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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/sp__ref_8cpp_source.html below:

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

71 #define THIS_FILE "sp_ref.cpp" 108  "MEDLINE"

,

"PLASMID"

,

"SPECIES"

,

"STRAIN"

,

"TISSUE"

,

"TRANSPOSON"

,

nullptr 124  if

(name.find(

'.'

) == string_view::npos)

129  auto

it = tokens.begin();

131  for

(;

next

(it) != tokens.end(); ++it)

165

bptr = dbp.

mBuf

.

ptr

+ col_data;

166

eptr = bptr + dbp.

mBuf

.

len

;

167  while

(

isdigit

(*bptr) == 0 && bptr < eptr)

189  for

(ptr1 =

str

; *ptr1 !=

'\0'

;) {

194  while

(*ptr1 !=

'\0'

&& *ptr1 !=

';'

)

197  while

(*ptr1 ==

';'

|| *ptr1 ==

' '

)

247  for

(ptr2 = ptr1; ptr2 !=

str

&& *ptr2 !=

' '

;)

257

prbp->

vol

.assign(ptr2, ptr1);

264

prbp->

pages

.assign(ptr1, ptr2);

266

std::vector<Char> pages(ptr1, ptr2);

269

prbp->

pages

.assign(pages.begin(), pages.end());

302  for

(

str

+= 4; *

str

==

' '

;)

324

prbp->

affil

.assign(ptr2, ptr1);

326  while

(*ptr1 ==

','

|| *ptr1 ==

' '

)

329  if

(prbp->

country

!=

"U.S.A."

)

340  if

(! prbp->

year

.empty())

366  if

(! prbp || !

str

||

str

[0] ==

'\0'

)

378  while

(*p ==

' '

|| *p ==

'\t'

|| *p ==

';'

)

386  if

(prbp->

muid

== 0)

396  if

(prbp->

doi

.empty())

397

prbp->

doi

= (q + 4);

455  while

(

len

> 0 &&

str

[

len

- 1] ==

';'

) {

460  switch

(subdbp.mType) {

474  for

(s =

str

+ 8; *s ==

' '

;)

487  for

(s =

str

; *s ==

'\"'

|| *s ==

' '

|| *s ==

'\t'

||

488

*s ==

'\n'

|| *s ==

';'

;)

492  for

(p = s; *p !=

'\0'

;)

494  for

(p--; *p ==

'\"'

|| *p ==

' '

|| *p ==

'\t'

||

495

*p ==

'\n'

|| *p ==

';'

;

528  static const char

*

months

[12] = {

"JAN"

,

"FEB"

,

"MAR"

,

"APR"

,

"MAY"

,

"JUN"

,

"JUL"

,

"AUG"

,

"SEP"

,

"OCT"

,

"NOV"

,

"DEC"

};

530  for

(s =

str

; *s !=

'\0'

&& *s !=

')'

;)

539  for

(cal = 0; cal < 12; cal++) {

559  int

cur_year = now.

GetYear

();

561  if

(year < 1900 || year > cur_year) {

575

new_title->SetName(title_str);

576

title.

Set

().push_back(new_title);

588  if

(prbp->

year

.empty())

593  if

(! prbp->

vol

.empty()) {

594  if

(prbp->

vol

.front() ==

'0'

)

600  if

(! prbp->

pages

.empty()) {

601  if

(prbp->

pages

.front() ==

'0'

)

621  while

(! prbp->

journal

.empty() && prbp->

journal

.back() ==

'.'

)

624

bptr = prbp->

journal

.c_str();

625  for

(s = bptr; *s !=

'('

&& *s !=

'\0'

;)

640

sub.

SetImp

().SetDate(*date);

644  for

(s = bptr; *s !=

')'

&& *s !=

'\0'

;)

669  if

(! prbp || prbp->

journal

.empty())

683  string

temp1 = bptr.substr(0, ed_pos);

684  const char

* temp2 = &bptr[ed_pos];

696  auto

here = tokens.begin();

697  for

(

auto

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

703  for

(

auto

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

704  len

+= it->size() + 2;

709

title.reserve(

len

);

710  for

(

auto

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

712

title.append(

", "

);

720  if

(authors.

Empty

()

) {

732  else if

((page =

StringIStr

(temp2,

"P."

)) != 0)

738  for

(temp2 = page; *temp2 !=

'\0'

&& *temp2 !=

','

;)

741

book.

SetImp

().SetPages(

string

(page, temp2));

744  const Char

* eptr = bptr.c_str() + bptr.size() - 1;

754  const Char

* year = eptr;

760

book.

SetImp

().SetDate(*date);

764  while

(*temp2 ==

' '

)

766  if

(*temp2 !=

'('

) {

773  for

(p = year; p > temp2 && (*p ==

' '

|| *p ==

','

);)

778

book.

SetImp

().SetPub().SetStr(affil);

782  if

(vol_pos !=

NPOS

) {

783

vol = bptr.c_str() + 4;

784  for

(s = vol; *s !=

'\0'

&&

isdigit

(*s) != 0;)

787

book.

SetImp

().SetVolume(

string

(vol, s));

821  if

(! prbp || prbp->

journal

.empty())

824

std::vector<Char> bptr(prbp->

journal

.begin(), prbp->

journal

.end());

828  if

(eds_pos ==

NPOS

)

831

ptr = &bptr[0] + eds_pos;

837  for

(ptr += 6; *ptr ==

';'

|| *ptr ==

' '

|| *ptr ==

'\t'

;)

840  if

(! p || p == ptr) {

846  for

(p--; *p ==

' '

|| *p ==

'\t'

|| *p ==

','

; p--) {

853  if

(p == ptr && *p ==

'\0'

) {

860  for

(q += 3, p = q; *q >=

'0'

&& *q <=

'9'

;)

862  if

(q == p || (*q !=

':'

&& *q !=

'-'

)) {

869  for

(p = q; *q >=

'0'

&& *q <=

'9'

;)

871  if

(q == p || *q !=

'-'

) {

881  while

(*q >=

'0'

&& *q <=

'9'

)

883  if

(*(q - 1) ==

'-'

) {

890  for

(p = q; *q ==

' '

|| *q ==

','

;)

892  if

(q == p || *q ==

'\0'

) {

908  for

(p--; *p ==

' '

|| *p ==

'\t'

|| *p ==

','

; p--) {

915  if

(p == q && *p ==

'\0'

) {

923

publisher =

StringSave

(string_view(q, p - q));

926  for

(p++, q = p; *p >=

'0'

&& *p <=

'9'

;)

928  if

(p - q != 4 || *p !=

')'

) {

940

imp.

SetPub

().SetStr(publisher);

976  if

(! prbp || prbp->

journal

.empty())

982  for

(q = p; *q !=

' '

&& *q !=

','

&& *q !=

'\0'

;)

994  for

(

char

& c : num)

995  if

(

'a'

<= c && c <=

'z'

)

999  for

(

char

c : num) {

1000  if

(! (

'A'

<= c && c <=

'Z'

))

1005

country[0] = num[0];

1006

country[1] = num[1];

1013  while

(*q !=

'\0'

&&

isdigit

(*q) == 0)

1021  if

(! std_date || std_date.

Empty

()) {

1055  bool

is_set =

false

;

1056  if

(! prbp->

journal

.empty()) {

1059

}

else if

(! prbp->

cit

.empty()) {

1061

prbp->

cit

.clear();

1065  if

(prbp->

title

&& ! prbp->

title

->empty()) {

1117  if

(prbp->

title

&& ! prbp->

title

->empty())

1127  if

(! prbp->

journal

.empty()) {

1129

title->SetJta(prbp->

journal

);

1130  journal

.SetTitle().Set().push_back(title);

1136  id

->SetOther().SetDb(

"AGRICOLA"

);

1137  id

->SetOther().SetTag().SetStr(prbp->

agricola

);

1139

article.

SetIds

().Set().push_back(

id

);

1142  if

(! prbp->

doi

.empty()) {

1144  id

->SetDoi().Set(prbp->

doi

);

1146

article.

SetIds

().Set().push_back(

id

);

1201

ret->SetPub().Set().push_back(pub);

1204  if

(prbp->

muid

> 0) {

1207

ret->SetPub().Set().push_back(pub);

1213

ret->SetPub().Set().push_back(pub);

1218  bool

is_set =

false

;

1225  msg

=

"Thesis format error (CitGen created)"

;

1229  msg

=

"Article format error (CitGen created)"

;

1235  msg

=

"Submission format error (CitGen created)"

;

1239  msg

=

"Book format error (CitGen created)"

;

1245  msg

=

"Patent format error (cit-gen created)"

;

1257

ret->SetPub().Set().push_back(pub);

1259  if

(! prbp->

comment

.empty())

1260

ret->SetComment(prbp->

comment

);

1270  if

(! prbp->

title

)

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

struct DataBlk::@1166 mBuf

#define ERR_REFERENCE_IllegalFormat

#define ERR_REFERENCE_Patent

#define ERR_REFERENCE_Fail_to_parse

#define ERR_REFERENCE_MultipleIdentifiers

#define ERR_REFERENCE_UnkRefRcToken

#define ERR_REFERENCE_IllegalDate

#define ERR_REFERENCE_UnkRefSubType

#define ERR_REFERENCE_YearEquZero

int fta_atoi(string_view sv)

bool StringEquNI(const char *s1, const char *s2, size_t n)

bool StringEquN(const char *s1, const char *s2, size_t n)

size_t StringLen(const char *s)

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

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

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

SStrictId_Entrez::TId TEntrezId

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

#define ENTREZ_ID_FROM(T, value)

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.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

char Char

Alias for char.

uint16_t Uint2

2-byte (16-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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

Check if a string starts with a specified prefix value.

static void TrimSuffixInPlace(string &str, const CTempString suffix, ECase use_case=eCase)

Trim suffix from a string (in-place)

static string Sanitize(CTempString str, TSS_Flags flags=fSS_print)

Sanitize a string, allowing only specified classes of characters.

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.

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

Truncate whitespace in a string.

@ fAllowTrailingSymbols

Ignore trailing non-numerics characters.

@ eTrunc_End

Truncate trailing whitespace only.

@ eNocase

Case insensitive compare.

@ eCurrent

Use current time. See also CCurrentTime.

void ResetImp(void)

Reset Imp data member.

void SetPages(const TPages &value)

Assign a value to Pages data member.

void SetIds(TIds &value)

Assign a value to Ids data member.

bool IsSetAffil(void) const

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

void SetTitle(TTitle &value)

Assign a value to Title data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetDate(TDate &value)

Assign a value to Date data member.

bool IsSetPub(void) const

publisher, required for book Check if a value has been assigned to Pub data member.

void SetDoc_type(const TDoc_type &value)

Assign a value to Doc_type data member.

void SetTitle(TTitle &value)

Assign a value to Title data member.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

void SetFrom(TFrom &value)

Assign a value 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 SetSerial_number(TSerial_number value)

Assign a value to Serial_number data member.

bool IsSetAuthors(void) const

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

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetPub(TPub &value)

Assign a value to Pub data member.

void SetImp(TImp &value)

Assign a value to Imp data member.

bool IsSetDate(void) const

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

void SetNumber(const TNumber &value)

Assign a value to Number data member.

void SetCit(TCit &value)

Assign a value to Cit data member.

void SetCit(const TCit &value)

Assign a value to Cit data member.

void SetVolume(const TVolume &value)

Assign a value to Volume data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetDate(TDate &value)

Assign a value to Date data member.

void SetType(TType value)

Assign a value to Type data member.

bool IsSetDate(void) const

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

void SetTitle(const TTitle &value)

Assign a value to Title data member.

const TImp & GetImp(void) const

Get the Imp member data.

void SetMedium(TMedium value)

Assign a value to Medium data member.

void SetTitle(const TTitle &value)

Assign a value to Title 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.

void SetDate_issue(TDate_issue &value)

Assign a value to Date_issue data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

Tdata & Set(void)

Assign a value to data member.

@ ePrepub_in_press

accepted, not published

void SetYear(TYear value)

Assign a value to Year data member.

void SetMonth(TMonth value)

Assign a value to Month data member.

TStd & SetStd(void)

Select the variant.

TYear GetYear(void) const

Get the Year member data.

TStr & SetStr(void)

Select the variant.

TPmid & SetPmid(void)

Select the variant.

TMuid & SetMuid(void)

Select the variant.

TMan & SetMan(void)

Select the variant.

TSub & SetSub(void)

Select the variant.

TGen & SetGen(void)

Select the variant.

TPatent & SetPatent(void)

Select the variant.

TArticle & SetArticle(void)

Select the variant.

const CharType(& source)[N]

User-defined methods of the data storage class.

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 msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static void CkSPComTopics(ParserPtr pp, const char *str)

static string ParseYear(const char *str)

static void SetCitTitle(CTitle &title, const string &title_str)

static bool GetImprintPtr(ParRefBlkPtr prbp, CImprint &imp)

static bool GetCitGen(ParRefBlkPtr prbp, CCit_gen &cit_gen)

static CRef< CDate > get_s_date(const Char *str, bool bstring)

static bool GetCitBook(ParRefBlkPtr prbp, CCit_art &article)

static void DisrootImprint(CCit_sub &sub)

static void GetSprotIds(ParRefBlk *prbp, char *str)

static bool GetCitPatent(ParRefBlkPtr prbp, Parser::ESource source, CCit_pat &pat)

const char * ParFlat_SPRefRcToken[]

static CRef< CPubdesc > GetPubRef(ParRefBlkPtr prbp, Parser::ESource source)

static bool GetCitBookOld(ParRefBlkPtr prbp, CCit_art &article)

static ParRefBlkPtr SprotRefString(ParserPtr pp, const DataBlk &dbp, Uint2 col_data)

static bool GetCitSubmit(ParRefBlkPtr prbp, CCit_sub &sub)

static void ParseRLDataSP(ParserPtr pp, ParRefBlkPtr prbp, char *str)

static bool NotName(string_view name)

static Int4 GetDataFromRN(const DataBlk &dbp, Uint2 col_data)

static bool ParseJourLine(ParserPtr pp, ParRefBlkPtr prbp, const char *str)

static void FreeParRefBlkPtr(ParRefBlkPtr prbp)

CRef< CPubdesc > sp_refs(ParserPtr pp, const DataBlk &dbp, Uint2 col_data)

static bool GetCitLetThesis(ParRefBlkPtr prbp, CCit_let &cit_let)

static bool GetCitArticle(ParRefBlkPtr prbp, CCit_art &article)

CRef< CAuth_list > authors

void PointToNextToken(char *&ptr)

string GetBlkDataReplaceNewLine(string_view instr, Uint2 indent)

CRef< CDate_std > get_full_date(string_view date_view, bool is_ref, Parser::ESource source)

Int2 fta_StringMatch(const Char **array, string_view text)

string GetTheCurrentToken(char **ptr)

Char * StringIStr(const Char *where, const Char *what)

void CleanTailNonAlphaChar(string &str)

void get_auth_from_toks(TTokenList::const_iterator beg, TTokenList::const_iterator end, ERefFormat format, CRef< CAuth_list > &auths)

TTokenList get_tokens(string_view str, string_view delimeter)

CRef< CDate > get_date(const Char *year)

void get_auth(string_view pt, ERefFormat format, string_view jour, CRef< CAuth_list > &auths)

Int4 valid_pages_range(char *pages, const Char *title, Int4 er, bool inpress)

void get_auth_consortium(string_view str, CRef< CAuth_list > &auths)


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