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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cleanup__pub_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/cleanup/cleanup_pub.cpp Source File

any_change =

;

any_change =

;

(comment.empty()) {

(cleaner.

(fix_initials, strip_serial)) {

it = id_set.begin();

(it != id_set.end()) {

(it != id_set.end() && !(*it)->IsPubmed()) {

(it != id_set.end()) {

id_set.erase(

(it2, id_set.end(), matcher), id_set.end());

change =

;

it = pe_set.begin();

(it != pe_set.end()) {

(cleaner->Clean(fix_initials, strip_serial)) {

(cleaner->IsEmpty()) {

it = pe_set.erase(it);

& ids = last_article->

().Set();

old_size = ids.size();

change |= (ids.size() != old_size);

id_it = ids.rbegin();

(id_it != ids.rend()) {

((*id_it)->IsPubmed()) {

last_article_pubmed_id = (*id_it)->GetPubmed();

new_pub->

().

(last_article_pubmed_id);

last_article->

().Set().push_back(new_article_id);

(!equiv.

()) {

has_id =

,

(

it : equiv.

()) {

((it->IsPmid() && it->GetPmid() > 0) ||

(it->IsMuid() && it->GetMuid() > 0)) {

(it->IsArticle()) {

any_change =

;

it =

.begin();

(it !=

.end()) {

((*it)->IsEquiv()) {

(sub_equiv.

().begin(), sub_equiv.

().end(), back_inserter(

));

it =

.erase(it);

(pub.

()) {

old_cit_size = cit.size();

(old_cit_size != cit.size()) {

any_change =

;

(imp.IsSetPub()) {

authors.SetAffil(imp.SetPub());

(authors.IsSetAffil()) {

& affil = authors.SetAffil();

&

= affil.SetStr();

& kBadAffil1 =

;

& kBadAffil2 =

;

=

.substr(kBadAffil1.length());

=

.substr(kBadAffil2.length());

authors.ResetAffil();

(imp.IsSetDate()) {

change =

;

change |= cleaner.

(fix_initials, strip_serial);

}

(from.IsProc()) {

change |= cleaner.

(fix_initials, strip_serial);

}

(from.IsJournal()) {

change |= cleaner.

(fix_initials, strip_serial);

change =

;

change =

;

change =

;

change = cleaner.

(fix_initials, strip_serial);

any_change =

;

change =

;

change =

;

(cleaner.

(fix_initials, strip_serial)) {

change =

;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void remove_if(Container &c, Predicate *__pred)

static bool CleanArticle(CCit_art &, bool fix_initials, bool strip_serial)

bool Clean(bool fix_initials, bool strip_serial) override

bool Clean(bool fix_initials, bool strip_serial) override

bool Clean(bool fix_initials, bool strip_serial) override

bool Clean(bool fix_initials, bool strip_serial) override

bool Clean(bool fix_initials, bool strip_serial) override

bool Clean(bool fix_initials, bool strip_serial) override

bool Clean(bool fix_initials, bool strip_serial) override

static bool CleanPubdesc(CPubdesc &pubdesc, bool strip_serial)

static bool x_CleanPubdescComment(string &str)

static bool CleanupAffil(CAffil &af)

static bool CleanupAuthList(CAuth_list &al, bool fix_initials=true)

static bool IsEmpty(const CAuth_list::TAffil &affil)

bool Clean(bool fix_initials, bool strip_serial) override

@ eImprintBC_AllowStatusChange

@ eImprintBC_ForbidStatusChange

static bool CleanImprint(CImprint &imprint, EImprintBC is_status_change_allowed)

static bool ShouldWeFixInitials(const CPub_equiv &equiv)

static bool s_Flatten(CPub_equiv &equiv)

bool Clean(bool fix_initials, bool strip_serial) override

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

static size_t s_PubPriority(CPub::E_Choice val)

#define FIX_IMPRINT_FIELD(x)

CRef< CPubCleaner > PubCleanerFactory(CPub &pub)

static bool s_PubWhichCompare(const CRef< CPub > &pub1, const CRef< CPub > &pub2)

void RemoveDuplicatePubMedArticleIds(CArticleIdSet::Tdata &id_set)

bool CleanDoubleQuote(string &str)

Change double to single quotes.

bool CleanVisString(string &str)

bool RemoveSpaces(string &str)

remove all spaces from a string

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

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

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

const TPrim & Get(void) const

void Reset(void)

Reset reference object.

#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.

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

Check if a string starts with a specified prefix value.

static void TrimPrefixInPlace(string &str, const CTempString prefix, ECase use_case=eCase)

Trim prefix from a string (in-place)

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

@ eNocase

Case insensitive compare.

BEGIN_STD_SCOPE bool is_sorted(Iterator iter1, Iterator iter2)

is_sorted is provided by some implementations of the STL and may be included in future releases of al...

void ResetPages(void)

Reset Pages data member.

void SetBook(TBook &value)

Assign a value to Book data member.

bool IsSetVolume(void) const

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

void ResetImp(void)

Reset Imp data member.

bool IsSetPages(void) const

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

const TIssue & GetIssue(void) const

Get the Issue member data.

bool IsSetDate(void) const

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

void SetIds(TIds &value)

Assign a value to Ids data member.

TSerial_number GetSerial_number(void) const

Get the Serial_number member data.

bool IsSetAuthors(void) const

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

bool IsSetAuthors(void) const

authors (ANSI requires) Check if a value has been assigned to Authors data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetDate(TDate &value)

Assign a value to Date data member.

const TVolume & GetVolume(void) const

Get the Volume member data.

bool IsSetVolume(void) const

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

const TPages & GetPages(void) const

Get the Pages member data.

bool IsSetPrepub(void) const

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

const TPages & GetPages(void) const

Get the Pages member data.

bool IsSetApplicants(void) const

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

const TPmid & GetPmid(void) const

Get the Pmid member data.

void SetApplicants(TApplicants &value)

Assign a value to Applicants data member.

bool IsSetAssignees(void) const

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

void SetImp(TImp &value)

Assign a value to Imp data member.

bool IsSetSerial_number(void) const

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

void SetFrom(TFrom &value)

Assign a value to From data member.

void ResetIssue(void)

Reset Issue data member.

bool IsSetFrom(void) const

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

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetCountry(const TCountry &value)

Assign a value to Country data member.

void SetAssignees(TAssignees &value)

Assign a value to Assignees data member.

bool IsSetAuthors(void) const

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

void SetPages(const TPages &value)

Assign a value to Pages data member.

bool IsSetImp(void) const

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

void ResetSerial_number(void)

Reset Serial_number data member.

TPrepub GetPrepub(void) const

Get the Prepub member data.

bool IsSetPubstatus(void) const

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

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void ResetPrepub(void)

Reset Prepub data member.

bool IsSetCit(void) const

anything, not parsable Check if a value has been assigned to Cit data member.

const TVolume & GetVolume(void) const

Get the Volume member data.

list< CRef< CArticleId > > Tdata

const TTitle & GetTitle(void) const

Get the Title member data.

void SetImp(TImp &value)

Assign a value to Imp data member.

TPubmed & SetPubmed(void)

Select the variant.

bool IsSetDate(void) const

replaces imp, will become required Check if a value has been assigned to Date data member.

void SetCit(TCit &value)

Assign a value to Cit data member.

const TPubmed & GetPubmed(void) const

Get the variant data.

bool IsSetTitle(void) const

eg.

bool IsSetAuthors(void) const

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

void SetCit(const TCit &value)

Assign a value to Cit data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

bool IsSetJournal(void) const

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

bool IsPubmed(void) const

Check if variant Pubmed is selected.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

bool IsSetPmid(void) const

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

bool IsSetIds(void) const

lots of ids Check if a value has been assigned to Ids data member.

bool IsSetAuthors(void) const

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

TType GetType(void) const

Get the Type member data.

bool IsSetBook(void) const

citation to meeting Check if a value has been assigned to Book data member.

bool IsSetCit(void) const

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

bool IsSetImp(void) const

this only used to get date.

void SetPrepub(TPrepub value)

Assign a value to Prepub data member.

void SetImp(TImp &value)

Assign a value to Imp data member.

bool IsSetIssue(void) const

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

TMuid GetMuid(void) const

Get the Muid member data.

void ResetVolume(void)

Reset Volume data member.

bool IsSetPages(void) const

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

bool IsSetType(void) const

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

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

bool IsSetMuid(void) const

medline uid Check if a value has been assigned to Muid data member.

TPubstatus GetPubstatus(void) const

Get the Pubstatus member data.

const TCountry & GetCountry(void) const

Get the Country member data.

bool IsSetImp(void) const

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

bool IsSetCountry(void) const

Patent Document Country Check if a value has been assigned to Country data member.

@ ePubStatus_aheadofprint

epublish, but will be followed by print

@ ePubStatus_epublish

published electronically by publisher

@ ePrepub_in_press

accepted, not published

void SetCit(TCit &value)

Assign a value to Cit data member.

bool IsSetCit(void) const

article citation Check if a value has been assigned to Cit data member.

const TCit & GetCit(void) const

Get the Cit member data.

bool IsPmid(void) const

Check if variant Pmid is selected.

TProc & SetProc(void)

Select the variant.

TPmid & SetPmid(void)

Select the variant.

E_Choice

Choice variants.

list< CRef< CPub > > Tdata

TBook & SetBook(void)

Select the variant.

const TPmid & GetPmid(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

const Tdata & Get(void) const

Get the member data.

TEquiv & SetEquiv(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

TMan & SetMan(void)

Select the variant.

TSub & SetSub(void)

Select the variant.

TGen & SetGen(void)

Select the variant.

TMedline & SetMedline(void)

Select the variant.

TJournal & SetJournal(void)

Select the variant.

TPatent & SetPatent(void)

Select the variant.

bool IsArticle(void) const

Check if variant Article is selected.

TArticle & SetArticle(void)

Select the variant.

@ e_Pat_id

identify a patent

@ e_Gen

general or generic unparsed

@ e_not_set

No variant selected.

@ e_Proc

proceedings of a meeting

@ e_Equiv

to cite a variety of ways

@ e_Man

manuscript, thesis, or letter

bool IsSetComment(void) const

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

void ResetComment(void)

Reset Comment data member.

void SetPub(TPub &value)

Assign a value to Pub data member.

bool IsSetPub(void) const

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

void SetComment(const TComment &value)

Assign a value to Comment data member.

const TPub & GetPub(void) const

Get the Pub member data.

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

User-defined methods of the data storage class.

bool StripSpaces(string &str)

bool operator()(CRef< CArticleId > other_id)

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