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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/reference__item_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/format/reference_item.cpp Source File

(ESerialFirst serial_first,

is_refseq);

(affil.

()) {

}

(affil.

()) {

(

.GetMapper()) {

}

(

.GetMapper()) {

(&

), m_PubType(ePub_sub), m_Category(eSubmission),

new_pubdesc->SetFig( *new_fig );

new_pubdesc->SetMaploc( *new_maploc );

new_pubdesc->SetPoly_a( *new_poly_a );

( ! ( prev_stop + 1 >= curr_start ) ) {

( authorsSame && locationsEqual && curr_ref.

() != prev_ref.

() ) {

& curr_unique_str = curr_ref.

();

& prev_unique_str = prev_ref.

();

is_circular =

( prev_id && curr_id && prev_id->

( *curr_id ) ) {

new_loc->

( *prev_id );

prev_ref.

( new_loc );

( (same_muid || same_pmid) &&

( refs.size() < 2 ) {

(

.IsEMBL() ||

.IsDDBJ() ) {

( !

.CanGetTLSeqEntryCtx() ||

!

.GetTLSeqEntryCtx().GetCanSourcePubsBeFused() )

CReferenceItem::TReferences::iterator curr = refs.begin();

( curr != refs.end() ) {

curr = refs.erase(curr);

combine_allowed =

;

combine_allowed =

;

combine_allowed =

;

( curr != refs.begin() ) {

combine_allowed =

;

( combine_allowed ) {

curr = refs.erase(curr);

stable_sort(refs.begin(), refs.end(),

(!

.Config().IsModeDump()) {

stable_sort(refs.begin(), refs.end(),

= refs.size();

current_serial = 1;

(

= 0;

<

; ++

) {

current_serial = refs[

]->m_Serial + 1;

refs[

]->m_Serial = current_serial++;

( !ps.

() ) {

(!pub.

()) {

( !

.IsSetCit() )

(!

.IsSetJournal() && !

.IsSetDate() &&

.IsSetSerial_number() &&

.GetSerial_number() > 0) {

& pub = **it;

(pub.

()) {

= pub_unique.length();

(

> 0 && pub_unique[

- 1] ==

) {

pub_unique.resize(

);

(

.IsGenbankFormat() ||

.Config().IsFormatGBSeq() ||

.Config().IsFormatINSDSeq() ) {

(pub.

()) {

(

.IsSetSerial_number() &&

.GetSerial_number() > 0 &&

.IsSetSerial_number() &&

.GetSerial_number() == 0) {

end = cit.find_first_of(

, pos);

= cit.substr(pos, end - pos);

(

.CanGetAuthors()) {

=

;

(

>=

|| ch < '0' || ch >

)

;

(i < max && ch >=

&& ch <=

) {

(

>=

)

;

(

>=

|| ch < '0' || ch >

)

;

(i < max && ch >=

&& ch <=

) {

(

>=

)

;

not_in_press =

;

is_epublish =

;

not_in_press =

;

not_in_press =

;

((*it)->Which()) {

= (*it)->GetPubmed().Get();

= (*it)->GetMedline().Get();

& doi = (*it)->GetDoi();

(not_in_press && is_epublish) {

& pii = (*it)->GetPii();

& dbt = (*it)->GetOther();

& db = dbt.

();

(oid.

() && not_in_press && is_epublish) {

& pii = oid.

();

(

.IsSetBook()) {

}

(

.IsSetMeet()) {

(

.IsSetTitle()) {

(

.CanGetImp()) {

(

.IsStd()) {

(

.Which()) {

(!(*it)->CanGetName()) {

& name = authors.back();

authors.insert(authors.end(),

.GetMl().begin(),

.GetMl().end());

authors.insert(authors.end(),

.GetStr().begin(),

.GetStr().end());

(authors.empty()) {

ostringstream auth_line;

TStrList::const_iterator

= --(authors.end());

auth_line << separator << *it;

( ( it ==

) &&

}

(it ==

) {

separator =

;

auth = auth_line.str();

( auth.empty() ) {

= title.length() - 1;

(title[

- 1] !=

|| title[

- 2] !=

) {

title.erase(

);

& pub = **it;

( pub.

() ) {

(

.length() > 3 ) {

,

,

,

,

,

,

,

*

kDoiLink =

;

( sc_Remarks.find(comment.c_str()) == sc_Remarks.end() ) {

.push_back(comment);

( (*it)->IsGibbsq() ) {

gibbsq = (*it)->GetGibbsq();

str1 =

;

str2 =

;

.push_back(

);

( (*it)->IsArticle() ) {

( (*it)->GetArticle().GetFrom().IsJournal() ) {

(*it)->GetArticle().GetFrom().GetJournal();

!ret.

().empty() ) {

.push_back(

+ ret.

() +

);

.push_back(

);

!ret.

().empty() ) {

.push_back(

+ ret.

() +

);

.push_back(

);

!ret.

().empty() ) {

.push_back(

+ ret.

() +

);

.push_back(

);

( pubstatus ) {

.push_back(

);

.push_back(

);

( !

.Config().IsFormatGBSeq() && !

.Config().IsFormatINSDSeq() ) {

( (*it)->GetArticle().CanGetIds() ) {

hasPmidOrMuid =

;

( (*it)->IsPubmed() && (*it)->GetPubmed().Get() !=

) {

hasPmidOrMuid =

;

}

( (*it)->IsMedline() && (*it)->GetMedline().Get() !=

) {

hasPmidOrMuid =

;

( ! hasPmidOrMuid ) {

& doi = (*it)->GetDoi().Get();

<<

<< kDoiLink << doi <<

.push_back(

+ doi );

}

( (*it)->IsSub() ) {

& sub = (*it)->GetSub();

(

.Config().IsFormatGBSeq() ||

.Config().IsFormatINSDSeq() ) {

}

(y1 > y2) {

}

(m1 > m2) {

}

(day1 > day2) {

m_SerialFirst(serial_first), m_IsRefSeq(is_refseq)

LessThan::operator()

( m_SerialFirst == eSerialFirst_Yes && ref1->GetSerial() != ref2->GetSerial() ) {

ref1->GetSerial() < ref2->GetSerial();

( ref1->GetCategory() != ref2->GetCategory() ) {

ref1->GetCategory() < ref2->GetCategory();

(ref1->IsSetDate() && !ref2->IsSetDate()) {

}

(!ref1->IsSetDate() && ref2->IsSetDate()) {

! m_IsRefSeq;

(ref1->IsSetDate() && ref2->IsSetDate()) {

!(ref1->GetPMID() == ref2->GetPMID()) ) {

m_IsRefSeq ? (ref1->GetPMID() > ref2->GetPMID()) :

(ref1->GetPMID() < ref2->GetPMID());

!(ref1->GetMUID() == ref2->GetMUID()) ) {

m_IsRefSeq ? (ref1->GetMUID() > ref2->GetMUID()) :

(ref1->GetMUID() < ref2->GetMUID());

( ref1->IsJustUids() && !ref2->IsJustUids() ) {

}

( !ref1->IsJustUids() && ref2->IsJustUids() ) {

(ref1->GetReftype() != ref2->GetReftype()) {

ref1->GetReftype() < ref2->GetReftype();

auth1, auth2;

(ref1->IsSetAuthors()) {

( ! ref1->GetConsortium().empty() ) {

( ! auth1.empty() ) {

auth1 += ref1->GetConsortium();

(ref2->IsSetAuthors()) {

( ! ref2->GetConsortium().empty() ) {

( ! auth2.empty() ) {

auth2 += ref2->GetConsortium();

& uniquestr1 = ref1->GetUniqueStr();

& uniquestr2 = ref2->GetUniqueStr();

}

(f1 && ! f2) {

}

(f1 && f2) {

}

(

<

) {

( !m_SerialFirst ) {

ref1->GetSerial() < ref2->GetSerial();

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

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

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

CScope & GetScope(void) const

vector< string > * TCache

void Format(IFormatter &formatter, IFlatTextOStream &text_os) const override

CCacheItem(CBioseqContext &ctx, TCache csh, int length, bool is_prot)

EItem GetItemType() const override

ECompare

How *this relates to another date.

@ eCompare_before

*this comes first.

@ eCompare_same

They're equivalent.

@ eCompare_after

*this comes second.

@ eCompare_unknown

Comparison is impossible.

CBioseqContext * GetContext(void)

void x_SetObject(const CSerialObject &obj)

bool operator()(const char ch)

void GetLabel(string *label, ETypeLabel type=eGenbank) const

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

Concatenate a label for this pub to label.

const CAuth_list & GetAuthors(void) const

bool IsSetAuthors(void) const

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

CConstRef< CSeq_loc > m_Loc

void x_Init(const CPub &pub, CBioseqContext &ctx)

static void Rearrange(TReferences &refs, CBioseqContext &ctx)

void x_GatherInfo(CBioseqContext &ctx) override

CConstRef< CPubdesc > m_Pubdesc

TEntrezId GetMUID(void) const

CConstRef< CDate > m_Date

void SetRemark(const CPubdesc::TFig *new_fig, const CPubdesc::TMaploc *new_maploc, const CPubdesc::TPoly_a *new_poly_a)

void x_GatherRemark(CBioseqContext &ctx)

static void FormatAffil(const CAffil &affil, string &result, bool gen_sub=false)

void Format(IFormatter &formatter, IFlatTextOStream &text_os) const override

format

void x_CreateUniqueStr(void) const

void SetLoc(const CConstRef< CSeq_loc > &loc)

~CReferenceItem()

destructor

static void GetAuthNames(const CAuth_list &alp, TStrList &authors)

void x_CapitalizeTitleIfNecessary(void)

void x_AddImprint(const CImprint &imp, CBioseqContext &ctx)

bool Matches(const CPub_set &ps) const

CConstRef< CCit_gen > m_Gen

CConstRef< CCit_sub > m_Sub

const string & GetRemark(void) const

void x_AddAuthors(const CAuth_list &auth)

CReferenceItem(const CSeqdesc &desc, CBioseqContext &ctx)

constructors

const string & GetUniqueStr(void) const

CConstRef< CCit_book > m_Book

TEntrezId GetPMID(void) const

vector< CRef< CReferenceItem > > TReferences

TCategory GetCategory(void) const

TReftype GetReftype(void) const

const CAuth_list & GetAuthors(void) const

const CPubdesc & GetPubdesc(void) const

static void FormatAuthors(const CAuth_list &alp, string &auth)

CConstRef< CCit_pat > m_Patent

CConstRef< CCit_jour > m_Journal

static void ChangeMedlineAuthorsToISO(CRef< CPub > pub)

CConstRef< CAuth_list > m_Authors

EItem GetItemType() const override

bool IsJustUids(void) const

const CSeq_loc & GetLoc(void) const

void x_InitProc(const CCit_book &book, CBioseqContext &ctx)

bool IsSetAuthors(void) const

namespace ncbi::objects::

const string & GetTitle(C_E::E_Choice type=C_E::e_not_set) const

If the internal list contains a title (of the specified type, if given), returns the corresponding st...

@ eLabel_V1

Traditional GetLabel semantics, modeled on the C Toolkit's PubLabelUnique.

@ fLabel_Unique

Append a unique tag [V1].

virtual void FormatCache(const CCacheItem &csh, IFlatTextOStream &text_os)=0

virtual void FormatReference(const CReferenceItem &keys, IFlatTextOStream &text_os)=0

ESerialFirst m_SerialFirst

LessThan(ESerialFirst serial_first, bool is_refseq)

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const struct name_t names[]

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

static void DLIST_NAME() remove(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_THROW(exception_class, err_code, message)

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

const TPrim & Get(void) const

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TRange GetTotalRange(void) const

EOpFlags

CSeq_loc operations.

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

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

bool Empty(void) const THROWS_NONE

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

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

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

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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

Convert int to string.

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 string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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

Case-insensitive equality of a substring with another string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ eNocase

Case insensitive compare.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TTitle & GetTitle(void) const

Get the Title member data.

const TDate & GetDate(void) const

Get the Date member data.

bool IsSetDescr(void) const

description of changes for public view Check if a value has been assigned to Descr data member.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

const TCit & GetCit(void) const

Get the Cit member data.

bool CanGetName(void) const

Check if it is safe to call GetName method.

const TBook & GetBook(void) const

Get the Book member data.

bool IsSetExp(void) const

citation and/or explanation Check if a value has been assigned to Exp data member.

const TJournal & GetJournal(void) const

Get the variant data.

bool IsSetTitle(void) const

title of journal Check if a value has been assigned to Title data member.

bool IsSetPrepub(void) const

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

const TFrom & GetFrom(void) const

Get the From member data.

bool IsSetTitle(void) const

Title of book Check if a value has been assigned to Title data member.

bool CanGetPubstatus(void) const

Check if it is safe to call GetPubstatus method.

bool CanGetImp(void) const

Check if it is safe to call GetImp method.

bool CanGetImp(void) const

Check if it is safe to call GetImp method.

bool IsSetStreet(void) const

street address, not ANSI Check if a value has been assigned to Street data member.

const TStr & GetStr(void) const

Get the variant data.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

bool CanGetDate(void) const

Check if it is safe to call GetDate method.

const TTitle & GetTitle(void) const

Get the Title member data.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

bool IsSetCity(void) const

Author Affiliation, City Check if a value has been assigned to City data member.

const TApp_date & GetApp_date(void) const

Get the App_date member data.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

bool IsSetAuthors(void) const

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

bool IsSetImp(void) const

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

TPrepub GetPrepub(void) const

Get the Prepub member data.

const TDate_issue & GetDate_issue(void) const

Get the Date_issue member data.

bool IsSetPubstatus(void) const

current status of this publication Check if a value has been assigned to Pubstatus data member.

const TStreet & GetStreet(void) const

Get the Street member data.

const TName & GetName(void) const

Get the Name member data.

const TAffil & GetAffil(void) const

Get the Affil member data.

const TSub & GetSub(void) const

Get the Sub member data.

const TProc & GetProc(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CAuthor > > TStd

list< CRef< C_E > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsStr(void) const

Check if variant Str is selected.

list< CRef< CArticleId > > Tdata

bool IsSetRetract(void) const

retraction info Check if a value has been assigned to Retract data member.

bool IsSetNames(void) const

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

bool IsSetAuthors(void) const

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

const TRetract & GetRetract(void) const

Get the Retract member data.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

bool CanGetNames(void) const

Check if it is safe to call GetNames method.

bool IsSetDiv(void) const

Author Affiliation, Division Check if a value has been assigned to Div data member.

const TCountry & GetCountry(void) const

Get the Country member data.

const TStd & GetStd(void) const

Get the variant data.

const TPostal_code & GetPostal_code(void) const

Get the Postal_code member data.

bool IsSetDate(void) const

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

bool IsSetTitle(void) const

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

EPrepub

for prepublication citations

const TImp & GetImp(void) const

Get the Imp member data.

const TImp & GetImp(void) const

Get the Imp member data.

bool IsSetAuthors(void) const

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

bool CanGet(void) const

Check if it is safe to call Get method.

TType GetType(void) const

Get the Type member data.

TType GetType(void) const

Get the Type member data.

const TNames & GetNames(void) const

Get the Names member data.

bool IsSetCit(void) const

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

bool IsMl(void) const

Check if variant Ml is selected.

const TIds & GetIds(void) const

Get the Ids member data.

bool IsSetApp_date(void) const

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

const TDate & GetDate(void) const

Get the Date member data.

bool IsStd(void) const

Check if variant Std is selected.

bool CanGetAuthors(void) const

Check if it is safe to call GetAuthors method.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

const TTitle & GetTitle(void) const

Get the Title member data.

bool IsSetPostal_code(void) const

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

bool IsSetCountry(void) const

Author Affiliation, Country Check if a value has been assigned to Country data member.

const TImp & GetImp(void) const

Get the Imp member data.

const TTitle & GetTitle(void) const

Get the Title member data.

const TCity & GetCity(void) const

Get the City member data.

bool IsSetAffil(void) const

Author Affiliation, Name Check if a value has been assigned to Affil data member.

bool IsSetType(void) const

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

const Tdata & Get(void) const

Get the member data.

const TExp & GetExp(void) const

Get the Exp member data.

const TDiv & GetDiv(void) const

Get the Div member data.

TPubstatus GetPubstatus(void) const

Get the Pubstatus member data.

bool IsSetDate_issue(void) const

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

bool IsSetSub(void) const

Author Affiliation, County Sub Check if a value has been assigned to Sub data member.

bool CanGetTitle(void) const

Check if it is safe to call GetTitle method.

const TBook & GetBook(void) const

Get the variant data.

@ e_Other

generic catch all

@ e_Pubmed

see types below

@ ePubStatus_aheadofprint

epublish, but will be followed by print

@ ePubStatus_epublish

published electronically by publisher

@ ePrepub_in_press

accepted, not published

@ eType_retracted

this citation retracted

@ eType_erratum

this is a published erratum

@ eType_in_error

an erratum was published about this

@ e_Ml

MEDLINE, semi-structured.

bool IsStr(void) const

Check if variant Str is selected.

bool IsConsortium(void) const

Check if variant Consortium is selected.

bool IsMl(void) const

Check if variant Ml is selected.

bool IsSetYear(void) const

full year (including 1900) Check if a value has been assigned to Year data member.

bool IsStd(void) const

Check if variant Std is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TSeason & GetSeason(void) const

Get the Season member data.

bool IsName(void) const

Check if variant Name is selected.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetDay(void) const

day of month (1-31) Check if a value has been assigned to Day data member.

const TStr & GetStr(void) const

Get the variant data.

const TConsortium & GetConsortium(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetSeason(void) const

for "spring", "may-june", etc Check if a value has been assigned to Season data member.

bool IsSetMonth(void) const

month (1-12) Check if a value has been assigned to Month data member.

TYear GetYear(void) const

Get the Year member data.

TMonth GetMonth(void) const

Get the Month member data.

E_Choice Which(void) const

Which variant is currently selected.

const TName & GetName(void) const

Get the variant data.

TDay GetDay(void) const

Get the Day member data.

const TStd & GetStd(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool CanGetPmid(void) const

Check if it is safe to call GetPmid method.

bool CanGetCit(void) const

Check if it is safe to call GetCit method.

bool CanGetUid(void) const

Check if it is safe to call GetUid method.

const TCit & GetCit(void) const

Get the Cit member data.

TUid GetUid(void) const

Get the Uid member data.

const TPmid & GetPmid(void) const

Get the Pmid member data.

bool IsPmid(void) const

Check if variant Pmid is selected.

const TMedline & GetMedline(void) const

Get the variant data.

list< CRef< CPub > > Tdata

const TMan & GetMan(void) const

Get the variant data.

const TPmid & GetPmid(void) const

Get the variant data.

const TArticle & GetArticle(void) const

Get the variant data.

const TJournal & GetJournal(void) const

Get the variant data.

const TSub & GetSub(void) const

Get the variant data.

bool IsPat_id(void) const

Check if variant Pat_id is selected.

const TPub & GetPub(void) const

Get the variant data.

const TPatent & GetPatent(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TProc & GetProc(void) const

Get the variant data.

const TEquiv & GetEquiv(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsEquiv(void) const

Check if variant Equiv is selected.

list< CRef< CPub > > TPub

bool IsPub(void) const

Check if variant Pub is selected.

const TGen & GetGen(void) const

Get the variant data.

TMuid GetMuid(void) const

Get the variant data.

bool IsMuid(void) const

Check if variant Muid is selected.

bool IsArticle(void) const

Check if variant Article is selected.

TArticle & SetArticle(void)

Select the variant.

bool IsGen(void) const

Check if variant Gen is selected.

const TBook & GetBook(void) const

Get the variant data.

@ e_Gen

general or generic unparsed

@ e_Proc

proceedings of a meeting

@ e_Equiv

to cite a variety of ways

@ e_Man

manuscript, thesis, or letter

const TPub & GetPub(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

bool IsPub(void) const

Check if variant Pub is selected.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsSetComment(void) const

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

bool CanGetPub(void) const

Check if it is safe to call GetPub method.

const TComment & GetComment(void) const

Get the Comment member data.

TPoly_a GetPoly_a(void) const

Get the Poly_a member data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSetFig(void) const

figure in paper Check if a value has been assigned to Fig data member.

bool IsSetMaploc(void) const

map location reported in paper Check if a value has been assigned to Maploc data member.

list< CRef< CSeq_id > > TId

const TFig & GetFig(void) const

Get the Fig member data.

bool IsPub(void) const

Check if variant Pub is selected.

bool IsSetPub(void) const

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

const TPub & GetPub(void) const

Get the Pub member data.

bool IsSetPoly_a(void) const

poly A tail indicated in figure? Check if a value has been assigned to Poly_a data member.

const TMaploc & GetMaploc(void) const

Get the Maploc member data.

@ eReftype_seq

refers to sequence

const TCit & GetCit(void) const

Get the Cit member data.

bool IsSetCit(void) const

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

unsigned int

A callback function used to compare two keys in a database.

const TYPE & Get(const CNamedParameterList *param)

const struct ncbi::grid::netcache::search::fields::SIZE size

bool StripSpaces(string &str)

void ExpandTildes(string &s, ETildeStyle style)

bool ConvertQuotesNotInHTMLTags(string &str)

bool CommentHasSuspiciousHtml(const string &str)

void AddPeriod(string &str)

void CleanAndCompress(string &dest, const CTempString &instr)

void ConvertQuotes(string &str)

CStaticArraySet< const char *, PCase_CStr > TStaticRemarkSet

static bool PiiOk(const string &str)

static bool s_ContainsNoLowercase(const string &str)

static const char *const sc_RemarkText[]

static void s_MergeDuplicates(CReferenceItem::TReferences &refs, CBioseqContext &ctx)

static CDate::ECompare s_CompareDates(const CDate &d1, const CDate &d2)

static void s_CombineRefs(CReferenceItem &prev_ref, CReferenceItem &curr_ref, CBioseqContext &ctx)

static void s_RemovePeriod(string &title)

static bool s_ShouldRemoveRef(const CReferenceItem &prev_ref, const CReferenceItem &curr_ref)

static bool s_IsOnlySerial(const CPub &pub)

DEFINE_STATIC_ARRAY_MAP(TStaticRemarkSet, sc_Remarks, sc_RemarkText)

static const sljit_gpr r1

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

static const sljit_gpr r2

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