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NCBI C++ ToolKit: src/app/table2asn/feature_table_reader.cpp Source File

kAssemblyGap_feature =

;

kGapType_qual =

;

kLinkageEvidence_qual =

;

CSeq_descr::Tdata::iterator it = src.

().Set().begin();

(it != src.

().Set().end())

((**it).Which())

dest.

().Set().push_back(*it);

dest.

().Set().push_back(*it);

mapids[] = {

SSeqAnnotCompare

* m = mapids;

strchr(m, c)-m;

mapwhich(left->

().

()) < mapwhich(right->GetData().Which());

(!(**annot_it).IsFtable())

;

& feature = **feature_it;

FindMaximumId(

& entry,

&

)

FindMaximumId(entry.

(),

);

FindMaximumId(**set_it,

);

((**xref_it).IsSetData())

((**xref_it).GetData().IsProt() &&

(**xref_it).GetData().GetProt().IsSetName())

protein_name = (**xref_it).GetData().GetProt().GetName().front();

->SetLocal().SetStr(id_label);

(!hid || !it->IsBetter(hid)) {

GetNewProteinId(seh.

(), id_base);

NewProteinName(

& feature,

make_hypotethic)

(protein_name.empty() && make_hypotethic)

protein_name =

;

(

pId : pProtEntry->GetSeq().GetId()) {

seqid->Assign(*bioseq.

().begin()->GetPointerOrNull());

best.push_back(orfs.front());

((**it).GetTotalRange().GetLength() >

best.front()->GetTotalRange().GetLength() )

(

it: seq.

()) {

(

it: seq_ids) {

(!BioseqHasId(bioseq, it))

bioseq.

().push_back(it);

(

it: ids) {

(it->IsGenbank() || best.

())

(

it = seq_ftable.begin(); it != seq_ftable.end(); ++it) {

prot_feat = *it;

seq_ftable.erase(it);

= &it->SetData().SetFtable();

= &annot->SetData().SetFtable();

bioseq.

().push_back(annot);

(prot_feat.

())

->push_back(prot_feat);

prot_feat =

->front();

GetGenomicCodeOfBioseq(

& bioseq)

(closest_biosource.

())

append_nonduplicated_item = [](list<string>& current_list,

list<string>& other_list)

unordered_set<string> current_set;

(

& item : current_list) {

current_set.insert(item);

(

& item : other_list) {

(current_set.find(item) == current_set.end()) {

current_list.push_back(item);

append_nonduplicated_item(current_ref.

(),

append_nonduplicated_item(current_ref.

(),

other_ref.

());

append_nonduplicated_item(current_ref.

(),

(

& pDBtag : other_ref.

()) {

current_ref.

().push_back(pDBtag);

nameFromRNAProduct{

};

nameFromRNAProduct =

;

prot_ref.

().push_back(product_name);

(pMrna.

() || nameFromRNAProduct) {

(extName.empty()) {

(

& protName : prot_ref.

()) {

prot_ref.

().push_back(extName);

was_extended =

;

(protein.

())

protein_entry->

(*protein);

(protein->

().empty())

* protein_ids =

;

qual_to_remove =

;

protein_ids = &cd_feature.

(qual_to_remove);

(protein_ids->empty())

qual_to_remove =

;

protein_ids = &cd_feature.

(qual_to_remove);

(protein_ids->empty())

(protein_ids->empty())

protein_ids = &cd_feature.

(

);

(protein_ids->empty()) {

MergeSeqIds(*protein, {

});

MergeSeqIds(*protein, new_ids);

(protein->

().empty())

(!bioseq.

().empty()) {

protein->

().push_back(GetNewProteinId(*token.

, base_name));

(

prot_id : protein->

()) {

prot_feat = MoveParentProt(seq_ftable, *prot_id);

CreateOrSetFTable(*protein, prot_feat);

prot_ref.

().empty()) &&

prot_ref.

().push_back(

);

prot_feat->

().SetInt().SetId().Assign(*GetAccessionId(protein->

()));

cd_feature.

().SetWhole().Assign(*GetAccessionId(protein->

()));

cd_feature.

().clear();

& ext = mrna->

().SetRna().SetExt();

(ext.IsName() && ext.SetName().empty()))

ext.SetName() = prot_ref.

().front();

protein_entry;

*left < *right;

* pNucSeq=

;

& bioseqSet = nuc_prot.

();

(

& pSubEntry : bioseqSet.GetSeq_set()) {

& bioseq = pSubEntry->GetSeq();

(bioseq.

()) {

inserter(proteinIds, proteinIds.

()),

[](

& pId) { return pId.GetPointer(); });

(

pAnnot : pNucSeq->

()) {

(pAnnot->IsFtable()) {

(

pSeqFeat : pAnnot->GetData().GetFtable()) {

!pSeqFeat->IsSetData() ||

!pSeqFeat->GetData().IsCdregion()) {

(!pSeqFeat->IsSetProduct() ||

!pSeqFeat->GetProduct().GetId() ||

proteinIds.

(pSeqFeat->GetProduct().GetId())

== proteinIds.

()) {

(entry.

())

(entry.

())

seq_ftable.sort(SSeqAnnotCompare());

feat_it = seq_ftable.begin();

(feat_it != seq_ftable.end())

(

.IsCdregion())

(!

.GetCdregion().IsSetCode())

= GetGenomicCodeOfBioseq(*token.

);

.SetCdregion().SetCode().SetId(

);

(!

.GetCdregion().IsSetFrame())

set_ftable.push_back(feature);

feat_it = seq_ftable.erase(feat_it);

(!entry.

() ||

entry_it = find_if(seq_set.begin(), seq_set.end(),

pEntry->GetSeq().IsSetInst() &&

pEntry->GetSeq().IsNa() &&

pEntry->GetSeq().IsSetAnnot());

(entry_it == seq_set.end()) {

& bioseq = token.

;

bioseq.

(&((*entry_it)->SetSeq()));

& annots = bioseq->

();

find_if(annots.begin(), annots.end(),

(annot_it == annots.end()) {

main_ftable = *annot_it;

(annot_it != annots.end()) {

pAnnot = *annot_it;

main_ftable->

().SetFtable().splice(

end(main_ftable->SetData().SetFtable()),

pAnnot->

().SetFtable());

annot_it = annots.erase(annot_it);

seq_ftable = main_ftable->SetData().SetFtable();

(seq_ftable.empty()) {

bioseq->

().remove(main_ftable);

main_ftable->SetData().SetFtable() = std::move(seq_ftable);

(!set_ftable.empty()) {

unique_ptr<CFastaReader> pReader(

CFastaReader(0,

));

pReader->SetPostponedMods({

,

});

(

->IsSetDescr())

(

->GetDescr().Get().empty())

->SetSeq().ResetDescr();

->SetSet().ResetDescr();

->SetSet().SetSeq_set().push_back(

);

list<CConstRef<CBioseq>> proteins;

(possible_proteins.

()) {

proteins.emplace_back(&(possible_proteins.

()));

proteins.emplace_back(&(pSubEntry->GetSeq()));

it = proteins.begin();

(it != proteins.end()) {

it = proteins.erase(it);

((**annot_it).IsFtable())

((**feat_it).CanGetData())

((**feat_it).GetData().Which())

(entry.

())

MoveSomeDescr(entry, bioseq);

(ival.

() < bioseqLength - 4) {

ival.

(bioseqLength - 1);

changed =

;

( partial5 && partial3 ) {

}

( partial5 ) {

}

( partial3 ) {

((*annot_it)->IsFtable()) {

((*feat_it)->IsSetData() && (*feat_it)->GetData().IsProt() && !(*feat_it)->GetData().GetProt().IsSetProcessed()) {

prot_feat = *feat_it;

prot_feat->

().SetProt();

->SetData().SetFtable().push_back(prot_feat);

prot_id->Assign(*(protein.

().front()));

prot_feat->

().SetInt().SetId(*prot_id);

(partial5 || partial3) {

(!eh.

()) {

(

&&

->IsSetSeq_set()) {

CBioseq_set::TDescr::Tdata::const_iterator it =

->GetDescr().Get().begin();

(it !=

->GetDescr().Get().end()) {

(!(*it)->IsMolinfo() && !(*it)->IsTitle()) {

->Assign(**it);

it =

->GetDescr().Get().begin();

(; annot_ci; ++annot_ci) {

((*annot_ci).IsFtable()) {

m_feh = aeh.AddFeat(*m_Feat);

& idString,

objects::ILineErrorListener& logger)

(

& modName : duplicateMods) {

message =

+ modName +

;

logger.PutError(*unique_ptr<CLineError>(

,

,

, message)));

& protein,

partial5,

partial3)

& proteinIds = pOriginalProtIds.empty() ?

(

pId : proteinIds) {

idString = pId->AsFastaString();

& modList = it->second.second;

lineNumber = it->second.first;

(

&

: modList) {

(!

.AddMods(

.GetName(),

.GetValue())) {

duplicateMods.

(

.GetName());

(!

.GetAllMods().empty()) {

.ApplyAllMods(protein);

(

->IsSeq()) {

.ApplyAllMods(

->SetSeq(),

, cds_loc);

(

pEntry :

->SetSet().SetSeq_set()) {

(pEntry->IsSeq() && pEntry->GetSeq().IsNa()) {

.ApplyAllMods(pEntry->SetSeq(),

, cds_loc);

(

pId : protein.

()) {

(seh.

()) {

(seh.

()) {

(bit->IsSynonym(*pId)) {

(nuc_count > 1) {

CSeq_loc& genomicLoc,

alignment = prosplign.

(scope, proteinId, genomicLoc,

(!filter.

(*alignment)) {

found_start_codon =

;

found_stop_codon =

;

list<CRef<CSeq_loc>> exonLocs;

(alignment->IsSetSegs() && alignment->GetSegs().IsSpliced()) {

seq_id->

(*(genomicLoc.GetId()));

& splicedSegs = alignment->GetSegs().GetSpliced();

isMinusStrand = (splicedSegs.IsSetGenomic_strand() &&

(

pExon : splicedSegs.GetExons()) {

pExonLoc =

(

CSeq_loc(*seq_id,

pExon->GetGenomic_start(),

pExon->GetGenomic_end()));

(isMinusStrand) {

}

(pExon->IsSetGenomic_strand()) {

pExonLoc->SetStrand(pExon->GetGenomic_strand());

exonLocs.push_back(pExonLoc);

(

pModifier : splicedSegs.GetModifiers()) {

(pModifier->IsStart_codon_found()) {

found_start_codon = pModifier->GetStart_codon_found();

(pModifier->IsStop_codon_found()) {

found_stop_codon = pModifier->GetStop_codon_found();

(exonLocs.empty()) {

pCDSLoc =

(

CSeq_loc());

(exonLocs.size() == 1) {

pCDSLoc->Assign(*(exonLocs.front()));

pCDSLoc->SetMix().Set() = exonLocs;

(!found_start_codon) {

(found_stop_codon) {

& finalInterval = pCDSLoc->IsMix() ?

pCDSLoc->SetMix().Set().back()->SetInt() :

pCds->SetLocation(loc);

pCds->SetPartial(

);

pCds->SetData().SetCdregion();

pCds->SetProduct().SetWhole(productId);

id_match{

};

bioseq_id->

(*(bsh_match.GetSeqId()));

match_loc(

CSeq_loc(*bioseq_id, 0, bsh_match.GetBioseqLength() - 1));

pOriginalIds = move(protein_entry->

().

());

protein_entry->

().

().push_back(product_id);

=

+

+

;

protein_entry->

(), partial5, partial3);

AddSeqEntry(bsh_match.GetParentEntry(), protein_entry);

new_cds =

(*cds_loc, (partial5 || partial3),

AddFeature(seh, new_cds);

title = protein_name;

(!org_name.empty())

(CBioseq::TAnnot::iterator annot_it = bioseq.

().begin(); annot_it != bioseq.

().end(); )

((**annot_it).IsFtable() && (**annot_it).GetData().GetFtable().empty())

annot_it = bioseq.

().erase(annot_it);

(feat.

(

) ==

);

& sGT = feature_gap.

(kGapType_qual);

gap_type = gap_type_info->

;

& sLE_name = (**sLE_qual).GetQual();

(sLE_name != kLinkageEvidence_qual)

(it == linkage_evidence_to_value_map.

())

(

) + (**sLE_qual).GetVal(),

(

) + sGT,

(

) + sGT,

evidences.

(evidence);

(

) + sGT,

(

bioseq_it(seh); bioseq_it; ++bioseq_it)

(

feature_it(*bioseq_it, annot_sel); feature_it; )

(feature_it->IsSetData() && feature_it->GetData().IsImp())

& imp = feature_it->GetData().GetImp();

& feature_gap = feature_it->GetOriginalFeature();

pBioseq =

*

(bioseq_it->GetCompleteBioseq().GetPointer());

,

& bioseq = (

&)*bioseq_it->GetEditHandle().GetCompleteBioseq();

(

pAnnot : bioseq.

()) {

(!pAnnot->IsSetData() ||

&

= pAnnot->SetData().SetFtable();

fit =

.begin();

(fit !=

.end()) {

pSeqFeat = *fit;

(pSeqFeat->IsSetData() &&

pSeqFeat->GetData().IsImp() &&

pSeqFeat->GetData().GetImp().IsSetKey() &&

pSeqFeat->GetData().GetImp().GetKey() == kAssemblyGap_feature) {

(

(bioseq, *pSeqFeat)) {

fit =

.erase(fit);

,

CSeqTranslator::ChangeDeltaProteinToRawProtein(Ref(&bioseq));

(loc.Which()) {

&loc.GetWhole();

&(loc.GetInt().GetId());

&(loc.GetPnt().GetId());

(!loc.GetPacked_int().Get().empty()) {

&(loc.GetPacked_int().Get().front()->GetId());

(loc.GetPacked_pnt().IsSetId()) {

&(loc.GetPacked_pnt().GetId());

= list<CRef<CSeq_feat>>::const_iterator;

list<SRegionIterators>& its)

(

annot_it = annots.begin();

annot_it != annots.end();

& annot = **annot_it;

(annot.IsFtable()) {

&

= annot.GetData().GetFtable();

list<SRegionIterators::TFeatIt> feat_its;

(

feat_it =

.begin(); feat_it !=

.end(); ++feat_it) {

& pFeat = *feat_it;

(pFeat->IsSetData() &&

pFeat->GetData().IsRegion()) {

feat_its.push_back(feat_it);

(!feat_its.empty()) {

(!seq_entry.

()) {

& bioseq_set = seq_entry.

();

(!bioseq_set.IsSetClass() ||

(bioseq_set.IsSetSeq_set()) {

(

pEntry : bioseq_set.SetSeq_set()) {

(bioseq_set.IsSetSeq_set());

list<SRegionIterators> region_its;

(

pSubEntry : bioseq_set.SetSeq_set()) {

& seq = pSubEntry->SetSeq();

region_its.empty()) {

pScope->AddTopLevelSeqEntry(seq_entry);

(

its : region_its) {

(

feat_it : its.feat_its) {

pRegion = *feat_it;

pRegion->SetLocation(*pMappedLoc);

(*its.annot_it)->SetData().SetFtable().

(feat_it);

((*its.annot_it)->GetData().GetFtable().empty()) {

pNucSeq->

().erase(its.annot_it);

(

pSubEntry : bioseq_set.SetSeq_set()) {

& bioseq = pSubEntry->SetSeq();

(bioseq.

()) {

(

pId : bioseq.

()) {

(it != mapped_regions.

() && (it->first->Compare(*pId) ==

)) {

it = mapped_regions.

(it);

bioseq.

().push_back(pAnnot);

(mapped_regions.

()) {

(entry.

()) {

& bioseq_set = entry.

();

(!bioseq_set.IsSetSeq_set()) {

any_change =

;

(!bioseq_set.IsSetClass() ||

(

pSubEntry : bioseq_set.SetSeq_set()) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

void g_LogGeneralParsingError(EDiagSev sev, const string &idString, const string &msg, objects::ILineErrorListener &listener)

string GetIdHashOrValue(const string &base, int offset)

void transform(Container &c, UnaryFunction *op)

CAlignFilter exposes a query language for inspecting properties and scores placed on Seq-align object...

bool Match(const objects::CSeq_align &align)

Match a single alignment.

CSeqdesc & Set(bool skip_lookup=false)

int GetGenCode(int def=1) const

CConstRef< CSeqdesc > GetClosestDescriptor(CSeqdesc::E_Choice choice, int *level=NULL) const

TSeqPos GetLength(void) const

static bool ExtendToStopIfShortAndNotPartial(CSeq_feat &f, CBioseq_Handle bsh, bool check_for_stop=true)

Extends a coding region up to 50 nt.

static bool ParseCodeBreaks(CSeq_feat &feat, CScope &scope)

Parses all valid transl_except Gb-quals into code-breaks for cdregion, then removes the transl_except...

static bool ExtendStopPosition(CSeq_feat &f, const CSeq_feat *cdregion, size_t extension=0)

static CRef< CSeq_loc > GetProteinLocationFromNucleotideLocation(const CSeq_loc &nuc_loc, CScope &scope)

static bool MoveProteinSpecificFeats(CSeq_entry_Handle seh)

Moves protein-specific features from nucleotide sequences in the Seq-entry to the appropriate protein...

static bool LocationMayBeExtendedToMatch(const CSeq_loc &orig, const CSeq_loc &improved)

Checks whether it is possible to extend the original location up to improved one.

void xParseCdregions(objects::CSeq_entry &entry, TAsyncToken &)

objects::CFastaReader::TPostponedModMap m_PrtModMap

void AddProteins(const objects::CSeq_entry &possible_proteins, objects::CSeq_entry &entry)

void MoveRegionsToProteins(objects::CSeq_entry &entry)

void xMoveCdRegions(objects::CSeq_entry_Handle entry_h, objects::CSeq_annot::TData::TFtable &seq_ftable, objects::CSeq_annot::TData::TFtable &set_ftable, TAsyncToken &)

void FindOpenReadingFrame(objects::CSeq_entry &entry) const

bool xAddProteinToSeqEntry(const objects::CBioseq &protein, objects::CSeq_entry_Handle seh)

void ConvertNucSetToSet(CRef< objects::CSeq_entry > &entry) const

CFeatureTableReader(CTable2AsnContext &context)

CTable2AsnContext & m_context

void MakeGapsFromFeatures(objects::CSeq_entry_Handle seh) const

CRef< objects::CSeq_entry > ReadProtein(ILineReader &line_reader)

void ChangeDeltaProteinToRawProtein(objects::CSeq_entry &entry) const

void xConvertSeqIntoSeqSet(objects::CSeq_entry &entry, bool nuc_prod_set) const

static void RemoveEmptyFtable(objects::CBioseq &bioseq)

CRef< objects::CSeq_feat > x_AddProteinFeatureToProtein(CRef< objects::CSeq_entry > nuc, CConstRef< objects::CSeq_loc > cds_loc, const list< CRef< objects::CSeq_id >> &pOriginalProtIds, objects::CBioseq &protein, bool partial5, bool partial3)

CRef< objects::CDelta_seq > MakeGap(objects::CBioseq &bioseq, const objects::CSeq_feat &feature_gap) const

void xMergeCDSFeatures_impl(objects::CSeq_entry &, TAsyncToken &)

void MergeCDSFeatures(objects::CSeq_entry &, TAsyncToken &)

void MoveProteinSpecificFeats(objects::CSeq_entry &entry)

CRef< objects::CSeq_entry > m_replacement_protein

bool xCheckIfNeedConversion(const objects::CSeq_entry &entry) const

CRef< objects::CSeq_entry > xTranslateProtein(const objects::CBioseq &bioseq, objects::CSeq_feat &cd_feature, list< CRef< CSeq_feat >> &seq_ftable, TAsyncToken &)

CRef< CDelta_seq > CreateGap(CBioseq &bioseq, TSeqPos gap_start, TSeqPos gap_length)

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

static CLineError * Create(EProblem eProblem, EDiagSev eSeverity, const std::string &strSeqId, unsigned int uLine, const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), const std::string &strErrorMessage=string(""), const TVecOfLines &vecOfOtherLines=TVecOfLines())

Use this because the constructor is protected.

vector< CRef< objects::CSeq_loc > > TLocVec

static CRef< objects::CSeq_annot > MakeCDSAnnot(const TLocVec &orfs, int genetic_code=1, objects::CSeq_id *id=NULL)

/ This version returns an annot full of CDS features.

static void FindOrfs(const string &seq, TLocVec &results, unsigned int min_length_bp=3, int genetic_code=1, const vector< string > &allowable_starts=vector< string >(), bool longest_orfs=true, size_t max_seq_gap=k_default_max_seq_gap)

Find ORFs in both orientations.

CProSplignOptions_Base & SetAltStarts(bool allow_alt_start)

Output filtering parameters.

@ ePassThrough

all zeroes - no filtering

@ eWithHoles

default filtering parameters

spliced protein to genomic alignment

CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Aligns protein to a region on genomic sequence.

void GetLabel(string *label) const

bool IsFtable(void) const

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

const TAnnot & GetAnnot(void) const

bool IsSetAnnot(void) const

void SetDescr(CSeq_descr &value)

list< CRef< CSeq_annot > > TAnnot

CSeq_entry * GetParentEntry(void) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

const CProt_ref * GetProtXref(void) const

get protein (if present) from Seq-feat.xref list

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

void RemoveQualifier(const string &qual_name)

Remove all qualifiers with the given name; do nothing if no such qualifier exists.

bool AddSeqFeatXref(const CSeqFeatXref::TId &id)

@ eLinkEvid_UnspecifiedOnly

only the "unspecified" linkage-evidence is allowed

@ eLinkEvid_Forbidden

no linkage-evidence is allowed

@ eLinkEvid_Required

any linkage-evidence is allowed, and at least one is required

static const SGapTypeInfo * NameToGapTypeInfo(const CTempString &sName)

From a gap-type string, get the SGapTypeInfo, insensitive to case, etc.

static bool GetOrgName(string &name, const objects::CSeq_entry &entry)

objects::ILineErrorListener * m_logger

bool m_use_hypothetic_protein

SPrtAlnOptions prtAlnOptions

static bool IsDBLink(const objects::CSeqdesc &desc)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

@ eProblem_GeneralParsingError

Abstract base class for lightweight line-by-line reading.

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

void SetMolinfoForProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

CRef< objects::CSeq_feat > AddEmptyProteinFeatureToProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

bool SetMolinfoCompleteness(objects::CMolInfo &mi, bool partial5, bool partial3)

Operators to edit gaps in sequences.

static void s_SetProtRef(const CSeq_feat &cds, CConstRef< CSeq_feat > pMrna, CProt_ref &prot_ref)

static CBioseq_Handle s_MatchProteinById(const CBioseq &protein, CSeq_entry_Handle seh)

static void s_AppendProtRefInfo(CProt_ref &current_ref, const CProt_ref &other_ref)

static void s_ReportDuplicateMods(const set< string > &duplicateMods, const string &idString, TSeqPos lineNumber, objects::ILineErrorListener &logger)

static bool s_MoveProteinSpecificFeats(CSeq_entry &entry)

static bool s_TranslateCds(const CSeq_feat &cds, CScope &scope)

static CRef< CSeq_loc > s_GetCDSLoc(CScope &scope, const CSeq_id &proteinId, const CSeq_loc &genomicLoc, TSeqPos bioseqLength, const CTable2AsnContext::SPrtAlnOptions &prtAlnOptions)

static bool s_HasUnprocessedCdregions(const CSeq_entry &nuc_prot)

static CRef< CSeq_feat > s_MakeCDSFeat(CSeq_loc &loc, bool isPartial, CSeq_id &productId)

static const CSeq_id * s_GetIdFromLocation(const CSeq_loc &loc)

static bool s_UnknownEstimatedLength(const CSeq_feat &feat)

static CBioseq_Handle s_GetSingleNucSeq(CSeq_entry_Handle seh)

static void s_GatherRegionIterators(list< CRef< CSeq_annot >> &annots, list< SRegionIterators > &its)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

@ eDiag_Error

Error message.

const string & GetMsg(void) const

Get message string.

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

Set object to copy of another one.

CNcbiIos & MSerial_VerifyNo(CNcbiIos &io)

#define ENUM_METHOD_NAME(EnumName)

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

#define MSerial_AsnText

I/O stream manipulators –.

static string CanonicalizeString(const CTempString &sValue)

@ fAddMods

Parse defline mods and add to SeqEntry.

@ fNoUserObjs

Don't save raw deflines in User-objects.

@ fForceType

Force specified type regardless of accession.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_YES

SeqIds compared, but are different.

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_ValidLocal

Treat otherwise unidentified strings as raw accessions, provided that they pass rudimentary validatio...

@ eContent

Untagged human-readable accession or the like.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

TSeqPos GetStop(ESeqLocExtremes ext) const

bool CopyFeaturePartials(CSeq_feat &dst, const CSeq_feat &src)

CopyFeaturePartials A function to copy the start and end partialness from one feature to another.

bool AdjustProteinMolInfoToMatchCDS(CMolInfo &molinfo, const CSeq_feat &cds)

AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region.

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

string GetProteinName(const CBioseq_Handle &seq)

Return protein name from corresponding Prot-ref feature.

static CCdregion::EFrame FindBestFrame(const CSeq_feat &cds, CScope &scope)

Find "best" frame for a coding region.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq().

CSeq_entry_EditHandle GetSeq_entryEditHandle(const CSeq_entry &entry)

CBioseq_set_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

vector< CSeq_id_Handle > TId

TClass GetClass(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &v) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CBioseq_set_EditHandle GetParentBioseq_set(void) const

Get parent bioseq-set edit handle.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

TSet ConvertSeqToSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the entry from Bioseq to Bioseq-set.

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from the TSE of this Seq-entry.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

CSeq_entry_EditHandle AttachEntry(CSeq_entry &entry, int index=-1) const

Attach an existing seq-entry.

bool IsSetClass(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_EditHandle AttachEntry(CSeq_entry &entry, int index=-1) const

Attach an existing seq-entry.

CConstRef< TObject > GetCompleteObject(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool AddSeqdesc(CSeqdesc &v) const

const TId & GetId(void) const

int GetSeq_entry_Index(const CSeq_entry_Handle &handle) const

bool IsSynonym(const CSeq_id &id) const

Check if this id can be used to obtain this bioseq handle.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

virtual bool IsType(TTypeInfo type) const

static const char label[]

bool IsSetLocus_tag(void) const

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

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

bool IsId(void) const

Check if variant Id is selected.

TId GetId(void) const

Get the variant data.

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.

const TDb & GetDb(void) const

Get the Db member data.

const TActivity & GetActivity(void) const

Get the Activity member data.

TEc & SetEc(void)

Assign a value to Ec data member.

const TName & GetName(void) const

Get the Name member data.

bool IsSetDb(void) const

ids in other dbases Check if a value has been assigned to Db data member.

bool IsSetEc(void) const

E.C.

void SetDesc(const TDesc &value)

Assign a value to Desc data member.

TProcessed GetProcessed(void) const

Get the Processed member data.

void SetProcessed(TProcessed value)

Assign a value to Processed data member.

bool IsSetName(void) const

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

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetActivity(void) const

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

const TEc & GetEc(void) const

Get the Ec member data.

TDb & SetDb(void)

Assign a value to Db data member.

TName & SetName(void)

Assign a value to Name data member.

bool IsSetExt(void) const

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

const TName & GetName(void) const

Get the variant data.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsName(void) const

Check if variant Name is selected.

@ e_not_set

No variant selected.

TXref & SetXref(void)

Assign a value to Xref data member.

const TKey & GetKey(void) const

Get the Key member data.

void ResetPartial(void)

Reset Partial data member.

bool IsSetData(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

bool IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetKey(void) const

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

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsSetXref(void) const

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

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetId(void) const

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

const TProduct & GetProduct(void) const

Get the Product member data.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

const TRna & GetRna(void) const

Get the variant data.

bool IsSetProduct(void) const

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

bool IsSetLocation(void) const

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

@ e_Het

cofactor, prosthetic grp, etc, bound to seq

@ e_not_set

No variant selected.

@ 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

@ e_Rsite

restriction site (for maps really)

@ e_Comment

just a comment

@ e_Non_std_residue

non-standard residue here in seq

void SetTo(TTo value)

Assign a value to To data member.

const TWhole & GetWhole(void) const

Get the variant data.

TFrom GetFrom(void) const

Get the From member data.

void SetFrom(TFrom value)

Assign a value to From data member.

bool IsSetStrand(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

bool IsWhole(void) const

Check if variant Whole is selected.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSetClass(void) const

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

TSet & SetSet(void)

Select the variant.

TClass GetClass(void) const

Get the Class member data.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetSeq_set(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

void SetClass(TClass value)

Assign a value to Class data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_genbank

converted genbank

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetCompleteness(void) const

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

TId & SetId(void)

Assign a value to Id data member.

void ResetId(void)

Reset Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

TTitle & SetTitle(void)

Select the variant.

bool IsSetAnnot(void) const

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

bool IsSetRepr(void) const

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

bool IsSetMol(void) const

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

const TSource & GetSource(void) const

Get the variant data.

bool IsSetBiomol(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

void ResetAnnot(void)

Reset Annot data member.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

void SetInst(TInst &value)

Assign a value to Inst data member.

virtual void Reset(void)

Reset the whole object.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

list< CRef< CSeq_feat > > TFtable

bool IsSetId(void) const

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

void SetTech(TTech value)

Assign a value to Tech data member.

TMolinfo & SetMolinfo(void)

Select the variant.

@ eCompleteness_complete

complete biological entity

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ eTech_concept_trans

conceptual translation

@ e_User

user defined object

@ e_Update_date

date of last update

@ e_Pub

a reference to the publication

@ e_Molinfo

info on the molecule and techniques

@ e_Create_date

date entry first created/released

@ e_Title

a title for this sequence

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

bm::gap_word_t gap_length(const bm::gap_word_t *buf) noexcept

Returs GAP block length.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is whole

void VisitAllBioseqs(objects::CSeq_entry &entry, _M &&m)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

Utility macros and typedefs for exploring NCBI objects from seq.asn.

Utility macros and typedefs for exploring NCBI objects from seqset.asn.

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Holds information about a given gap-type string.

CSeq_gap::EType m_eType

The underlying type that the string corresponds to.

ELinkEvid m_eLinkEvid

Indicates what linkage-evidences are compatible with this.

Compare objects pointed to by (smart) pointer.

bool operator()(const CSeq_id *const left, const CSeq_id *const right) const

list< CRef< CSeq_feat > >::const_iterator TFeatIt

list< CRef< CSeq_annot > >::iterator TAnnotIt

CRef< objects::CBioseq > bioseq

CRef< objects::CSeq_feat > ParentGene(const objects::CSeq_feat &cds)

CRef< objects::CSeq_feat > ParentMrna(const objects::CSeq_feat &cds)

static void s_ExtendIntervalToEnd(objects::CSeq_interval &ival, objects::CBioseq_Handle bsh)

bool AssignLocalIdIfEmpty(CSeq_feat &feature, int &id)

static CS_CONTEXT * context

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