call GetGenomic_strand method. More...
 
void CSpliced_exon_Base::ResetGenomic_strand (void)
 Reset Genomic_strand data member. More...
 
TGenomic_strand CSpliced_exon_Base::GetGenomic_strand (void) const
 Get the Genomic_strand member data. More...
 
void CSpliced_exon_Base::SetGenomic_strand (TGenomic_strand value)
 Assign a value to Genomic_strand data member. More...
 
TGenomic_strandCSpliced_exon_Base::SetGenomic_strand (void)
 Assign a value to Genomic_strand data member. More...
 
bool CSpliced_exon_Base::IsSetParts (void) const
 basic seqments always are in biologic order Check if a value has been assigned to Parts data member. More...
 
bool CSpliced_exon_Base::CanGetParts (void) const
 Check if it is safe to call GetParts method. More...
 
void CSpliced_exon_Base::ResetParts (void)
 Reset Parts data member. More...
 
const TPartsCSpliced_exon_Base::GetParts (void) const
 Get the Parts member data. More...
 
TPartsCSpliced_exon_Base::SetParts (void)
 Assign a value to Parts data member. More...
 
bool CSpliced_exon_Base::IsSetScores (void) const
 scores for this exon Check if a value has been assigned to Scores data member. More...
 
bool CSpliced_exon_Base::CanGetScores (void) const
 Check if it is safe to call GetScores method. More...
 
void CSpliced_exon_Base::ResetScores (void)
 Reset Scores data member. More...
 
const TScoresCSpliced_exon_Base::GetScores (void) const
 Get the Scores member data. More...
 
void CSpliced_exon_Base::SetScores (TScores &value)
 Assign a value to Scores data member. More...
 
TScoresCSpliced_exon_Base::SetScores (void)
 Assign a value to Scores data member. More...
 
bool CSpliced_exon_Base::IsSetAcceptor_before_exon (void) const
 splice sites Check if a value has been assigned to Acceptor_before_exon data member. More...
 
bool CSpliced_exon_Base::CanGetAcceptor_before_exon (void) const
 Check if it is safe to call GetAcceptor_before_exon method. More...
 
void CSpliced_exon_Base::ResetAcceptor_before_exon (void)
 Reset Acceptor_before_exon data member. More...
 
const TAcceptor_before_exonCSpliced_exon_Base::GetAcceptor_before_exon (void) const
 Get the Acceptor_before_exon member data. More...
 
void CSpliced_exon_Base::SetAcceptor_before_exon (TAcceptor_before_exon &value)
 Assign a value to Acceptor_before_exon data member. More...
 
TAcceptor_before_exonCSpliced_exon_Base::SetAcceptor_before_exon (void)
 Assign a value to Acceptor_before_exon data member. More...
 
bool CSpliced_exon_Base::IsSetDonor_after_exon (void) const
 Check if a value has been assigned to Donor_after_exon data member. More...
 
bool CSpliced_exon_Base::CanGetDonor_after_exon (void) const
 Check if it is safe to call GetDonor_after_exon method. More...
 
void CSpliced_exon_Base::ResetDonor_after_exon (void)
 Reset Donor_after_exon data member. More...
 
const TDonor_after_exonCSpliced_exon_Base::GetDonor_after_exon (void) const
 Get the Donor_after_exon member data. More...
 
void CSpliced_exon_Base::SetDonor_after_exon (TDonor_after_exon &value)
 Assign a value to Donor_after_exon data member. More...
 
TDonor_after_exonCSpliced_exon_Base::SetDonor_after_exon (void)
 Assign a value to Donor_after_exon data member. More...
 
bool CSpliced_exon_Base::IsSetPartial (void) const
 flag: is this exon complete or partial? Check if a value has been assigned to Partial data member. More...
 
bool CSpliced_exon_Base::CanGetPartial (void) const
 Check if it is safe to call GetPartial method. More...
 
void CSpliced_exon_Base::ResetPartial (void)
 Reset Partial data member. More...
 
TPartial CSpliced_exon_Base::GetPartial (void) const
 Get the Partial member data. More...
 
void CSpliced_exon_Base::SetPartial (TPartial value)
 Assign a value to Partial data member. More...
 
TPartialCSpliced_exon_Base::SetPartial (void)
 Assign a value to Partial data member. More...
 
bool CSpliced_exon_Base::IsSetExt (void) const
 extra info Check if a value has been assigned to Ext data member. More...
 
bool CSpliced_exon_Base::CanGetExt (void) const
 Check if it is safe to call GetExt method. More...
 
void CSpliced_exon_Base::ResetExt (void)
 Reset Ext data member. More...
 
const TExtCSpliced_exon_Base::GetExt (void) const
 Get the Ext member data. More...
 
TExtCSpliced_exon_Base::SetExt (void)
 Assign a value to Ext data member. More...
 
virtual void CSpliced_exon_Base::Reset (void)
 Reset the whole object. More...
 
 CSpliced_exon_Base::CSpliced_exon_Base (const CSpliced_exon_Base &)
 
CSpliced_exon_BaseCSpliced_exon_Base::operator= (const CSpliced_exon_Base &)
 
 CSpliced_exon_chunk::CSpliced_exon_chunk (void)
 
 CSpliced_exon_chunk::~CSpliced_exon_chunk (void)
 
 CSpliced_exon_chunk::CSpliced_exon_chunk (const CSpliced_exon_chunk &value)
 
CSpliced_exon_chunkCSpliced_exon_chunk::operator= (const CSpliced_exon_chunk &value)
 
 CSpliced_exon_chunk_Base::CSpliced_exon_chunk_Base (void)
 
virtual CSpliced_exon_chunk_Base::~CSpliced_exon_chunk_Base (void)
 
 CSpliced_exon_chunk_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
virtual void CSpliced_exon_chunk_Base::Reset (void)
 Reset the whole object. More...
 
virtual void CSpliced_exon_chunk_Base::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CSpliced_exon_chunk_Base::Which (void) const
 Which variant is currently selected. More...
 
void CSpliced_exon_chunk_Base::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CSpliced_exon_chunk_Base::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CSpliced_exon_chunk_Base::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CSpliced_exon_chunk_Base::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CSpliced_exon_chunk_Base::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CSpliced_exon_chunk_Base::IsMatch (void) const
 Check if variant Match is selected. More...
 
TMatch CSpliced_exon_chunk_Base::GetMatch (void) const
 Get the variant data. More...
 
TMatchCSpliced_exon_chunk_Base::SetMatch (void)
 Select the variant. More...
 
void CSpliced_exon_chunk_Base::SetMatch (TMatch value)
 Select the variant and set its data. More...
 
bool CSpliced_exon_chunk_Base::IsMismatch (void) const
 Check if variant Mismatch is selected. More...
 
TMismatch CSpliced_exon_chunk_Base::GetMismatch (void) const
 Get the variant data. More...
 
TMismatchCSpliced_exon_chunk_Base::SetMismatch (void)
 Select the variant. More...
 
void CSpliced_exon_chunk_Base::SetMismatch (TMismatch value)
 Select the variant and set its data. More...
 
bool CSpliced_exon_chunk_Base::IsDiag (void) const
 Check if variant Diag is selected. More...
 
TDiag CSpliced_exon_chunk_Base::GetDiag (void) const
 Get the variant data. More...
 
TDiagCSpliced_exon_chunk_Base::SetDiag (void)
 Select the variant. More...
 
void CSpliced_exon_chunk_Base::SetDiag (TDiag value)
 Select the variant and set its data. More...
 
bool CSpliced_exon_chunk_Base::IsProduct_ins (void) const
 Check if variant Product_ins is selected. More...
 
TProduct_ins CSpliced_exon_chunk_Base::GetProduct_ins (void) const
 Get the variant data. More...
 
TProduct_insCSpliced_exon_chunk_Base::SetProduct_ins (void)
 Select the variant. More...
 
void CSpliced_exon_chunk_Base::SetProduct_ins (TProduct_ins value)
 Select the variant and set its data. More...
 
bool CSpliced_exon_chunk_Base::IsGenomic_ins (void) const
 Check if variant Genomic_ins is selected. More...
 
TGenomic_ins CSpliced_exon_chunk_Base::GetGenomic_ins (void) const
 Get the variant data. More...
 
TGenomic_insCSpliced_exon_chunk_Base::SetGenomic_ins (void)
 Select the variant. More...
 
void CSpliced_exon_chunk_Base::SetGenomic_ins (TGenomic_ins value)
 Select the variant and set its data. More...
 
 CSpliced_exon_chunk_Base::CSpliced_exon_chunk_Base (const CSpliced_exon_chunk_Base &)
 
CSpliced_exon_chunk_BaseCSpliced_exon_chunk_Base::operator= (const CSpliced_exon_chunk_Base &)
 
void CSpliced_exon_chunk_Base::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 
 CSpliced_seg_Base::CSpliced_seg_Base (void)
 
virtual CSpliced_seg_Base::~CSpliced_seg_Base (void)
 
 CSpliced_seg_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() CSpliced_seg_Base::EProduct_type (void)
 Access to EProduct_type's attributes (values, names) as defined in spec. More...
 
bool CSpliced_seg_Base::IsSetProduct_id (void) const
 product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member. More...
 
bool CSpliced_seg_Base::CanGetProduct_id (void) const
 Check if it is safe to call GetProduct_id method. More...
 
void CSpliced_seg_Base::ResetProduct_id (void)
 Reset Product_id data member. More...
 
const TProduct_idCSpliced_seg_Base::GetProduct_id (void) const
 Get the Product_id member data. More...
 
void CSpliced_seg_Base::SetProduct_id (TProduct_id &value)
 Assign a value to Product_id data member. More...
 
TProduct_idCSpliced_seg_Base::SetProduct_id (void)
 Assign a value to Product_id data member. More...
 
bool CSpliced_seg_Base::IsSetGenomic_id (void) const
 Check if a value has been assigned to Genomic_id data member. More...
 
bool CSpliced_seg_Base::CanGetGenomic_id (void) const
 Check if it is safe to call GetGenomic_id method. More...
 
void CSpliced_seg_Base::ResetGenomic_id (void)
 Reset Genomic_id data member. More...
 
const TGenomic_idCSpliced_seg_Base::GetGenomic_id (void) const
 Get the Genomic_id member data. More...
 
void CSpliced_seg_Base::SetGenomic_id (TGenomic_id &value)
 Assign a value to Genomic_id data member. More...
 
TGenomic_idCSpliced_seg_Base::SetGenomic_id (void)
 Assign a value to Genomic_id data member. More...
 
bool CSpliced_seg_Base::IsSetProduct_strand (void) const
 should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member. More...
 
bool CSpliced_seg_Base::CanGetProduct_strand (void) const
 Check if it is safe to call GetProduct_strand method. More...
 
void CSpliced_seg_Base::ResetProduct_strand (void)
 Reset Product_strand data member. More...
 
TProduct_strand CSpliced_seg_Base::GetProduct_strand (void) const
 Get the Product_strand member data. More...
 
void CSpliced_seg_Base::SetProduct_strand (TProduct_strand value)
 Assign a value to Product_strand data member. More...
 
TProduct_strandCSpliced_seg_Base::SetProduct_strand (void)
 Assign a value to Product_strand data member. More...
 
bool CSpliced_seg_Base::IsSetGenomic_strand (void) const
 Check if a value has been assigned to Genomic_strand data member. More...
 
bool CSpliced_seg_Base::CanGetGenomic_strand (void) const
 Check if it is safe to call GetGenomic_strand method. More...
 
void CSpliced_seg_Base::ResetGenomic_strand (void)
 Reset Genomic_strand data member. More...
 
TGenomic_strand CSpliced_seg_Base::GetGenomic_strand (void) const
 Get the Genomic_strand member data. More...
 
void CSpliced_seg_Base::SetGenomic_strand (TGenomic_strand value)
 Assign a value to Genomic_strand data member. More...
 
TGenomic_strandCSpliced_seg_Base::SetGenomic_strand (void)
 Assign a value to Genomic_strand data member. More...
 
bool CSpliced_seg_Base::IsSetProduct_type (void) const
 Check if a value has been assigned to Product_type data member. More...
 
bool CSpliced_seg_Base::CanGetProduct_type (void) const
 Check if it is safe to call GetProduct_type method. More...
 
void CSpliced_seg_Base::ResetProduct_type (void)
 Reset Product_type data member. More...
 
TProduct_type CSpliced_seg_Base::GetProduct_type (void) const
 Get the Product_type member data. More...
 
void CSpliced_seg_Base::SetProduct_type (TProduct_type value)
 Assign a value to Product_type data member. More...
 
TProduct_typeCSpliced_seg_Base::SetProduct_type (void)
 Assign a value to Product_type data member. More...
 
bool CSpliced_seg_Base::IsSetExons (void) const
 set of segments involved each segment corresponds to one exon exons are always in biological order Check if a value has been assigned to Exons data member. More...
 
bool CSpliced_seg_Base::CanGetExons (void) const
 Check if it is safe to call GetExons method. More...
 
void CSpliced_seg_Base::ResetExons (void)
 Reset Exons data member. More...
 
const TExonsCSpliced_seg_Base::GetExons (void) const
 Get the Exons member data. More...
 
TExonsCSpliced_seg_Base::SetExons (void)
 Assign a value to Exons data member. More...
 
bool CSpliced_seg_Base::IsSetPoly_a (void) const
 start of poly(A) tail on the transcript For sense transcripts: aligned product positions < poly-a <= product-length poly-a == product-length indicates inferred poly(A) tail at transcript's end For antisense transcripts: -1 <= poly-a < aligned product positions poly-a == -1 indicates inferred poly(A) tail at transcript's start Check if a value has been assigned to Poly_a data member. More...
 
bool CSpliced_seg_Base::CanGetPoly_a (void) const
 Check if it is safe to call GetPoly_a method. More...
 
void CSpliced_seg_Base::ResetPoly_a (void)
 Reset Poly_a data member. More...
 
TPoly_a CSpliced_seg_Base::GetPoly_a (void) const
 Get the Poly_a member data. More...
 
void CSpliced_seg_Base::SetPoly_a (TPoly_a value)
 Assign a value to Poly_a data member. More...
 
TPoly_aCSpliced_seg_Base::SetPoly_a (void)
 Assign a value to Poly_a data member. More...
 
bool CSpliced_seg_Base::IsSetProduct_length (void) const
 length of the product, in bases/residues from this (or from poly-a if present), a 3' unaligned length can be extracted Check if a value has been assigned to Product_length data member. More...
 
bool CSpliced_seg_Base::CanGetProduct_length (void) const
 Check if it is safe to call GetProduct_length method. More...
 
void CSpliced_seg_Base::ResetProduct_length (void)
 Reset Product_length data member. More...
 
TProduct_length CSpliced_seg_Base::GetProduct_length (void) const
 Get the Product_length member data. More...
 
void CSpliced_seg_Base::SetProduct_length (TProduct_length value)
 Assign a value to Product_length data member. More...
 
TProduct_lengthCSpliced_seg_Base::SetProduct_length (void)
 Assign a value to Product_length data member. More...
 
bool CSpliced_seg_Base::IsSetModifiers (void) const
 alignment descriptors / modifiers this provides us a set for extension Check if a value has been assigned to Modifiers data member. More...
 
bool CSpliced_seg_Base::CanGetModifiers (void) const
 Check if it is safe to call GetModifiers method. More...
 
void CSpliced_seg_Base::ResetModifiers (void)
 Reset Modifiers data member. More...
 
const TModifiersCSpliced_seg_Base::GetModifiers (void) const
 Get the Modifiers member data. More...
 
TModifiersCSpliced_seg_Base::SetModifiers (void)
 Assign a value to Modifiers data member. More...
 
virtual void CSpliced_seg_Base::Reset (void)
 Reset the whole object. More...
 
 CSpliced_seg_Base::CSpliced_seg_Base (const CSpliced_seg_Base &)
 
CSpliced_seg_BaseCSpliced_seg_Base::operator= (const CSpliced_seg_Base &)
 
 CSpliced_seg_modifier::CSpliced_seg_modifier (void)
 
 CSpliced_seg_modifier::~CSpliced_seg_modifier (void)
 
 CSpliced_seg_modifier::CSpliced_seg_modifier (const CSpliced_seg_modifier &value)
 
CSpliced_seg_modifierCSpliced_seg_modifier::operator= (const CSpliced_seg_modifier &value)
 
 CSpliced_seg_modifier_Base::CSpliced_seg_modifier_Base (void)
 
virtual CSpliced_seg_modifier_Base::~CSpliced_seg_modifier_Base (void)
 
 CSpliced_seg_modifier_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
virtual void CSpliced_seg_modifier_Base::Reset (void)
 Reset the whole object. More...
 
virtual void CSpliced_seg_modifier_Base::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CSpliced_seg_modifier_Base::Which (void) const
 Which variant is currently selected. More...
 
void CSpliced_seg_modifier_Base::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CSpliced_seg_modifier_Base::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CSpliced_seg_modifier_Base::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CSpliced_seg_modifier_Base::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CSpliced_seg_modifier_Base::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CSpliced_seg_modifier_Base::IsStart_codon_found (void) const
 Check if variant Start_codon_found is selected. More...
 
TStart_codon_found CSpliced_seg_modifier_Base::GetStart_codon_found (void) const
 Get the variant data. More...
 
TStart_codon_foundCSpliced_seg_modifier_Base::SetStart_codon_found (void)
 Select the variant. More...
 
void CSpliced_seg_modifier_Base::SetStart_codon_found (TStart_codon_found value)
 Select the variant and set its data. More...
 
bool CSpliced_seg_modifier_Base::IsStop_codon_found (void) const
 Check if variant Stop_codon_found is selected. More...
 
TStop_codon_found CSpliced_seg_modifier_Base::GetStop_codon_found (void) const
 Get the variant data. More...
 
TStop_codon_foundCSpliced_seg_modifier_Base::SetStop_codon_found (void)
 Select the variant. More...
 
void CSpliced_seg_modifier_Base::SetStop_codon_found (TStop_codon_found value)
 Select the variant and set its data. More...
 
 CSpliced_seg_modifier_Base::CSpliced_seg_modifier_Base (const CSpliced_seg_modifier_Base &)
 
CSpliced_seg_modifier_BaseCSpliced_seg_modifier_Base::operator= (const CSpliced_seg_modifier_Base &)
 
void CSpliced_seg_modifier_Base::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 
 CStd_seg_Base::CStd_seg_Base (void)
 
virtual CStd_seg_Base::~CStd_seg_Base (void)
 
 CStd_seg_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CStd_seg_Base::IsSetDim (void) const
 dimensionality Check if a value has been assigned to Dim data member. More...
 
bool CStd_seg_Base::CanGetDim (void) const
 Check if it is safe to call GetDim method. More...
 
void CStd_seg_Base::ResetDim (void)
 Reset Dim data member. More...
 
void CStd_seg_Base::SetDefaultDim (void)
 Assign default value to Dim data member. More...
 
TDim CStd_seg_Base::GetDim (void) const
 Get the Dim member data. More...
 
void CStd_seg_Base::SetDim (TDim value)
 Assign a value to Dim data member. More...
 
TDimCStd_seg_Base::SetDim (void)
 Assign a value to Dim data member. More...
 
bool CStd_seg_Base::IsSetIds (void) const
 Check if a value has been assigned to Ids data member. More...
 
bool CStd_seg_Base::CanGetIds (void) const
 Check if it is safe to call GetIds method. More...
 
void CStd_seg_Base::ResetIds (void)
 Reset Ids data member. More...
 
const TIdsCStd_seg_Base::GetIds (void) const
 Get the Ids member data. More...
 
TIdsCStd_seg_Base::SetIds (void)
 Assign a value to Ids data member. More...
 
bool CStd_seg_Base::IsSetLoc (void) const
 Check if a value has been assigned to Loc data member. More...
 
bool CStd_seg_Base::CanGetLoc (void) const
 Check if it is safe to call GetLoc method. More...
 
void CStd_seg_Base::ResetLoc (void)
 Reset Loc data member. More...
 
const TLocCStd_seg_Base::GetLoc (void) const
 Get the Loc member data. More...
 
TLocCStd_seg_Base::SetLoc (void)
 Assign a value to Loc data member. More...
 
bool CStd_seg_Base::IsSetScores (void) const
 Check if a value has been assigned to Scores data member. More...
 
bool CStd_seg_Base::CanGetScores (void) const
 Check if it is safe to call GetScores method. More...
 
void CStd_seg_Base::ResetScores (void)
 Reset Scores data member. More...
 
const TScoresCStd_seg_Base::GetScores (void) const
 Get the Scores member data. More...
 
TScoresCStd_seg_Base::SetScores (void)
 Assign a value to Scores data member. More...
 
virtual void CStd_seg_Base::Reset (void)
 Reset the whole object. More...
 
 CStd_seg_Base::CStd_seg_Base (const CStd_seg_Base &)
 
CStd_seg_BaseCStd_seg_Base::operator= (const CStd_seg_Base &)
 

Variables

Uint4 CDense_diag_Base::m_set_State [1]
 
int CDense_diag_Base::m_Dim
 
vector< CRef< CSeq_id > > CDense_diag_Base::m_Ids
 
vector< TSeqPosCDense_diag_Base::m_Starts
 
TSeqPos CDense_diag_Base::m_Len
 
vector< ENa_strandCDense_diag_Base::m_Strands
 
vector< CRef< CScore > > CDense_diag_Base::m_Scores
 
Uint4 CDense_seg_Base::m_set_State [1]
 
int CDense_seg_Base::m_Dim
 
int CDense_seg_Base::m_Numseg
 
vector< CRef< CSeq_id > > CDense_seg_Base::m_Ids
 
vector< TSignedSeqPosCDense_seg_Base::m_Starts
 
vector< TSeqPosCDense_seg_Base::m_Lens
 
vector< ENa_strandCDense_seg_Base::m_Strands
 
vector< CRef< CScore > > CDense_seg_Base::m_Scores
 
Uint4 CPacked_seg_Base::m_set_State [1]
 
int CPacked_seg_Base::m_Dim
 
int CPacked_seg_Base::m_Numseg
 
vector< CRef< CSeq_id > > CPacked_seg_Base::m_Ids
 
vector< TSeqPosCPacked_seg_Base::m_Starts
 
vector< char > CPacked_seg_Base::m_Present
 
vector< TSeqPosCPacked_seg_Base::m_Lens
 
vector< ENa_strandCPacked_seg_Base::m_Strands
 
vector< CRef< CScore > > CPacked_seg_Base::m_Scores
 
E_Choice CProduct_pos_Base::m_choice
 
static const char *const CProduct_pos_Base::sm_SelectionNames []
 
TNucpos   CProduct_pos_Base::m_Nucpos
 
NCBI_NS_NCBI::CSerialObject *   CProduct_pos_Base::m_object
 
union {
   TNucpos   CProduct_pos_Base::m_Nucpos
 
   NCBI_NS_NCBI::CSerialObject *   CProduct_pos_Base::m_object
 
}; 
 
Uint4 CProt_pos_Base::m_set_State [1]
 
TSeqPos CProt_pos_Base::m_Amin
 
TSeqPos CProt_pos_Base::m_Frame
 
E_Choice CScore_Base::C_Value::m_choice
 
static const char *const CScore_Base::C_Value::sm_SelectionNames []
 
TReal   CScore_Base::C_Value::m_Real
 
TInt   CScore_Base::C_Value::m_Int
 
union {
   TReal   CScore_Base::C_Value::m_Real
 
   TInt   CScore_Base::C_Value::m_Int
 
}; 
 
Uint4 CScore_Base::m_set_State [1]
 
CRef< TIdCScore_Base::m_Id
 
C_Value CScore_Base::m_Value
 
Uint4 CScore_set_Base::m_set_State [1]
 
list< CRef< CScore > > CScore_set_Base::m_data
 
E_Choice CSeq_align_Base::C_Segs::m_choice
 
static const char *const CSeq_align_Base::C_Segs::sm_SelectionNames []
 
NCBI_NS_NCBI::CUnionBuffer< TDendiag >   CSeq_align_Base::C_Segs::m_Dendiag
 
NCBI_NS_NCBI::CUnionBuffer< TStd >   CSeq_align_Base::C_Segs::m_Std
 
NCBI_NS_NCBI::CSerialObject *   CSeq_align_Base::C_Segs::m_object
 
union {
   NCBI_NS_NCBI::CUnionBuffer< TDendiag >   CSeq_align_Base::C_Segs::m_Dendiag
 
   NCBI_NS_NCBI::CUnionBuffer< TStd >   CSeq_align_Base::C_Segs::m_Std
 
   NCBI_NS_NCBI::CSerialObject *   CSeq_align_Base::C_Segs::m_object
 
}; 
 
Uint4 CSeq_align_Base::m_set_State [1]
 
EType CSeq_align_Base::m_Type
 
int CSeq_align_Base::m_Dim
 
vector< CRef< CScore > > CSeq_align_Base::m_Score
 
CRef< TSegsCSeq_align_Base::m_Segs
 
list< CRef< CSeq_loc > > CSeq_align_Base::m_Bounds
 
list< CRef< CObject_id > > CSeq_align_Base::m_Id
 
list< CRef< CUser_object > > CSeq_align_Base::m_Ext
 
Uint4 CSeq_align_set_Base::m_set_State [1]
 
list< CRef< CSeq_align > > CSeq_align_set_Base::m_data
 
Uint4 CSparse_align_Base::m_set_State [1]
 
CRef< TFirst_idCSparse_align_Base::m_First_id
 
CRef< TSecond_idCSparse_align_Base::m_Second_id
 
int CSparse_align_Base::m_Numseg
 
vector< intCSparse_align_Base::m_First_starts
 
vector< intCSparse_align_Base::m_Second_starts
 
vector< TSeqPosCSparse_align_Base::m_Lens
 
vector< ENa_strandCSparse_align_Base::m_Second_strands
 
vector< CRef< CScore > > CSparse_align_Base::m_Seg_scores
 
Uint4 CSparse_seg_Base::m_set_State [1]
 
CRef< TMaster_idCSparse_seg_Base::m_Master_id
 
vector< CRef< CSparse_align > > CSparse_seg_Base::m_Rows
 
vector< CRef< CScore > > CSparse_seg_Base::m_Row_scores
 
vector< CRef< CSparse_seg_ext > > CSparse_seg_Base::m_Ext
 
Uint4 CSparse_seg_ext_Base::m_set_State [1]
 
int CSparse_seg_ext_Base::m_Index
 
Uint4 CSplice_site_Base::m_set_State [1]
 
string CSplice_site_Base::m_Bases
 
Uint4 CSpliced_exon_Base::m_set_State [1]
 
CRef< TProduct_startCSpliced_exon_Base::m_Product_start
 
CRef< TProduct_endCSpliced_exon_Base::m_Product_end
 
TSeqPos CSpliced_exon_Base::m_Genomic_start
 
TSeqPos CSpliced_exon_Base::m_Genomic_end
 
CRef< TProduct_idCSpliced_exon_Base::m_Product_id
 
CRef< TGenomic_idCSpliced_exon_Base::m_Genomic_id
 
ENa_strand CSpliced_exon_Base::m_Product_strand
 
ENa_strand CSpliced_exon_Base::m_Genomic_strand
 
list< CRef< CSpliced_exon_chunk > > CSpliced_exon_Base::m_Parts
 
CRef< TScoresCSpliced_exon_Base::m_Scores
 
CRef< TAcceptor_before_exonCSpliced_exon_Base::m_Acceptor_before_exon
 
CRef< TDonor_after_exonCSpliced_exon_Base::m_Donor_after_exon
 
bool CSpliced_exon_Base::m_Partial
 
list< CRef< CUser_object > > CSpliced_exon_Base::m_Ext
 
E_Choice CSpliced_exon_chunk_Base::m_choice
 
static const char *const CSpliced_exon_chunk_Base::sm_SelectionNames []
 
TMatch   CSpliced_exon_chunk_Base::m_Match
 
TMismatch   CSpliced_exon_chunk_Base::m_Mismatch
 
TDiag   CSpliced_exon_chunk_Base::m_Diag
 
TProduct_ins   CSpliced_exon_chunk_Base::m_Product_ins
 
TGenomic_ins   CSpliced_exon_chunk_Base::m_Genomic_ins
 
union {
   TMatch   CSpliced_exon_chunk_Base::m_Match
 
   TMismatch   CSpliced_exon_chunk_Base::m_Mismatch
 
   TDiag   CSpliced_exon_chunk_Base::m_Diag
 
   TProduct_ins   CSpliced_exon_chunk_Base::m_Product_ins
 
   TGenomic_ins   CSpliced_exon_chunk_Base::m_Genomic_ins
 
}; 
 
Uint4 CSpliced_seg_Base::m_set_State [1]
 
CRef< TProduct_idCSpliced_seg_Base::m_Product_id
 
CRef< TGenomic_idCSpliced_seg_Base::m_Genomic_id
 
ENa_strand CSpliced_seg_Base::m_Product_strand
 
ENa_strand CSpliced_seg_Base::m_Genomic_strand
 
EProduct_type CSpliced_seg_Base::m_Product_type
 
list< CRef< CSpliced_exon > > CSpliced_seg_Base::m_Exons
 
TSeqPos CSpliced_seg_Base::m_Poly_a
 
TSeqPos CSpliced_seg_Base::m_Product_length
 
list< CRef< CSpliced_seg_modifier > > CSpliced_seg_Base::m_Modifiers
 
E_Choice CSpliced_seg_modifier_Base::m_choice
 
static const char *const CSpliced_seg_modifier_Base::sm_SelectionNames []
 
TStart_codon_found   CSpliced_seg_modifier_Base::m_Start_codon_found
 
TStop_codon_found   CSpliced_seg_modifier_Base::m_Stop_codon_found
 
union {
   TStart_codon_found   CSpliced_seg_modifier_Base::m_Start_codon_found
 
   TStop_codon_found   CSpliced_seg_modifier_Base::m_Stop_codon_found
 
}; 
 
Uint4 CStd_seg_Base::m_set_State [1]
 
int CStd_seg_Base::m_Dim
 
vector< CRef< CSeq_id > > CStd_seg_Base::m_Ids
 
vector< CRef< CSeq_loc > > CStd_seg_Base::m_Loc
 
vector< CRef< CScore > > CStd_seg_Base::m_Scores
 

Detailed Description

Typedef Documentation

◆ TAcceptor_before_exon

Definition at line 107 of file Spliced_exon_.hpp.

◆ TAmin

Definition at line 82 of file Prot_pos_.hpp.

◆ TBases

Definition at line 86 of file Splice_site_.hpp.

◆ TBounds

Definition at line 400 of file Seq_align_.hpp.

◆ Tdata [1/2]

typedef list< CRef< CScore > > CScore_set_Base::Tdata

Definition at line 90 of file Score_set_.hpp.

◆ Tdata [2/2]

Definition at line 91 of file Seq_align_set_.hpp.

◆ TDendiag

Definition at line 194 of file Seq_align_.hpp.

◆ TDenseg

Definition at line 195 of file Seq_align_.hpp.

◆ TDiag

Definition at line 148 of file Spliced_exon_chunk_.hpp.

◆ TDim [1/5]

Definition at line 92 of file Dense_diag_.hpp.

◆ TDim [2/5]

Definition at line 104 of file Dense_seg_.hpp.

◆ TDim [3/5]

Definition at line 92 of file Packed_seg_.hpp.

◆ TDim [4/5]

Definition at line 397 of file Seq_align_.hpp.

◆ TDim [5/5]

Definition at line 91 of file Std_seg_.hpp.

◆ TDisc

Definition at line 198 of file Seq_align_.hpp.

◆ TDonor_after_exon

Definition at line 108 of file Spliced_exon_.hpp.

◆ TExons

Definition at line 105 of file Spliced_seg_.hpp.

◆ TExt [1/3]

Definition at line 402 of file Seq_align_.hpp.

◆ TExt [2/3]

Definition at line 101 of file Sparse_seg_.hpp.

◆ TExt [3/3]

Definition at line 110 of file Spliced_exon_.hpp.

◆ TFirst_id

Definition at line 91 of file Sparse_align_.hpp.

◆ TFirst_starts

Definition at line 94 of file Sparse_align_.hpp.

◆ TFrame

Definition at line 83 of file Prot_pos_.hpp.

◆ TGenomic_end

Definition at line 100 of file Spliced_exon_.hpp.

◆ TGenomic_id [1/2]

Definition at line 102 of file Spliced_exon_.hpp.

◆ TGenomic_id [2/2]

Definition at line 101 of file Spliced_seg_.hpp.

◆ TGenomic_ins

Definition at line 150 of file Spliced_exon_chunk_.hpp.

◆ TGenomic_start

Definition at line 99 of file Spliced_exon_.hpp.

◆ TGenomic_strand [1/2]

Definition at line 104 of file Spliced_exon_.hpp.

◆ TGenomic_strand [2/2]

Definition at line 103 of file Spliced_seg_.hpp.

◆ TId [1/2]

Definition at line 240 of file Score_.hpp.

◆ TId [2/2]

typedef list< CRef< CObject_id > > CSeq_align_Base::TId

Definition at line 401 of file Seq_align_.hpp.

◆ TIds [1/4]

typedef vector< CRef< CSeq_id > > CDense_diag_Base::TIds

Definition at line 93 of file Dense_diag_.hpp.

◆ TIds [2/4]

typedef vector< CRef< CSeq_id > > CDense_seg_Base::TIds

Definition at line 106 of file Dense_seg_.hpp.

◆ TIds [3/4]

typedef vector< CRef< CSeq_id > > CPacked_seg_Base::TIds

Definition at line 94 of file Packed_seg_.hpp.

◆ TIds [4/4]

typedef vector< CRef< CSeq_id > > CStd_seg_Base::TIds

Definition at line 92 of file Std_seg_.hpp.

◆ TIndex

Definition at line 81 of file Sparse_seg_ext_.hpp.

◆ TInt

Definition at line 163 of file Score_.hpp.

◆ TLen

Definition at line 95 of file Dense_diag_.hpp.

◆ TLens [1/3]

typedef vector< TSeqPos > CDense_seg_Base::TLens

Definition at line 108 of file Dense_seg_.hpp.

◆ TLens [2/3]

typedef vector< TSeqPos > CPacked_seg_Base::TLens

Definition at line 97 of file Packed_seg_.hpp.

◆ TLens [3/3]

Definition at line 96 of file Sparse_align_.hpp.

◆ TLoc

typedef vector< CRef< CSeq_loc > > CStd_seg_Base::TLoc

Definition at line 93 of file Std_seg_.hpp.

◆ TMaster_id

Definition at line 98 of file Sparse_seg_.hpp.

◆ TMatch

Definition at line 146 of file Spliced_exon_chunk_.hpp.

◆ TmemberIndex [1/13]

Definition at line 109 of file Dense_diag_.hpp.

◆ TmemberIndex [2/13]

Definition at line 123 of file Dense_seg_.hpp.

◆ TmemberIndex [3/13]

Definition at line 113 of file Packed_seg_.hpp.

◆ TmemberIndex [4/13]

Definition at line 91 of file Prot_pos_.hpp.

◆ TmemberIndex [5/13]

Definition at line 249 of file Score_.hpp.

◆ TmemberIndex [6/13]

Definition at line 415 of file Seq_align_.hpp.

◆ TmemberIndex [7/13]

Definition at line 112 of file Sparse_align_.hpp.

◆ TmemberIndex [8/13]

Definition at line 111 of file Sparse_seg_.hpp.

◆ TmemberIndex [9/13]

Definition at line 88 of file Sparse_seg_ext_.hpp.

◆ TmemberIndex [10/13]

Definition at line 93 of file Splice_site_.hpp.

◆ TmemberIndex [11/13]

Definition at line 130 of file Spliced_exon_.hpp.

◆ TmemberIndex [12/13]

Definition at line 123 of file Spliced_seg_.hpp.

◆ TmemberIndex [13/13]

Definition at line 104 of file Std_seg_.hpp.

◆ TMismatch

Definition at line 147 of file Spliced_exon_chunk_.hpp.

◆ TModifiers

Definition at line 108 of file Spliced_seg_.hpp.

◆ TNucpos

Definition at line 144 of file Product_pos_.hpp.

◆ TNumseg [1/3]

Definition at line 105 of file Dense_seg_.hpp.

◆ TNumseg [2/3]

Definition at line 93 of file Packed_seg_.hpp.

◆ TNumseg [3/3]

Definition at line 93 of file Sparse_align_.hpp.

◆ TPacked

Definition at line 197 of file Seq_align_.hpp.

◆ Tparent [1/26]

Definition at line 81 of file Dense_diag_.hpp.

◆ Tparent [2/26]

Definition at line 93 of file Dense_seg_.hpp.

◆ Tparent [3/26]

Definition at line 67 of file Packed_seg.hpp.

◆ Tparent [4/26]

Definition at line 81 of file Packed_seg_.hpp.

◆ Tparent [5/26]

Definition at line 74 of file Product_pos_.hpp.

◆ Tparent [6/26]

Definition at line 71 of file Prot_pos_.hpp.

◆ Tparent [7/26]

Definition at line 75 of file Score_.hpp.

◆ Tparent [8/26]

Definition at line 92 of file Score_.hpp.

◆ Tparent [9/26]

Definition at line 67 of file Score_set.hpp.

◆ Tparent [10/26]

Definition at line 79 of file Score_set_.hpp.

◆ Tparent [11/26]

Definition at line 89 of file Seq_align_.hpp.

◆ Tparent [12/26]

Definition at line 119 of file Seq_align_.hpp.

◆ Tparent [13/26]

Definition at line 80 of file Seq_align_set_.hpp.

◆ Tparent [14/26]

Definition at line 80 of file Sparse_align_.hpp.

◆ Tparent [15/26]

Definition at line 87 of file Sparse_seg_.hpp.

◆ Tparent [16/26]

Definition at line 67 of file Sparse_seg_ext.hpp.

◆ Tparent [17/26]

Definition at line 70 of file Sparse_seg_ext_.hpp.

◆ Tparent [18/26]

Definition at line 67 of file Splice_site.hpp.

◆ Tparent [19/26]

Definition at line 75 of file Splice_site_.hpp.

◆ Tparent [20/26]

Definition at line 86 of file Spliced_exon_.hpp.

◆ Tparent [21/26]

Definition at line 67 of file Spliced_exon_chunk.hpp.

◆ Tparent [22/26]

Definition at line 73 of file Spliced_exon_chunk_.hpp.

◆ Tparent [23/26]

Definition at line 81 of file Spliced_seg_.hpp.

◆ Tparent [24/26]

Definition at line 67 of file Spliced_seg_modifier.hpp.

◆ Tparent [25/26]

Definition at line 70 of file Spliced_seg_modifier_.hpp.

◆ Tparent [26/26]

Definition at line 80 of file Std_seg_.hpp.

◆ TPartial

Definition at line 109 of file Spliced_exon_.hpp.

◆ TParts

Definition at line 105 of file Spliced_exon_.hpp.

◆ TPoly_a

Definition at line 106 of file Spliced_seg_.hpp.

◆ TPresent

typedef vector< char > CPacked_seg_Base::TPresent

Definition at line 96 of file Packed_seg_.hpp.

◆ TProduct_end

Definition at line 98 of file Spliced_exon_.hpp.

◆ TProduct_id [1/2]

Definition at line 101 of file Spliced_exon_.hpp.

◆ TProduct_id [2/2]

Definition at line 100 of file Spliced_seg_.hpp.

◆ TProduct_ins

Definition at line 149 of file Spliced_exon_chunk_.hpp.

◆ TProduct_length

Definition at line 107 of file Spliced_seg_.hpp.

◆ TProduct_start

Definition at line 97 of file Spliced_exon_.hpp.

◆ TProduct_strand [1/2]

Definition at line 103 of file Spliced_exon_.hpp.

◆ TProduct_strand [2/2]

Definition at line 102 of file Spliced_seg_.hpp.

◆ TProduct_type

Definition at line 104 of file Spliced_seg_.hpp.

◆ TProtpos

Definition at line 145 of file Product_pos_.hpp.

◆ TReal

Definition at line 162 of file Score_.hpp.

◆ TRow_scores

Definition at line 100 of file Sparse_seg_.hpp.

◆ TRows

Definition at line 99 of file Sparse_seg_.hpp.

◆ TScore

typedef vector< CRef< CScore > > CSeq_align_Base::TScore

Definition at line 398 of file Seq_align_.hpp.

◆ TScores [1/5]

typedef vector< CRef< CScore > > CDense_diag_Base::TScores

Definition at line 97 of file Dense_diag_.hpp.

◆ TScores [2/5]

typedef vector< CRef< CScore > > CDense_seg_Base::TScores

Definition at line 110 of file Dense_seg_.hpp.

◆ TScores [3/5]

typedef vector< CRef< CScore > > CPacked_seg_Base::TScores

Definition at line 99 of file Packed_seg_.hpp.

◆ TScores [4/5]

Definition at line 106 of file Spliced_exon_.hpp.

◆ TScores [5/5]

typedef vector< CRef< CScore > > CStd_seg_Base::TScores

Definition at line 94 of file Std_seg_.hpp.

◆ TSecond_id

Definition at line 92 of file Sparse_align_.hpp.

◆ TSecond_starts

Definition at line 95 of file Sparse_align_.hpp.

◆ TSecond_strands

Definition at line 97 of file Sparse_align_.hpp.

◆ TSeg_scores

Definition at line 98 of file Sparse_align_.hpp.

◆ TSegs

Definition at line 399 of file Seq_align_.hpp.

◆ TSparse

Definition at line 200 of file Seq_align_.hpp.

◆ TSpliced

Definition at line 199 of file Seq_align_.hpp.

◆ TStart_codon_found

Definition at line 140 of file Spliced_seg_modifier_.hpp.

◆ TStarts [1/3]

Definition at line 94 of file Dense_diag_.hpp.

◆ TStarts [2/3]

Definition at line 107 of file Dense_seg_.hpp.

◆ TStarts [3/3]

Definition at line 95 of file Packed_seg_.hpp.

◆ TStd

Definition at line 196 of file Seq_align_.hpp.

◆ TStop_codon_found

Definition at line 141 of file Spliced_seg_modifier_.hpp.

◆ TStrands [1/3]

Definition at line 96 of file Dense_diag_.hpp.

◆ TStrands [2/3]

Definition at line 109 of file Dense_seg_.hpp.

◆ TStrands [3/3]

Definition at line 98 of file Packed_seg_.hpp.

◆ TType

Definition at line 396 of file Seq_align_.hpp.

◆ TValue

Definition at line 241 of file Score_.hpp.

Enumeration Type Documentation

◆ E_Choice [1/5]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Nucpos 
e_Protpos 

Definition at line 86 of file Product_pos_.hpp.

◆ E_Choice [2/5]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Real 
e_Int 

Definition at line 104 of file Score_.hpp.

◆ E_Choice [3/5]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Dendiag 
e_Denseg 
e_Std 
e_Packed 
e_Disc 
e_Spliced 
e_Sparse 

Definition at line 131 of file Seq_align_.hpp.

◆ E_Choice [4/5]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Match 

both sequences represented, product and genomic sequences match

e_Mismatch 

both sequences represented, product and genomic sequences do not match

e_Diag 

both sequences are represented, there is sufficient similarity between product and genomic sequences. Can be used to replace stretches of matches and mismatches, mostly for protein to genomic where definition of match or mismatch depends on translation table

e_Product_ins 

insertion in product sequence (i.e. gap in the genomic sequence)

e_Genomic_ins 

insertion in genomic sequence (i.e. gap in the product sequence)

Definition at line 85 of file Spliced_exon_chunk_.hpp.

◆ E_Choice [5/5]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Start_codon_found 

protein aligns from the start and the first codon on both product and genomic is start codon

e_Stop_codon_found 

protein aligns to it's end and there is stop codon on the genomic right after the alignment

Definition at line 82 of file Spliced_seg_modifier_.hpp.

◆ E_ChoiceStopper [1/5]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Protpos+1

Definition at line 92 of file Product_pos_.hpp.

◆ E_ChoiceStopper [2/5]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Int+1

Definition at line 110 of file Score_.hpp.

◆ E_ChoiceStopper [3/5]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Sparse+1

Definition at line 142 of file Seq_align_.hpp.

◆ E_ChoiceStopper [4/5]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Genomic_ins+1

Definition at line 94 of file Spliced_exon_chunk_.hpp.

◆ E_ChoiceStopper [5/5]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Stop_codon_found+1

Definition at line 88 of file Spliced_seg_modifier_.hpp.

◆ E_memberIndex [1/13]

Enumerator
e__allMandatory 
e_dim 
e_ids 
e_starts 
e_len 
e_strands 
e_scores 

Definition at line 100 of file Dense_diag_.hpp.

◆ E_memberIndex [2/13]

Enumerator
e__allMandatory 
e_dim 
e_numseg 
e_ids 
e_starts 
e_lens 
e_strands 
e_scores 

Definition at line 113 of file Dense_seg_.hpp.

◆ E_memberIndex [3/13]

Enumerator
e__allMandatory 
e_dim 
e_numseg 
e_ids 
e_starts 
e_present 
e_lens 
e_strands 
e_scores 

Definition at line 102 of file Packed_seg_.hpp.

◆ E_memberIndex [4/13]

Enumerator
e__allMandatory 
e_amin 
e_frame 

Definition at line 86 of file Prot_pos_.hpp.

◆ E_memberIndex [5/13]

Enumerator
e__allMandatory 
e_id 
e_value 

Definition at line 244 of file Score_.hpp.

◆ E_memberIndex [6/13]

Enumerator
e__allMandatory 
e_type 
e_dim 
e_score 
e_segs 
e_bounds 
e_id 
e_ext 

Definition at line 405 of file Seq_align_.hpp.

◆ E_memberIndex [7/13]

Enumerator
e__allMandatory 
e_first_id 
e_second_id 
e_numseg 
e_first_starts 
e_second_starts 
e_lens 
e_second_strands 
e_seg_scores 

Definition at line 101 of file Sparse_align_.hpp.

◆ E_memberIndex [8/13]

Enumerator
e__allMandatory 
e_master_id 
e_rows 
e_row_scores 
e_ext 

Definition at line 104 of file Sparse_seg_.hpp.

◆ E_memberIndex [9/13]

Enumerator
e__allMandatory 
e_index 

Definition at line 84 of file Sparse_seg_ext_.hpp.

◆ E_memberIndex [10/13]

Enumerator
e__allMandatory 
e_bases 

Definition at line 89 of file Splice_site_.hpp.

◆ E_memberIndex [11/13]

Enumerator
e__allMandatory 
e_product_start 
e_product_end 
e_genomic_start 
e_genomic_end 
e_product_id 
e_genomic_id 
e_product_strand 
e_genomic_strand 
e_parts 
e_scores 
e_acceptor_before_exon 
e_donor_after_exon 
e_partial 
e_ext 

Definition at line 113 of file Spliced_exon_.hpp.

◆ E_memberIndex [12/13]

Enumerator
e__allMandatory 
e_product_id 
e_genomic_id 
e_product_strand 
e_genomic_strand 
e_product_type 
e_exons 
e_poly_a 
e_product_length 
e_modifiers 

Definition at line 111 of file Spliced_seg_.hpp.

◆ E_memberIndex [13/13]

Enumerator
e__allMandatory 
e_dim 
e_ids 
e_loc 
e_scores 

Definition at line 97 of file Std_seg_.hpp.

◆ EProduct_type

Enumerator
eProduct_type_transcript 
eProduct_type_protein 

Definition at line 91 of file Spliced_seg_.hpp.

◆ EType

enum CSeq_align_Base::EType ( void  )
Enumerator
eType_not_set 
eType_global 
eType_diags 

unbroken, but not ordered, diagonals

eType_partial 

mapping pieces together

eType_disc 

discontinuous alignment

eType_other 

Definition at line 99 of file Seq_align_.hpp.

Function Documentation

◆ C_Segs() [1/2]

CSeq_align_Base::C_Segs::C_Segs ( const C_Segs )
private

◆ C_Segs() [2/2]

END_CHOICE_INFO CSeq_align_Base::C_Segs::C_Segs ( void  )

Definition at line 283 of file Seq_align_.cpp.

◆ C_Value() [1/2]

CScore_Base::C_Value::C_Value ( const C_Value )
private

◆ C_Value() [2/2]

END_CHOICE_INFO CScore_Base::C_Value::C_Value ( void  )

Definition at line 108 of file Score_.cpp.

◆ CanGet() [1/2]

bool CScore_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 159 of file Score_set_.hpp.

◆ CanGet() [2/2]

bool CSeq_align_set_Base::CanGet ( void  ) const
inline

◆ CanGetAcceptor_before_exon()

bool CSpliced_exon_Base::CanGetAcceptor_before_exon ( void  ) const
inline

Check if it is safe to call GetAcceptor_before_exon method.

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

Definition at line 1030 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetAcceptor_before_exon().

Referenced by CProteinAlignText::CProteinAlignText(), and CSpliced_exon_Base::GetAcceptor_before_exon().

◆ CanGetAmin()

bool CProt_pos_Base::CanGetAmin ( void  ) const
inline

Check if it is safe to call GetAmin method.

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

Definition at line 207 of file Prot_pos_.hpp.

References CProt_pos_Base::IsSetAmin().

Referenced by CProt_pos_Base::GetAmin().

◆ CanGetBases()

bool CSplice_site_Base::CanGetBases ( void  ) const
inline

Check if it is safe to call GetBases method.

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

Definition at line 168 of file Splice_site_.hpp.

References CSplice_site_Base::IsSetBases().

Referenced by CProteinAlignText::CProteinAlignText(), and CSplice_site_Base::GetBases().

◆ CanGetBounds()

bool CSeq_align_Base::CanGetBounds ( void  ) const
inline

Check if it is safe to call GetBounds method.

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

Definition at line 945 of file Seq_align_.hpp.

Referenced by CProteinAlignText::GetGenomicBounds().

◆ CanGetDim() [1/5]

bool CDense_diag_Base::CanGetDim ( void  ) const
inline

Check if it is safe to call GetDim method.

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

Definition at line 354 of file Dense_diag_.hpp.

◆ CanGetDim() [2/5]

bool CDense_seg_Base::CanGetDim ( void  ) const
inline

Check if it is safe to call GetDim method.

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

Definition at line 402 of file Dense_seg_.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSeqAlign(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().

◆ CanGetDim() [3/5]

bool CPacked_seg_Base::CanGetDim ( void  ) const
inline

Check if it is safe to call GetDim method.

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

Definition at line 426 of file Packed_seg_.hpp.

◆ CanGetDim() [4/5]

bool CSeq_align_Base::CanGetDim ( void  ) const
inline

Check if it is safe to call GetDim method.

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

Definition at line 843 of file Seq_align_.hpp.

References CSeq_align_Base::IsSetDim().

Referenced by CSeq_align_Base::GetDim(), and CSeq_align::GetSeqRange().

◆ CanGetDim() [5/5]

bool CStd_seg_Base::CanGetDim ( void  ) const
inline

Check if it is safe to call GetDim method.

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

Definition at line 276 of file Std_seg_.hpp.

◆ CanGetDonor_after_exon()

bool CSpliced_exon_Base::CanGetDonor_after_exon ( void  ) const
inline

Check if it is safe to call GetDonor_after_exon method.

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

Definition at line 1051 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetDonor_after_exon().

Referenced by CProteinAlignText::CProteinAlignText(), and CSpliced_exon_Base::GetDonor_after_exon().

◆ CanGetExons()

bool CSpliced_seg_Base::CanGetExons ( void  ) const
inline

Check if it is safe to call GetExons method.

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

Definition at line 686 of file Spliced_seg_.hpp.

Referenced by CScore_LastSpliceSite::Get(), CFeatureGenerator::SImplementation::StitchSmallHoles(), and CFeatureGenerator::SImplementation::TrimHolesToCodons().

◆ CanGetExt() [1/3]

bool CSeq_align_Base::CanGetExt ( void  ) const
inline

Check if it is safe to call GetExt method.

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

Definition at line 995 of file Seq_align_.hpp.

Referenced by IsGnomonConstructed().

◆ CanGetExt() [2/3]

bool CSparse_seg_Base::CanGetExt ( void  ) const
inline

Check if it is safe to call GetExt method.

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

Definition at line 353 of file Sparse_seg_.hpp.

◆ CanGetExt() [3/3]

bool CSpliced_exon_Base::CanGetExt ( void  ) const
inline

Check if it is safe to call GetExt method.

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

Definition at line 1119 of file Spliced_exon_.hpp.

◆ CanGetFirst_id()

bool CSparse_align_Base::CanGetFirst_id ( void  ) const
inline

Check if it is safe to call GetFirst_id method.

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

Definition at line 425 of file Sparse_align_.hpp.

◆ CanGetFirst_starts()

bool CSparse_align_Base::CanGetFirst_starts ( void  ) const
inline

Check if it is safe to call GetFirst_starts method.

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

Definition at line 532 of file Sparse_align_.hpp.

◆ CanGetFrame()

bool CProt_pos_Base::CanGetFrame ( void  ) const
inline

Check if it is safe to call GetFrame method.

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

Definition at line 254 of file Prot_pos_.hpp.

◆ CanGetGenomic_end()

bool CSpliced_exon_Base::CanGetGenomic_end ( void  ) const
inline

Check if it is safe to call GetGenomic_end method.

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

Definition at line 801 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetGenomic_end().

Referenced by CSpliced_exon_Base::GetGenomic_end().

◆ CanGetGenomic_id() [1/2]

bool CSpliced_exon_Base::CanGetGenomic_id ( void  ) const
inline

Check if it is safe to call GetGenomic_id method.

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

Definition at line 869 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetGenomic_id().

Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSpliced_exon_Base::GetGenomic_id(), and CFeatureGenerator::SImplementation::HasMixedGenomicIds().

◆ CanGetGenomic_id() [2/2]

bool CSpliced_seg_Base::CanGetGenomic_id ( void  ) const
inline

Check if it is safe to call GetGenomic_id method.

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

Definition at line 524 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::IsSetGenomic_id().

Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSpliced_seg_Base::GetGenomic_id(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), and s_GetAlignmentContent().

◆ CanGetGenomic_start()

bool CSpliced_exon_Base::CanGetGenomic_start ( void  ) const
inline

Check if it is safe to call GetGenomic_start method.

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

Definition at line 754 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetGenomic_start().

Referenced by CSpliced_exon_Base::GetGenomic_start().

◆ CanGetGenomic_strand() [1/2]

bool CSpliced_exon_Base::CanGetGenomic_strand ( void  ) const
inline

Check if it is safe to call GetGenomic_strand method.

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

Definition at line 937 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetGenomic_strand().

Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CSpliced_exon_Base::GetGenomic_strand(), and CSpliced_seg::IsConsistentBiologicalOrder().

◆ CanGetGenomic_strand() [2/2]

bool CSpliced_seg_Base::CanGetGenomic_strand ( void  ) const
inline

◆ CanGetId() [1/2]

bool CScore_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 438 of file Score_.hpp.

References CScore_Base::IsSetId().

Referenced by CScore_Base::GetId(), and CHitMatrixDataSource::x_UpdateScoreMap().

◆ CanGetId() [2/2]

bool CSeq_align_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 970 of file Seq_align_.hpp.

Referenced by GetModelId().

◆ CanGetIds() [1/4]

bool CDense_diag_Base::CanGetIds ( void  ) const
inline

Check if it is safe to call GetIds method.

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

Definition at line 404 of file Dense_diag_.hpp.

◆ CanGetIds() [2/4]

bool CDense_seg_Base::CanGetIds ( void  ) const
inline

Check if it is safe to call GetIds method.

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

Definition at line 499 of file Dense_seg_.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().

◆ CanGetIds() [3/4]

bool CPacked_seg_Base::CanGetIds ( void  ) const
inline

Check if it is safe to call GetIds method.

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

Definition at line 523 of file Packed_seg_.hpp.

◆ CanGetIds() [4/4]

bool CStd_seg_Base::CanGetIds ( void  ) const
inline

Check if it is safe to call GetIds method.

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

Definition at line 326 of file Std_seg_.hpp.

◆ CanGetIndex()

bool CSparse_seg_ext_Base::CanGetIndex ( void  ) const
inline

Check if it is safe to call GetIndex method.

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

Definition at line 164 of file Sparse_seg_ext_.hpp.

References CSparse_seg_ext_Base::IsSetIndex().

Referenced by CSparse_seg_ext_Base::GetIndex().

◆ CanGetLen()

bool CDense_diag_Base::CanGetLen ( void  ) const
inline

Check if it is safe to call GetLen method.

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

Definition at line 454 of file Dense_diag_.hpp.

References CDense_diag_Base::IsSetLen().

Referenced by CDense_diag_Base::GetLen().

◆ CanGetLens() [1/3]

bool CDense_seg_Base::CanGetLens ( void  ) const
inline

Check if it is safe to call GetLens method.

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

Definition at line 549 of file Dense_seg_.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().

◆ CanGetLens() [2/3]

bool CPacked_seg_Base::CanGetLens ( void  ) const
inline

Check if it is safe to call GetLens method.

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

Definition at line 601 of file Packed_seg_.hpp.

◆ CanGetLens() [3/3]

bool CSparse_align_Base::CanGetLens ( void  ) const
inline

Check if it is safe to call GetLens method.

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

Definition at line 582 of file Sparse_align_.hpp.

◆ CanGetLoc()

bool CStd_seg_Base::CanGetLoc ( void  ) const
inline

Check if it is safe to call GetLoc method.

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

Definition at line 351 of file Std_seg_.hpp.

◆ CanGetMaster_id()

bool CSparse_seg_Base::CanGetMaster_id ( void  ) const
inline

Check if it is safe to call GetMaster_id method.

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

Definition at line 282 of file Sparse_seg_.hpp.

References CSparse_seg_Base::IsSetMaster_id().

Referenced by CSparse_seg_Base::GetMaster_id().

◆ CanGetModifiers()

bool CSpliced_seg_Base::CanGetModifiers ( void  ) const
inline

Check if it is safe to call GetModifiers method.

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

Definition at line 805 of file Spliced_seg_.hpp.

◆ CanGetNumseg() [1/3]

bool CDense_seg_Base::CanGetNumseg ( void  ) const
inline

Check if it is safe to call GetNumseg method.

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

Definition at line 452 of file Dense_seg_.hpp.

References CDense_seg_Base::IsSetNumseg().

Referenced by BOOST_AUTO_TEST_CASE(), CDense_seg_Base::GetNumseg(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().

◆ CanGetNumseg() [2/3]

bool CPacked_seg_Base::CanGetNumseg ( void  ) const
inline

Check if it is safe to call GetNumseg method.

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

Definition at line 476 of file Packed_seg_.hpp.

References CPacked_seg_Base::IsSetNumseg().

Referenced by CPacked_seg_Base::GetNumseg().

◆ CanGetNumseg() [3/3]

bool CSparse_align_Base::CanGetNumseg ( void  ) const
inline

Check if it is safe to call GetNumseg method.

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

Definition at line 485 of file Sparse_align_.hpp.

References CSparse_align_Base::IsSetNumseg().

Referenced by CSparse_align_Base::GetNumseg().

◆ CanGetPartial()

bool CSpliced_exon_Base::CanGetPartial ( void  ) const
inline

Check if it is safe to call GetPartial method.

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

Definition at line 1072 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetPartial().

Referenced by CSpliced_exon_Base::GetPartial().

◆ CanGetParts()

bool CSpliced_exon_Base::CanGetParts ( void  ) const
inline

Check if it is safe to call GetParts method.

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

Definition at line 984 of file Spliced_exon_.hpp.

◆ CanGetPoly_a()

bool CSpliced_seg_Base::CanGetPoly_a ( void  ) const
inline

◆ CanGetPresent()

bool CPacked_seg_Base::CanGetPresent ( void  ) const
inline

Check if it is safe to call GetPresent method.

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

Definition at line 573 of file Packed_seg_.hpp.

References CPacked_seg_Base::IsSetPresent().

Referenced by CPacked_seg_Base::GetPresent().

◆ CanGetProduct_end()

bool CSpliced_exon_Base::CanGetProduct_end ( void  ) const
inline

Check if it is safe to call GetProduct_end method.

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

Definition at line 724 of file Spliced_exon_.hpp.

Referenced by CScore_LastSpliceSite::Get().

◆ CanGetProduct_id() [1/2]

bool CSpliced_exon_Base::CanGetProduct_id ( void  ) const
inline

Check if it is safe to call GetProduct_id method.

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

Definition at line 848 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetProduct_id().

Referenced by CSpliced_exon_Base::GetProduct_id().

◆ CanGetProduct_id() [2/2]

bool CSpliced_seg_Base::CanGetProduct_id ( void  ) const
inline

Check if it is safe to call GetProduct_id method.

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

Definition at line 503 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::IsSetProduct_id().

Referenced by CSpliced_seg_Base::GetProduct_id(), s_GetAlignmentContent(), and CFeatureGenerator::SImplementation::TrimHolesToCodons().

◆ CanGetProduct_length()

bool CSpliced_seg_Base::CanGetProduct_length ( void  ) const
inline

Check if it is safe to call GetProduct_length method.

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

Definition at line 758 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::IsSetProduct_length().

Referenced by CScore_StartStopCodon::Get(), and CSpliced_seg_Base::GetProduct_length().

◆ CanGetProduct_start()

bool CSpliced_exon_Base::CanGetProduct_start ( void  ) const
inline

Check if it is safe to call GetProduct_start method.

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

Definition at line 694 of file Spliced_exon_.hpp.

◆ CanGetProduct_strand() [1/2]

bool CSpliced_exon_Base::CanGetProduct_strand ( void  ) const
inline

Check if it is safe to call GetProduct_strand method.

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

Definition at line 890 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetProduct_strand().

Referenced by ConvertSplicedToPairwiseAln(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg::IsConsistentBiologicalOrder(), and CSpliced_seg::Validate().

◆ CanGetProduct_strand() [2/2]

bool CSpliced_seg_Base::CanGetProduct_strand ( void  ) const
inline

◆ CanGetProduct_type()

bool CSpliced_seg_Base::CanGetProduct_type ( void  ) const
inline

Check if it is safe to call GetProduct_type method.

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

Definition at line 639 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::IsSetProduct_type().

Referenced by CScore_LastSpliceSite::Get(), CSpliced_seg_Base::GetProduct_type(), and CPslRecord::xValidateSegment().

◆ CanGetRow_scores()

bool CSparse_seg_Base::CanGetRow_scores ( void  ) const
inline

Check if it is safe to call GetRow_scores method.

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

Definition at line 328 of file Sparse_seg_.hpp.

◆ CanGetRows()

bool CSparse_seg_Base::CanGetRows ( void  ) const
inline

Check if it is safe to call GetRows method.

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

Definition at line 303 of file Sparse_seg_.hpp.

◆ CanGetScore()

bool CSeq_align_Base::CanGetScore ( void  ) const
inline

Check if it is safe to call GetScore method.

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

Definition at line 890 of file Seq_align_.hpp.

Referenced by CPslWriter::WriteAlign().

◆ CanGetScores() [1/5]

bool CDense_diag_Base::CanGetScores ( void  ) const
inline

Check if it is safe to call GetScores method.

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

Definition at line 526 of file Dense_diag_.hpp.

◆ CanGetScores() [2/5]

bool CDense_seg_Base::CanGetScores ( void  ) const
inline

Check if it is safe to call GetScores method.

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

Definition at line 599 of file Dense_seg_.hpp.

◆ CanGetScores() [3/5]

bool CPacked_seg_Base::CanGetScores ( void  ) const
inline

Check if it is safe to call GetScores method.

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

Definition at line 651 of file Packed_seg_.hpp.

◆ CanGetScores() [4/5]

bool CSpliced_exon_Base::CanGetScores ( void  ) const
inline

Check if it is safe to call GetScores method.

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

Definition at line 1009 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::IsSetScores().

Referenced by CSpliced_exon_Base::GetScores().

◆ CanGetScores() [5/5]

bool CStd_seg_Base::CanGetScores ( void  ) const
inline

Check if it is safe to call GetScores method.

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

Definition at line 376 of file Std_seg_.hpp.

◆ CanGetSecond_id()

bool CSparse_align_Base::CanGetSecond_id ( void  ) const
inline

Check if it is safe to call GetSecond_id method.

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

Definition at line 455 of file Sparse_align_.hpp.

◆ CanGetSecond_starts()

bool CSparse_align_Base::CanGetSecond_starts ( void  ) const
inline

Check if it is safe to call GetSecond_starts method.

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

Definition at line 557 of file Sparse_align_.hpp.

◆ CanGetSecond_strands()

bool CSparse_align_Base::CanGetSecond_strands ( void  ) const
inline

Check if it is safe to call GetSecond_strands method.

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

Definition at line 607 of file Sparse_align_.hpp.

◆ CanGetSeg_scores()

bool CSparse_align_Base::CanGetSeg_scores ( void  ) const
inline

Check if it is safe to call GetSeg_scores method.

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

Definition at line 632 of file Sparse_align_.hpp.

◆ CanGetSegs()

bool CSeq_align_Base::CanGetSegs ( void  ) const
inline

◆ CanGetStarts() [1/3]

bool CDense_diag_Base::CanGetStarts ( void  ) const
inline

Check if it is safe to call GetStarts method.

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

Definition at line 429 of file Dense_diag_.hpp.

◆ CanGetStarts() [2/3]

bool CDense_seg_Base::CanGetStarts ( void  ) const
inline

Check if it is safe to call GetStarts method.

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

Definition at line 524 of file Dense_seg_.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().

◆ CanGetStarts() [3/3]

bool CPacked_seg_Base::CanGetStarts ( void  ) const
inline

Check if it is safe to call GetStarts method.

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

Definition at line 548 of file Packed_seg_.hpp.

◆ CanGetStrands() [1/3]

bool CDense_diag_Base::CanGetStrands ( void  ) const
inline

Check if it is safe to call GetStrands method.

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

Definition at line 501 of file Dense_diag_.hpp.

Referenced by CDense_diag::GetSeqStrand().

◆ CanGetStrands() [2/3]

bool CDense_seg_Base::CanGetStrands ( void  ) const
inline

◆ CanGetStrands() [3/3]

bool CPacked_seg_Base::CanGetStrands ( void  ) const
inline

Check if it is safe to call GetStrands method.

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

Definition at line 626 of file Packed_seg_.hpp.

◆ CanGetType()

bool CSeq_align_Base::CanGetType ( void  ) const
inline

Check if it is safe to call GetType method.

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

Definition at line 796 of file Seq_align_.hpp.

References CSeq_align_Base::IsSetType().

Referenced by CSeq_align_Base::GetType().

◆ CanGetValue()

bool CScore_Base::CanGetValue ( void  ) const
inline

Check if it is safe to call GetValue method.

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

Definition at line 459 of file Score_.hpp.

References CScore_Base::IsSetValue().

Referenced by CScore_Base::GetValue().

◆ CDense_diag_Base() [1/2]

CDense_diag_Base::CDense_diag_Base ( const CDense_diag_Base )
private

◆ CDense_diag_Base() [2/2]

END_CLASS_INFO CDense_diag_Base::CDense_diag_Base ( void  )

Definition at line 102 of file Dense_diag_.cpp.

References CDense_diag_Base::m_set_State.

◆ CDense_seg_Base() [1/2]

CDense_seg_Base::CDense_seg_Base ( const CDense_seg_Base )
private

◆ CDense_seg_Base() [2/2]

END_CLASS_INFO CDense_seg_Base::CDense_seg_Base ( void  )

Definition at line 110 of file Dense_seg_.cpp.

References CDense_seg_Base::m_set_State.

◆ CheckSelected() [1/5]

void CProduct_pos_Base::CheckSelected ( E_Choice  index) const
inline

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

Parameters
indexExpected selection.

Definition at line 237 of file Product_pos_.hpp.

References CProduct_pos_Base::m_choice, and CProduct_pos_Base::ThrowInvalidSelection().

Referenced by CProduct_pos_Base::GetNucpos(), and CProduct_pos_Base::GetProtpos().

◆ CheckSelected() [2/5]

void CScore_Base::C_Value::CheckSelected ( E_Choice  index) const
inline

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

Parameters
indexExpected selection.

Definition at line 355 of file Score_.hpp.

◆ CheckSelected() [3/5]

void CSeq_align_Base::C_Segs::CheckSelected ( E_Choice  index) const
inline

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

Parameters
indexExpected selection.

Definition at line 697 of file Seq_align_.hpp.

◆ CheckSelected() [4/5]

void CSpliced_exon_chunk_Base::CheckSelected ( E_Choice  index) const
inline

◆ CheckSelected() [5/5]

void CSpliced_seg_modifier_Base::CheckSelected ( E_Choice  index) const
inline

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

Parameters
indexExpected selection.

Definition at line 234 of file Spliced_seg_modifier_.hpp.

References CSpliced_seg_modifier_Base::m_choice, and CSpliced_seg_modifier_Base::ThrowInvalidSelection().

Referenced by CSpliced_seg_modifier_Base::GetStart_codon_found(), and CSpliced_seg_modifier_Base::GetStop_codon_found().

◆ CPacked_seg() [1/2]

CPacked_seg::CPacked_seg ( const CPacked_seg value)
private

◆ CPacked_seg() [2/2]

CPacked_seg::CPacked_seg ( void  )
inline

Definition at line 86 of file Packed_seg.hpp.

◆ CPacked_seg_Base() [1/2]

CPacked_seg_Base::CPacked_seg_Base ( const CPacked_seg_Base )
private

◆ CPacked_seg_Base() [2/2]

END_CLASS_INFO CPacked_seg_Base::CPacked_seg_Base ( void  )

Definition at line 118 of file Packed_seg_.cpp.

References CPacked_seg_Base::m_set_State.

◆ CProduct_pos_Base() [1/2]

CProduct_pos_Base::CProduct_pos_Base ( const CProduct_pos_Base )
private

◆ CProduct_pos_Base() [2/2]

END_CHOICE_INFO CProduct_pos_Base::CProduct_pos_Base ( void  )

Definition at line 136 of file Product_pos_.cpp.

◆ CProt_pos_Base() [1/2]

CProt_pos_Base::CProt_pos_Base ( const CProt_pos_Base )
private

◆ CProt_pos_Base() [2/2]

END_CLASS_INFO CProt_pos_Base::CProt_pos_Base ( void  )

Definition at line 68 of file Prot_pos_.cpp.

References CProt_pos_Base::m_set_State.

◆ CScore_Base() [1/2]

CScore_Base::CScore_Base ( const CScore_Base )
private

◆ CScore_Base() [2/2]

END_CLASS_INFO CScore_Base::CScore_Base ( void  )

Definition at line 167 of file Score_.cpp.

References CScore_Base::m_set_State.

◆ CScore_set() [1/2]

CScore_set::CScore_set ( const CScore_set value)
private

◆ CScore_set() [2/2]

CScore_set::CScore_set ( void  )
inline

Definition at line 86 of file Score_set.hpp.

◆ CScore_set_Base() [1/2]

CScore_set_Base::CScore_set_Base ( const CScore_set_Base )
private

◆ CScore_set_Base() [2/2]

END_CLASS_INFO CScore_set_Base::CScore_set_Base ( void  )

Definition at line 68 of file Score_set_.cpp.

References CScore_set_Base::m_set_State.

◆ CSeq_align_Base() [1/2]

CSeq_align_Base::CSeq_align_Base ( const CSeq_align_Base )
private

◆ CSeq_align_Base() [2/2]

END_CLASS_INFO CSeq_align_Base::CSeq_align_Base ( void  )

◆ CSeq_align_set_Base() [1/2]

CSeq_align_set_Base::CSeq_align_set_Base ( const CSeq_align_set_Base )
private

◆ CSeq_align_set_Base() [2/2]

END_CLASS_INFO CSeq_align_set_Base::CSeq_align_set_Base ( void  )

Definition at line 68 of file Seq_align_set_.cpp.

References CSeq_align_set_Base::m_set_State.

◆ CSparse_align_Base() [1/2]

CSparse_align_Base::CSparse_align_Base ( const CSparse_align_Base )
private

◆ CSparse_align_Base() [2/2]

END_CLASS_INFO CSparse_align_Base::CSparse_align_Base ( void  )

◆ CSparse_seg_Base() [1/2]

CSparse_seg_Base::CSparse_seg_Base ( const CSparse_seg_Base )
private

◆ CSparse_seg_Base() [2/2]

END_CLASS_INFO CSparse_seg_Base::CSparse_seg_Base ( void  )

Definition at line 111 of file Sparse_seg_.cpp.

References CSparse_seg_Base::m_set_State.

◆ CSparse_seg_ext() [1/2]

CSparse_seg_ext::CSparse_seg_ext ( const CSparse_seg_ext value)
private

◆ CSparse_seg_ext() [2/2]

CSparse_seg_ext::CSparse_seg_ext ( void  )
inline

Definition at line 86 of file Sparse_seg_ext.hpp.

◆ CSparse_seg_ext_Base() [1/2]

CSparse_seg_ext_Base::CSparse_seg_ext_Base ( const CSparse_seg_ext_Base )
private

◆ CSparse_seg_ext_Base() [2/2]

END_CLASS_INFO CSparse_seg_ext_Base::CSparse_seg_ext_Base ( void  )

Definition at line 66 of file Sparse_seg_ext_.cpp.

References CSparse_seg_ext_Base::m_set_State.

◆ CSplice_site() [1/2]

CSplice_site::CSplice_site ( const CSplice_site value)
private

◆ CSplice_site() [2/2]

CSplice_site::CSplice_site ( void  )
inline

Definition at line 86 of file Splice_site.hpp.

◆ CSplice_site_Base() [1/2]

CSplice_site_Base::CSplice_site_Base ( const CSplice_site_Base )
private

◆ CSplice_site_Base() [2/2]

END_CLASS_INFO CSplice_site_Base::CSplice_site_Base ( void  )

Definition at line 72 of file Splice_site_.cpp.

References CSplice_site_Base::m_set_State.

◆ CSpliced_exon_Base() [1/2]

CSpliced_exon_Base::CSpliced_exon_Base ( const CSpliced_exon_Base )
private

◆ CSpliced_exon_Base() [2/2]

END_CLASS_INFO CSpliced_exon_Base::CSpliced_exon_Base ( void  )

◆ CSpliced_exon_chunk() [1/2]

CSpliced_exon_chunk::CSpliced_exon_chunk ( const CSpliced_exon_chunk value)
private

◆ CSpliced_exon_chunk() [2/2]

CSpliced_exon_chunk::CSpliced_exon_chunk ( void  )
inline

Definition at line 86 of file Spliced_exon_chunk.hpp.

◆ CSpliced_exon_chunk_Base() [1/2]

CSpliced_exon_chunk_Base::CSpliced_exon_chunk_Base ( const CSpliced_exon_chunk_Base )
private

◆ CSpliced_exon_chunk_Base() [2/2]

END_CHOICE_INFO CSpliced_exon_chunk_Base::CSpliced_exon_chunk_Base ( void  )

Definition at line 121 of file Spliced_exon_chunk_.cpp.

◆ CSpliced_seg_Base() [1/2]

CSpliced_seg_Base::CSpliced_seg_Base ( const CSpliced_seg_Base )
private

◆ CSpliced_seg_Base() [2/2]

END_CLASS_INFO CSpliced_seg_Base::CSpliced_seg_Base ( void  )

Definition at line 140 of file Spliced_seg_.cpp.

References CSpliced_seg_Base::m_set_State.

◆ CSpliced_seg_modifier() [1/2]

CSpliced_seg_modifier::CSpliced_seg_modifier ( const CSpliced_seg_modifier value)
private

◆ CSpliced_seg_modifier() [2/2]

CSpliced_seg_modifier::CSpliced_seg_modifier ( void  )