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

Code generated by DATATOOL from 'seqalign.asn' (module 'NCBI-Seqalign')

typedef CSerialObject CDense_diag_Base::Tparent typedef int CDense_diag_Base::TDim typedef vector< CRef< CSeq_id > > CDense_diag_Base::TIds typedef vector< TSeqPos > CDense_diag_Base::TStarts typedef TSeqPos CDense_diag_Base::TLen typedef vector< ENa_strand > CDense_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< TSignedSeqPos > CDense_seg_Base::TStarts typedef vector< TSeqPos > CDense_seg_Base::TLens typedef vector< ENa_strand > CDense_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< TSeqPos > CPacked_seg_Base::TStarts typedef vector< char > CPacked_seg_Base::TPresent typedef vector< TSeqPos > CPacked_seg_Base::TLens typedef vector< ENa_strand > CPacked_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< int > CSparse_align_Base::TFirst_starts typedef vector< int > CSparse_align_Base::TSecond_starts typedef vector< TSeqPos > CSparse_align_Base::TLens typedef vector< ENa_strand > CSparse_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 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
} 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...
TDim & CDense_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 TIds & CDense_diag_Base::GetIds (void) const Get the Ids member data. More...
TIds & CDense_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 TStarts & CDense_diag_Base::GetStarts (void) const Get the Starts member data. More...
TStarts & CDense_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...
TLen & CDense_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 TStrands & CDense_diag_Base::GetStrands (void) const Get the Strands member data. More...
TStrands & CDense_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 TScores & CDense_diag_Base::GetScores (void) const Get the Scores member data. More...
TScores & CDense_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_Base & CDense_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...
TDim & CDense_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...
TNumseg & CDense_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 TIds & CDense_seg_Base::GetIds (void) const Get the Ids member data. More...
TIds & CDense_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 TStarts & CDense_seg_Base::GetStarts (void) const Get the Starts member data. More...
TStarts & CDense_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 TLens & CDense_seg_Base::GetLens (void) const Get the Lens member data. More...
TLens & CDense_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 TStrands & CDense_seg_Base::GetStrands (void) const Get the Strands member data. More...
TStrands & CDense_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 TScores & CDense_seg_Base::GetScores (void) const Get the Scores member data. More...
TScores & CDense_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_Base & CDense_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_seg & CPacked_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...
TDim & CPacked_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...
TNumseg & CPacked_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 TIds & CPacked_seg_Base::GetIds (void) const Get the Ids member data. More...
TIds & CPacked_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 TStarts & CPacked_seg_Base::GetStarts (void) const Get the Starts member data. More...
TStarts & CPacked_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 TPresent & CPacked_seg_Base::GetPresent (void) const Get the Present member data. More...
TPresent & CPacked_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 TLens & CPacked_seg_Base::GetLens (void) const Get the Lens member data. More...
TLens & CPacked_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 TStrands & CPacked_seg_Base::GetStrands (void) const Get the Strands member data. More...
TStrands & CPacked_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 TScores & CPacked_seg_Base::GetScores (void) const Get the Scores member data. More...
TScores & CPacked_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_Base & CPacked_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...
TNucpos & CProduct_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 TProtpos & CProduct_pos_Base::GetProtpos (void) const Get the variant data. More...
TProtpos & CProduct_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_Base & CProduct_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...
TAmin & CProt_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...
TFrame & CProt_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_Base & CProt_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...
TReal & CScore_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...
TInt & CScore_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_Value & CScore_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 TId & CScore_Base::GetId (void) const Get the Id member data. More...
void CScore_Base::SetId (TId &value) Assign a value to Id data member. More...
TId & CScore_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 TValue & CScore_Base::GetValue (void) const Get the Value member data. More...
TValue & CScore_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_Base & CScore_Base::operator= (const CScore_Base &) CScore_set::CScore_set (void) CScore_set::~CScore_set (void) CScore_set::CScore_set (const CScore_set &value) CScore_set & CScore_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 Tdata & CScore_set_Base::Get (void) const Get the member data. More...
Tdata & CScore_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_Base & CScore_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 TDendiag & CSeq_align_Base::C_Segs::GetDendiag (void) const Get the variant data. More...
TDendiag & CSeq_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 TDenseg & CSeq_align_Base::C_Segs::GetDenseg (void) const Get the variant data. More...
TDenseg & CSeq_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 TStd & CSeq_align_Base::C_Segs::GetStd (void) const Get the variant data. More...
TStd & CSeq_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 TPacked & CSeq_align_Base::C_Segs::GetPacked (void) const Get the variant data. More...
TPacked & CSeq_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 TDisc & CSeq_align_Base::C_Segs::GetDisc (void) const Get the variant data. More...
TDisc & CSeq_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 TSpliced & CSeq_align_Base::C_Segs::GetSpliced (void) const Get the variant data. More...
TSpliced & CSeq_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 TSparse & CSeq_align_Base::C_Segs::GetSparse (void) const Get the variant data. More...
TSparse & CSeq_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_Segs & CSeq_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...
TType & CSeq_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...
TDim & CSeq_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 TScore & CSeq_align_Base::GetScore (void) const Get the Score member data. More...
TScore & CSeq_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 TSegs & CSeq_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...
TSegs & CSeq_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 TBounds & CSeq_align_Base::GetBounds (void) const Get the Bounds member data. More...
TBounds & CSeq_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 TId & CSeq_align_Base::GetId (void) const Get the Id member data. More...
TId & CSeq_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 TExt & CSeq_align_Base::GetExt (void) const Get the Ext member data. More...
TExt & CSeq_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_Base & CSeq_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 Tdata & CSeq_align_set_Base::Get (void) const Get the member data. More...
Tdata & CSeq_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_Base & CSeq_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_id & CSparse_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_id & CSparse_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_id & CSparse_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_id & CSparse_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...
TNumseg & CSparse_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_starts & CSparse_align_Base::GetFirst_starts (void) const Get the First_starts member data. More...
TFirst_starts & CSparse_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_starts & CSparse_align_Base::GetSecond_starts (void) const Get the Second_starts member data. More...
TSecond_starts & CSparse_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 TLens & CSparse_align_Base::GetLens (void) const Get the Lens member data. More...
TLens & CSparse_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_strands & CSparse_align_Base::GetSecond_strands (void) const Get the Second_strands member data. More...
TSecond_strands & CSparse_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_scores & CSparse_align_Base::GetSeg_scores (void) const Get the Seg_scores member data. More...
TSeg_scores & CSparse_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_Base & CSparse_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_id & CSparse_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_id & CSparse_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 TRows & CSparse_seg_Base::GetRows (void) const Get the Rows member data. More...
TRows & CSparse_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_scores & CSparse_seg_Base::GetRow_scores (void) const Get the Row_scores member data. More...
TRow_scores & CSparse_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 TExt & CSparse_seg_Base::GetExt (void) const Get the Ext member data. More...
TExt & CSparse_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_Base & CSparse_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_ext & CSparse_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...
TIndex & CSparse_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_Base & CSparse_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_site & CSplice_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 TBases & CSplice_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) TBases & CSplice_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_Base & CSplice_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_start & CSpliced_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_start & CSpliced_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_end & CSpliced_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_end & CSpliced_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_start & CSpliced_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_end & CSpliced_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_id & CSpliced_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_id & CSpliced_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_id & CSpliced_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_id & CSpliced_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_strand & CSpliced_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_strand & CSpliced_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 TParts & CSpliced_exon_Base::GetParts (void) const Get the Parts member data. More...
TParts & CSpliced_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 TScores & CSpliced_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...
TScores & CSpliced_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_exon & CSpliced_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_exon & CSpliced_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_exon & CSpliced_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_exon & CSpliced_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...
TPartial & CSpliced_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 TExt & CSpliced_exon_Base::GetExt (void) const Get the Ext member data. More...
TExt & CSpliced_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_Base & CSpliced_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_chunk & CSpliced_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...
TMatch & CSpliced_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...
TMismatch & CSpliced_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...
TDiag & CSpliced_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_ins & CSpliced_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_ins & CSpliced_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_Base & CSpliced_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_id & CSpliced_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_id & CSpliced_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_id & CSpliced_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_id & CSpliced_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_strand & CSpliced_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_strand & CSpliced_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_type & CSpliced_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 TExons & CSpliced_seg_Base::GetExons (void) const Get the Exons member data. More...
TExons & CSpliced_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_a & CSpliced_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_length & CSpliced_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 TModifiers & CSpliced_seg_Base::GetModifiers (void) const Get the Modifiers member data. More...
TModifiers & CSpliced_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_Base & CSpliced_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_modifier & CSpliced_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_found & CSpliced_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_found & CSpliced_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_Base & CSpliced_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...
TDim & CStd_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 TIds & CStd_seg_Base::GetIds (void) const Get the Ids member data. More...
TIds & CStd_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 TLoc & CStd_seg_Base::GetLoc (void) const Get the Loc member data. More...
TLoc & CStd_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 TScores & CStd_seg_Base::GetScores (void) const Get the Scores member data. More...
TScores & CStd_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_Base & CStd_seg_Base::operator= (const CStd_seg_Base &) ◆ TAcceptor_before_exon ◆ TAmin ◆ TBases ◆ TBounds ◆ Tdata [1/2] ◆ Tdata [2/2] ◆ TDendiag ◆ TDenseg ◆ TDiag ◆ TDim [1/5] ◆ TDim [2/5] ◆ TDim [3/5] ◆ TDim [4/5] ◆ TDim [5/5] ◆ TDisc ◆ TDonor_after_exon ◆ TExons ◆ TExt [1/3] ◆ TExt [2/3] ◆ TExt [3/3] ◆ TFirst_id ◆ TFirst_starts ◆ TFrame ◆ TGenomic_end ◆ TGenomic_id [1/2] ◆ TGenomic_id [2/2] ◆ TGenomic_ins ◆ TGenomic_start ◆ TGenomic_strand [1/2] ◆ TGenomic_strand [2/2] ◆ TId [1/2] ◆ TId [2/2] ◆ TIds [1/4] ◆ TIds [2/4] ◆ TIds [3/4] ◆ TIds [4/4] ◆ TIndex ◆ TInt ◆ TLen ◆ TLens [1/3] ◆ TLens [2/3] ◆ TLens [3/3] ◆ TLoc ◆ TMaster_id ◆ TMatch ◆ TmemberIndex [1/13] ◆ TmemberIndex [2/13] ◆ TmemberIndex [3/13] ◆ TmemberIndex [4/13] ◆ TmemberIndex [5/13] ◆ TmemberIndex [6/13] ◆ TmemberIndex [7/13] ◆ TmemberIndex [8/13] ◆ TmemberIndex [9/13] ◆ TmemberIndex [10/13] ◆ TmemberIndex [11/13] ◆ TmemberIndex [12/13] ◆ TmemberIndex [13/13] ◆ TMismatch ◆ TModifiers ◆ TNucpos ◆ TNumseg [1/3] ◆ TNumseg [2/3] ◆ TNumseg [3/3] ◆ TPacked ◆ Tparent [1/26] ◆ Tparent [2/26] ◆ Tparent [3/26] ◆ Tparent [4/26] ◆ Tparent [5/26] ◆ Tparent [6/26] ◆ Tparent [7/26] ◆ Tparent [8/26] ◆ Tparent [9/26] ◆ Tparent [10/26] ◆ Tparent [11/26] ◆ Tparent [12/26] ◆ Tparent [13/26] ◆ Tparent [14/26] ◆ Tparent [15/26] ◆ Tparent [16/26] ◆ Tparent [17/26] ◆ Tparent [18/26] ◆ Tparent [19/26] ◆ Tparent [20/26] ◆ Tparent [21/26] ◆ Tparent [22/26] ◆ Tparent [23/26] ◆ Tparent [24/26] ◆ Tparent [25/26] ◆ Tparent [26/26] ◆ TPartial ◆ TParts ◆ TPoly_a ◆ TPresent ◆ TProduct_end ◆ TProduct_id [1/2] ◆ TProduct_id [2/2] ◆ TProduct_ins ◆ TProduct_length ◆ TProduct_start ◆ TProduct_strand [1/2] ◆ TProduct_strand [2/2] ◆ TProduct_type ◆ TProtpos ◆ TReal ◆ TRow_scores ◆ TRows ◆ TScore ◆ TScores [1/5] ◆ TScores [2/5] ◆ TScores [3/5] ◆ TScores [4/5] ◆ TScores [5/5] ◆ TSecond_id ◆ TSecond_starts ◆ TSecond_strands ◆ TSeg_scores ◆ TSegs ◆ TSparse ◆ TSpliced ◆ TStart_codon_found ◆ TStarts [1/3] ◆ TStarts [2/3] ◆ TStarts [3/3] ◆ TStd ◆ TStop_codon_found ◆ TStrands [1/3] ◆ TStrands [2/3] ◆ TStrands [3/3] ◆ TType ◆ TValue ◆ 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] ◆ E_memberIndex [10/13] ◆ 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 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.

◆ C_Segs() [1/2] ◆ C_Segs() [2/2] ◆ C_Value() [1/2] ◆ C_Value() [2/2] ◆ 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 ◆ CanGetAmin() bool CProt_pos_Base::CanGetAmin ( void ) const inline ◆ CanGetBases() bool CSplice_site_Base::CanGetBases ( void ) const inline ◆ CanGetBounds() bool CSeq_align_Base::CanGetBounds ( void ) const inline ◆ 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 ◆ 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 ◆ 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 ◆ CanGetExons() bool CSpliced_seg_Base::CanGetExons ( void ) const inline ◆ CanGetExt() [1/3] bool CSeq_align_Base::CanGetExt ( void ) const inline ◆ 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 ◆ CanGetGenomic_id() [1/2] bool CSpliced_exon_Base::CanGetGenomic_id ( void ) const inline ◆ CanGetGenomic_id() [2/2] bool CSpliced_seg_Base::CanGetGenomic_id ( void ) const inline ◆ CanGetGenomic_start() bool CSpliced_exon_Base::CanGetGenomic_start ( void ) const inline ◆ CanGetGenomic_strand() [1/2] bool CSpliced_exon_Base::CanGetGenomic_strand ( void ) const inline ◆ CanGetGenomic_strand() [2/2] bool CSpliced_seg_Base::CanGetGenomic_strand ( void ) const inline ◆ CanGetId() [1/2] bool CScore_Base::CanGetId ( void ) const inline ◆ 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 ◆ 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 ◆ CanGetLen() bool CDense_diag_Base::CanGetLen ( void ) const inline ◆ CanGetLens() [1/3] bool CDense_seg_Base::CanGetLens ( void ) const inline ◆ 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 ◆ 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 ◆ CanGetNumseg() [2/3] bool CPacked_seg_Base::CanGetNumseg ( void ) const inline ◆ CanGetNumseg() [3/3] bool CSparse_align_Base::CanGetNumseg ( void ) const inline ◆ CanGetPartial() bool CSpliced_exon_Base::CanGetPartial ( void ) const inline ◆ 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 ◆ CanGetProduct_end() bool CSpliced_exon_Base::CanGetProduct_end ( void ) const inline ◆ CanGetProduct_id() [1/2] bool CSpliced_exon_Base::CanGetProduct_id ( void ) const inline ◆ CanGetProduct_id() [2/2] bool CSpliced_seg_Base::CanGetProduct_id ( void ) const inline ◆ CanGetProduct_length() bool CSpliced_seg_Base::CanGetProduct_length ( void ) const inline ◆ 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 ◆ CanGetProduct_strand() [2/2] bool CSpliced_seg_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 545 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::IsSetProduct_strand().

Referenced by ConvertSplicedToPairwiseAln(), CScore_LastSpliceSite::Get(), CSpliced_seg_Base::GetProduct_strand(), CSpliced_seg::GetSeqStrand(), CSpliced_seg::IsConsistentBiologicalOrder(), s_GetAlignmentSpans_Intron(), CSpliced_seg::Validate(), CGff3FlybaseWriter::xAssignAlignmentSplicedLocation(), CGff3Writer::xAssignAlignmentSplicedTarget(), and CPslRecord::xInitializeStrands().

◆ CanGetProduct_type() bool CSpliced_seg_Base::CanGetProduct_type ( void ) const inline ◆ 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 ◆ 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 ◆ 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

Check if it is safe to call GetSegs method.

Returns

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

Definition at line 915 of file Seq_align_.hpp.

Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::CleanAlignment(), IsProteinAlign(), CTabularFormatter_Cigar::Print(), CTabularFormatter_Traceback::Print(), s_AlignToSeqRanges(), s_CleanSeqAlign(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CHitMatrixDataSource::x_GetAlignedSeqIds(), CHitMatrixDataSource::x_GetSeqAlignIds(), CVectorTrimPanel::x_TrimAlignments(), and CHitMatrixDataSource::x_UpdateScoreMap().

◆ 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 ◆ 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 ◆ 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 ◆ CanGetValue() bool CScore_Base::CanGetValue ( void ) const inline ◆ CDense_diag_Base() [1/2] ◆ CDense_diag_Base() [2/2] ◆ CDense_seg_Base() [1/2] ◆ CDense_seg_Base() [2/2] ◆ CheckSelected() [1/5] void CProduct_pos_Base::CheckSelected ( E_Choice index ) const inline ◆ 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: index Expected 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: index Expected 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 ◆ CPacked_seg() [1/2] ◆ 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() [2/2] ◆ CProduct_pos_Base() [1/2] ◆ CProduct_pos_Base() [2/2] ◆ CProt_pos_Base() [1/2] ◆ CProt_pos_Base() [2/2] ◆ CScore_Base() [1/2] ◆ CScore_Base() [2/2] ◆ CScore_set() [1/2] ◆ 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() [2/2] ◆ CSeq_align_Base() [1/2] ◆ CSeq_align_Base() [2/2] ◆ CSeq_align_set_Base() [1/2] ◆ CSeq_align_set_Base() [2/2] ◆ CSparse_align_Base() [1/2] ◆ CSparse_align_Base() [2/2] ◆ CSparse_seg_Base() [1/2] ◆ CSparse_seg_Base() [2/2] ◆ CSparse_seg_ext() [1/2] ◆ CSparse_seg_ext() [2/2] ◆ CSparse_seg_ext_Base() [1/2] ◆ CSparse_seg_ext_Base() [2/2] ◆ CSplice_site() [1/2] ◆ 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() [2/2] ◆ CSpliced_exon_Base() [1/2] ◆ CSpliced_exon_Base() [2/2] ◆ CSpliced_exon_chunk() [1/2] ◆ CSpliced_exon_chunk() [2/2] ◆ CSpliced_exon_chunk_Base() [1/2] ◆ CSpliced_exon_chunk_Base() [2/2] ◆ CSpliced_seg_Base() [1/2] ◆ CSpliced_seg_Base() [2/2] ◆ CSpliced_seg_modifier() [1/2] ◆ CSpliced_seg_modifier() [2/2] ◆ CSpliced_seg_modifier_Base() [1/2] ◆ CSpliced_seg_modifier_Base() [2/2] ◆ CStd_seg_Base() [1/2] ◆ CStd_seg_Base() [2/2] ◆ DECLARE_INTERNAL_TYPE_INFO() [1/20] CDense_diag_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [2/20] CDense_seg_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [3/20] CPacked_seg_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [4/20] CProduct_pos_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [5/20] CProt_pos_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [6/20] CScore_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [7/20] CScore_Base::C_Value::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [8/20] CScore_set_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [9/20] CSeq_align_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [10/20] CSeq_align_Base::C_Segs::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [11/20] CSeq_align_set_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [12/20] CSparse_align_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [13/20] CSparse_seg_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [14/20] CSparse_seg_ext_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [15/20] CSplice_site_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [16/20] CSpliced_exon_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [17/20] CSpliced_exon_chunk_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [18/20] CSpliced_seg_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [19/20] CSpliced_seg_modifier_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [20/20] CStd_seg_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DoNotDeleteThisObject() void CScore_Base::DoNotDeleteThisObject ( void ) virtual ◆ DoSelect() [1/5] ◆ DoSelect() [2/5] ◆ DoSelect() [3/5] ◆ DoSelect() [4/5]

Definition at line 61 of file Spliced_exon_chunk_.cpp.

References CSpliced_exon_chunk_Base::e_Diag, CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, CSpliced_exon_chunk_Base::m_choice, CSpliced_exon_chunk_Base::m_Diag, CSpliced_exon_chunk_Base::m_Genomic_ins, CSpliced_exon_chunk_Base::m_Match, CSpliced_exon_chunk_Base::m_Mismatch, and CSpliced_exon_chunk_Base::m_Product_ins.

◆ DoSelect() [5/5] ◆ EProduct_type()

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

◆ EType()

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

◆ Get() [1/2] ◆ Get() [2/2]

Get the member data.

Returns: Reference to the member data.

Definition at line 166 of file Seq_align_set_.hpp.

References CSeq_align_set_Base::m_data.

◆ GetAcceptor_before_exon() ◆ GetAmin()

Get the Amin member data.

Returns: Copy of the member data.

Definition at line 220 of file Prot_pos_.hpp.

References CProt_pos_Base::CanGetAmin(), CProt_pos_Base::m_Amin, and CSerialObject::ThrowUnassigned().

◆ GetBases() ◆ GetBounds() ◆ GetDendiag()

Get the variant data.

Returns: Reference to the data.

Definition at line 726 of file Seq_align_.hpp.

Referenced by CSeqsRange::Add(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CRemoveSeqFromAlignDlg::GetAlignLabel(), GetBlockCount(), GetDDSetFromSeqAlign(), GetMasterGIFromSeqAlign(), GetReportableSeqIdForAlignment(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), CSeq_align::GetSeqStrand(), CCdCore::Has3DMaster(), CCdCore::HasSeqId(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_Fingerprint_Seq_align(), s_GetAlnScores(), s_GetSubjectId(), CValidError_align::ValidateSeqAlign(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CValidError_align::x_GetIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetDenseg()

Get the variant data.

Returns: Reference to the data.

Definition at line 153 of file Seq_align_.cpp.

◆ GetDiag()

Get the variant data.

Returns: Copy of the variant data.

Definition at line 410 of file Spliced_exon_chunk_.hpp.

References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Diag, and CSpliced_exon_chunk_Base::m_Diag.

Referenced by ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), s_ExonToDenseg(), s_GetCountIdentityMismatch(), SBlocks::SBlocks(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CReportEntry::x_CheckExonGap(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().

◆ GetDim() [1/5]

Get the Dim member data.

Returns: Copy of the member data.

Definition at line 373 of file Dense_diag_.hpp.

References CDense_diag_Base::m_Dim.

Referenced by CSeqsRange::Add(), CDense_diag::CheckNumRows(), ConvertDendiagToPairwiseAln(), CDense_diag::CreateRowSeq_interval(), CDense_diag::GetSeqStart(), CDense_diag::GetSeqStrand(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CDense_diag::OffsetRow(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAnnotObject_Info::x_ProcessAlign(), CValidError_align::x_ValidateDendiag(), and CValidError_align::x_ValidateSeqLength().

◆ GetDim() [2/5]

Get the Dim member data.

Returns: Copy of the member data.

Definition at line 421 of file Dense_seg_.hpp.

References CDense_seg_Base::m_Dim.

Referenced by CSeqsRange::Add(), CAlnMixMatches::Add(), CAlnMixSequences::Add(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), BOOST_AUTO_TEST_CASE(), CDense_seg::CheckNumRows(), CDense_seg::CheckNumSegs(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), ConvertToPairwise(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateTranslatedDensegFromNADenseg(), CAlignmentAssistant::DeleteSelection(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractSlice(), CFeaturePropagator::FindRow(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CAlignmentAssistant::GetFeatures(), CPaintAlignment::GetSegments(), CPhyTreeCalc::GetSeqAlign(), CDense_seg::GetSeqStart(), CDense_seg::GetSeqStop(), CValidError_align::IsTpaAlignment(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CDense_seg::OffsetRow(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CDense_seg::CReserveHook::PreReadClassMember(), CAlnAsnReader::Read(), CDenseSegReserveStartsHook::ReadClassMember(), CDenseSegReserveStrandsHook::ReadClassMember(), CDense_seg::RemapToLoc(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), s_AlignToSeqRanges(), s_CalculateMatchingColumns(), s_CompressDiscToDenseq(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DenseSegLength(), s_FindSegment(), s_GetAlignmentLength(), s_GetGapCount(), s_GetIndels(), s_GetNumIdsToUse(), s_Seq_align_Seq_loc(), s_SeqAlignToBlastSeqLoc(), s_TestAlignmentFromMSAs(), COverlapScorer::ScoreAlignments(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CDense_seg::SwapRows(), CAlignmentAssistant::TranslateLocations(), CReportTrim::TrimAlignments(), CDense_seg::TrimEndGaps(), TrimSeqAlign(), CAlnWriter::WriteAlignDenseSeg(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CAlignCleanup::x_Cleanup_AlignVec(), CInversionMergeAligner::x_CreateDiscAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAppHitFilter::x_DumpOutput(), CAlnMix::x_ExtendDSWithWidths(), CVectorTrimPanel::x_FindSegment(), CReportTrim::x_FindSegment(), CDense_seg::x_FindSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CInversionMergeAligner::x_IsAllGap(), CUnorderedSplitter::x_IsAllGap(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CInstancedAligner::x_RunCleanup(), x_TestAlignmentQuerySubjStrandCombinations(), CVectorTrimPanel::x_TrimAlignments(), CValidError_align::x_ValidateAlignPercentIdentity(), and CPslRecord::xValidateSegment().

◆ GetDim() [3/5] ◆ GetDim() [4/5]

Get the Dim member data.

Returns: Copy of the member data.

Definition at line 856 of file Seq_align_.hpp.

References CSeq_align_Base::CanGetDim(), CSeq_align_Base::m_Dim, and CSerialObject::ThrowUnassigned().

Referenced by BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CDesktopAlignItem::GetDescription(), CSeq_align_Handle::GetDim(), CSeq_align_Mapper_Base::GetDstAlign(), GetPssmIdFromSeqAlign(), GetReportableSeqIdForAlignment(), CSeq_align::GetSeqRange(), CValidError_imp::PostErr(), CDesktopAlignItem::s_ContainsFarPointers(), s_TestCalc(), s_TestResultAlignment(), CLDS2_AnnotType_Hook::SkipObject(), CSeq_align::SplitOnLongDiscontinuity(), and CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile().

◆ GetDim() [5/5]

Get the Dim member data.

Returns: Copy of the member data.

Definition at line 295 of file Std_seg_.hpp.

References CStd_seg_Base::m_Dim.

Referenced by CStd_seg::CheckNumRows(), CSeq_align::CreateDensegFromStdseg(), CStd_seg::CreateRowSeq_loc(), CStdSegHit::CStdSegHit(), CStd_seg::GetSeqRange(), CStd_seg::GetSeqStart(), CStd_seg::GetSeqStop(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CStd_seg::RemapToLoc(), s_GetAlignmentLength(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), and CValidError_align::x_ValidateStd().

◆ GetDisc()

Get the variant data.

Returns: Reference to the data.

Definition at line 197 of file Seq_align_.cpp.

Referenced by CAlnMix::Add(), CSeqsRange::Add(), BuildAlignDataSource(), ExtractFirstSeqAlign(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CAlignFormatUtil::ExtractSeqalignSetFromDiscSegs(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeq_align::GetSeqStrand(), CAlnContainer::insert(), PatchTargetSequence(), PrintSAM(), PrintTabular(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CTestSingleAln_All::RunTest(), s_AlignToSeqRanges(), s_CountSegments(), s_ExtractSeqId(), s_Fingerprint_Seq_align(), s_GetAlignmentLength(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlignmentTooltip(), s_GetCountIdentityMismatch(), s_GetGapCount(), SAlignmentScoringModel::s_GetIdentOdds_disc(), s_GetIndels(), s_Render_PairwiseAlign(), s_ScoreAlignments(), s_Seq_align_Seq_loc(), s_SeqAlignToXMLHit(), CSeq_align::SplitOnLongDiscontinuity(), CValidError_align::ValidateSeqAlign(), CPslWriter::WriteAlign(), CAlnTableDS::x_AddAlign(), CSeq_annot_Info::x_AddAlignKeys(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CQuerySet::x_ContainsAlignment(), CCleanupAlignmentsJob::x_CreateProjectItems(), CCIGAR_Formatter::x_FormatAlignmentRows(), CCommonComponentScorer::x_GetSeqHistCompList(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CTreeAlignMerger::x_MakeMergeableGroups(), CAnnotObject_Info::x_ProcessAlign(), CAppHitFilter::x_ReadInputHits(), CTabularFormatter_DiscStrand::x_RecurseStrands(), CHitMatrixDataSource::x_TestAndSelectAlign(), and CGff3Writer::xWriteAlignDisc().

◆ GetDonor_after_exon() ◆ GetExons()

Get the Exons member data.

Returns: Reference to the member data.

Definition at line 692 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::m_Exons.

◆ GetExt() [1/3]

Get the Ext member data.

Returns: Reference to the member data.

Definition at line 1001 of file Seq_align_.hpp.

References CSeq_align_Base::m_Ext.

Referenced by BOOST_AUTO_TEST_CASE(), CSGAlignmentJob::FilterDuplicatesAndBadReads(), CSeq_align::FindExt(), CSeq_align_Mapper_Base::GetDstAlign(), CProductStringBuilder::GetProductString(), CScoreBuilder::GetTraceback(), IsGnomonConstructed(), CTabularFormatter_BestPlacementGroup::Print(), CTabularFormatter_AssemblyInfo::Print(), CDemoApp::Run(), s_CheckTraceMateAlign(), and s_PopulateExtSet().

◆ GetExt() [2/3] ◆ GetExt() [3/3] ◆ GetFirst_id()

Get the First_id member data.

Returns: Reference to the member data.

Definition at line 431 of file Sparse_align_.hpp.

References CSparse_align_Base::m_First_id, and CSparse_align_Base::ResetFirst_id().

Referenced by CSeqsRange::Add(), ConvertToPairwise(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeq_id(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetFirst_starts()

Get the First_starts member data.

Returns: Reference to the member data.

Definition at line 538 of file Sparse_align_.hpp.

References CSparse_align_Base::m_First_starts.

Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetFrame() ◆ GetGenomic_end()

Get the Genomic_end member data.

Returns: Copy of the member data.

Definition at line 814 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::CanGetGenomic_end(), CSpliced_exon_Base::m_Genomic_end, and CSerialObject::ThrowUnassigned().

Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSeq_align::ExonLengthRange(), CScore_EdgeExonInfo::Get(), CFeatureGenerator::SImplementation::GetExonStructure(), CSpliced_exon::GetRowSeq_range(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSeq_align::IntronLengthRange(), CSpliced_seg::IsConsistentBiologicalOrder(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_ExonToDenseg(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_ValidateExon(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CReportEntry::x_CheckExonGap(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAnnotObject_Info::x_ProcessAlign(), CGff3Writer::xAssignAlignmentSplicedLocation(), and CGff3FlybaseWriter::xAssignAlignmentSplicedTarget().

◆ GetGenomic_id() [1/2]

Get the Genomic_id member data.

Returns: Reference to the member data.

Definition at line 875 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::CanGetGenomic_id(), CSpliced_exon_Base::m_Genomic_id, and CSerialObject::ThrowUnassigned().

Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSpliced_exon::CreateRowSeq_interval(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_newlogic(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetGenomic_id() [2/2]

Get the Genomic_id member data.

Returns: Reference to the member data.

Definition at line 530 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::CanGetGenomic_id(), CSpliced_seg_Base::m_Genomic_id, and CSerialObject::ThrowUnassigned().

Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::AdjustAlignment(), CSpliced_seg::AsDiscSeg(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSpliced_exon::CreateRowSeq_interval(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CFeatureGenerator::SImplementation::GetExonStructure(), CProteinAlignText::GetGenomicBounds(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CProSplignText::Output(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_Fingerprint_Spliced_seg(), s_GetAlignmentContent(), s_SplicedToDisc(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CAlnWriter::WriteAlignSplicedSeg(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CAlnSpanVertModel::x_Init(), CSeq_loc_Mapper_Base::x_InitSpliced(), CGff3Writer::xAssignAlignmentSplicedMethod(), CGff3Writer::xAssignAlignmentSplicedSeqId(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), CGff3Writer::xAssignAlignmentSplicedType(), and CPslRecord::xInitializeSequenceInfo().

◆ GetGenomic_ins()

Get the variant data.

Returns: Copy of the variant data.

Definition at line 464 of file Spliced_exon_chunk_.hpp.

References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Genomic_ins, and CSpliced_exon_chunk_Base::m_Genomic_ins.

Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSpliced_exon::GetRowSeq_insertions(), CFeatureGenerator::SImplementation::MaximizeTranslation(), ProjectExon_oldlogic(), CSplign::s_ComputeStats(), s_ExonToDenseg(), SBlocks::SBlocks(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CReportEntry::x_CheckExonGap(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().

◆ GetGenomic_start()

Get the Genomic_start member data.

Returns: Copy of the member data.

Definition at line 767 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::CanGetGenomic_start(), CSpliced_exon_Base::m_Genomic_start, and CSerialObject::ThrowUnassigned().

Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSeq_align::ExonLengthRange(), CScore_EdgeExonInfo::Get(), CFeatureGenerator::SImplementation::GetExonStructure(), CSpliced_exon::GetRowSeq_range(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSeq_align::IntronLengthRange(), CSpliced_seg::IsConsistentBiologicalOrder(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_ExonToDenseg(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_ValidateExon(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CReportEntry::x_CheckExonGap(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CAnnotObject_Info::x_ProcessAlign(), CGff3Writer::xAssignAlignmentSplicedLocation(), and CGff3FlybaseWriter::xAssignAlignmentSplicedTarget().

◆ GetGenomic_strand() [1/2]

Get the Genomic_strand member data.

Returns: Copy of the member data.

Definition at line 950 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::CanGetGenomic_strand(), CSpliced_exon_Base::m_Genomic_strand, and CSerialObject::ThrowUnassigned().

Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), ProjectExon_newlogic(), s_ExonToDenseg(), s_GetAlignmentMismatches(), CSeq_align_Mapper_Base::x_GetDstExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAnnotObject_Info::x_ProcessAlign(), and CGff3Writer::xAssignAlignmentSplicedLocation().

◆ GetGenomic_strand() [2/2]

Get the Genomic_strand member data.

Returns: Copy of the member data.

Definition at line 605 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::CanGetGenomic_strand(), CSpliced_seg_Base::m_Genomic_strand, and CSerialObject::ThrowUnassigned().

Referenced by CSpliced_seg::AsDiscSeg(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSpliced_exon::CreateRowSeq_interval(), CProteinAlignText::GetGenomicBounds(), CSpliced_exon::GetRowSeq_insertions(), CSpliced_seg::GetSeqStrand(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), CProSplignText::Output(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Intron(), s_GetCIGARForSort(), s_SplicedToDisc(), CReportEntry::SetAlignment(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CCDSTranslationPanel::x_SetLocationForProtein(), CGff3Writer::xAssignAlignmentSplicedLocation(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), and CPslRecord::xInitializeStrands().

◆ GetId() [1/2]

Get the Id member data.

Returns: Reference to the member data.

Definition at line 444 of file Score_.hpp.

References CScore_Base::CanGetId(), CScore_Base::m_Id, and CSerialObject::ThrowUnassigned().

Referenced by s_GetAlignmentTooltip(), s_GetBitScore(), s_GetEvalue(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), sInheritScores(), sPrepareSeqAlign(), testNuclHitList(), CAlnTableDS::x_AdjustColumns(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), CMultiAligner::x_SetDomainHits(), CHitMatrixDataSource::x_UpdateScoreMap(), CGff3FlybaseWriter::xAssignAlignmentDensegScores(), and CGff3FlybaseWriter::xAssignAlignmentSplicedScores().

◆ GetId() [2/2] ◆ GetIds() [1/4]

Get the Ids member data.

Returns: Reference to the member data.

Definition at line 410 of file Dense_diag_.hpp.

References CDense_diag_Base::m_Ids.

Referenced by CSeqsRange::Add(), CDense_diag::CheckNumRows(), CDense_diag::CreateRowSeq_interval(), GetPendingSeqId(), CCdCore::HasSeqId(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), s_Fingerprint_Dense_diag(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAnnotObject_Info::x_ProcessAlign(), CValidError_align::x_ValidateDendiag(), and CValidError_align::x_ValidateSeqLength().

◆ GetIds() [2/4]

Get the Ids member data.

Returns: Reference to the member data.

Definition at line 505 of file Dense_seg_.hpp.

References CDense_seg_Base::m_Ids.

Referenced by CSeqsRange::Add(), CAlnMixSequences::Add(), CAlignmentAssistant::AdjustAlign(), CDense_seg::CheckNumRows(), ConvertToPairwise(), CreateAlignRow(), CAlnVec::CreateConsensus(), CSeq_align::CreateDensegFromDisc(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), Denseg2DenseDiagList(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), CDense_seg::GetSeq_id(), CPhyTreeCalc::GetSeqIds(), CContigAssembly::IsAtLeastHalfDovetail(), CValidError_align::IsTpaAlignment(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CTestBlastp_All::RunTest(), s_CheckTraceMateAlign(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DensegHasAccessionWithZeroVersion(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), s_Fingerprint_Dense_seg(), s_GetAlignmentContent(), s_GetAlignmentTooltip(), s_GetNumIdsToUse(), s_GetSubjectId(), s_Seq_align_Seq_loc(), s_TestAlignmentFromMSAs(), s_TestCalc(), CPhyTreeCalc::SetQuery(), CReportTrim::TrimAlignments(), TrimSeqAlign(), CUpdateAlign::x_ChangeIDsToFarPointers(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAlnMix::x_ExtendDSWithWidths(), CMultiAligner::x_FindRPSHits(), CApplyRNAITSDlg::x_GetAlignments(), CValidError_align::x_GetIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CUpdateAlign::x_MapNonPresentIDs(), CUpdateAlign::x_RemoveIDsFromAlign(), CApplyRNAITSDlg::x_SeqIdsAlignedWith(), CMultiAligner::x_SetDomainHits(), and CVectorTrimPanel::x_TrimAlignments().

◆ GetIds() [3/4] ◆ GetIds() [4/4] ◆ GetIndex() ◆ GetInt()

Get the variant data.

Returns: Copy of the variant data.

Definition at line 411 of file Score_.hpp.

Referenced by GetFloatScore(), GetIntScore(), s_CompareValues(), s_GetAlignmentTooltip(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), sPrepareSeqAlign(), testNuclHitList(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), and CMultiAligner::x_SetDomainHits().

◆ GetLen()

Get the Len member data.

Returns: Copy of the member data.

Definition at line 467 of file Dense_diag_.hpp.

References CDense_diag_Base::CanGetLen(), CDense_diag_Base::m_Len, and CSerialObject::ThrowUnassigned().

Referenced by CSeqsRange::Add(), ConvertDendiagToPairwiseAln(), CDense_diag::CreateRowSeq_interval(), CDense_diag::GetSeqStop(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), s_Fingerprint_Dense_diag(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), and CValidError_align::x_ValidateSeqLength().

◆ GetLens() [1/3]

Get the Lens member data.

Returns: Reference to the member data.

Definition at line 555 of file Dense_seg_.hpp.

References CDense_seg_Base::m_Lens.

Referenced by CSeqsRange::Add(), CAlnMixMatches::Add(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CContigAssembly::BandedGlobalAlignment(), CContigAssembly::BestLocalSubAlignment(), BOOST_AUTO_TEST_CASE(), CAlignShadow::CAlignShadow(), CDense_seg::CheckNumSegs(), CAlnVecPrinter::ClustalStyle(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateTranslatedDensegFromNADenseg(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CEditSeqEndsWithAlign::FindPosition(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CFastaAlignmentBuilder::GetCompletedAlignment(), CPaintAlignment::GetSegments(), CDense_seg::GetSeqStop(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CAlignmentAssistant::OnReverseStrand(), CAlnVecPrinter::PopsetStyle(), CTabularFormatter_Cigar::Print(), PrintSAM(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_AlignToSeqRanges(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DenseSegLength(), s_FindSegment(), s_Fingerprint_Dense_seg(), s_GetAlignmentLength(), s_GetCigarString(), s_GetGapCount(), s_GetIndels(), s_SeqAlignToBlastSeqLoc(), s_TestAlignmentFromMSAs(), s_TestResultAlignment(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CSeq_align::SplitOnLongDiscontinuity(), CDense_seg::TrimEndGaps(), TrimSeqAlign(), UpdateDensegAlignment(), CDense_seg::Validate(), CAlnWriter::WriteAlignDenseSeg(), CFastaReader::x_AddMultiwayAlignment(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CAlignCleanup::x_Cleanup_AlignVec(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAlnMix::x_ExtendDSWithWidths(), CVectorTrimPanel::x_FindSegment(), CReportTrim::x_FindSegment(), CDense_seg::x_FindSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CDenseg_CI::x_InitIterator(), CDenseg_CI::x_InitSegment(), x_TestAlignmentQuerySubjStrandCombinations(), and CPslRecord::xInitializeStatsAndBlocks().

◆ GetLens() [2/3] ◆ GetLens() [3/3] ◆ GetLoc()

Get the Loc member data.

Returns: Reference to the member data.

Definition at line 357 of file Std_seg_.hpp.

References CStd_seg_Base::m_Loc.

Referenced by CStd_seg::CheckNumRows(), CSeq_align::CreateDensegFromStdseg(), CStd_seg::CreateRowSeq_loc(), CStdSegHit::CStdSegHit(), CStd_seg::GetSeqRange(), CStd_seg::GetSeqStart(), CStd_seg::GetSeqStop(), CStdSegHit::HasAlignment(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), s_Fingerprint_Std_seg(), s_GetAlignmentLength(), s_GetAlignmentSpans_Exon(), s_GetGapCount(), s_GetStdsegMasterFrame(), CStd_seg::SwapRows(), CHitMatrixDataSource::x_GoodSeg(), CSeq_loc_Mapper_Base::x_InitAlign(), CValidError_align::x_ValidateSeqLength(), and CValidError_align::x_ValidateStd().

◆ GetMaster_id() ◆ GetMatch()

Get the variant data.

Returns: Copy of the variant data.

Definition at line 356 of file Spliced_exon_chunk_.hpp.

References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Match, and CSpliced_exon_chunk_Base::m_Match.

Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), CSplign::s_ComputeStats(), s_ExonToDenseg(), s_GetCountIdentityMismatch(), SBlocks::SBlocks(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CReportEntry::x_CheckExonGap(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().

◆ GetMismatch()

Get the variant data.

Returns: Copy of the variant data.

Definition at line 383 of file Spliced_exon_chunk_.hpp.

References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Mismatch, and CSpliced_exon_chunk_Base::m_Mismatch.

Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), CSplign::s_ComputeStats(), s_ExonToDenseg(), s_GetCountIdentityMismatch(), SBlocks::SBlocks(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CReportEntry::x_CheckExonGap(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().

◆ GetModifiers() ◆ GetNucpos()

Get the variant data.

Returns: Copy of the variant data.

Definition at line 266 of file Product_pos_.hpp.

References CProduct_pos_Base::CheckSelected(), CProduct_pos_Base::e_Nucpos, and CProduct_pos_Base::m_Nucpos.

Referenced by CSeqsRange::Add(), as_nucpos(), CProduct_pos::AsSeqPos(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CScore_LastSpliceSite::Get(), CTabularFormatter_ExonIntrons::Print(), s_ExonToDenseg(), s_ValidateExon(), CProductStringBuilder::x_AddExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CAlnSpanVertModel::x_PopulateRowsSpliced(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetNumseg() [1/3]

Get the Numseg member data.

Returns: Copy of the member data.

Definition at line 465 of file Dense_seg_.hpp.

References CDense_seg_Base::CanGetNumseg(), CDense_seg_Base::m_Numseg, and CSerialObject::ThrowUnassigned().

Referenced by CSeqsRange::Add(), CAlnMixMatches::Add(), CAlignmentAssistant::AdjustAlign(), CContigAssembly::Align(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CDense_seg::CheckNumSegs(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateTranslatedDensegFromNADenseg(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CAlignmentAssistant::GetFeatures(), CPaintAlignment::GetSegments(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CRemoveSeqFromAlignDlg::ModifyAlign(), CDense_seg::OffsetRow(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CDense_seg::CReserveHook::PreReadClassMember(), CTabularFormatter_Cigar::Print(), CDenseSegReserveStartsHook::ReadClassMember(), CDenseSegReserveLensHook::ReadClassMember(), CDenseSegReserveStrandsHook::ReadClassMember(), CDense_seg::RemapToLoc(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), s_AlignToSeqRanges(), s_CalculateMatchingColumns(), s_ComputeTraceback(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_FindSegment(), s_GetAlignmentLength(), s_GetGapCount(), s_GetIndels(), s_SeqAlignToBlastSeqLoc(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CAlignCompare::SAlignment::Slice(), CSeq_align::SplitOnLongDiscontinuity(), CDense_seg::SwapRows(), CDense_seg::TrimEndGaps(), TrimSeqAlign(), CAlnWriter::WriteAlignDenseSeg(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAppHitFilter::x_DumpOutput(), CAlnMix::x_ExtendDSWithWidths(), CVectorTrimPanel::x_FindSegment(), CReportTrim::x_FindSegment(), CDense_seg::x_FindSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CDenseg_CI::x_InitIterator(), CInversionMergeAligner::x_IsAllGap(), CUnorderedSplitter::x_IsAllGap(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CUpdateAlign::x_RemoveIDsFromAlign(), CInstancedAligner::x_RunCleanup(), and CInstancedAligner::x_RunMMGlobal().

◆ GetNumseg() [2/3] ◆ GetNumseg() [3/3] ◆ GetPacked() ◆ GetPartial() ◆ GetParts()

Get the Parts member data.

Returns: Reference to the member data.

Definition at line 990 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::m_Parts.

Referenced by BOOST_AUTO_TEST_CASE(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CProSplign::CImplementation::HasStartOnNuc(), CSeq_align_Mapper_Base::InitExon(), CFeatureGenerator::SImplementation::RecalculateExonIdty(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), s_GetAlignmentMismatches(), s_GetCountIdentityMismatch(), s_ValidateExon(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CReportEntry::x_CheckExonGap(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().

◆ GetPoly_a()

Get the Poly_a member data.

Returns: Copy of the member data.

Definition at line 724 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::CanGetPoly_a(), CSpliced_seg_Base::m_Poly_a, and CSerialObject::ThrowUnassigned().

Referenced by CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), SAlignmentScoringModel::GetPolyA_length(), s_GetPercentCoverage(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CAlnSpanVertModel::x_PopulateRowsSpliced(), and CFeatureGenerator::SImplementation::x_SetComment().

◆ GetPresent() ◆ GetProduct_end()

Get the Product_end member data.

Returns: Reference to the member data.

Definition at line 730 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::m_Product_end, and CSpliced_exon_Base::ResetProduct_end().

Referenced by CSeqsRange::Add(), AreAbuttingOnProduct(), BOOST_AUTO_TEST_CASE(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_LastSpliceSite::Get(), CScore_EdgeExonInfo::Get(), CFeatureGenerator::SImplementation::GetExonStructure(), CSpliced_exon::GetRowSeq_range(), GetTerminalPartialness(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_GetCountIdentityMismatch(), s_ValidateExon(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAnnotObject_Info::x_ProcessAlign(), CGff3FlybaseWriter::xAssignAlignmentSplicedLocation(), and CGff3Writer::xAssignAlignmentSplicedTarget().

◆ GetProduct_id() [1/2] ◆ GetProduct_id() [2/2]

Get the Product_id member data.

Returns: Reference to the member data.

Definition at line 509 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::CanGetProduct_id(), CSpliced_seg_Base::m_Product_id, and CSerialObject::ThrowUnassigned().

Referenced by CSeqsRange::Add(), CSpliced_seg::AsDiscSeg(), CProteinAlignText::CProteinAlignText(), CSpliced_exon::CreateRowSeq_interval(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CInternalStopFinder::GetCDSNucleotideSequence(), CSeq_align::GetSeq_id(), CSeq_align_Mapper_Base::InitExon(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CProSplignText::Output(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Spliced_seg(), s_GetAlignmentContent(), s_SplicedToDisc(), CProSplign::CImplementation::SeekStartStop(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CAlnWriter::WriteAlignSplicedSeg(), CAlnSpanVertModel::x_Init(), CSeq_loc_Mapper_Base::x_InitSpliced(), CGff3Writer::xAssignAlignmentSplicedMethod(), CGff3FlybaseWriter::xAssignAlignmentSplicedSeqId(), CGff3Writer::xAssignAlignmentSplicedTarget(), CGff3Writer::xAssignAlignmentSplicedType(), CPslRecord::xInitializeSequenceInfo(), and CGff3Writer::xSplicedSegHasProteinProd().

◆ GetProduct_ins()

Get the variant data.

Returns: Copy of the variant data.

Definition at line 437 of file Spliced_exon_chunk_.hpp.

References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Product_ins, and CSpliced_exon_chunk_Base::m_Product_ins.

Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSpliced_exon::GetRowSeq_insertions(), CFeatureGenerator::SImplementation::MaximizeTranslation(), ProjectExon_oldlogic(), CSplign::s_ComputeStats(), s_ExonToDenseg(), s_GetCountIdentityMismatch(), SBlocks::SBlocks(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().

◆ GetProduct_length()

Get the Product_length member data.

Returns: Copy of the member data.

Definition at line 771 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::CanGetProduct_length(), CSpliced_seg_Base::m_Product_length, and CSerialObject::ThrowUnassigned().

Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CProteinAlignText::CProteinAlignText(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), CScore_SequenceLength::Get(), CScore_StartStopCodon::Get(), SAlignmentScoringModel::GetCoverage(), SAlignmentScoringModel::GetPolyA_length(), CProductStringBuilder::GetProductString(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), PrintSAM(), PrintTabular(), s_GetPercentCoverage(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CSpliced_seg::Validate(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CAlnSpanVertModel::x_PopulateRowsSpliced(), and CFeatureGenerator::SImplementation::x_SetComment().

◆ GetProduct_start()

Get the Product_start member data.

Returns: Reference to the member data.

Definition at line 700 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::m_Product_start, and CSpliced_exon_Base::ResetProduct_start().

Referenced by CSeqsRange::Add(), AreAbuttingOnProduct(), BOOST_AUTO_TEST_CASE(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_EdgeExonInfo::Get(), CFeatureGenerator::SImplementation::GetExonStructure(), CSpliced_exon::GetRowSeq_range(), GetTerminalPartialness(), CProSplign::CImplementation::HasStartOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_GetCountIdentityMismatch(), s_ValidateExon(), CProSplign::CImplementation::SeekStartStop(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CSeq_align_Mapper_Base::x_GetDstExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CAnnotObject_Info::x_ProcessAlign(), CGff3FlybaseWriter::xAssignAlignmentSplicedLocation(), and CGff3Writer::xAssignAlignmentSplicedTarget().

◆ GetProduct_strand() [1/2]

Get the Product_strand member data.

Returns: Copy of the member data.

Definition at line 903 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::CanGetProduct_strand(), CSpliced_exon_Base::m_Product_strand, and CSerialObject::ThrowUnassigned().

Referenced by ConvertSplicedToPairwiseAln(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), s_ExonToDenseg(), s_GetAlignmentMismatches(), CSpliced_seg::Validate(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetProduct_strand() [2/2]

Get the Product_strand member data.

Returns: Copy of the member data.

Definition at line 558 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::CanGetProduct_strand(), CSpliced_seg_Base::m_Product_strand, and CSerialObject::ThrowUnassigned().

Referenced by CSpliced_seg::AsDiscSeg(), ConvertSplicedToPairwiseAln(), CSpliced_exon::CreateRowSeq_interval(), CScore_LastSpliceSite::Get(), CScore_Polya::Get(), CSpliced_exon::GetRowSeq_insertions(), CSpliced_seg::GetSeqStrand(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::InternalUnaligned(), CSpliced_seg::IsConsistentBiologicalOrder(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Intron(), s_GetPercentCoverage(), s_SplicedToDisc(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeq_loc_Mapper_Base::x_InitSpliced(), CGff3FlybaseWriter::xAssignAlignmentSplicedLocation(), CGff3Writer::xAssignAlignmentSplicedTarget(), and CPslRecord::xInitializeStrands().

◆ GetProduct_type()

Get the Product_type member data.

Returns: Copy of the member data.

Definition at line 652 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::CanGetProduct_type(), CSpliced_seg_Base::m_Product_type, and CSerialObject::ThrowUnassigned().

Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), CSpliced_seg::AsDiscSeg(), BOOST_AUTO_TEST_CASE(), CTestSingleAln::CanTest(), ConvertSplicedToPairwiseAln(), CInternalStopFinder::FindStartStopRanges(), CScore_LastSpliceSite::Get(), CScore_FrameShifts::Get(), CScore_StartStopCodon::Get(), CScore_TblastnScore::Get(), CScoreBuilder::GetBlastScoreSpliced(), CInternalStopFinder::GetCDSNucleotideSequence(), CProductStringBuilder::GetProductString(), CSpliced_seg::GetSeqRange(), GetTerminalPartialness(), CSpliced_seg::InternalUnaligned(), IsProteinAlign(), SAlignmentScoringModel::isProtSS(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_ExonIntrons::Print(), CFeatureGenerator::SImplementation::RecalculateScores(), s_GetSplicedSegIdentityMismatch(), s_IsProteinToGenomic(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstExon(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CScoreBuilderBase::x_GetMatrixCounts(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedType(), CGff3Writer::xSplicedSegHasProteinProd(), and CPslRecord::xValidateSegment().

◆ GetProtpos()

Get the variant data.

Returns: Reference to the data.

Definition at line 100 of file Product_pos_.cpp.

References CProduct_pos_Base::CheckSelected(), CProduct_pos_Base::e_Protpos, and CProduct_pos_Base::m_object.

Referenced by CSeqsRange::Add(), as_nucpos(), CProduct_pos::AsSeqPos(), BOOST_AUTO_TEST_CASE(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CTabularFormatter_ExonIntrons::Print(), s_Fingerprint_Product_pos(), CProSplign::CImplementation::SeekStartStop(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CAnnotObject_Info::x_ProcessAlign(), and CGff3FlybaseWriter::xAssignAlignmentSplicedLocation().

◆ GetReal()

Get the variant data.

Returns: Copy of the variant data.

Definition at line 384 of file Score_.hpp.

Referenced by GetFloatScore(), GetIntScore(), s_CompareValues(), s_GetAlignmentTooltip(), s_GetBitScore(), s_GetEvalue(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), testNuclHitList(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), and CMultiAligner::x_SetDomainHits().

◆ GetRow_scores() ◆ GetRows()

Get the Rows member data.

Returns: Reference to the member data.

Definition at line 309 of file Sparse_seg_.hpp.

References CSparse_seg_Base::m_Rows.

Referenced by CSeqsRange::Add(), CSparse_seg::CheckNumRows(), ConvertSparseToPairwiseAln(), ConvertToPairwise(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSparse_seg::GetSeq_id(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), CSparse_seg::GetSeqStrand(), CRemoveSeqFromAlignDlg::ModifyAlign(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Sparse_seg(), CSparse_seg::Validate(), CAlnWriter::WriteAlignSparseSeg(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetScore()

Get the Score member data.

Returns: Reference to the member data.

Definition at line 896 of file Seq_align_.hpp.

References CSeq_align_Base::m_Score.

Referenced by CSAM_CIGAR_Formatter::AddRow(), CValidError_align::AlignmentScorePercentIdOk(), BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CSeq_align_Handle::GetScore(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), s_GetAlignmentTooltip(), s_GetAlnScores(), s_PopulateScoreSet(), sInheritScores(), sPrepareSeqAlign(), testNuclHitList(), CPslWriter::WriteAlign(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), CCIGAR_Formatter::x_FormatAlignmentRows(), CSeq_align::x_GetNamedScore(), CSeq_align_Mapper_Base::x_Init(), CSeqAlignFilter::x_ReadExtraGis(), CMultiAligner::x_SetDomainHits(), CHitMatrixDataSource::x_UpdateScoreMap(), CGff3Writer::xAssignAlignmentScores(), and CGff3FlybaseWriter::xAssignAlignmentScores().

◆ GetScores() [1/5] ◆ GetScores() [2/5] ◆ GetScores() [3/5] ◆ GetScores() [4/5] ◆ GetScores() [5/5] ◆ GetSecond_id()

Get the Second_id member data.

Returns: Reference to the member data.

Definition at line 461 of file Sparse_align_.hpp.

References CSparse_align_Base::m_Second_id, and CSparse_align_Base::ResetSecond_id().

◆ GetSecond_starts() ◆ GetSecond_strands()

Get the Second_strands member data.

Returns: Reference to the member data.

Definition at line 613 of file Sparse_align_.hpp.

References CSparse_align_Base::m_Second_strands.

Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), CSparse_seg::GetSeqStrand(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetSeg_scores() ◆ GetSegs()

Get the Segs member data.

Returns: Reference to the member data.

Definition at line 921 of file Seq_align_.hpp.

References CSeq_align_Base::m_Segs, and CSeq_align_Base::ResetSegs().

◆ GetSparse()

Get the variant data.

Returns: Reference to the data.

Definition at line 241 of file Seq_align_.cpp.

Referenced by CSeqsRange::Add(), CSeq_align::CheckNumRows(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqRange(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CRemoveSeqFromAlignDlg::ModifyAlign(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Seq_align(), CSeq_align::Validate(), CAlnWriter::WriteAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), and CAnnotObject_Info::x_ProcessAlign().

◆ GetSpliced()

Get the variant data.

Returns: Reference to the data.

Definition at line 219 of file Seq_align_.cpp.

◆ GetStart_codon_found() ◆ GetStarts() [1/3]

Get the Starts member data.

Returns: Reference to the member data.

Definition at line 435 of file Dense_diag_.hpp.

References CDense_diag_Base::m_Starts.

Referenced by CSeqsRange::Add(), CDense_diag::CheckNumRows(), ConvertDendiagToPairwiseAln(), CreateDense_diagFromAnchoredAln(), CDense_diag::CreateRowSeq_interval(), CDense_diag::GetSeqStart(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CDense_diag::OffsetRow(), s_Fingerprint_Dense_diag(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAnnotObject_Info::x_ProcessAlign(), CValidError_align::x_ValidateDendiag(), and CValidError_align::x_ValidateSeqLength().

◆ GetStarts() [2/3]

Get the Starts member data.

Returns: Reference to the member data.

Definition at line 530 of file Dense_seg_.hpp.

References CDense_seg_Base::m_Starts.

Referenced by CSeqsRange::Add(), CAlnMixMatches::Add(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CAlignShadow::CAlignShadow(), CDense_seg::CheckNumSegs(), CAlnVecPrinter::ClustalStyle(), CDense_seg::Compact(), CDUpdater::ComputePercentIdentity(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CEditSeqEndsWithAlign::FindPosition(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CPaintAlignment::GetSegments(), CDense_seg::GetSeqStart(), CDense_seg::GetSeqStop(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CRemoveSeqFromAlignDlg::ModifyAlign(), CDense_seg::OffsetRow(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CAlnVecPrinter::PopsetStyle(), CTabularFormatter_Cigar::Print(), PrintSAM(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_AlignToSeqRanges(), s_CalculateMatchingColumns(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DenseSegLength(), s_FindSegment(), s_Fingerprint_Dense_seg(), s_GetAlignmentLength(), s_GetCigarString(), s_GetGapCount(), s_GetIndels(), s_SeqAlignToBlastSeqLoc(), s_TestAlignmentFromMSAs(), s_TestResultAlignment(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CAlignCompare::SAlignment::Slice(), CSeq_align::SplitOnLongDiscontinuity(), CDense_seg::TrimEndGaps(), TrimSeqAlign(), UpdateDensegAlignment(), CDense_seg::Validate(), CAlnWriter::WriteAlignDenseSeg(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CAlignCleanup::x_Cleanup_AlignVec(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAppHitFilter::x_DumpOutput(), CVectorTrimPanel::x_FindSegment(), CReportTrim::x_FindSegment(), CDense_seg::x_FindSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CDenseg_CI::x_InitIterator(), CDenseg_CI::x_InitSegment(), CInversionMergeAligner::x_IsAllGap(), CUnorderedSplitter::x_IsAllGap(), CUpdateAlign::x_RemoveIDsFromAlign(), CInstancedAligner::x_RunMMGlobal(), x_TestAlignmentQuerySubjStrandCombinations(), and CPslRecord::xInitializeStatsAndBlocks().

◆ GetStarts() [3/3] ◆ GetStd()

Get the variant data.

Returns: Reference to the data.

Definition at line 752 of file Seq_align_.hpp.

Referenced by CSeqsRange::Add(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeqUtils::GetLocPlacements(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), CSeq_align::GetSeqStrand(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Seq_align(), s_GetAlignmentLength(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlnMapplingLocs(), s_GetAlnScores(), s_GetGapCount(), s_GetSubjectId(), testNuclHitList(), CValidError_align::ValidateSeqAlign(), CHitMatrixDataSource::x_CreateHit_Std(), CValidError_align::x_GetIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CAnnotObject_Info::x_ProcessAlign(), CHitMatrixDataSource::x_TestAndSelectAlign(), and CValidError_align::x_ValidateAlignPercentIdentity().

◆ GetStop_codon_found() ◆ GetStrands() [1/3] ◆ GetStrands() [2/3]

Get the Strands member data.

Returns: Reference to the member data.

Definition at line 580 of file Dense_seg_.hpp.

References CDense_seg_Base::m_Strands.

Referenced by CAlnMixMatches::Add(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CContigAssembly::BandedGlobalAlignment(), CAlignShadow::CAlignShadow(), CDense_seg::CheckNumSegs(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CPaintAlignment::GetSegments(), CDense_seg::GetSeqStart(), CDense_seg::GetSeqStop(), CDense_seg::GetSeqStrand(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_Fingerprint_Dense_seg(), s_GetIndels(), s_SeqAlignSetToXMLHsps(), s_SeqAlignToBlastSeqLoc(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CBlastTabularInfo::SetFields(), CDense_seg::TrimEndGaps(), CDense_seg::Validate(), CAlnWriter::WriteAlignDenseSeg(), CAlignCleanup::x_Cleanup_AlignVec(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CContigAssembly::x_IsAllowedStrands(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CUpdateAlign::x_RemoveIDsFromAlign(), CInstancedAligner::x_RunCleanup(), and x_TestAlignmentQuerySubjStrandCombinations().

◆ GetStrands() [3/3] ◆ GetType()

Get the Type member data.

Returns: Copy of the member data.

Definition at line 809 of file Seq_align_.hpp.

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

Referenced by CTestSingleAln::CanTest(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CSeq_align_Mapper_Base::GetDstAlign(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), CSeq_align_Handle::GetType(), CValidError_imp::PostErr(), s_TestResultAlignment(), CValidError_align::ValidateSeqAlign(), and CValidError_align::x_ValidateFastaLike().

◆ GetValue()

Get the Value member data.

Returns: Reference to the member data.

Definition at line 465 of file Score_.hpp.

References CScore_Base::CanGetValue(), CScore_Base::m_Value, and CSerialObject::ThrowUnassigned().

Referenced by GetFloatScore(), GetIntScore(), s_GetAlignmentTooltip(), s_GetBitScore(), s_GetEvalue(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), sPrepareSeqAlign(), testNuclHitList(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), CMultiAligner::x_SetDomainHits(), and CHitMatrixDataSource::x_UpdateScoreMap().

◆ IsDendiag() bool CSeq_align_Base::C_Segs::IsDendiag ( void ) const inline

Check if variant Dendiag is selected.

Dendiag type is defined as 'typedef list< CRef< CDense_diag > > TDendiag'.

Returns

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

Definition at line 720 of file Seq_align_.hpp.

Referenced by CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CAlignFormatUtil::GetAlignmentLength(), GetBlockCount(), GetDDSetFromSeqAlign(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), GetReportableSeqIdForAlignment(), CCdCore::Has3DMaster(), s_DivvyUpAlignments_ProcessAnnot(), s_GetSubjectId(), s_SeqAlignSetToXMLHsps(), CBlastTabularInfo::SetFields(), CAlignFilter::x_FuncCall(), CSeqAlignFilter::x_UpdateGiInSeqalign(), and CModifySeqId::x_UpdateSeqAlign().

◆ IsDenseg() bool CSeq_align_Base::C_Segs::IsDenseg ( void ) const inline

Check if variant Denseg is selected.

Denseg type is defined as 'typedef CDense_seg TDenseg'.

Returns

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

Definition at line 740 of file Seq_align_.hpp.

Referenced by CAlnMix::Add(), CAlnVwrApp::AddAlnToMix(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CFeaturePropagator::CFeaturePropagator(), ConvertRawToDeltaByNsCommand_impl(), ConvertRawToDeltaByNsHugeFileCmd_impl(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), Denseg2DenseDiagList(), CEditSeqEndsWithAlign::FindPosition(), CScoreBuilder::GetBlastScore(), CScoreBuilder::GetBlastScoreDenseg(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), CTabularFormatter_Cigar::Print(), CTabularFormatter_Traceback::Print(), PrintTabular(), s_CheckTraceMateAlign(), s_CleanSeqAlign(), s_ComputeTraceback(), s_DivvyUpAlignments_ProcessAnnot(), s_GetSubjectId(), s_IsProteinToGenomic(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), s_ScoreAlignments(), s_TestAlignmentFromMSAs(), s_UpdateSubjectInSeqalign(), COverlapScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), SeqAlignConvert(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CAlignCleanup::x_Cleanup_AlignVec(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CHitMatrixDataSource::x_CreateHit_Denseg(), CTreeBuilderJob::x_CreateProjectItems(), CCIGAR_Formatter::x_FormatAlignmentRows(), CAlignFilter::x_FuncCall(), CApplyRNAITSDlg::x_GetAlignments(), CUpdateSeqPanel::x_InitDrawingParams(), CApplyRNAITSDlg::x_IsThereAlignment(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CApplyRNAITSDlg::x_SetupAlnMgr(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CModifySeqId::x_UpdateSeqAlign(), CValidError_align::x_ValidateAlignPercentIdentity(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi129295(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi7450545(), and CEditObjectFeaturePropagate::xInit().

◆ IsDiag() bool CSpliced_exon_chunk_Base::IsDiag ( void ) const inline ◆ IsDisc() bool CSeq_align_Base::C_Segs::IsDisc ( void ) const inline

Check if variant Disc is selected.

Disc type is defined as 'typedef CSeq_align_set TDisc'.

Returns

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

Definition at line 772 of file Seq_align_.hpp.

Referenced by CAlnMix::Add(), BuildAlignDataSource(), CFeaturePropagator::CFeaturePropagator(), ExtractFirstSeqAlign(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CAlignFormatUtil::ExtractSeqalignSetFromDiscSegs(), SAlignmentScoringModel::GetIdentOdds(), PatchTargetSequence(), PrintSAM(), PrintTabular(), CTestSingleAln_All::RunTest(), s_CleanSeqAlign(), s_ExtractSeqId(), s_SeqAlignToXMLHit(), CAlnTableDS::x_AddAlign(), CSeq_annot_Info::x_AddAlignKeys(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CQuerySet::x_ContainsAlignment(), CCleanupAlignmentsJob::x_CreateProjectItems(), CAlignFilter::x_FuncCall(), CCommonComponentScorer::x_GetSeqHistCompList(), CTreeAlignMerger::x_MakeMergeableGroups(), CIdMapperTestApp::x_RecurseMapSeqAligns(), and CTabularFormatter_DiscStrand::x_RecurseStrands().

◆ IsGenomic_ins() bool CSpliced_exon_chunk_Base::IsGenomic_ins ( void ) const inline

Check if variant Genomic_ins is selected.

Genomic_ins type is defined as 'typedef TSeqPos TGenomic_ins'.

Returns

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

Definition at line 458 of file Spliced_exon_chunk_.hpp.

References CSpliced_exon_chunk_Base::e_Genomic_ins, and CSpliced_exon_chunk_Base::m_choice.

Referenced by CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::HasStartOnNuc(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_oldlogic(), s_ExonToDenseg(), SBlocks::SBlocks(), CReportEntry::x_CheckExonGap(), CSeq_align_Mapper_Base::x_GetDstSpliced(), and CSeq_loc_Mapper_Base::x_IterateExonParts().

◆ IsInt() bool CScore_Base::C_Value::IsInt ( void ) const inline ◆ IsMatch() bool CSpliced_exon_chunk_Base::IsMatch ( void ) const inline ◆ IsMismatch() bool CSpliced_exon_chunk_Base::IsMismatch ( void ) const inline ◆ IsNucpos() bool CProduct_pos_Base::IsNucpos ( void ) const inline ◆ IsPacked() bool CSeq_align_Base::C_Segs::IsPacked ( void ) const inline ◆ IsProduct_ins() bool CSpliced_exon_chunk_Base::IsProduct_ins ( void ) const inline

Check if variant Product_ins is selected.

Product_ins type is defined as 'typedef TSeqPos TProduct_ins'.

Returns

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

Definition at line 431 of file Spliced_exon_chunk_.hpp.

References CSpliced_exon_chunk_Base::e_Product_ins, and CSpliced_exon_chunk_Base::m_choice.

◆ IsProtpos() bool CProduct_pos_Base::IsProtpos ( void ) const inline ◆ IsReal() bool CScore_Base::C_Value::IsReal ( void ) const inline ◆ IsSet() [1/2] bool CScore_set_Base::IsSet ( void ) const inline

Check if a value has been assigned to data member.

Data member is mandatory; its type is defined as 'typedef list< CRef< CScore > > Tdata'

Returns

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

Definition at line 153 of file Score_set_.hpp.

References CScore_set_Base::m_set_State.

◆ IsSet() [2/2] bool CSeq_align_set_Base::IsSet ( void ) const inline

Check if a value has been assigned to data member.

Data member is mandatory; its type is defined as 'typedef list< CRef< CSeq_align > > Tdata'

Returns

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

Definition at line 154 of file Seq_align_set_.hpp.

References CSeq_align_set_Base::m_set_State.

Referenced by HitDistributor::addBatch(), CAlignmentCollectionScore::Get(), CBlastFormatUtil::InsertSubjectScores(), CFarPointerSeq::RunBlast(), CCreateSeqHistForTpa::RunBlast(), s_RoundScores(), s_RunBlast2NASeq(), CAlignmentCollectionScore::Set(), CIgBlastTabularInfo::SetAirrFormatData(), CIgBlastTabularInfo::SetIgAnnotation(), CDUpdater::update(), CAutogeneratedCleanup::x_BasicCleanupSeqAlignSet(), CNGAlignJob::x_CreateProjectItems(), and CFindOverlapJob::x_CreateProjectItems().

◆ IsSetAcceptor_before_exon() bool CSpliced_exon_Base::IsSetAcceptor_before_exon ( void ) const inline ◆ IsSetAmin() bool CProt_pos_Base::IsSetAmin ( void ) const inline ◆ IsSetBases() bool CSplice_site_Base::IsSetBases ( void ) const inline ◆ IsSetBounds() bool CSeq_align_Base::IsSetBounds ( void ) const inline ◆ IsSetDim() [1/5] bool CDense_diag_Base::IsSetDim ( void ) const inline ◆ IsSetDim() [2/5] bool CDense_seg_Base::IsSetDim ( void ) const inline ◆ IsSetDim() [3/5] bool CPacked_seg_Base::IsSetDim ( void ) const inline ◆ IsSetDim() [4/5] bool CSeq_align_Base::IsSetDim ( void ) const inline

dimensionality Check if a value has been assigned to Dim data member.

Data member Dim is optional; its type is defined as 'typedef int TDim'

Returns

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

Definition at line 837 of file Seq_align_.hpp.

References CSeq_align_Base::m_set_State.

Referenced by CSeq_align_Base::CanGetDim(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CDesktopAlignItem::GetDescription(), CSeq_align_Mapper_Base::GetDstAlign(), GetPssmIdFromSeqAlign(), GetReportableSeqIdForAlignment(), CSeq_align_Handle::IsSetDim(), CDesktopAlignItem::s_ContainsFarPointers(), CSeq_align_Base::SetDim(), CLDS2_AnnotType_Hook::SkipObject(), and CSeq_align::SplitOnLongDiscontinuity().

◆ IsSetDim() [5/5] bool CStd_seg_Base::IsSetDim ( void ) const inline ◆ IsSetDonor_after_exon() bool CSpliced_exon_Base::IsSetDonor_after_exon ( void ) const inline ◆ IsSetExons() bool CSpliced_seg_Base::IsSetExons ( void ) const inline ◆ IsSetExt() [1/3] bool CSeq_align_Base::IsSetExt ( void ) const inline

extra info Check if a value has been assigned to Ext data member.

Data member Ext is optional; its type is defined as 'typedef list< CRef< CUser_object > > TExt'

Returns

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

Definition at line 989 of file Seq_align_.hpp.

References CSeq_align_Base::m_set_State.

Referenced by CSGAlignmentJob::FilterDuplicatesAndBadReads(), CSeq_align::FindExt(), CSeq_align_Mapper_Base::GetDstAlign(), CProductStringBuilder::GetProductString(), CScoreBuilder::GetTraceback(), CTabularFormatter_BestPlacementGroup::Print(), CTabularFormatter_AssemblyInfo::Print(), s_CheckTraceMateAlign(), and s_PopulateExtSet().

◆ IsSetExt() [2/3] bool CSparse_seg_Base::IsSetExt ( void ) const inline ◆ IsSetExt() [3/3] bool CSpliced_exon_Base::IsSetExt ( void ) const inline ◆ IsSetFirst_id() bool CSparse_align_Base::IsSetFirst_id ( void ) const inline ◆ IsSetFirst_starts() bool CSparse_align_Base::IsSetFirst_starts ( void ) const inline

starts on the first sequence [numseg] Check if a value has been assigned to First_starts data member.

Data member First_starts is mandatory; its type is defined as 'typedef vector< int > TFirst_starts'

Returns

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

Definition at line 526 of file Sparse_align_.hpp.

References CSparse_align_Base::m_set_State.

◆ IsSetFrame() bool CProt_pos_Base::IsSetFrame ( void ) const inline ◆ IsSetGenomic_end() bool CSpliced_exon_Base::IsSetGenomic_end ( void ) const inline ◆ IsSetGenomic_id() [1/2] bool CSpliced_exon_Base::IsSetGenomic_id ( void ) const inline

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

Data member Genomic_id is optional; its type is defined as 'typedef CSeq_id TGenomic_id'

Returns

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

Definition at line 863 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::m_Genomic_id.

Referenced by CSeqsRange::Add(), CSpliced_exon_Base::CanGetGenomic_id(), CSpliced_exon::CreateRowSeq_interval(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_newlogic(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), CSpliced_seg::Validate(), CAutogeneratedCleanup::x_BasicCleanupSplicedExon(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().

◆ IsSetGenomic_id() [2/2] bool CSpliced_seg_Base::IsSetGenomic_id ( void ) const inline

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

Data member Genomic_id is optional; its type is defined as 'typedef CSeq_id TGenomic_id'

Returns

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

Definition at line 518 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::m_Genomic_id.

Referenced by CSeqsRange::Add(), CSpliced_seg_Base::CanGetGenomic_id(), CSpliced_exon::CreateRowSeq_interval(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeq_align_Mapper_Base::InitExon(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Spliced_seg(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CAutogeneratedCleanup::x_BasicCleanupSplicedSeg(), and CSeq_loc_Mapper_Base::x_InitSpliced().

◆ IsSetGenomic_start() bool CSpliced_exon_Base::IsSetGenomic_start ( void ) const inline ◆ IsSetGenomic_strand() [1/2] bool CSpliced_exon_Base::IsSetGenomic_strand ( void ) const inline

genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_strand data member.

Data member Genomic_strand is optional; its type is defined as 'typedef ENa_strand TGenomic_strand'

Returns

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

Definition at line 931 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::m_set_State.

Referenced by CSpliced_exon_Base::CanGetGenomic_strand(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_newlogic(), s_ExonToDenseg(), s_GetAlignmentMismatches(), CSpliced_exon_Base::SetGenomic_strand(), CSeq_align_Mapper_Base::x_GetDstExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAnnotObject_Info::x_ProcessAlign(), and CGff3Writer::xAssignAlignmentSplicedLocation().

◆ IsSetGenomic_strand() [2/2] bool CSpliced_seg_Base::IsSetGenomic_strand ( void ) const inline

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

Data member Genomic_strand is optional; its type is defined as 'typedef ENa_strand TGenomic_strand'

Returns

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

Definition at line 586 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::m_set_State.

Referenced by CSpliced_seg::AsDiscSeg(), CSpliced_seg_Base::CanGetGenomic_strand(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), s_GetAlignmentMismatches(), s_GetCIGARForSort(), CReportEntry::SetAlignment(), CSpliced_seg_Base::SetGenomic_strand(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CCDSTranslationPanel::x_SetLocationForProtein(), CGff3Writer::xAssignAlignmentSplicedLocation(), and CGff3FlybaseWriter::xAssignAlignmentSplicedTarget().

◆ IsSetId() [1/2] bool CScore_Base::IsSetId ( void ) const inline ◆ IsSetId() [2/2] bool CSeq_align_Base::IsSetId ( void ) const inline ◆ IsSetIds() [1/4] bool CDense_diag_Base::IsSetIds ( void ) const inline ◆ IsSetIds() [2/4] bool CDense_seg_Base::IsSetIds ( void ) const inline

sequences in order Check if a value has been assigned to Ids data member.

Data member Ids is mandatory; its type is defined as 'typedef vector< CRef< CSeq_id > > TIds'

Returns

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

Definition at line 493 of file Dense_seg_.hpp.

References CDense_seg_Base::m_set_State.

Referenced by CAlignmentAssistant::GetFeatures(), CDense_seg::GetSeq_id(), CAlignmentAssistant::ReportUnresolvedBioseqs(), s_DensegHasAccessionWithZeroVersion(), s_FixZeroVersions(), s_GetNumIdsToUse(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), CAutogeneratedCleanup::x_BasicCleanupDenseg(), and CApplyRNAITSDlg::x_GetAlignments().

◆ IsSetIds() [3/4] bool CPacked_seg_Base::IsSetIds ( void ) const inline ◆ IsSetIds() [4/4] bool CStd_seg_Base::IsSetIds ( void ) const inline ◆ IsSetIndex() bool CSparse_seg_ext_Base::IsSetIndex ( void ) const inline ◆ IsSetLen() bool CDense_diag_Base::IsSetLen ( void ) const inline ◆ IsSetLens() [1/3] bool CDense_seg_Base::IsSetLens ( void ) const inline ◆ IsSetLens() [2/3] bool CPacked_seg_Base::IsSetLens ( void ) const inline

length of each segment Check if a value has been assigned to Lens data member.

Data member Lens is mandatory; its type is defined as 'typedef vector< TSeqPos > TLens'

Returns

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

Definition at line 595 of file Packed_seg_.hpp.

References CPacked_seg_Base::m_set_State.

◆ IsSetLens() [3/3] bool CSparse_align_Base::IsSetLens ( void ) const inline

lengths of segments [numseg] Check if a value has been assigned to Lens data member.

Data member Lens is mandatory; its type is defined as 'typedef vector< TSeqPos > TLens'

Returns

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

Definition at line 576 of file Sparse_align_.hpp.

References CSparse_align_Base::m_set_State.

◆ IsSetLoc() bool CStd_seg_Base::IsSetLoc ( void ) const inline ◆ IsSetMaster_id() bool CSparse_seg_Base::IsSetMaster_id ( void ) const inline ◆ IsSetModifiers() bool CSpliced_seg_Base::IsSetModifiers ( void ) const inline ◆ IsSetNumseg() [1/3] bool CDense_seg_Base::IsSetNumseg ( void ) const inline ◆ IsSetNumseg() [2/3] bool CPacked_seg_Base::IsSetNumseg ( void ) const inline ◆ IsSetNumseg() [3/3] bool CSparse_align_Base::IsSetNumseg ( void ) const inline ◆ IsSetPartial() bool CSpliced_exon_Base::IsSetPartial ( void ) const inline ◆ IsSetParts() bool CSpliced_exon_Base::IsSetParts ( void ) const inline

basic seqments always are in biologic order Check if a value has been assigned to Parts data member.

Data member Parts is optional; its type is defined as 'typedef list< CRef< CSpliced_exon_chunk > > TParts'

Returns

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

Definition at line 978 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::m_set_State.

Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), AlignModelToSeqalign(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), CFeatureGenerator::SImplementation::MaximizeTranslation(), ProjectExon_newlogic(), CFeatureGenerator::SImplementation::RecalculateExonIdty(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), s_GetAlignmentMismatches(), s_GetCountIdentityMismatch(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CReportEntry::x_CheckExonGap(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAlnSpanVertModel::x_PopulateRowsSpliced().

◆ IsSetPoly_a() bool CSpliced_seg_Base::IsSetPoly_a ( void ) const inline

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.

Data member Poly_a is optional; its type is defined as 'typedef TSeqPos TPoly_a'

Returns

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

Definition at line 705 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::m_set_State.

Referenced by CSpliced_seg_Base::CanGetPoly_a(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), SAlignmentScoringModel::GetPolyA_length(), GetUnalignedLength_3p(), s_GetPercentCoverage(), CSpliced_seg_Base::SetPoly_a(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CFeatureGenerator::SImplementation::x_MapFeature(), and CAlnSpanVertModel::x_PopulateRowsSpliced().

◆ IsSetPresent() bool CPacked_seg_Base::IsSetPresent ( void ) const inline ◆ IsSetProduct_end() bool CSpliced_exon_Base::IsSetProduct_end ( void ) const inline ◆ IsSetProduct_id() [1/2] bool CSpliced_exon_Base::IsSetProduct_id ( void ) const inline

product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member.

Data member Product_id is optional; its type is defined as 'typedef CSeq_id TProduct_id'

Returns

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

Definition at line 842 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::m_Product_id.

Referenced by CSeqsRange::Add(), CSpliced_exon_Base::CanGetProduct_id(), CSpliced_exon::CreateRowSeq_interval(), CSeq_align_Mapper_Base::InitExon(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), CSpliced_seg::Validate(), CAutogeneratedCleanup::x_BasicCleanupSplicedExon(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().

◆ IsSetProduct_id() [2/2] bool CSpliced_seg_Base::IsSetProduct_id ( void ) const inline

product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member.

Data member Product_id is optional; its type is defined as 'typedef CSeq_id TProduct_id'

Returns

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

Definition at line 497 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::m_Product_id.

Referenced by CSeqsRange::Add(), CSpliced_seg_Base::CanGetProduct_id(), CSpliced_exon::CreateRowSeq_interval(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeq_align_Mapper_Base::InitExon(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Spliced_seg(), CSpliced_seg::Validate(), CAutogeneratedCleanup::x_BasicCleanupSplicedSeg(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CGff3Writer::xAssignAlignmentSplicedMethod().

◆ IsSetProduct_length() bool CSpliced_seg_Base::IsSetProduct_length ( void ) const inline

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.

Data member Product_length is optional; its type is defined as 'typedef TSeqPos TProduct_length'

Returns

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

Definition at line 752 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::m_set_State.

Referenced by CSpliced_seg_Base::CanGetProduct_length(), CScore_Polya::Get(), SAlignmentScoringModel::GetCoverage(), SAlignmentScoringModel::GetPolyA_length(), CProductStringBuilder::GetProductString(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), PrintTabular(), s_GetPercentCoverage(), CSpliced_seg_Base::SetProduct_length(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), and CAlnSpanVertModel::x_PopulateRowsSpliced().

◆ IsSetProduct_start() bool CSpliced_exon_Base::IsSetProduct_start ( void ) const inline ◆ IsSetProduct_strand() [1/2] bool CSpliced_exon_Base::IsSetProduct_strand ( void ) const inline

should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.

Data member Product_strand is optional; its type is defined as 'typedef ENa_strand TProduct_strand'

Returns

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

Definition at line 884 of file Spliced_exon_.hpp.

References CSpliced_exon_Base::m_set_State.

Referenced by CSpliced_exon_Base::CanGetProduct_strand(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), s_ExonToDenseg(), s_GetAlignmentMismatches(), CSpliced_exon_Base::SetProduct_strand(), CSpliced_seg::Validate(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().

◆ IsSetProduct_strand() [2/2] bool CSpliced_seg_Base::IsSetProduct_strand ( void ) const inline

should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.

Data member Product_strand is optional; its type is defined as 'typedef ENa_strand TProduct_strand'

Returns

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

Definition at line 539 of file Spliced_seg_.hpp.

References CSpliced_seg_Base::m_set_State.

Referenced by CSpliced_seg::AsDiscSeg(), CSpliced_seg_Base::CanGetProduct_strand(), CSpliced_exon::CreateRowSeq_interval(), CScore_Polya::Get(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::InternalUnaligned(), s_GetAlignmentMismatches(), s_GetPercentCoverage(), CSpliced_seg_Base::SetProduct_strand(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstSpliced(), and CSeq_loc_Mapper_Base::x_InitSpliced().

◆ IsSetProduct_type() bool CSpliced_seg_Base::IsSetProduct_type ( void ) const inline ◆ IsSetRow_scores() bool CSparse_seg_Base::IsSetRow_scores ( void ) const inline ◆ IsSetRows() bool CSparse_seg_Base::IsSetRows ( void ) const inline ◆ IsSetScore() bool CSeq_align_Base::IsSetScore ( void ) const inline

for whole alignment Check if a value has been assigned to Score data member.

Data member Score is optional; its type is defined as 'typedef vector< CRef< CScore > > TScore'

Returns

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

Definition at line 884 of file Seq_align_.hpp.

References CSeq_align_Base::m_set_State.

Referenced by CGBProjectHelper::AddProjectItemsFromRID(), CSAM_CIGAR_Formatter::AddRow(), CValidError_align::AlignmentScorePercentIdOk(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ClearScores(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CSeq_align_Handle::IsSetScore(), CFeatureGenerator::SImplementation::RecalculateScores(), CSeq_align::ResetNamedScore(), s_GetAlignmentTooltip(), s_PopulateScoreSet(), sInheritScores(), sPrepareSeqAlign(), CCIGAR_Formatter::x_FormatAlignmentRows(), CSeq_align::x_GetNamedScore(), CSeq_align_Mapper_Base::x_Init(), CSeq_align::x_SetNamedScore(), CGff3Writer::xAssignAlignmentScores(), and CGff3FlybaseWriter::xAssignAlignmentScores().

◆ IsSetScores() [1/5] bool CDense_diag_Base::IsSetScores ( void ) const inline ◆ IsSetScores() [2/5] bool CDense_seg_Base::IsSetScores ( void ) const inline ◆ IsSetScores() [3/5] bool CPacked_seg_Base::IsSetScores ( void ) const inline ◆ IsSetScores() [4/5] bool CSpliced_exon_Base::IsSetScores ( void ) const inline ◆ IsSetScores() [5/5] bool CStd_seg_Base::IsSetScores ( void ) const inline ◆ IsSetSecond_id() bool CSparse_align_Base::IsSetSecond_id ( void ) const inline ◆ IsSetSecond_starts() bool CSparse_align_Base::IsSetSecond_starts ( void ) const inline

starts on the second sequence [numseg] Check if a value has been assigned to Second_starts data member.

Data member Second_starts is mandatory; its type is defined as 'typedef vector< int > TSecond_starts'

Returns

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

Definition at line 551 of file Sparse_align_.hpp.

References CSparse_align_Base::m_set_State.

◆ IsSetSecond_strands() bool CSparse_align_Base::IsSetSecond_strands ( void ) const inline

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

Data member Second_strands is optional; its type is defined as 'typedef vector< ENa_strand > TSecond_strands'

Returns

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

Definition at line 601 of file Sparse_align_.hpp.

References CSparse_align_Base::m_set_State.

Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), CSparse_seg::GetSeqStrand(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), and CAnnotObject_Info::x_ProcessAlign().

◆ IsSetSeg_scores() bool CSparse_align_Base::IsSetSeg_scores ( void ) const inline ◆ IsSetSegs() bool CSeq_align_Base::IsSetSegs ( void ) const inline

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

Data member Segs is mandatory; its type is defined as 'typedef C_Segs TSegs'

Returns

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

Definition at line 909 of file Seq_align_.hpp.

References CSeq_align_Base::m_Segs.

Referenced by ConvertRawToDeltaByNsCommand_impl(), ConvertRawToDeltaByNsHugeFileCmd_impl(), CEditSeqEndsWithAlign::FindPosition(), CRemoveSeqFromAlignDlg::GetAlignLabel(), GetReportableSeqIdForAlignment(), CRemoveSeqFromAlignDlg::ModifyAlign(), CValidError_imp::PostErr(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), CValidError_align::ValidateSeqAlign(), CAutogeneratedCleanup::x_BasicCleanupSeqAlign(), CHitMatrixDataSource::x_CreateHit(), CHitMatrixDataSource::x_CreateHits(), CApplyRNAITSDlg::x_GetAlignments(), CApplyRNAITSDlg::x_IsThereAlignment(), CCDSTranslationPanel::x_SetLocationForProtein(), CApplyRNAITSDlg::x_SetupAlnMgr(), CModifySeqId::x_UpdateSeqAlign(), CValidError_align::x_ValidateAlignPercentIdentity(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi40456275(), CGff3Writer::xWriteAlign(), and CGff3Writer::xWriteAlignSpliced().

◆ IsSetStarts() [1/3] bool CDense_diag_Base::IsSetStarts ( void ) const inline

start OFFSETS in ids order Check if a value has been assigned to Starts data member.

Data member Starts is mandatory; its type is defined as 'typedef vector< TSeqPos > TStarts'

Returns

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

Definition at line 423 of file Dense_diag_.hpp.

References CDense_diag_Base::m_set_State.

◆ IsSetStarts() [2/3] bool CDense_seg_Base::IsSetStarts ( void ) const inline ◆ IsSetStarts() [3/3] bool CPacked_seg_Base::IsSetStarts ( void ) const inline

start OFFSETS in ids order for whole alignment Check if a value has been assigned to Starts data member.

Data member Starts is mandatory; its type is defined as 'typedef vector< TSeqPos > TStarts'

Returns

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

Definition at line 542 of file Packed_seg_.hpp.

References CPacked_seg_Base::m_set_State.

◆ IsSetStrands() [1/3] bool CDense_diag_Base::IsSetStrands ( void ) const inline ◆ IsSetStrands() [2/3] bool CDense_seg_Base::IsSetStrands ( void ) const inline

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

Data member Strands is optional; its type is defined as 'typedef vector< ENa_strand > TStrands'

Returns

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

Definition at line 568 of file Dense_seg_.hpp.

References CDense_seg_Base::m_set_State.

Referenced by CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CreateAlignSetFromPairwiseAln(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CPaintAlignment::GetSegments(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::RemovePureGapSegs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_CutDensegSegment(), s_Fingerprint_Dense_seg(), s_GetIndels(), s_Seq_align_Seq_loc(), s_SeqAlignSetToXMLHsps(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CBlastTabularInfo::SetFields(), CDense_seg::SwapRows(), CDense_seg::TrimEndGaps(), CAlnWriter::WriteAlignDenseSeg(), CAlignCleanup::x_Cleanup_AlignVec(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), and CUpdateAlign::x_RemoveIDsFromAlign().

◆ IsSetStrands() [3/3] bool CPacked_seg_Base::IsSetStrands ( void ) const inline ◆ IsSetType() bool CSeq_align_Base::IsSetType ( void ) const inline ◆ IsSetValue() bool CScore_Base::IsSetValue ( void ) const inline ◆ IsSparse() bool CSeq_align_Base::C_Segs::IsSparse ( void ) const inline ◆ IsSpliced() bool CSeq_align_Base::C_Segs::IsSpliced ( void ) const inline

Check if variant Spliced is selected.

Spliced type is defined as 'typedef CSpliced_seg TSpliced'.

Returns

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

Definition at line 778 of file Seq_align_.hpp.

◆ IsStart_codon_found() bool CSpliced_seg_modifier_Base::IsStart_codon_found ( void ) const inline ◆ IsStd() bool CSeq_align_Base::C_Segs::IsStd ( void ) const inline

Check if variant Std is selected.

Std type is defined as 'typedef list< CRef< CStd_seg > > TStd'.

Returns

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

Definition at line 746 of file Seq_align_.hpp.

Referenced by CAlnMix::Add(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CFeaturePropagator::CFeaturePropagator(), CreateAnchoredAlnFromAln(), CreateAnchoredAlnVec(), CScore_CdsScore::Get(), CAlignFormatUtil::GetAlignmentLength(), CScoreBuilder::GetBlastScore(), CSeqUtils::GetLocPlacements(), GetReportableSeqIdForAlignment(), s_CleanSeqAlign(), s_GetAlnMapplingLocs(), s_GetPercentCoverage(), s_GetSubjectId(), s_SeqAlignSetToXMLHsps(), SeqAlignConvert(), CBlastTabularInfo::SetFields(), testNuclHitList(), CHitMatrixDataSource::x_CreateHit_Std(), CAlignFilter::x_FuncCall(), CProSplignJob::x_GenerateCompartments(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CModifySeqId::x_UpdateSeqAlign(), and CValidError_align::x_ValidateAlignPercentIdentity().

◆ IsStop_codon_found() bool CSpliced_seg_modifier_Base::IsStop_codon_found ( void ) const inline ◆ operator const Tdata &() [1/2]

Conversion operator to 'const Tdata' type.

Definition at line 178 of file Score_set_.hpp.

◆ operator const Tdata &() [2/2] ◆ operator Tdata &() [1/2] ◆ operator Tdata &() [2/2] ◆ operator=() [1/26] ◆ operator=() [2/26] ◆ operator=() [3/26] ◆ operator=() [4/26] ◆ operator=() [5/26] ◆ operator=() [6/26] ◆ operator=() [7/26] ◆ operator=() [8/26] ◆ operator=() [9/26] ◆ operator=() [10/26] ◆ operator=() [11/26] ◆ operator=() [12/26] ◆ operator=() [13/26] ◆ operator=() [14/26] ◆ operator=() [15/26] ◆ operator=() [16/26] ◆ operator=() [17/26] ◆ operator=() [18/26] ◆ operator=() [19/26] ◆ operator=() [20/26] ◆ operator=() [21/26] ◆ operator=() [22/26] ◆ operator=() [23/26] ◆ operator=() [24/26] ◆ operator=() [25/26] ◆ operator=() [26/26] ◆ Reset() [1/20] void CDense_diag_Base::Reset ( void ) virtual ◆ Reset() [2/20] void CDense_seg_Base::Reset ( void ) virtual ◆ Reset() [3/20] void CPacked_seg_Base::Reset ( void ) virtual ◆ Reset() [4/20] void CProduct_pos_Base::Reset ( void ) virtual ◆ Reset() [5/20] void CProt_pos_Base::Reset ( void ) virtual ◆ Reset() [6/20] void CScore_Base::C_Value::Reset ( void ) ◆ Reset() [7/20] void CScore_Base::Reset ( void ) virtual ◆ Reset() [8/20] void CScore_set_Base::Reset ( void ) ◆ Reset() [9/20] ◆ Reset() [10/20] void CSeq_align_Base::Reset ( void ) virtual

Reset the whole object.

Definition at line 333 of file Seq_align_.cpp.

References CSeq_align_Base::ResetBounds(), CSeq_align_Base::ResetDim(), CSeq_align_Base::ResetExt(), CSeq_align_Base::ResetId(), CSeq_align_Base::ResetScore(), CSeq_align_Base::ResetSegs(), and CSeq_align_Base::ResetType().

Referenced by HitDistributor::distribute(), CSeqEdit_Cmd_ReplaceAnnot_Base::C_Data::C_Align::SetNvalue(), CSeqEdit_Cmd_ReplaceAnnot_Base::C_Data::C_Align::SetOvalue(), BlockModel::toSeqAlign(), and CSeq_align_Base::C_Segs::~C_Segs().

◆ Reset() [11/20] void CSeq_align_set_Base::Reset ( void ) ◆ Reset() [12/20] void CSparse_align_Base::Reset ( void ) virtual ◆ Reset() [13/20] void CSparse_seg_Base::Reset ( void ) virtual ◆ Reset() [14/20] void CSparse_seg_ext_Base::Reset ( void ) virtual ◆ Reset() [15/20] void CSplice_site_Base::Reset ( void ) virtual ◆ Reset() [16/20] void CSpliced_exon_Base::Reset ( void ) virtual

Reset the whole object.

Definition at line 181 of file Spliced_exon_.cpp.

◆ Reset() [17/20] void CSpliced_exon_chunk_Base::Reset ( void ) virtual ◆ Reset() [18/20] void CSpliced_seg_Base::Reset ( void ) virtual ◆ Reset() [19/20] void CSpliced_seg_modifier_Base::Reset ( void ) virtual ◆ Reset() [20/20] void CStd_seg_Base::Reset ( void ) virtual ◆ ResetAcceptor_before_exon() void CSpliced_exon_Base::ResetAcceptor_before_exon ( void ) ◆ ResetAmin() void CProt_pos_Base::ResetAmin ( void ) inline ◆ ResetBases() void CSplice_site_Base::ResetBases ( void ) ◆ ResetBounds() void CSeq_align_Base::ResetBounds ( void ) ◆ ResetDim() [1/5] void CDense_diag_Base::ResetDim ( void ) inline ◆ ResetDim() [2/5] void CDense_seg_Base::ResetDim ( void ) inline ◆ ResetDim() [3/5] void CPacked_seg_Base::ResetDim ( void ) inline ◆ ResetDim() [4/5] void CSeq_align_Base::ResetDim ( void ) inline ◆ ResetDim() [5/5] void CStd_seg_Base::ResetDim ( void ) inline ◆ ResetDonor_after_exon() void CSpliced_exon_Base::ResetDonor_after_exon ( void ) ◆ ResetExons() void CSpliced_seg_Base::ResetExons ( void ) ◆ ResetExt() [1/3] void CSeq_align_Base::ResetExt ( void ) ◆ ResetExt() [2/3] void CSparse_seg_Base::ResetExt ( void ) ◆ ResetExt() [3/3] void CSpliced_exon_Base::ResetExt ( void ) ◆ ResetFirst_id() void CSparse_align_Base::ResetFirst_id ( void ) ◆ ResetFirst_starts() void CSparse_align_Base::ResetFirst_starts ( void ) ◆ ResetFrame() void CProt_pos_Base::ResetFrame ( void ) inline ◆ ResetGenomic_end() void CSpliced_exon_Base::ResetGenomic_end ( void ) inline ◆ ResetGenomic_id() [1/2] void CSpliced_exon_Base::ResetGenomic_id ( void ) ◆ ResetGenomic_id() [2/2] void CSpliced_seg_Base::ResetGenomic_id ( void ) ◆ ResetGenomic_start() void CSpliced_exon_Base::ResetGenomic_start ( void ) inline ◆ ResetGenomic_strand() [1/2] void CSpliced_exon_Base::ResetGenomic_strand ( void ) inline ◆ ResetGenomic_strand() [2/2] void CSpliced_seg_Base::ResetGenomic_strand ( void ) inline ◆ ResetId() [1/2] void CScore_Base::ResetId ( void ) ◆ ResetId() [2/2] void CSeq_align_Base::ResetId ( void ) ◆ ResetIds() [1/4] void CDense_diag_Base::ResetIds ( void ) ◆ ResetIds() [2/4] void CDense_seg_Base::ResetIds ( void ) ◆ ResetIds() [3/4] void CPacked_seg_Base::ResetIds ( void ) ◆ ResetIds() [4/4] void CStd_seg_Base::ResetIds ( void ) ◆ ResetIndex() void CSparse_seg_ext_Base::ResetIndex ( void ) inline ◆ ResetLen() void CDense_diag_Base::ResetLen ( void ) inline ◆ ResetLens() [1/3] void CDense_seg_Base::ResetLens ( void )

Reset Lens data member.

Definition at line 64 of file Dense_seg_.cpp.

References CDense_seg_Base::m_Lens, and CDense_seg_Base::m_set_State.

Referenced by ImproveAlignment(), CDense_seg_Base::Reset(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFuseAbuttingIntervals(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), and TestPartialWhenCutStopDoNotExtend().

◆ ResetLens() [2/3] void CPacked_seg_Base::ResetLens ( void ) ◆ ResetLens() [3/3] void CSparse_align_Base::ResetLens ( void ) ◆ ResetLoc() void CStd_seg_Base::ResetLoc ( void ) ◆ ResetMaster_id() void CSparse_seg_Base::ResetMaster_id ( void ) ◆ ResetModifiers() void CSpliced_seg_Base::ResetModifiers ( void ) ◆ ResetNumseg() [1/3] void CDense_seg_Base::ResetNumseg ( void ) inline ◆ ResetNumseg() [2/3] void CPacked_seg_Base::ResetNumseg ( void ) inline ◆ ResetNumseg() [3/3] void CSparse_align_Base::ResetNumseg ( void ) inline ◆ ResetPartial() void CSpliced_exon_Base::ResetPartial ( void ) inline ◆ ResetParts() void CSpliced_exon_Base::ResetParts ( void ) ◆ ResetPoly_a() void CSpliced_seg_Base::ResetPoly_a ( void ) inline ◆ ResetPresent() void CPacked_seg_Base::ResetPresent ( void ) ◆ ResetProduct_end() void CSpliced_exon_Base::ResetProduct_end ( void ) ◆ ResetProduct_id() [1/2] void CSpliced_exon_Base::ResetProduct_id ( void ) ◆ ResetProduct_id() [2/2] ◆ ResetProduct_length() void CSpliced_seg_Base::ResetProduct_length ( void ) inline ◆ ResetProduct_start() void CSpliced_exon_Base::ResetProduct_start ( void ) ◆ ResetProduct_strand() [1/2] void CSpliced_exon_Base::ResetProduct_strand ( void ) inline ◆ ResetProduct_strand() [2/2] void CSpliced_seg_Base::ResetProduct_strand ( void ) inline ◆ ResetProduct_type() void CSpliced_seg_Base::ResetProduct_type ( void ) inline ◆ ResetRow_scores() void CSparse_seg_Base::ResetRow_scores ( void ) ◆ ResetRows() void CSparse_seg_Base::ResetRows ( void ) ◆ ResetScore() void CSeq_align_Base::ResetScore ( void ) ◆ ResetScores() [1/5] void CDense_diag_Base::ResetScores ( void ) ◆ ResetScores() [2/5] void CDense_seg_Base::ResetScores ( void ) ◆ ResetScores() [3/5] void CPacked_seg_Base::ResetScores ( void ) ◆ ResetScores() [4/5] void CSpliced_exon_Base::ResetScores ( void ) ◆ ResetScores() [5/5] void CStd_seg_Base::ResetScores ( void ) ◆ ResetSecond_id() void CSparse_align_Base::ResetSecond_id ( void ) ◆ ResetSecond_starts() void CSparse_align_Base::ResetSecond_starts ( void ) ◆ ResetSecond_strands() void CSparse_align_Base::ResetSecond_strands ( void ) ◆ ResetSeg_scores() void CSparse_align_Base::ResetSeg_scores ( void ) ◆ ResetSegs() void CSeq_align_Base::ResetSegs ( void ) ◆ ResetSelection() [1/5] void CProduct_pos_Base::ResetSelection ( void ) virtual ◆ ResetSelection() [2/5] void CScore_Base::C_Value::ResetSelection ( void ) ◆ ResetSelection() [3/5] void CSeq_align_Base::C_Segs::ResetSelection ( void ) ◆ ResetSelection() [4/5] void CSpliced_exon_chunk_Base::ResetSelection ( void ) virtual ◆ ResetSelection() [5/5] void CSpliced_seg_modifier_Base::ResetSelection ( void ) virtual ◆ ResetStarts() [1/3] void CDense_diag_Base::ResetStarts ( void ) ◆ ResetStarts() [2/3] void CDense_seg_Base::ResetStarts ( void )

Reset Starts data member.

Definition at line 58 of file Dense_seg_.cpp.

References CDense_seg_Base::m_set_State, and CDense_seg_Base::m_Starts.

◆ ResetStarts() [3/3] void CPacked_seg_Base::ResetStarts ( void ) ◆ ResetStrands() [1/3] void CDense_diag_Base::ResetStrands ( void ) ◆ ResetStrands() [2/3] void CDense_seg_Base::ResetStrands ( void ) ◆ ResetStrands() [3/3] void CPacked_seg_Base::ResetStrands ( void ) ◆ ResetType() void CSeq_align_Base::ResetType ( void ) inline ◆ ResetValue() void CScore_Base::ResetValue ( void ) ◆ Select() [1/10]