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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/citation_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/flatfile/citation.cpp Source File

&(

->GetEquiv());

(

& pub :

->Get()) {

(pub->IsGen() && pub->GetGen().IsSetSerial_number()) {

= pub->GetGen().GetSerial_number();

(

->IsEquiv()) {

(

& cur_pub :

->GetEquiv().Get()) {

(cur_pub->IsGen() && cur_pub->GetGen().IsSetSerial_number()) {

= cur_pub->GetGen().GetSerial_number();

(

& descr : descrs) {

(descr->IsPub()) {

pubs.push_back(pub_info);

(

& annot : annots) {

(! annot->IsSetData() || ! annot->GetData().IsFtable())

(

& feat : annot->GetData().GetFtable()) {

(feat->IsSetData()) {

(feat->IsSetLocation())

= feat->GetLocation().GetId();

(feat->GetData().IsPub()) {

pub_info.

(&feat->GetData().GetPub().GetPub());

pubs.push_back(pub_info);

}

(feat->GetData().IsImp() && feat->IsSetCit()) {

& pub_set = feat->GetCit();

(

& pub : pub_set.

()) {

pubs.push_back(pub_info);

* pub =

;

(

& cur_pub : pub_equiv->

()) {

(cur_pub->IsMuid() || cur_pub->IsPmid()) {

(new_pub.

()) {

new_pub->

(*cur_pub);

new_pub_equiv->

().push_back(new_pub);

new_pub->

(*cur_pub);

new_pub_equiv->

().push_back(new_pub);

new_pub->

(*new_pub_equiv);

pubs.push_back(new_pub);

(! equiv_pubs.empty())

pub = *equiv_pubs.begin();

pub = pub_info.

();

pubs.push_back(new_pub);

(pub && pub->

()) {

(equiv_pubs.size() > 1) {

TPubList::const_iterator cur_pub = equiv_pubs.begin();

pubs.push_back(new_pub);

pubs.push_back(new_pub);

pubs.push_back(new_pub);

(

& annot : annots) {

(! annot->IsSetData() || ! annot->GetData().IsFtable())

(

& feat : annot->SetData().SetFtable()) {

(feat->IsSetQual()) {

(TQualVector::iterator qual = quals.begin(); qual != quals.end();) {

((*qual)->IsSetQual() && (*qual)->GetQual() ==

) {

qual = quals.erase(qual);

(

& pub : pubs) {

(pub.GetSerial() == ser_num) {

(bioseq && pub.GetBioseq() && bioseq != pub.GetBioseq())

(! cit_pubs.empty())

feat->SetCit().SetPub().swap(cit_pubs);

std::vector<CPubInfo> pubs;

(

& entry : seq_entries) {

(bio_set->IsSetDescr())

(bio_set->IsSetAnnot())

(bioseq->IsSetDescr())

(bioseq->IsSetAnnot())

(

& entry : seq_entries) {

(bio_set->IsSetAnnot())

(pubs, bio_set->SetAnnot(),

);

(bioseq->IsSetAnnot())

(pubs, bioseq->SetAnnot(), &(*bioseq));

void ProcessCitations(TEntryList &seq_entries)

static void FindCitInDescr(std::vector< CPubInfo > &pubs, const TSeqdescList &descrs, const CBioseq *bioseq)

void SetMinimumPub(const CPubInfo &pub_info, TPubList &pubs)

static void ProcessCit(const std::vector< CPubInfo > &pubs, CBioseq::TAnnot &annots, const CBioseq *bioseq)

static void FindCitInFeats(std::vector< CPubInfo > &pubs, const CBioseq::TAnnot &annots)

static int GetCitSerialFromQual(const CGb_qual &qual)

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

const objects::CBioseq * bioseq_

const objects::CPub_equiv * GetPubEquiv() const

const objects::CPub * GetPub() const

const objects::CPub_equiv * pub_equiv_

void SetPubEquiv(const objects::CPub_equiv *pub_equiv)

void SetBioseq(const objects::CBioseq *bioseq)

void SetPub(const objects::CPub *pub)

const objects::CPub * pub_

bool GetLabel(string *label, ELabelType type=eContent, TLabelFlags flags=0, ELabelVersion version=eLabel_DefaultVersion) const

Concatenate a label for this pub to label.

Template class for iteration on objects of class C (non-medifiable version)

Template class for iteration on objects of class C.

@ fLabel_Unique

Append a unique tag [V1].

#define ERR_QUALIFIER_NoRefForCiteQual

list< CRef< objects::CSeq_entry > > TEntryList

std::list< CRef< objects::CPub > > TPubList

std::list< CRef< objects::CSeqdesc > > TSeqdescList

int fta_atoi(string_view sv)

#define FtaErrPost(sev, level,...)

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

Set object to copy of another one.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

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 Empty(void) const THROWS_NONE

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

char Char

Alias for char.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static const char label[]

bool IsSetSerial_number(void) const

for GenBank style references Check if a value has been assigned to Serial_number data member.

void SetCit(const TCit &value)

Assign a value to Cit data member.

bool IsPmid(void) const

Check if variant Pmid is selected.

Tdata & Set(void)

Assign a value to data member.

const TPub & GetPub(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

TEquiv & SetEquiv(void)

Select the variant.

TGen & SetGen(void)

Select the variant.

const TGen & GetGen(void) const

Get the variant data.

bool IsMuid(void) const

Check if variant Muid is selected.

bool IsGen(void) const

Check if variant Gen is selected.

const TVal & GetVal(void) const

Get the Val member data.

list< CRef< CSeq_annot > > TAnnot

std::vector< CRef< objects::CGb_qual > > TQualVector

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