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NCBI C++ ToolKit: src/objtools/cleanup/autogenerated_cleanup.cpp Source File

m_NewCleanup.DateStdBC(date.SetStd());

<

Tcontainer_ncbi_cref_cseq_

erval_>

(arg0.

()) {

(

pInt : arg0.

()) {

(packed_point.

()) {

(arg0.

()) {

<

TSeqLocContainer>

(

pLoc : locs) {

<

TSeqIdContainer>

madeChange{

};

(

pId : ids) {

<

TDenseDiagContainer>

(

pDenseDiag : dense_diags) {

(align_set.

()) {

(

pAlign : align_set.

()) {

(

pSparseAlign : arg0.

()) {

(

pSplicedExon : arg0.

()) {

(arg0.

()) {

(

pStdSeg : arg0.

()) {

<

TSeqAlignContainer>

(

pAlign : aligns) {

(arg0.

()) {

}

(arg0.

()) {

& affil_str = arg0.

();

(arg0.

()) {

(

pAuthor : arg0.

()) {

(arg0.

()) {

(

& pPubStatusDate : arg0.

()) {

(arg0.

()) {

(arg0.

()) {

(

pElement : arg0.

()) {

(pElement && pElement->IsName()) {

(arg0.

()) {

(

pCitBook : arg0.

()) {

(

pCitJournal : arg0.

()) {

(

pMedlineEntry : arg0.

()) {

(

pPatent : arg0.

()) {

(

pProc : arg0.

()) {

isSeqFeatCitPub =

;

(

pPub : arg0.

()) {

<

Tcontainer_ncbi_cref_cdbtag_>

<

Tcontainer_std_

_>

(

& pOrgMod : orgMods) {

& orgMod = *pOrgMod;

<

Tcontainer_ncbi_cref_corgname_>

(arg0.

()) {

(arg0.

()) {

<

Tcontainer_ncbi_cref_cclone_seq_>

(arg0.

()) {

<

Tcontainer_std_

_>

(arg0.

()) {

<

Tcontainer_std_

_>

<

Tcontainer_std_

_>

<

Tcontainer_std_

_>

(cleanup_parent_feat) {

(arg0.

()) {

(

pPub : arg0.

()) {

(arg0.

()) {

(! equiv.

()) {

(

pPub : equiv.

()) {

(! pPub->IsEquiv()) {

pubs.push_back(pPub);

(labels.size() != pubs.size()) {

labels.resize(pubs.size());

vector<string>::size_type index = 0;

(

pPub : pubs) {

labels[index++] =

;

list<CRef<CPub>> pubs;

vector<string> old_labels(pubs.size());

(! pubs.empty()) {

vector<string> new_labels(pubs.size());

<

Tcontainer_ncbi_cref_crna_qual_>

(arg0.

()) {

(arg0.

()) {

(

pGeneRef : arg0.

()) {

<

Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence>

(arg0.Which()) {

Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence::e_Variation:

<

Tcontainer_ncbi_cref_c_e_consequence_>

(arg0.

()) {

<

Tcontainer_ncbi_cref_cdelta_item_>

<

Tcvariation_ref_container_ncbi_cref_c_e_somatic_origin_c_e_somatic_origin>

(arg0.IsSetSource()) {

<

Tcontainer_ncbi_cref_c_e_somatic_origin_>

(

Tcontainer_ncbi_cref_c_e_somatic_origin_, iter, arg0)

(arg0.IsSetVariations()) {

(

pVariation : arg0.SetVariations()) {

(arg0.

()) {

(arg0.

()) {

clean_parent_feat =

;

(arg0.

()) {

<

Tcontainer_ncbi_cref_cgb_qual_>

<

Tcontainer_ncbi_cref_cinferencesupport_>

(

Tcontainer_ncbi_cref_cinferencesupport_, iter, arg0)

<

Tcontainer_ncbi_cref_cmodelev

enceitem_>

(

Tcontainer_ncbi_cref_cmodelevidenceitem_, iter, arg0)

<

Tcontainer_ncbi_cref_cmodelev

encesupport_>

(

Tcontainer_ncbi_cref_cmodelevidencesupport_, iter, arg0)

(

pSubSource : biosrc.

()) {

(arg0.

()) {

(

pXref : arg0.

()) {

new_feat->

(arg0_raw);

new_feat.

(&arg0_raw);

(

pXref : arg0.

()) {

(

pFeat : feats) {

<

Tcontainer_ncbi_cref_cseq_graph_>

(arg0.

()) {

(arg0.

()) {

<

Tcontainer_ncbi_cref_cseqtable_column_>

(

Tcontainer_ncbi_cref_cseqtable_column_, iter, arg0)

(arg0.

()) {

(arg0.

()) {

(arg0.

()) {

(

pAnnotdesc : arg0.

()) {

(

feat_it(annotHandle); feat_it; ++feat_it) {

}

(annotHandle.

()) {

(

graph_it(annotHandle); graph_it; ++graph_it) {

new_graph->Assign(graph_it->GetOriginalGraph());

graph_it->GetSeq_graph_Handle().Replace(*new_graph);

}

(annotHandle.

()) {

(

align_it(annotHandle); align_it; ++align_it) {

new_align->Assign(align_it.GetOriginalSeq_align());

align_it.GetSeq_align_Handle().Replace(*new_align);

(replace.IsSetDate()) {

(arg0.

()) {

pNewDesc->Assign(*pDesc);

(arg0.

()) {

(

pDeltaSeq : arg0.

()) {

(pDeltaSeq && pDeltaSeq->IsLoc()) {

(arg0.

()) {

(arg0.

()) {

(arg0.

()) {

(arg0.

()) {

(

pAnnot : annots) {

(; annot_it; ++annot_it) {

(arg0.

()) {

(arg0.

()) {

(

pDesc : arg0.

()) {

(arg0.

()) {

(arg0.

()) {

(

pEntry : arg0.

()) {

in_submit_block =

;

static void s_GetLabels(const list< CRef< CPub >> &pubs, vector< string > &labels)

static void s_GetPubsFromEquiv(const CPub_equiv &equiv, list< CRef< CPub >> &pubs)

@Affil.hpp User-defined methods of the data storage class.

@Auth_list.hpp User-defined methods of the data storage class.

This file was generated by application DATATOOL.

void x_BasicCleanupContactInfo(CContact_info &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_ETC(Tcontainer_ncbi_cref_c_e_somatic_origin_ &arg0)

void x_BasicCleanupSeqLocMix(CSeq_loc_mix &arg0)

void x_BasicCleanupSeqfeatCit(CPub_set &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_product_ETC(std::string &arg0)

void x_BasicCleanupSeqAnnotData_seq_table_seq_table_columns_E_E_data_data_real_scaled(CScaled_real_multi_data &arg0)

void x_BasicCleanupCodeBreak(CCode_break &arg0)

void x_BasicCleanupSeqPoint(CSeq_point &seq_point)

void x_BasicCleanupGeneRef(CGene_ref &arg0, bool cleanup_parent_feat)

void x_BasicCleanupBioseqDesc(CSeqdesc &desc)

void x_BasicCleanupPatentPriority(CPatent_priority &arg0)

void x_BasicCleanupTxinit(CTxinit &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_ETC(CRNA_gen &arg0)

void x_BasicCleanupCitBook(CCit_book &arg0)

void x_BasicCleanupDescRegion(std::string &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_ETC(CCdregion &arg0)

void x_BasicCleanupAlignSegs(CSeq_align::C_Segs &arg0)

void x_BasicCleanupSeqAnnotData_seq_table_seq_table_columns_E_E_data_data_int_scaled(CScaled_int_multi_data &arg0)

void x_BasicCleanupPackedSeqInt(CPacked_seqint &arg0)

void x_BasicCleanupSeqFeatXref(CSeqFeatXref &arg0)

void x_BasicCleanupPubStatusDateSet(CPubStatusDateSet &arg0)

void BasicCleanupSeqEntry(CSeq_entry &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_clone_seq_clone_seq_ETC(Tcontainer_ncbi_cref_cclone_seq_ &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_clone_seq_clone_seq_E_E_ETC(CClone_seq &arg0)

bool x_BasicCleanupSeqIds(TSeqIdContainer &ids)

void x_BasicCleanupSeqBond(CSeq_bond &seq_bond)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_ETC(Tcontainer_ncbi_cref_crna_qual_ &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC(Tcontainer_std_string_ &arg0)

void x_BasicCleaupSparseSeg(CSparse_seg &arg0)

void x_BasicCleanupPackedPoint(CPacked_seqpnt &arg0)

void x_BasicCleanupBioseq_inst(const CBioseq_Handle &bsh)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_ETC(CRNA_gen &arg0)

void x_BasicCleanupSplicedExon(CSpliced_exon &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_ETC(CVariation_inst &arg0)

void x_BasicCleanupSeqFeat_data_data_region_ETC(std::string &arg0)

void x_BasicCleanupSeqFeatSupport(CSeqFeatSupport &arg0)

CNewCleanup_imp & m_NewCleanup

void x_BasicCleanupOrgRef(COrg_ref &arg0, CBioSource *pBiosrc)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_clone_seq_clone_seq_E_ETC(CClone_seq &arg0)

CSeq_feat * m_pCurrentSeqFeat

void x_BasicCleanupSeqAnnotData_seq_table_seq_table_columns_E_ETC(CSeqTable_column &arg0)

void x_BasicCleanupSeqFeat_qual_ETC(Tcontainer_ncbi_cref_cgb_qual_ &arg0)

void x_BasicCleanupAuthListNames(CAuth_list::C_Names &arg0)

void x_BasicCleanupPackedSeg(CPacked_seg &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_tRNA_tRNA_ETC(CTrna_ext &arg0)

void x_BasicCleanupOrgNameName_hybrid(CMultiOrgName &arg0)

void x_BasicCleanupNumbering(CNumbering &arg0)

void x_BasicCleanupPub(CPub &arg0, bool isSeqFeatCitPub=false)

void x_BasicCleanupDescTitle(std::string &arg0)

void x_BasicCleanupSeqInts(Tcontainer_ncbi_cref_cseq_interval_ &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_ETC(CDelta_item &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_E_ETC(CRNA_qual &arg0)

void x_BasicCleanupSeqFeat_dbxref_ETC(Tcontainer_ncbi_cref_cdbtag_ &arg0)

void x_BasicCleanupSeqAnnotGraph(Tcontainer_ncbi_cref_cseq_graph_ &arg0)

void x_BasicCleanupSeqAnnotData_seq_table_seq_table_columns_E_E_data_data_int_scaled_int_scaled(CScaled_int_multi_data &arg0)

void x_BasicCleanupCitGen(CCit_gen &arg0)

void x_BasicCleanupProtRef(CProt_ref &arg0, bool cleanup_parent_feat)

void x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_ETC(CEvidenceBasis &arg0)

bool x_BasicCleanupSeqId(CSeq_id &id)

bool x_BasicCleanupDate(CDate &date)

This file was generated by application DATATOOL.

void x_BasicCleanupSeqFeat_support_support_model_evidence_ETC(Tcontainer_ncbi_cref_cmodelevidencesupport_ &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_ETC(CImp_feat &arg0)

void x_FallBackSeqAnnotMethod(const CSeq_annot_Handle &annotHandle)

std::optional< CMolInfo::TBiomol > mBiomol

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence(Tcontainer_ncbi_cref_c_e_consequence_ &arg0)

void x_BasicCleanupAnnotDesc(CAnnotdesc &arg0)

void x_BasicCleanupTitle(CTitle &arg0)

void x_BasicCleanupSeqSubmit_sub(CSubmit_block &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_ETC(CRNA_qual &arg0)

void x_BasicCleanupSeqLocEquiv(CSeq_loc_equiv &arg0)

void x_BasicCleanupBioseqDescr(const CBioseq_Handle &bsh)

void x_BasicCleanupSeqAnnotData_seq_table_seq_table_columns_E_E_sparse_other_sparse_other_ETC(CSeqTable_single_data &arg0)

void x_BasicCleanupBiosource(CBioSource &arg0)

void x_BasicCleanupMapExt(CMap_ext &arg0)

void x_BasicCleanupSeqTable(CSeq_table &arg0)

void x_BasicCleanupSeqAlignSet(CSeq_align_set &arg0)

void x_BasicCleanupSeqAnnotData_seq_table_seq_table_columns_ETC(Tcontainer_ncbi_cref_cseqtable_column_ &arg0)

void x_BasicCleanupSeqFeat_support_support_inference_E_E_ETC(CInferenceSupport &arg0)

void x_BasicCleanupCitArtFrom(CCit_art::C_From &arg0)

void x_BasicCleanupSeqAnnots(list< CRef< CSeq_annot >> &annots)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_ETC(CDelta_item::C_Seq &arg0)

void x_BasicCleanupSeqHistDeleted(CSeq_hist::C_Deleted &arg0)

void x_BasicCleanupPDBBlock(CPDB_block &arg0)

void x_BasicCleanupPubStatusDate(CPubStatusDate &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_ETC(CRNA_ref::C_Ext &arg0)

void x_BasicCleanupMeeting(CMeeting &arg0)

void x_BasicCleanupSeqFeat_support_support_inference_ETC(Tcontainer_ncbi_cref_cinferencesupport_ &arg0)

void BasicCleanupBioseqSet(CBioseq_set &arg0)

void x_BasicCleanupSegExt(CSeg_ext &arg0)

void x_BasicCleanupSeqAligns(TSeqAlignContainer &aligns)

void x_BasicCleanupNumRef(CNum_ref &arg0)

void x_BasicCleanupSeqLocs(TSeqLocContainer &locs)

void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_protein_ETC(Tcontainer_ncbi_cref_cmodelevidenceitem_ &arg0)

void x_BasicCleanupSeqFeats(list< CRef< CSeq_feat >> &feats)

void x_BasicCleanupAffil(CAffil &arg0)

void x_BasicCleanupCitJournal(CCit_jour &arg0)

void x_BasicCleanupVariationRef(CVariation_ref &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_desc_ETC(std::string &arg0)

void x_BasicCleanupSeqAnnotData_seq_table_seq_table_columns_E_E_data_data_real_scaled_real_scaled(CScaled_real_multi_data &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC(std::string &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_ETC(Tcontainer_std_string_ &arg0)

void x_BasicCleanupSeqInt(CSeq_interval &seq_int)

void x_BasicCleanupDeltaExt(CDelta_ext &delta_ext, CSeq_inst::ERepr repr)

void x_BasicCleanupDenseDiag(CDense_diag &arg0)

void x_BasicCleanupAnnotDescr(CAnnot_descr &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC(CImp_feat &arg0)

void BasicCleanupSeqSubmit(CSeq_submit &arg0)

void x_BasicCleanupSeqExt(CSeq_ext &ext, CSeq_inst::ERepr repr)

void x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_ETC(CEvidenceBasis &arg0)

void x_BasicCleanupGBBlock(CGB_block &arg0)

void x_BasicCleanupHybridOrgName(COrgName &arg0)

void x_BasicCleanupCdregion(CCdregion &arg0)

void x_BasicCleanupImprint(CImprint &arg0)

void x_BasicCleanupSeqFeat_data_data_rna(CRNA_ref &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_ETC(Tcontainer_ncbi_cref_cdelta_item_ &arg0)

void BasicCleanupBioseqHandle(const CBioseq_Handle &bsh)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_E_ETC(std::string &arg0)

void x_BasicCleanupSeqFeat_support_support_inference_E_ETC(CInferenceSupport &arg0)

void x_BasicCleanupAffilStd(CAffil::C_Std &arg0)

void x_BasicCleanupOrgNameName(COrgName::C_Name &arg0)

void x_BasicCleanupSeqAlign(CSeq_align &arg0)

void x_BasicCleanupCitLet(CCit_let &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_name_ETC(std::string &arg0)

void x_BasicCleanupSeqEntry_set(CBioseq_set &arg0)

void x_BasicCleanupSeqHist(CSeq_hist &arg0)

void x_BasicCleanupCitArt(CCit_art &arg0)

void x_BasicCleanupMedlineEntry(CMedline_entry &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E(Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence &arg0)

void x_BasicCleanupCitSub(CCit_sub &arg0, bool in_submit_block=false)

void x_BasicCleanupPubEquiv(CPub_equiv &arg0)

void x_BasicCleanupEMBLBlock(CEMBL_block &arg0)

void x_BasicCleanupOrgName(COrgName &arg0, CBioSource *pBiosrc=nullptr)

void BasicCleanupSeqAnnot(CSeq_annot &arg0)

void x_BasicCleanupBioseqSetDesc(CSeqdesc &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_ETC(CRNA_ref &arg0)

void x_BasicCleanupSeqSubmit_data(CSeq_submit::C_Data &arg0)

void x_BasicCleanupSplicedSeg(CSpliced_seg &arg0)

void x_BasicCleanupSeqFeat_location_ETC(CSeq_loc &arg0)

void x_BasicCleanupSparseAlign(CSparse_align &arg0)

void x_BasicCleanupSeqTableMultiData(CSeqTable_multi_data &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_name_E_ETC(std::string &arg0)

void x_BasicCleanupSeqAnnotData(CSeq_annot::C_Data &arg0)

void x_BasicCleanupAuthor(CAuthor &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data(CVariation_ref::C_Data &arg0)

void x_BasicCleanupBioseqSet_descr_ETC(CSeq_descr &arg0)

void x_BasicCleanupCitProc(CCit_proc &arg0)

void x_BasicCleanupDescComment(std::string &arg0)

void x_BasicCleanupCitPat(CCit_pat &arg0)

void x_BasicCleanupSeqLoc(CSeq_loc &seq_loc)

void x_BasicCleanupSeqFeat_xref_E_E_data_ETC(CSeqFeatData &arg0)

void x_BasicCleanupDenseDiags(TDenseDiagContainer &dense_diags)

void x_BasicCleanupSeqFeat_data(CSeqFeatData &arg0)

void x_BasicCleanupSeqHistRec(CSeq_hist_rec &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_tRNA_ETC(CTrna_ext &arg0)

void x_BasicCleanupDenseg(CDense_seg &denseg)

void x_BasicCleanupStdSeg(CStd_seg &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_clone_seq_ETC(CClone_seq_set &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_ETC(CClone_ref &arg0)

void x_BasicCleanupOrgMods(list< CRef< COrgMod >> &orgMods)

void x_BasicCleanupModelEvidenceSupport(CModelEvidenceSupport &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set(CVariation_ref::C_Data::C_Set &arg0)

void x_BasicCleanupOrgNameName_hybrid_hybrid(Tcontainer_ncbi_cref_corgname_ &arg0)

void BasicCleanupSeqFeat(CSeq_feat &arg0_raw)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_E_ETC(Tcvariation_ref_container_ncbi_cref_c_e_somatic_origin_c_e_somatic_origin &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_ETC(CDelta_item &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_desc_ETC(std::string &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_ETC(std::string &arg0)

void x_BasicCleanupSeqFeat_comment(std::string &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_ETC(CRNA_qual_set &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ec_ETC(Tcontainer_std_string_ &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_name_ETC(Tcontainer_std_string_ &arg0)

void x_BasicCleanupSPBlock(CSP_block &arg0)

void x_BasicCleanupAuthList(CAuth_list &arg0, bool fix_initials=false)

void x_BasicCleanupOrgRefMod(Tcontainer_std_string_ &arg0)

void x_BasicCleanupPIRBlock(CPIR_block &arg0)

void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_protein_E_ETC(CModelEvidenceItem &arg0)

void x_BasicCleanupSeqGraph(CSeq_graph &arg0)

void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_ETC(CClone_ref &arg0)

void x_BasicCleanupBioseqSet_annot_E_E_desc_desc_E_E_align_ETC(CAlign_def &arg0)

void x_BasicCleanupSeqAnnotData_seq_table_seq_table_columns_E_E_sparse_other_ETC(CSeqTable_single_data &arg0)

void x_BasicCleanupSeqfeatPub(CPubdesc &arg0, bool is_xref=false)

@Imp_feat.hpp User-defined methods of the data storage class.

CModelEvidenceSupport –.

void x_CopyGBBlockDivToOrgnameDiv(CSeq_entry &seq_entry)

void RnaFeatBC(CRNA_ref &rr, CSeq_feat &sf)

void LabelMapAppend(const vector< string > &old_labels, const vector< string > &new_labels)

void x_PostSeqFeat(CSeq_feat &seq_feat)

void x_CleanupStringJunkMarkChanged(std::string &str)

void ProtSeqBC(const CBioseq_Handle &bsh)

void PCRReactionSetBC(CPCRReactionSet &pcr_reaction_set)

void x_BothStrandBC(CSeq_loc &loc)

void ProtNameBC(std::string &str)

void x_RememberSeqFeatCitPubs(CPub &pub)

void x_PostOrgRef(COrg_ref &org)

void x_ClearEmptyDescr(CBioseq_set &bioseq_set)

void x_PostBiosource(CBioSource &biosrc)

void BiosourceFeatBC(CBioSource &biosrc, CSeq_feat &seqfeat)

void AddPartialToProteinTitle(const CBioseq_Handle &bsh)

void GenerefBC(CGene_ref &gr)

void CdregionFeatBC(CCdregion &cds, CSeq_feat &seqfeat)

void x_OrgModBC(COrgMod &orgmod)

void ConvertSeqLocWholeToInt(CSeq_loc &loc)

void x_RemoveFlankingQuotes(string &val)

void x_ExpandCombinedQuals(CSeq_feat::TQual &quals)

void x_CleanupOrgModAndSubSourceOther(COrgName &orgname, CBioSource &biosrc)

void ClearEmptyDescr(const CBioseq_Handle &bsh)

void EnteringEntry(CSeq_entry &se)

void SeqsetBC(CBioseq_set &bss)

void GeneFeatBC(CGene_ref &gr, CSeq_feat &sf)

void PostProtFeatfBC(CProt_ref &pr)

void x_CompressStringSpacesMarkChanged(std::string &str)

void ImpFeatBC(CSeq_feat &sf)

bool RemoveSingleStrand(const CBioseq_Handle &bsh)

bool MolInfoBC(CMolInfo &molinfo)

void UserObjectBC(CUser_object &user_object)

void x_ConvertDoubleQuotesMarkChanged(std::string &str)

void ProtActivityBC(std::string &str)

void SiteFeatBC(const CSeqFeatData::ESite &site, CSeq_feat &sf)

void RnarefBC(CRNA_ref &rr)

void BiosourceBC(CBioSource &bsc)

void PubdescBC(CPubdesc &pub)

void GBblockBC(CGB_block &gbk)

void x_SubSourceBC(CSubSource &subsrc)

bool BasicCleanupSeqIds(const CBioseq_Handle &bsh)

void DbtagBC(CDbtag &dbt)

void x_RemoveSpacesBetweenTildesMarkChanged(std::string &str)

void FixUnsetMolFromBiomol(CMolInfo::TBiomol biomol, const CBioseq_Handle &bsh)

void x_NotePubdescOrAnnotPubs(const CPub_equiv &pub_equiv)

void x_RememberMuidThatMightBeConvertibleToPmid(CPub &pub)

void SeqfeatBC(CSeq_feat &sf)

void ProtFeatfBC(CProt_ref &pr, CSeq_feat &sf)

void x_AuthListBCWithFixInitials(CAuth_list &al)

void x_RememberPubOldLabel(CPub &pub)

void x_CleanupECNumberList(CProt_ref::TEc &ec_num_list)

void x_CleanupStringMarkChanged(std::string &str)

void ProtrefBC(CProt_ref &pr)

void GBblockOriginBC(string &str)

void SeqLocBC(CSeq_loc &loc)

void OrgrefModBC(string &str)

void x_GBQualToOrgRef(COrg_ref &org, CSeq_feat &seqfeat)

void OrgrefBC(COrg_ref &org)

bool SeqIdBC(CSeq_id &seq_id)

void EMBLblockBC(CEMBL_block &emb)

void x_TrimInternalSemicolonsMarkChanged(std::string &str)

void x_DecodeXMLMarkChanged(std::string &str)

void x_ModernizePCRPrimers(CBioSource &biosrc)

void x_FixUpEllipsis(string &str)

void x_StripSpacesMarkChanged(std::string &str)

void RemoveZeroLengthLiterals(CDelta_ext &delta_ext)

@Pubdesc.hpp User-defined methods of the data storage class.

@RNA_ref.hpp User-defined methods of the data storage class.

void SetRegion(const TRegion &v)

void SetBiosrc(TBiosrc &v)

void SetSite(const TSite &v)

void SetVariation(TVariation &v)

void SetTxinit(TTxinit &v)

void SetCdregion(TCdregion &v)

@Seq_descr.hpp User-defined methods of the data storage class.

CSeq_feat_EditHandle –.

namespace ncbi::objects::

@ fLabel_Unique

Append a unique tag [V1].

#define CLEAN_STRING_LIST(o, x)

#define CLEAN_AND_COMPRESS_STRING_MEMBER_JUNK(o, x)

#define CLEAN_AND_COMPRESS_STRING_MEMBER(o, x)

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

void SetPacked_int(TPacked_int &v)

void SetPacked_pnt(TPacked_pnt &v)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

const TInst_Hist & GetInst_Hist(void) const

const TInst_Ext & GetInst_Ext(void) const

bool IsFtable(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool IsSetInst_Hist(void) const

bool IsSetInst_Ext(void) const

void Update(void) const

Update index after manual modification of the object.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

bool HasAnnots(void) const

CRef< CSeqdesc > ReplaceSeqdesc(const CSeqdesc &old_desc, CSeqdesc &new_desc) const

const TDescr & GetDescr(void) const

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

bool IsSetInst(void) const

bool IsSetInst_Repr(void) const

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

TInst_Repr GetInst_Repr(void) const

void SetInst_Hist(TInst_Hist &v) const

void SetInst_Ext(TInst_Ext &v) const

bool IsSetDescr(void) const

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

bool Seq_annot_IsSetDesc(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

static const char label[]

void SetUpdate_date(TUpdate_date &value)

Assign a value to Update_date data member.

bool IsSetCreation_date(void) const

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

void SetCreation_date(TCreation_date &value)

Assign a value to Creation_date data member.

bool IsSetUpdate_date(void) const

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

bool IsSetEntry_date(void) const

replaces date Check if a value has been assigned to Entry_date data member.

bool IsSetOrigin(void) const

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

void SetOrigin(const TOrigin &value)

Assign a value to Origin data member.

void SetEntry_date(TEntry_date &value)

Assign a value to Entry_date data member.

void SetBook(TBook &value)

Assign a value to Book data member.

TStd & SetStd(void)

Select the variant.

TPriority & SetPriority(void)

Assign a value to Priority data member.

bool IsSetPriority(void) const

Priorities Check if a value has been assigned to Priority data member.

void SetApp_date(TApp_date &value)

Assign a value to App_date data member.

bool IsSetDate(void) const

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

bool IsSetAffil(void) const

author affiliation Check if a value has been assigned to Affil data member.

bool IsSetAuthors(void) const

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

bool IsSetAuthors(void) const

authors (ANSI requires) Check if a value has been assigned to Authors data member.

void SetTitle(TTitle &value)

Assign a value to Title data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetCprt(TCprt &value)

Assign a value to Cprt data member.

void SetDate(TDate &value)

Assign a value to Date data member.

bool IsSetDate(void) const

time may be added later Check if a value has been assigned to Date data member.

void SetPlace(TPlace &value)

Assign a value to Place data member.

bool IsSetApplicants(void) const

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

bool IsSetPub(void) const

publisher, required for book Check if a value has been assigned to Pub data member.

void SetApplicants(TApplicants &value)

Assign a value to Applicants data member.

bool IsSetAssignees(void) const

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

void SetImp(TImp &value)

Assign a value to Imp data member.

bool IsSetTitle(void) const

title of paper (ANSI requires) Check if a value has been assigned to Title data member.

void SetFrom(TFrom &value)

Assign a value to From data member.

bool IsSetDate(void) const

date of application Check if a value has been assigned to Date data member.

bool IsSetAffil(void) const

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

bool IsSetHistory(void) const

dates for this record Check if a value has been assigned to History data member.

void SetAffil(TAffil &value)

Assign a value to Affil data member.

bool IsSetFrom(void) const

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

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetDate(TDate &value)

Assign a value to Date data member.

void SetAssignees(TAssignees &value)

Assign a value to Assignees data member.

bool IsSetAuthors(void) const

not necessarily authors of the paper Check if a value has been assigned to Authors data member.

bool IsSetImp(void) const

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

TBook & SetBook(void)

Select the variant.

void SetDate(TDate &value)

Assign a value to Date data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetPub(TPub &value)

Assign a value to Pub data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetPlace(void) const

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

bool IsStr(void) const

Check if variant Str is selected.

void SetImp(TImp &value)

Assign a value to Imp data member.

TStr & SetStr(void)

Select the variant.

bool IsSetDate(void) const

replaces imp, will become required Check if a value has been assigned to Date data member.

void SetCit(TCit &value)

Assign a value to Cit data member.

void SetAffil(TAffil &value)

Assign a value to Affil data member.

bool IsSetNames(void) const

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

bool IsSetAuthors(void) const

author/inventor Check if a value has been assigned to Authors data member.

void SetNames(TNames &value)

Assign a value to Names data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetDate(TDate &value)

Assign a value to Date data member.

bool IsSetDate(void) const

date of publication Check if a value has been assigned to Date data member.

TProc & SetProc(void)

Select the variant.

void SetHistory(THistory &value)

Assign a value to History data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetAuthors(void) const

authors Check if a value has been assigned to Authors data member.

void SetDate(TDate &value)

Assign a value to Date data member.

bool IsSetBook(void) const

citation to meeting Check if a value has been assigned to Book data member.

Tdata & Set(void)

Assign a value to data member.

TJournal & SetJournal(void)

Select the variant.

bool IsSetCit(void) const

same fields as a book Check if a value has been assigned to Cit data member.

bool IsSetImp(void) const

this only used to get date.

bool IsSetApp_date(void) const

Patent Appl File Date Check if a value has been assigned to App_date data member.

void SetDate(TDate &value)

Assign a value to Date data member.

bool IsSetCprt(void) const

copyright date, " " " Check if a value has been assigned to Cprt data member.

bool IsStd(void) const

Check if variant Std is selected.

bool IsSetDate(void) const

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

bool IsSetMeet(void) const

time and location of meeting Check if a value has been assigned to Meet data member.

void SetMeet(TMeet &value)

Assign a value to Meet data member.

void SetImp(TImp &value)

Assign a value to Imp data member.

void SetDate_issue(TDate_issue &value)

Assign a value to Date_issue data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

TStd & SetStd(void)

Select the variant.

bool IsSetDate_issue(void) const

Patent Issue/Pub Date Check if a value has been assigned to Date_issue data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetImp(void) const

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

Tdata & Set(void)

Assign a value to data member.

bool IsStd(void) const

Check if variant Std is selected.

bool IsSetOrg(void) const

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

bool IsSetSubtype(void) const

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

bool IsSetPcr_primers(void) const

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

void SetPcr_primers(TPcr_primers &value)

Assign a value to Pcr_primers data member.

void SetOrg(TOrg &value)

Assign a value to Org data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

TSyn & SetSyn(void)

Assign a value to Syn data member.

bool IsSetSyn(void) const

synonyms for locus Check if a value has been assigned to Syn data member.

void SetAllele(const TAllele &value)

Assign a value to Allele data member.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

bool IsSetDesc(void) const

descriptive name Check if a value has been assigned to Desc data member.

void SetLocus(const TLocus &value)

Assign a value to Locus data member.

bool IsSetAllele(void) const

Official allele designation Check if a value has been assigned to Allele data member.

bool IsSetMaploc(void) const

descriptive map location Check if a value has been assigned to Maploc data member.

void SetLocus_tag(const TLocus_tag &value)

Assign a value to Locus_tag data member.

void SetMaploc(const TMaploc &value)

Assign a value to Maploc data member.

void SetDesc(const TDesc &value)

Assign a value to Desc data member.

void SetEm(TEm &value)

Assign a value to Em data member.

void SetCit(TCit &value)

Assign a value to Cit data member.

bool IsSetCit(void) const

article citation Check if a value has been assigned to Cit data member.

bool IsSetEm(void) const

Entry Month Check if a value has been assigned to Em data member.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

THybrid & SetHybrid(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

void SetCommon(const TCommon &value)

Assign a value to Common data member.

bool IsSetCommon(void) const

common name Check if a value has been assigned to Common data member.

TDb & SetDb(void)

Assign a value to Db data member.

void SetName(TName &value)

Assign a value to Name data member.

bool IsSetMod(void) const

unstructured modifiers Check if a value has been assigned to Mod data member.

Tdata & Set(void)

Assign a value to data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetMod(void) const

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

bool IsSetOrgname(void) const

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

TMod & SetMod(void)

Assign a value to Mod data member.

TMod & SetMod(void)

Assign a value to Mod data member.

void SetOrgname(TOrgname &value)

Assign a value to Orgname data member.

bool IsSetName(void) const

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

@ e_Hybrid

hybrid between organisms

TActivity & SetActivity(void)

Assign a value to Activity data member.

bool IsSetDesc(void) const

description (instead of name) Check if a value has been assigned to Desc data member.

TEc & SetEc(void)

Assign a value to Ec data member.

bool IsSetEc(void) const

E.C.

void SetDesc(const TDesc &value)

Assign a value to Desc data member.

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

bool IsSetActivity(void) const

activities Check if a value has been assigned to Activity data member.

TName & SetName(void)

Assign a value to Name data member.

TProc & SetProc(void)

Select the variant.

TMedline & SetMedline(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

TProc & SetProc(void)

Select the variant.

TBook & SetBook(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

TBook & SetBook(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

TArticle & SetArticle(void)

Select the variant.

const Tdata & Get(void) const

Get the member data.

TEquiv & SetEquiv(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

TMan & SetMan(void)

Select the variant.

TJournal & SetJournal(void)

Select the variant.

TSub & SetSub(void)

Select the variant.

TGen & SetGen(void)

Select the variant.

TPub & SetPub(void)

Select the variant.

TPatent & SetPatent(void)

Select the variant.

TMedline & SetMedline(void)

Select the variant.

TJournal & SetJournal(void)

Select the variant.

TPatent & SetPatent(void)

Select the variant.

TArticle & SetArticle(void)

Select the variant.

@ e_Proc

proceedings of a meeting

@ e_Gen

general or generic unparsed

@ e_Proc

proceedings of a meeting

@ e_Equiv

to cite a variety of ways

@ e_Man

manuscript, thesis, or letter

void SetQual(const TQual &value)

Assign a value to Qual data member.

TTRNA & SetTRNA(void)

Select the variant.

TName & SetName(void)

Select the variant.

void SetVal(const TVal &value)

Assign a value to Val data member.

bool IsSetProduct(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

void SetAnticodon(TAnticodon &value)

Assign a value to Anticodon data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

void SetClass(const TClass &value)

Assign a value to Class data member.

Tdata & Set(void)

Assign a value to data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetVal(void) const

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

bool IsSetQuals(void) const

e.g., tag_peptide qualifier for tmRNAs Check if a value has been assigned to Quals data member.

bool IsSetClass(void) const

for ncRNAs, the class of non-coding RNA: examples: antisense_RNA, guide_RNA, snRNA Check if a value h...

TGen & SetGen(void)

Select the variant.

bool IsSetQual(void) const

in a tag (qual), value (val) format Check if a value has been assigned to Qual data member.

void SetQuals(TQuals &value)

Assign a value to Quals data member.

void SetProduct(const TProduct &value)

Assign a value to Product data member.

@ e_Name

for naming "other" type

void SetSparse_other(TSparse_other &value)

Assign a value to Sparse_other data member.

void SetData(TData &value)

Assign a value to Data data member.

E_Choice Which(void) const

Which variant is currently selected.

TLoc & SetLoc(void)

Select the variant.

TInterval & SetInterval(void)

Select the variant.

TId & SetId(void)

Select the variant.

TId & SetId(void)

Select the variant.

TLoc & SetLoc(void)

Select the variant.

bool IsSetSparse_other(void) const

single value for indexes not listed in sparse table Check if a value has been assigned to Sparse_othe...

bool IsSetData(void) const

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

bool IsSetData(void) const

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

TReal_scaled & SetReal_scaled(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetData(void) const

row data Check if a value has been assigned to Data data member.

TInt_delta & SetInt_delta(void)

Select the variant.

TInterval & SetInterval(void)

Select the variant.

TInt_scaled & SetInt_scaled(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetColumns(void) const

data in columns Check if a value has been assigned to Columns data member.

E_Choice Which(void) const

Which variant is currently selected.

void SetDefault(TDefault &value)

Assign a value to Default data member.

bool IsSetDefault(void) const

default value for sparse table, or if row data is too short Check if a value has been assigned to Def...

TColumns & SetColumns(void)

Assign a value to Columns data member.

@ e_Int_scaled

scaled data (int/bit -> int)

@ e_Loc

a set of locations, one per row

@ e_Int_delta

delta-encoded data (int/bit -> int)

@ e_Real_scaled

scaled data (int/bit -> real)

Tdata & Set(void)

Assign a value to data member.

TIds & SetIds(void)

Assign a value to Ids data member.

void SetGenomic_id(TGenomic_id &value)

Assign a value to Genomic_id data member.

void SetProduct_id(TProduct_id &value)

Assign a value to Product_id data member.

void SetFirst_id(TFirst_id &value)

Assign a value to First_id data member.

TDenseg & SetDenseg(void)

Select the variant.

bool IsSetBounds(void) const

regions of sequence over which align was computed Check if a value has been assigned to Bounds data m...

E_Choice Which(void) const

Which variant is currently selected.

TStd & SetStd(void)

Select the variant.

TPacked & SetPacked(void)

Select the variant.

bool IsSetFirst_id(void) const

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

void SetProduct_id(TProduct_id &value)

Assign a value to Product_id data member.

bool IsSetIds(void) const

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

void SetMaster_id(TMaster_id &value)

Assign a value to Master_id data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

bool IsSetSegs(void) const

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

TExons & SetExons(void)

Assign a value to Exons data member.

bool IsSetSecond_id(void) const

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

TSparse & SetSparse(void)

Select the variant.

TRows & SetRows(void)

Assign a value to Rows data member.

TLoc & SetLoc(void)

Assign a value to Loc data member.

bool IsSetProduct_id(void) const

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

bool IsSetProduct_id(void) const

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

bool IsSetIds(void) const

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

TIds & SetIds(void)

Assign a value to Ids data member.

TDendiag & SetDendiag(void)

Select the variant.

void SetSecond_id(TSecond_id &value)

Assign a value to Second_id data member.

TDisc & SetDisc(void)

Select the variant.

bool IsSetExons(void) const

set of segments involved each segment corresponds to one exon exons are always in biological order Ch...

bool IsSetMaster_id(void) const

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

void SetGenomic_id(TGenomic_id &value)

Assign a value to Genomic_id data member.

TSpliced & SetSpliced(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetIds(void) const

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

TIds & SetIds(void)

Assign a value to Ids data member.

bool IsSetGenomic_id(void) const

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

bool IsSetLoc(void) const

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

TBounds & SetBounds(void)

Assign a value to Bounds data member.

bool IsSetRows(void) const

pairwise alignments constituting this multiple alignment Check if a value has been assigned to Rows d...

bool IsSetIds(void) const

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

bool IsSetGenomic_id(void) const

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

TIds & SetIds(void)

Assign a value to Ids data member.

bool IsSetTitle(void) const

for user defined label Check if a value has been assigned to Title data member.

TXref & SetXref(void)

Assign a value to Xref data member.

TModel_evidence & SetModel_evidence(void)

Assign a value to Model_evidence data member.

bool IsSetComment(void) const

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

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetSeq(void) const

clone sequence location Check if a value has been assigned to Seq data member.

bool IsSetIdentification(void) const

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

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

void SetSeq(TSeq &value)

Assign a value to Seq data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsSetBasis(void) const

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

bool IsSetSupport(void) const

will replace /experiment, /inference, model-evidence Check if a value has been assigned to Support da...

bool IsSetModel_evidence(void) const

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

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetCit(TCit &value)

Assign a value to Cit data member.

Tdata & Set(void)

Assign a value to data member.

bool IsSetEst(void) const

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

TMrna & SetMrna(void)

Assign a value to Mrna data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

void SetClone_seq(TClone_seq &value)

Assign a value to Clone_seq data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

void SetSupport(TSupport &value)

Assign a value to Support data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

bool IsSetMrna(void) const

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

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsSetId(void) const

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

TProtein & SetProtein(void)

Assign a value to Protein data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetData(TData &value)

Assign a value to Data data member.

TCode_break & SetCode_break(void)

Assign a value to Code_break data member.

TInference & SetInference(void)

Assign a value to Inference data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

void SetId(TId &value)

Assign a value to Id data member.

TAccessions & SetAccessions(void)

Assign a value to Accessions data member.

bool IsSetCit(void) const

citations for this feature Check if a value has been assigned to Cit data member.

void SetIdentification(TIdentification &value)

Assign a value to Identification data member.

TEst & SetEst(void)

Assign a value to Est data member.

void SetBasis(TBasis &value)

Assign a value to Basis data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsSetLoc(void) const

location of exception Check if a value has been assigned to Loc data member.

bool IsSetInference(void) const

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

bool IsSetLocation(void) const

location on sequence Check if a value has been assigned to Location data member.

bool IsSetCode_break(void) const

individual exceptions Check if a value has been assigned to Code_break data member.

bool IsSetClone_seq(void) const

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

bool IsSetAccessions(void) const

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

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

bool IsSetProtein(void) const

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

@ e_Region

named region (globin locus)

@ e_Seq

to annotate origin from another seq

@ e_Txinit

transcription initiation

@ e_Num

a numbering system

@ e_Pub

publication applies to this seq

@ e_User

user defined structure

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetA(TA &value)

Assign a value to A data member.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

Tdata & Set(void)

Assign a value to data member.

bool IsSetA(void) const

connection to a least one residue Check if a value has been assigned to A data member.

void SetId(TId &value)

Assign a value to Id data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

Tdata & Set(void)

Assign a value to data member.

Tdata & Set(void)

Assign a value to data member.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

void SetB(TB &value)

Assign a value to B data member.

bool IsSetId(void) const

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

bool IsSetB(void) const

other end may not be available Check if a value has been assigned to B data member.

@ e_Equiv

equivalent sets of locations

@ e_Empty

to NULL one Seq-id in a collection

bool IsSetLoc(void) const

region this applies to Check if a value has been assigned to Loc data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

TSet & SetSet(void)

Select the variant.

bool IsSetDate(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

bool IsSetAnnot(void) const

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

bool IsSetSeq_set(void) const

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

bool IsSetDescr(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

void SetDate(TDate &value)

Assign a value to Date data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

TAlign & SetAlign(void)

Select the variant.

TSeq_table & SetSeq_table(void)

Select the variant.

bool IsSetComment(void) const

any comment on this pub in context Check if a value has been assigned to Comment data member.

bool IsSetDeleted(void) const

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

Tdata & Set(void)

Assign a value to data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetReplaced_by(void) const

these seqs make this one obsolete Check if a value has been assigned to Replaced_by data member.

void SetDeleted(TDeleted &value)

Assign a value to Deleted data member.

TIds & SetIds(void)

Assign a value to Ids data member.

TPir & SetPir(void)

Select the variant.

void SetAligns(TAligns &value)

Assign a value to Aligns data member.

ERepr

representation class

void SetPub(TPub &value)

Assign a value to Pub data member.

TTitle & SetTitle(void)

Select the variant.

TPub & SetPub(void)

Select the variant.

bool IsSetAssembly(void) const

how was this assembled? Check if a value has been assigned to Assembly data member.

TOrg & SetOrg(void)

Select the variant.

bool IsSetIds(void) const

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

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TFtable & SetFtable(void)

Select the variant.

TGenbank & SetGenbank(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

TPdb & SetPdb(void)

Select the variant.

bool IsSetBiomol(void) const

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

TPub & SetPub(void)

Select the variant.

bool IsSetData(void) const

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

TSp & SetSp(void)

Select the variant.

const Tdata & Get(void) const

Get the member data.

bool IsSetReplaces(void) const

seq makes these seqs obsolete Check if a value has been assigned to Replaces data member.

TDelta & SetDelta(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

E_Choice Which(void) const

Which variant is currently selected.

void SetDate(TDate &value)

Assign a value to Date data member.

bool IsSetAligns(void) const

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

TName & SetName(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetDesc(void) const

used only for stand alone Seq-annots Check if a value has been assigned to Desc data member.

void SetReplaces(TReplaces &value)

Assign a value to Replaces data member.

TIds & SetIds(void)

Assign a value to Ids data member.

TNum & SetNum(void)

Select the variant.

TComment & SetComment(void)

Select the variant.

TRegion & SetRegion(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

TAlign & SetAlign(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

TSource & SetSource(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

TBiomol GetBiomol(void) const

Get the Biomol member data.

TGraph & SetGraph(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice Which(void) const

Which variant is currently selected.

TSeg & SetSeg(void)

Select the variant.

bool IsSetPub(void) const

the citation(s) Check if a value has been assigned to Pub data member.

TUser & SetUser(void)

Select the variant.

bool IsSetNum(void) const

numbering from paper Check if a value has been assigned to Num data member.

TEmbl & SetEmbl(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

TDate & SetDate(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

void SetReplaced_by(TReplaced_by &value)

Assign a value to Replaced_by data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

TLocs & SetLocs(void)

Select the variant.

bool IsSetDate(void) const

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

Tdata & Set(void)

Assign a value to data member.

const TPub & GetPub(void) const

Get the Pub member data.

TIds & SetIds(void)

Select the variant.

TAssembly & SetAssembly(void)

Assign a value to Assembly data member.

TUpdate_date & SetUpdate_date(void)

Select the variant.

TModelev & SetModelev(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

void SetNum(TNum &value)

Assign a value to Num data member.

TMolinfo & SetMolinfo(void)

Select the variant.

TCreate_date & SetCreate_date(void)

Select the variant.

TRef & SetRef(void)

Select the variant.

TCreate_date & SetCreate_date(void)

Select the variant.

TSrc & SetSrc(void)

Select the variant.

TUpdate_date & SetUpdate_date(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetIds(void) const

used for the one ref seqid for now Check if a value has been assigned to Ids data member.

E_Choice Which(void) const

Which variant is currently selected.

TMap & SetMap(void)

Select the variant.

TRegion & SetRegion(void)

Select the variant.

TRef & SetRef(void)

Select the variant.

@ eRepr_delta

sequence made by changes (delta) to others

@ e_Ref

by reference to another sequence

@ e_Ids

used for communication between tools

@ e_Locs

used for communication between tools

@ e_Seg

segmented sequences

@ e_Map

ordered map of markers

@ e_Ref

hot link to another sequence (a view)

@ e_Embl

EMBL specific information.

@ e_Org

if all from one organism

@ e_Num

a numbering system

@ e_User

user defined object

@ e_Update_date

date of last update

@ e_Pub

a reference to the publication

@ e_Pir

PIR specific info.

@ e_Genbank

GenBank specific info.

@ e_Sp

SWISSPROT specific info.

@ e_Comment

a more extensive comment

@ e_Modelev

model evidence for XM records

@ e_Region

overall region (globin locus)

@ e_Molinfo

info on the molecule and techniques

@ e_Create_date

date entry first created/released

@ e_Title

a title for this sequence

@ e_Pdb

PDB specific information.

@ e_Name

a name for this sequence

@ e_Source

source of materials, includes Org-ref

@ e_Pub

a reference to the publication

@ e_Align

definition of the SeqAligns

@ e_Region

all contents cover this region

@ e_Update_date

date of last update

@ e_Create_date

date entry first created/released

@ e_Src

source sequence from which annot came

TEntrys & SetEntrys(void)

Select the variant.

bool IsSetData(void) const

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

void SetReldate(TReldate &value)

Assign a value to Reldate data member.

void SetSub(TSub &value)

Assign a value to Sub data member.

void SetContact(TContact &value)

Assign a value to Contact data member.

void SetCit(TCit &value)

Assign a value to Cit data member.

TDelete & SetDelete(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetReldate(void) const

release by date Check if a value has been assigned to Reldate data member.

TAnnots & SetAnnots(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetSub(void) const

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

bool IsSetCit(void) const

citation for this submission Check if a value has been assigned to Cit data member.

bool IsSetContact(void) const

who to contact Check if a value has been assigned to Contact data member.

void SetContact(TContact &value)

Assign a value to Contact data member.

bool IsSetContact(void) const

WARNING: this will replace the above Check if a value has been assigned to Contact data member.

bool IsSetGene(void) const

gene(s) transcribed Check if a value has been assigned to Gene data member.

TProtein & SetProtein(void)

Assign a value to Protein data member.

bool IsSetProtein(void) const

protein(s) produced Check if a value has been assigned to Protein data member.

TGene & SetGene(void)

Assign a value to Gene data member.

void SetTxorg(TTxorg &value)

Assign a value to Txorg data member.

bool IsSetTxorg(void) const

organism supplying transcription apparatus Check if a value has been assigned to Txorg data member.

bool IsSetSomatic_origin(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

TSomatic_origin & SetSomatic_origin(void)

Assign a value to Somatic_origin data member.

TConsequence & SetConsequence(void)

Assign a value to Consequence data member.

bool IsSetSeq(void) const

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

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetConsequence(void) const

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

TLoc & SetLoc(void)

Select the variant.

void SetSeq(TSeq &value)

Assign a value to Seq data member.

TSet & SetSet(void)

Select the variant.

TInstance & SetInstance(void)

Select the variant.

TDelta & SetDelta(void)

Assign a value to Delta data member.

bool IsSetData(void) const

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

@ e_Instance

actual sequence-edit at feat.location

bool IsSetReplace(void) const

replacement history Check if a value has been assigned to Replace data member.

bool IsSetDeposition(void) const

deposition date month,year Check if a value has been assigned to Deposition data member.

void SetDeposition(TDeposition &value)

Assign a value to Deposition data member.

void SetReplace(TReplace &value)

Assign a value to Replace data member.

TSeqref & SetSeqref(void)

Assign a value to Seqref data member.

bool IsSetSeqref(void) const

xref to other sequences Check if a value has been assigned to Seqref data member.

void SetAnnotupd(TAnnotupd &value)

Assign a value to Annotupd data member.

bool IsSetSequpd(void) const

sequence update Check if a value has been assigned to Sequpd data member.

void SetCreated(TCreated &value)

Assign a value to Created data member.

bool IsSetSeqref(void) const

xref to other sequences Check if a value has been assigned to Seqref data member.

bool IsSetAnnotupd(void) const

annotation update Check if a value has been assigned to Annotupd data member.

void SetSequpd(TSequpd &value)

Assign a value to Sequpd data member.

bool IsSetCreated(void) const

creation date Check if a value has been assigned to Created data member.

TSeqref & SetSeqref(void)

Assign a value to Seqref data member.

Magic spell ;-) needed for some weird compilers... very empiric.

#define CLEAN_STRING_MEMBER(o, x)

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