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NCBI C++ ToolKit: src/objtools/writers/gff3_writer.cpp Source File

& wrapSize,

& wrapPoint)

wrapSize = wrapPoint = 0;

(subInts.empty()) {

(bioH.CanGetInst_Topology()) {

&

= *subInts.front();

(!

.CanGetStrand()) {

frontStrand =

.GetStrand();

pCompare = subInts.begin()++;

(pCompare != subInts.end()) {

& interval = **pCompare;

(!interval.CanGetStrand() || interval.GetStrand() != frontStrand) {

(!bioH.CanGetInst_Length()) {

wrapSize = bioH.GetInst_Length();

subInts.back()->GetFrom() :

subInts.front()->GetFrom();

vector<CRef<CScore> > SCORES;

SCORES& scoresFrom = alignFrom.

();

(SCORES::const_iterator itFrom = scoresFrom.begin();

itFrom != scoresFrom.end(); ++itFrom) {

& scoreFrom = **itFrom;

& keyFrom = scoreFrom.

().

();

SCORES& scoresTo = alignTo.

();

SCORES::const_iterator itTo;

(itTo = scoresTo.begin(); itTo != scoresTo.end(); ++itTo) {

& scoreTo = **itTo;

& keyTo = scoreTo.

().

();

(keyTo == keyFrom) {

(itTo == scoresTo.end()) {

alignTo.

().push_back(*itFrom);

SCORES& scoresTo = alignFrom.

();

SCORES::const_iterator itTo;

(itTo = scoresTo.begin(); itTo != scoresTo.end(); ++itTo) {

& scoreTo = **itTo;

(idTo.

(idFrom)) {

(itTo == scoresTo.end()) {

alignTo.

().push_back(*itFrom);

* strProtMatch =

;

* strEstMatch =

;

* strCdnaMatch =

;

sortAlignments) :

m_sDefaultMethod(

),

m_SortAlignments(sortAlignments),

sortAlignments) :

m_SortAlignments(

),

& strAssName,

& strAssAcc )

(

);

+= (

+ e.

() +

);

& alignId)

cerr <<

<< endl;

(

.

()) {

(CSeq_align::TId::const_iterator it = ids.begin();

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

((*it)->IsStr()) {

= (*it)->GetStr();

(

.

()) {

& alignId)

list<CRef<CSeq_align> > ALIGNS;

(ALIGNS::const_iterator cit =

.begin(); cit !=

.end(); ++cit) {

& alignId)

list<CRef<CSpliced_exon> > EXONS;

(EXONS::const_iterator cit = exons.begin(); cit != exons.end(); ++cit) {

);

record.

(

);

(!genomicH || !productH) {

record.

(seqStart, seqStop, seqStrand);

list<CRef<CScore> > SCORES;

(SCORES::const_iterator cit = scores.begin(); cit != scores.end();

tgtWidth = isProteinProd ? 3 : 1;

list<CRef<CSpliced_exon_chunk> > CHUNKS;

CHUNKS& chunks = exon.

();

(CHUNKS::const_iterator cit = chunks.begin(); cit != chunks.end(); ++cit) {

(chunk.

()) {

del_length = chunk.

()/tgtWidth;

(del_length > 0) {

forward_shift = chunk.

()%tgtWidth;

(forward_shift > 0) {

reverse_shift = chunk.

()%tgtWidth;

(reverse_shift > 0) {

insert_length = chunk.

()/tgtWidth;

(insert_length > 0) {

tgtWidth = isProteinProd ? 3 : 1;

seqStrand =

;

target +=

+ seqStart;

target +=

+ seqStop;

target +=

+ seqStrand;

vector<CRef<CScore> > SCORES;

SCORES& scores = align.

();

(SCORES::const_iterator cit = scores.begin(); cit != scores.end();

& alignId)

);

(std::exception&) {};

vector<CRef<CScore> > SCORES;

SCORES& scores = denseSeg.

();

(SCORES::const_iterator cit = scores.begin(); cit != scores.end();

(std::exception&) {};

(std::exception&) {};

(std::exception&) {};

(std::exception&) {};

(start2 < 0 && start_seg < numSegs) {

start2 = alnMap.

(0, start_seg++);

stop_seg = numSegs-1;

(stop2 < 0 && stop_seg >= 0) {

stop2 = alnMap.

(0, stop_seg--);

(start2, stop2);

stop2 += alnMap.

(start_seg-1)-1;

stop2 += alnMap.

(stop_seg+1)-1;

tgtWidth;

(std::exception&) {};

(

seg = 0; seg < numSegs; ++seg) {

reverse_shift = tgtPiece.

()%tgtWidth;

(reverse_shift > 0) {

insert_length = tgtPiece.

()/tgtWidth;

(insert_length > 0) {

del_length = srcPiece.

()/tgtWidth;

(del_length > 0) {

forward_shift = srcPiece.

()%tgtWidth;

(forward_shift > 0) {

(

(tgtFlags, srcFlags)) {

srcRow)

seqStart = alnMap.

(srcRow);

seqStop = alnMap.

(srcRow);

record.

(seqStart, seqStop, seqStrand);

srcRow)

<<

<<

;

<<

<<

;

<<

<<

;

<<

<<

;

;

<<

<<

<<

<< start <<

<< stop <<

;

base_url =

;

<<

<< base_url <<

<< tax_id <<

;

<<

<< base_url <<

<< orgname <<

;

(!align1 && align2) {

((align1 && !align2) ||

(!align1 && !align2) ) {

make_key = [](

pair<CConstRef<CSeq_align>,

>& p,

& scope) {

alignId = p.second;

subject_accession;

target_accession;

(CSeq_align::TId::const_iterator it = ids.begin();

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

((*it)->IsStr()) {

(*it)->GetStr();

((range.

() <= pos) &&

(range.

() >= pos)) {

(!cc->IsSetAnnot()) {

& annots = cc->

();

(annots.empty()) {

&

= cc->GetAnnot().front();

& display_range =

();

(

align_it(bsh, display_range, sel); align_it; ++align_it) {

alignCache.push_back(make_pair(pAlign,alignId));

(

alignPair : alignCache) {

(*(alignPair.first), alignPair.second);

align_it(bsh, display_range, sel);

feature::CFeatTree& featTree = fc.

();

vector<CMappedFeat> vChildren;

featTree.GetChildrenTo(mf, vChildren);

(

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

& display_range =

();

feat_iter(bsh, display_range, sel);

(

&

: fc.

().GetChildren(root) ) {

(

.IsSetProduct() ) {

(

prod_id =

.GetProduct().GetId() ) {

vector<CMappedFeat> vRoots = fc.

().GetRootFeatures();

(

& bh : bhs ) {

( bh && bh.IsProtein() ) {

all_prot_loc->

().Set().push_back(loc);

pre_load_prots.push_back(bh);

( !pre_load_prots.empty() ) {

(

pit = vRoots.begin(); pit != vRoots.end(); ++pit) {

& display_range =

();

feat_iter(bsh, display_range, sel);

);

);

cerr <<

<< endl;

cerr <<

<< e.

() << endl;

(isTransSpliced) {

inPoint, outPoint;

list< CRef< CSeq_interval > >& sublocs = PackedInt.

().

();

parentId = pRna->

();

list< CRef< CSeq_interval > >::const_iterator it;

wrapSize(0), wrapPoint(0);

(!isTransSpliced) {

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

pChild->

(subint, wrapSize, wrapPoint);

(isTransSpliced){

rnaId = pRna->

();

list< CRef< CSeq_interval > >& sublocs = PackedInt.

().

();

wrapSize(0), wrapPoint(0);

(!isTransSpliced) {

(

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

pChild->

(subint, wrapSize, wrapPoint);

(!me || !me->

(

)) {

method(

);

(method ==

) {

seqStart(0);

seqStop(0);

seqStart, seqStop)) {

(seqStart < bstop) {

(seqStop < bstop) {

(seqStart < bstart) {

(seqStop < bstart) {

vector<string> acceptedClasses = {

,

,

ncrna_class = mf.

(

);

(ncrna_class.empty()) {

(ncrna_class ==

) {

(ncrna_class.empty()) {

cit = std::find(

acceptedClasses.begin(), acceptedClasses.end(), ncrna_class);

(cit == acceptedClasses.end()) {

recomb_class = mf.

(

);

(!recomb_class.empty() && recomb_class !=

) {

cit = std::find(validClasses.begin(), validClasses.end(), recomb_class);

(cit == validClasses.end()) {

note = recomb_class;

regulatory_class = mf.

(

);

(!regulatory_class.empty() && regulatory_class !=

) {

cit = std::find(validClasses.begin(), validClasses.end(), regulatory_class);

(cit == validClasses.end()) {

note = regulatory_class;

(!note.empty()) {

(!comment.empty()) {

note +=

+ comment;

(!note.empty()) {

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

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

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

) {

record.

(

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

transcript_id;

record.

(

, transcript_id);

vector<string>

;

(!

.IsSetExt()) {

,

,

,

,

,

,

,

,

,

,

(

& qual: quals) {

(!qual->IsSetQual() || !qual->IsSetVal()) {

= qual->GetQual();

&

= qual->GetVal();

(

==

) {

(

==

) {

(

==

) {

gff3_attributes.find(

) == gff3_attributes.end()) {

.SetInt().SetFrom(0);

);

(!display_range.IsWhole()) {

pLoc->

(*sequence::CFeatTrim::Apply(*pLoc, display_range));

list< CRef< CSeq_interval > >& sublocs = pLoc->

().Set();

list< CRef<CSeq_interval> >::iterator it;

list< CRef<CSeq_interval> >::iterator it_ceil=sublocs.end();

list< CRef<CSeq_interval> >::iterator it_floor=sublocs.end();

(sublocs.size() > 1) {

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

(it_floor != sublocs.end() && it_ceil != sublocs.end()) {

( it_ceil != sublocs.end() && it_floor != sublocs.end() ) {

(*it_ceil)->

( (*it_ceil)->GetTo() + (*it_floor)->GetTo() + 1 );

sublocs.erase(it_floor);

defaultId(

);

ids = bsh.

();

= ids.front();

method(

);

seqStart = 0;

record.

(seqStart, seqStop, seqStrand);

vector<CRef<CDbtag> > DBTAGS;

DBTAGS& tags = orgRef.

();

(DBTAGS::const_iterator cit = tags.begin(); cit != tags.end(); ++cit) {

vector<string> ignoredKeys = {

list<CRef<COrgMod> > MODS;

MODS& mods = orgName.

();

(MODS::const_iterator cit = mods.begin(); cit != mods.end(); ++cit) {

ignoredIt = std::find(ignoredKeys.begin(), ignoredKeys.end(),

);

(ignoredIt != ignoredKeys.end()) {

list<CRef<CSubSource> >

;

(SUBS::const_iterator cit = subs.begin(); cit != subs.end(); ++cit) {

pCds->

(parentOverride->Id());

(display_range.

()) {

iPhase =

(sequence::CFeatTrim::GetCdsFrame(feature, display_range)-1, 0);

iTotSize = -iPhase;

list< CRef< CSeq_interval > > sublocs( PackedInt.

().

() );

list< CRef< CSeq_interval > >::const_iterator it;

cdsId = pCds->

();

wrapSize(0), wrapPoint(0);

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

pExon->

(subint, wrapSize, wrapPoint);

iTotSize = (iTotSize + subint.

());

posInCodon = (3+iTotSize)%3;

iPhase = posInCodon ? 3-posInCodon : 0;

list< CRef< CSeq_interval > >& sublocs = PackedInt.

().

();

parentId = pRna->

();

list< CRef< CSeq_interval > >::const_iterator it;

wrapSize(0), wrapPoint(0);

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

pChild->

(subint, wrapSize, wrapPoint);

parentId = pSegment->

();

list< CRef< CSeq_interval > >& sublocs = PackedInt.

().

();

wrapSize(0), wrapPoint(0);

(

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

pChild->

(subint, wrapSize, wrapPoint);

{

,

},

{

,

},

{

,

},

{

,

},

fixupIt = proteinOnCdsFixups.

(pRecord->

());

(fixupIt != proteinOnCdsFixups.

()) {

pRecord->

(fixupIt->second);

parentId = parentIt->second->Id();

(

.IsSetName()) {

& packedInt = *pMappedLoc;

(packedInt.IsPacked_int() && packedInt.GetPacked_int().CanGet());

list< CRef< CSeq_interval > > sublocs( packedInt.GetPacked_int().Get() );

wrapSize(0), wrapPoint(0);

(

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

pExon->

(subint, wrapSize, wrapPoint);

seqLength )

(sublocs.size() == 1) {

curInterval = 1;

(

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

pChild->SetLocation(subint, 0);

pChild->SetAttribute(

, part);

(

& parent_type : parent_types) {

mf, parent_type, &fc.

());

+ record.

() +

);

<<

<<

;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool WriteAlignments(CAlign_CI first)

TSegTypeFlags GetSegType(TNumrow row, TNumseg seg, int offset=0) const

TSignedSeqPos GetStart(TNumrow row, TNumseg seg, int offset=0) const

const CSeq_id & GetSeqId(TNumrow row) const

TDim GetNumRows(void) const

unsigned int TSegTypeFlags

TSeqPos GetLen(TNumseg seg, int offset=0) const

const CDense_seg & GetDenseg(void) const

TSeqPos GetSeqStop(TNumrow row) const

TSignedRange GetRange(TNumrow row, TNumseg seg, int offset=0) const

int StrandSign(TNumrow row) const

TNumseg GetNumSegs(void) const

TSeqPos GetSeqStart(TNumrow row) const

CSeq_annot_Handle GetAnnot(void) const

const string & GetTaxname(void) const

string GetRepliconName(void) const

bool IsSetOrgname(void) const

CRef< CDense_seg > FillUnaligned() const

Create a new dense-seg with added all unaligned pieces (implicit inserts), if any,...

const TWidths & GetWidths(void) const

bool GetBestId(CSeq_id_Handle, CScope &, string &) const

CWriterBase implementation that formats Genbank objects as plain GFF files.

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

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

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

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

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

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

CMappedFeat xGenerateMissingTranscript(CGffFeatureContext &, const CMappedFeat &)

void SetRecordId(const string &recordId)

void SetParent(const string &parent)

void SetRecordId(const string &recordId)

virtual bool xAssignAlignmentSplicedLocation(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

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

Write a raw Seq-align to the internal output stream.

virtual bool xWriteSource(CBioseq_Handle)

bool xAssignAlignmentSplicedType(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool xWriteFeatureRecords(const CGffFeatureRecord &, const CSeq_loc &, unsigned int)

CBioseq_Handle m_BioseqHandle

bool WriteFooter() override

Write a file trailer.

bool xAssignAlignmentSpliced(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

bool xWriteFeature(CFeat_CI feat_it) override

bool xAssignAlignmentSplicedMethod(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool xAssignFeatureAttributeParentGene(CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xWriteAlign(const CSeq_align &, const string &="") override

virtual bool xWriteRecord(const CGffBaseRecord &)

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

virtual bool xWriteFeatureGeneric(CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignAlignmentSplicedTarget(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool xWriteFeatureCDJVSegment(CGffFeatureContext &, const CMappedFeat &)

virtual bool xWriteFeatureGene(CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeParent(CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignSourceType(CGff3SourceRecord &)

unsigned int m_uPendingCdsId

unsigned int m_uPendingMrnaId

list< pair< CConstRef< CSeq_align >, string > > TAlignCache

virtual bool xAssignAlignmentDensegScores(CGffAlignRecord &, const CAlnMap &, unsigned int)

TRegionMapNew m_RegionMapNew

virtual bool xWriteAlignDenseg(const CSeq_align &, const string &="")

virtual bool xWriteSequenceHeader(CBioseq_Handle)

virtual bool xWriteFeatureCds(CGffFeatureContext &, const CMappedFeat &)

virtual bool xWriteAlignDisc(const CSeq_align &, const string &="")

virtual bool xWriteSequence(CBioseq_Handle)

virtual void x_SortAlignments(TAlignCache &alignCache, CScope &scope)

bool xAssignFeatureAttributeTranscriptId(CGffFeatureRecord &, const CMappedFeat &)

virtual bool xAssignFeatureAttributeParentCds(CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignFeatureAttributeParentVDJsegmentCregion(CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

TFeatureMap m_PrernaMapNew

bool xAssignAlignmentDensegType(CGffAlignRecord &, const CAlnMap &, unsigned int)

bool xAssignAlignmentDensegMethod(CGffAlignRecord &, const CAlnMap &, unsigned int)

virtual bool xAssignAlignmentSplicedGap(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

bool xAssignFeatureAttributeName(CGffFeatureRecord &, const CMappedFeat &)

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

bool WriteHeader() override

Write a file header.

virtual bool xWriteFeatureRna(CGffFeatureContext &, const CMappedFeat &)

virtual bool xAssignAlignmentDensegTarget(CGffAlignRecord &, const CAlnMap &, unsigned int)

virtual bool xWriteProteinFeature(CGffFeatureContext &, const CMappedFeat &)

bool xAssignAlignmentDenseg(CGffAlignRecord &, const CAlnMap &, unsigned int)

virtual bool xWriteAlignSpliced(const CSeq_align &, const string &="")

bool xAssignSourceAttributesOrgMod(CGff3SourceRecord &, const CBioSource &)

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

unique_ptr< CGffIdGenerator > m_pIdGenerator

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

virtual bool xAssignAlignmentDensegSeqId(CGffAlignRecord &, const CAlnMap &, unsigned int)

bool xSplicedSegHasProteinProd(const CSpliced_seg &spliced)

virtual bool xAssignFeatureAttributeParentMrna(CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignSourceAttributeDbxref(CGff3SourceRecord &, const CBioSource &)

bool xAssignSourceAttributeGbKey(CGff3SourceRecord &)

bool xAssignSourceAttributes(CGff3SourceRecord &, CBioseq_Handle)

bool xAssignAlignmentSplicedAttributes(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual SAnnotSelector & xSetJunkFilteringAnnotSelector()

bool xAssignSourceAttributeIsCircular(CGff3SourceRecord &, CBioseq_Handle)

bool xAssignAlignmentDensegGap(CGffAlignRecord &, const CAlnMap &, unsigned int)

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

bool xAssignAlignmentSplicedPhase(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool xWriteProteinSequence(CBioseq_Handle)

bool xAssignSourceMethod(CGff3SourceRecord &, CBioseq_Handle)

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

bool x_WriteBioseqHandle(CBioseq_Handle) override

virtual bool xAssignAlignmentSplicedSeqId(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

bool xWriteAllChildren(CGffFeatureContext &, const CMappedFeat &) override

void SetBioseqHandle(CBioseq_Handle bsh)

virtual bool x_WriteFeatureContext(CGffFeatureContext &)

bool xAssignSourceAttributesBioSource(CGff3SourceRecord &, CBioseq_Handle)

bool xAssignSourceAttributeName(CGff3SourceRecord &, const CBioSource &)

bool xAssignFeatureAttributeID(CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool xWriteNucleotideFeature(CGffFeatureContext &, const CMappedFeat &)

bool xAssignSource(CGff3SourceRecord &, CBioseq_Handle)

virtual bool xPassesFilterByViewMode(CBioseq_Handle)

TFeatureMap m_VDJsegmentCregionMapNew

virtual bool xAssignAlignmentScores(CGffAlignRecord &, const CSeq_align &)

unsigned int m_uPendingAlignId

virtual bool xAssignFeatureAttributeParentpreRNA(CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignSourceAttributeMolType(CGff3SourceRecord &, CBioseq_Handle)

bool x_WriteSeqAnnotHandle(CSeq_annot_Handle) override

bool xAssignSourceSeqId(CGff3SourceRecord &, CBioseq_Handle)

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

bool xAssignSourceEndpoints(CGff3SourceRecord &, CBioseq_Handle)

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

bool xAssignFeatureAttributeNcrnaClass(CGffFeatureRecord &, const CMappedFeat &)

bool xAssignFeatureAttributeDbxref(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

virtual bool xAssignAlignmentDensegLocation(CGffAlignRecord &, const CAlnMap &, unsigned int)

void xWriteAlignment(const CGffAlignRecord &record)

unsigned int m_uPendingTrnaId

unsigned int m_uPendingGenericId

virtual bool xWriteNucleotideSequence(CBioseq_Handle)

virtual bool xAssignAlignmentSplicedScores(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool xWriteFeatureProtein(CGffFeatureContext &, const CMappedFeat &, const CMappedFeat &)

virtual bool xWriteNucleotideFeatureTransSpliced(CGffFeatureContext &, const CMappedFeat &)

bool xAssignSourceAttributeGenome(CGff3SourceRecord &, const CBioSource &)

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

bool xAssignSourceAttributesSubSource(CGff3SourceRecord &, const CBioSource &)

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

virtual bool xAssignFeatureAttributeParentRegion(CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

unsigned int m_uPendingGeneId

virtual bool xWriteFeatureTrna(CGffFeatureContext &, const CMappedFeat &)

CGff3Writer(CScope &, CNcbiOstream &, unsigned int=fNormal, bool sortAlignments=false)

void AddInsertion(unsigned int)

void AddMatch(unsigned int)

void AddReverseShift(unsigned int)

void AddDeletion(unsigned int)

string StrAttributes() const

void AddForwardShift(unsigned int)

void SetPhase(unsigned int)

virtual string StrType() const

virtual string StrSeqStop() const

virtual string StrAttributes() const

const CSeq_loc & GetLocation() const

bool DropAttributes(const string &)

virtual string StrScore() const

void SetSeqId(const string &)

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

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

void SetType(const string &)

virtual string StrPhase() const

void SetMethod(const string &)

void SetStrand(ENa_strand)

bool SetAttribute(const string &, const string &)

virtual string StrSeqStart() const

void SetScore(const CScore &)

virtual string StrSeqId() const

bool AddAttribute(const string &, const string &)

virtual string StrStrand() const

bool CanGetLocation() const

virtual string StrMethod() const

void AssignShouldInheritPseudo(bool shouldInheritPseudo)

feature::CFeatTree & FeatTree()

CBioseq_Handle BioseqHandle() const

CMappedFeat FindBestGeneParent(const CMappedFeat &mf)

void InitLocation(const CSeq_loc &)

const CSeq_loc & Location() const

void SetLocation(const CSeq_interval &, unsigned int, unsigned int=0)

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

bool Match(const CObject_id &oid2) const

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

static string GetRnaTypeName(const CRNA_ref::EType rna_type)

ESubtype GetSubtype(void) const

static const vector< string > & GetRecombinationClassList()

@ eSubtype_transit_peptide

@ eSubtype_misc_structure

@ eSubtype_mobile_element

@ eSubtype_transit_peptide_aa

@ eSubtype_non_std_residue

@ eSubtype_sig_peptide_aa

@ eSubtype_mat_peptide_aa

static const vector< string > & GetRegulatoryClassList()

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

void Validate(bool full_test=false) const

namespace ncbi::objects::

TSeqPos GetLength(void) const

static bool FeatureToSoType(const CSeq_feat &, string &)

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

static bool IsTransspliced(const CSeq_feat &feature)

static void ChangeToPackedInt(CSeq_loc &loc)

static bool IsSequenceCircular(CBioseq_Handle)

static bool IsProteinSequence(CBioseq_Handle)

static bool GetSubSourceSubType(const CSubSource &, string &, string &)

static bool GetOrgModSubType(const COrgMod &, string &, string &)

static bool GetDbTag(const CDbtag &, string &)

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

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

static bool GetIdType(CBioseq_Handle, string &)

static bool IsNucleotideSequence(CBioseq_Handle)

static CConstRef< CUser_object > GetModelEvidence(CMappedFeat)

static bool GetGenomeString(const CBioSource &, string &)

static bool GetBiomol(CBioseq_Handle, string &)

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

CRange< TSeqPos > m_Range

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

virtual SAnnotSelector & SetAnnotSelector(void)

unique_ptr< CGenbankIdResolve > mpIdResolve

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

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

bool Empty(const CNcbiOstrstream &src)

static const char location[]

void sGetWrapInfo(const list< CRef< CSeq_interval > > &subInts, CGffFeatureContext &fc, unsigned int &wrapSize, unsigned int &wrapPoint)

bool s_RangeContains(const CRange< TSeqPos > &range, const TSeqPos pos)

string s_GetAlignID(const CSeq_align &align)

bool sGetMethodFromModelEvidence(const CMappedFeat &mf, string &method)

#define IS_DELETION(sf, tf)

void sx_CollectProductIds(CGffFeatureContext &fc, CScope::TIds &product_ids, const CMappedFeat &root=CMappedFeat())

bool sInheritScores(const CSeq_align &alignFrom, CSeq_align &alignTo)

string sBestMatchType(const CSeq_id &source)

static string s_GetSequenceRegionId(const CGenbankIdResolve &id_resolver, CBioseq_Handle &bsh)

#define IS_INSERTION(sf, tf)

unsigned int TSeqPos

Type for sequence locations and lengths.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

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

Set object to copy of another one.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

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

EAccessionInfo

For IdentifyAccession (below)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ eContent

Untagged human-readable accession or the like.

void SetPacked_int(TPacked_int &v)

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

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

Override Assign() to incorporate cache invalidation.

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.

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

CMappedFeat GetBestParentForFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype parent_subtype, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CMappedFeat GetBestMrnaForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

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,...

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

string GetAccessionForId(const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession string for a Seq-id.

const CBioSource * GetBioSourceForBioseq(const CBioseq_Handle &bsh)

Find a BioSource for the given Bioseq: If it's a protein then look for the source feature of the prod...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

@ eGetId_ForceAcc

return only an accession based seq-id

double GetProteinWeight(const CBioseq_Handle &handle, const CSeq_loc *location=0, TGetProteinWeight opts=0)

Handles the standard 20 amino acids and Sec and Pyl; treats Asx as Asp, Glx as Glu,...

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

TCDD_Entries GetCDDAnnots(const TIds &idhs)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< CBioseq_Handle > TBioseqHandles

vector< CTSE_Handle > TCDD_Entries

Get CDD annotations for all ids.

TBioseqHandles GetBioseqHandlesFromTSE(const TIds &ids, const CTSE_Handle &tse)

Bulk get bioseq handles for sequence withing one TSE.

vector< CSeq_id_Handle > TIds

void SetFuzzOption(TFuzzOption newOption)

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

@ eProductToLocation

Map from the feature's product to location.

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

CConstRef< CSeq_id > GetLocalIdOrNull(void) const

bool IsSetComment(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const CSeqFeatData & GetData(void) const

bool CanGetInst(void) const

TSeqPos GetBioseqLength(void) const

const CSeq_id_Handle & GetSeq_id_Handle(void) const

Get handle of id used to obtain this bioseq handle.

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

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

bool IsSetProduct(void) const

TInst_Topology GetInst_Topology(void) const

const string & GetComment(void) const

bool CanGetInst_Strand(void) const

TInst_Length GetInst_Length(void) const

CConstRef< CSeq_id > GetNonLocalIdOrNull(void) const

Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are l...

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeqFeatData::ESubtype GetFeatSubtype(void) const

CSeqFeatData::E_Choice GetFeatType(void) const

const CSeq_feat::TQual & GetQual(void) const

const TId & GetId(void) const

bool IsSetData(void) const

const TInst & GetInst(void) const

CSeq_id_Handle GetProductId(void) const

SAnnotSelector & SetSourceLoc(const CSeq_loc &loc)

Set filter for source location of annotations.

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetLimitSeqAnnot(const CSeq_annot_Handle &limit)

Limit annotations to those from the seq-annot only.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

const CSeq_loc & GetProduct(void) const

SAnnotSelector & SetResolveNone(void)

SetResolveNone() is equivalent to SetResolveMethod(eResolve_None).

CSeq_id_Handle GetLocationId(void) const

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

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

TObjectType & GetNCObject(void) const

Get object.

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

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

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

Convert int to string.

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

Convert UInt to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string URLEncode(const CTempString str, EUrlEncode flag=eUrlEnc_SkipMarkChars)

URL-encode string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

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.

const TOrg & GetOrg(void) const

Get the Org member data.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetData(void) const

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

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetDb(void) const

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

const TDb & GetDb(void) const

Get the Db member data.

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.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

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.

TType GetType(void) const

Get the Type member data.

bool IsSetExt(void) const

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

bool IsGen(void) const

Check if variant Gen is selected.

const TGen & GetGen(void) const

Get the variant data.

bool IsSetType(void) const

Check if a value has been assigned to Type 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...

const TExt & GetExt(void) const

Get the Ext member data.

const TClass & GetClass(void) const

Get the Class member data.

const TId & GetId(void) const

Get the Id member data.

const TDenseg & GetDenseg(void) const

Get the variant data.

bool IsSetProduct_type(void) const

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

TScore & SetScore(void)

Assign a value to Score data member.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

E_Choice Which(void) const

Which variant is currently selected.

TMatch GetMatch(void) const

Get the variant data.

bool IsSetId(void) const

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

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

bool IsSetScores(void) const

score for each seg Check if a value has been assigned to Scores data member.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

bool IsSetSegs(void) const

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

TDiag GetDiag(void) const

Get the variant data.

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

TMismatch GetMismatch(void) const

Get the variant data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

list< CRef< CObject_id > > TId

bool IsSetGenomic_strand(void) const

genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_str...

bool CanGetProduct_strand(void) const

Check if it is safe to call GetProduct_strand method.

const TParts & GetParts(void) const

Get the Parts member data.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

bool IsSetProduct_id(void) const

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

const TSpliced & GetSpliced(void) const

Get the variant data.

TGenomic_ins GetGenomic_ins(void) const

Get the variant data.

bool IsSetGenomic_strand(void) const

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

const TScores & GetScores(void) const

Get the Scores member data.

const TExons & GetExons(void) const

Get the Exons member data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

const Tdata & Get(void) const

Get the member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

const TScore & GetScore(void) const

Get the Score member data.

const TScores & GetScores(void) const

Get the Scores member data.

TProduct_ins GetProduct_ins(void) const

Get the variant data.

const TDisc & GetDisc(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsSetScores(void) const

scores for this exon Check if a value has been assigned to Scores data member.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Product_ins

insertion in product sequence (i.e. gap in the genomic sequence)

@ e_Diag

both sequences are represented, there is sufficient similarity between product and genomic sequences....

@ e_Genomic_ins

insertion in genomic sequence (i.e. gap in the product sequence)

@ e_Match

both sequences represented, product and genomic sequences match

@ e_Mismatch

both sequences represented, product and genomic sequences do not match

bool IsProt(void) const

Check if variant Prot is selected.

const TRegion & GetRegion(void) const

Get the variant data.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

vector< CRef< CGb_qual > > TQual

const TRna & GetRna(void) const

Get the variant data.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsSetFrame(void) const

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

void SetTo(TTo value)

Assign a value to To data member.

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool IsSetTo(void) const

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

bool CanGet(void) const

Check if it is safe to call Get method.

TTo GetTo(void) const

Get the To member data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsSetFrom(void) const

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

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

TLength GetLength(void) const

Get the Length member data.

@ e_Source

source of materials, includes Org-ref

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

std::false_type tagStrNocase

constexpr auto sort(_Init &&init)

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

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

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

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

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

bool operator()(const pair< CConstRef< CSeq_align >, string > &p1, const pair< CConstRef< CSeq_align >, string > &p2)

SCompareAlignments(CScope &scope)

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