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NCBI C++ ToolKit: src/objtools/writers/gff_writer.cpp Source File

label_type =

.IsGeneral() ?

.GetLabel(&

, label_type);

uFlags ) :

m_bHeaderWritten(

)

uFlags ) :

m_bHeaderWritten(

)

& strAssemblyName,

& strAssemblyAccession )

& strAssemblyName,

& strAssemblyAccession )

(

fit(*aci); fit; ++fit) {

(currentId != lastId) {

& strAssemblyName,

& strAssemblyAccession )

& display_range =

();

feat_iter(bsh, display_range, sel);

feature::CFeatTree& featTree = fc.

();

vector<CMappedFeat> vChildren;

featTree.GetChildrenTo(mf, vChildren);

(

cit = vChildren.begin(); cit != vChildren.end(); ++cit) {

& strAssemblyName,

& strAssemblyAccession )

(

; feat_iter; ++feat_iter) {

& strAssName,

& strAssAcc )

<<

<<

;

& strName,

& strAccession )

( !strName.empty() ) {

<<

<< strName <<

;

( !strAccession.empty() ) {

<<

<< strAccession <<

;

vector< CRef< CGb_qual > >& quals = mf.

();

vector< CRef< CGb_qual > >::const_iterator it = quals.begin();

( ; it != quals.end(); ++it ) {

( !(*it)->CanGetQual() || !(*it)->CanGetVal() ) {

( (*it)->GetQual() ==

) {

start(0);

stop(0);

(

!= dbxref.find(

)) {

dbxref =

(

) + dbxref;

dbxref =

(

) + dbxref;

dbxref =

(

) + dbxref;

&

,

(

& pDbxref : mf.

()) {

parent = fc.

().GetParent( mf );

(geneRef && geneRef->IsSuppressed()) {

(

& pDbxref : parent.

()) {

(!dbxref.empty()) {

(gene_feat && gene_feat.IsSetDbxref() &&

gene_feat.IsSetData() && !gene_feat.GetData().GetGene().IsSuppressed()) {

(

& pDbxref : gene_feat.GetDbxref() ) {

display_range.

() < feat_range.

())) {

(

!= 1 &&

!= 255) {

(!protein_id.empty()) {

( pProtRef && pProtRef->

() ) {

(

.IsSetExt() &&

.GetExt().IsTRNA()) {

(!display_range.

())

trimmed_trna = sequence::CFeatTrim::Apply(

.GetExt().GetTRNA(), display_range);

.GetExt().GetTRNA() :

(

.IsSetExt() &&

.GetExt().IsName()) {

(

.IsSetExt() &&

.GetExt().IsGen() &&

.GetExt().GetGen().IsSetProduct() ) {

record.

(

,

.GetExt().GetGen().GetProduct());

( CSeq_feat::TQual::const_iterator cit = quals.begin();

cit != quals.end(); ++cit) {

((*cit)->IsSetQual() && (*cit)->IsSetVal() &&

(*cit)->GetQual() ==

) {

list<CRef<CCode_break> >& code_breaks = cds.

();

(!display_range.

()) {

trimmed_cb = sequence::CFeatTrim::Apply(*code_break, display_range);

list<CRef<CCode_break> >::const_iterator it = code_breaks.begin();

(; it != code_breaks.end(); ++it) {

noRef.

();

(geneRef.IsSetLocus()) {

(geneRef.IsSetLocus_tag()) {

record.

(

, geneRef.GetLocus_tag());

(geneRef.IsSetDesc()) {

record.

(

, geneRef.GetDesc());

(geneRef.IsSetSyn()) {

& syns = geneRef.GetSyn();

it = syns.begin();

(it != syns.end()) {

old_locus_tags;

vector<CRef<CGb_qual> > quals = mf.

();

(vector<

>::const_iterator it = quals.begin();

it != quals.end(); ++it) {

((**it).IsSetQual() && (**it).IsSetVal()) {

qual = (**it).GetQual();

(qual !=

) {

(!old_locus_tags.empty()) {

old_locus_tags +=

;

old_locus_tags += (**it).GetVal();

(!old_locus_tags.empty()) {

record.

(

, old_locus_tags);

vector<string> experiments;

& quals = mf.

();

(

& qual: quals) {

(qual->GetQual() ==

) {

experiments.push_back(qual->GetVal());

(!experiments.empty()) {

modelEvidence;

(!modelEvidence.empty()) {

record.

(

, modelEvidence);

(quals.empty()) {

(CSeq_feat::TQual::const_iterator cit = quals.begin();

cit != quals.end(); ++cit) {

((*cit)->GetQual() ==

) {

record.

(

, (*cit)->GetVal());

(!pseudoGene.empty()) {

(!pseudoGene.empty()) {

&

= mf.

(

);

(!

.

()) {

(

.CanGetActivity() && !

.GetActivity().empty()) {

& go_component = mf.

(

);

(!go_component.empty()) {

& ext = mf.

();

(!ext.IsSetType() || !ext.GetType().IsStr()) {

(ext.GetType().GetStr() ==

) {

& goFields = ext.

();

(

& goField: goFields) {

(!goField->IsSetLabel() || !goField->GetLabel().IsStr()) {

& goLabel = goField->GetLabel().GetStr();

(goLabel ==

&& goField->IsSetData()

&& goField->GetData().IsFields()) {

& fields = goField->GetData().GetFields();

vector<string> goStrings;

(goLabel ==

&& goField->IsSetData()

&& goField->GetData().IsFields()) {

& fields = goField->GetData().GetFields();

vector<string> goStrings;

(goLabel ==

&& goField->IsSetData()

&& goField->GetData().IsFields()) {

& fields = goField->GetData().GetFields();

vector<string> goStrings;

(!goIds.empty()) {

record.

(

, vector<string>(goIds.begin(), goIds.end()));

}

(ext.GetType().GetStr() ==

) {

(field_label.

() && field_label.

() ==

) {

(

& goField: goFields) {

(!goField->IsSetLabel() || !goField->GetLabel().IsStr()) {

& goLabel = goField->GetLabel().GetStr();

(goLabel ==

&& goField->IsSetData()

&& goField->GetData().IsFields()) {

& fields = goField->GetData().GetFields();

vector<string> goStrings;

(goLabel ==

&& goField->IsSetData()

&& goField->GetData().IsFields()) {

& fields = goField->GetData().GetFields();

vector<string> goStrings;

(goLabel ==

&& goField->IsSetData()

&& goField->GetData().IsFields()) {

& fields = goField->GetData().GetFields();

vector<string> goStrings;

(!goIds.empty()) {

record.

(

, vector<string>(goIds.begin(), goIds.end()));

(

.CanGetEc()) {

list<string> ec =

.GetEc();

, vector<string>(ec.begin(), ec.end()));

( CSeq_feat::TQual::const_iterator cit = quals.begin();

acceptableTranscriptTypes.end();

pMissingTranscript->

(

);

saeh.

(*pMissingTranscript);

.FeatTree().AddFeature(tf);

(sublocs.size() == 1) {

&

= *sublocs.front();

lastStart =

.GetFrom();

(

itComp = sublocs.begin()++; itComp != sublocs.end(); itComp++) {

& comp = **itComp;

compStart = comp.GetFrom();

lastStart = compStart;

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

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

virtual bool xAssignFeatureAttributeProduct(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

static bool IsTranscriptType(const CMappedFeat &)

bool xAssignFeatureAttributeIsOrdered(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool WriteAlign(const CSeq_align &, const string &asmblyName="", const string &asmblyAccession="") override

Write a Seq-align object.

virtual bool xAssignFeatureAttributeNote(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureType(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeFunction(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureAttributeProteinId(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureAttributeDbxref(CGffFeatureRecord &, CGffFeatureContext &, const string &label, const CMappedFeat &)

bool xAssignFeatureAttributeMapLoc(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeature(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeRptFamily(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeCodeBreak(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool WriteAnnot(const CSeq_annot &annot, const string &asmblyName="", const string &asmblyAccession="") override

Write a trailer marking the end of a parsing context.

static bool HasAccaptableTranscriptParent(CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureAttributePseudo(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool x_WriteAssemblyInfo(const string &, const string &)

virtual bool xAssignFeatureStrand(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xWriteAllChildren(CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureAttributesFormatIndependent(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool x_WriteAnnot(const CSeq_annot &)

CGff2Writer(CScope &scope, CNcbiOstream &ostr, unsigned int flags=fNormal)

Constructor.

bool WriteBioseqHandle(CBioseq_Handle bsh, const string &asmblyName="", const string &asmblyAccession="") override

Write Bioseq contained in given handle Essentially, will write all features that live on the given Bi...

virtual bool x_WriteAlign(const CSeq_align &)

virtual bool xAssignFeatureAttributeRibosomalSlippage(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeGeneBiotype(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xGeneratingMissingTranscripts() const

virtual bool xWriteFeature(CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributePseudoGene(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool x_WriteSeqAnnotHandle(CSeq_annot_Handle)

bool xAssignFeatureAttributeEcNumbers(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributesGoMarkup(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool x_WriteSeqEntryHandle(CSeq_entry_Handle)

virtual bool xAssignFeatureSeqId(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeModelEvidence(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureEndpoints(CGffFeatureRecord &record, CGffFeatureContext &, const CMappedFeat &mapped_feat)

virtual bool xAssignFeatureAttributePartial(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool WriteSeqAnnotHandle(CSeq_annot_Handle sah, const string &asmblyName="", const string &asmblyAccession="") override

Write Seq-annot contained in given handle Essentially, write out embedded feature table.

virtual bool xAssignFeatureMethod(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureAttributesQualifiers(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool WriteHeader() override

Write a file header identifying the file content as GFF version 2.

virtual bool xAssignFeatureAttributes(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureAttributesFormatSpecific(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool WriteSeqEntryHandle(CSeq_entry_Handle seh, const string &asmblyName="", const string &asmblyAccession="") override

Write Seq-entry contained in a given handle.

virtual bool xAssignFeatureAttributesGene(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeOldLocusTag(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureAttributeTranslationTable(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool x_WriteBioseqHandle(CBioseq_Handle)

bool xAssignFeatureAttributeExonNumber(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeExperiment(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool x_WriteSequenceHeader(CBioseq_Handle)

virtual bool xAssignFeatureBasic(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureScore(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeaturePhase(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

static bool xIntervalsNeedPartNumbers(const list< CRef< CSeq_interval >> &)

CMappedFeat xGenerateMissingTranscript(CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeException(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

void SetSeqId(const string &)

void SetLocation(unsigned int, unsigned int, ENa_strand=objects::eNa_strand_unknown)

void SetType(const string &)

void SetMethod(const string &)

void SetStrand(ENa_strand)

bool SetAttribute(const string &, const string &)

void SetScore(const CScore &)

bool SetAttributes(const string &, const vector< string > &)

bool AddAttribute(const string &, const string &)

bool ShouldInheritPseudo() const

void AssignShouldInheritPseudo(bool shouldInheritPseudo)

feature::CFeatTree & FeatTree()

bool HasSequenceBioSource() const

CMappedFeat FindBestGeneParent(const CMappedFeat &mf)

bool IsSequenceGenomicRecord() const

void SetGbKeyFrom(CMappedFeat)

void SetEndpoints(unsigned int start, unsigned int stop, ENa_strand strand)

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

T & Get(void)

Create the variable if not created yet, return the reference.

bool IsLegalQualifier(EQualifier qual) const

Test wheather a certain qualifier is legal for the feature.

namespace ncbi::objects::

static bool IsTransspliced(const CSeq_feat &feature)

static bool GetTrnaAntiCodon(const CTrna_ext &, string &)

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

static bool IsLocationOrdered(const CSeq_loc &)

static bool GetDbTag(const CDbtag &, string &)

static bool GetStringForModelEvidence(CMappedFeat mf, string &mestr)

static bool GetCodeBreak(const CCode_break &, string &)

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

static ENa_strand GetEffectiveStrand(const CSeq_interval &)

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

static bool GetTrnaCodons(const CTrna_ext &, string &)

static bool GetTrnaProductName(const CTrna_ext &, string &)

Defines and provides stubs for a general interface to a variety of file formatters.

virtual const CRange< TSeqPos > & GetRange(void) const

bool GetBestId(CSeq_id_Handle idh, CScope &scope, string &best_id) const

virtual SAnnotSelector & SetAnnotSelector(void)

unique_ptr< CGenbankIdResolve > mpIdResolve

#define MAKE_CONST_SET(name, type,...)

static const struct name_t names[]

static const char location[]

static string s_GetDbxrefFromProduct(const CMappedFeat &mf)

const CGene_ref & sGetClosestGeneRef(CGffFeatureContext &fc, const CMappedFeat &mf)

static auto s_GffIdFormatter

const TResidue codons[4][4]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

@ eContent

Untagged human-readable accession or the like.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

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 GetFeatureGeneBiotypeFaster(feature::CFeatTree &ft, CMappedFeat mf, string &biotype)

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_ForceAcc

return only an accession based seq-id

@ eGetId_ForceGi

return only a gi-based seq-id

void RemoveSeq_annot(const CSeq_annot_Handle &annot)

Revoke Seq-annot previously added using AddSeq_annot().

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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.

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add Seq-annot, return its CSeq_annot_Handle.

CBioseq_Handle GetObjectHandle(const CBioseq &bioseq, EMissing action=eMissing_Default)

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

bool IsSetExcept(void) const

bool GetExcept(void) const

bool GetPseudo(void) const

TClass GetClass(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

bool IsSetDbxref(void) const

const CSeqFeatData & GetData(void) const

const CProt_ref * GetProtXref(void) const

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

bool IsSetExcept_text(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

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

CSeq_feat_EditHandle AddFeat(const CSeq_feat &new_obj) const

bool IsSetProduct(void) const

const CUser_object & GetExt(void) const

const string & GetExcept_text(void) const

bool IsSetClass(void) const

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeq_feat::TDbxref & GetDbxref(void) const

bool IsSetQual(void) const

CSeqFeatData::ESubtype GetFeatSubtype(void) const

CSeqFeatData::E_Choice GetFeatType(void) const

const CGene_ref * GetGeneXref(void) const

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

bool IsSetPseudo(void) const

const CSeq_feat::TQual & GetQual(void) const

bool IsSetExt(void) const

bool IsSetData(void) const

CSeq_id_Handle GetProductId(void) const

bool IsSetPartial(void) const

const CSeq_loc & GetLocation(void) const

bool GetPartial(void) const

bool IsMapped(void) const

Fast way to check if mapped feature is different from the original one.

const CSeq_loc & GetProduct(void) const

SAnnotSelector & SetSortOrder(ESortOrder sort_order)

Set sort order of annotations.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

@ eSortOrder_Normal

default - increasing start, decreasing length

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.

bool NotEmpty(void) const

TThisType IntersectionWith(const TThisType &r) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetMaploc(void) const

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

const TMaploc & GetMaploc(void) const

Get the Maploc member data.

bool IsStr(void) const

Check if variant Str is selected.

const TData & GetData(void) const

Get the Data member data.

const TFields & GetFields(void) const

Get the variant data.

bool IsFields(void) const

Check if variant Fields is selected.

bool IsSetLabel(void) const

field label Check if a value has been assigned to Label data member.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

bool IsSetData(void) const

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

vector< CRef< CUser_field > > TData

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

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

const TVal & GetVal(void) const

Get the Val member data.

void ResetPartial(void)

Reset Partial data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

E_Choice

Choice variants.

void SetExcept(TExcept value)

Assign a value to Except data member.

bool IsGene(void) const

Check if variant Gene is selected.

const TCode & GetCode(void) const

Get the Code member data.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetQual(void) const

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

const TGene & GetGene(void) const

Get the variant data.

TPartial GetPartial(void) const

Get the Partial member data.

void SetExcept_text(const TExcept_text &value)

Assign a value to Except_text data member.

const TProt & GetProt(void) const

Get the variant data.

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

const TRna & GetRna(void) const

Get the variant data.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

bool IsSetCode_break(void) const

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

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_genbank

converted genbank

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

constexpr bool empty(list< Ts... >) noexcept

Static variables safety - create on demand, destroy on application termination.

static CS_CONTEXT * context

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