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

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);

(

.GetConfig().DoHTML()) {

item.

(*

, text_os);

vector<string>& accs,

os << separator <<*it;

(acc.length() !=

.length()) {

(

= 0;

< acc.length() && !

((

) acc[

]); ++

) {

(acc[

] !=

[

]) {

(

< acc.length()) {

kAccCutoff = 20;

kBinCutoff = 5;

(xtra.size() < kAccCutoff) {

vector<string> TAccBin;

vector <TAccBin> TAccBins;

TAccBin* curr_bin =

;

CAccessionItem::TExtra_accessions::const_iterator

= xtra.begin();

bins.push_back(TAccBin());

curr_bin = &bins.back();

curr_bin->push_back(*it);

(TAccBins, bin_it, bins) {

(bin_it->size() <= kBinCutoff) {

os << separator<< bin_it->front() <<

<< bin_it->back();

separator)

ostringstream acc_line;

acc_line << separator;

acc_line << separator;

acc_line.str();

.resize(width,

);

:

;

htmlaware)

internalIndentation )

(

, padded_tag, where);

(where ==

) {

.push_back(padded_tag);

( internalIndentation > 0 ) {

padded_indent = *

;

padded_indent.resize( padded_indent.size() + internalIndentation,

);

* strHtmlHead =

;

* strCgiHead =

;

.AddLine( strCgiHead ) :

.AddLine( strHtmlHead );

strHtmlTail(

strCgiTail(

);

.AddLine( strCgiTail ) :

.AddLine( strHtmlTail );

& delim,

os << (

.IsProt() ?

:

);

os << *delim_p << range.

() + 1 << to << range.

() + 1;

(

.Which()) {

.GetStd().size();

.GetMl().size();

.GetStr().size();

date.

(&year,

);

(

& issue,

& part_sup,

& part_supi)

* digits =

;

firstText, firstNumber, dash, lastText, lastNumber;

firstDigit = pages.find_first_of( digits );

(

== firstDigit ) {

( 0 == firstDigit ) {

( it != pages.end() ) {

( *it !=

) {

( it != pages.end() ) {

( ::

( *it ) ||

== *it ) {

( it == pages.end() ) {

( it != pages.end() && ::

(*it) ) {

( it != pages.end() && *it !=

) {

string::iterator locationRightAfterFirstDash = it;

( it != pages.end() && *it ==

) {

( it == pages.end() ) {

pages.erase( locationRightAfterFirstDash, pages.end() );

pages += firstNumber;

( it == pages.end() ) {

( it != pages.end() ) {

( *it !=

) {

( it != pages.end() ) {

( ::

( *it ) ||

== *it ) {

firstNumberEmpty = firstNumber.empty();

firstTextEmpty = firstText.empty();

lastNumberEmpty = lastNumber.empty();

lastTextEmpty = lastText.empty();

( (lastNumberEmpty && firstTextEmpty) ||

(firstNumberEmpty && lastTextEmpty) ) {

( it != pages.end() ) {

lastNumber = firstNumber;

lastText = firstText;

pages = firstNumber + firstText +

+ lastNumber + lastText;

}

( !

(*it) ) {

pages = firstNumber + firstText +

+ lastNumber + lastText;

( it != pages.end() ) {

( ::

( *it ) ||

== *it ) {

( it != pages.end() ) {

( *it !=

) {

( it == pages.end() ) {

( it != pages.end() && *it !=

) {

( it == pages.end() ) {

( it != pages.end() ) {

( ::

( *it ) ||

== *it ) {

( it != pages.end() ) {

( *it !=

) {

( it != pages.end() ) {

( ! firstText.empty() ) {

( firstText.length() != 1 ) {

( ! lastText.empty() ) {

( lastText != firstText ) {

( lastText.empty() && lastNumber.empty() ) {

pages = ( (0 == firstDigit) ?

(firstNumber + firstText) : (firstText + firstNumber) );

( firstNumber.empty() && ! lastNumber.empty() ) {

( ! firstNumber.empty() && lastNumber.empty() ) {

( lastNumber.length() < firstNumber.length() ) {

lastNumber = firstNumber.substr( 0,

firstNumber.length() - lastNumber.length() ) + lastNumber;

( lastText.empty() ) {

lastText = firstText;

( 0 == firstDigit ) {

pages = firstNumber + firstText +

+ lastNumber + lastText;

pages = firstText + firstNumber +

+ lastText + lastNumber;

( year.empty() ) {

(title.length() < 3) {

(!authstr.empty()

) {

jour << ((num_auth == 1) ?

:

) <<

;

issue, part_sup, part_supi;

jour <<

<< volume;

jour <<

(issue, part_sup, part_supi);

jour <<

<< pages;

jour <<

<<

;

jour << affil <<

;

jour <<

;

jour <<

<< affil;

jour <<

;

(

.IsSetDate()) {

& date =

.GetDate();

(date.

() ||

.GetDate().GetDate(&year,

);

(

.IsSetAuthors() &&

.GetAuthors().IsSetAffil()) {

(

.IsSetDate()) {

(

.IsSetPages()) {

pages =

.GetPages();

(

.IsSetJournal()) {

( cit.at( cit.length() - 1) ==

) {

= cit.substr(pos, cit.length() - pos - 1 );

in_press =

;

(

+= prefix) += in_press;

date =

;

((

+=

) += date) +=

;

( !embl_affil ) {

+=

;

}

(do_embl) {

+=

;

is_html = cfg.

();

use_pre_grant_formatting = ! pat.

();

use_pre_grant_formatting &= (

use_pre_grant_formatting = use_pre_grant_formatting &&

( use_pre_grant_formatting ) {

any_good_patents =

;

&

= **id_iter;

(

.IsPatent() &&

.GetPatent().IsSetCit() &&

.GetPatent().GetCit().IsSetId() &&

.GetPatent().GetCit().

().IsApp_number() &&

any_good_patents =

;

( ! any_good_patents ) {

use_pre_grant_formatting =

;

( use_pre_grant_formatting ) {

header =

;

header =

;

header =

;

do_us_patent_html =

( do_us_patent_html ) {

( do_us_patent_html ) {

( use_pre_grant_formatting ) {

jour <<

<<

;

}

(affil.

()) {

jour << prefix << std.

() <<

;

jour << prefix << std.

() <<

;

jour << prefix << std.

();

jour << prefix << std.

();

jour <<

<<

<< std.

() <<

;

(affil.

()) {

jour <<

<< authors <<

<< affil.

();

}

(affil.

()) {

jour << authors <<

;

jour << prefix << std.

() <<

;

jour << prefix << std.

() <<

;

jour << prefix << std.

();

jour << prefix << std.

();

jour <<

<<

<< std.

() <<

;

(!

.Config().CitArtIsoJta()) {

strict =

;

(it->Which()) {

((*it)->IsIso_jta()) {

iso_jta = (*it)->GetIso_jta();

}

((*it)->IsMl_jta()) {

ml_jta = (*it)->GetMl_jta();

(title.length() < 3) {

issue, part_sup, part_supi;

jour <<

<< volume;

jour <<

(issue, part_sup, part_supi);

jour <<

<< pages;

jour <<

<< pages;

jour <<

<< year;

jour <<

;

jour <<

;

& prefix,

list<string>&

)

(

, prefix, keywords);

User-defined methods of the data storage class.

const string & GetWGSAccession(void) const

const string & GetTSAAccession(void) const

const TExtra_accessions & GetExtraAccessions(void) const

const string & GetAccession(void) const

vector< string > TExtra_accessions

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

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

void GetDate(string *label, bool year_only=false) const

Append a standardized string representation of the date to the label.

const TFormat & GetFormat(void) const

bool IsFormatGBSeq(void) const

const TMode & GetMode(void) const

bool NoAffilOnUnpub(void) const

bool IsFormatINSDSeq(void) const

bool DropBadCitGens(void) const

bool IsFormatGenbank(void) const

bool IsFormatEMBL(void) const

bool IsModeEntrez(void) const

const CFlatFileConfig & GetConfig(void) const

static const string s_GenbankMol[]

string x_FormatAccession(const CAccessionItem &acc, char separator) const

static CFlatItemFormatter * New(CFlatFileConfig::TFormat format)

void End(IFlatTextOStream &) override

virtual SIZE_TYPE GetWidth(void) const

static const string s_EmblMol[]

virtual string & Pad(const string &s, string &out, EPadContext where) const

~CFlatItemFormatter() override

void x_FormatRefJournal(const CReferenceItem &ref, string &journal, CBioseqContext &ctx) const

void x_GetKeywords(const CKeywordsItem &kws, const string &prefix, list< string > &l) const

void SetContext(CFlatFileContext &ctx)

static string & x_Pad(const string &s, string &out, SIZE_TYPE width, const string &indent=kEmptyStr)

CRef< CFlatFileContext > m_Ctx

void x_FormatRefLocation(ostream &os, const CSeq_loc &loc, const string &to, const string &delim, CBioseqContext &ctx) const

void Format(const IFlatItem &item, IFlatTextOStream &text_os)

virtual list< string > & Wrap(list< string > &l, SIZE_TYPE width, const string &tag, const string &body, EPadContext where=ePara, bool htmlaware=false) const

TWrapFlags & SetWrapFlags(void)

CBioseqContext * GetContext(void)

const TKeywords & GetKeywords(void) const

bool IsSetSub(void) const

TPubType GetPubType(void) const

TSeqid GetPatSeqid(void) const

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

bool IsSetJournal(void) const

bool IsSetBook(void) const

const CCit_gen & GetGen(void) const

const CCit_pat & GetPatent(void) const

const string & GetPII(void) const

const CCit_sub & GetSub(void) const

const string & GetOldPII(void) const

const CCit_book & GetBook(void) const

bool IsSetGen(void) const

const CCit_jour & GetJournal(void) const

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

bool IsSetPatent(void) const

bool IsElectronic(void) const

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

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...

virtual void Format(IFormatter &formatter, IFlatTextOStream &text_os) const =0

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

std::ofstream out("events_result.xml")

main entry point for tests

static const struct name_t names[]

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

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,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

vector< CSeq_id_Handle > TId

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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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 unsigned long StringToULong(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned long.

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 unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

static void Wrap(const string &str, SIZE_TYPE width, IWrapDest &dest, TWrapFlags flags, const string *prefix, const string *prefix1)

static string & ToUpper(string &str)

Convert string to upper case – string& version.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fWrap_HTMLPre

Wrap as pre-formatted HTML?

@ eNocase

Case insensitive compare.

const TTitle & GetTitle(void) const

Get the Title member data.

bool IsSetVolume(void) const

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

const TDate & GetDate(void) const

Get the Date member data.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

const TPart_supi & GetPart_supi(void) const

Get the Part_supi member data.

const TDoc_type & GetDoc_type(void) const

Get the Doc_type member data.

bool IsSetNumber(void) const

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

bool IsSetAffil(void) const

author affiliation Check if a value has been assigned to Affil data member.

const TVolume & GetVolume(void) const

Get the Volume member data.

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.

bool IsSetTitle(void) const

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

bool IsSetAssignees(void) const

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

const TAffil & GetAffil(void) const

Get the Affil member data.

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.

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 TIssue & GetIssue(void) const

Get the Issue member data.

bool CanGetPrepub(void) const

Check if it is safe to call GetPrepub method.

const TApp_date & GetApp_date(void) const

Get the App_date member data.

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 TAffil & GetAffil(void) const

Get the Affil member data.

const TPart_sup & GetPart_sup(void) const

Get the Part_sup member data.

const TPub & GetPub(void) const

Get the Pub member data.

const TSub & GetSub(void) const

Get the Sub member data.

list< CRef< C_E > > Tdata

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDate(void) const

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

bool CanGetCountry(void) const

Check if it is safe to call GetCountry method.

bool CanGetApp_number(void) const

Check if it is safe to call GetApp_number method.

bool CanGetNumber(void) const

Check if it is safe to call GetNumber method.

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.

bool CanGetPub(void) const

Check if it is safe to call GetPub method.

bool IsSetIssue(void) const

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

bool IsSetDoc_type(void) const

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

const TNumber & GetNumber(void) const

Get the Number member data.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

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.

bool IsSetDate(void) const

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

EPrepub

for prepublication citations

bool IsSetPart_sup(void) const

part/sup of volume Check if a value has been assigned to Part_sup data member.

const TImp & GetImp(void) const

Get the Imp member data.

const TNames & GetNames(void) const

Get the Names 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 IsSetApp_number(void) const

Patent Doc Appl Number Check if a value has been assigned to App_number data member.

const TApp_number & GetApp_number(void) const

Get the App_number member data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsSetPart_supi(void) const

part/sup on issue Check if a value has been assigned to Part_supi data member.

const TTitle & GetTitle(void) const

Get the Title member data.

const TAssignees & GetAssignees(void) const

Get the Assignees member data.

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.

bool CanGetAuthors(void) const

Check if it is safe to call GetAuthors method.

bool IsSetPages(void) const

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

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.

const Tdata & Get(void) const

Get the 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.

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 IsSetSub(void) const

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

@ ePrepub_in_press

accepted, not published

@ ePrepub_submitted

submitted, not accepted

@ e_Ml

MEDLINE, semi-structured.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

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 TStr & GetStr(void) const

Get the variant data.

TYear GetYear(void) const

Get the Year member data.

const TStd & GetStd(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Tpg

Third Party Annot/Seq Genbank.

list< CRef< CSeq_id > > TId

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

static void s_FormatYear(const CDate &date, string &year)

static void s_FormatJournal(const CReferenceItem &ref, string &journal, CBioseqContext &ctx)

static size_t s_NumAuthors(const CCit_book::TAuthors &authors)

static void s_FormatCitBookArt(const CReferenceItem &ref, string &journal, bool do_gb)

static void s_FormatCitGen(const CReferenceItem &ref, string &journal, const CFlatFileConfig &cfg, CBioseqContext &ctx)

static void s_FormatThesis(const CReferenceItem &ref, string &journal)

static bool s_IsSuccessor(const string &acc, const string &prev)

static void s_FormatSecondaryAccessions(CNcbiOstream &os, const CAccessionItem::TExtra_accessions &xtra, char separator)

static string s_DoSup(const string &issue, const string &part_sup, const string &part_supi)

static bool s_StrictIsoJta(CBioseqContext &ctx)

static void s_PrintAccessions(CNcbiOstream &os, const vector< string > &accs, char separator)

static void s_FormatPatent(const CReferenceItem &ref, string &journal, const CBioseqContext &ctx)

static void s_FormatCitSub(const CReferenceItem &ref, string &journal, bool do_embl)

static void s_FormatCitBook(const CReferenceItem &ref, string &journal)

static void s_FixPages(string &pages)

bool TrimSpacesAndJunkFromEnds(string &str, bool allow_ellipsis=false)

void DateToString(const CDate &date, string &str, EDateToString format_choice=eDateToString_regular)

bool StripSpaces(string &str)

void ExpandTildes(string &s, ETildeStyle style)

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

void TrimSpaces(string &str, size_t indent=0)

const char * strLinkBaseUSPTO

void ConvertQuotes(string &str)

void Out(T t, int w, CNcbiOstream &to=cout)

CRef< CPub > journal(ParserPtr pp, char *bptr, char *eptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, bool has_muid, CRef< CCit_art > &cit_art, Int4 er)

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

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