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CWriteUtil Class Reference

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#include <objtools/writers/write_util.hpp>

Static Public Member Functions

static CRef< CUser_object > GetDescriptor (const CSeq_annot &annot, const string &)
 
static bool GetGenomeString (const CBioSource &, string &)
 
static bool GetOrgModSubType (const COrgMod &, string &, string &)
 
static bool GetSubSourceSubType (const CSubSource &, string &, string &)
 
static bool GetBiomol (CBioseq_Handle, string &)
 
static bool GetIdType (CBioseq_Handle, string &)
 
static bool GetIdType (const CSeq_id &, string &)
 
static bool GetAaName (const CCode_break &, string &)
 
static bool GetCodeBreak (const CCode_break &, string &)
 
static bool GetTrnaProductName (const CTrna_ext &, string &)
 
static bool GetBestId (CSeq_id_Handle, CScope &, string &)
 
static bool GetBestId (const CMappedFeat &, string &)
 
static bool GetTrnaCodons (const CTrna_ext &, string &)
 
static bool GetTrnaAntiCodon (const CTrna_ext &, string &)
 
static bool GetDbTag (const CDbtag &, string &)
 
static bool IsLocationOrdered (const CSeq_loc &)
 
static bool IsSequenceCircular (CBioseq_Handle)
 
static bool NeedsQuoting (const string &)
 
static void ChangeToPackedInt (CSeq_loc &loc)
 
static CConstRef< CUser_object > GetUserObjectByType (const CUser_object &uo, const string &strType)
 
static CConstRef< CUser_object > GetUserObjectByType (const list< CRef< CUser_object > > &uos, const string &strType)
 
static CConstRef< CUser_object > GetModelEvidence (CMappedFeat)
 
static bool GetStringForModelEvidence (CMappedFeat mf, string &mestr)
 
static bool GetStringForGoMarkup (const vector< CRef< CUser_field > > &fields, string &goMarkup, bool relaxed=false)
 
static bool GetStringsForGoMarkup (const vector< CRef< CUser_field > > &fields, vector< string > &goMarkup, bool relaxed=false)
 
static bool GetListOfGoIds (const vector< CRef< CUser_field > > &fields, list< std::string > &goIds, bool relaxed=false)
 
static bool IsThreeFeatFormat (const CSeq_annot &)
 
static bool GetThreeFeatType (const CSeq_feat &, string &)
 
static bool GetThreeFeatScore (const CSeq_feat &, int &)
 
static bool GetThreeFeatRgb (const CSeq_feat &, string &)
 
static bool CompareFeatures (const CMappedFeat &lhs, const CMappedFeat &rhs)
 
static string GetStringId (const CSeq_loc &loc)
 
static bool IsNucleotideSequence (CBioseq_Handle)
 
static bool IsProteinSequence (CBioseq_Handle)
 
static bool IsTransspliced (const CSeq_feat &feature)
 
static bool IsTransspliced (const CMappedFeat &mf)
 
static bool GetTranssplicedEndpoints (const CSeq_loc &loc, unsigned int &inPoint, unsigned int &outPoint)
 
static ENa_strand GetEffectiveStrand (const CSeq_interval &)
 

Detailed Description

Definition at line 51 of file write_util.hpp.

Member Function Documentation

◆ ChangeToPackedInt()

void CWriteUtil::ChangeToPackedInt ( CSeq_loc &  loc)
static

Definition at line 622 of file write_util.cpp.

References CSeq_loc::Assign(), CSeq_loc::ChangeToPackedInt(), copy(), CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Null, CSeq_loc_mix_Base::Get(), CSeq_bond_Base::GetA(), CSeq_loc_Base::GetBond(), CSeq_loc_Base::GetMix(), ITERATE, Ref(), CSeq_loc::SetPacked_int(), and CSeq_loc_Base::Which().

Referenced by CGff3Writer::xAssignFeature(), CGff3Writer::xWriteFeatureProtein(), and CBedWriter::xWriteFeaturesTracked().

◆ CompareFeatures()

bool CWriteUtil::CompareFeatures ( const CMappedFeat &  lhs,
const CMappedFeat &  rhs 
)
static

Definition at line 1217 of file write_util.cpp.

References eExtreme_Positional, CSeqFeatData::eSubtype_region, CSeq_feat_Handle::GetData(), CSeq_feat_Handle::GetFeatSubtype(), CMappedFeat::GetLocation(), CSeqFeatData_Base::GetRegion(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), GetStringId(), int, and CSeq_loc::IsSetStrand().

Referenced by CGtfWriter::x_WriteBioseqHandle(), CGff3Writer::x_WriteFeatureContext(), and CBedWriter::xWriteTrackedAnnot().

◆ GetAaName()

bool CWriteUtil::GetAaName ( const CCode_break &  cb,
string &  aaName 
)
static

Definition at line 233 of file write_util.cpp.

References CCode_break_Base::C_Aa::e_Ncbi8aa, CSeq_data_Base::e_Ncbieaa, CCode_break_Base::C_Aa::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CCode_break_Base::C_Aa::e_Ncbistdaa, CCode_break_Base::GetAa(), CSeqportUtil::GetMapToIndex(), CCode_break_Base::C_Aa::GetNcbi8aa(), CCode_break_Base::C_Aa::GetNcbieaa(), CCode_break_Base::C_Aa::GetNcbistdaa(), and CCode_break_Base::C_Aa::Which().

Referenced by GetCodeBreak(), and CFastaOstreamEx::x_GetCodeBreak().

◆ GetBestId() [1/2]

bool CWriteUtil::GetBestId ( const CMappedFeat &  mf,
string &  best_id 
)
static

Definition at line 685 of file write_util.cpp.

References CGenbankIdResolve::Get(), and CGenbankIdResolve::GetBestId().

◆ GetBestId() [2/2]

bool CWriteUtil::GetBestId ( CSeq_id_Handle  idh,
CScope &  scope,
string &  best_id 
)
static

Definition at line 675 of file write_util.cpp.

References CGenbankIdResolve::Get(), and CGenbankIdResolve::GetBestId().

Referenced by CMacroBioData_BioSourceIter::GetBestDescr(), CMacroBioData_PubdescIter::GetBestDescr(), CMacroBioData_SeqIter::GetBestDescr(), CMakeBadSpecificHostTable::MakeTable(), CMacroFunction_ApplyCDS::TheFunction(), CMacroFunction_ApplyRNA::TheFunction(), CMacroFunction_ApplyGene::TheFunction(), CMacroFunction_ApplyOtherFeature::TheFunction(), and CMacroBioData_SeqdescIter::x_GetSeqId().

◆ GetBiomol()

bool CWriteUtil::GetBiomol ( CBioseq_Handle  bsh,
string &  mol_str 
)
static

Definition at line 494 of file write_util.cpp.

References CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_genomic_mRNA, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_ncRNA, CMolInfo_Base::eBiomol_other, CMolInfo_Base::eBiomol_other_genetic, CMolInfo_Base::eBiomol_pre_RNA, CMolInfo_Base::eBiomol_rRNA, CMolInfo_Base::eBiomol_scRNA, CMolInfo_Base::eBiomol_snoRNA, CMolInfo_Base::eBiomol_snRNA, CMolInfo_Base::eBiomol_tmRNA, CMolInfo_Base::eBiomol_transcribed_RNA, CMolInfo_Base::eBiomol_tRNA, EMIT, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, CMolInfo_Base::GetBiomol(), CBioseq_Handle::GetInst_Mol(), CBioseq_Handle::GetParentEntry(), CMolInfo_Base::IsSetBiomol(), and md.

Referenced by CGff3Writer::xAssignSourceAttributeMolType().

◆ GetCodeBreak()

bool CWriteUtil::GetCodeBreak ( const CCode_break &  cb,
string &  cbString 
)
static

Definition at line 266 of file write_util.cpp.

References CSeq_loc_Base::e_Int, eExtreme_Positional, eNa_strand_minus, GetAaName(), CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CCode_break_Base::GetLoc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), NStr::IntToString(), CCode_break_Base::IsSetLoc(), CSeq_interval_Base::IsSetStrand(), and CSeq_loc_Base::Which().

Referenced by CGff2Writer::xAssignFeatureAttributeCodeBreak().

◆ GetDbTag()

bool CWriteUtil::GetDbTag ( const CDbtag &  dbtag,
string &  dbTagStr 
)
static

Definition at line 461 of file write_util.cpp.

References CDbtag_Base::GetDb(), CObject_id_Base::GetId(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CObject_id_Base::IsId(), CDbtag_Base::IsSetDb(), CDbtag_Base::IsSetTag(), CObject_id_Base::IsStr(), str(), and NStr::UIntToString().

Referenced by CGff3Writer::xAssignFeatureAttributeDbxref(), and CGff3Writer::xAssignSourceAttributeDbxref().

◆ GetDescriptor()

CRef< CUser_object > CWriteUtil::GetDescriptor ( const CSeq_annot &  annot,
const string &  strType 
)
static

Definition at line 57 of file write_util.cpp.

References CSerialObject::Assign(), CAnnot_descr_Base::Get(), CSeq_annot_Base::GetDesc(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeq_annot_Base::IsSetDesc(), and CRef< C, Locker >::Reset().

◆ GetEffectiveStrand()

ENa_strand CWriteUtil::GetEffectiveStrand ( const CSeq_interval &  interval)
static

Definition at line 1411 of file write_util.cpp.

References eNa_strand_minus, eNa_strand_plus, CSeq_interval_Base::GetStrand(), and CSeq_interval_Base::IsSetStrand().

Referenced by CGff2Writer::xIntervalsNeedPartNumbers().

◆ GetGenomeString()

bool CWriteUtil::GetGenomeString ( const CBioSource &  bs,
string &  genome_str 
)
static

Definition at line 84 of file write_util.cpp.

References CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromatophore, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_chromosome, CBioSource_Base::eGenome_cyanelle, CBioSource_Base::eGenome_endogenous_virus, CBioSource_Base::eGenome_extrachrom, CBioSource_Base::eGenome_genomic, CBioSource_Base::eGenome_hydrogenosome, CBioSource_Base::eGenome_insertion_seq, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_macronuclear, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_nucleomorph, CBioSource_Base::eGenome_plasmid, CBioSource_Base::eGenome_plastid, CBioSource_Base::eGenome_proplastid, CBioSource_Base::eGenome_proviral, CBioSource_Base::eGenome_transposon, CBioSource_Base::eGenome_unknown, CBioSource_Base::eGenome_virion, EMIT, CBioSource_Base::GetGenome(), and CBioSource_Base::IsSetGenome().

Referenced by CGff3Writer::xAssignSourceAttributeGenome().

◆ GetIdType() [1/2]

bool CWriteUtil::GetIdType ( CBioseq_Handle  bsh,
string &  idType 
)
static

Definition at line 166 of file write_util.cpp.

References eGetId_Best, eGetId_Canonical, GetId(), and CSeq_id_Handle::GetSeqId().

Referenced by CGff3Writer::xAssignAlignmentDensegMethod(), CGff3Writer::xAssignAlignmentSplicedMethod(), CGff3Writer::xAssignFeatureMethod(), CGtfWriter::xAssignFeatureMethod(), and CGff3Writer::xAssignSourceMethod().

◆ GetIdType() [2/2]

bool CWriteUtil::GetIdType ( const CSeq_id &  seqId,
string &  idType 
)
static

Definition at line 125 of file write_util.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_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, EMIT, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::SelectionName(), NStr::ToUpper(), and CSeq_id_Base::Which().

◆ GetListOfGoIds()

bool CWriteUtil::GetListOfGoIds ( const vector< CRef< CUser_field > > &  fields,
list< std::string > &  goIds,
bool  relaxed = false 
)
static

Definition at line 1185 of file write_util.cpp.

Referenced by CGff2Writer::xAssignFeatureAttributesGoMarkup().

◆ GetModelEvidence()

CConstRef< CUser_object > CWriteUtil::GetModelEvidence ( CMappedFeat  mf)
static

Definition at line 841 of file write_util.cpp.

References CSeq_feat_Handle::GetExt(), CSeq_feat_Handle::GetExts(), GetUserObjectByType(), CSeq_feat_Handle::IsSetExt(), and CSeq_feat_Handle::IsSetExts().

Referenced by GetStringForModelEvidence(), and sGetMethodFromModelEvidence().

◆ GetOrgModSubType()

bool CWriteUtil::GetOrgModSubType ( const COrgMod &  mod,
string &  subtype,
string &  subname 
)
static

Definition at line 188 of file write_util.cpp.

References COrgMod::GetSubtypeName(), mod(), and subname.

Referenced by CGff3Writer::xAssignSourceAttributesOrgMod().

◆ GetStringForGoMarkup()

bool CWriteUtil::GetStringForGoMarkup ( const vector< CRef< CUser_field > > &  fields,
string &  goMarkup,
bool  relaxed = false 
)
static

Definition at line 1125 of file write_util.cpp.

References GetStringsForGoMarkup(), NStr::Join(), and strings.

◆ GetStringForModelEvidence()

bool CWriteUtil::GetStringForModelEvidence ( CMappedFeat  mf,
string &  mestr 
)
static

Definition at line 889 of file write_util.cpp.

References CUser_field_Base::CanGetData(), CUser_field_Base::GetData(), CUser_object_Base::GetData(), CUser_field_Base::C_Data::GetFields(), CUser_field_Base::C_Data::GetInt(), CUser_field_Base::GetLabel(), GetModelEvidence(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_field_Base::C_Data::IsInt(), CUser_field_Base::IsSetData(), CUser_field_Base::IsSetLabel(), CObject_id_Base::IsStr(), ITERATE, label, prefix, s_CountAccessions(), and text().

Referenced by CGff2Writer::xAssignFeatureAttributeModelEvidence().

◆ GetStringId()

string CWriteUtil::GetStringId ( const CSeq_loc &  loc)
static

Definition at line 1274 of file write_util.cpp.

References CSeq_id::AsFastaString(), and CSeq_loc::GetId().

Referenced by CompareFeatures().

◆ GetStringsForGoMarkup()

bool CWriteUtil::GetStringsForGoMarkup ( const vector< CRef< CUser_field > > &  fields,
vector< string > &  goMarkup,
bool  relaxed = false 
)
static

Definition at line 1140 of file write_util.cpp.

References NStr::IntToString().

Referenced by GetStringForGoMarkup(), and CGff2Writer::xAssignFeatureAttributesGoMarkup().

◆ GetSubSourceSubType()

bool CWriteUtil::GetSubSourceSubType ( const CSubSource &  sub,
string &  subtype,
string &  subname 
)
static

Definition at line 203 of file write_util.cpp.

References EMIT, CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_metagenomic, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_transgenic, CSubSource_Base::GetName(), CSubSource_Base::GetSubtype(), CSubSource::GetSubtypeName(), CSubSource_Base::IsSetName(), and CSubSource_Base::IsSetSubtype().

Referenced by CGff3Writer::xAssignSourceAttributesSubSource().

◆ GetThreeFeatRgb()

bool CWriteUtil::GetThreeFeatRgb ( const CSeq_feat &  feat,
string &  color 
)
static

Definition at line 1082 of file write_util.cpp.

References color, CSeq_feat_Base::GetExts(), GetUserObjectByType(), and CSeq_feat_Base::IsSetExts().

Referenced by CThreeFeatRecord::GetBedFeature().

◆ GetThreeFeatScore()

bool CWriteUtil::GetThreeFeatScore ( const CSeq_feat &  feat,
int &  score 
)
static

Definition at line 1064 of file write_util.cpp.

References CSeq_feat_Base::GetExts(), GetUserObjectByType(), and CSeq_feat_Base::IsSetExts().

Referenced by CThreeFeatRecord::GetBedFeature().

◆ GetThreeFeatType()

bool CWriteUtil::GetThreeFeatType ( const CSeq_feat &  feat,
string &  threeFeatType 
)
static

Definition at line 1046 of file write_util.cpp.

References CSeq_feat_Base::GetExts(), GetUserObjectByType(), and CSeq_feat_Base::IsSetExts().

Referenced by CThreeFeatRecord::AddFeature(), and IsThreeFeatFormat().

◆ GetTranssplicedEndpoints()

bool CWriteUtil::GetTranssplicedEndpoints ( const CSeq_loc &  loc,
unsigned int &  inPoint,
unsigned int &  outPoint 
)
static

Definition at line 1375 of file write_util.cpp.

References CSeq_loc::Assign(), CSeq_loc::ChangeToPackedInt(), eExtreme_Biological, CPacked_seqint_Base::Get(), CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetPacked_int(), CPacked_seqint::GetStart(), CPacked_seqint::GetStop(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::IsMix(), and CSeq_loc_Base::IsPacked_int().

Referenced by CGff2Writer::xAssignFeatureEndpoints(), CGff3Writer::xAssignFeatureEndpoints(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().

◆ GetTrnaAntiCodon()

bool CWriteUtil::GetTrnaAntiCodon ( const CTrna_ext &  trna,
string &  acStr 
)
static

Definition at line 428 of file write_util.cpp.

References CSeq_loc_Base::e_Int, eExtreme_Positional, eNa_strand_minus, CTrna_ext_Base::GetAnticodon(), CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), NStr::IntToString(), CTrna_ext_Base::IsSetAnticodon(), CSeq_interval_Base::IsSetStrand(), string, and CSeq_loc_Base::Which().

Referenced by CGff2Writer::xAssignFeatureAttributeProduct().

◆ GetTrnaCodons()

bool CWriteUtil::GetTrnaCodons ( const CTrna_ext &  trna,
string &  codonStr 
)
static

Definition at line 374 of file write_util.cpp.

References codons, CTrna_ext_Base::IsSetCodon(), and s_ComposeCodonRecognizedStr().

Referenced by CGff2Writer::xAssignFeatureAttributeProduct().

◆ GetTrnaProductName()

bool CWriteUtil::GetTrnaProductName ( const CTrna_ext &  trna,
string &  name 
)
static

Definition at line 404 of file write_util.cpp.

References CTrna_ext_Base::GetAa(), CTrna_ext_Base::C_Aa::GetNcbieaa(), CTrna_ext_Base::C_Aa::IsNcbieaa(), and CTrna_ext_Base::IsSetAa().

Referenced by CFastaOstreamEx::x_AddRNAProductAttribute(), and CGff2Writer::xAssignFeatureAttributeProduct().

◆ GetUserObjectByType() [1/2]

CConstRef< CUser_object > CWriteUtil::GetUserObjectByType ( const CUser_object &  uo,
const string &  strType 
)
static

Definition at line 794 of file write_util.cpp.

References CUser_field_Base::C_Data::e_Object, CUser_field_Base::GetData(), CUser_object_Base::GetData(), CUser_field_Base::C_Data::GetObject(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CUser_field_Base::IsSetData(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), and CUser_field_Base::C_Data::Which().

Referenced by GetModelEvidence(), GetThreeFeatRgb(), GetThreeFeatScore(), GetThreeFeatType(), GetUserObjectByType(), and CGtfWriter::xAssignFeatureMethod().

◆ GetUserObjectByType() [2/2]

CConstRef< CUser_object > CWriteUtil::GetUserObjectByType ( const list< CRef< CUser_object > > &  uos,
const string &  strType 
)
static

Definition at line 823 of file write_util.cpp.

References GetUserObjectByType().

◆ IsLocationOrdered()

bool CWriteUtil::IsLocationOrdered ( const CSeq_loc &  loc)
static

Definition at line 569 of file write_util.cpp.

References CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Null, CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetMix(), ITERATE, and CSeq_loc_Base::Which().

Referenced by CGff2Writer::xAssignFeatureAttributeIsOrdered().

◆ IsNucleotideSequence()

bool CWriteUtil::IsNucleotideSequence ( CBioseq_Handle  bsh)
static

Definition at line 1285 of file write_util.cpp.

References CBioseq_Handle::CanGetDescr(), CBioseq_Handle::CanGetInst_Mol(), CMolInfo_Base::eBiomol_other, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eBiomol_unknown, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, CSeq_descr_Base::Get(), CBioseq_Handle::GetBioseqMolType(), and CBioseq_Handle::GetDescr().

Referenced by CGff3Writer::xPassesFilterByViewMode().

◆ IsProteinSequence()

bool CWriteUtil::IsProteinSequence ( CBioseq_Handle  bsh)
static

Definition at line 1322 of file write_util.cpp.

References CBioseq_Handle::CanGetDescr(), CBioseq_Handle::CanGetInst_Mol(), CMolInfo_Base::eBiomol_other, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eBiomol_unknown, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, CSeq_descr_Base::Get(), CBioseq_Handle::GetBioseqMolType(), and CBioseq_Handle::GetDescr().

Referenced by CGff3Writer::xPassesFilterByViewMode(), and CGff3Writer::xWriteSequence().

◆ IsSequenceCircular()

bool CWriteUtil::IsSequenceCircular ( CBioseq_Handle  bsh)
static

Definition at line 592 of file write_util.cpp.

References CSeq_inst_Base::eTopology_circular, CBioseq_Handle::GetInst_Topology(), and CBioseq_Handle::IsSetInst_Topology().

Referenced by CGff3Writer::xAssignFeature(), CGff3Writer::xAssignFeatureEndpoints(), and CGff3Writer::xAssignSourceAttributeIsCircular().

◆ IsThreeFeatFormat()

bool CWriteUtil::IsThreeFeatFormat ( const CSeq_annot &  annot)
static

Definition at line 1100 of file write_util.cpp.

References dummy, ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), GetThreeFeatType(), and CSeq_annot::IsFtable().

Referenced by CBedWriter::xWriteTrackedAnnot().

◆ IsTransspliced() [1/2]

bool CWriteUtil::IsTransspliced ( const CMappedFeat &  mf)
static

Definition at line 1366 of file write_util.cpp.

References CMappedFeat::GetMappedFeature(), and IsTransspliced().

◆ IsTransspliced() [2/2]

bool CWriteUtil::IsTransspliced ( const CSeq_feat &  feature)
static

Definition at line 1358 of file write_util.cpp.

References CSeq_feat_Base::GetExcept_text(), and CSeq_feat_Base::IsSetExcept_text().

Referenced by IsTransspliced(), CGff2Writer::xAssignFeatureEndpoints(), CGff3Writer::xAssignFeatureEndpoints(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteFeatureProtein(), CGff3Writer::xWriteFeatureRna(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().

◆ NeedsQuoting()

bool CWriteUtil::NeedsQuoting ( const string &  str)
static

Definition at line 604 of file write_util.cpp.

References str().

The documentation for this class was generated from the following files:
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Modified on Sat Dec 02 09:21:25 2023 by modify_doxy.py rev. 669887