NCBI C++ ToolKit
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typedef CSeq_point CSeq_bond_Base::TA |
Definition at line 86 of file Seq_bond_.hpp.
typedef string CTextseq_id_Base::TAccession |
Definition at line 86 of file Textseq_id_.hpp.
typedef CSeq_point CSeq_bond_Base::TB |
Definition at line 87 of file Seq_bond_.hpp.
typedef CSeq_bond CSeq_loc_Base::TBond |
Definition at line 171 of file Seq_loc_.hpp.
typedef int CPDB_seq_id_Base::TChain |
Definition at line 92 of file PDB_seq_id_.hpp.
typedef string CPDB_seq_id_Base::TChain_id |
Definition at line 94 of file PDB_seq_id_.hpp.
typedef CId_pat CPatent_seq_id_Base::TCit |
Definition at line 86 of file Patent_seq_id_.hpp.
typedef list< CRef< CSeq_interval > > CPacked_seqint_Base::Tdata |
Definition at line 89 of file Packed_seqint_.hpp.
typedef list< CRef< CSeq_id > > CSeq_id_set_Base::Tdata |
Definition at line 89 of file Seq_id_set_.hpp.
typedef list< CRef< CSeq_loc > > CSeq_loc_equiv_Base::Tdata |
Definition at line 90 of file Seq_loc_equiv_.hpp.
typedef list< CRef< CSeq_loc > > CSeq_loc_mix_Base::Tdata |
Definition at line 90 of file Seq_loc_mix_.hpp.
typedef string CGiimport_id_Base::TDb |
Definition at line 86 of file Giimport_id_.hpp.
typedef CTextseq_id CSeq_id_Base::TDdbj |
Definition at line 181 of file Seq_id_.hpp.
typedef CTextseq_id CSeq_id_Base::TEmbl |
Definition at line 174 of file Seq_id_.hpp.
typedef CSeq_id CSeq_loc_Base::TEmpty |
Definition at line 163 of file Seq_loc_.hpp.
typedef CSeq_loc_equiv CSeq_loc_Base::TEquiv |
Definition at line 170 of file Seq_loc_.hpp.
typedef CFeat_id CSeq_loc_Base::TFeat |
Definition at line 172 of file Seq_loc_.hpp.
typedef TSeqPos CSeq_interval_Base::TFrom |
Definition at line 90 of file Seq_interval_.hpp.
typedef CInt_fuzz CPacked_seqpnt_Base::TFuzz |
Definition at line 93 of file Packed_seqpnt_.hpp.
typedef CInt_fuzz CSeq_point_Base::TFuzz |
Definition at line 93 of file Seq_point_.hpp.
Definition at line 94 of file Seq_interval_.hpp.
Definition at line 95 of file Seq_interval_.hpp.
typedef CTextseq_id CSeq_id_Base::TGenbank |
Definition at line 173 of file Seq_id_.hpp.
typedef CDbtag CSeq_id_Base::TGeneral |
Definition at line 179 of file Seq_id_.hpp.
typedef NCBI_NS_NCBI::TGi CSeq_id_Base::TGi |
Definition at line 180 of file Seq_id_.hpp.
typedef int CSeq_id_Base::TGibbmt |
Definition at line 171 of file Seq_id_.hpp.
typedef int CSeq_id_Base::TGibbsq |
Definition at line 170 of file Seq_id_.hpp.
typedef CGiimport_id CSeq_id_Base::TGiim |
Definition at line 172 of file Seq_id_.hpp.
typedef CTextseq_id CSeq_id_Base::TGpipe |
Definition at line 187 of file Seq_id_.hpp.
typedef int CGiimport_id_Base::TId |
Definition at line 85 of file Giimport_id_.hpp.
typedef CSeq_id CPacked_seqpnt_Base::TId |
Definition at line 92 of file Packed_seqpnt_.hpp.
typedef CSeq_id CSeq_interval_Base::TId |
Definition at line 93 of file Seq_interval_.hpp.
typedef CSeq_id CSeq_point_Base::TId |
Definition at line 92 of file Seq_point_.hpp.
typedef CSeq_interval CSeq_loc_Base::TInt |
Definition at line 165 of file Seq_loc_.hpp.
typedef CObject_id CSeq_id_Base::TLocal |
Definition at line 169 of file Seq_id_.hpp.
Definition at line 96 of file Giimport_id_.hpp.
Definition at line 104 of file Packed_seqpnt_.hpp.
Definition at line 94 of file Patent_seq_id_.hpp.
Definition at line 104 of file PDB_seq_id_.hpp.
Definition at line 95 of file Seq_bond_.hpp.
Definition at line 107 of file Seq_interval_.hpp.
Definition at line 103 of file Seq_point_.hpp.
Definition at line 98 of file Textseq_id_.hpp.
typedef CSeq_loc_mix CSeq_loc_Base::TMix |
Definition at line 169 of file Seq_loc_.hpp.
typedef CPDB_mol_id CPDB_seq_id_Base::TMol |
Definition at line 91 of file PDB_seq_id_.hpp.
typedef string CTextseq_id_Base::TName |
Definition at line 85 of file Textseq_id_.hpp.
Definition at line 188 of file Seq_id_.hpp.
typedef CTextseq_id CSeq_id_Base::TOther |
Definition at line 178 of file Seq_id_.hpp.
Definition at line 166 of file Seq_loc_.hpp.
Definition at line 168 of file Seq_loc_.hpp.
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Definition at line 67 of file Giimport_id.hpp.
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Definition at line 74 of file Giimport_id_.hpp.
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Definition at line 78 of file Packed_seqint_.hpp.
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Definition at line 80 of file Packed_seqpnt_.hpp.
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Definition at line 74 of file Patent_seq_id_.hpp.
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Definition at line 67 of file PDB_mol_id.hpp.
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Definition at line 76 of file PDB_mol_id_.hpp.
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Definition at line 80 of file PDB_seq_id_.hpp.
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Definition at line 75 of file Seq_bond_.hpp.
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Definition at line 81 of file Seq_id_.hpp.
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Definition at line 67 of file Seq_id_set.hpp.
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Definition at line 78 of file Seq_id_set_.hpp.
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Definition at line 79 of file Seq_interval_.hpp.
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Definition at line 84 of file Seq_loc_.hpp.
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Definition at line 79 of file Seq_loc_equiv_.hpp.
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Definition at line 79 of file Seq_loc_mix_.hpp.
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Definition at line 79 of file Seq_point_.hpp.
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Definition at line 74 of file Textseq_id_.hpp.
typedef CPatent_seq_id CSeq_id_Base::TPatent |
Definition at line 177 of file Seq_id_.hpp.
typedef CPDB_seq_id CSeq_id_Base::TPdb |
Definition at line 183 of file Seq_id_.hpp.
typedef CTextseq_id CSeq_id_Base::TPir |
Definition at line 175 of file Seq_id_.hpp.
typedef CSeq_point CSeq_loc_Base::TPnt |
Definition at line 167 of file Seq_loc_.hpp.
typedef TSeqPos CSeq_point_Base::TPoint |
Definition at line 90 of file Seq_point_.hpp.
typedef vector< TSeqPos > CPacked_seqpnt_Base::TPoints |
Definition at line 94 of file Packed_seqpnt_.hpp.
typedef CTextseq_id CSeq_id_Base::TPrf |
Definition at line 182 of file Seq_id_.hpp.
typedef CDate CPDB_seq_id_Base::TRel |
Definition at line 93 of file PDB_seq_id_.hpp.
typedef string CGiimport_id_Base::TRelease |
Definition at line 87 of file Giimport_id_.hpp.
typedef string CTextseq_id_Base::TRelease |
Definition at line 87 of file Textseq_id_.hpp.
typedef int CPatent_seq_id_Base::TSeqid |
Definition at line 85 of file Patent_seq_id_.hpp.
Definition at line 91 of file Packed_seqpnt_.hpp.
Definition at line 92 of file Seq_interval_.hpp.
typedef ENa_strand CSeq_point_Base::TStrand |
Definition at line 91 of file Seq_point_.hpp.
typedef CTextseq_id CSeq_id_Base::TSwissprot |
Definition at line 176 of file Seq_id_.hpp.
typedef TSeqPos CSeq_interval_Base::TTo |
Definition at line 91 of file Seq_interval_.hpp.
typedef CTextseq_id CSeq_id_Base::TTpd |
Definition at line 186 of file Seq_id_.hpp.
typedef CTextseq_id CSeq_id_Base::TTpe |
Definition at line 185 of file Seq_id_.hpp.
typedef CTextseq_id CSeq_id_Base::TTpg |
Definition at line 184 of file Seq_id_.hpp.
typedef int CTextseq_id_Base::TVersion |
Definition at line 88 of file Textseq_id_.hpp.
typedef CSeq_id CSeq_loc_Base::TWhole |
Definition at line 164 of file Seq_loc_.hpp.
Choice variants.
Definition at line 93 of file Seq_id_.hpp.
Choice variants.
Definition at line 96 of file Seq_loc_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Named_annot_track+1 |
Definition at line 117 of file Seq_id_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Feat+1 |
Definition at line 111 of file Seq_loc_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_id | |
e_db | |
e_release |
Definition at line 90 of file Giimport_id_.hpp.
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Enumerator | |
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e__allMandatory | |
e_strand | |
e_id | |
e_fuzz | |
e_points |
Definition at line 97 of file Packed_seqpnt_.hpp.
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Enumerator | |
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e__allMandatory | |
e_seqid | |
e_cit |
Definition at line 89 of file Patent_seq_id_.hpp.
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Enumerator | |
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e__allMandatory | |
e_mol | |
e_chain | |
e_rel | |
e_chain_id |
Definition at line 97 of file PDB_seq_id_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_a | |
e_b |
Definition at line 90 of file Seq_bond_.hpp.
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Enumerator | |
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e__allMandatory | |
e_from | |
e_to | |
e_strand | |
e_id | |
e_fuzz_from | |
e_fuzz_to |
Definition at line 98 of file Seq_interval_.hpp.
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Enumerator | |
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e__allMandatory | |
e_point | |
e_strand | |
e_id | |
e_fuzz |
Definition at line 96 of file Seq_point_.hpp.
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Enumerator | |
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e__allMandatory | |
e_name | |
e_accession | |
e_release | |
e_version |
Definition at line 91 of file Textseq_id_.hpp.
enum ENa_strand |
strand of nucleic acid
Access to ENa_strand's attributes (values, names) as defined in spec.
Enumerator | |
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eNa_strand_unknown | |
eNa_strand_plus | |
eNa_strand_minus | |
eNa_strand_both | in forward orientation |
eNa_strand_both_rev | in reverse orientation |
eNa_strand_other |
Definition at line 64 of file Na_strand_.hpp.
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Check if it is safe to call Get method.
Definition at line 158 of file Packed_seqint_.hpp.
Referenced by CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGtfWriter::xWriteFeatureExons(), CGff3Writer::xWriteFeatureRecords(), CGff3Writer::xWriteFeatureRna(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
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Check if it is safe to call Get method.
Definition at line 158 of file Seq_id_set_.hpp.
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Check if it is safe to call Get method.
Definition at line 159 of file Seq_loc_equiv_.hpp.
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Check if it is safe to call Get method.
Definition at line 159 of file Seq_loc_mix_.hpp.
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Check if it is safe to call GetA method.
Definition at line 207 of file Seq_bond_.hpp.
Referenced by FTASeqLocCheck(), s_AddSeqBondString(), CFlatSeqLoc::x_Add(), and CSeq_loc::x_CheckId().
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Check if it is safe to call GetAccession method.
Definition at line 334 of file Textseq_id_.hpp.
References CTextseq_id_Base::IsSetAccession().
Referenced by CGffRecord::AssignSeqId(), CSeq_id::ComposeOSLT(), extractBioseqInfo(), FTASeqLocCheck(), GetAccAndVersion(), CTextseq_id_Base::GetAccession(), GetAccessionAndDatabaseSource(), SeqDB_SimplifySeqid(), CSeqDBVol::x_CheckVersions(), CVectorScreen::x_FindAccession(), CDBSourceItem::x_FormatDBSourceID(), CBioseqContext::x_SetId(), and CSingleFeatValidator::x_ValidateSeqFeatProduct().
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Check if it is safe to call GetB method.
Definition at line 237 of file Seq_bond_.hpp.
References CSeq_bond_Base::IsSetB().
Referenced by CSeq_bond_Base::GetB(), GetReverseComplement(), s_AddSeqBondString(), SeqLocPrintUseBestID(), CFlatSeqLoc::x_Add(), and CSeq_loc::x_CheckId().
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Check if it is safe to call GetChain method.
Definition at line 335 of file PDB_seq_id_.hpp.
Referenced by CGencollIdMapper::x_FixImperfectId().
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Check if it is safe to call GetChain_id method.
Definition at line 406 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::IsSetChain_id().
Referenced by CPDB_seq_id_Base::GetChain_id().
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Check if it is safe to call GetCit method.
Definition at line 253 of file Patent_seq_id_.hpp.
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Check if it is safe to call GetDb method.
Definition at line 296 of file Giimport_id_.hpp.
References CGiimport_id_Base::IsSetDb().
Referenced by GetAccessionAndDatabaseSource(), and CGiimport_id_Base::GetDb().
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Check if it is safe to call GetFrom method.
Definition at line 370 of file Seq_interval_.hpp.
References CSeq_interval_Base::IsSetFrom().
Referenced by CSeq_interval_Base::GetFrom(), s_SeqIntervalDelete(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CGffFeatureRecord::SetLocation(), SplitLocationForGap(), CNewCleanup_imp::x_SeqIntervalBC(), and CVectorTrimPanel::x_SeqIntervalDelete().
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Check if it is safe to call GetFuzz method.
Definition at line 361 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::IsSetFuzz().
Referenced by CPacked_seqpnt_Base::GetFuzz(), and CFlatSeqLoc::x_Add().
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Check if it is safe to call GetFuzz method.
Definition at line 414 of file Seq_point_.hpp.
References CSeq_point_Base::IsSetFuzz().
Referenced by CSeq_point_Base::GetFuzz(), CSGFeatureJob::x_CalcIntervals(), CFeatGlyph::x_DrawFeatureBar(), and CFeatGlyph::x_DrawRSites().
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Check if it is safe to call GetFuzz_from method.
Definition at line 541 of file Seq_interval_.hpp.
References CSeq_interval_Base::IsSetFuzz_from().
Referenced by CSeq_interval_Base::GetFuzz_from(), PrintSeqIntUseBestID(), and s_FixIntervalProtToCds().
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Check if it is safe to call GetFuzz_to method.
Definition at line 562 of file Seq_interval_.hpp.
References CSeq_interval_Base::IsSetFuzz_to().
Referenced by CSeq_interval_Base::GetFuzz_to(), PrintSeqIntUseBestID(), and s_FixIntervalProtToCds().
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Check if it is safe to call GetId method.
Definition at line 249 of file Giimport_id_.hpp.
References CGiimport_id_Base::IsSetId().
Referenced by CGiimport_id_Base::GetId().
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Check if it is safe to call GetId method.
Definition at line 331 of file Packed_seqpnt_.hpp.
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Check if it is safe to call GetId method.
Definition at line 511 of file Seq_interval_.hpp.
Referenced by CBedFeatureRecord::AssignLocation().
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Check if it is safe to call GetId method.
Definition at line 384 of file Seq_point_.hpp.
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Check if it is safe to call GetMol method.
Definition at line 300 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::IsSetMol().
Referenced by CPDB_seq_id_Base::GetMol(), CWriteDB_IsamIndex::x_AddPdb(), and CGencollIdMapper::x_FixImperfectId().
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Check if it is safe to call GetName method.
Definition at line 287 of file Textseq_id_.hpp.
References CTextseq_id_Base::IsSetName().
Referenced by CSeq_id::ComposeOSLT(), GetAccessionAndDatabaseSource(), CTextseq_id_Base::GetName(), s_GetNameForBioseq(), SeqDB_SimplifySeqid(), CDBSourceItem::x_FormatDBSourceID(), CBioseqContext::x_SetId(), and CSingleFeatValidator::x_ValidateSeqFeatProduct().
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Check if it is safe to call GetPoint method.
Definition at line 290 of file Seq_point_.hpp.
References CSeq_point_Base::IsSetPoint().
Referenced by CSeq_point_Base::GetPoint(), CFlatSeqLoc::x_Add(), and CFeatGlyph::x_DrawRSites().
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Check if it is safe to call GetPoints method.
Definition at line 382 of file Packed_seqpnt_.hpp.
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Check if it is safe to call GetRel method.
Definition at line 385 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::IsSetRel().
Referenced by CPDB_seq_id_Base::GetRel(), and CDBSourceItem::x_FormatDBSourceID().
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Check if it is safe to call GetRelease method.
Definition at line 343 of file Giimport_id_.hpp.
References CGiimport_id_Base::IsSetRelease().
Referenced by CGiimport_id_Base::GetRelease().
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Check if it is safe to call GetRelease method.
Definition at line 381 of file Textseq_id_.hpp.
References CTextseq_id_Base::IsSetRelease().
Referenced by CTextseq_id_Base::GetRelease().
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Check if it is safe to call GetSeqid method.
Definition at line 206 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::IsSetSeqid().
Referenced by CPatent_seq_id_Base::GetSeqid().
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Check if it is safe to call GetStrand method.
Definition at line 284 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::IsSetStrand().
Referenced by CPacked_seqpnt_Base::GetStrand(), and s_AddSeqPackedPointString().
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Check if it is safe to call GetStrand method.
Definition at line 464 of file Seq_interval_.hpp.
References CSeq_interval_Base::IsSetStrand().
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_align::CreateDensegFromStdseg(), CReadBlastApp::getFromTo(), CEditingActionFeatAnticodon::GetIntervalString(), GetIntervalString(), CSeq_interval_Base::GetStrand(), PrintSeqIntUseBestID(), TMaskedQueryRegions::RestrictToSeqInt(), s_AddSeqIntString(), s_FixIntervalProtToCds(), CNewCleanup_imp::x_BothStrandBC(), CLocusItem::x_SetTopology(), CBlastFilterTest::x_TestLowerCaseMaskWith(), and CGff2Record::xUpdateFeatureData().
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Check if it is safe to call GetStrand method.
Definition at line 337 of file Seq_point_.hpp.
References CSeq_point_Base::IsSetStrand().
Referenced by CSeq_point_Base::GetStrand(), s_AddSeqPointString(), s_SeqPntRevCmp(), CNewCleanup_imp::x_BothStrandBC(), and CFeatGlyph::x_DrawRSites().
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Check if it is safe to call GetTo method.
Definition at line 417 of file Seq_interval_.hpp.
References CSeq_interval_Base::IsSetTo().
Referenced by GetRetranslateCDSCommand(), CSeq_interval_Base::GetTo(), RetranslateCdregion(), RetranslateCDS(), CRetranslateCDS::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), s_SeqIntervalDelete(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CGffFeatureRecord::SetLocation(), SplitLocationForGap(), CVectorTrimPanel::x_RetranslateCDS(), CNewCleanup_imp::x_SeqIntervalBC(), and CVectorTrimPanel::x_SeqIntervalDelete().
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Check if it is safe to call GetVersion method.
Definition at line 428 of file Textseq_id_.hpp.
References CTextseq_id_Base::IsSetVersion().
Referenced by CGffRecord::AssignSeqId(), extractBioseqInfo(), GetAccAndVersion(), CPSGS_AsyncResolveBase::GetEffectiveVersion(), CTextseq_id_Base::GetVersion(), s_Fingerprint_Textseq_id(), SeqDB_SimplifySeqid(), CSeqDBVol::x_CheckVersions(), CDBSourceItem::x_FormatDBSourceID(), and CGencollIdMapper::x_Init().
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Definition at line 86 of file Giimport_id.hpp.
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END_CLASS_INFO CGiimport_id_Base::CGiimport_id_Base | ( | void | ) |
Definition at line 82 of file Giimport_id_.cpp.
References CGiimport_id_Base::m_set_State.
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 752 of file Seq_id_.hpp.
References CSeq_id_Base::m_choice, and CSeq_id_Base::ThrowInvalidSelection().
Referenced by CSeq_id_Base::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CSeq_id_Base::GetGpipe(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), and CSeq_id_Base::GetTpg().
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 481 of file Seq_loc_.hpp.
References CSeq_loc_Base::m_choice, and CSeq_loc_Base::ThrowInvalidSelection().
Referenced by CSeq_loc_Base::GetBond(), CSeq_loc_Base::GetEmpty(), CSeq_loc_Base::GetEquiv(), CSeq_loc_Base::GetFeat(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), and CSeq_loc_Base::GetWhole().
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END_CLASS_INFO CPacked_seqint_Base::CPacked_seqint_Base | ( | void | ) |
Definition at line 68 of file Packed_seqint_.cpp.
References CPacked_seqint_Base::m_set_State.
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END_CLASS_INFO CPacked_seqpnt_Base::CPacked_seqpnt_Base | ( | void | ) |
Definition at line 111 of file Packed_seqpnt_.cpp.
References CObject::IsAllocatedInPool(), CPacked_seqpnt_Base::m_set_State, and CPacked_seqpnt_Base::ResetId().
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END_CLASS_INFO CPatent_seq_id_Base::CPatent_seq_id_Base | ( | void | ) |
Definition at line 83 of file Patent_seq_id_.cpp.
References CObject::IsAllocatedInPool(), CPatent_seq_id_Base::m_set_State, and CPatent_seq_id_Base::ResetCit().
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Explicit constructor from the primitive type.
Definition at line 72 of file PDB_mol_id.hpp.
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Definition at line 69 of file PDB_mol_id.hpp.
Definition at line 102 of file PDB_mol_id_.hpp.
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Definition at line 97 of file PDB_mol_id_.hpp.
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END_CLASS_INFO CPDB_seq_id_Base::CPDB_seq_id_Base | ( | void | ) |
Definition at line 102 of file PDB_seq_id_.cpp.
References CPDB_seq_id_Base::m_set_State.
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END_CLASS_INFO CSeq_bond_Base::CSeq_bond_Base | ( | void | ) |
Definition at line 100 of file Seq_bond_.cpp.
References CObject::IsAllocatedInPool(), CSeq_bond_Base::m_set_State, and CSeq_bond_Base::ResetA().
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END_CHOICE_INFO CSeq_id_Base::CSeq_id_Base | ( | void | ) |
Definition at line 599 of file Seq_id_.cpp.
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Definition at line 86 of file Seq_id_set.hpp.
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END_CLASS_INFO CSeq_id_set_Base::CSeq_id_set_Base | ( | void | ) |
Definition at line 68 of file Seq_id_set_.cpp.
References CSeq_id_set_Base::m_set_State.
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END_CLASS_INFO CSeq_interval_Base::CSeq_interval_Base | ( | void | ) |
Definition at line 126 of file Seq_interval_.cpp.
References CObject::IsAllocatedInPool(), CSeq_interval_Base::m_set_State, and CSeq_interval_Base::ResetId().
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END_CHOICE_INFO CSeq_loc_Base::CSeq_loc_Base | ( | void | ) |
Definition at line 393 of file Seq_loc_.cpp.
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END_CLASS_INFO CSeq_loc_equiv_Base::CSeq_loc_equiv_Base | ( | void | ) |
Definition at line 68 of file Seq_loc_equiv_.cpp.
References CSeq_loc_equiv_Base::m_set_State.
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END_CLASS_INFO CSeq_loc_mix_Base::CSeq_loc_mix_Base | ( | void | ) |
Definition at line 68 of file Seq_loc_mix_.cpp.
References CSeq_loc_mix_Base::m_set_State.
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END_CLASS_INFO CSeq_point_Base::CSeq_point_Base | ( | void | ) |
Definition at line 105 of file Seq_point_.cpp.
References CObject::IsAllocatedInPool(), CSeq_point_Base::m_set_State, and CSeq_point_Base::ResetId().
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END_CLASS_INFO CTextseq_id_Base::CTextseq_id_Base | ( | void | ) |
Definition at line 90 of file Textseq_id_.cpp.
References CTextseq_id_Base::m_set_State.
CGiimport_id_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CPacked_seqint_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CPacked_seqpnt_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CPatent_seq_id_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CPDB_seq_id_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_bond_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_id_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_id_set_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_interval_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_loc_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_loc_equiv_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_loc_mix_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_point_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CTextseq_id_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CPDB_mol_id_Base::DECLARE_STD_ALIAS_TYPE_INFO | ( | ) |
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Definition at line 90 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id_Base::m_choice, CSeq_id_Base::m_Gi, CSeq_id_Base::m_Gibbmt, CSeq_id_Base::m_Gibbsq, and CSeq_id_Base::m_object.
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Definition at line 86 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_Base::m_choice, and CSeq_loc_Base::m_object.
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Get the member data.
Definition at line 164 of file Packed_seqint_.hpp.
References CPacked_seqint_Base::m_data.
Referenced by CPacked_seqint::AddIntervals(), NTweakExon::AsString(), BOOST_AUTO_TEST_CASE(), Canonicalize(), NTweakExon::CheckIdAndStrand(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSequenceSearchForm::ConstructQuery(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CorrectIntervalOrder(), CSeqUtils::CreateSeq_loc(), CSeqUtils::GetCdsMappingInfoFromRna(), IBISInteraction::GetFootprint(), CReadBlastApp::getFromTo(), IBISInteraction::GetGi(), CPacked_seqint::GetLength(), CRemoteBlast::GetMasks(), GetPositionsForAlignAnnot(), GetReverseComplement(), CPacked_seqint::GetStart(), CPacked_seqint::GetStartInt(), CPacked_seqint::GetStop(), CPacked_seqint::GetStopInt(), CPacked_seqint::GetStrand(), CWriteUtil::GetTranssplicedEndpoints(), CPacked_seqint::IsPartialStart(), CPacked_seqint::IsPartialStop(), CPacked_seqint::IsSetStrand(), CPacked_seqint::IsTruncatedStart(), CPacked_seqint::IsTruncatedStop(), CFastaObjectLoader::LoadFromStream(), CGtfLocationMerger::MergeLocationForGene(), CSeqUtils::MixLocToLoc(), NormalizeLoc(), PreserveTerminalCodons(), s_AddLocString(), s_CountIntervals(), s_CreateBlastMask(), s_Fingerprint_Packed_seqint(), s_FlattenLoc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), s_Load_Packed_seqint(), s_LocationToStartStopPairs(), s_SeqLoc2MaskedSubjRanges(), SeqLocAdjustForTrim(), SeqLocPartialCheck(), SeqLocPrintUseBestID(), CBedImportData::Serialize(), CCleanup::SetCodeBreakLocation(), CPacked_seqint::SetPartialStart(), CPacked_seqint::SetPartialStop(), SplitLocationForGap(), NTweakExon::Validate(), CUCSCRegionWriter::WriteAnnot(), CSeqMap::x_Add(), CFlatSeqLoc::x_Add(), x_Assign(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CValidError_imp::x_CheckPackedInt(), x_CompareConsecutiveIntervals(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CValidError_imp::x_ReportInvalidFuzz(), CBioseq::x_SeqLoc_To_DeltaExt(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGtfWriter::xWriteFeatureExons(), CGff3Writer::xWriteFeatureRecords(), CGff3Writer::xWriteFeatureRna(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
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Get the member data.
Definition at line 164 of file Seq_id_set_.hpp.
References CSeq_id_set_Base::m_data.
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Get the member data.
Definition at line 165 of file Seq_loc_equiv_.hpp.
References CSeq_loc_equiv_Base::m_data.
Referenced by CSeq_loc_equiv::Add(), CHandleRangeMap::AddLocation(), CSeq_loc_Conversion::ConvertEquiv(), CSeq_loc_Conversion_Set::ConvertEquiv(), GetReverseComplement(), NormalizeLoc(), s_Fingerprint_Seq_loc_equiv(), s_GetLabel(), SeqLocPrintUseBestID(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), x_Assign(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_CI_Impl::x_ProcessLocation().
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Get the member data.
Definition at line 165 of file Seq_loc_mix_.hpp.
References CSeq_loc_mix_Base::m_data.
Referenced by CHandleRangeMap::AddLocation(), CSeq_loc_mix::AddSeqLoc(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CWriteUtil::ChangeToPackedInt(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_loc_mix::GetFirstLoc(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), CSeq_loc_mix::GetLastLoc(), GetLength(), GetReverseComplement(), GetSeqLocation(), CSeq_loc_mix::GetStart(), CSeq_loc_mix::GetStop(), CSeq_loc_mix::GetStrand(), CGuiObjectInfoPrimer::GetToolTip(), CEditingActionFeatAnticodon::GetValue(), CLocationEditPolicy::HasNulls(), CLocationPanel::Init(), CWriteUtil::IsLocationOrdered(), CFeaturePropagator::IsOrdered(), CSeq_loc_mix::IsPartialStart(), CSeq_loc_mix::IsPartialStop(), CSeq_loc_mix::IsSetStrand(), CSeq_loc_mix::IsTruncatedStart(), CSeq_loc_mix::IsTruncatedStop(), CSeq_loc_Conversion::MakeDstMix(), CSeq_loc_CI_Impl::MakeLoc(), CFeaturePropagator::MakeOrdered(), NormalizeLoc(), SRelLoc::Resolve(), s_AddLocString(), s_CalcCoverageCount(), s_CountIntervals(), s_Fingerprint_Seq_loc_mix(), s_FlattenLoc(), s_GetCodeBreak(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), s_IsOrdered(), s_NeedsFlattening(), s_NormalizeNullsBetween(), s_SeqLoc2MaskedSubjRanges(), SeqLocPrintUseBestID(), CLocationPanel::TransferDataToWindow(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), x_Assign(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSGFeatureJob::x_CreateCloneFeature(), CFeatureTableReader_Imp::x_FinishFeature(), CFeatureTableReader_Imp::x_GetPointStrand(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CGFFReader::x_ResolveLoc(), CBioseq::x_SeqLoc_To_DeltaExt(), and CCDSTranslationPanel::x_SetLocationForProtein().
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Get the A member data.
Definition at line 213 of file Seq_bond_.hpp.
References CSeq_bond_Base::m_A, and CSeq_bond_Base::ResetA().
Referenced by CHandleRangeMap::AddLocation(), CWriteUtil::ChangeToPackedInt(), CSeq_loc_Conversion::ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), fta_seqloc_del_far(), GetReverseComplement(), CSeq_bond::GetStart(), CSeq_bond::GetStop(), CSeq_bond::GetStrand(), CSeq_bond::IsSetStrand(), s_AddSeqBondString(), s_Fingerprint_Seq_bond(), s_GetLabel(), s_GetStrand(), SeqLocPrintUseBestID(), CFlatSeqLoc::x_Add(), x_Assign(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_CI_Impl::x_ProcessLocation().
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Get the Accession member data.
Definition at line 340 of file Textseq_id_.hpp.
References CTextseq_id_Base::CanGetAccession(), CTextseq_id_Base::m_Accession, and CSerialObject::ThrowUnassigned().
Referenced by AllowOrphanedProtein(), CTextseq_id::AsFastaString(), CSeq_id_Descr::Assign(), CGffRecord::AssignSeqId(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CAlnMix::ChooseSeqId(), CTextseq_id::Compare(), CSeq_id::ComposeOSLT(), CpSeqId(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), extractBioseqInfo(), CSeq_id_Textseq_Tree::FindInfo(), CSeq_id_Textseq_Tree::FindMatch(), CSeq_id_Textseq_Tree::FindOrCreate(), CWGSFileInfo::FindProtAcc(), CSeq_id_Textseq_Tree::FindReverseMatch(), flat2asn_range_func(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), fta_fix_seq_id(), FTASeqLocCheck(), get_accession_from_id(), GetAccAndVersion(), GetAccessionAndDatabaseSource(), GetAccVer(), CDefaultSynonymMapper::GetBestSynonym(), GetDirectLabel(), CWGSDataLoader_Impl::GetFileInfoByAcc(), CWGSDataLoader_Impl::GetFileInfoByProtAcc(), GetLabel(), GetProtRefSeqId(), CVDBGraphDb_Impl::GetSeqInfo(), GetWGSMasterSeq_id(), CSeq_id::IdentifyAccession(), CValidError_bioseq::IsTSAAccession(), CValidError_bioseq::IsWGSAccession(), CValidError_bioseq::IsWp(), Make_SeqID_String(), CTextseq_id::Match(), CSeq_id_Textseq_Info::Pack(), CSeq_id_Textseq_PlainInfo::ParseCaseVariant(), CWGSResolver_Ids::ParseWGSPrefix(), s_AssignTextseq_id(), s_DeflineCompare(), s_Fingerprint_Textseq_id(), s_GetBestSynonym(), s_GetIdLabel(), s_GetModelEvidance(), s_ValidateAcc(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CValidError_imp::Setup(), StrippedAccVer(), CWGSFileInfo::SAccFileInfo::ValidateAcc(), CValidError_imp::ValidateBioSource(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseq::ValidateOrgContext(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqIds(), x_Assign(), CFeatureGenerator::SImplementation::x_CheckMatch(), CSeqDBVol::x_CheckVersions(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CGenbankGatherer::x_DoSingleSection(), CSeq_id_Textseq_Tree::x_Equals(), CVectorScreen::x_FindAccession(), CSeq_id_Textseq_Tree::x_FindStrInfo(), CGencollIdMapper::x_FixImperfectId(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), CGencollIdMapper::x_Init(), CTopLevelSeqEntryContext::x_InitSeqs(), CCdregionValidator::x_IsProductMisplaced(), CFlatGatherer::x_MergeEqualBioSources(), CDeflineGenerator::x_SetFlags(), CBioseqContext::x_SetId(), CLocusItem::x_SetName(), CFeatureGenerator::SImplementation::x_SetQualForGapFilledModel(), CValidError_bioseq::x_ShowBioProjectWarning(), CSeq_id_Textseq_Tree::x_Unindex(), and CFastaOstream::x_WriteAsFasta().
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Get the B member data.
Definition at line 243 of file Seq_bond_.hpp.
References CSeq_bond_Base::CanGetB(), CSeq_bond_Base::m_B, and CSerialObject::ThrowUnassigned().
Referenced by CHandleRangeMap::AddLocation(), CSeq_loc_Conversion::ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), GetReverseComplement(), CSeq_bond::GetStart(), CSeq_bond::GetStop(), CSeq_bond::GetStrand(), CSeq_bond::IsSetStrand(), s_AddSeqBondString(), s_GetLabel(), s_GetStrand(), SeqLocPrintUseBestID(), CFlatSeqLoc::x_Add(), x_Assign(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_CI_Impl::x_ProcessLocation().
const CSeq_loc_Base::TBond & CSeq_loc_Base::GetBond | ( | void | ) | const |
Get the variant data.
Definition at line 326 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Bond, and CSeq_loc_Base::m_object.
Referenced by CHandleRangeMap::AddLocation(), CSeq_loc::Assign(), CWriteUtil::ChangeToPackedInt(), CSeq_loc_Conversion::ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), fta_seqloc_del_far(), FTASeqLocCheck(), GetLength(), GetReverseComplement(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::IsSetStrand(), ReverseComplementLocation(), s_AddLocString(), s_Fingerprint_Seq_loc(), s_GetLabel(), s_GetStrand(), SeqLocPrintUseBestID(), CSeq_loc::SetId(), UpgradeSeqLocId(), CFlatSeqLoc::x_Add(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_CI_Impl::x_ProcessLocation().
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Get the Chain member data.
Definition at line 354 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_Chain.
Referenced by CPDB_seq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CheckSPDupPDBXrefs(), CSeq_id::ComposeOSLT(), CPDB_seq_id::GetEffectiveChain_id(), CPDB_seq_id::IsChainConflict(), Make_GI_or_PDB_String_CN3D(), Make_SeqID_String(), CPDB_seq_id::Match(), CSeq_id_PDB_Info::Normalize(), LessBySeqId::operator()(), s_Fingerprint_PDB_seq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CValidError_bioseq::ValidateSeqId(), x_Assign(), CGencollIdMapper::x_FixImperfectId(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), and CDeflineGenerator::x_SetFlags().
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Get the Chain_id member data.
Definition at line 412 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::CanGetChain_id(), CPDB_seq_id_Base::m_Chain_id, and CSerialObject::ThrowUnassigned().
Referenced by CPDB_seq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CPDB_seq_id::Compare(), CSeq_id::ComposeOSLT(), CPDB_seq_id::IsChainConflict(), CPDB_seq_id::Match(), CSeq_id_PDB_Info::Normalize(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CValidError_bioseq::ValidateSeqId(), x_Assign(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), and CDeflineGenerator::x_SetFlags().
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Get the Cit member data.
Definition at line 259 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::m_Cit, and CPatent_seq_id_Base::ResetCit().
Referenced by CPatent_seq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CPatent_seq_id::Compare(), CSeq_id::ComposeOSLT(), CSeq_id_Patent_Tree::FindOrCreate(), CPatent_seq_id::Match(), s_Fingerprint_Patent_seq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), x_Assign(), CSeq_id_Patent_Tree::x_FindInfo(), CDeflineGenerator::x_SetFlags(), and CSeq_id_Patent_Tree::x_Unindex().
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Get the Db member data.
Definition at line 302 of file Giimport_id_.hpp.
References CGiimport_id_Base::CanGetDb(), CGiimport_id_Base::m_Db, and CSerialObject::ThrowUnassigned().
Referenced by GetAccessionAndDatabaseSource(), SChildLess::operator()(), s_Fingerprint_Giimport_id(), and x_Assign().
const CSeq_id_Base::TDdbj & CSeq_id_Base::GetDdbj | ( | void | ) | const |
Get the variant data.
Definition at line 391 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Ddbj, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_AssignSeq_id(), s_Fingerprint_Seq_id(), CRemoveName::x_GetReplacementIds(), CAccessionToLocalId::x_GetReplacementIds(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TEmbl & CSeq_id_Base::GetEmbl | ( | void | ) | const |
Get the variant data.
Definition at line 259 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Embl, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_AssignSeq_id(), s_Fingerprint_Seq_id(), CRemoveName::x_GetReplacementIds(), CAccessionToLocalId::x_GetReplacementIds(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_loc_Base::TEmpty & CSeq_loc_Base::GetEmpty | ( | void | ) | const |
Get the variant data.
Definition at line 150 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Empty, and CSeq_loc_Base::m_object.
Referenced by CHandleRangeMap::AddLocation(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CSeq_loc_Conversion::GetId(), s_Fingerprint_Seq_loc(), s_GetLabel(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_CI_Impl::x_ProcessLocation().
const CSeq_loc_Base::TEquiv & CSeq_loc_Base::GetEquiv | ( | void | ) | const |
Get the variant data.
Definition at line 304 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Equiv, and CSeq_loc_Base::m_object.
Referenced by CSeq_loc_equiv::Add(), CHandleRangeMap::AddLocation(), CSeq_loc::Assign(), CSeq_loc_Conversion::ConvertEquiv(), CSeq_loc_Conversion_Set::ConvertEquiv(), GetReverseComplement(), NormalizeLoc(), s_Fingerprint_Seq_loc(), s_GetLabel(), SeqLocPrintUseBestID(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_CI_Impl::x_ProcessLocation().
const CSeq_loc_Base::TFeat & CSeq_loc_Base::GetFeat | ( | void | ) | const |
Get the variant data.
Definition at line 348 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Feat, and CSeq_loc_Base::m_object.
Referenced by CSeq_loc::Assign(), and s_Fingerprint_Seq_loc().
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Get the From member data.
Definition at line 383 of file Seq_interval_.hpp.
References CSeq_interval_Base::CanGetFrom(), CSeq_interval_Base::m_From, and CSerialObject::ThrowUnassigned().
Referenced by AgpRead(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), check_short_CDS(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_align::CreateDensegFromStdseg(), CRawWiggleRecord::Dump(), CBioseqEditor::EditSelection(), EndAdded(), CGBObjectLoader::Execute(), AlignmentCollection::FindSeqInterval(), variation::FindSSRLoc(), FixMixLoc(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), fta_get_acc_minmax_strand(), CReadBlastApp::getFromTo(), CSeq_interval::GetLength(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CStd_seg::GetSeqRange(), CSeq_interval::GetStart(), CSeq_interval::GetStop(), CWriteUtil::GetTranssplicedEndpoints(), CWriteUtil::GetTrnaAntiCodon(), IsLocFullLength(), IsNotDuplicateInterval(), IsValid(), CSeq_loc_Conversion::MakeDstMix(), CDDAnnotateDialog::NewOrEditMotif(), CStd_seg::OffsetRow(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), PrintSeqIntUseBestID(), CStd_seg::RemapToLoc(), TMaskedQueryRegions::RestrictToSeqInt(), RevComp(), ReverseComplementLocation(), CFeatTreeSampleApp::Run(), s_AddSeqIntString(), s_CheckInterval(), s_ExtendIntervalToEnd(), s_Fingerprint_Seq_interval(), s_FixIntervalProtToCds(), s_GetCodeBreak(), s_GetLabel(), s_GetSeq_intervalLabel(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_LocationToStartStopPairs(), s_LocToRange(), s_OOFBlastHSP2SeqAlign(), s_RemoveBogusFuzzFromIntervals_Helper(), s_SeqIntervalDelete(), s_SeqIntervalToSeqLocInfo(), s_SeqLoc2MaskedSubjRanges(), s_SubLocDeltaSeq(), s_SubsequentIntron(), sConvertIntToPoint(), CClippedScorer::ScoreAlignments(), SeqIntCheckCpp(), SeqIntPartialCheck(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CBedFeatureRecord::SetBlocks(), CGffFeatureRecord::SetLocation(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), SplitLocationForGap(), sx_AddBits(), CBlastTabular::sx_MineSegment(), TestOneCDS(), CdBlaster::truncateBioseq(), CAssemblyGapValidator::Validate(), NTweakExon::Validate(), CUCSCRegionWriter::WriteAnnot(), CSeqMap::x_Add(), CFeatureItem::x_AddQualsCdregionIdx(), CPhrap_Contig::x_AddReadLocFeats(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CMultiAligner::x_AlignFillerBlocks(), x_Assign(), CGvfWriteRecord::x_AssignAttributeStartRange(), CSeq_loc::x_CalculateTotalRangeCheckId(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CCdsGlyph::x_DrawProtSeqWithMapping(), CDisplaySeqalign::x_FillLocList(), CUnorderedSplitter::x_FixAlignment(), CFastaOstreamEx::x_GetCodeBreak(), CMultiAligner::x_GetSeqalign(), CAnnotTypes_CI::x_Init(), CGencollIdMapper::x_IsLoc_Int_InAGap(), x_IsNotAdjacent(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGFFReader::x_ParseAlignRecord(), CGC_Assembly_Parser::x_ParseGCSequence(), CSeq_loc_CI_Impl::x_ProcessInterval(), variation::CVariationUtil::x_Remap(), CValidError_imp::x_ReportInvalidFuzz(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CNewCleanup_imp::x_SeqIntervalBC(), CVectorTrimPanel::x_SeqIntervalDelete(), CLocusItem::x_SetTopology(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CBlastFilterTest::x_TestLowerCaseMaskWith(), CSingleFeatValidator::x_ValidateImpFeatLoc(), CGff3Writer::xAssignFeature(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), XGappedSeqLocsToDeltaSeqs(), CUCSCRegionReader::xParseFeatureUCSCFormat(), CGff3Reader::xVerifyExonLocation(), and CBedGraphWriter::xWriteSingleFeature().
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Get the Fuzz member data.
Definition at line 367 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::CanGetFuzz(), CPacked_seqpnt_Base::m_Fuzz, and CSerialObject::ThrowUnassigned().
Referenced by CSeq_loc_Conversion::ConvertPacked_pnt(), CPacked_seqpnt::IsPartialStart(), CPacked_seqpnt::IsPartialStop(), CPacked_seqpnt::IsTruncatedStart(), CPacked_seqpnt::IsTruncatedStop(), NormalizeLoc(), SeqLocPartialCheck(), CFlatSeqLoc::x_Add(), x_Assign(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), and CSeq_loc_CI_Impl::x_ProcessLocation().
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Get the Fuzz member data.
Definition at line 420 of file Seq_point_.hpp.
References CSeq_point_Base::CanGetFuzz(), CSeq_point_Base::m_Fuzz, and CSerialObject::ThrowUnassigned().
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), CSeq_loc_Conversion::ConvertPoint(), FixMixLoc(), GetLowHighFromSeqLoc(), CSeq_point::IsLeftOf(), CSeq_point::IsPartialStart(), CSeq_point::IsPartialStop(), variation::IsPureFuzzPoint(), CSeq_point::IsRightOf(), CSeq_point::IsTruncatedStart(), CSeq_point::IsTruncatedStop(), SSNP_Info::ParseSeq_feat(), s_GetLabel(), s_IsBetween(), s_Load_Seq_point(), s_PrintLocAsJavascriptArray(), SeqLocPartialCheck(), variation_ref::CHgvsParser::x_abs_pos(), variation::CHgvsParser::x_abs_pos(), CFlatSeqLoc::x_Add(), x_Assign(), CSGFeatureJob::x_CalcIntervals(), CFeatGlyph::x_DrawFeatureBar(), CFeatGlyph::x_DrawRSites(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessPoint(), CValidError_imp::x_ReportInvalidFuzz(), and CNewCleanup_imp::x_SeqPointBC().
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Get the Fuzz_from member data.
Definition at line 547 of file Seq_interval_.hpp.
References CSeq_interval_Base::CanGetFuzz_from(), CSeq_interval_Base::m_Fuzz_from, and CSerialObject::ThrowUnassigned().
Referenced by CSeq_loc_Conversion::ConvertInterval(), FixMixLoc(), GetLowHighFromSeqLoc(), CSeq_interval::IsPartialStart(), CSeq_interval::IsPartialStop(), CSeq_interval::IsTruncatedStart(), CSeq_interval::IsTruncatedStop(), PrintSeqIntUseBestID(), ReverseComplementLocation(), s_FixIntervalProtToCds(), s_GetLabel(), s_RemoveBogusFuzzFromIntervals_Helper(), SeqIntPartialCheck(), x_Assign(), CGvfWriteRecord::x_AssignAttributeStartRange(), CFeatGlyph::x_DrawFeatureBar_sv(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFeatGlyph::x_GetUndefinedBp_from(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessInterval(), and CValidError_imp::x_ReportInvalidFuzz().
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Get the Fuzz_to member data.
Definition at line 568 of file Seq_interval_.hpp.
References CSeq_interval_Base::CanGetFuzz_to(), CSeq_interval_Base::m_Fuzz_to, and CSerialObject::ThrowUnassigned().
Referenced by CSeq_loc_Conversion::ConvertInterval(), FixMixLoc(), GetLowHighFromSeqLoc(), CSeq_interval::IsPartialStart(), CSeq_interval::IsPartialStop(), CSeq_interval::IsTruncatedStart(), CSeq_interval::IsTruncatedStop(), PrintSeqIntUseBestID(), ReverseComplementLocation(), s_FixIntervalProtToCds(), s_GetLabel(), s_RemoveBogusFuzzFromIntervals_Helper(), SeqIntPartialCheck(), x_Assign(), CGvfWriteRecord::x_AssignAttributeEndRange(), CFeatGlyph::x_DrawFeatureBar_sv(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFeatGlyph::x_GetUndefinedBp_to(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessInterval(), and CValidError_imp::x_ReportInvalidFuzz().
const CSeq_id_Base::TGenbank & CSeq_id_Base::GetGenbank | ( | void | ) | const |
Get the variant data.
Definition at line 237 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Genbank, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_AssignSeq_id(), s_Fingerprint_Seq_id(), CRemoveName::x_GetReplacementIds(), CAccessionToLocalId::x_GetReplacementIds(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TGeneral & CSeq_id_Base::GetGeneral | ( | void | ) | const |
Get the variant data.
Definition at line 369 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_General, and CSeq_id_Base::m_object.
Referenced by CFeatGapInfo::AdjustProteinSeq(), CSeq_id::AdjustScore(), CSeq_id::Assign(), CSeq_id::BaseBlastScore(), CSeq_id::BaseFastaAAScore(), CSeq_id::BaseFastaNAScore(), BOOST_AUTO_TEST_CASE(), CReadDispatcher::CannotProcess(), CannotProcess(), CGeneralToLocalId::CGeneralToLocalId(), CLocalToGeneralId::CLocalToGeneralId(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), CGuiObjectInfoSeq_id::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractAccession(), ExtractGnomonModelNum(), CBlastDBExtractor::ExtractSeqId(), CSeq_id_General_Tree::FindMatch(), GetAccessionAndDatabaseSource(), CWholeFileAnnotation::GetAndUseAnnot(), GetCDDPssmIdFromSeqId(), CWGSDataLoader_Impl::GetFileInfo(), GetGeneralOrLocal(), CWriteUtil::GetIdType(), CSeq_id::GetMatchingIds(), GetNewGeneralProtId(), CVDBBlastUtil::GetOIDFromVDBSeqId(), CSeq_id_General_PlainInfo::GetPackedSeqId(), GetProteinId(), CCommentItem::GetStringForTPA(), GetTitle(), CGeneralIDField::GetVal(), CEditingActionEntireGeneralId::GetValue(), CEditingActionGeneralIdDb::GetValue(), CEditingActionGeneralIdTag::GetValue(), CTraceDataProxy::HasData(), CSGTraceGraphDS::HasData(), CSeq_id::IdentifyAccession(), CGuiSeqInfoSeq_id::IsDNA(), CEditingActionFileId::IsSetValue(), CEditingActionGeneralIdDb::IsSetValue(), CEditingActionGeneralIdTag::IsSetValue(), CSGSequenceDS::IsTraceAssembly(), CTraceDataProxy::LoadData(), CSGTraceGraphDS::LoadData(), CId1Reader::LoadSeq_idSeq_ids(), CSeq_id_General_PlainInfo::ParseCaseVariant(), CTabularFormatter_SeqId::Print(), s_AssignSeq_id(), s_CheckTraceMateAlign(), s_FindSmartSeqId(), s_Fingerprint_Seq_id(), s_GetAlignmentTooltip(), CMacroFunction_MakeBoldXrefs::s_GetBarcodeId(), s_GetSRASeqMetadata(), s_ShouldUseOriginalID(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CSeqDBImpl::SeqidToOids(), CValidError_imp::Setup(), TestCollidingAccessionFixes(), CValidError_bioseq::ValidateIDSetAgainstDb(), CVDBBlastUtil::VDBIdType(), CFeatureItem::x_AddQualProteinId(), CWriteDB_IsamIndex::x_AddStringIds(), CWriteDB_IsamIndex::x_AddTraceIds(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CVectorScreen::x_FindTypeGeneral(), CDBSourceItem::x_GatherInfo(), CPrimaryItem::x_GetStrForPrimary(), CFileIDField::x_IsNCBIFILEId(), CId2ReaderBase::x_ProcessGetBlobId(), CCdregionValidator::x_ReportTranslationProblems(), CValidError_bioseq::x_TranscriptIDsMatch(), CSingleFeatValidator::x_ValidateLocusTagGeneralMatch(), CSeq_id::x_WriteContentAsFasta(), and XISAGappedSeqLoc().
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Get the variant data.
Definition at line 889 of file Seq_id_.hpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Gi, and CSeq_id_Base::m_Gi.
Referenced by CReadUtil::AsSeqId(), CSeq_id::Assign(), CGffRecord::AssignSeqId(), BOOST_AUTO_TEST_CASE(), CTestProtProd_EntrezNeighbors::CanTest(), CAlnMix::ChooseSeqId(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), CTableImportDataSource::ConvertToSeqAnnot(), DensegConvert(), ExtractGi(), CBlastDBExtractor::ExtractLinksInteger(), CBlastDBExtractor::ExtractMembershipInteger(), CSeqAlignFilter::FilterByGiList(), CSeqAlignFilter::FilterByGiListFromFile(), g_DoesNotReferencePrimary(), GetAccessionAndDatabaseSource(), CCdCore::GetGI(), AlignmentCollection::GetGI(), IBISInteraction::GetGi(), CLocationListCtrl::GetIdFromForm(), CSeqUtils::GetLocPlacements(), CWGSDb_Impl::GetMasterGi(), GetMasterGIFromSeqAlign(), CSeq_feat_Handle::GetSNPGi(), TaxClient::GetTaxIDForSeqId(), CTaxTreeDS_ObjMgr::GetTaxMap(), GiFootPrint::GiFootPrint(), CId1Reader::LoadGiBlob_ids(), CId1Reader::LoadGiSeq_ids(), Make_GI_or_PDB_String_CN3D(), Make_SeqID_String(), CSeqUtils::MapStringId(), CSeq_annot_SNP_Info::OffsetGi(), PatchTargetSequence(), CTestProtProd_EntrezNeighbors::RunTest(), s_AssignSeq_id(), s_CheckQuals_cdregion(), CPsiBlastTestFixture::s_CountNumberUniqueGIs(), s_DeflineCompare(), s_DupIdsBioseq(), s_FindGi(), s_Fingerprint_Seq_id(), s_GetAlnMapplingLocs(), s_GetRefSeq_id(), s_GetSequencesIntoScope(), s_IdXrefsNotReciprocal(), s_Matches(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), sx_GetRefSeq_id(), CDUpdater::update(), CValidError_bioseq::ValidateDeltaLoc(), CWriteDB_Volume::WriteSequence(), CWriteDB_IsamIndex::x_AddGis(), CFeatureItem::x_AddQualProteinId(), CFeatureItem::x_AddQualsRna(), CSeq_annot_SNP_Info::x_CheckId(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CTaxTreeToolJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CGencollIdMapper::x_FindChromosomeSequence(), CGencollIdMapper::x_FixImperfectId(), CDBSourceItem::x_FormatDBSourceID(), CDBSourceItem::x_GatherInfo(), CProjectFileWriter::x_GetGi(), CAppHitFilter::x_LoadConstraints(), CGFFReader::x_ResolveNewSeqName(), CPSGS_CDDProcessor::x_SendAnnotInfo(), CSeqAlignFilter::x_UpdateGiInSeqalign(), and CSeq_id::x_WriteContentAsFasta().
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Get the variant data.
Definition at line 814 of file Seq_id_.hpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Gibbmt, and CSeq_id_Base::m_Gibbmt.
Referenced by CSeq_id::Assign(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), GetAccessionAndDatabaseSource(), s_Fingerprint_Seq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), and CSeq_id::x_WriteContentAsFasta().
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Get the variant data.
Definition at line 787 of file Seq_id_.hpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Gibbsq, and CSeq_id_Base::m_Gibbsq.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), GetAccessionAndDatabaseSource(), s_Fingerprint_Seq_id(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TGiim & CSeq_id_Base::GetGiim | ( | void | ) | const |
Get the variant data.
Definition at line 215 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Giim, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), GetAccessionAndDatabaseSource(), s_Fingerprint_Seq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TGpipe & CSeq_id_Base::GetGpipe | ( | void | ) | const |
Get the variant data.
Definition at line 523 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Gpipe, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_AssignSeq_id(), s_Fingerprint_Seq_id(), and CSeq_id::x_WriteContentAsFasta().
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Get the Id member data.
Definition at line 262 of file Giimport_id_.hpp.
References CGiimport_id_Base::CanGetId(), CGiimport_id_Base::m_Id, and CSerialObject::ThrowUnassigned().
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id_Giim_Tree::FindOrCreate(), GetAccessionAndDatabaseSource(), SChildLess::operator()(), s_Fingerprint_Giimport_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), x_Assign(), CSeq_id_Giim_Tree::x_FindInfo(), CFeatGlyph::x_GetFeatureId(), CSeq_id_Giim_Tree::x_Unindex(), and CSeq_id::x_WriteContentAsFasta().
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Get the Id member data.
Definition at line 337 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_Id, and CPacked_seqpnt_Base::ResetId().
Referenced by CHandleRangeMap::AddLocation(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), fta_seqloc_del_far(), IsValid(), NormalizeLoc(), PrintPntAndPntsUseBestID(), ReverseComplementLocation(), s_Fingerprint_Packed_seqpnt(), s_GetLabel(), UpgradeSeqLocId(), CSeqMap::x_Add(), CFlatSeqLoc::x_Add(), x_Assign(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), CSeq_loc_CI_Impl::x_ProcessLocation(), and CBioseq::x_SeqLoc_To_DeltaExt().
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Get the Id member data.
Definition at line 517 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_Id, and CSeq_interval_Base::ResetId().
Referenced by CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CRawWiggleRecord::Dump(), EndAdded(), SeqTreeAsnizer::fillSeqItem(), AlignmentCollection::FindSeqInterval(), FixMixLoc(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), GetLowHighFromSeqLoc(), CBlastInput::GetNextSeqBatch(), GetOverlappingFeatures(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), HasExcludedAnnotation(), IsNotDuplicateInterval(), IsValid(), OkToAdjustLoc(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), PrintSeqIntUseBestID(), TMaskedQueryRegions::RestrictToSeqInt(), ReverseComplementLocation(), s_CheckIfMatchesBioseq(), s_Fingerprint_Seq_interval(), s_FixIntervalProtToCds(), s_GetLabel(), s_GetSeq_intervalLabel(), s_IsVirtualSeqInt(), SeqIntPartialCheck(), CBedImportData::Serialize(), CGtfImportData::Serialize(), TryOneCaseMixLoc(), UpgradeSeqLocId(), CSeqMap::x_Add(), x_Assign(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CValidError_imp::x_CheckSeqInt(), CDisplaySeqalign::x_FillLocList(), CUnorderedSplitter::x_FixAlignment(), CCommonComponentScorer::x_GetDeltaExtCompList(), CMultiAligner::x_GetSeqalign(), CPsiBlastInputData::x_GetSubjectSequence(), CAnnotTypes_CI::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), x_IsCorrectlyOrdered(), CGencollIdMapper::x_IsLoc_Int_InAGap(), x_IsNotAdjacent(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGC_Assembly_Parser::x_ParseGCSequence(), CSeq_loc_CI_Impl::x_ProcessInterval(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CValidError_imp::x_ReportInvalidFuzz(), CAnnot_Collector::x_SearchRange(), CNewCleanup_imp::x_SeqIntervalBC(), and CBedGraphWriter::xWriteSingleFeature().
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Get the Id member data.
Definition at line 390 of file Seq_point_.hpp.
References CSeq_point_Base::m_Id, and CSeq_point_Base::ResetId().
Referenced by CHandleRangeMap::AddLocation(), CSeq_loc_Conversion_Set::ConvertBond(), CSeq_loc_Conversion::ConvertPoint(), CSeq_loc_Conversion_Set::ConvertPoint(), FixMixLoc(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), GetLowHighFromSeqLoc(), CSeq_align::GetSeqRange(), IsValid(), OkToAdjustLoc(), SSNP_Info::ParseSeq_feat(), PrintPntAndPntsUseBestID(), ReverseComplementLocation(), s_Fingerprint_Seq_point(), s_GetLabel(), s_Load_Seq_point(), UpgradeSeqLocId(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), x_Assign(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), variation_ref::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_fuzzy_pos(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessPoint(), variation_ref::CHgvsParser::x_range(), variation::CHgvsParser::x_range(), CValidError_imp::x_ReportInvalidFuzz(), CNewCleanup_imp::x_SeqPointBC(), and CAdjustForConsensusSpliceSite::x_UpdateMixLocations().
const CSeq_loc_Base::TInt & CSeq_loc_Base::GetInt | ( | void | ) | const |
Get the variant data.
Definition at line 194 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Int, and CSeq_loc_Base::m_object.
Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), AgpRead(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), check_short_CDS(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CSeq_loc_Conversion::ConvertSimpleMix(), CBioseqEditor::EditSelection(), variation::FindSSRLoc(), FixMixLoc(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), GenelocContained(), CWriteUtil::GetCodeBreak(), CAddGlobalCodeBreak::GetCommand(), GetCoverage(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), CBlobSplitterImpl::GetLength(), GetLength(), GetLowHighFromSeqLoc(), CBlastInput::GetNextSeqBatch(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), GetRetranslateCDSCommand(), GetReverseComplement(), CLocationListCtrl::GetSeq_loc(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), GetStrand(), CSeq_loc::GetStrand(), CWriteUtil::GetTrnaAntiCodon(), CEditingActionFeatAnticodon::GetValue(), HasExcludedAnnotation(), IBISAnnotateDialog::HighlightAnnotation(), CDDAnnotateDialog::HighlightAnnotation(), CLocationPanel::Init(), CBedImportData::Initialize(), IsLocFullLength(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CDDAnnotateDialog::NewOrEditMotif(), CStd_seg::OffsetRow(), SSNP_Info::ParseSeq_feat(), CStd_seg::RemapToLoc(), RetranslateCdregion(), RetranslateCDS(), CRetranslateCDS::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), RevComp(), CFeatTreeSampleApp::Run(), s_AddLocString(), s_Fingerprint_Seq_loc(), s_FixIntervalProtToCds(), s_GetLabel(), s_GetStrand(), s_GetTrimmedLength(), s_GetUngapLoc(), s_LocationToStartStopPairs(), s_MixStringAppend(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocDelete(), s_SubsequentIntron(), sConvertIntToPoint(), CClippedScorer::ScoreAlignments(), SeqIntCheckCpp(), SeqLocPartialCheck(), SeqLocPrintUseBestID(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), sx_AddBits(), CBlastTabular::sx_MineSegment(), TestOneCDS(), CSingleCDSExceptionPanel::TransferDataFromWindow(), CLocationPanel::TransferDataToWindow(), TrimStopsFromCompleteCDS(), CdBlaster::truncateBioseq(), TryOneCaseMixLoc(), CAssemblyGapValidator::Validate(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CFeatureItem::x_AddQualsCdregionIdx(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CMultiAligner::x_AlignFillerBlocks(), CGvfWriteRecord::x_AssignAttributeEndRange(), CGvfWriteRecord::x_AssignAttributeStartRange(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedInt(), CSeq_loc::x_CheckId(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CFeatGlyph::x_DrawFeatureBar_sv(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFastaOstreamEx::x_GetCodeBreak(), CMultiAligner::x_GetSeqalign(), CPsiBlastInputData::x_GetSubjectSequence(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CSeq_align_Mapper_Base::x_Init(), CAnnotTypes_CI::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CSeqTableInfo::x_IsSorted(), CLocationPanel::x_LoadSeqLoc(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGFFReader::x_ParseAlignRecord(), CGC_Assembly_Parser::x_ParseGCSequence(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessLocation(), CIdMapperTestApp::x_RecurseMapSeqAligns(), variation::CVariationUtil::x_Remap(), CVectorTrimPanel::x_RetranslateCDS(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CVectorTrimPanel::x_SeqLocDelete(), CLocusItem::x_SetTopology(), CSingleFeatValidator::x_ValidateImpFeatLoc(), CUCSCRegionReader::xParseFeatureUCSCFormat(), CGff3Reader::xUpdateAnnotGeneric(), CGff3Reader::xUpdateAnnotRna(), CGtfAnnotAssembler::xUpdateCds(), CGff2Record::xUpdateFeatureData(), CGtfAnnotAssembler::xUpdateGene(), and CGff3Reader::xVerifyExonLocation().
const CSeq_id_Base::TLocal & CSeq_id_Base::GetLocal | ( | void | ) | const |
Get the variant data.
Definition at line 193 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Local, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), CGffRecord::AssignSeqId(), BOOST_AUTO_TEST_CASE(), CLocalToGeneralId::CLocalToGeneralId(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), CRemoveSeqId::CRemoveSeqId(), GetAccessionAndDatabaseSource(), GetGeneralOrLocal(), CSeq_id::GetMatchingIds(), GetNewLocalProtId(), CSeq_id_Local_Info::GetPackedSeqId(), IsConsensus(), IsLocalID(), CLoadStructComments::LoadWithAccessions(), Make_SeqID_String(), CSeqIdValidate::operator()(), CSeq_id_Local_Info::ParseCaseVariant(), s_AddCDS(), s_AssignSeq_id(), s_CheckTraceMateAlign(), s_Fingerprint_Seq_id(), s_GetIdLabel(), s_GetLabel(), s_ReplaceLocalId(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), SeqIdMatchesMaster(), TestCollidingAccessionFixes(), CWriteDB_IsamIndex::x_AddLocal(), CEditSeqId::x_CollectChangedIds(), CInversionMergeAligner::x_CreateDiscAlignment(), CGencollIdMapper::x_FixImperfectId(), CAgpConverter::x_InitializeCopyOfTemplate(), CSeq_loc_Mapper::x_IsUCSCRandomChr(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CSeq_id::x_WriteContentAsFasta(), and CWiggleWriter::xWriteSingleGraphFixedStep().
const CSeq_loc_Base::TMix & CSeq_loc_Base::GetMix | ( | void | ) | const |
Get the variant data.
Definition at line 282 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Mix, and CSeq_loc_Base::m_object.
Referenced by CHandleRangeMap::AddLocation(), CAlignCDSAddPanel::AddOneCommand(), CAlignRNAAddPanel::AddOneCommand(), CAlignOtherAddPanel::AddOneCommand(), CSeq_loc_mix::AddSeqLoc(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CWriteUtil::ChangeToPackedInt(), CSeq_loc::ChangeToPackedInt(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CWriteUtil::GetCodeBreak(), CSeq_loc_Conversion::GetDstMix(), GetEmblInstContig(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), GetGenBankInstContig(), GetLength(), GetReverseComplement(), GetSeqLocation(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CGuiObjectInfoPrimer::GetToolTip(), CEditingActionFeatAnticodon::GetValue(), CLocationEditPolicy::HasNulls(), CLocationPanel::Init(), CWriteUtil::IsLocationOrdered(), CFeaturePropagator::IsOrdered(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CSeq_loc_CI_Impl::MakeLoc(), CFeaturePropagator::MakeOrdered(), NormalizeLoc(), s_AddLocString(), s_CalcCoverageCount(), s_CountIntervals(), s_Fingerprint_Seq_loc(), s_FlattenLoc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), s_IsOrdered(), s_NeedsFlattening(), s_NormalizeNullsBetween(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocDelete(), SeqLocPrintUseBestID(), CLocationPanel::TransferDataToWindow(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CSGFeatureJob::x_CreateCloneFeature(), CFeatureTableReader_Imp::x_FinishFeature(), CFeatureTableReader_Imp::x_GetPointStrand(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CGFFReader::x_ResolveLoc(), CBioseq::x_SeqLoc_To_DeltaExt(), CVectorTrimPanel::x_SeqLocDelete(), CCDSTranslationPanel::x_SetLocationForProtein(), and XMLGetInstContig().
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Get the Mol member data.
Definition at line 306 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::CanGetMol(), CPDB_seq_id_Base::m_Mol, and CSerialObject::ThrowUnassigned().
Referenced by CPDB_seq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CheckSPDupPDBXrefs(), CPDB_seq_id::Compare(), CSeq_id::ComposeOSLT(), ExtractPdbMolChain(), GetAccessionAndDatabaseSource(), Make_GI_or_PDB_String_CN3D(), Make_SeqID_String(), CPDB_seq_id::Match(), CSeq_id_PDB_Info::Normalize(), LessBySeqId::operator()(), s_CompareIdList(), s_Fingerprint_PDB_seq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CWriteDB_IsamIndex::x_AddPdb(), x_Assign(), CGencollIdMapper::x_FixImperfectId(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), and CWriteDB_LMDB::x_InsertEntry().
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Get the Name member data.
Definition at line 293 of file Textseq_id_.hpp.
References CTextseq_id_Base::CanGetName(), CTextseq_id_Base::m_Name, and CSerialObject::ThrowUnassigned().
Referenced by CTextseq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CTextseq_id::Compare(), CSeq_id::ComposeOSLT(), CpSeqId(), CSeq_id_Textseq_Tree::FindMatch(), CSeq_id_Textseq_Tree::FindOrCreate(), CSeq_id_Textseq_Tree::FindReverseMatch(), GetAccessionAndDatabaseSource(), GetLabel(), IsSegBioseq(), CTextseq_id::Match(), CWGSResolver_Ids::ParseWGSPrefix(), s_AssignTextseq_id(), s_GetNameForBioseq(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqIds(), x_Assign(), CSeq_id_Textseq_Tree::x_Equals(), CSeq_id_Textseq_Tree::x_FindStrInfo(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), CBioseqContext::x_SetId(), CLocusItem::x_SetName(), CSeq_id_Textseq_Tree::x_Unindex(), and CSingleFeatValidator::x_ValidateSeqFeatProduct().
const CSeq_id_Base::TNamed_annot_track & CSeq_id_Base::GetNamed_annot_track | ( | void | ) | const |
Get the variant data.
Definition at line 545 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Named_annot_track, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_AssignSeq_id(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TOther & CSeq_id_Base::GetOther | ( | void | ) | const |
Get the variant data.
Definition at line 347 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Other, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), CGffRecord::AssignSeqId(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), Make_SeqID_String(), s_AssignSeq_id(), s_DeflineCompare(), s_Fingerprint_Seq_id(), CValidError_imp::Setup(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseq::ValidateOrgContext(), CRemoveName::x_GetReplacementIds(), CCdregionValidator::x_IsProductMisplaced(), CFeatureGenerator::SImplementation::x_SetQualForGapFilledModel(), CValidError_bioseq::x_ShowBioProjectWarning(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_loc_Base::TPacked_int & CSeq_loc_Base::GetPacked_int | ( | void | ) | const |
Get the variant data.
Definition at line 216 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Packed_int, and CSeq_loc_Base::m_object.
Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSequenceSearchForm::ConstructQuery(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), ConvertPackedIntToInterval(), CSeqUtils::GetCdsMappingInfoFromRna(), IBISInteraction::GetFootprint(), CReadBlastApp::getFromTo(), IBISInteraction::GetGi(), GetLength(), CRemoteBlast::GetMasks(), GetPositionsForAlignAnnot(), GetReverseComplement(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CWriteUtil::GetTranssplicedEndpoints(), CLocationPanel::Init(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CFastaObjectLoader::LoadFromStream(), CGtfLocationMerger::MergeLocationForGene(), NormalizeLoc(), PackedSeqLocToMaskedQueryRegions(), PreserveTerminalCodons(), ProjectExon(), s_AddLocString(), s_CountIntervals(), s_Fingerprint_Seq_loc(), s_FlattenLoc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), s_LocationToStartStopPairs(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocDelete(), SeqLocPartialCheck(), SeqLocPrintUseBestID(), CBedImportData::Serialize(), CCleanup::SetCodeBreakLocation(), CLocationPanel::TransferDataToWindow(), NTweakExon::TweakExon(), NTweakExon::Validate(), CUCSCRegionWriter::WriteAnnot(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedInt(), CSeq_loc::x_CheckId(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CLocationPanel::x_LoadSeqLoc(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CBioseq::x_SeqLoc_To_DeltaExt(), CVectorTrimPanel::x_SeqLocDelete(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGtfWriter::xWriteFeatureExons(), CGff3Writer::xWriteFeatureRecords(), CGff3Writer::xWriteFeatureRna(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
const CSeq_loc_Base::TPacked_pnt & CSeq_loc_Base::GetPacked_pnt | ( | void | ) | const |
Get the variant data.
Definition at line 260 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Packed_pnt, and CSeq_loc_Base::m_object.
Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), fta_seqloc_del_far(), CWriteUtil::GetCodeBreak(), GetLength(), GetReverseComplement(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), GetStrand(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), NormalizeLoc(), PackSeqPntCheckCpp(), PrintPntAndPntsUseBestID(), s_AddLocString(), s_CanAdd(), s_CountIntervals(), s_Fingerprint_Seq_loc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_GetTrimmedLength(), SeqLocPartialCheck(), SplitLocationForGap(), UpgradeSeqLocId(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedPnt(), CSeq_loc::x_CheckId(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), CBioseq::x_SeqLoc_To_DeltaExt(), and CBioseqContext::x_SetOpticalMapPoints().
const CSeq_id_Base::TPatent & CSeq_id_Base::GetPatent | ( | void | ) | const |
Get the variant data.
Definition at line 325 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Patent, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), GetAccessionAndDatabaseSource(), s_Fingerprint_Seq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CSeq_id::WriteAsFasta(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TPdb & CSeq_id_Base::GetPdb | ( | void | ) | const |
Get the variant data.
Definition at line 435 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Pdb, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), ExtractPdbMolChain(), CSeq_id_PDB_Tree::FindMatch(), CSeq_id_PDB_Tree::FindReverseMatch(), GetAccessionAndDatabaseSource(), CSeq_id::GetMatchingIds(), CCdCore::GetPDB(), Make_GI_or_PDB_String_CN3D(), Make_SeqID_String(), CSeq_id_PDB_Info::Normalize(), LessBySeqId::operator()(), s_CompareIdList(), s_Fingerprint_Seq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CWriteDB_IsamIndex::x_AddPdb(), CAutogeneratedCleanup::x_BasicCleanupSeqId(), CGencollIdMapper::x_FixImperfectId(), CWriteDB_LMDB::x_InsertEntry(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TPir & CSeq_id_Base::GetPir | ( | void | ) | const |
Get the variant data.
Definition at line 281 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Pir, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_Fingerprint_Seq_id(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_loc_Base::TPnt & CSeq_loc_Base::GetPnt | ( | void | ) | const |
Get the variant data.
Definition at line 238 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Pnt, and CSeq_loc_Base::m_object.
Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), FixMixLoc(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), CWriteUtil::GetCodeBreak(), GetLowHighFromSeqLoc(), GetReverseComplement(), CSeq_align::GetSeqRange(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), GetStrand(), CSeq_loc::GetStrand(), CLocationPanel::Init(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CStd_seg::OffsetRow(), SSNP_Info::ParseSeq_feat(), PrintPntAndPntsUseBestID(), s_AddLocString(), s_CanAdd(), s_Fingerprint_Seq_loc(), s_GetLabel(), s_GetStrand(), s_IsBetween(), s_LocationToStartStopPairs(), s_MixStringAppend(), s_PrintLocAsJavascriptArray(), s_SubsequentIntron(), SeqLocPartialCheck(), SeqPntCheckCpp(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), SplitLocationForGap(), CLocationPanel::TransferDataToWindow(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CSGFeatureJob::x_CalcIntervals(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedPnt(), CSeq_loc::x_CheckId(), CFeatGlyph::x_DrawRSites(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CSeq_align_Mapper_Base::x_Init(), CLocationPanel::x_LoadSeqLoc(), variation_ref::CHgvsParser::x_location(), variation::CHgvsParser::x_location(), CReportEntry::x_MapPos(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessLocation(), CBioseqContext::x_SetOpticalMapPoints(), and CAdjustForConsensusSpliceSite::x_UpdateMixLocations().
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Get the Point member data.
Definition at line 303 of file Seq_point_.hpp.
References CSeq_point_Base::CanGetPoint(), CSeq_point_Base::m_Point, and CSerialObject::ThrowUnassigned().
Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion_Set::ConvertBond(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertPoint(), CSeq_loc_Conversion_Set::ConvertPoint(), FixMixLoc(), fta_get_acc_minmax_strand(), GetLowHighFromSeqLoc(), CSeq_align::GetSeqRange(), CSeq_bond::GetStart(), CSeq_loc::GetStart(), CSeq_bond::GetStop(), CSeq_loc::GetStop(), variation::IsPureFuzzPoint(), IsValid(), CStd_seg::OffsetRow(), SSNP_Info::ParseSeq_feat(), ReverseComplementLocation(), s_AddSeqPointString(), s_Fingerprint_Seq_point(), s_GetCodeBreak(), s_GetLabel(), s_Load_Seq_point(), s_LocationToStartStopPairs(), s_PrintLocAsJavascriptArray(), s_SubsequentIntron(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), SeqPntCheckCpp(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), SplitLocationForGap(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), x_Assign(), CSGFeatureJob::x_CalcIntervals(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedPnt(), CFeatGlyph::x_DrawRSites(), variation_ref::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_general_pos(), variation_ref::CHgvsParser::x_location(), variation::CHgvsParser::x_location(), CReportEntry::x_MapPos(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessPoint(), variation_ref::CHgvsParser::x_range(), variation::CHgvsParser::x_range(), CValidError_imp::x_ReportInvalidFuzz(), variation_ref::CHgvsParser::x_SeqPntToStr(), CNewCleanup_imp::x_SeqPointBC(), CBioseqContext::x_SetOpticalMapPoints(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), and xgbint_ver().
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Get the Points member data.
Definition at line 388 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_Points.
Referenced by CSeq_loc::Add(), CHandleRangeMap::AddLocation(), BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CorrectIntervalOrder(), GetLength(), CPacked_seqpnt::GetStart(), CPacked_seqpnt::GetStop(), CCommentItem::GetStringForOpticalMap(), IsValid(), NormalizeLoc(), PackSeqPntCheckCpp(), s_AddSeqPackedPointString(), s_CountIntervals(), s_Fingerprint_Packed_seqpnt(), s_GetCodeBreak(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetTrimmedLength(), CSeqMap::x_Add(), CFlatSeqLoc::x_Add(), x_Assign(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_ChangeToPackedPnt(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessLocation(), and CBioseq::x_SeqLoc_To_DeltaExt().
const CSeq_id_Base::TPrf & CSeq_id_Base::GetPrf | ( | void | ) | const |
Get the variant data.
Definition at line 413 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Prf, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_Fingerprint_Seq_id(), and CSeq_id::x_WriteContentAsFasta().
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Get the Rel member data.
Definition at line 391 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::CanGetRel(), CPDB_seq_id_Base::m_Rel, and CSerialObject::ThrowUnassigned().
Referenced by CSeq_id_PDB_Tree::FindMatch(), CSeq_id_PDB_Info::Normalize(), x_Assign(), and CDBSourceItem::x_FormatDBSourceID().
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Get the Release member data.
Definition at line 349 of file Giimport_id_.hpp.
References CGiimport_id_Base::CanGetRelease(), CGiimport_id_Base::m_Release, and CSerialObject::ThrowUnassigned().
Referenced by SChildLess::operator()(), s_Fingerprint_Giimport_id(), and x_Assign().
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Get the Release member data.
Definition at line 387 of file Textseq_id_.hpp.
References CTextseq_id_Base::CanGetRelease(), CTextseq_id_Base::m_Release, and CSerialObject::ThrowUnassigned().
Referenced by BOOST_AUTO_TEST_CASE(), s_AssignTextseq_id(), s_Fingerprint_Textseq_id(), x_Assign(), CSeq_id_Textseq_Tree::x_Equals(), and CSeq_id_Textseq_Tree::x_FindMatchByName().
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Get the Seqid member data.
Definition at line 219 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::CanGetSeqid(), CPatent_seq_id_Base::m_Seqid, and CSerialObject::ThrowUnassigned().
Referenced by CPatent_seq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CPatent_seq_id::Compare(), CSeq_id::ComposeOSLT(), CSeq_id_Patent_Tree::FindOrCreate(), GetAccessionAndDatabaseSource(), CPatent_seq_id::Match(), s_Fingerprint_Patent_seq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), x_Assign(), CSeq_id_Patent_Tree::x_FindInfo(), CDeflineGenerator::x_SetFlags(), and CSeq_id_Patent_Tree::x_Unindex().
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Get the Strand member data.
Definition at line 297 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::CanGetStrand(), CPacked_seqpnt_Base::m_Strand, and CSerialObject::ThrowUnassigned().
Referenced by CHandleRangeMap::AddLocation(), BOOST_AUTO_TEST_CASE(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CorrectIntervalOrder(), CPacked_seqpnt::FlipStrand(), GetStrand(), CSeq_loc::GetStrand(), NormalizeLoc(), s_AddSeqPackedPointString(), s_GetCodeBreak(), s_GetStrand(), CSeqMap::x_Add(), CFlatSeqLoc::x_Add(), x_Assign(), CPacked_seqpnt::x_IsMinusStrand(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), CSeq_loc_CI_Impl::x_ProcessLocation(), and CBioseq::x_SeqLoc_To_DeltaExt().
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Get the Strand member data.
Definition at line 477 of file Seq_interval_.hpp.
References CSeq_interval_Base::CanGetStrand(), CSeq_interval_Base::m_Strand, and CSerialObject::ThrowUnassigned().
Referenced by CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_align::CreateDensegFromStdseg(), EndAdded(), CSeq_interval::FlipStrand(), fta_get_acc_minmax_strand(), CWriteUtil::GetEffectiveStrand(), CReadBlastApp::getFromTo(), CEditingActionFeatAnticodon::GetIntervalString(), GetIntervalString(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), CSeqMap::GetSeqMapForSeq_loc(), GetStrand(), CSeq_loc::GetStrand(), CWriteUtil::GetTrnaAntiCodon(), CBedImportData::Initialize(), CSeq_loc_Conversion::MakeDstMix(), NTweakExon::MinusStrand(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), PrintSeqIntUseBestID(), CStd_seg::RemapToLoc(), TMaskedQueryRegions::RestrictToSeqInt(), RevComp(), s_AddSeqIntString(), s_ExtendIntervalToEnd(), s_FixIntervalProtToCds(), s_GetCodeBreak(), s_GetLabel(), s_GetSeq_intervalLabel(), s_GetStrand(), SeqIntPartialCheck(), SeqLocAdjustForTrim(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CGffFeatureRecord::SetLocation(), CBedFeatureRecord::SetLocation(), CUCSCRegionWriter::WriteAnnot(), CSeqMap::x_Add(), x_Assign(), CNewCleanup_imp::x_BothStrandBC(), CValidError_imp::x_CheckSeqInt(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CAnnotTypes_CI::x_Init(), x_IsCorrectlyOrdered(), CSeq_interval::x_IsMinusStrand(), x_IsNotAdjacent(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGFFReader::x_ParseAlignRecord(), CSeq_loc_CI_Impl::x_ProcessInterval(), x_SameStrand(), CAnnot_Collector::x_SearchRange(), CNewCleanup_imp::x_SeqIntervalBC(), CLocusItem::x_SetTopology(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), and CGff2Record::xUpdateFeatureData().
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Get the Strand member data.
Definition at line 350 of file Seq_point_.hpp.
References CSeq_point_Base::CanGetStrand(), CSeq_point_Base::m_Strand, and CSerialObject::ThrowUnassigned().
Referenced by CHandleRangeMap::AddLocation(), CSeq_loc_Conversion::ConvertPoint(), CSeq_point::FlipStrand(), fta_get_acc_minmax_strand(), GetLowHighFromSeqLoc(), GetStrand(), CSeq_bond::GetStrand(), CSeq_loc::GetStrand(), s_AddSeqPointString(), s_GetCodeBreak(), s_GetLabel(), s_GetStrand(), s_Load_Seq_point(), s_SeqPntRevCmp(), CBedFeatureRecord::SetLocation(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), x_Assign(), CNewCleanup_imp::x_BothStrandBC(), CSeq_loc::x_ChangeToPackedPnt(), CFeatGlyph::x_DrawRSites(), variation_ref::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_fuzzy_pos(), CSeq_point::x_IsMinusStrand(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessPoint(), variation_ref::CHgvsParser::x_range(), variation::CHgvsParser::x_range(), and CNewCleanup_imp::x_SeqPointBC().
const CSeq_id_Base::TSwissprot & CSeq_id_Base::GetSwissprot | ( | void | ) | const |
Get the variant data.
Definition at line 303 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Swissprot, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_Fingerprint_Seq_id(), CSeq_id::WriteAsFasta(), and CSeq_id::x_WriteContentAsFasta().
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Get the To member data.
Definition at line 430 of file Seq_interval_.hpp.
References CSeq_interval_Base::CanGetTo(), CSeq_interval_Base::m_To, and CSerialObject::ThrowUnassigned().
Referenced by AgpRead(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), check_short_CDS(), CollapseDiscontinuitiesInUTR(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertMixToInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), CSeq_align::CreateDensegFromStdseg(), CRawWiggleRecord::Dump(), EndAdded(), CGBObjectLoader::Execute(), AlignmentCollection::FindSeqInterval(), variation::FindSSRLoc(), FixMixLoc(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), fta_get_acc_minmax_strand(), CReadBlastApp::getFromTo(), CSeq_interval::GetLength(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CStd_seg::GetSeqRange(), CSeq_interval::GetStart(), CSeq_interval::GetStop(), CWriteUtil::GetTranssplicedEndpoints(), CWriteUtil::GetTrnaAntiCodon(), IsLocFullLength(), IsNotDuplicateInterval(), IsValid(), CSeq_loc_Conversion::MakeDstMix(), CDDAnnotateDialog::NewOrEditMotif(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), PrintSeqIntUseBestID(), CStd_seg::RemapToLoc(), TMaskedQueryRegions::RestrictToSeqInt(), RevComp(), ReverseComplementLocation(), CFeatTreeSampleApp::Run(), s_AddSeqIntString(), s_CheckInterval(), s_ExtendIntervalToEnd(), s_Fingerprint_Seq_interval(), s_FixIntervalProtToCds(), s_GetCodeBreak(), s_GetLabel(), s_GetSeq_intervalLabel(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_LocationToStartStopPairs(), s_LocToRange(), s_OOFBlastHSP2SeqAlign(), s_RemoveBogusFuzzFromIntervals_Helper(), s_SeqIntervalDelete(), s_SeqIntervalToSeqLocInfo(), s_SeqLoc2MaskedSubjRanges(), s_SubsequentIntron(), CClippedScorer::ScoreAlignments(), SeqIntCheckCpp(), SeqIntPartialCheck(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CGffFeatureRecord::SetLocation(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetThick(), SplitLocationForGap(), CBlastTabular::sx_MineSegment(), TestOneCDS(), TrimStopsFromCompleteCDS(), CdBlaster::truncateBioseq(), CAssemblyGapValidator::Validate(), NTweakExon::Validate(), CUCSCRegionWriter::WriteAnnot(), CFeatureItem::x_AddQualsCdregionIdx(), CPhrap_Contig::x_AddReadLocFeats(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CMultiAligner::x_AlignFillerBlocks(), x_Assign(), CGvfWriteRecord::x_AssignAttributeEndRange(), CSeq_loc::x_CalculateTotalRangeCheckId(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CCdsGlyph::x_DrawProtSeqWithMapping(), CDisplaySeqalign::x_FillLocList(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFastaOstreamEx::x_GetCodeBreak(), CAnnotTypes_CI::x_Init(), x_IsCorrectlyOrdered(), CGencollIdMapper::x_IsLoc_Int_InAGap(), x_IsNotAdjacent(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessInterval(), CValidError_imp::x_ReportInvalidFuzz(), CAnnot_Collector::x_SearchRange(), CNewCleanup_imp::x_SeqIntervalBC(), CVectorTrimPanel::x_SeqIntervalDelete(), CLocusItem::x_SetTopology(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CBlastFilterTest::x_TestLowerCaseMaskWith(), CSingleFeatValidator::x_ValidateImpFeatLoc(), CGff3Writer::xAssignFeature(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGtfWriter::xAssignFeaturesTranscript(), XGappedSeqLocsToDeltaSeqs(), CGff3Reader::xVerifyExonLocation(), and CBedGraphWriter::xWriteSingleFeature().
const CSeq_id_Base::TTpd & CSeq_id_Base::GetTpd | ( | void | ) | const |
Get the variant data.
Definition at line 501 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Tpd, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_Fingerprint_Seq_id(), CRemoveName::x_GetReplacementIds(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TTpe & CSeq_id_Base::GetTpe | ( | void | ) | const |
Get the variant data.
Definition at line 479 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Tpe, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_Fingerprint_Seq_id(), CRemoveName::x_GetReplacementIds(), and CSeq_id::x_WriteContentAsFasta().
const CSeq_id_Base::TTpg & CSeq_id_Base::GetTpg | ( | void | ) | const |
Get the variant data.
Definition at line 457 of file Seq_id_.cpp.
References CSeq_id_Base::CheckSelected(), CSeq_id_Base::e_Tpg, and CSeq_id_Base::m_object.
Referenced by CSeq_id::Assign(), CSeq_id::Compare(), CSeq_id::GetTextseq_Id(), s_Fingerprint_Seq_id(), CRemoveName::x_GetReplacementIds(), and CSeq_id::x_WriteContentAsFasta().
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Get the Version member data.
Definition at line 441 of file Textseq_id_.hpp.
References CTextseq_id_Base::CanGetVersion(), CTextseq_id_Base::m_Version, and CSerialObject::ThrowUnassigned().
Referenced by CTextseq_id::AsFastaString(), CGffRecord::AssignSeqId(), BOOST_AUTO_TEST_CASE(), CTextseq_id::Compare(), CSeq_id::ComposeOSLT(), CpSeqId(), extractBioseqInfo(), CWGSFileInfo::FindProtAcc(), flat2asn_range_func(), get_accession_from_id(), GetAccAndVersion(), GetAccVer(), GetDirectLabel(), CPSGS_AsyncResolveBase::GetEffectiveVersion(), GetLabel(), CSeq_id::GetLabel(), GetNormalizedSeqId(), CVDBGraphDb_Impl::GetSeqInfo(), CTextseq_id::Match(), CSeq_id_Textseq_Info::ParseAcc(), CWGSClient::Resolve(), s_AssignTextseq_id(), s_Fingerprint_Textseq_id(), s_GetModelEvidance(), s_ValidateAcc(), SeqDB_SimplifySeqid(), CValidError_imp::Setup(), StrippedAccVer(), CWGSFileInfo::SAccFileInfo::ValidateAcc(), CValidError_bioseq::ValidateSeqIds(), x_Assign(), CFeatureGenerator::SImplementation::x_CheckMatch(), CSeqDBVol::x_CheckVersions(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CSeq_id_Textseq_Tree::x_Equals(), CSeq_id_Textseq_Tree::x_FindMatchByAcc(), CSeq_id_Textseq_Tree::x_FindRevMatchByAcc(), CSeq_id_Textseq_Tree::x_FindRevMatchByAccNonPacked(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), CSeq_id_Textseq_Tree::x_GetVersion(), CGencollIdMapper::x_Init(), and CFastaOstream::x_WriteAsFasta().
const CSeq_loc_Base::TWhole & CSeq_loc_Base::GetWhole | ( | void | ) | const |
Get the variant data.
Definition at line 172 of file Seq_loc_.cpp.
References CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::e_Whole, and CSeq_loc_Base::m_object.
Referenced by CHandleRangeMap::AddLocation(), CFeatGapInfo::AdjustProteinSeq(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CFeaturePropagator::ConstructProteinFeatureForPropagatedCodingRegion(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CNewCleanup_imp::ConvertSeqLocWholeToInt(), CApplyRNAITSDlg::GetCommand(), GetCoverage(), GetLength(), CBlastInput::GetNextSeqBatch(), GetOverlappingFeatures(), CSeqMap::GetSeqMapForSeq_loc(), GetValidatorLocationLabel(), CCleanup::RepackageProteins(), s_ConvertWholeToInt(), s_Fingerprint_Seq_loc(), s_GetCdsSequence(), CCompareSeqRegions::s_GetGeneId(), s_GetLabel(), SeqLocPartialCheck(), TranslateCodingRegionForValidation(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CImportFeatTable::x_DoImportCDS(), CAdjustFeaturesForGaps::x_DoOne(), CCreateGeneModelTask::x_GetCommand(), CMultiAligner::x_GetSeqalign(), CAnnotTypes_CI::x_Init(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGC_Assembly_Parser::x_ParseGCSequence(), CSeq_loc_CI_Impl::x_ProcessLocation(), CIdMapperTestApp::x_RecurseMapSeqAligns(), and CFeatureTableReader::xTranslateProtein().
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Check if variant Bond is selected.
Bond type is defined as 'typedef CSeq_bond TBond'.
Definition at line 564 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Bond, and CSeq_loc_Base::m_choice.
Referenced by fta_seqloc_del_far(), CSeq_loc_CI_Impl::GetBondBegin(), CSeq_loc_CI_Impl::GetBondEnd(), SeqLocPrintUseBestID(), and SrchCdRegion().
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Check if variant Ddbj is selected.
Ddbj type is defined as 'typedef CTextseq_id TDdbj'.
Definition at line 910 of file Seq_id_.hpp.
References CSeq_id_Base::e_Ddbj, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), s_GetNameForBioseq(), and CValidError_bioseq::ValidateDeltaLoc().
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Check if variant Embl is selected.
Embl type is defined as 'typedef CTextseq_id TEmbl'.
Definition at line 847 of file Seq_id_.hpp.
References CSeq_id_Base::e_Embl, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), s_GetNameForBioseq(), and CValidError_bioseq::ValidateDeltaLoc().
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Check if variant Empty is selected.
Empty type is defined as 'typedef CSeq_id TEmpty'.
Definition at line 516 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Empty, and CSeq_loc_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), variation::CVariationUtil::CheckPlacement(), CStdSegHit::CStdSegHit(), fta_check_con_for_wgs(), GetSeqLocation(), CStdSegHit::HasAlignment(), CNSeq::Init(), CLocMapper_Default::Map(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CCompareSeqRegions::NextComparisonGroup(), CFeatureLoadingJob::Run(), s_CombineDustMasksWithUserProvidedMasks(), s_GetAlignmentSpans_Interval(), s_GetGapCount(), s_GetTrimmedLength(), s_SeqLoc2MaskedSubjRanges(), s_UpdateCodeBreaksAndAnticodons(), CClippedScorer::ScoreAlignments(), SrchCdRegion(), CFeatGapInfo::x_AdjustAnticodons(), CFeatGapInfo::x_AdjustCodebreaks(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CSGAlignmentJob::x_CreateFeatGlyph(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CSeq_loc_Mapper_Base::x_InitAlign(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), variation::CHgvsParser::x_PlacementCoordsToStr(), CIdMapperTestApp::x_RecurseMapSeqAligns(), variation::CVariationUtil::x_Remap(), and CValidError_align::x_ValidateSeqLength().
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Check if variant Equiv is selected.
Equiv type is defined as 'typedef CSeq_loc_equiv TEquiv'.
Definition at line 558 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Equiv, and CSeq_loc_Base::m_choice.
Referenced by CSeq_loc_equiv::Add(), CheckForeignLoc(), SeqLocPrintUseBestID(), SrchCdRegion(), and CFeatureGenerator::SImplementation::x_CreateCdsFeature().
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Check if variant Feat is selected.
Feat type is defined as 'typedef CFeat_id TFeat'.
Definition at line 570 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Feat, and CSeq_loc_Base::m_choice.
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Check if variant Genbank is selected.
Genbank type is defined as 'typedef CTextseq_id TGenbank'.
Definition at line 841 of file Seq_id_.hpp.
References CSeq_id_Base::e_Genbank, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), GetBestBioseqLabel(), s_GetNameForBioseq(), CValidError_bioseq::ValidateDeltaLoc(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CImportFeatTable::x_DoImportCDS(), CCompareWithBiosample::x_LoadData(), and CGtfReader::xFeatureSetDataCds().
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Check if variant General is selected.
General type is defined as 'typedef CDbtag TGeneral'.
Definition at line 877 of file Seq_id_.hpp.
References CSeq_id_Base::e_General, and CSeq_id_Base::m_choice.
Referenced by CSeq_id::AdjustScore(), BOOST_AUTO_TEST_CASE(), CGeneralToLocalId::CGeneralToLocalId(), seqsubmit_split::SIdCompare::compare_seq(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractAccession(), ExtractGnomonModelNum(), CBlastDBExtractor::ExtractSeqId(), GetAccessionAndDatabaseSource(), CWholeFileAnnotation::GetAndUseAnnot(), GetCDDPssmIdFromSeqId(), GetGeneralOrLocal(), GetId(), CVDBBlastUtil::GetOIDFromVDBSeqId(), GetProteinId(), CCommentItem::GetStringForTPA(), CGeneralIDField::GetVal(), CTraceDataProxy::HasData(), CSGTraceGraphDS::HasData(), CEditingActionFileId::IsSetValue(), CEditingActionEntireGeneralId::IsSetValue(), CEditingActionGeneralIdDb::IsSetValue(), CEditingActionGeneralIdTag::IsSetValue(), CSGSequenceDS::IsTraceAssembly(), CTraceDataProxy::LoadData(), CSGTraceGraphDS::LoadData(), CTabularFormatter_SeqId::Print(), s_CheckTraceMateAlign(), s_GetAlignmentTooltip(), CMacroFunction_MakeBoldXrefs::s_GetBarcodeId(), TestCollidingAccessionFixes(), CFeatureItem::x_AddQualDbXref(), CFeatureItem::x_AddQualProteinId(), CWriteDB_IsamIndex::x_AddTraceIds(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CImportFeatTable::x_DoImportCDS(), CVectorScreen::x_FindTypeGeneral(), CPrimaryItem::x_GetStrForPrimary(), CFileIDField::x_IsNCBIFILEId(), CId2ReaderBase::x_ProcessGetBlobId(), CCdregionValidator::x_ReportTranslationProblems(), CValidError_bioseq::x_TranscriptIDsMatch(), CSeq_id_General_Tree::x_Unindex(), CSingleFeatValidator::x_ValidateLocusTagGeneralMatch(), seqsubmit_split::SIdCompare::xGetGeneralId(), and XISAGappedSeqLoc().
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Check if variant Gi is selected.
Gi type is defined as 'typedef NCBI_NS_NCBI::TGi TGi'.
Definition at line 883 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gi, and CSeq_id_Base::m_choice.
Referenced by CReadUtil::AsSeqId(), BlastHitList2SeqAlign_OMF(), BLASTPrelminSearchHitListToStdSeg(), BOOST_AUTO_TEST_CASE(), CAlnMix::ChooseSeqId(), CGuiObjectInfoSeq_id::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), DensegConvert(), CBlastDBExtractor::ExtractLinksInteger(), CBlastDBExtractor::ExtractMembershipInteger(), CFlatSeqIdQVal::Format(), CFtableFormatter::FormatFeatHeader(), CGBSeqFormatter::FormatFeature(), AlignmentCollection::Get_GI_or_PDB_String_FromAlignment(), CCdCore::Get_GI_or_PDB_String_FromAlignment(), GetAccessionAndDatabaseSource(), CCdCore::GetGI(), AlignmentCollection::GetGI(), IBISInteraction::GetGi(), CLocationListCtrl::GetIdFromForm(), GetLabel(), CSeqUtils::GetLocPlacements(), GetMasterGIFromSeqAlign(), GetProductLabel(), CShowBlastDefline::GetSeqIdListString(), GetSequenceLengthAndId(), CCommentItem::GetStringForTPA(), TaxClient::GetTaxIDForSeqId(), CTaxTreeDS_ObjMgr::GetTaxMap(), GiFootPrint::GiFootPrint(), CSeq_id::IsAllowedSNPScaleLimit(), CGuiSeqInfoSeq_id::IsDNA(), CGuiSeqInfoSeq_id::IsProtein(), Make_GI_or_PDB_String_CN3D(), Make_SeqID_String(), CSeqUtils::MapStringId(), CSeq_annot_SNP_Info::OffsetGi(), PatchTargetSequence(), CBlast_def_line_set::RemoveGIs(), CGBDocument::ReplaceGiSeqIds(), s_BLAST_OneSubjectResults2CSeqAlign(), s_CheckQuals_cdregion(), s_DeflineCompare(), s_DupIdsBioseq(), s_FindGi(), s_GetAlignedSeqGi(), s_GetAlnMapplingLocs(), s_GetRefSeq_id(), s_GetSeqLabel(), s_GetSequencesIntoScope(), s_IdXrefsNotReciprocal(), s_Matches(), s_ModifySeqAlnWithFilteredSeqIDs(), s_ProcessSeqIDsForV5(), s_UpdateSeqAlnWithFilteredSeqIDs(), sx_GetRefSeq_id(), CCDSTranslationPanel::TransferDataToWindow(), CValidError_bioseq::ValidateDeltaLoc(), CSeq_id::WriteAsFasta(), WriteBlastSeqidlistFile(), CWriteDB_Volume::WriteSequence(), CWriteDB_IsamIndex::x_AddGis(), CFeatureItem::x_AddQualDbXref(), CFeatureItem::x_AddQualProteinId(), CGencollIdMapper::x_ApplyPatternToId(), CSeq_annot_SNP_Info::x_CheckId(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CTaxTreeToolJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CGencollIdMapper::x_FindChromosomeSequence(), CGencollIdMapper::x_FixImperfectId(), CDBSourceItem::x_GatherInfo(), CCreateGeneModelTask::x_GetCommand(), CPrimaryItem::x_GetStrForPrimary(), CBlastKmerResults::x_InitScoreVec(), CWriteDB_LMDB::x_InsertEntry(), CAppHitFilter::x_LoadConstraints(), CGencollIdMapper::x_RecursiveSeqFix(), CGFFReader::x_ResolveNewSeqName(), CBuildDatabase::x_ResolveRemoteId(), CPSGS_CDDProcessor::x_SendAnnotInfo(), SWGSCreateInfo::x_SetId(), CSeqAlignFilter::x_UpdateGiInSeqalign(), and CFastaOstream::x_WriteAsFasta().
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Check if variant Gibbmt is selected.
Gibbmt type is defined as 'typedef int TGibbmt'.
Definition at line 808 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gibbmt, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), and GetAccessionAndDatabaseSource().
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Check if variant Gibbsq is selected.
Gibbsq type is defined as 'typedef int TGibbsq'.
Definition at line 781 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gibbsq, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), and GetAccessionAndDatabaseSource().
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Check if variant Giim is selected.
Giim type is defined as 'typedef CGiimport_id TGiim'.
Definition at line 835 of file Seq_id_.hpp.
References CSeq_id_Base::e_Giim, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), GetAccessionAndDatabaseSource(), and CSeq_id_Giim_Tree::x_Unindex().
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Check if variant Gpipe is selected.
Gpipe type is defined as 'typedef CTextseq_id TGpipe'.
Definition at line 946 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gpipe, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), and FTASeqLocCheck().
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Check if variant Int is selected.
Int type is defined as 'typedef CSeq_interval TInt'.
Definition at line 528 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Int, and CSeq_loc_Base::m_choice.
Referenced by CSeq_loc::Add(), CAdjustForConsensusSpliceSite::AdjustCDS(), variation_ref::CVariationUtil::AdjustDelinsToInterval(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), BOOST_AUTO_TEST_CASE(), ChangeNucProtSetNucId(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CCdsToMatPeptide::ConvertInner(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CSeq_loc_Conversion::ConvertSimpleMix(), CGBObjectLoader::Execute(), CCleanup::ExpandGeneToIncludeChildren(), FixMixLoc(), CHTMLFormatterEx::FormatLocation(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), GenelocContained(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), CAddGlobalCodeBreak::GetCommand(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), GetLowHighFromSeqLoc(), CBlastInput::GetNextSeqBatch(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), CCleanup::GetProteinLocationFromNucleotideLocation(), GetRetranslateCDSCommand(), CLocationListCtrl::GetSeq_loc(), GetSeqLocation(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CEditingActionFeatAnticodon::GetValue(), HasExcludedAnnotation(), IBISAnnotateDialog::HighlightAnnotation(), CDDAnnotateDialog::HighlightAnnotation(), IsLocFullLength(), IsTransSpliced(), MakeDDFromSeqLoc(), CGtfLocationMerger::MergeLocationForGene(), CDDAnnotateDialog::NewOrEditMotif(), variation::SFastLocSubtract::operator()(), CReadBlastApp::overlaps(), CCleanup::ParseCodeBreak(), ProjectAndCollapseCDS(), RetranslateCdregion(), RetranslateCDS(), CRetranslateCDS::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), RevComp(), CNewCleanup_imp::RnaFeatBC(), variation::CVariationUtil::s_AddIntronicOffsets(), s_ConvertToBlastQueries(), s_FixIntervalProtToCds(), s_GetAlignmentSpans_Interval(), s_GetTrimmedLength(), s_GetUngapLoc(), s_LocationToStartStopPairs(), s_MixStringAppend(), s_RemapToSubjectLoc(), variation::CVariationUtil::s_ResolveIntronicOffsets(), s_SeqLoc2MaskedSubjRanges(), s_SubLocDeltaSeq(), s_SubsequentIntron(), SeqLocPrintUseBestID(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CSeqTableSetLocFuzzFromLim::SetInt(), CSeqTableSetLocFuzzToLim::SetInt(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), CBlastTabular::sx_MineSegment(), CSingleCDSExceptionPanel::TransferDataFromWindow(), TrimStopsFromCompleteCDS(), CdBlaster::truncateBioseq(), CAssemblyGapValidator::Validate(), CFlatSeqLoc::x_Add(), CFeatureItem::x_AddQualsCdregionIdx(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CGvfWriteRecord::x_AssignAttributeEndRange(), CGvfWriteRecord::x_AssignAttributeStartRange(), CSeq_loc::x_ChangeToPackedInt(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CProSplignJob::x_CreateProjectItems(), CFeatGlyph::x_DrawFeatureBar_sv(), CNewCleanup_imp::x_ExtendSingleGeneOnMrna(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CGuiObjectInfoSeq_feat::x_GetLocLengthRow(), CMultiAligner::x_GetSeqalign(), CFeatTrim::x_GetStartOffset(), CAlignedFeatureGraph::x_GetTooltip(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), variation::CVariationUtil::x_InferNAfromAA(), CAnnotTypes_CI::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeqTableInfo::x_IsSorted(), CGFFReader::x_ParseAlignRecord(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CIdMapperTestApp::x_RecurseMapSeqAligns(), variation::CVariationUtil::x_Remap(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CVectorTrimPanel::x_RetranslateCDS(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CProSplignTool::x_SelectCompatibleInputObjects(), CSplignTool::x_SelectCompatibleInputObjects(), CBioseqContext::x_SetLocation(), CLocusItem::x_SetTopology(), CAdjustForConsensusSpliceSite::x_UpdateExonFeatures(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), CValidError_graph::x_ValidateGraphLocation(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CSingleFeatValidator::x_ValidateImpFeatLoc(), xgbloc_ver(), and CGtfAnnotAssembler::xUpdateGene().
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Check if variant Local is selected.
Local type is defined as 'typedef CObject_id TLocal'.
Definition at line 775 of file Seq_id_.hpp.
References CSeq_id_Base::e_Local, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), CCreateProteinId::create_protein_ids(), CRemoveSeqId::CRemoveSeqId(), CSeqFormatter::DumpAll(), CCreateCoverageTask::Execute(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractSeqId(), SeqSwapper::findReplacements(), CTextAlnReader::GenerateID(), GetAccessionAndDatabaseSource(), GetGeneralOrLocal(), CBioseq::GetLocalId(), CBioseq::GetNonLocalId(), CTableDataGCAssembly::GetObjectValue(), CShowBlastDefline::GetSeqIdListString(), CTableDataGCAssembly::GetStringValue(), CSeqTextPanel::InitObject(), CVcfTableView::InitView(), IsConsensus(), IsLocalID(), CLoadStructComments::LoadWithAccessions(), Make_SeqID_String(), CSeqIdValidate::operator()(), OverrideLenIfAccession(), CSeqFastaReader::PostProcessIDs(), CBlastFormat::PrintReport(), CBlastInputReader::ReadOneSeq(), RelaxedMatch(), s_BestLocalRank(), s_BestNonLocalRank(), s_CheckTraceMateAlign(), s_FindLocalId(), s_GetIdLabel(), s_GetLabel(), s_MatchSeqIds(), s_ReplaceLocalId(), s_SeqAlignToXMLHit(), s_UseFastaReaderDeflines(), CNewCleanup_imp::SeqIdBC(), CStructuredCommentsReader::SeqIdMatchesCommentId(), SeqIdMatchesMaster(), CEditSeqId::x_CollectChangedIds(), CInversionMergeAligner::x_CreateDiscAlignment(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), CImportFeatTable::x_DoImportCDS(), CSGSegmentSmearJob::x_Execute(), CVectorScreen::x_FindLocalId(), CGencollIdMapper::x_FixImperfectId(), CBlastHitMatrix::x_GetLabels(), CTableColumnTypeGuesser::x_GuessType(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CCSraDb_Impl::x_MakeRefSeq_ids(), CGC_Assembly_Parser::x_ParseGCSequence(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CBlastFormat::x_ReverseQuery(), CFeaturePanel::x_StartAssemblyJob(), and CSeq_id_Local_Tree::x_Unindex().
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Check if variant Mix is selected.
Mix type is defined as 'typedef CSeq_loc_mix TMix'.
Definition at line 552 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Mix, and CSeq_loc_Base::m_choice.
Referenced by AddLoc(), CAlignCDSAddPanel::AddOneCommand(), CAlignRNAAddPanel::AddOneCommand(), CAlignOtherAddPanel::AddOneCommand(), CSeq_loc_mix::AddSeqLoc(), CAdjustForConsensusSpliceSite::AdjustCDS(), BOOST_AUTO_TEST_CASE(), Canonicalize(), ChangeNucProtSetNucId(), CheckForeignLoc(), CollapseDiscontinuitiesInUTR(), CSeq_loc::Compare(), CSeq_loc::CompareSubLoc(), CCleanup::ExtendStopPosition(), FinalCleanup(), GetEmblInstContig(), CAntiCodonColumn::GetFromFeat(), CReadBlastApp::getFromTo(), GetGenBankInstContig(), GetOverlappingFeatures(), GetSeqLocation(), CGuiObjectInfoPrimer::GetToolTip(), CWriteUtil::GetTranssplicedEndpoints(), CEditingActionFeatAnticodon::GetValue(), CFeaturePropagator::IsOrdered(), CSeq_loc_CI_Impl::MakeLoc(), CFeaturePropagator::MakeOrdered(), CGencollIdMapper::Map(), CAnnotObjectType_Less::operator()(), PreserveTerminalCodons(), CFeatureTableReader_Imp::ReadSequinFeatureTable(), RevComp(), CSeq_loc_Conversion::s_ConvertToMix(), s_GetTrimmedLength(), s_IsOrdered(), s_NeedsFlattening(), s_NormalizeNullsBetween(), s_SeqLoc2MaskedSubjRanges(), SeqLocPrintUseBestID(), SrchGene(), CFlatSeqLoc::x_Add(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CSGFeatureJob::x_CalcIntervals(), CSGFeatureJob::x_CreateCloneFeature(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CFeatureTableReader_Imp::x_FinishFeature(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CFeatureTableReader_Imp::x_GetPointStrand(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeatureGenerator::SImplementation::x_MapFeature(), CFeaturePropagator::x_MapLocation(), CSeq_loc_Mapper_Base::x_PushLocToDstMix(), x_PushRange(), variation::CVariationUtil::x_Remap(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CCDSTranslationPanel::x_SetLocationForProtein(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), CFeatureTableReader_Imp::x_UpdatePointStrand(), xgbloc_ver(), and XMLGetInstContig().
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Check if variant Named_annot_track is selected.
Named_annot_track type is defined as 'typedef CTextseq_id TNamed_annot_track'.
Definition at line 952 of file Seq_id_.hpp.
References CSeq_id_Base::e_Named_annot_track, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE().
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Check if variant Null is selected.
Definition at line 504 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Null, and CSeq_loc_Base::m_choice.
Referenced by FeatUtil::AddLocations(), CEditSequence::AdjustFeatureLocations(), CEditSequence::AdjustProtFeatureLocations(), CFeatTrim::Apply(), CDiscrepancyVisitorImpl< _Name >::Autofix(), Canonicalize(), CBioseqIndex::CBioseqIndex(), CLocationEditPolicy::ConvertToJoin(), variation::CreateUnknownProtConsequenceVariation(), GetDeltaSeqSummary(), CSeq_loc_mix::GetFirstLoc(), CReadBlastApp::getFromTo(), GetIdHandle(), CSeq_loc_mix::GetLastLoc(), CNSeq::Init(), C5ColImportData::Initialize(), CFastaObjectLoader::LoadFromStream(), CIdMapper::Map(), CLocMapper_Default::Map(), CGencollIdMapper::Map(), CSeq_loc_Mapper_Base::Map(), CFeatureGenerator::SImplementation::MergeSeq_locs(), CCompareSeqRegions::NextComparisonGroup(), CBedAnnotAssembler::ProcessRecord(), ProjectAndCollapseCDS(), RemapOtherProtFeats(), CFeatureLoadingJob::Run(), s_CombineDustMasksWithUserProvidedMasks(), s_FinishLoc(), s_FlattenLoc(), s_GetAlignmentSpans_Interval(), s_GetTrimmedLength(), s_MixStringAppend(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocAnyNull(), s_UpdateCodeBreaksAndAnticodons(), CBedImportData::Serialize(), CSeq_loc_mix::SetFirstLoc(), CSeq_loc_mix::SetLastLoc(), variation::CVariationUtil::TranslateNAtoAA(), TruncateToCDS(), CFlatSeqLoc::x_Add(), CFeatGapInfo::x_AdjustAnticodons(), CFeatGapInfo::x_AdjustCodebreaks(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSGAlignmentJob::x_CreateFeatGlyph(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), IEditingActionFeat::x_GetSublocOnBioseq(), CBioseqContext::x_IsDeltaLitOnly(), CGencollIdMapper::x_Map_Down(), CGencollIdMapper::x_Map_Up(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_id_Resolver__ChrNamesFromGC::x_MapLoc(), CFeaturePropagator::x_MapLocation(), variation::CHgvsParser::x_PlacementCoordsToStr(), CXcompareAnnotsApplication::x_ProcessMappingRange(), CXcompareAnnotsApplication::x_ProcessMappingRanges(), CSeq_loc_Mapper_Base::x_PushLocToDstMix(), CSeq_loc_Mapper_Base::x_PushRangesToDstMix(), CIdMapperTestApp::x_RecurseMapSeqAligns(), variation::CVariationUtil::x_Remap(), CReportTrim::x_RetranslateCDS(), CMasterContext::x_SetNumParts(), CFeatTrim::x_TrimLocation(), CCdregionValidator::x_ValidateCodebreak(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CValidError_align::x_ValidateSeqLength(), and xgbloc_ver().
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Check if variant Other is selected.
Other type is defined as 'typedef CTextseq_id TOther'.
Definition at line 871 of file Seq_id_.hpp.
References CSeq_id_Base::e_Other, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), Make_SeqID_String(), CValidError_imp::RequireLocalProduct(), s_DeflineCompare(), CValidError_bioseq::ValidateDeltaLoc(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CCdregionValidator::x_IsProductMisplaced(), CBulkEditFeatDlg::x_IsRefSeq(), CGenericPropsPanel::x_IsRefSeq(), CAlignFilter::x_Query_Op(), and CFeatureGenerator::SImplementation::x_SetQualForGapFilledModel().
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Check if variant Packed_int is selected.
Packed_int type is defined as 'typedef CPacked_seqint TPacked_int'.
Definition at line 534 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Packed_int, and CSeq_loc_Base::m_choice.
Referenced by CSeq_loc::Add(), CAdjustForConsensusSpliceSite::AdjustCDS(), BOOST_AUTO_TEST_CASE(), Canonicalize(), CollapseDiscontinuitiesInUTR(), CSeq_loc::CompareSubLoc(), CSequenceSearchForm::ConstructQuery(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CFeaturePropagator::CreateRowSeq_loc(), FinalCleanup(), CReadBlastApp::getFromTo(), CRemoteBlast::GetMasks(), GetOverlappingFeatures(), GetPositionsForAlignAnnot(), CWriteUtil::GetTranssplicedEndpoints(), IBISAnnotateDialog::HighlightAnnotation(), CDDAnnotateDialog::HighlightAnnotation(), CFastaObjectLoader::LoadFromStream(), MakeDDFromSeqLoc(), CSeq_loc_CI_Impl::MakeLoc(), CDDAnnotateDialog::NewOrEditMotif(), CAnnotObjectType_Less::operator()(), PackedSeqLocToMaskedQueryRegions(), PreserveTerminalCodons(), s_CombineDustMasksWithUserProvidedMasks(), s_ConvertToBlastQueries(), s_FlattenLoc(), s_GetTrimmedLength(), s_LocationToStartStopPairs(), s_SeqLoc2MaskedSubjRanges(), SeqLocPrintUseBestID(), NTweakExon::TweakExon(), CFlatSeqLoc::x_Add(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CSeq_loc::x_ChangeToPackedInt(), CAdjustForConsensusSpliceSite::x_CreateNewLocation(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CFeatGlyph::x_GetUndefinedBp_from(), CFeatGlyph::x_GetUndefinedBp_to(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeaturePropagator::x_MapLocation(), IEditingActionFeat::x_MergeFeatureLocation(), variation::CVariationUtil::x_Remap(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteFeatureRecords(), CGff3Writer::xWriteFeatureRna(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
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Check if variant Packed_pnt is selected.
Packed_pnt type is defined as 'typedef CPacked_seqpnt TPacked_pnt'.
Definition at line 546 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Packed_pnt, and CSeq_loc_Base::m_choice.
Referenced by CSeq_loc::Add(), CSequenceTrack::CSequenceTrack(), fta_check_con_for_wgs(), fta_seqloc_del_far(), GetOverlappingFeatures(), CSeq_loc_CI_Impl::MakeLoc(), PrintPntAndPntsUseBestID(), s_GetTrimmedLength(), SeqLocPrintUseBestID(), CSeq_loc::x_ChangeToPackedPnt(), and CFeaturePropagator::x_MapLocation().
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Check if variant Patent is selected.
Patent type is defined as 'typedef CPatent_seq_id TPatent'.
Definition at line 865 of file Seq_id_.hpp.
References CSeq_id_Base::e_Patent, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), GetAccessionAndDatabaseSource(), CSeq_id::WriteAsFasta(), and CSeq_id_Patent_Tree::x_Unindex().
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Check if variant Pdb is selected.
Pdb type is defined as 'typedef CPDB_seq_id TPdb'.
Definition at line 922 of file Seq_id_.hpp.
References CSeq_id_Base::e_Pdb, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), SeqSwapper::findReplacements(), AlignmentCollection::Get_GI_or_PDB_String_FromAlignment(), CCdCore::Get_GI_or_PDB_String_FromAlignment(), GetAccessionAndDatabaseSource(), CCdCore::GetGI(), AlignmentCollection::GetGI(), CCdCore::GetPDB(), AlignmentCollection::IsPdb(), Make_GI_or_PDB_String_CN3D(), Make_SeqID_String(), CDUpdater::mergePending(), LessBySeqId::operator()(), PdbBadRank(), ReMasterCdWithoutUnifiedBlocks(), RemasterWithStructure(), s_CompareIdList(), s_PreProcessAccessionsForDBv5(), CCdCore::SynchronizeMaster3D(), CAutogeneratedCleanup::x_BasicCleanupSeqId(), CGencollIdMapper::x_FixImperfectId(), CWriteDB_LMDB::x_InsertEntry(), and CSeq_id_PDB_Tree::x_Unindex().
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Check if variant Pir is selected.
Pir type is defined as 'typedef CTextseq_id TPir'.
Definition at line 853 of file Seq_id_.hpp.
References CSeq_id_Base::e_Pir, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), FTASeqLocCheck(), GetBlastSeqIdString(), s_PreProcessAccessionsForDBv5(), s_ProcessSeqIDsForV5(), s_UseFastaReaderDeflines(), CSeqDBImpl::SeqidToOids(), WriteBlastSeqidlistFile(), and CWriteDB_LMDB::x_InsertEntry().
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Check if variant Pnt is selected.
Pnt type is defined as 'typedef CSeq_point TPnt'.
Definition at line 540 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Pnt, and CSeq_loc_Base::m_choice.
Referenced by CSeq_loc::Add(), CAlignCDSAddPanel::AddOneCommand(), CAdjustForConsensusSpliceSite::AdjustCDS(), variation::CVariationUtil::AttachProteinConsequences(), BOOST_AUTO_TEST_CASE(), FixMixLoc(), CHTMLFormatterEx::FormatLocation(), fta_check_con_for_wgs(), fta_get_acc_minmax_strand(), fta_seqloc_del_far(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), CCleanup::GetProteinLocationFromNucleotideLocation(), CSeq_align::GetSeqRange(), variation::SFastLocSubtract::operator()(), CCleanup::ParseCodeBreak(), PrintPntAndPntsUseBestID(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_GetLength(), s_GetTrimmedLength(), s_IsBetween(), s_LocationToStartStopPairs(), s_MixStringAppend(), s_PrintLocAsJavascriptArray(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), s_SubsequentIntron(), SeqLocPrintUseBestID(), CReportEntry::SetCds(), CSeqTableSetLocFuzzFromLim::SetInt(), CBedFeatureRecord::SetLocation(), CBedFeatureRecord::SetNoThick(), CBedFeatureRecord::SetThick(), CFlatSeqLoc::x_Add(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), CSGFeatureJob::x_CalcIntervals(), CSeq_loc::x_ChangeToPackedPnt(), CFeatGlyph::x_DrawRSites(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CGuiObjectInfoSeq_feat::x_GetLocLengthRow(), CAlignedFeatureGraph::x_GetTooltip(), variation_ref::CHgvsParser::x_location(), variation::CHgvsParser::x_location(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation::CVariationUtil::x_Remap(), CReportEntry::x_SetRnaCds(), variation::CHgvsParser::x_ssr(), CAdjustForConsensusSpliceSite::x_UpdateLocation(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), and xgbloc_ver().
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Check if variant Prf is selected.
Prf type is defined as 'typedef CTextseq_id TPrf'.
Definition at line 916 of file Seq_id_.hpp.
References CSeq_id_Base::e_Prf, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), FTASeqLocCheck(), GetBlastSeqIdString(), s_PreProcessAccessionsForDBv5(), s_ProcessSeqIDsForV5(), s_UseFastaReaderDeflines(), CSeqDBImpl::SeqidToOids(), WriteBlastSeqidlistFile(), and CWriteDB_LMDB::x_InsertEntry().
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Check if a value has been assigned to data member.
Data member is mandatory; its type is defined as 'typedef list< CRef< CSeq_interval > > Tdata'
Definition at line 152 of file Packed_seqint_.hpp.
References CPacked_seqint_Base::m_set_State.
Referenced by SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), SplitLocationForGap(), CAutogeneratedCleanup::x_BasicCleanupPackedSeqInt(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), and CFeaturePropagator::x_MapLocation().
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Check if a value has been assigned to data member.
Data member is mandatory; its type is defined as 'typedef list< CRef< CSeq_id > > Tdata'
Definition at line 152 of file Seq_id_set_.hpp.
References CSeq_id_set_Base::m_set_State.
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Check if a value has been assigned to data member.
Data member is mandatory; its type is defined as 'typedef list< CRef< CSeq_loc > > Tdata'
Definition at line 153 of file Seq_loc_equiv_.hpp.
References CSeq_loc_equiv_Base::m_set_State.
Referenced by SplitLocationForGap(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_location_location_equiv_ETC(), and CAutogeneratedCleanup::x_BasicCleanupSeqLocEquiv().
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Check if a value has been assigned to data member.
Data member is mandatory; its type is defined as 'typedef list< CRef< CSeq_loc > > Tdata'
Definition at line 153 of file Seq_loc_mix_.hpp.
References CSeq_loc_mix_Base::m_set_State.
Referenced by CAlignCDSAddPanel::AddOneCommand(), CAlignRNAAddPanel::AddOneCommand(), CAlignOtherAddPanel::AddOneCommand(), CFeaturePropagator::MakeOrdered(), s_GetCodeBreak(), s_NormalizeNullsBetween(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), SplitLocationForGap(), CAutogeneratedCleanup::x_BasicCleanupSeqLocMix(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CFeaturePropagator::x_MapLocation(), and CFlatGatherer::x_RemoveBogusFuzzFromIntervals().
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connection to a least one residue Check if a value has been assigned to A data member.
Data member A is mandatory; its type is defined as 'typedef CSeq_point TA'
Definition at line 201 of file Seq_bond_.hpp.
References CSeq_bond_Base::m_A.
Referenced by fta_seqloc_del_far(), GetLength(), ReverseComplementLocation(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), UpgradeSeqLocId(), and CAutogeneratedCleanup::x_BasicCleanupSeqBond().
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Check if a value has been assigned to Accession data member.
Data member Accession is optional; its type is defined as 'typedef string TAccession'
Definition at line 328 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_set_State.
Referenced by AllowOrphanedProtein(), CTextseq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CTextseq_id_Base::CanGetAccession(), CBioseqIndex::CBioseqIndex(), CTextseq_id::Compare(), CpSeqId(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), CSeq_id_Textseq_Tree::FindInfo(), CSeq_id_Textseq_Tree::FindMatch(), CSeq_id_Textseq_Tree::FindOrCreate(), CSeq_id_Textseq_Tree::FindReverseMatch(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), fta_fix_seq_id(), get_accession_from_id(), GetAccession(), GetAccVer(), GetDirectLabel(), CWGSDataLoader_Impl::GetFileInfo(), GetFilteredRedundantSeqids(), GetLabel(), CBioseq::GetLabel(), CVDBGraphDb_Impl::GetSeqInfo(), GetWGSMasterSeq_id(), HasNameAndAccession(), CSeq_id::IdentifyAccession(), IsSegBioseq(), CValidError_bioseq::IsTSAAccession(), CValidError_bioseq::IsWGSAccession(), CValidError_bioseq::IsWp(), CTextseq_id::Match(), CWGSResolver_Ids::ParseWGSPrefix(), s_AssignTextseq_id(), s_Fingerprint_Textseq_id(), s_GetIdLabel(), s_GetModelEvidance(), s_IsRefSeqInSep(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CTextseq_id_Base::SetAccession(), CValidError_imp::Setup(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateOrgContext(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqIds(), x_Assign(), CGenbankGatherer::x_DoSingleSection(), CSeq_id_Textseq_Tree::x_Equals(), CSeq_id_Textseq_Tree::x_FindMatchByName(), CSeq_id_Textseq_Tree::x_FindStrInfo(), CGencollIdMapper::x_FixImperfectId(), x_GetId(), x_GetLabel_Content(), CTopLevelSeqEntryContext::x_InitSeqs(), CCdregionValidator::x_IsProductMisplaced(), CDeflineGenerator::x_SetFlags(), CLocusItem::x_SetName(), CValidError_bioseq::x_ShowBioProjectWarning(), CSeq_id_Textseq_Tree::x_Unindex(), CSingleFeatValidator::x_ValidateSeqFeatProduct(), and CFastaOstream::x_WriteAsFasta().
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other end may not be available Check if a value has been assigned to B data member.
Data member B is optional; its type is defined as 'typedef CSeq_point TB'
Definition at line 231 of file Seq_bond_.hpp.
References CSeq_bond_Base::m_B.
Referenced by CHandleRangeMap::AddLocation(), CSeq_bond_Base::CanGetB(), CSeq_loc_Conversion::ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), GetLength(), CSeq_bond::GetStart(), CSeq_bond::GetStop(), CSeq_bond::GetStrand(), CSeq_bond::IsSetStrand(), ReverseComplementLocation(), s_GetLabel(), s_GetStrand(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), UpgradeSeqLocId(), x_Assign(), CAutogeneratedCleanup::x_BasicCleanupSeqBond(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_CI_Impl::x_ProcessLocation().
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Deprecated: 'chain' can't support multiple character PDB chain identifiers (introduced in 2015).
'chain-id' stores chain identifiers of any length. Check if a value has been assigned to Chain data member.
Data member Chain is optional with default 32; its type is defined as 'typedef int TChain'
Definition at line 329 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_set_State.
Referenced by BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CSeq_id::ComposeOSLT(), CPDB_seq_id::GetEffectiveChain_id(), CPDB_seq_id::IsChainConflict(), CPDB_seq_id::Match(), CSeq_id_PDB_Info::Normalize(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CPDB_seq_id_Base::SetChain(), CValidError_bioseq::ValidateSeqId(), x_Assign(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), and CDeflineGenerator::x_SetFlags().
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chain identifier; length-independent generalization of 'chain' Check if a value has been assigned to Chain_id data member.
Data member Chain_id is optional; its type is defined as 'typedef string TChain_id'
Definition at line 400 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_set_State.
Referenced by CPDB_seq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CPDB_seq_id_Base::CanGetChain_id(), CBioseqIndex::CBioseqIndex(), CPDB_seq_id::Compare(), CSeq_id::ComposeOSLT(), CPDB_seq_id::GetEffectiveChain_id(), CPDB_seq_id::IsChainConflict(), CPDB_seq_id::Match(), CSeq_id_PDB_Info::Normalize(), s_CompareIdList(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CPDB_seq_id_Base::SetChain_id(), CValidError_bioseq::ValidateSeqId(), x_Assign(), CDBSourceItem::x_FormatDBSourceID(), x_GetLabel_Content(), and CDeflineGenerator::x_SetFlags().
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patent citation Check if a value has been assigned to Cit data member.
Data member Cit is mandatory; its type is defined as 'typedef CId_pat TCit'
Definition at line 247 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::m_Cit.
Referenced by CBioseqIndex::CBioseqIndex(), and CDeflineGenerator::x_SetFlags().
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dbase used in Check if a value has been assigned to Db data member.
Data member Db is optional; its type is defined as 'typedef string TDb'
Definition at line 290 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_set_State.
Referenced by CGiimport_id_Base::CanGetDb(), SChildLess::operator()(), s_Fingerprint_Giimport_id(), CGiimport_id_Base::SetDb(), and x_Assign().
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Check if a value has been assigned to From data member.
Data member From is mandatory; its type is defined as 'typedef TSeqPos TFrom'
Definition at line 364 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_set_State.
Referenced by CBedFeatureRecord::AssignLocation(), CSeq_interval_Base::CanGetFrom(), FixMixLoc(), ReverseComplementLocation(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_RemoveBogusFuzzFromIntervals_Helper(), CSeq_interval_Base::SetFrom(), CUCSCRegionWriter::WriteAnnot(), CValidError_imp::x_ReportInvalidFuzz(), and CGff3Writer::xAssignFeature().
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Check if a value has been assigned to Fuzz data member.
Data member Fuzz is optional; its type is defined as 'typedef CInt_fuzz TFuzz'
Definition at line 355 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_Fuzz.
Referenced by CPacked_seqpnt_Base::CanGetFuzz(), CSeq_loc_Conversion::ConvertPacked_pnt(), CPacked_seqpnt::IsPartialStart(), CPacked_seqpnt::IsPartialStop(), CPacked_seqpnt::IsTruncatedStart(), CPacked_seqpnt::IsTruncatedStop(), NormalizeLoc(), ReverseComplementLocation(), CSeq_loc_Conversion::s_ConvertToMix(), SeqLocPartialCheck(), x_Assign(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), and CSeq_loc_CI_Impl::x_ProcessLocation().
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Check if a value has been assigned to Fuzz data member.
Data member Fuzz is optional; its type is defined as 'typedef CInt_fuzz TFuzz'
Definition at line 408 of file Seq_point_.hpp.
References CSeq_point_Base::m_Fuzz.
Referenced by CSeq_point_Base::CanGetFuzz(), CSeq_loc_Conversion::ConvertPoint(), FixMixLoc(), GetLowHighFromSeqLoc(), CSeq_point::IsLeftOf(), CSeq_point::IsPartialStart(), CSeq_point::IsPartialStop(), variation::IsPureFuzzPoint(), CSeq_point::IsRightOf(), CSeq_point::IsTruncatedStart(), CSeq_point::IsTruncatedStop(), SSNP_Info::ParseSeq_feat(), ReverseComplementLocation(), s_GetLabel(), s_IsBetween(), s_Load_Seq_point(), s_PrintLocAsJavascriptArray(), SeqLocPartialCheck(), CFlatSeqLoc::x_Add(), x_Assign(), CSeq_loc::x_ChangeToPackedPnt(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessPoint(), variation_ref::CHgvsParser::x_range(), variation::CHgvsParser::x_range(), CValidError_imp::x_ReportInvalidFuzz(), and CNewCleanup_imp::x_SeqPointBC().
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Check if a value has been assigned to Fuzz_from data member.
Data member Fuzz_from is optional; its type is defined as 'typedef CInt_fuzz TFuzz_from'
Definition at line 535 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_Fuzz_from.
Referenced by CSeq_interval_Base::CanGetFuzz_from(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), EndAdded(), FixMixLoc(), GetLowHighFromSeqLoc(), CSeq_interval::IsPartialStart(), CSeq_interval::IsPartialStop(), CSeq_interval::IsTruncatedStart(), CSeq_interval::IsTruncatedStop(), SSNP_Info::ParseSeq_feat(), ReverseComplementLocation(), s_GetLabel(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_RemoveBogusFuzzFromIntervals_Helper(), sConvertIntToPoint(), SeqIntPartialCheck(), x_Assign(), CGvfWriteRecord::x_AssignAttributeStartRange(), CFeatGlyph::x_DrawFeatureBar_sv(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFeatGlyph::x_GetUndefinedBp_from(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessInterval(), variation::CVariationUtil::x_Remap(), and CValidError_imp::x_ReportInvalidFuzz().
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Check if a value has been assigned to Fuzz_to data member.
Data member Fuzz_to is optional; its type is defined as 'typedef CInt_fuzz TFuzz_to'
Definition at line 556 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_Fuzz_to.
Referenced by CSeq_interval_Base::CanGetFuzz_to(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), EndAdded(), FixMixLoc(), GetLowHighFromSeqLoc(), CSeq_interval::IsPartialStart(), CSeq_interval::IsPartialStop(), CSeq_interval::IsTruncatedStart(), CSeq_interval::IsTruncatedStop(), SSNP_Info::ParseSeq_feat(), ReverseComplementLocation(), s_GetLabel(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_RemoveBogusFuzzFromIntervals_Helper(), SeqIntPartialCheck(), x_Assign(), CGvfWriteRecord::x_AssignAttributeEndRange(), CFeatGlyph::x_DrawFeatureBar_sv(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFeatGlyph::x_GetUndefinedBp_to(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), variation::CHgvsParser::x_PlacementCoordsToStr(), CSeq_loc_CI_Impl::x_ProcessInterval(), variation::CVariationUtil::x_Remap(), and CValidError_imp::x_ReportInvalidFuzz().
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the id to use here Check if a value has been assigned to Id data member.
Data member Id is mandatory; its type is defined as 'typedef int TId'
Definition at line 243 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_set_State.
Referenced by CGiimport_id_Base::CanGetId(), and CGiimport_id_Base::SetId().
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Check if a value has been assigned to Id data member.
Data member Id is mandatory; its type is defined as 'typedef CSeq_id TId'
Definition at line 325 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_Id.
Referenced by NormalizeLoc(), s_Fingerprint_Packed_seqpnt(), UpgradeSeqLocId(), and CAutogeneratedCleanup::x_BasicCleanupPackedPoint().
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WARNING: this used to be optional Check if a value has been assigned to Id data member.
Data member Id is mandatory; its type is defined as 'typedef CSeq_id TId'
Definition at line 505 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_Id.
Referenced by BOOST_AUTO_TEST_CASE(), FixMixLoc(), fta_get_acc_minmax_strand(), OkToAdjustLoc(), ReverseComplementLocation(), s_Fingerprint_Seq_interval(), s_IsVirtualSeqInt(), sConvertIntToPoint(), UpgradeSeqLocId(), CAutogeneratedCleanup::x_BasicCleanupSeqInt(), and CNewCleanup_imp::x_SeqIntervalBC().
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WARNING: this used to be optional Check if a value has been assigned to Id data member.
Data member Id is mandatory; its type is defined as 'typedef CSeq_id TId'
Definition at line 378 of file Seq_point_.hpp.
References CSeq_point_Base::m_Id.
Referenced by FixMixLoc(), fta_get_acc_minmax_strand(), OkToAdjustLoc(), ReverseComplementLocation(), s_Fingerprint_Seq_point(), s_Load_Seq_point(), UpgradeSeqLocId(), CAutogeneratedCleanup::x_BasicCleanupSeqPoint(), CSeq_loc::x_ChangeToPackedPnt(), CValidError_imp::x_ReportInvalidFuzz(), and CNewCleanup_imp::x_SeqPointBC().
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the molecule name Check if a value has been assigned to Mol data member.
Data member Mol is mandatory; its type is defined as 'typedef CPDB_mol_id TMol'
Definition at line 294 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_set_State.
Referenced by CPDB_seq_id_Base::CanGetMol().
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Check if a value has been assigned to Name data member.
Data member Name is optional; its type is defined as 'typedef string TName'
Definition at line 281 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_set_State.
Referenced by CTextseq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CTextseq_id_Base::CanGetName(), CTextseq_id::Compare(), CpSeqId(), CSeq_id_Textseq_Tree::FindInfo(), CSeq_id_Textseq_Tree::FindMatch(), CSeq_id_Textseq_Tree::FindOrCreate(), CSeq_id_Textseq_Tree::FindReverseMatch(), GetLabel(), CVDBGraphDb_Impl::GetSeqInfo(), HasNameAndAccession(), IsAccessionNoVersion(), IsSegBioseq(), CTextseq_id::Match(), CWGSResolver_Ids::ParseWGSPrefix(), s_AssignTextseq_id(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CTextseq_id_Base::SetName(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqIds(), x_Assign(), CSeq_id_Textseq_Tree::x_Equals(), CSeq_id_Textseq_Tree::x_FindStrInfo(), x_GetLabel_Content(), CLocusItem::x_SetName(), CSeq_id_Textseq_Tree::x_Unindex(), and CSingleFeatValidator::x_ValidateSeqFeatProduct().
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Check if a value has been assigned to Point data member.
Data member Point is mandatory; its type is defined as 'typedef TSeqPos TPoint'
Definition at line 284 of file Seq_point_.hpp.
References CSeq_point_Base::m_set_State.
Referenced by CSeq_point_Base::CanGetPoint(), FixMixLoc(), ReverseComplementLocation(), SeqLocAdjustForInsert(), CSeq_point_Base::SetPoint(), CValidError_imp::x_ReportInvalidFuzz(), and CBioseqContext::x_SetOpticalMapPoints().
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Check if a value has been assigned to Points data member.
Data member Points is mandatory; its type is defined as 'typedef vector< TSeqPos > TPoints'
Definition at line 376 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_set_State.
Referenced by CorrectIntervalOrder(), ReverseComplementLocation(), s_GetCodeBreak(), and CFeaturePropagator::x_MapLocation().
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release date, month and year Check if a value has been assigned to Rel data member.
Data member Rel is optional; its type is defined as 'typedef CDate TRel'
Definition at line 379 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_Rel.
Referenced by CPDB_seq_id_Base::CanGetRel(), CSeq_id_PDB_Tree::FindMatch(), CSeq_id_PDB_Tree::FindReverseMatch(), CSeq_id_PDB_Info::Normalize(), x_Assign(), and CAutogeneratedCleanup::x_BasicCleanupSeqId().
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the release Check if a value has been assigned to Release data member.
Data member Release is optional; its type is defined as 'typedef string TRelease'
Definition at line 337 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_set_State.
Referenced by CGiimport_id_Base::CanGetRelease(), SChildLess::operator()(), s_Fingerprint_Giimport_id(), CGiimport_id_Base::SetRelease(), and x_Assign().
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Check if a value has been assigned to Release data member.
Data member Release is optional; its type is defined as 'typedef string TRelease'
Definition at line 375 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_set_State.
Referenced by BOOST_AUTO_TEST_CASE(), CTextseq_id_Base::CanGetRelease(), CSeq_id_Textseq_Tree::FindInfo(), CSeq_id_Textseq_Tree::FindOrCreate(), CVDBGraphDb_Impl::GetSeqInfo(), IsAccessionNoVersion(), s_AssignTextseq_id(), s_Fingerprint_Textseq_id(), CTextseq_id_Base::SetRelease(), x_Assign(), CSeq_id_Textseq_Tree::x_Equals(), and CSeq_id_Textseq_Tree::x_FindMatchByName().
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number of sequence in patent Check if a value has been assigned to Seqid data member.
Data member Seqid is mandatory; its type is defined as 'typedef int TSeqid'
Definition at line 200 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::m_set_State.
Referenced by CPatent_seq_id_Base::CanGetSeqid(), CBioseqIndex::CBioseqIndex(), CPatent_seq_id_Base::SetSeqid(), and CDeflineGenerator::x_SetFlags().
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Check if a value has been assigned to Strand data member.
Data member Strand is optional; its type is defined as 'typedef ENa_strand TStrand'
Definition at line 278 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_set_State.
Referenced by CHandleRangeMap::AddLocation(), CPacked_seqpnt_Base::CanGetStrand(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CorrectIntervalOrder(), CPacked_seqpnt::FlipStrand(), GetStrand(), CSeq_loc::GetStrand(), CSeq_loc::IsSetStrand(), NormalizeLoc(), CSeq_loc_Conversion::s_ConvertToMix(), s_GetStrand(), CPacked_seqpnt_Base::SetStrand(), CSeqMap::x_Add(), CFlatSeqLoc::x_Add(), x_Assign(), CPacked_seqpnt::x_IsMinusStrand(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), CSeq_loc_CI_Impl::x_ProcessLocation(), and CBioseq::x_SeqLoc_To_DeltaExt().
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Check if a value has been assigned to Strand data member.
Data member Strand is optional; its type is defined as 'typedef ENa_strand TStrand'
Definition at line 458 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_set_State.
Referenced by CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), CSeq_interval_Base::CanGetStrand(), CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion::ConvertSimpleMix(), EndAdded(), CSeq_interval::FlipStrand(), fta_get_acc_minmax_strand(), CWriteUtil::GetEffectiveStrand(), GetLowHighFromSeqLoc(), GetOverlappingFeatures(), CSeqMap::GetSeqMapForSeq_loc(), GetStrand(), CSeq_loc::GetStrand(), CWriteUtil::GetTrnaAntiCodon(), CSeq_loc::IsSetStrand(), CSeq_loc_Conversion::MakeDstMix(), NTweakExon::MinusStrand(), CAssemblyTrackingPanel::OnPopulateBtnClick(), SCigarAlignment::operator()(), SSNP_Info::ParseSeq_feat(), RevComp(), s_ExtendIntervalToEnd(), s_GetCodeBreak(), s_GetLabel(), s_GetSeq_intervalLabel(), s_GetStrand(), SeqIntPartialCheck(), SeqLocAdjustForTrim(), CGffFeatureRecord::SetLocation(), CBedFeatureRecord::SetLocation(), CSeq_interval_Base::SetStrand(), CUCSCRegionWriter::WriteAnnot(), CSeqMap::x_Add(), x_Assign(), CValidError_imp::x_CheckSeqInt(), CSeq_align_Mapper_Base::x_Init(), CAnnotTypes_CI::x_Init(), x_IsCorrectlyOrdered(), CSeq_interval::x_IsMinusStrand(), x_IsNotAdjacent(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CGFFReader::x_ParseAlignRecord(), CSeq_loc_CI_Impl::x_ProcessInterval(), x_SameStrand(), CAnnot_Collector::x_SearchRange(), CNewCleanup_imp::x_SeqIntervalBC(), CGtfWriter::xAssignFeaturesCds(), and CGtfWriter::xAssignFeaturesGene().
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Check if a value has been assigned to Strand data member.
Data member Strand is optional; its type is defined as 'typedef ENa_strand TStrand'
Definition at line 331 of file Seq_point_.hpp.
References CSeq_point_Base::m_set_State.
Referenced by CHandleRangeMap::AddLocation(), CSeq_point_Base::CanGetStrand(), CSeq_loc_Conversion::ConvertPoint(), CSeq_point::FlipStrand(), fta_get_acc_minmax_strand(), GetLowHighFromSeqLoc(), GetStrand(), CSeq_bond::GetStrand(), CSeq_loc::GetStrand(), CSeq_bond::IsSetStrand(), CSeq_loc::IsSetStrand(), SSNP_Info::ParseSeq_feat(), s_GetCodeBreak(), s_GetLabel(), s_GetStrand(), s_Load_Seq_point(), CBedFeatureRecord::SetLocation(), CSeq_point_Base::SetStrand(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), x_Assign(), CSeq_loc::x_ChangeToPackedPnt(), CSeq_align_Mapper_Base::x_Init(), CSeq_point::x_IsMinusStrand(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_CI_Impl::x_ProcessPoint(), and CNewCleanup_imp::x_SeqPointBC().
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Check if a value has been assigned to To data member.
Data member To is mandatory; its type is defined as 'typedef TSeqPos TTo'
Definition at line 411 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_set_State.
Referenced by CBedFeatureRecord::AssignLocation(), CSeq_interval_Base::CanGetTo(), FixMixLoc(), ReverseComplementLocation(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_RemoveBogusFuzzFromIntervals_Helper(), CSeq_interval_Base::SetTo(), CUCSCRegionWriter::WriteAnnot(), CValidError_imp::x_ReportInvalidFuzz(), and CGff3Writer::xAssignFeature().
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Check if a value has been assigned to Version data member.
Data member Version is optional; its type is defined as 'typedef int TVersion'
Definition at line 422 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_set_State.
Referenced by CTextseq_id::AsFastaString(), BOOST_AUTO_TEST_CASE(), CTextseq_id_Base::CanGetVersion(), CheckAccession(), CAlnMix::ChooseSeqId(), CTextseq_id::Compare(), CSeq_id::ComposeOSLT(), CpSeqId(), CpSeqIdAcOnly(), CWGSFileInfo::FindProtAcc(), flat2asn_range_func(), get_accession_from_id(), GetAccVer(), CDefaultSynonymMapper::GetBestSynonym(), GetDirectLabel(), GetLabel(), CSeq_id::GetLabel(), GetNormalizedSeqId(), CVDBGraphDb_Impl::GetSeqInfo(), IsAccessionNoVersion(), CTextseq_id::Match(), CSeq_id_Textseq_Info::ParseAcc(), CWGSClient::Resolve(), s_AssignTextseq_id(), s_GetBestSynonym(), s_GetModelEvidance(), s_ValidateAcc(), CValidError_imp::Setup(), CTextseq_id_Base::SetVersion(), StrippedAccVer(), CWGSFileInfo::SAccFileInfo::ValidateAcc(), CValidError_bioseq::ValidateSeqIds(), x_Assign(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CComponentSearchJob::x_DoSearch(), CSeq_id_Textseq_Tree::x_Equals(), CSeq_id_Textseq_Tree::x_FindMatchByAcc(), CSeq_id_Textseq_Tree::x_FindRevMatchByAcc(), CSeq_id_Textseq_Tree::x_FindRevMatchByAccNonPacked(), CGencollIdMapper::x_FixImperfectId(), x_GetLabel_Content(), CSeq_id_Textseq_Tree::x_GetVersion(), CBuildDatabase::x_ResolveRemoteId(), and CFastaOstream::x_WriteAsFasta().
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Check if variant Swissprot is selected.
Swissprot type is defined as 'typedef CTextseq_id TSwissprot'.
Definition at line 859 of file Seq_id_.hpp.
References CSeq_id_Base::e_Swissprot, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), FTASeqLocCheck(), CSeq_id::WriteAsFasta(), and CDBSourceItem::x_FormatDBSourceID().
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Check if variant Tpd is selected.
Tpd type is defined as 'typedef CTextseq_id TTpd'.
Definition at line 940 of file Seq_id_.hpp.
References CSeq_id_Base::e_Tpd, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), s_GetNameForBioseq(), and CValidError_bioseq::ValidateDeltaLoc().
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Check if variant Tpe is selected.
Tpe type is defined as 'typedef CTextseq_id TTpe'.
Definition at line 934 of file Seq_id_.hpp.
References CSeq_id_Base::e_Tpe, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), s_GetNameForBioseq(), and CValidError_bioseq::ValidateDeltaLoc().
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Check if variant Tpg is selected.
Tpg type is defined as 'typedef CTextseq_id TTpg'.
Definition at line 928 of file Seq_id_.hpp.
References CSeq_id_Base::e_Tpg, and CSeq_id_Base::m_choice.
Referenced by BOOST_AUTO_TEST_CASE(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), FTASeqLocCheck(), s_GetNameForBioseq(), and CValidError_bioseq::ValidateDeltaLoc().
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Check if variant Whole is selected.
Whole type is defined as 'typedef CSeq_id TWhole'.
Definition at line 522 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Whole, and CSeq_loc_Base::m_choice.
Referenced by CGBProjectHelper::AddProjectItemsFromRID(), CFeatGapInfo::AdjustForRelevantGapIntervals(), CFeatGapInfo::AdjustProteinSeq(), BOOST_AUTO_TEST_CASE(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CNewCleanup_imp::ConvertSeqLocWholeToInt(), CProSplign::FindGlobalAlignment(), CGenbankFormatter::FormatAccession(), fta_check_con_for_wgs(), fta_seqloc_del_far(), CApplyRNAITSDlg::GetCommand(), CProteinAlignText::GetGenomicBounds(), GetIdStartStopStrandStr(), CBlastInput::GetNextSeqBatch(), GetOverlappingFeatures(), CSeqMap::GetSeqMapForSeq_loc(), GetStop(), GetValidatorLocationLabel(), CViewGraphic::InitView(), RemapAlignToLoc(), CDense_seg::RemapToLoc(), CCleanup::RepackageProteins(), s_CombineDustMasksWithUserProvidedMasks(), s_ConvertWholeToInt(), s_CreateObjList(), s_EliminateDuplicates(), s_GetCdsSequence(), s_RemapToSubjectLoc(), s_ShouldRemoveRef(), CSeqUtils::SeqLocToBioseq(), TranslateCodingRegionForValidation(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddQualsProt(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CBLASTSeqToolJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CProSplignJob::x_CreateProjectItems(), CImportFeatTable::x_DoImportCDS(), CComponentSearchJob::x_DoSearch(), CGenbankGatherer::x_DoSingleSection(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CCreateGeneModelTask::x_GetCommand(), CMultiAligner::x_GetSeqalign(), CSeq_align_Mapper_Base::x_Init(), CAnnotTypes_CI::x_Init(), variation::CHgvsParser::x_no_change(), variation::CHgvsParser::x_PlacementCoordsToStr(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CProSplignTool::x_SelectCompatibleInputObjects(), CSplignTool::x_SelectCompatibleInputObjects(), CBioseqContext::x_SetLocation(), CLocusItem::x_SetTopology(), CSingleFeatValidator::x_ValidateFeatPartialness(), CSingleFeatValidator::x_ValidateSeqFeatLoc(), CValidError_align::x_ValidateSeqLength(), CGff3Writer::xAssignFeature(), and CFeatureTableReader::xTranslateProtein().
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Conversion operator to 'const Tdata' type.
Definition at line 177 of file Packed_seqint_.hpp.
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Conversion operator to 'const Tdata' type.
Definition at line 177 of file Seq_id_set_.hpp.
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Conversion operator to 'const Tdata' type.
Definition at line 178 of file Seq_loc_equiv_.hpp.
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Conversion operator to 'const Tdata' type.
Definition at line 178 of file Seq_loc_mix_.hpp.
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Conversion operator to 'Tdata' type.
Definition at line 183 of file Packed_seqint_.hpp.
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Conversion operator to 'Tdata' type.
Definition at line 183 of file Seq_id_set_.hpp.
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Conversion operator to 'Tdata' type.
Definition at line 184 of file Seq_loc_equiv_.hpp.
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Conversion operator to 'Tdata' type.
Definition at line 184 of file Seq_loc_mix_.hpp.
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Definition at line 108 of file PDB_mol_id_.hpp.
References str(), and WriteObject().
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Definition at line 119 of file PDB_mol_id_.hpp.
References ReadObject(), and str().
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Reset the whole object.
Definition at line 62 of file Giimport_id_.cpp.
References CGiimport_id_Base::ResetDb(), CGiimport_id_Base::ResetId(), and CGiimport_id_Base::ResetRelease().
void CPacked_seqint_Base::Reset | ( | void | ) |
Reset data member.
Definition at line 51 of file Packed_seqint_.cpp.
References CPacked_seqint_Base::m_data, and CPacked_seqint_Base::m_set_State.
Referenced by SeqLocAdjustForTrim().
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Reset the whole object.
Definition at line 89 of file Packed_seqpnt_.cpp.
References CPacked_seqpnt_Base::ResetFuzz(), CPacked_seqpnt_Base::ResetId(), CPacked_seqpnt_Base::ResetPoints(), and CPacked_seqpnt_Base::ResetStrand().
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Reset the whole object.
Definition at line 65 of file Patent_seq_id_.cpp.
References CPatent_seq_id_Base::ResetCit(), and CPatent_seq_id_Base::ResetSeqid().
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Reset the whole object.
Definition at line 80 of file PDB_seq_id_.cpp.
References CPDB_seq_id_Base::ResetChain(), CPDB_seq_id_Base::ResetChain_id(), CPDB_seq_id_Base::ResetMol(), and CPDB_seq_id_Base::ResetRel().
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Reset the whole object.
Definition at line 82 of file Seq_bond_.cpp.
References CSeq_bond_Base::ResetA(), and CSeq_bond_Base::ResetB().
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Reset the whole object.
Definition at line 56 of file Seq_id_.cpp.
References CSeq_id_Base::e_not_set, CSeq_id_Base::m_choice, and CSeq_id_Base::ResetSelection().
Referenced by CSeq_id::Assign(), CAlnMix::ChooseSeqId(), DbxrefToSeqID(), CCDSTranslationPanel::GetProductId(), CTMgr_GenomeContext_Base::C_Assembly_and_sequence::SetSequence(), and CSeq_id_Base::~CSeq_id_Base().
void CSeq_id_set_Base::Reset | ( | void | ) |
Reset data member.
Definition at line 51 of file Seq_id_set_.cpp.
References CSeq_id_set_Base::m_data, and CSeq_id_set_Base::m_set_State.
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Reset the whole object.
Definition at line 100 of file Seq_interval_.cpp.
References CSeq_interval_Base::ResetFrom(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_interval_Base::ResetId(), CSeq_interval_Base::ResetStrand(), and CSeq_interval_Base::ResetTo().
Referenced by CSeqTree_node_Base::C_Children::C_Footprint::SetSeqRange().
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Reset the whole object.
Definition at line 59 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_not_set, CSeq_loc_Base::m_choice, and CSeq_loc_Base::ResetSelection().
Referenced by CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CGff3LocationMerger::GetLocation(), CSNPDbFeatIterator::GetSeq_feat(), CBedImportData::Initialize(), NormalizeLoc(), CBedAnnotAssembler::ProcessRecord(), s_BuildMaskedRanges(), SplitLocationForGap(), CAnnotMapping_Info::UpdateMappedSeq_loc(), xgbloc_ver(), CExonNumberAssigner::xInitialize(), and CSeq_loc_Base::~CSeq_loc_Base().
void CSeq_loc_equiv_Base::Reset | ( | void | ) |
Reset data member.
Definition at line 51 of file Seq_loc_equiv_.cpp.
References CSeq_loc_equiv_Base::m_data, and CSeq_loc_equiv_Base::m_set_State.
void CSeq_loc_mix_Base::Reset | ( | void | ) |
Reset data member.
Definition at line 51 of file Seq_loc_mix_.cpp.
References CSeq_loc_mix_Base::m_data, and CSeq_loc_mix_Base::m_set_State.
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Reset the whole object.
Definition at line 83 of file Seq_point_.cpp.
References CSeq_point_Base::ResetFuzz(), CSeq_point_Base::ResetId(), CSeq_point_Base::ResetPoint(), and CSeq_point_Base::ResetStrand().
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Reset the whole object.
Definition at line 68 of file Textseq_id_.cpp.
References CTextseq_id_Base::ResetAccession(), CTextseq_id_Base::ResetName(), CTextseq_id_Base::ResetRelease(), and CTextseq_id_Base::ResetVersion().
Referenced by CSeq_id::GetMatchingTextseqIds(), and GetWGSMasterSeq_id().
void CSeq_bond_Base::ResetA | ( | void | ) |
Reset A data member.
Definition at line 51 of file Seq_bond_.cpp.
References CSeq_bond_Base::m_A.
Referenced by CSeq_bond_Base::CSeq_bond_Base(), CSeq_bond_Base::GetA(), CSeq_bond_Base::Reset(), and CSeq_bond_Base::SetA().
void CTextseq_id_Base::ResetAccession | ( | void | ) |
Reset Accession data member.
Definition at line 56 of file Textseq_id_.cpp.
References CTextseq_id_Base::m_Accession, and CTextseq_id_Base::m_set_State.
Referenced by CTextseq_id_Base::Reset(), CTextseq_id::Set(), and x_Assign().
void CSeq_bond_Base::ResetB | ( | void | ) |
Reset B data member.
Definition at line 65 of file Seq_bond_.cpp.
References CSeq_bond_Base::m_B.
Referenced by CSeq_bond_Base::Reset(), and x_Assign().
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Reset Chain data member.
Definition at line 341 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_Chain, and CPDB_seq_id_Base::m_set_State.
Referenced by CSeq_id_PDB_Info::GetPackedSeqId(), CPDB_seq_id_Base::Reset(), CPDB_seq_id::ResetChainIdentifiers(), CSeq_id::Set(), CPDB_seq_id::SetChainIdentifiers(), CPDB_seq_id_Base::SetDefaultChain(), and x_Assign().
void CPDB_seq_id_Base::ResetChain_id | ( | void | ) |
Reset Chain_id data member.
Definition at line 74 of file PDB_seq_id_.cpp.
References CPDB_seq_id_Base::m_Chain_id, and CPDB_seq_id_Base::m_set_State.
Referenced by CSeq_id_PDB_Info::GetPackedSeqId(), CPDB_seq_id_Base::Reset(), CPDB_seq_id::ResetChainIdentifiers(), CSeq_id::Set(), and x_Assign().
void CPatent_seq_id_Base::ResetCit | ( | void | ) |
Reset Cit data member.
Definition at line 51 of file Patent_seq_id_.cpp.
References CPatent_seq_id_Base::m_Cit.
Referenced by CPatent_seq_id_Base::CPatent_seq_id_Base(), CPatent_seq_id_Base::GetCit(), CPatent_seq_id_Base::Reset(), and CPatent_seq_id_Base::SetCit().
void CGiimport_id_Base::ResetDb | ( | void | ) |
Reset Db data member.
Definition at line 50 of file Giimport_id_.cpp.
References CGiimport_id_Base::m_Db, and CGiimport_id_Base::m_set_State.
Referenced by CGiimport_id_Base::Reset(), CSeq_id::Set(), and x_Assign().
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Reset From data member.
Definition at line 376 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_From, and CSeq_interval_Base::m_set_State.
Referenced by CSeq_interval_Base::Reset(), and ReverseComplementLocation().
void CPacked_seqpnt_Base::ResetFuzz | ( | void | ) |
Reset Fuzz data member.
Definition at line 66 of file Packed_seqpnt_.cpp.
References CPacked_seqpnt_Base::m_Fuzz.
Referenced by CPacked_seqpnt_Base::Reset(), CPacked_seqpnt::SetPartialStart(), CPacked_seqpnt::SetPartialStop(), CPacked_seqpnt::SetTruncatedStart(), CPacked_seqpnt::SetTruncatedStop(), and x_Assign().
void CSeq_point_Base::ResetFuzz | ( | void | ) |
Reset Fuzz data member.
Definition at line 66 of file Seq_point_.cpp.
References CSeq_point_Base::m_Fuzz.
Referenced by CSeq_point_Base::Reset(), CSeq_point::SetLeftOf(), CSeq_point::SetPartialStart(), CSeq_point::SetPartialStop(), CSeq_point::SetRightOf(), CSeq_point::SetTruncatedStart(), CSeq_point::SetTruncatedStop(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeq_loc_CI_Impl::UpdatePoint(), CSeqTableLocColumns::UpdateSeq_loc(), x_Assign(), and SSNP_Info::x_UpdateSeq_feat().
void CSeq_interval_Base::ResetFuzz_from | ( | void | ) |
Reset Fuzz_from data member.
Definition at line 66 of file Seq_interval_.cpp.
References CSeq_interval_Base::m_Fuzz_from.
Referenced by CSeq_interval_Base::Reset(), ReverseComplementLocation(), s_FixIntervalProtToCds(), s_RemoveBogusFuzzFromIntervals_Helper(), CSeq_interval::SetPartialStart(), CSeq_interval::SetPartialStop(), CSeq_interval::SetTruncatedStart(), CSeq_interval::SetTruncatedStop(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), x_Assign(), and CSeqMap::x_DoUpdateSeq_inst().
void CSeq_interval_Base::ResetFuzz_to | ( | void | ) |
Reset Fuzz_to data member.
Definition at line 83 of file Seq_interval_.cpp.
References CSeq_interval_Base::m_Fuzz_to.
Referenced by CSeq_interval_Base::Reset(), ReverseComplementLocation(), s_FixIntervalProtToCds(), s_RemoveBogusFuzzFromIntervals_Helper(), CSeq_interval::SetPartialStart(), CSeq_interval::SetPartialStop(), CSeq_interval::SetTruncatedStart(), CSeq_interval::SetTruncatedStop(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), x_Assign(), and CSeqMap::x_DoUpdateSeq_inst().
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Reset Id data member.
Definition at line 255 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_Id, and CGiimport_id_Base::m_set_State.
Referenced by CGiimport_id_Base::Reset().
void CPacked_seqpnt_Base::ResetId | ( | void | ) |
Reset Id data member.
Definition at line 52 of file Packed_seqpnt_.cpp.
References CPacked_seqpnt_Base::m_Id.
Referenced by CPacked_seqpnt_Base::CPacked_seqpnt_Base(), CPacked_seqpnt_Base::GetId(), CPacked_seqpnt_Base::Reset(), and CPacked_seqpnt_Base::SetId().
void CSeq_interval_Base::ResetId | ( | void | ) |
Reset Id data member.
Definition at line 52 of file Seq_interval_.cpp.
References CSeq_interval_Base::m_Id.
Referenced by CSeq_interval_Base::CSeq_interval_Base(), CSeq_interval_Base::GetId(), CSeq_interval_Base::Reset(), and CSeq_interval_Base::SetId().
void CSeq_point_Base::ResetId | ( | void | ) |
Reset Id data member.
Definition at line 52 of file Seq_point_.cpp.
References CSeq_point_Base::m_Id.
Referenced by CSeq_point_Base::CSeq_point_Base(), CSeq_point_Base::GetId(), CSeq_point_Base::Reset(), and CSeq_point_Base::SetId().
void CPDB_seq_id_Base::ResetMol | ( | void | ) |
Reset Mol data member.
Definition at line 51 of file PDB_seq_id_.cpp.
References CPDB_seq_id_Base::m_Mol, CPDB_seq_id_Base::m_set_State, and CAliasBase< TPrim >::Set().
Referenced by CPDB_seq_id_Base::Reset().
void CTextseq_id_Base::ResetName | ( | void | ) |
Reset Name data member.
Definition at line 50 of file Textseq_id_.cpp.
References CTextseq_id_Base::m_Name, and CTextseq_id_Base::m_set_State.
Referenced by CBioseq::GetLabel(), CTextseq_id_Base::Reset(), CTextseq_id::Set(), CIdMapperGCAssembly::x_AddUnversionedMapping(), x_Assign(), CRemoveName::x_GetReplacementIds(), and CScope_Impl::x_GetSynonyms().
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Reset Point data member.
Definition at line 296 of file Seq_point_.hpp.
References CSeq_point_Base::m_Point, and CSeq_point_Base::m_set_State.
Referenced by CSeq_point_Base::Reset().
void CPacked_seqpnt_Base::ResetPoints | ( | void | ) |
Reset Points data member.
Definition at line 83 of file Packed_seqpnt_.cpp.
References CPacked_seqpnt_Base::m_Points, and CPacked_seqpnt_Base::m_set_State.
Referenced by CPacked_seqpnt_Base::Reset(), and ReverseComplementLocation().
void CPDB_seq_id_Base::ResetRel | ( | void | ) |
Reset Rel data member.
Definition at line 57 of file PDB_seq_id_.cpp.
References CPDB_seq_id_Base::m_Rel.
Referenced by CPDB_seq_id_Base::Reset(), CSeq_id::Set(), and x_Assign().
void CGiimport_id_Base::ResetRelease | ( | void | ) |
Reset Release data member.
Definition at line 56 of file Giimport_id_.cpp.
References CGiimport_id_Base::m_Release, and CGiimport_id_Base::m_set_State.
Referenced by CGiimport_id_Base::Reset(), CSeq_id::Set(), and x_Assign().
void CTextseq_id_Base::ResetRelease | ( | void | ) |
Reset Release data member.
Definition at line 62 of file Textseq_id_.cpp.
References CTextseq_id_Base::m_Release, and CTextseq_id_Base::m_set_State.
Referenced by CSeq_id::GetMatchingTextseqIds(), CTextseq_id_Base::Reset(), CTextseq_id::Set(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and x_Assign().
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Reset the selection (set it to e_not_set).
Definition at line 62 of file Seq_id_.cpp.
References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id_Base::m_choice, and CSeq_id_Base::m_object.
Referenced by CSeq_id_Base::Reset(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGiim(), CSeq_id_Base::SetGpipe(), CSeq_id_Base::SetLocal(), CSeq_id_Base::SetNamed_annot_track(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CSeq_id_Base::SetSwissprot(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), and CSeq_id_Base::SetTpg().
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Reset the selection (set it to e_not_set).
Definition at line 65 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_Base::m_choice, and CSeq_loc_Base::m_object.
Referenced by CSeq_loc_Base::Reset(), CSeq_loc_Base::SetBond(), CSeq_loc_Base::SetEmpty(), CSeq_loc_Base::SetEquiv(), CSeq_loc_Base::SetFeat(), CSeq_loc_Base::SetInt(), CSeq_loc_Base::SetMix(), CSeq_loc_Base::SetPacked_int(), CSeq_loc_Base::SetPacked_pnt(), CSeq_loc_Base::SetPnt(), and CSeq_loc_Base::SetWhole().
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Reset Seqid data member.
Definition at line 212 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::m_Seqid, and CPatent_seq_id_Base::m_set_State.
Referenced by CPatent_seq_id_Base::Reset().
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Reset Strand data member.
Definition at line 290 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_set_State, and CPacked_seqpnt_Base::m_Strand.
Referenced by CPacked_seqpnt_Base::Reset(), CSeq_loc::ResetStrand(), and x_Assign().
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Reset Strand data member.
Definition at line 470 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_set_State, and CSeq_interval_Base::m_Strand.
Referenced by CSeq_interval_Base::Reset(), CSeq_loc::ResetStrand(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), x_Assign(), CSeqMap::x_DoUpdateSeq_inst(), CNewCleanup_imp::x_SeqIntervalBC(), and SSNP_Info::x_UpdateSeq_feat().
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Reset Strand data member.
Definition at line 343 of file Seq_point_.hpp.
References CSeq_point_Base::m_set_State, and CSeq_point_Base::m_Strand.
Referenced by CSeq_point_Base::Reset(), CSeq_loc::ResetStrand(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeq_loc_CI_Impl::UpdatePoint(), CSeqTableLocColumns::UpdateSeq_loc(), x_Assign(), CNewCleanup_imp::x_SeqPointBC(), and SSNP_Info::x_UpdateSeq_feat().
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Reset To data member.
Definition at line 423 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_set_State, and CSeq_interval_Base::m_To.
Referenced by CSeq_interval_Base::Reset(), and ReverseComplementLocation().
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Reset Version data member.
Definition at line 434 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_set_State, and CTextseq_id_Base::m_Version.
Referenced by CSeq_id::GetMatchingTextseqIds(), CTextseq_id_Base::Reset(), CTextseq_id::Set(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and x_Assign().
void CSeq_id_Base::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CSeq_loc_Base::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CSeq_id_Base::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
Referenced by CSeq_id_Descr::Assign(), CSeq_id_Textseq_Info::GetPackedSeqId(), s_Match_id(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGi(), CSeq_id_Base::SetGibbmt(), CSeq_id_Base::SetGibbsq(), CSeq_id_Base::SetGiim(), CSeq_id_Base::SetGpipe(), CSeq_id_Base::SetLocal(), CSeq_id_Base::SetNamed_annot_track(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CSeq_id_Base::SetSwissprot(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), and CSeq_id_Base::SetTpg().
void CSeq_loc_Base::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
Referenced by CSeq_loc_Base::SetBond(), CSeq_loc_Base::SetEmpty(), CSeq_loc_Base::SetEquiv(), CSeq_loc_Base::SetFeat(), CSeq_loc_Base::SetInt(), CSeq_loc_Base::SetMix(), CSeq_loc_Base::SetNull(), CSeq_loc_Base::SetPacked_int(), CSeq_loc_Base::SetPacked_pnt(), CSeq_loc_Base::SetPnt(), and CSeq_loc_Base::SetWhole().
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Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 183 of file Seq_id_.cpp.
References CSeq_id_Base::sm_SelectionNames.
Referenced by CSeq_id_not_set_Tree::Dump(), CSeq_id_int_Tree::Dump(), CSeq_id_Gi_Tree::Dump(), CSeq_id_Textseq_Tree::Dump(), CSeq_id_Local_Tree::Dump(), CSeq_id_General_Tree::Dump(), CSeq_id_Giim_Tree::Dump(), CSeq_id_Patent_Tree::Dump(), CSeq_id_PDB_Tree::Dump(), CWriteUtil::GetIdType(), and CSeq_id::Set().
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Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 140 of file Seq_loc_.cpp.
References CSeq_loc_Base::sm_SelectionNames.
Referenced by CSeq_loc::Add(), CSeq_loc::ChangeToPackedInt(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), and CSeq_loc_CI_Impl::x_ProcessLocation().
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Assign a value to data member.
Definition at line 170 of file Packed_seqint_.hpp.
References CPacked_seqint_Base::m_data, and CPacked_seqint_Base::m_set_State.
Referenced by CPacked_seqint::AddInterval(), CPacked_seqint::AddIntervals(), NTweakExon::AdjustBiostops(), CCleanup::ClearInternalPartials(), NTweakExon::CollapseNonframeshiftting(), NTweakExon::ConvertOverlapsToGaps(), CorrectIntervalOrder(), CSeqUtils::CreateSeq_loc(), CDDAnnotateDialog::EditAnnotation(), CPacked_seqint::FlipStrand(), CRegexp_loc::GetLoc(), GetReverseComplement(), CSeqUtils::MixLocToLoc(), CDDAnnotateDialog::NewAnnotation(), CPacked_seqint::ResetStrand(), s_Load_Packed_seqint(), s_Load_Seq_interval(), s_Load_Seq_point(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CPacked_seqint::SetStartInt(), CPacked_seqint::SetStopInt(), CPacked_seqint::SetStrand(), CPacked_seqint::SetTruncatedStart(), CPacked_seqint::SetTruncatedStop(), SplitLocationForGap(), NTweakExon::SubsumeMicroIntervals(), x_Assign(), and CAutogeneratedCleanup::x_BasicCleanupPackedSeqInt().
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Assign a value to data member.
Definition at line 170 of file Seq_id_set_.hpp.
References CSeq_id_set_Base::m_data, and CSeq_id_set_Base::m_set_State.
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Assign a value to data member.
Definition at line 171 of file Seq_loc_equiv_.hpp.
References CSeq_loc_equiv_Base::m_data, and CSeq_loc_equiv_Base::m_set_State.
Referenced by CSeq_loc_equiv::Add(), GetReverseComplement(), CSeq_loc_CI_Impl::MakeLoc(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), SplitLocationForGap(), x_Assign(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_location_location_equiv_ETC(), and CAutogeneratedCleanup::x_BasicCleanupSeqLocEquiv().
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Assign a value to data member.
Definition at line 171 of file Seq_loc_mix_.hpp.
References CSeq_loc_mix_Base::m_data, and CSeq_loc_mix_Base::m_set_State.
Referenced by CSeq_loc_mix::AddInterval(), CSeq_loc_mix::AddSeqLoc(), CSeq_loc::ChangeToMix(), CCleanup::ClearInternalPartials(), DealWithGenes(), CSeq_loc_mix::FlipStrand(), CValidError_bioseq::GetLocFromSeq(), GetReverseComplement(), CSeq_loc_Conversion::MakeDstMix(), PreserveTerminalCodons(), CSeq_loc_mix::ResetStrand(), SRelLoc::Resolve(), s_FlattenSeqLocMix(), CInvertProcess::SeqEntryProcess(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CSeq_loc_mix::SetFirstLoc(), CSeq_loc_mix::SetLastLoc(), CSeq_loc_mix::SetPartialStart(), CSeq_loc_mix::SetPartialStop(), CSeq_loc_mix::SetStrand(), CSeq_loc_mix::SetTruncatedStart(), CSeq_loc_mix::SetTruncatedStop(), SplitLocationForGap(), x_Assign(), CAutogeneratedCleanup::x_BasicCleanupSeqLocMix(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().
void CSeq_bond_Base::SetA | ( | CSeq_bond_Base::TA & | value | ) |
Assign a value to A data member.
value | Reference to value. |
Definition at line 60 of file Seq_bond_.cpp.
References CSeq_bond_Base::m_A, and rapidjson::value.
Referenced by CSeq_loc_Conversion::ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), GetReverseComplement(), GetSPSeqLoc(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CSeq_loc::SetId(), x_Assign(), CAutogeneratedCleanup::x_BasicCleanupSeqBond(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().
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Assign a value to A data member.
Definition at line 222 of file Seq_bond_.hpp.
References CSeq_bond_Base::m_A, and CSeq_bond_Base::ResetA().
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Assign a value to Accession data member.
value | Value to assign |
Definition at line 349 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_Accession, CTextseq_id_Base::m_set_State, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGoodAlign(), fta_get_gi_for_seq_id(), CSeq_id::GetMatchingTextseqIds(), CSeq_id_Textseq_PlainInfo::GetPackedSeqId(), GetWGSMasterSeq_id(), s_AssignTextseq_id(), TestBadProtId(), TestGoodNucId(), TestGoodProtId(), TestNewAccessionOnNuc(), TestNewAccessionOnNucProt(), TestNewAccessionOnStandaloneProt(), TestOneLongGeneral(), and x_Assign().
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Definition at line 356 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_Accession, CTextseq_id_Base::m_set_State, and rapidjson::value.
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Assign a value to Accession data member.
Definition at line 363 of file Textseq_id_.hpp.
References CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::m_Accession, CTextseq_id_Base::m_set_State, and CSerialObject::UnassignedString().
Referenced by CTextseq_id::Set().
void CSeq_bond_Base::SetB | ( | CSeq_bond_Base::TB & | value | ) |
Assign a value to B data member.
value | Reference to value. |
Definition at line 70 of file Seq_bond_.cpp.
References CSeq_bond_Base::m_B, and rapidjson::value.
Referenced by CSeq_loc_Conversion::ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), GetSPSeqLoc(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CSeq_loc::SetId(), x_Assign(), CAutogeneratedCleanup::x_BasicCleanupSeqBond(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().
CSeq_bond_Base::TB & CSeq_bond_Base::SetB | ( | void | ) |
Assign a value to B data member.
Definition at line 75 of file Seq_bond_.cpp.
References CSeq_bond_Base::m_B.
void CSeq_loc_Base::SetBond | ( | CSeq_loc_Base::TBond & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 338 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Bond, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TBond & CSeq_loc_Base::SetBond | ( | void | ) |
Select the variant.
Definition at line 332 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Bond, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
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Assign a value to Chain data member.
value | Value to assign |
Definition at line 360 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_Chain, CPDB_seq_id_Base::m_set_State, and rapidjson::value.
Referenced by CSeq_id_PDB_Info::Normalize(), CSeq_id::Set(), and x_Assign().
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Assign a value to Chain data member.
Definition at line 367 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::m_Chain, CPDB_seq_id_Base::m_set_State, and CSerialObject::UnassignedByte().
Referenced by CPDB_seq_id::SetChainIdentifiers().
Assign a value to Chain_id data member.
value | Value to assign |
Definition at line 421 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_Chain_id, CPDB_seq_id_Base::m_set_State, and rapidjson::value.
Referenced by CSeq_id_PDB_Info::Normalize(), CSeq_id::Set(), SetTextId(), and x_Assign().
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Definition at line 428 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_Chain_id, CPDB_seq_id_Base::m_set_State, and rapidjson::value.
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Assign a value to Chain_id data member.
Definition at line 435 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::IsSetChain_id(), CPDB_seq_id_Base::m_Chain_id, CPDB_seq_id_Base::m_set_State, and CSerialObject::UnassignedString().
Referenced by CPDB_seq_id::SetChainIdentifiers().
void CPatent_seq_id_Base::SetCit | ( | CPatent_seq_id_Base::TCit & | value | ) |
Assign a value to Cit data member.
value | Reference to value. |
Definition at line 60 of file Patent_seq_id_.cpp.
References CPatent_seq_id_Base::m_Cit, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), CWGSDb_Impl::GetPatentSeq_id(), CSeq_id::Set(), and x_Assign().
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Assign a value to Cit data member.
Definition at line 268 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::m_Cit, and CPatent_seq_id_Base::ResetCit().
Assign a value to Db data member.
value | Value to assign |
Definition at line 311 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_Db, CGiimport_id_Base::m_set_State, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), and x_Assign().
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Definition at line 318 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_Db, CGiimport_id_Base::m_set_State, and rapidjson::value.
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Assign a value to Db data member.
Definition at line 325 of file Giimport_id_.hpp.
References CGiimport_id_Base::IsSetDb(), CGiimport_id_Base::m_Db, CGiimport_id_Base::m_set_State, and CSerialObject::UnassignedString().
void CSeq_id_Base::SetDdbj | ( | CSeq_id_Base::TDdbj & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 403 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TDdbj & CSeq_id_Base::SetDdbj | ( | void | ) |
Select the variant.
Definition at line 397 of file Seq_id_.cpp.
References CSeq_id_Base::e_Ddbj, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_FIXTURE_TEST_CASE(), s_AssignSeq_id(), CSeq_id::Set(), SetTextId(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and CRemoveName::x_GetReplacementIds().
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Assign default value to Chain data member.
Definition at line 348 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::ResetChain().
void CSeq_id_Base::SetEmbl | ( | CSeq_id_Base::TEmbl & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 271 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Embl, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TEmbl & CSeq_id_Base::SetEmbl | ( | void | ) |
Select the variant.
Definition at line 265 of file Seq_id_.cpp.
References CSeq_id_Base::e_Embl, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), s_AssignSeq_id(), CSeq_id::Set(), SetTextId(), TestOneLongGeneral(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and CRemoveName::x_GetReplacementIds().
void CSeq_loc_Base::SetEmpty | ( | CSeq_loc_Base::TEmpty & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 162 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Empty, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TEmpty & CSeq_loc_Base::SetEmpty | ( | void | ) |
Select the variant.
Definition at line 156 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Empty, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
void CSeq_loc_Base::SetEquiv | ( | CSeq_loc_Base::TEquiv & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 316 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Equiv, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TEquiv & CSeq_loc_Base::SetEquiv | ( | void | ) |
Select the variant.
Definition at line 310 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Equiv, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
void CSeq_loc_Base::SetFeat | ( | CSeq_loc_Base::TFeat & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 360 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Feat, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TFeat & CSeq_loc_Base::SetFeat | ( | void | ) |
Select the variant.
Definition at line 354 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Feat, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
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Assign a value to From data member.
value | Value to assign |
Definition at line 392 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_From, CSeq_interval_Base::m_set_State, and rapidjson::value.
Referenced by CSeq_loc_mix::AddInterval(), CPacked_seqint::AddInterval(), Blast_GetSeqLocInfoVector(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), NTweakExon::Collapse(), CSeq_loc_Conversion_Set::Convert(), CRawWiggleRecord::CRawWiggleRecord(), CSpliced_exon::CreateRowSeq_interval(), CDense_diag::CreateRowSeq_interval(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSourceFeatureItem::CSourceFeatureItem(), EndAdded(), CGBObjectLoader::Execute(), CdBlaster::FillOutSeqLoc(), CSimpleB2SWrapper::FillOutSeqLoc(), fta_do_fix_seq_loc_id(), fta_get_seqloc_int_whole(), fta_make_seq_int(), CSeqUtils::GetCdsMappingInfoFromRna(), CCSraRefSeqIterator::GetCoverageGraph(), CDDAnnotateDialog::GetCurrentHighlightedIntervals(), CSeq_loc_Conversion::GetDstInterval(), CHistogramGlyph::GetHTMLActiveAreas(), IBISAnnotateDialog::GetIntervalsForSet(), CGtfLocationRecord::GetLocation(), GetOverlappingFeatures(), GetProteinWeights(), CCSraAlignIterator::GetQualityGraph(), CCodingPropensity::GetScore(), CSNPDbFeatIterator::GetSeq_feat(), CWGSScaffoldIterator::GetSeq_inst(), GetSeqLocIntSP(), GetSPSeqLoc(), CBedImportData::Initialize(), CGencollIdMapper::IsLocInAGap(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CBamRefSeqInfo::LoadPileupChunk(), LoadSequencesToScope(), MakeDDFromSeqLoc(), CSeq_loc_Conversion::MakeDstMix(), MakeEntryForDeltaConversion(), CSeq_loc_CI_Impl::MakeInterval(), MakeMaskingBioseq(), MakeSeqLocFromDD(), ProjectExon_newlogic(), CGlimmerReader::Read(), SRelLoc::Resolve(), ReverseComplementLocation(), s_BuildMaskedRanges(), s_ConvertBlastnMasks(), s_CreateMappingInfo(), s_ExtendIntervalToEnd(), s_FixIntervalProtToCds(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetIntronsAndSpliceSiteLocs(), s_MakePackedInt(), s_OOFBlastHSP2SeqAlign(), s_Seq_align_Seq_loc(), s_SeqIntervalDelete(), s_SetSplitQuerySeqInterval(), s_SubLocDeltaSeq(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), NTweakExon::SetBioStart(), NTweakExon::SetBioStop(), CRawBedRecord::SetInterval(), SetNewInterval(), SimpleSeqLocFromBioseq(), sParseRange(), Split_Qscore_SeqGraph_By_DeltaSeq(), SplitLocationForGap(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), x_Assign(), CVariationNormalization_base< T >::x_ConvertPointToInterval(), CSGAlignmentJob::x_CreateFeatGlyph(), CCpgSearchJob::x_DoSearch(), CSeqMap::x_DoUpdateSeq_inst(), SGraphMaker::x_EndGraph(), CFeaturePropagator::x_ExtendToStopCodon(), CLocationListCtrl::x_GetInterval(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CWGSSeqIterator::x_GetQualityAnnot(), CCSraShortReadIterator::x_GetQualityGraph(), CFeatureGenerator::SImplementation::x_MapFeature(), x_PushRange(), CNewCleanup_imp::x_SeqIntervalBC(), CVectorTrimPanel::x_SeqIntervalDelete(), CWig2tableApplication::x_SetTotalLoc(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CAdjustForConsensusSpliceSite::x_UpdateInterval(), CAdjustForConsensusSpliceSite::x_UpdateIntervals(), SSNP_Info::x_UpdateSeq_feat(), XGapToSeqLocEx(), CFeatTableEdit::xGetGeneLocation(), CGff3LocationMerger::xGetRecordLocation(), CReaderBase::xSetBrowserRegion(), CMicroArrayReader::xSetFeatureLocation(), CBedReader::xSetFeatureLocationBlock(), CBedReader::xSetFeatureLocationRna(), CWiggleReader::xSetTotalLoc(), and CGff3Reader::xUpdateAnnotGeneric().
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Assign a value to From data member.
Definition at line 399 of file Seq_interval_.hpp.
References CSeq_interval_Base::IsSetFrom(), CSeq_interval_Base::m_From, CSeq_interval_Base::m_set_State, and CSerialObject::UnassignedByte().
Referenced by CSeq_interval::CSeq_interval().
void CPacked_seqpnt_Base::SetFuzz | ( | CPacked_seqpnt_Base::TFuzz & | value | ) |
Assign a value to Fuzz data member.
value | Reference to value. |
Definition at line 71 of file Packed_seqpnt_.cpp.
References CPacked_seqpnt_Base::m_Fuzz, and rapidjson::value.
Referenced by CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_CI_Impl::MakeLocPacked_pnt(), ReverseComplementLocation(), CSeq_loc_Conversion::s_ConvertToMix(), x_Assign(), and CSeq_loc::x_ChangeToPackedPnt().
void CSeq_point_Base::SetFuzz | ( | CSeq_point_Base::TFuzz & | value | ) |
Assign a value to Fuzz data member.
value | Reference to value. |
Definition at line 71 of file Seq_point_.cpp.
References CSeq_point_Base::m_Fuzz, and rapidjson::value.
Referenced by fta_make_seq_pnt(), CSeq_loc_Conversion::GetDstPoint(), CBulkLocationPanel::GetLocForBioseq(), GetSPSeqLoc(), NormalizeLoc(), SRelLoc::Resolve(), ReverseComplementLocation(), sConvertIntToPoint(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeq_loc_CI_Impl::UpdatePoint(), variation_ref::CHgvsParser::x_abs_pos(), variation::CHgvsParser::x_abs_pos(), x_Assign(), CSeq_loc::x_ChangeToPackedPnt(), variation_ref::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_fuzzy_pos(), CLocationListCtrl::x_GetInterval(), x_PushRange(), variation_ref::CHgvsParser::x_range(), variation::CHgvsParser::x_range(), variation_ref::CHgvsParser::x_SeqLocToStr(), CNewCleanup_imp::x_SeqPointBC(), SSNP_Info::x_UpdateSeq_feat(), and xgbint_ver().
CPacked_seqpnt_Base::TFuzz & CPacked_seqpnt_Base::SetFuzz | ( | void | ) |
Assign a value to Fuzz data member.
Definition at line 76 of file Packed_seqpnt_.cpp.
References CPacked_seqpnt_Base::m_Fuzz.
Referenced by CPacked_seqpnt::SetPartialStart(), CPacked_seqpnt::SetPartialStop(), CPacked_seqpnt::SetTruncatedStart(), and CPacked_seqpnt::SetTruncatedStop().
CSeq_point_Base::TFuzz & CSeq_point_Base::SetFuzz | ( | void | ) |
Assign a value to Fuzz data member.
Definition at line 76 of file Seq_point_.cpp.
References CSeq_point_Base::m_Fuzz.
Referenced by CSeq_point::SetLeftOf(), CSeq_point::SetPartialStart(), CSeq_point::SetPartialStop(), CSeq_point::SetRightOf(), CSeq_point::SetTruncatedStart(), and CSeq_point::SetTruncatedStop().
void CSeq_interval_Base::SetFuzz_from | ( | CSeq_interval_Base::TFuzz_from & | value | ) |
Assign a value to Fuzz_from data member.
value | Reference to value. |
Definition at line 71 of file Seq_interval_.cpp.
References CSeq_interval_Base::m_Fuzz_from, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), fta_make_seq_int(), CScore_StartStopCodon::Get(), CSeq_loc_Conversion::GetDstInterval(), GetProtRefAnnot(), GetSPSeqLoc(), CSeq_loc_CI_Impl::MakeInterval(), SRelLoc::Resolve(), ReverseComplementLocation(), s_FixIntervalProtToCds(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), s_Load_Seq_point(), SetNewInterval(), SplitLocationForGap(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CPhrap_Contig::x_AddReadLocFeats(), x_Assign(), IEditingActionFeat::x_MergeFeatureLocation(), x_PushRange(), and x_SingleRange().
CSeq_interval_Base::TFuzz_from & CSeq_interval_Base::SetFuzz_from | ( | void | ) |
Assign a value to Fuzz_from data member.
Definition at line 76 of file Seq_interval_.cpp.
References CSeq_interval_Base::m_Fuzz_from.
Referenced by CSeq_interval::SetPartialStart(), CSeq_interval::SetPartialStop(), CSeq_interval::SetTruncatedStart(), and CSeq_interval::SetTruncatedStop().
void CSeq_interval_Base::SetFuzz_to | ( | CSeq_interval_Base::TFuzz_to & | value | ) |
Assign a value to Fuzz_to data member.
value | Reference to value. |
Definition at line 88 of file Seq_interval_.cpp.
References CSeq_interval_Base::m_Fuzz_to, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), fta_make_seq_int(), CScore_StartStopCodon::Get(), CSeq_loc_Conversion::GetDstInterval(), GetProtRefAnnot(), GetSPSeqLoc(), CSeq_loc_CI_Impl::MakeInterval(), SRelLoc::Resolve(), ReverseComplementLocation(), s_FixIntervalProtToCds(), s_GiveOneResidueIntervalsBogusFuzz_Helper(), SetNewInterval(), SplitLocationForGap(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CPhrap_Contig::x_AddReadLocFeats(), x_Assign(), IEditingActionFeat::x_MergeFeatureLocation(), x_PushRange(), and x_SingleRange().
CSeq_interval_Base::TFuzz_to & CSeq_interval_Base::SetFuzz_to | ( | void | ) |
Assign a value to Fuzz_to data member.
Definition at line 93 of file Seq_interval_.cpp.
References CSeq_interval_Base::m_Fuzz_to.
Referenced by CSeq_interval::SetPartialStart(), CSeq_interval::SetPartialStop(), CSeq_interval::SetTruncatedStart(), and CSeq_interval::SetTruncatedStop().
void CSeq_id_Base::SetGenbank | ( | CSeq_id_Base::TGenbank & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 249 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Genbank, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TGenbank & CSeq_id_Base::SetGenbank | ( | void | ) |
Select the variant.
Definition at line 243 of file Seq_id_.cpp.
References CSeq_id_Base::e_Genbank, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGoodAlign(), fta_get_gi_for_seq_id(), s_AssignSeq_id(), CSeq_id::Set(), SetTextId(), TestBadProtId(), TestGoodNucId(), TestGoodProtId(), TestNewAccessionOnNuc(), TestNewAccessionOnNucProt(), TestNewAccessionOnStandaloneProt(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and CRemoveName::x_GetReplacementIds().
void CSeq_id_Base::SetGeneral | ( | CSeq_id_Base::TGeneral & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 381 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_General, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TGeneral & CSeq_id_Base::SetGeneral | ( | void | ) |
Select the variant.
Definition at line 375 of file Seq_id_.cpp.
References CSeq_id_Base::e_General, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by Sequence::AddMMDBAnnotTag(), AddPIDToSeqId(), CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CLocalToGeneralId::CLocalToGeneralId(), CSeq_id_General_PlainInfo::CSeq_id_General_PlainInfo(), CSeq_id_General_Tree::FindMatch(), fta_create_wgs_dbtag(), fta_parse_tpa_tsa_block(), IIndexedFeatureReader::GetAnnotId(), GetNewGeneralProtId(), CSeq_id_General_Id_Info::GetPackedSeqId(), CSeq_id_General_Str_Info::GetPackedSeqId(), GetProtRefSeqId(), CCSraDb_Impl::MakeShortReadId(), PssmMaker::modifyQuery(), CProcessor_ExtAnnot::Process(), CDUpdater::reformatBioseq(), CAgpconvertApplication::Run(), s_AddGeneralAndLocal(), s_AssignSeq_id(), CSeq_id::Set(), sx_MakeUniqueId(), TestTrimForFrame(), TryOneCDSCase(), CEditSeqId::x_CollectChangedIds(), CWriteDB_Impl::x_ExtractDeflines(), CWriteDB_Impl::x_GetFastaReaderDeflines(), and CSeqDBVol::x_GetHdrAsn1().
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Select the variant and set its data.
value | Variant data. |
Definition at line 903 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gi, eDoNotResetVariant, CSeq_id_Base::m_Gi, CSeq_id_Base::Select(), and rapidjson::value.
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Select the variant.
Definition at line 896 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gi, eDoNotResetVariant, CSeq_id_Base::m_Gi, and CSeq_id_Base::Select().
Referenced by AddPIDToSeqId(), CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CGBObjectLoader::Execute(), SeqTreeAsnizer::fillAsnSeqTreeNode(), CSimpleOM::GetBioseqHandle(), CSeq_id_Gi_Tree::GetGiHandle(), CWGSSeqIterator::GetGiSeq_id(), CWGSProteinIterator::GetGiSeq_id(), CLocationListCtrl::GetIdFromForm(), CSeq_id_Gi_Info::GetPackedSeqId(), CWGSResolver_Ids::GetPrefixes(), CWGSClient::GetSeqIds(), GetSeqIdsForGI(), CId1FetchApp::LookUpGI(), CSeq_annot_SNP_Info::OffsetGi(), CSplitCacheApp::ProcessGi(), CHgvsReader::ReadSeqAnnot(), CFeatTreeSampleApp::Run(), CSampleObjmgrApplication::Run(), CTestProtProd_EntrezNeighbors::RunTest(), s_AssignSeq_id(), CSeq_id::Set(), CSeq_annot_SNP_Info::SetGi(), TestOneOtherAcc(), CCreateGeneModelTask::x_GetCommand(), CSeq_annot_SNP_Info_Reader::x_Read(), and CSeqAlignFilter::x_UpdateGiInSeqalign().
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Select the variant and set its data.
value | Variant data. |
Definition at line 828 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gibbmt, eDoNotResetVariant, CSeq_id_Base::m_Gibbmt, CSeq_id_Base::Select(), and rapidjson::value.
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Select the variant.
Definition at line 821 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gibbmt, eDoNotResetVariant, CSeq_id_Base::m_Gibbmt, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), and CSeq_id::Set().
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Select the variant and set its data.
value | Variant data. |
Definition at line 801 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gibbsq, eDoNotResetVariant, CSeq_id_Base::m_Gibbsq, CSeq_id_Base::Select(), and rapidjson::value.
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Select the variant.
Definition at line 794 of file Seq_id_.hpp.
References CSeq_id_Base::e_Gibbsq, eDoNotResetVariant, CSeq_id_Base::m_Gibbsq, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), and CSeq_id::Set().
void CSeq_id_Base::SetGiim | ( | CSeq_id_Base::TGiim & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 227 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Giim, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TGiim & CSeq_id_Base::SetGiim | ( | void | ) |
Select the variant.
Definition at line 221 of file Seq_id_.cpp.
References CSeq_id_Base::e_Giim, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), and CSeq_id::Set().
void CSeq_id_Base::SetGpipe | ( | CSeq_id_Base::TGpipe & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 535 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Gpipe, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TGpipe & CSeq_id_Base::SetGpipe | ( | void | ) |
Select the variant.
Definition at line 529 of file Seq_id_.cpp.
References CSeq_id_Base::e_Gpipe, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), s_AssignSeq_id(), CSeq_id::Set(), SetTextId(), and CIdMapperGCAssembly::x_AddUnversionedMapping().
void CPacked_seqpnt_Base::SetId | ( | CPacked_seqpnt_Base::TId & | value | ) |
Assign a value to Id data member.
value | Reference to value. |
Definition at line 61 of file Packed_seqpnt_.cpp.
References CPacked_seqpnt_Base::m_Id, and rapidjson::value.
Referenced by CSeq_loc_Conversion::ConvertPacked_pnt(), CPhrap_Seq::CreatePadsFeat(), CSeq_loc_CI_Impl::MakeLocPacked_pnt(), CSeq_loc_Conversion::s_ConvertToMix(), CSeq_loc::SetId(), x_Assign(), CAutogeneratedCleanup::x_BasicCleanupPackedPoint(), and CSeq_loc::x_ChangeToPackedPnt().
void CSeq_interval_Base::SetId | ( | CSeq_interval_Base::TId & | value | ) |
Assign a value to Id data member.
value | Reference to value. |
Definition at line 61 of file Seq_interval_.cpp.
References CSeq_interval_Base::m_Id, and rapidjson::value.
Referenced by CSeq_loc_mix::AddInterval(), CPacked_seqint::AddInterval(), Blast_GetSeqLocInfoVector(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), CSeq_loc_Conversion_Set::Convert(), CRawWiggleRecord::CRawWiggleRecord(), CSpliced_exon::CreateRowSeq_interval(), CDense_diag::CreateRowSeq_interval(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSourceFeatureItem::CSourceFeatureItem(), CdBlaster::FillOutSeqLoc(), CSimpleB2SWrapper::FillOutSeqLoc(), fta_do_fix_seq_loc_id(), fta_get_seqloc_int_whole(), fta_make_seq_int(), CSeqUtils::GetCdsMappingInfoFromRna(), CCSraRefSeqIterator::GetCoverageGraph(), CDDAnnotateDialog::GetCurrentHighlightedIntervals(), CSeq_loc_Conversion::GetDstInterval(), CHistogramGlyph::GetHTMLActiveAreas(), IBISAnnotateDialog::GetIntervalsForSet(), CGtfLocationRecord::GetLocation(), GetOverlappingFeatures(), GetProteinWeights(), CCSraAlignIterator::GetQualityGraph(), CCodingPropensity::GetScore(), CSNPDbFeatIterator::GetSeq_feat(), CWGSScaffoldIterator::GetSeq_inst(), GetSeqLocIntSP(), GetSPSeqLoc(), CBedImportData::Initialize(), CGencollIdMapper::IsLocInAGap(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CBamRefSeqInfo::LoadPileupChunk(), LoadSequencesToScope(), MakeDDFromSeqLoc(), CSeq_loc_Conversion::MakeDstMix(), MakeEntryForDeltaConversion(), CSeq_loc_CI_Impl::MakeInterval(), MakeMaskingBioseq(), MakeSeqLocFromDD(), ProjectExon_newlogic(), SRelLoc::Resolve(), s_BuildMaskedRanges(), s_ConvertBlastnMasks(), s_CreateMappingInfo(), s_MakePackedInt(), s_Seq_align_Seq_loc(), CSeq_loc::SetId(), CRawBedRecord::SetInterval(), SimpleSeqLocFromBioseq(), Split_Qscore_SeqGraph_By_DeltaSeq(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), UpgradeSeqLocId(), x_Assign(), CAutogeneratedCleanup::x_BasicCleanupSeqInt(), CVariationNormalization_base< T >::x_ConvertPointToInterval(), CSGAlignmentJob::x_CreateFeatGlyph(), CCpgSearchJob::x_DoSearch(), CSeqMap::x_DoUpdateSeq_inst(), SGraphMaker::x_EndGraph(), CFeaturePropagator::x_ExtendToStopCodon(), CLocationListCtrl::x_GetInterval(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CWGSSeqIterator::x_GetQualityAnnot(), CCSraShortReadIterator::x_GetQualityGraph(), CGenBankLoadOptionPanel::x_ProccessText(), x_PushRange(), CWig2tableApplication::x_SetTotalLoc(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), SSNP_Info::x_UpdateSeq_feat(), XGapToSeqLocEx(), CFeatTableEdit::xGetGeneLocation(), CGff3LocationMerger::xGetRecordLocation(), CBedReader::xSetFeatureLocationBlock(), CBedReader::xSetFeatureLocationRna(), CWiggleReader::xSetTotalLoc(), and CGff3Reader::xUpdateAnnotGeneric().
void CSeq_point_Base::SetId | ( | CSeq_point_Base::TId & | value | ) |
Assign a value to Id data member.
value | Reference to value. |
Definition at line 61 of file Seq_point_.cpp.
References CSeq_point_Base::m_Id, and rapidjson::value.
Referenced by CSeq_loc_mix::AddInterval(), BOOST_AUTO_TEST_CASE(), fta_make_seq_pnt(), CSeq_loc_Conversion::GetDstPoint(), CBulkLocationPanel::GetLocForBioseq(), CSNPDbFeatIterator::GetSeq_feat(), GetSPSeqLoc(), CCdregionValidator::MapToNTCoords(), NormalizeLoc(), CAnalyzeShiftApp::ProcessHGVS(), SRelLoc::Resolve(), sConvertIntToPoint(), CSeq_loc::SetId(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeq_loc_CI_Impl::UpdatePoint(), CSeqTableLocColumns::UpdateSeq_loc(), UpgradeSeqLocId(), variation_ref::CHgvsParser::x_abs_pos(), variation::CHgvsParser::x_abs_pos(), x_Assign(), CAutogeneratedCleanup::x_BasicCleanupSeqPoint(), CSeq_loc::x_ChangeToPackedPnt(), CVariationNormalization_base< T >::x_ConvertIntervalToPoint(), variation_ref::CHgvsParser::x_general_pos(), variation::CHgvsParser::x_general_pos(), CLocationListCtrl::x_GetInterval(), x_PushRange(), variation_ref::CHgvsParser::x_range(), variation::CHgvsParser::x_range(), CGFFReader::x_ResolveLoc(), variation_ref::CHgvsParser::x_SeqLocToStr(), and SSNP_Info::x_UpdateSeq_feat().
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Assign a value to Id data member.
value | Value to assign |
Definition at line 271 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_Id, CGiimport_id_Base::m_set_State, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_id::Set(), and x_Assign().
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Assign a value to Id data member.
Definition at line 278 of file Giimport_id_.hpp.
References CGiimport_id_Base::IsSetId(), CGiimport_id_Base::m_Id, CGiimport_id_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Id data member.
Definition at line 346 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_Id, and CPacked_seqpnt_Base::ResetId().
Referenced by CPacked_seqpnt::CPacked_seqpnt().
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Assign a value to Id data member.
Definition at line 526 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_Id, and CSeq_interval_Base::ResetId().
Referenced by CSeq_interval::CSeq_interval().
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Assign a value to Id data member.
Definition at line 399 of file Seq_point_.hpp.
References CSeq_point_Base::m_Id, and CSeq_point_Base::ResetId().
Referenced by CSeq_point::CSeq_point().
void CSeq_loc_Base::SetInt | ( | CSeq_loc_Base::TInt & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 206 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Int, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TInt & CSeq_loc_Base::SetInt | ( | void | ) |
Select the variant.
Definition at line 200 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Int, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
void CSeq_id_Base::SetLocal | ( | CSeq_id_Base::TLocal & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 205 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Local, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TLocal & CSeq_id_Base::SetLocal | ( | void | ) |
Select the variant.
Definition at line 199 of file Seq_id_.cpp.
References CSeq_id_Base::e_Local, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by AgpRead(), CReadUtil::AsSeqId(), CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGenProdSetWithBigProduct(), BuildGoodGenProdSet(), BuildSmallGenomeSet(), CBioseq::CBioseq(), CGeneralToLocalId::CGeneralToLocalId(), CNWFormatter::CNWFormatter(), CRemoveSeqId::CRemoveSeqId(), CSeq_id_Local_Info::CSeq_id_Local_Info(), SeqTreeAsnizer::fillAsnSeqTreeNode(), CSeqIdGenerator::GenerateID(), IIndexedFeatureReader::GetAnnotId(), CPhrap_Seq::GetId(), CLocationListCtrl::GetIdFromForm(), GetNewLocalProtId(), CSeq_id_Local_Info::GetPackedSeqId(), GetProtRefSeqId(), CGencollIdMapper::Guess(), CIdMapperConfig::Initialize(), MakeProteinForGoodNucProtSet(), MakeProteinForNucProtSet(), MakeSmallGenomeSetNucId(), s_AddCDS(), s_AddGeneralAndLocal(), s_AssignSeq_id(), CAgpToSeqEntry::s_LocalSeqIdFromStr(), s_ReplaceLocalId(), CClippedScorer::ScoreAlignments(), CSeq_id::Set(), SetEmptyId(), CEditingActionFeatTranscriptId::SetValue(), CReadBlastApp::StoreBlast(), sx_MakeUniqueId(), TestBadProtId(), TestFeatInsideGap(), TestGoodNucId(), TestGoodProtId(), CRNAPanel::TransferDataFromWindow(), CIdMapperGCAssembly::x_AddAliasMappings(), CGencollIdMapper::x_ApplyPatternToId(), CEditSeqId::x_CollectChangedIds(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CGencollIdMapper::x_FindChromosomeSequence(), CGencollIdMapper::x_FixImperfectId(), CImportFeatTable::x_GetFixedId(), CGencollIdMapper::x_GetIdFromSeqAndSpec(), CAccessionToLocalId::x_GetReplacementIds(), CSeq_loc_Mapper::x_IsUCSCRandomChr(), CGencollIdMapper::x_NCBI34_Map_IdFix(), CUnorderedSplitter::x_SplitDeltaExt(), and CUnorderedSplitter::x_SplitSeqData().
void CSeq_loc_Base::SetMix | ( | CSeq_loc_Base::TMix & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 294 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Mix, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TMix & CSeq_loc_Base::SetMix | ( | void | ) |
Select the variant.
Definition at line 288 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Mix, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
Assign a value to Mol data member.
value | Value to assign |
Definition at line 315 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_Mol, CPDB_seq_id_Base::m_set_State, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_id_PDB_Info::GetPackedSeqId(), CSeq_id_PDB_Info::Normalize(), CSeq_id::Set(), and x_Assign().
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Assign a value to Mol data member.
Definition at line 322 of file PDB_seq_id_.hpp.
References CPDB_seq_id_Base::m_Mol, and CPDB_seq_id_Base::m_set_State.
Assign a value to Name data member.
value | Value to assign |
Definition at line 302 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_Name, CTextseq_id_Base::m_set_State, and rapidjson::value.
Referenced by CSeq_id::GetMatchingTextseqIds(), s_AssignTextseq_id(), and x_Assign().
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Definition at line 309 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_Name, CTextseq_id_Base::m_set_State, and rapidjson::value.
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Assign a value to Name data member.
Definition at line 316 of file Textseq_id_.hpp.
References CTextseq_id_Base::IsSetName(), CTextseq_id_Base::m_Name, CTextseq_id_Base::m_set_State, and CSerialObject::UnassignedString().
Referenced by CTextseq_id::Set().
void CSeq_id_Base::SetNamed_annot_track | ( | CSeq_id_Base::TNamed_annot_track & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 557 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TNamed_annot_track & CSeq_id_Base::SetNamed_annot_track | ( | void | ) |
Select the variant.
Definition at line 551 of file Seq_id_.cpp.
References CSeq_id_Base::e_Named_annot_track, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), s_AssignSeq_id(), CSeq_id::Set(), SetTextId(), and CIdMapperGCAssembly::x_AddUnversionedMapping().
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Select the variant.
Definition at line 510 of file Seq_loc_.hpp.
References CSeq_loc_Base::e_Null, eDoNotResetVariant, and CSeq_loc_Base::Select().
Referenced by CSeq_loc::SetNull().
void CSeq_id_Base::SetOther | ( | CSeq_id_Base::TOther & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 359 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Other, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TOther & CSeq_id_Base::SetOther | ( | void | ) |
Select the variant.
Definition at line 353 of file Seq_id_.cpp.
References CSeq_id_Base::e_Other, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), s_AssignSeq_id(), CSeq_id::Set(), SetTextId(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and CRemoveName::x_GetReplacementIds().
void CSeq_loc_Base::SetPacked_int | ( | CSeq_loc_Base::TPacked_int & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 228 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TPacked_int & CSeq_loc_Base::SetPacked_int | ( | void | ) |
Select the variant.
Definition at line 222 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Packed_int, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
void CSeq_loc_Base::SetPacked_pnt | ( | CSeq_loc_Base::TPacked_pnt & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 272 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TPacked_pnt & CSeq_loc_Base::SetPacked_pnt | ( | void | ) |
Select the variant.
Definition at line 266 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Packed_pnt, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
void CSeq_id_Base::SetPatent | ( | CSeq_id_Base::TPatent & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 337 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Patent, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TPatent & CSeq_id_Base::SetPatent | ( | void | ) |
Select the variant.
Definition at line 331 of file Seq_id_.cpp.
References CSeq_id_Base::e_Patent, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), CWGSDb_Impl::GetPatentSeq_id(), GetProtRefSeqId(), LoadFeat(), and CSeq_id::Set().
void CSeq_id_Base::SetPdb | ( | CSeq_id_Base::TPdb & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 447 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Pdb, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TPdb & CSeq_id_Base::SetPdb | ( | void | ) |
Select the variant.
Definition at line 441 of file Seq_id_.cpp.
References CSeq_id_Base::e_Pdb, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_AUTO_TEST_CASE(), fta_create_pdb_seq_id(), CSeq_id_PDB_Info::GetPackedSeqId(), MakePDBSeqId(), CSeq_id_PDB_Info::Normalize(), CSeq_id::Set(), SetTextId(), and CAutogeneratedCleanup::x_BasicCleanupSeqId().
void CSeq_id_Base::SetPir | ( | CSeq_id_Base::TPir & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 293 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Pir, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TPir & CSeq_id_Base::SetPir | ( | void | ) |
Select the variant.
Definition at line 287 of file Seq_id_.cpp.
References CSeq_id_Base::e_Pir, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_FIXTURE_TEST_CASE(), CSeq_id::Set(), SetTextId(), SPAppendPIRToHist(), and CIdMapperGCAssembly::x_AddUnversionedMapping().
void CSeq_loc_Base::SetPnt | ( | CSeq_loc_Base::TPnt & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 250 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Pnt, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TPnt & CSeq_loc_Base::SetPnt | ( | void | ) |
Select the variant.
Definition at line 244 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Pnt, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
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Assign a value to Point data member.
value | Value to assign |
Definition at line 312 of file Seq_point_.hpp.
References CSeq_point_Base::m_Point, CSeq_point_Base::m_set_State, and rapidjson::value.
Referenced by CSeq_loc_mix::AddInterval(), BOOST_AUTO_TEST_CASE(), fta_make_seq_pnt(), CSeq_loc_Conversion::GetDstPoint(), CBulkLocationPanel::GetLocForBioseq(), CSNPDbFeatIterator::GetSeq_feat(), GetSPSeqLoc(), CCdregionValidator::MapToNTCoords(), NormalizeLoc(), CAnalyzeShiftApp::ProcessHGVS(), SRelLoc::Resolve(), ReverseComplementLocation(), sConvertIntToPoint(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeq_loc_CI_Impl::UpdatePoint(), CSeqTableLocColumns::UpdateSeq_loc(), variation_ref::CHgvsParser::x_abs_pos(), variation::CHgvsParser::x_abs_pos(), x_Assign(), CVariationNormalization_base< T >::x_ConvertIntervalToPoint(), variation_ref::CHgvsParser::x_general_pos(), variation::CHgvsParser::x_general_pos(), CLocationListCtrl::x_GetInterval(), x_PushRange(), CGFFReader::x_ResolveLoc(), variation_ref::CHgvsParser::x_SeqLocToStr(), CNewCleanup_imp::x_SeqPointBC(), SSNP_Info::x_UpdateSeq_feat(), and xgbint_ver().
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Assign a value to Point data member.
Definition at line 319 of file Seq_point_.hpp.
References CSeq_point_Base::IsSetPoint(), CSeq_point_Base::m_Point, CSeq_point_Base::m_set_State, and CSerialObject::UnassignedByte().
Referenced by CSeq_point::CSeq_point().
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Assign a value to Points data member.
Definition at line 394 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_Points, and CPacked_seqpnt_Base::m_set_State.
Referenced by CPacked_seqpnt::AddPoint(), CPacked_seqpnt::AddPoints(), CSeq_loc_Conversion::ConvertPacked_pnt(), CorrectIntervalOrder(), CPacked_seqpnt::CPacked_seqpnt(), CPhrap_Seq::CreatePadsFeat(), CSeq_loc_CI_Impl::MakeLocPacked_pnt(), ReverseComplementLocation(), CSeq_loc_Conversion::s_ConvertToMix(), SeqLocAdjustForInsert(), and x_Assign().
void CSeq_id_Base::SetPrf | ( | CSeq_id_Base::TPrf & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 425 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Prf, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TPrf & CSeq_id_Base::SetPrf | ( | void | ) |
Select the variant.
Definition at line 419 of file Seq_id_.cpp.
References CSeq_id_Base::e_Prf, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_FIXTURE_TEST_CASE(), CSeq_id::Set(), SetTextId(), and CIdMapperGCAssembly::x_AddUnversionedMapping().
void CPDB_seq_id_Base::SetRel | ( | CPDB_seq_id_Base::TRel & | value | ) |
Assign a value to Rel data member.
value | Reference to value. |
Definition at line 62 of file PDB_seq_id_.cpp.
References CPDB_seq_id_Base::m_Rel, and rapidjson::value.
Referenced by CSeq_id_PDB_Info::GetPackedSeqId(), x_Assign(), and CAutogeneratedCleanup::x_BasicCleanupSeqId().
CPDB_seq_id_Base::TRel & CPDB_seq_id_Base::SetRel | ( | void | ) |
Assign a value to Rel data member.
Definition at line 67 of file PDB_seq_id_.cpp.
References CPDB_seq_id_Base::m_Rel.
Assign a value to Release data member.
value | Value to assign |
Definition at line 358 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_Release, CGiimport_id_Base::m_set_State, and rapidjson::value.
Referenced by x_Assign().
Assign a value to Release data member.
value | Value to assign |
Definition at line 396 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_Release, CTextseq_id_Base::m_set_State, and rapidjson::value.
Referenced by CSeq_id::GetMatchingTextseqIds(), s_AssignTextseq_id(), and x_Assign().
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Definition at line 365 of file Giimport_id_.hpp.
References CGiimport_id_Base::m_Release, CGiimport_id_Base::m_set_State, and rapidjson::value.
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Definition at line 403 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_Release, CTextseq_id_Base::m_set_State, and rapidjson::value.
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Assign a value to Release data member.
Definition at line 372 of file Giimport_id_.hpp.
References CGiimport_id_Base::IsSetRelease(), CGiimport_id_Base::m_Release, CGiimport_id_Base::m_set_State, and CSerialObject::UnassignedString().
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Assign a value to Release data member.
Definition at line 410 of file Textseq_id_.hpp.
References CTextseq_id_Base::IsSetRelease(), CTextseq_id_Base::m_Release, CTextseq_id_Base::m_set_State, and CSerialObject::UnassignedString().
Referenced by CTextseq_id::Set().
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Assign a value to Seqid data member.
value | Value to assign |
Definition at line 228 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::m_Seqid, CPatent_seq_id_Base::m_set_State, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), CWGSDb_Impl::GetPatentSeq_id(), CSeq_id::Set(), and x_Assign().
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Assign a value to Seqid data member.
Definition at line 235 of file Patent_seq_id_.hpp.
References CPatent_seq_id_Base::IsSetSeqid(), CPatent_seq_id_Base::m_Seqid, CPatent_seq_id_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Strand data member.
value | Value to assign |
Definition at line 306 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::m_set_State, CPacked_seqpnt_Base::m_Strand, and rapidjson::value.
Referenced by CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_CI_Impl::MakeLocPacked_pnt(), CSeq_loc_Conversion::s_ConvertToMix(), CSeq_loc::SetStrand(), x_Assign(), and CSeq_loc::x_ChangeToPackedPnt().
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Assign a value to Strand data member.
value | Value to assign |
Definition at line 486 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_set_State, CSeq_interval_Base::m_Strand, and rapidjson::value.
Referenced by CSeq_loc_mix::AddInterval(), CPacked_seqint::AddInterval(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), CSpliced_exon::CreateRowSeq_interval(), CDense_diag::CreateRowSeq_interval(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), fta_do_fix_seq_loc_id(), fta_make_seq_int(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeq_loc_Conversion::GetDstInterval(), CGtfLocationRecord::GetLocation(), GetOverlappingFeatures(), CCSraAlignIterator::GetQualityGraph(), CCodingPropensity::GetScore(), CWGSScaffoldIterator::GetSeq_inst(), CBedImportData::Initialize(), CSeq_loc_Conversion::MakeDstMix(), CSeq_loc_CI_Impl::MakeInterval(), ProjectExon_newlogic(), SRelLoc::Resolve(), s_BuildMaskedRanges(), s_CreateMappingInfo(), s_FixIntervalProtToCds(), s_Load_Seq_point(), CRawBedRecord::SetInterval(), CSeq_loc::SetStrand(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), x_Assign(), CNewCleanup_imp::x_BothStrandBC(), CVariationNormalization_base< T >::x_ConvertPointToInterval(), CSGAlignmentJob::x_CreateFeatGlyph(), CSeqMap::x_DoUpdateSeq_inst(), CLocationListCtrl::x_GetInterval(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), x_PushRange(), CNewCleanup_imp::x_SeqIntervalBC(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), SSNP_Info::x_UpdateSeq_feat(), CFeatTableEdit::xGetGeneLocation(), CGff3LocationMerger::xGetRecordLocation(), CReaderBase::xSetBrowserRegion(), CMicroArrayReader::xSetFeatureLocation(), CBedReader::xSetFeatureLocationBlock(), CBedReader::xSetFeatureLocationRna(), and CGff3Reader::xUpdateAnnotGeneric().
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Assign a value to Strand data member.
value | Value to assign |
Definition at line 359 of file Seq_point_.hpp.
References CSeq_point_Base::m_set_State, CSeq_point_Base::m_Strand, and rapidjson::value.
Referenced by CSeq_loc_mix::AddInterval(), BOOST_AUTO_TEST_CASE(), fta_make_seq_pnt(), CSeq_loc_Conversion::GetDstPoint(), CBulkLocationPanel::GetLocForBioseq(), CCdregionValidator::MapToNTCoords(), NormalizeLoc(), CAnalyzeShiftApp::ProcessHGVS(), SRelLoc::Resolve(), CSeq_loc::SetStrand(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeq_loc_CI_Impl::UpdatePoint(), CSeqTableLocColumns::UpdateSeq_loc(), variation_ref::CHgvsParser::x_abs_pos(), variation::CHgvsParser::x_abs_pos(), x_Assign(), CNewCleanup_imp::x_BothStrandBC(), CVariationNormalization_base< T >::x_ConvertIntervalToPoint(), variation_ref::CHgvsParser::x_general_pos(), variation::CHgvsParser::x_general_pos(), CLocationListCtrl::x_GetInterval(), x_PushRange(), CGFFReader::x_ResolveLoc(), CNewCleanup_imp::x_SeqPointBC(), and SSNP_Info::x_UpdateSeq_feat().
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Assign a value to Strand data member.
Definition at line 313 of file Packed_seqpnt_.hpp.
References CPacked_seqpnt_Base::IsSetStrand(), CPacked_seqpnt_Base::m_set_State, CPacked_seqpnt_Base::m_Strand, and CSerialObject::UnassignedByte().
Referenced by CPacked_seqpnt::CPacked_seqpnt(), and CPacked_seqpnt::FlipStrand().
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Assign a value to Strand data member.
Definition at line 493 of file Seq_interval_.hpp.
References CSeq_interval_Base::IsSetStrand(), CSeq_interval_Base::m_set_State, CSeq_interval_Base::m_Strand, and CSerialObject::UnassignedByte().
Referenced by CSeq_interval::CSeq_interval(), and CSeq_interval::FlipStrand().
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Assign a value to Strand data member.
Definition at line 366 of file Seq_point_.hpp.
References CSeq_point_Base::IsSetStrand(), CSeq_point_Base::m_set_State, CSeq_point_Base::m_Strand, and CSerialObject::UnassignedByte().
Referenced by CSeq_point::CSeq_point(), and CSeq_point::FlipStrand().
void CSeq_id_Base::SetSwissprot | ( | CSeq_id_Base::TSwissprot & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 315 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Swissprot, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TSwissprot & CSeq_id_Base::SetSwissprot | ( | void | ) |
Select the variant.
Definition at line 309 of file Seq_id_.cpp.
References CSeq_id_Base::e_Swissprot, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_FIXTURE_TEST_CASE(), GetSprotDescr(), CSeq_id::Set(), SetTextId(), and CIdMapperGCAssembly::x_AddUnversionedMapping().
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Assign a value to To data member.
value | Value to assign |
Definition at line 439 of file Seq_interval_.hpp.
References CSeq_interval_Base::m_set_State, CSeq_interval_Base::m_To, and rapidjson::value.
Referenced by CSeq_loc_mix::AddInterval(), CPacked_seqint::AddInterval(), Blast_GetSeqLocInfoVector(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToPackedInt(), NTweakExon::Collapse(), CSeq_loc_Conversion_Set::Convert(), CRawWiggleRecord::CRawWiggleRecord(), CSpliced_exon::CreateRowSeq_interval(), CDense_diag::CreateRowSeq_interval(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSourceFeatureItem::CSourceFeatureItem(), EndAdded(), CGBObjectLoader::Execute(), CdBlaster::FillOutSeqLoc(), CSimpleB2SWrapper::FillOutSeqLoc(), fta_do_fix_seq_loc_id(), fta_get_seqloc_int_whole(), fta_make_seq_int(), CSeqUtils::GetCdsMappingInfoFromRna(), CCSraRefSeqIterator::GetCoverageGraph(), CDDAnnotateDialog::GetCurrentHighlightedIntervals(), CSeq_loc_Conversion::GetDstInterval(), CHistogramGlyph::GetHTMLActiveAreas(), IBISAnnotateDialog::GetIntervalsForSet(), CGtfLocationRecord::GetLocation(), GetOverlappingFeatures(), GetProteinWeights(), CCSraAlignIterator::GetQualityGraph(), CCodingPropensity::GetScore(), CSNPDbFeatIterator::GetSeq_feat(), CWGSScaffoldIterator::GetSeq_inst(), GetSeqLocIntSP(), GetSPSeqLoc(), CBedImportData::Initialize(), CGencollIdMapper::IsLocInAGap(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CBamRefSeqInfo::LoadPileupChunk(), LoadSequencesToScope(), MakeDDFromSeqLoc(), CSeq_loc_Conversion::MakeDstMix(), MakeEntryForDeltaConversion(), CSeq_loc_CI_Impl::MakeInterval(), MakeMaskingBioseq(), MakeSeqLocFromDD(), ProjectExon_newlogic(), CGlimmerReader::Read(), SRelLoc::Resolve(), ReverseComplementLocation(), s_BuildMaskedRanges(), s_ConvertBlastnMasks(), s_CreateMappingInfo(), s_ExtendIntervalToEnd(), s_FixIntervalProtToCds(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetIntronsAndSpliceSiteLocs(), s_MakePackedInt(), s_OOFBlastHSP2SeqAlign(), s_Seq_align_Seq_loc(), s_SeqIntervalDelete(), s_SetSplitQuerySeqInterval(), s_SubLocDeltaSeq(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), NTweakExon::SetBioStart(), NTweakExon::SetBioStop(), CRawBedRecord::SetInterval(), SetNewInterval(), SimpleSeqLocFromBioseq(), sParseRange(), Split_Qscore_SeqGraph_By_DeltaSeq(), SplitLocationForGap(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSeqTableLocColumns::UpdateSeq_loc(), x_Assign(), CVariationNormalization_base< T >::x_ConvertPointToInterval(), CSGAlignmentJob::x_CreateFeatGlyph(), CCpgSearchJob::x_DoSearch(), CSeqMap::x_DoUpdateSeq_inst(), SGraphMaker::x_EndGraph(), CFeaturePropagator::x_ExtendToStopCodon(), CLocationListCtrl::x_GetInterval(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CWGSSeqIterator::x_GetQualityAnnot(), CCSraShortReadIterator::x_GetQualityGraph(), CFeatureGenerator::SImplementation::x_MapFeature(), x_PushRange(), CNewCleanup_imp::x_SeqIntervalBC(), CVectorTrimPanel::x_SeqIntervalDelete(), CWig2tableApplication::x_SetTotalLoc(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CAdjustForConsensusSpliceSite::x_UpdateInterval(), CAdjustForConsensusSpliceSite::x_UpdateIntervals(), SSNP_Info::x_UpdateSeq_feat(), CGff3Writer::xAssignFeature(), XGapToSeqLocEx(), CFeatTableEdit::xGetGeneLocation(), CGff3LocationMerger::xGetRecordLocation(), CReaderBase::xSetBrowserRegion(), CMicroArrayReader::xSetFeatureLocation(), CBedReader::xSetFeatureLocationBlock(), CBedReader::xSetFeatureLocationRna(), CWiggleReader::xSetTotalLoc(), and CGff3Reader::xUpdateAnnotGeneric().
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Assign a value to To data member.
Definition at line 446 of file Seq_interval_.hpp.
References CSeq_interval_Base::IsSetTo(), CSeq_interval_Base::m_set_State, CSeq_interval_Base::m_To, and CSerialObject::UnassignedByte().
Referenced by CSeq_interval::CSeq_interval().
void CSeq_id_Base::SetTpd | ( | CSeq_id_Base::TTpd & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 513 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Tpd, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TTpd & CSeq_id_Base::SetTpd | ( | void | ) |
Select the variant.
Definition at line 507 of file Seq_id_.cpp.
References CSeq_id_Base::e_Tpd, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_FIXTURE_TEST_CASE(), CSeq_id::Set(), SetTextId(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and CRemoveName::x_GetReplacementIds().
void CSeq_id_Base::SetTpe | ( | CSeq_id_Base::TTpe & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 491 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Tpe, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TTpe & CSeq_id_Base::SetTpe | ( | void | ) |
Select the variant.
Definition at line 485 of file Seq_id_.cpp.
References CSeq_id_Base::e_Tpe, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_FIXTURE_TEST_CASE(), CSeq_id::Set(), SetTextId(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and CRemoveName::x_GetReplacementIds().
void CSeq_id_Base::SetTpg | ( | CSeq_id_Base::TTpg & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 469 of file Seq_id_.cpp.
References CObject::AddReference(), CSeq_id_Base::e_Tpg, CSeq_id_Base::m_choice, CSeq_id_Base::m_object, CSeq_id_Base::ResetSelection(), and rapidjson::value.
CSeq_id_Base::TTpg & CSeq_id_Base::SetTpg | ( | void | ) |
Select the variant.
Definition at line 463 of file Seq_id_.cpp.
References CSeq_id_Base::e_Tpg, eDoNotResetVariant, CSeq_id_Base::m_object, and CSeq_id_Base::Select().
Referenced by CSeq_id::Assign(), BOOST_FIXTURE_TEST_CASE(), CSeq_id::Set(), SetTextId(), CIdMapperGCAssembly::x_AddUnversionedMapping(), and CRemoveName::x_GetReplacementIds().
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Assign a value to Version data member.
value | Value to assign |
Definition at line 450 of file Textseq_id_.hpp.
References CTextseq_id_Base::m_set_State, CTextseq_id_Base::m_Version, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGoodAlign(), GetDescrSPBlock(), CSeq_id::GetMatchingTextseqIds(), GetWGSMasterSeq_id(), s_AssignTextseq_id(), TestOneLongGeneral(), and x_Assign().
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Assign a value to Version data member.
Definition at line 457 of file Textseq_id_.hpp.
References CTextseq_id_Base::IsSetVersion(), CTextseq_id_Base::m_set_State, CTextseq_id_Base::m_Version, and CSerialObject::UnassignedByte().
Referenced by CTextseq_id::Set().
void CSeq_loc_Base::SetWhole | ( | CSeq_loc_Base::TWhole & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 184 of file Seq_loc_.cpp.
References CObject::AddReference(), CSeq_loc_Base::e_Whole, CSeq_loc_Base::m_choice, CSeq_loc_Base::m_object, CSeq_loc_Base::ResetSelection(), and rapidjson::value.
CSeq_loc_Base::TWhole & CSeq_loc_Base::SetWhole | ( | void | ) |
Select the variant.
Definition at line 178 of file Seq_loc_.cpp.
References CSeq_loc_Base::e_Whole, eDoNotResetVariant, CSeq_loc_Base::m_object, and CSeq_loc_Base::Select().
void CSeq_id_Base::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 188 of file Seq_id_.cpp.
References DIAG_COMPILE_INFO, CSeq_id_Base::m_choice, and CSeq_id_Base::sm_SelectionNames.
Referenced by CSeq_id_Base::CheckSelected().
void CSeq_loc_Base::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 145 of file Seq_loc_.cpp.
References DIAG_COMPILE_INFO, CSeq_loc_Base::m_choice, and CSeq_loc_Base::sm_SelectionNames.
Referenced by CSeq_loc_Base::CheckSelected().
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Which variant is currently selected.
Definition at line 746 of file Seq_id_.hpp.
References CSeq_id_Base::m_choice.
Referenced by CGBProjectHelper::AddProjectItemsFromRID(), CFeatGapInfo::AdjustProteinSeq(), AgpRead(), AllowOrphanedProtein(), AreSeqIdTypesMatched(), ArgToSeq_id(), CSeq_id::Assign(), CSeq_id_Descr::Assign(), CGffRecord::AssignSeqId(), CSeq_id::BaseBestRankScore(), CSeq_id::BaseBlastScore(), CSeq_id::BaseFastaAAScore(), CSeq_id::BaseFastaNAScore(), CSeq_id::BaseTextScore(), BOOST_AUTO_TEST_CASE(), CSeq_id::Compare(), CSeq_loc::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), DetectSeqIdTypeForIPG(), FinalCleanup(), g_DoesNotReferencePrimary(), CFlatFileGenerator::Generate(), GetAccessionAndDatabaseSource(), CWGSClient::GetBioseqInfo(), CAlignFormatUtil::GetDbType(), IPSGS_Processor::GetEffectiveSeqIdType(), CWriteUtil::GetIdType(), CAlignFormatUtil::GetLabel(), CBioseq::GetLabel(), CSeq_id::GetMatchingIds(), CSeq_id::GetMatchingTextseqIds(), GetSeq_idByType(), CSeq_id::GetTextseq_Id(), GetTitle(), CSeq_id::IdentifyAccession(), IPSGS_Processor::ParseInputSeqId(), s_AssignSeq_id(), s_Fingerprint_Seq_id(), s_GetBestIDForURL(), s_GetDescription(), s_GetLinkoutUrl(), s_GetSeqIdChoiceMask(), s_PSGRank(), s_ScoreForDBSource(), s_SetCloneInfo(), s_ShouldUseOriginalID(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CSeqDBImpl::SeqidToOids(), CNewCleanup_imp::SetGlobalFlags(), CValidError_imp::Setup(), CCleanup::ShouldStripPubSerial(), sx_MakeUniqueId(), CIdMapperConfig::TargetHandle(), TestCollidingAccessionFixes(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateOrgContext(), CVDBBlastUtil::VDBIdType(), CSeq_id::WriteAsFasta(), CFlatSeqLoc::x_AddID(), CFeatureItem::x_AddQualProteinId(), CAsn2FlatApp::x_AddSNPAnnots(), CWriteDB_IsamIndex::x_AddStringIds(), CIdMapperGCAssembly::x_AddUnversionedMapping(), CSequenceUpdater::x_ChangeIDInFeature(), CPSGS_CassBlobBase::x_DecideToRequestMoreChunksForSmartTSE(), CDeflineProcess::x_FastaSeqIdWrite(), CSeq_id_Textseq_Tree::x_FindStrInfo(), CGencollIdMapper::x_FixImperfectId(), CSeqVectorProcess::x_FsaSeqIdWrite(), CFastaOstream::x_GetBestId(), CWriteDB_Impl::x_GetFastaReaderDeflines(), CProjectFileWriter::x_GetGi(), CSeqDBVol::x_GetHdrAsn1(), CGridTableSeqIds::x_GetLabel(), CRemoveName::x_GetReplacementIds(), CAccessionToLocalId::x_GetReplacementIds(), CSeq_id_Mapper::x_GetTree(), CTableColumnTypeGuesser::x_GuessType(), CPhyTreeFormatter::x_InitTreeFeatures(), CFlatGatherer::x_MergeEqualBioSources(), CGencollIdMapper::x_RecursiveSeqFix(), CBuildDatabase::x_ResolveRemoteId(), CGFFReader::x_ResolveSeqName(), COligoSpecificityCheck::x_SavePrimerInfo(), CId2ReaderBase::x_SetResolve(), CValidError_bioseq::x_ShowBioProjectWarning(), CGencollIdMapper::x_StripPseudoSeq(), CTitleProcess::x_TitleSeqIdWrite(), CSingleFeatValidator::x_ValidateSeqFeatProduct(), CSeq_id::x_WriteContentAsFasta(), and CWiggleWriter::xWriteSingleGraphFixedStep().
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Which variant is currently selected.
Definition at line 475 of file Seq_loc_.hpp.
References CSeq_loc_Base::m_choice.
Referenced by CSeq_loc::Add(), AddFeat(), CHandleRangeMap::AddLocation(), variation_ref::CVariationUtil::AdjustDelinsToInterval(), CSeq_loc::Assign(), BOOST_AUTO_TEST_CASE(), CSeq_loc::ChangeToMix(), CWriteUtil::ChangeToPackedInt(), CSeq_loc::ChangeToPackedInt(), CCleanup::ClearInternalPartials(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CSeq_loc_Conversion::ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), CSeq_loc_Conversion::ConvertCdregion(), CSeq_loc_Conversion_Set::ConvertCdregion(), CSeq_loc_Conversion::ConvertEquiv(), CSeq_loc_Conversion_Set::ConvertEquiv(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion::ConvertRna(), CSeq_loc_Conversion_Set::ConvertRna(), CLocationEditPolicy::ConvertToOrder(), CorrectIntervalOrder(), CSeq_loc::FlipStrand(), FTASeqLocCheck(), CWriteUtil::GetCodeBreak(), GetCoverage(), GetLength(), GetReverseComplement(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), GetStrand(), CSeq_loc::GetStrand(), CWriteUtil::GetTrnaAntiCodon(), CEditingActionFeatTranslExcept::GetValue(), CLocationEditPolicy::HasNulls(), CLocationPanel::Init(), CSeq_loc_CI_Impl::InsertRange(), variation_ref::IsFirstSubsetOfSecond(), CWriteUtil::IsLocationOrdered(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), CSeq_loc::IsTruncatedStart(), CSeq_loc::IsTruncatedStop(), CCompareSeqRegions::NextComparisonGroup(), NormalizeLoc(), CStd_seg::OffsetRow(), SSNP_Info::ParseSeq_feat(), CSeq_align::RemapToLoc(), CStd_seg::RemapToLoc(), CSeq_loc::ResetStrand(), ReverseComplementLocation(), CFeatCompareJob_Align::Run(), s_AddCoalescedLocations(), s_AddLocString(), s_BioSeqHasContig(), s_CanAdd(), CSeq_loc_Conversion::s_ConvertToMix(), s_CountIntervals(), s_Fingerprint_Seq_loc(), s_GetLabel(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetStrand(), s_IntervalsMatchGaps(), s_IsEmpty(), s_SeqLoc2MaskedSubjRanges(), s_SeqLocDelete(), SeqLocAdjustForInsert(), SeqLocAdjustForTrim(), CNewCleanup_imp::SeqLocBC(), SeqLocPartialCheck(), CFeatureSearchJob::SeqLocToString(), CCleanup::SetCodeBreakLocation(), CSeq_loc::SetId(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeq_loc::SetStrand(), CSeq_loc::SetTruncatedStart(), CSeq_loc::SetTruncatedStop(), CFeatGapInfo::Split(), SplitLocationForGap(), CLocationPanel::TransferDataToWindow(), CAlignmentAssistant::TranslateLocations(), CFeatGapInfo::Trim(), UpgradeSeqLocId(), CValidError_graph::ValidateGraphsOnBioseq(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), variation::CVariationUtil::x_AdjustDelinsToInterval(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqLoc(), CNewCleanup_imp::x_BothStrandBC(), CBioseq_Info::x_CalcBioseqLength(), CSeq_loc::x_CalculateTotalRangeCheckId(), CSeq_loc::x_CheckId(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CSGFeatureJob::x_CreateFeature1(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CLocation_constraint::x_DoesStrandMatchConstraint(), CSeq_loc_Mapper_Base::x_FixNonsenseFuzz(), CFastaOstreamEx::x_GetCodeBreak(), CSeq_align_Mapper_Base::x_Init(), CBioseqIndex::x_InitFeats(), CBatchFeatJob::x_LoadFeatProducts(), CLocationPanel::x_LoadSeqLoc(), CFeatureGenerator::SImplementation::x_MapFeature(), CReportEntry::x_MapPos(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CMacroFunction_LocationType::x_Match(), x_MergeAndSort(), x_MergeNoSort(), CConvertFeatureBase::x_MoveFeatureToProtein(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CGC_Assembly_Parser::x_ParseGCSequence(), CSeq_loc_CI_Impl::x_ProcessInterval(), CSeq_loc_CI_Impl::x_ProcessLocation(), CSeq_loc_CI_Impl::x_ProcessPoint(), x_PushRange(), variation::CVariationUtil::x_Remap(), CBioseq::x_SeqLoc_To_DeltaExt(), CVectorTrimPanel::x_SeqLocDelete(), CBioseqContext::x_SetHasMultiIntervalGenes(), CBioseqContext::x_SetOpticalMapPoints(), x_SubAndSort(), x_SubNoSort(), x_ToBlastVec(), CValidError_graph::x_ValidateGraphLocation(), CGffIdGenerator::xExtractFeatureLocation(), and CGff3Reader::xUpdateAnnotRna().
CGiimport_id::~CGiimport_id | ( | void | ) |
Definition at line 50 of file Giimport_id.cpp.
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Definition at line 89 of file Giimport_id_.cpp.
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Definition at line 74 of file Packed_seqint_.cpp.
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Definition at line 121 of file Packed_seqpnt_.cpp.
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Definition at line 93 of file Patent_seq_id_.cpp.
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Definition at line 109 of file PDB_seq_id_.cpp.
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Definition at line 109 of file Seq_bond_.cpp.
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Definition at line 605 of file Seq_id_.cpp.
References CSeq_id_Base::Reset().
CSeq_id_set::~CSeq_id_set | ( | void | ) |
Definition at line 50 of file Seq_id_set.cpp.
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Definition at line 74 of file Seq_id_set_.cpp.
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Definition at line 136 of file Seq_interval_.cpp.
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Definition at line 399 of file Seq_loc_.cpp.
References CSeq_loc_Base::Reset().
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Definition at line 74 of file Seq_loc_equiv_.cpp.
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Definition at line 74 of file Seq_loc_mix_.cpp.
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Definition at line 115 of file Seq_point_.cpp.
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Definition at line 97 of file Textseq_id_.cpp.
union { ... } |
union { ... } |
Definition at line 187 of file Seq_bond_.hpp.
Referenced by CSeq_bond_Base::GetA(), CSeq_bond_Base::IsSetA(), CSeq_bond_Base::ResetA(), and CSeq_bond_Base::SetA().
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Definition at line 266 of file Textseq_id_.hpp.
Referenced by CTextseq_id_Base::GetAccession(), CTextseq_id_Base::ResetAccession(), and CTextseq_id_Base::SetAccession().
Definition at line 188 of file Seq_bond_.hpp.
Referenced by CSeq_bond_Base::GetB(), CSeq_bond_Base::IsSetB(), CSeq_bond_Base::ResetB(), and CSeq_bond_Base::SetB().
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Definition at line 279 of file PDB_seq_id_.hpp.
Referenced by CPDB_seq_id_Base::GetChain(), CPDB_seq_id_Base::ResetChain(), and CPDB_seq_id_Base::SetChain().
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Definition at line 281 of file PDB_seq_id_.hpp.
Referenced by CPDB_seq_id_Base::GetChain_id(), CPDB_seq_id_Base::ResetChain_id(), and CPDB_seq_id_Base::SetChain_id().
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Definition at line 722 of file Seq_id_.hpp.
Referenced by CSeq_id_Base::CheckSelected(), CSeq_id_Base::DoSelect(), CSeq_id_Base::IsDdbj(), CSeq_id_Base::IsEmbl(), CSeq_id_Base::IsGenbank(), CSeq_id_Base::IsGeneral(), CSeq_id_Base::IsGi(), CSeq_id_Base::IsGibbmt(), CSeq_id_Base::IsGibbsq(), CSeq_id_Base::IsGiim(), CSeq_id_Base::IsGpipe(), CSeq_id_Base::IsLocal(), CSeq_id_Base::IsNamed_annot_track(), CSeq_id_Base::IsOther(), CSeq_id_Base::IsPatent(), CSeq_id_Base::IsPdb(), CSeq_id_Base::IsPir(), CSeq_id_Base::IsPrf(), CSeq_id_Base::IsSwissprot(), CSeq_id_Base::IsTpd(), CSeq_id_Base::IsTpe(), CSeq_id_Base::IsTpg(), CSeq_id_Base::Reset(), CSeq_id_Base::ResetSelection(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGiim(), CSeq_id_Base::SetGpipe(), CSeq_id_Base::SetLocal(), CSeq_id_Base::SetNamed_annot_track(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CSeq_id_Base::SetSwissprot(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), CSeq_id_Base::SetTpg(), CSeq_id_Base::ThrowInvalidSelection(), and CSeq_id_Base::Which().
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Definition at line 454 of file Seq_loc_.hpp.
Referenced by CSeq_loc_Base::CheckSelected(), CSeq_loc_Base::DoSelect(), CSeq_loc_Base::IsBond(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsEquiv(), CSeq_loc_Base::IsFeat(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), CSeq_loc_Base::IsWhole(), CSeq_loc_Base::Reset(), CSeq_loc_Base::ResetSelection(), CSeq_loc_Base::SetBond(), CSeq_loc_Base::SetEmpty(), CSeq_loc_Base::SetEquiv(), CSeq_loc_Base::SetFeat(), CSeq_loc_Base::SetInt(), CSeq_loc_Base::SetMix(), CSeq_loc_Base::SetPacked_int(), CSeq_loc_Base::SetPacked_pnt(), CSeq_loc_Base::SetPnt(), CSeq_loc_Base::SetWhole(), CSeq_loc_Base::ThrowInvalidSelection(), and CSeq_loc_Base::Which().
Definition at line 187 of file Patent_seq_id_.hpp.
Referenced by CPatent_seq_id_Base::GetCit(), CPatent_seq_id_Base::IsSetCit(), CPatent_seq_id_Base::ResetCit(), and CPatent_seq_id_Base::SetCit().
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Definition at line 139 of file Packed_seqint_.hpp.
Referenced by CPacked_seqint_Base::Get(), CPacked_seqint_Base::Reset(), and CPacked_seqint_Base::Set().
Definition at line 139 of file Seq_id_set_.hpp.
Referenced by CSeq_id_set_Base::Get(), CSeq_id_set_Base::Reset(), and CSeq_id_set_Base::Set().
Definition at line 140 of file Seq_loc_equiv_.hpp.
Referenced by CSeq_loc_equiv_Base::Get(), CSeq_loc_equiv_Base::Reset(), and CSeq_loc_equiv_Base::Set().
Definition at line 140 of file Seq_loc_mix_.hpp.
Referenced by CSeq_loc_mix_Base::Get(), CSeq_loc_mix_Base::Reset(), and CSeq_loc_mix_Base::Set().
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Definition at line 229 of file Giimport_id_.hpp.
Referenced by CGiimport_id_Base::GetDb(), CGiimport_id_Base::ResetDb(), and CGiimport_id_Base::SetDb().
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Definition at line 346 of file Seq_interval_.hpp.
Referenced by CSeq_interval_Base::GetFrom(), CSeq_interval_Base::ResetFrom(), and CSeq_interval_Base::SetFrom().
Definition at line 264 of file Packed_seqpnt_.hpp.
Referenced by CPacked_seqpnt_Base::GetFuzz(), CPacked_seqpnt_Base::IsSetFuzz(), CPacked_seqpnt_Base::ResetFuzz(), and CPacked_seqpnt_Base::SetFuzz().
Definition at line 271 of file Seq_point_.hpp.
Referenced by CSeq_point_Base::GetFuzz(), CSeq_point_Base::IsSetFuzz(), CSeq_point_Base::ResetFuzz(), and CSeq_point_Base::SetFuzz().
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Definition at line 350 of file Seq_interval_.hpp.
Referenced by CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::ResetFuzz_from(), and CSeq_interval_Base::SetFuzz_from().
Definition at line 351 of file Seq_interval_.hpp.
Referenced by CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::ResetFuzz_to(), and CSeq_interval_Base::SetFuzz_to().
ncbi::TIntId CSeq_id_Base::m_Gi |
Definition at line 731 of file Seq_id_.hpp.
Referenced by CSeq_id_Base::DoSelect(), CSeq_id_Base::GetGi(), and CSeq_id_Base::SetGi().
ncbi::TIntId { ... } ::m_Gi |
Definition at line 731 of file Seq_id_.hpp.
TGibbmt CSeq_id_Base::m_Gibbmt |
Definition at line 730 of file Seq_id_.hpp.
Referenced by CSeq_id_Base::DoSelect(), CSeq_id_Base::GetGibbmt(), and CSeq_id_Base::SetGibbmt().
TGibbmt { ... } ::m_Gibbmt |
Definition at line 730 of file Seq_id_.hpp.
TGibbsq CSeq_id_Base::m_Gibbsq |
Definition at line 729 of file Seq_id_.hpp.
Referenced by CSeq_id_Base::DoSelect(), CSeq_id_Base::GetGibbsq(), and CSeq_id_Base::SetGibbsq().
TGibbsq { ... } ::m_Gibbsq |
Definition at line 729 of file Seq_id_.hpp.
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Definition at line 228 of file Giimport_id_.hpp.
Referenced by CGiimport_id_Base::GetId(), CGiimport_id_Base::ResetId(), and CGiimport_id_Base::SetId().
Definition at line 263 of file Packed_seqpnt_.hpp.
Referenced by CPacked_seqpnt_Base::GetId(), CPacked_seqpnt_Base::IsSetId(), CPacked_seqpnt_Base::ResetId(), and CPacked_seqpnt_Base::SetId().
Definition at line 349 of file Seq_interval_.hpp.
Referenced by CSeq_interval_Base::GetId(), CSeq_interval_Base::IsSetId(), CSeq_interval_Base::ResetId(), and CSeq_interval_Base::SetId().
Definition at line 270 of file Seq_point_.hpp.
Referenced by CSeq_point_Base::GetId(), CSeq_point_Base::IsSetId(), CSeq_point_Base::ResetId(), and CSeq_point_Base::SetId().
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Definition at line 278 of file PDB_seq_id_.hpp.
Referenced by CPDB_seq_id_Base::GetMol(), CPDB_seq_id_Base::ResetMol(), and CPDB_seq_id_Base::SetMol().
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Definition at line 265 of file Textseq_id_.hpp.
Referenced by CTextseq_id_Base::GetName(), CTextseq_id_Base::ResetName(), and CTextseq_id_Base::SetName().
NCBI_NS_NCBI::CSerialObject* { ... } ::m_object |
Definition at line 732 of file Seq_id_.hpp.
NCBI_NS_NCBI::CSerialObject* CSeq_id_Base::m_object |
Definition at line 732 of file Seq_id_.hpp.
Referenced by CSeq_id_Base::DoSelect(), CSeq_id_Base::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGiim(), CSeq_id_Base::GetGpipe(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), CSeq_id_Base::GetTpg(), CSeq_id_Base::ResetSelection(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGiim(), CSeq_id_Base::SetGpipe(), CSeq_id_Base::SetLocal(), CSeq_id_Base::SetNamed_annot_track(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CSeq_id_Base::SetSwissprot(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), and CSeq_id_Base::SetTpg().
NCBI_NS_NCBI::CSerialObject* CSeq_loc_Base::m_object |
Definition at line 461 of file Seq_loc_.hpp.
Referenced by CSeq_loc_Base::DoSelect(), CSeq_loc_Base::GetBond(), CSeq_loc_Base::GetEmpty(), CSeq_loc_Base::GetEquiv(), CSeq_loc_Base::GetFeat(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_loc_Base::GetWhole(), CSeq_loc_Base::ResetSelection(), CSeq_loc_Base::SetBond(), CSeq_loc_Base::SetEmpty(), CSeq_loc_Base::SetEquiv(), CSeq_loc_Base::SetFeat(), CSeq_loc_Base::SetInt(), CSeq_loc_Base::SetMix(), CSeq_loc_Base::SetPacked_int(), CSeq_loc_Base::SetPacked_pnt(), CSeq_loc_Base::SetPnt(), and CSeq_loc_Base::SetWhole().
NCBI_NS_NCBI::CSerialObject* { ... } ::m_object |
Definition at line 461 of file Seq_loc_.hpp.
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Definition at line 268 of file Seq_point_.hpp.
Referenced by CSeq_point_Base::GetPoint(), CSeq_point_Base::ResetPoint(), and CSeq_point_Base::SetPoint().
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Definition at line 265 of file Packed_seqpnt_.hpp.
Referenced by CPacked_seqpnt_Base::GetPoints(), CPacked_seqpnt_Base::ResetPoints(), and CPacked_seqpnt_Base::SetPoints().
Definition at line 280 of file PDB_seq_id_.hpp.
Referenced by CPDB_seq_id_Base::GetRel(), CPDB_seq_id_Base::IsSetRel(), CPDB_seq_id_Base::ResetRel(), and CPDB_seq_id_Base::SetRel().
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Definition at line 230 of file Giimport_id_.hpp.
Referenced by CGiimport_id_Base::GetRelease(), CGiimport_id_Base::ResetRelease(), and CGiimport_id_Base::SetRelease().
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Definition at line 267 of file Textseq_id_.hpp.
Referenced by CTextseq_id_Base::GetRelease(), CTextseq_id_Base::ResetRelease(), and CTextseq_id_Base::SetRelease().
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Definition at line 186 of file Patent_seq_id_.hpp.
Referenced by CPatent_seq_id_Base::GetSeqid(), CPatent_seq_id_Base::ResetSeqid(), and CPatent_seq_id_Base::SetSeqid().
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Definition at line 227 of file Giimport_id_.hpp.
Referenced by CGiimport_id_Base::CGiimport_id_Base(), CGiimport_id_Base::IsSetDb(), CGiimport_id_Base::IsSetId(), CGiimport_id_Base::IsSetRelease(), CGiimport_id_Base::ResetDb(), CGiimport_id_Base::ResetId(), CGiimport_id_Base::ResetRelease(), CGiimport_id_Base::SetDb(), CGiimport_id_Base::SetId(), and CGiimport_id_Base::SetRelease().
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Definition at line 138 of file Packed_seqint_.hpp.
Referenced by CPacked_seqint_Base::CPacked_seqint_Base(), CPacked_seqint_Base::IsSet(), CPacked_seqint_Base::Reset(), and CPacked_seqint_Base::Set().
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Definition at line 261 of file Packed_seqpnt_.hpp.
Referenced by CPacked_seqpnt_Base::CPacked_seqpnt_Base(), CPacked_seqpnt_Base::IsSetPoints(), CPacked_seqpnt_Base::IsSetStrand(), CPacked_seqpnt_Base::ResetPoints(), CPacked_seqpnt_Base::ResetStrand(), CPacked_seqpnt_Base::SetPoints(), and CPacked_seqpnt_Base::SetStrand().
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Definition at line 185 of file Patent_seq_id_.hpp.
Referenced by CPatent_seq_id_Base::CPatent_seq_id_Base(), CPatent_seq_id_Base::IsSetSeqid(), CPatent_seq_id_Base::ResetSeqid(), and CPatent_seq_id_Base::SetSeqid().
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Definition at line 277 of file PDB_seq_id_.hpp.
Referenced by CPDB_seq_id_Base::CPDB_seq_id_Base(), CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::IsSetChain_id(), CPDB_seq_id_Base::IsSetMol(), CPDB_seq_id_Base::ResetChain(), CPDB_seq_id_Base::ResetChain_id(), CPDB_seq_id_Base::ResetMol(), CPDB_seq_id_Base::SetChain(), CPDB_seq_id_Base::SetChain_id(), and CPDB_seq_id_Base::SetMol().
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Definition at line 186 of file Seq_bond_.hpp.
Referenced by CSeq_bond_Base::CSeq_bond_Base().
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Definition at line 138 of file Seq_id_set_.hpp.
Referenced by CSeq_id_set_Base::CSeq_id_set_Base(), CSeq_id_set_Base::IsSet(), CSeq_id_set_Base::Reset(), and CSeq_id_set_Base::Set().
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Definition at line 345 of file Seq_interval_.hpp.
Referenced by CSeq_interval_Base::CSeq_interval_Base(), CSeq_interval_Base::IsSetFrom(), CSeq_interval_Base::IsSetStrand(), CSeq_interval_Base::IsSetTo(), CSeq_interval_Base::ResetFrom(), CSeq_interval_Base::ResetStrand(), CSeq_interval_Base::ResetTo(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().
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Definition at line 139 of file Seq_loc_equiv_.hpp.
Referenced by CSeq_loc_equiv_Base::CSeq_loc_equiv_Base(), CSeq_loc_equiv_Base::IsSet(), CSeq_loc_equiv_Base::Reset(), and CSeq_loc_equiv_Base::Set().
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Definition at line 139 of file Seq_loc_mix_.hpp.
Referenced by CSeq_loc_mix_Base::CSeq_loc_mix_Base(), CSeq_loc_mix_Base::IsSet(), CSeq_loc_mix_Base::Reset(), and CSeq_loc_mix_Base::Set().
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Definition at line 267 of file Seq_point_.hpp.
Referenced by CSeq_point_Base::CSeq_point_Base(), CSeq_point_Base::IsSetPoint(), CSeq_point_Base::IsSetStrand(), CSeq_point_Base::ResetPoint(), CSeq_point_Base::ResetStrand(), CSeq_point_Base::SetPoint(), and CSeq_point_Base::SetStrand().
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Definition at line 264 of file Textseq_id_.hpp.
Referenced by CTextseq_id_Base::CTextseq_id_Base(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), CTextseq_id_Base::IsSetRelease(), CTextseq_id_Base::IsSetVersion(), CTextseq_id_Base::ResetAccession(), CTextseq_id_Base::ResetName(), CTextseq_id_Base::ResetRelease(), CTextseq_id_Base::ResetVersion(), CTextseq_id_Base::SetAccession(), CTextseq_id_Base::SetName(), CTextseq_id_Base::SetRelease(), and CTextseq_id_Base::SetVersion().
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Definition at line 262 of file Packed_seqpnt_.hpp.
Referenced by CPacked_seqpnt_Base::GetStrand(), CPacked_seqpnt_Base::ResetStrand(), and CPacked_seqpnt_Base::SetStrand().
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Definition at line 348 of file Seq_interval_.hpp.
Referenced by CSeq_interval_Base::GetStrand(), CSeq_interval_Base::ResetStrand(), and CSeq_interval_Base::SetStrand().
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Definition at line 269 of file Seq_point_.hpp.
Referenced by CSeq_point_Base::GetStrand(), CSeq_point_Base::ResetStrand(), and CSeq_point_Base::SetStrand().
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Definition at line 347 of file Seq_interval_.hpp.
Referenced by CSeq_interval_Base::GetTo(), CSeq_interval_Base::ResetTo(), and CSeq_interval_Base::SetTo().
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Definition at line 268 of file Textseq_id_.hpp.
Referenced by CTextseq_id_Base::GetVersion(), CTextseq_id_Base::ResetVersion(), and CTextseq_id_Base::SetVersion().
Definition at line 726 of file Seq_id_.hpp.
Referenced by CSeq_id_Base::SelectionName(), and CSeq_id_Base::ThrowInvalidSelection().
Definition at line 458 of file Seq_loc_.hpp.
Referenced by CSeq_loc_Base::SelectionName(), and CSeq_loc_Base::ThrowInvalidSelection().