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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/ref_8cpp_source.html below:

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

84 #define THIS_FILE "ref.cpp" 93  "to the EMBL/GenBank/DDBJ databases"

,

94  "to the EMBL/DDBJ/GenBank databases"

,

95  "to the DDBJ/GenBank/EMBL databases"

,

96  "to the DDBJ/EMBL/GenBank databases"

,

97  "to the GenBank/DDBJ/EMBL databases"

,

98  "to the GenBank/EMBL/DDBJ databases"

,

105  "Publication Status: Online-Only"

,

106  "Publication Status : Online-Only"

,

107  "Publication_Status: Online-Only"

,

108  "Publication_Status : Online-Only"

,

109  "Publication-Status: Online-Only"

,

110  "Publication-Status : Online-Only"

,

112  "Publication Status: Available-Online"

,

113  "Publication Status : Available-Online"

,

114  "Publication_Status: Available-Online"

,

115  "Publication_Status : Available-Online"

,

116  "Publication-Status: Available-Online"

,

117  "Publication-Status : Available-Online"

,

118  "Publication Status: Available-Online prior to print"

,

119  "Publication Status : Available-Online prior to print"

,

120  "Publication_Status: Available-Online prior to print"

,

121  "Publication_Status : Available-Online prior to print"

,

122  "Publication-Status: Available-Online prior to print"

,

123  "Publication-Status : Available-Online prior to print"

,

130  for

(

size_t

pos = 0; pos < comment.size();) {

131

pos = comment.find(

"; "

, pos);

132  if

(pos == string::npos)

137  for

(

size_t i

= pos;

i

< comment.size(); ++

i

) {

138  char

c = comment[

i

];

139  if

(c ==

' '

|| c ==

';'

)

145

comment.erase(pos,

n

);

167  const char

*

months

[12] = {

"Jan"

,

"Feb"

,

"Mar"

,

"Apr"

,

"May"

,

"Jun"

,

"Jul"

,

"Aug"

,

"Sep"

,

"Oct"

,

"Nov"

,

"Dec"

};

170  for

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

178  if

(year < 1900 || year > 1994) {

210  if

(

b

< e &&

str

[e - 1] ==

';'

)

212  while

(

b

< e && (

str

[

b

] ==

'\"'

||

str

[

b

] ==

'\''

))

214  while

(

b

< e && (

str

[e - 1] ==

'\"'

||

str

[e - 1] ==

'\''

))

248  for

(p += 8; *p ==

' '

;)

277  for

(q = p; *q !=

' '

&& *q !=

'\0'

;)

297  for

(p += 7; *p ==

' '

;)

331  while

(*q ==

' '

|| *q ==

'\t'

)

333  for

(

r

= q; *

r

>=

'0'

&& *

r

<=

'9'

;)

336  if

(

r

== q || *

r

!=

'\0'

)

341  if

(*p !=

' '

&& *p !=

'\t'

&& *p !=

','

&& *p !=

';'

&& *p !=

'.'

)

344  while

(*p ==

' '

|| *p ==

'\t'

|| *p ==

','

|| *p ==

';'

|| *p ==

'.'

) {

349  if

(*p !=

' '

&& *p !=

'\t'

&& *p !=

','

&& *p !=

';'

&& *p !=

'.'

)

419  for

(s = bptr +

len

; *s ==

' '

;)

423  for

(country = s, q = s;

isalpha

((

int

)*s) || *s ==

' '

; s++)

438  for

(

number

= s, q = s;

isdigit

((

int

)*s) != 0 || *s ==

','

; s++)

453  for

(

type

= s; *s !=

' '

&& *s !=

'/'

&& *s !=

'\0'

;)

467  for

(app = s, q = s; *s >=

'0'

&& *s <=

'9'

;)

469  if

(*s !=

'\0'

&& *s !=

','

&& *s !=

'.'

&& *s !=

' '

&& *s !=

';'

&&

475

}

else if

(*s !=

'\0'

)

476  for

(*s++ =

'\0'

; *s ==

' '

;)

484  if

(std_date.

Empty

()) {

500

cit_pat->SetCountry(country);

501

cit_pat->SetNumber(

msg

);

503

cit_pat->SetDoc_type(

type

?

type

:

""

);

504

cit_pat->SetDate_issue().SetStd(*std_date);

505

cit_pat->SetTitle(title.

Empty

() ?

""

: title->GetName());

508  CAuth_list

& pat_auth_list = cit_pat->SetAuthors();

509

pat_auth_list.

SetNames

().SetStr().push_back(

""

);

511

cit_pat->SetAuthors(*auth_list);

517  if

(s < eptr && *s !=

'\0'

)

525

ibp->

psip

->SetCit().SetCountry(country);

526

ibp->

psip

->SetCit().SetId().SetNumber(

msg

);

529

ibp->

psip

->SetCit().SetDoc_type(

type

);

547  if

(! parts || *parts ==

'\0'

)

550  for

(p = parts,

i

= 0, j = 0; *p !=

'\0'

; p++) {

556  if

(j >

i

||

i

- j > 1)

560  if

(*p !=

'\0'

||

i

< 2)

566  for

(p = start + 1; *p ==

' '

;)

571  for

(q = end - 1; *q ==

' '

&& q > p;)

599  if

(! bptr || ! eptr)

602

parts =

StringSave

(string_view(bptr, eptr - bptr));

604  for

(p = parts; *p !=

'\0'

; p++)

629  for

(p = q; *p ==

' '

;)

631  for

(q = p; *q !=

'\0'

&& *q !=

' '

;)

637  for

(p = q; *p ==

' '

;)

639  for

(q = p; *q !=

'\0'

;)

642  for

(q--; *q ==

' '

;)

653

(issue_str[0] ==

'P'

|| issue_str[0] ==

'p'

) && (issue_str[1] ==

'T'

|| issue_str[1] ==

't'

) &&

654

issue_str[2] ==

'\0'

) {

661  for

(p = parts; *p ==

' '

;)

663  for

(q = p; *q !=

'\0'

&& *q !=

' '

;)

669  for

(p = q; *p ==

' '

;)

671  for

(q = p; *q !=

'\0'

;)

674  for

(q--; *q ==

' '

;)

700  char

* tit =

nullptr

;

701  char

* volume =

nullptr

;

702  char

* pages =

nullptr

;

731

end_volume =

nullptr

;

734

unique_ptr<char[]> pBuf(

new char

[

len

+ 1]);

735  char

*

buf

= pBuf.get();

738  while

(eptr >

buf

&& (*eptr ==

' '

|| *eptr ==

'\t'

|| *eptr ==

'.'

))

743  for

(s = eptr - 1; s >

buf

&& *s !=

'('

;)

750  for

(s--; s >=

buf

&&

isspace

((

int

)*s) != 0;)

755  if

(

buf

[0] ==

'G'

&&

buf

[1] ==

'3'

)

759  for

(

i

= 0; ss <= year; ss++) {

762  else if

(*ss ==

')'

)

764  else if

(*ss >=

'0'

&& *ss <=

'9'

&&

i

== 0)

768  for

(s = end_pages; s >=

buf

&& *s != symbol;)

786  for

(s = end_pages; s >=

buf

&& *s != symbol;)

792  if

(*s == symbol && ss != year) {

796  for

(pages = s + 1;

isspace

(*pages) != 0;)

799  if

(end_volume > ss) {

801  if

(*end_tit ==

'('

)

838  else if

(

i

== -1 && is_er > 0) {

846  if

(!

get_parts

(volume, end_volume, imp)) {

867  if

(date.

Empty

()) {

879  for

(

char

* aux = end_tit - 1; aux > tit && *aux !=

'.'

&& *aux !=

')'

&& !

isalnum

(*aux); --aux)

883  journal

.SetTitle().Set().push_back(journal_title);

889  if

((is_er & 01) == 01) {

913

cit_art->

SetTitle

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

938  for

(s = bptr; *s !=

'\0'

&& *s !=

'('

;)

945  if

(s < eptr && *s !=

'\0'

&& auth_list.

NotEmpty

())

948

cit_gen->SetCit(

string

(bptr,

str

+ 1));

952

cit_gen->SetAuthors(*auth_list);

955

cit_gen->SetTitle(title);

981  bool

IS_AUTH =

false

;

1010

cit_book.

SetImp

().SetPrepub(pre);

1016  for

(s = tbptr + 4; *s ==

' '

;)

1018  for

(bptr = s; *s !=

';'

&& *s !=

'('

&& *s !=

'\0'

;)

1026

}

else if

(*s ==

';'

)

1029  while

(*tit ==

' '

|| *tit ==

';'

|| *tit ==

'\n'

)

1032  if

(IS_AUTH && *bptr !=

'\0'

) {

1034  get_auth

(bptr, ref_fmt, jour, book_auth_list);

1048  for

(ss = tit; *ss !=

'\0'

;)

1050  for

(s = ss; *s !=

':'

&& s != tit;)

1058

book_title->SetName(

""

);

1059  if

(*tit !=

'\0'

) {

1062

cit_book.

SetImp

().SetVolume(volume);

1068  for

(pages = s; *s !=

'\0'

&& *s !=

','

&& *s !=

';'

;)

1073  while

(*pages ==

' '

)

1085  string

new_title = book_title->GetName();

1088

book_title->SetName(new_title);

1093  for

(press = s; *s !=

'('

&& *s !=

'\0'

;)

1101  if

(date.

Empty

()) {

1111

cit_book.

SetImp

().SetDate(*date);

1114

cit_book.

SetTitle

().Set().push_back(book_title);

1117

cit_art->

SetTitle

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

1146

book.

SetImp

().SetPrepub(pre);

1149  for

(s = bptr; *s !=

'\0'

&& *s !=

'('

;)

1155

book.

SetImp

().SetDate(*date);

1171

book.

SetTitle

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

1176

empty_title->SetName(

""

);

1177

book.

SetTitle

().Set().push_back(empty_title);

1201  for

(bptr += 5;

isspace

(*bptr) != 0;)

1205  for

(s = bptr; *s !=

'\0'

&& *s !=

'('

;)

1216

cit_book->

SetImp

().SetPrepub(pre);

1220

cit_book->

SetImp

().SetDate(*date);

1223  for

(s = bptr; *s !=

'\0'

&& *s !=

'.'

;)

1227

book_title->SetName(

string

(bptr, s));

1228

cit_book->

SetTitle

().Set().push_back(book_title);

1264  for

(s = bptr; *s !=

'('

&& *s !=

'\0'

;)

1277  isdigit

((

int

)*(s + 1)) == 0) {

1283

date->

SetStd

(*std_date);

1299  for

(s += 8; *s !=

'\0'

&& *s !=

':'

;)

1302  if

(*s !=

'\0'

&& *(s + 1) !=

'\0'

) {

1312  for

(s += l_str; *s ==

' '

|| *s ==

'.'

;)

1321  if

(*s !=

'\0'

&& auth_list.

NotEmpty

()) {

1362  for

(s = bptr; *s !=

'('

&& *s !=

'\0'

;)

1370  if

(std_date.

Empty

())

1374

date->

SetStd

(*std_date);

1386  const Char

* s = title->GetName().c_str();

1387  size_t

l_str =

StringLen

(

"Published by"

);

1388  if

(

StringEquN

(s,

"Published by"

, l_str)) {

1423  for

(p++; *p ==

' '

|| *p ==

'\t'

;)

1425  for

(q = p; *p >=

'0'

&& *p <=

'9'

;)

1427  for

(

r

= p; *p ==

' '

|| *p ==

'\t'

|| *p ==

')'

;)

1429  if

(*p ==

'\n'

|| *p ==

'\0'

) {

1436  for

(q--; *q ==

' '

|| *q ==

'\t'

|| *q ==

'('

;)

1446

cit_gen->SetCit(bptr);

1448

cit_gen->SetAuthors(*auth_list);

1449

cit_gen->SetTitle(title->GetName());

1452

cit_gen->SetDate().SetStd().SetYear(year);

1469  const Char

* title_str = title.

Empty

() ?

nullptr

: title->GetName().c_str();

1478  while

(*nearend ==

' '

|| *nearend ==

'\t'

|| *nearend ==

'.'

)

1485

*(nearend + 1) =

'\0'

;

1491  if

(pre == 0 && *end ==

'('

&&

isdigit

(*(end + 1)) != 0) {

1492  for

(nearend = end - 1; nearend > bptr && *nearend !=

' '

;)

1496

*(nearend + 1) =

'\0'

;

1501  if

(my_len >= 6 && *p ==

'('

) {

1512  const Char

* title_str = title.

Empty

() ?

nullptr

: title->GetName().c_str();

1519  if

(article.

Empty

())

1528  if

(cit_let.

Empty

()) {

1537  if

(cit_sub.

Empty

()) {

1548  if

(cit_sub.

Empty

()) {

1564  if

(cit_pat.

Empty

()) {

1578  if

(book.

Empty

()) {

1588  if

(cit_gen.

Empty

()) {

1599  if

(cit_gen.

Empty

()) {

1613  if

(new_art.

Empty

()) {

1614  if

(! all_zeros && !

fta_StartsWith

(bptr,

"(er)"

sv) && er == 0)

1629  if

(! pchStart || ! pchCurrent || pchStart >= pchCurrent)

1632  for

(pchCurrent--; pchCurrent >= pchStart; pchCurrent--) {

1633  if

(

isspace

((

int

)*pchCurrent) != 0)

1635  if

(*pchCurrent ==

';'

)

1636  return

(pchCurrent);

1646  if

(!

str

|| *

str

==

'\0'

)

1662  char

* pchNumber =

nullptr

;

1677

pchNumber = end + 1;

1680

pchNumber = end + 1;

1690  for

(p = comm; *p ==

' '

|| *p ==

'\t'

|| *p ==

'\n'

;)

1701  if

(! entry || xil.empty())

1704  for

(

const auto

& xip : xil) {

1705  if

(xip.subtags.empty())

1710  for

(

const auto

& xipqual : xip.subtags) {

1718

quals.push_back(qual);

1725  if

(doi.empty() && agricola.empty())

1731  if

(! agricola.empty()) {

1733  id

->SetOther().SetDb(

"AGRICOLA"

);

1734  id

->SetOther().SetTag().SetStr(agricola);

1736

cit_art.

SetIds

().Set().push_front(

id

);

1739  if

(! doi.empty()) {

1741  id

->SetDoi().Set(doi);

1743

cit_art.

SetIds

().Set().push_front(

id

);

1787  if

(p &&

isdigit

((

int

)*p) != 0) {

1788

desc->SetPub().Set().push_back(

get_num

(p));

1817  if

(! q || q[1] !=

'\0'

) {

1825  for

(q = p; *q ==

' '

|| *q ==

'.'

|| *q ==

','

;)

1839  for

(q = p; *q ==

' '

|| *q ==

'.'

|| *q ==

','

;)

1856

*p !=

'\0'

&& *p !=

';'

) {

1858  if

(! title.empty()) {

1873  if

(*p ==

'\0'

|| *p ==

';'

) {

1888

desc->SetComment(comm);

1896  if

(cit_art.

Empty

())

1903

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

1910  for

(

const auto

& xip : dbp.

GetXmlData

()) {

1917  for

(

const auto

& xref : xrefs) {

1918  if

(! xref->IsSetQual())

1922

agricola = xref->GetVal();

1924

doi = xref->GetVal();

1929  if

(pub_ref.

Empty

()) {

1937

desc->SetPub().Set().push_back(pub_ref);

1958

p = dbp.

mBuf

.

ptr

+ col_data;

1962  if

(*p >=

'0'

&& *p <=

'9'

)

1963

desc->SetPub().Set().push_back(

get_num

(p));

1977  if

(*p < '0' || *p >

'9'

)

1987

desc->SetPub().Set().push_back(

get_num

(p));

2001  for

(q = p; *q ==

' '

|| *q ==

'.'

|| *q ==

','

;)

2014  for

(q = p; *q ==

' '

|| *q ==

'.'

|| *q ==

','

;)

2028

*p !=

'\0'

&& *p !=

';'

) {

2030  if

(! title.empty()) {

2045  if

(*p ==

'\0'

|| *p ==

';'

) {

2059

desc->SetComment(comm);

2074

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

2079  if

(pub_ref.

Empty

()) {

2087

desc->SetPub().Set().push_back(pub_ref);

2115

p = dbp.

mBuf

.

ptr

+ col_data;

2116  while

((*p < '0' || *p >

'9'

) && dbp.

mBuf

.

len

> 0)

2118  if

(*p >=

'0'

&& *p <=

'9'

)

2119

desc->SetPub().Set().push_back(

get_num

(p));

2153

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

2166  for

(q = p; *q ==

' '

|| *q ==

'.'

|| *q ==

','

;)

2182  for

(q = p; *q ==

' '

|| *q ==

'.'

|| *q ==

','

;)

2195  if

(*p !=

'\0'

&& *p !=

';'

) {

2197  if

(! title.empty()) {

2212  if

(*p ==

'\0'

|| *p ==

';'

) {

2229

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

2234  if

(pub_ref.

Empty

()) {

2244

desc->SetPub().Set().push_back(pub_ref);

2252  for

(TPubList::iterator pub = pubs.begin(); pub != pubs.end(); ++pub) {

2253

TPubList::iterator next_pub = pub;

2254  for

(++next_pub; next_pub != pubs.end(); ++next_pub) {

2255  if

((*next_pub)->Which() > (*pub)->Which())

2258  if

((*next_pub)->Which() == (*pub)->Which()) {

2259  if

(! (*pub)->IsMuid() || (*pub)->GetMuid() >= (*next_pub)->GetMuid())

2263

pub->Swap(*next_pub);

2271  static const size_t

MAX_LAST_NAME_LEN = 30;

2279  if

(! author->IsSetName() || ! author->GetName().IsName())

2282  const CName_std

& name = author->GetName().GetName();

2294  FtaErrPost

(sev,

ERR_REFERENCE_LongAuthorName

,

"Last name of author exceeds 30 characters in length. A format error in the reference data might have caused the author name to be parsed incorrectly. Name is \"{}\"."

, name.

GetLast

());

2327

}

else if

(pub.

IsSub

())

2329  if

(! soft_report) {

2350  else if

(pub.

IsProc

()) {

2374  for

(

const auto

& cur_pub : pub.

GetEquiv

().

Get

()) {

2387  for

(

auto

& pub : pub_equiv.

Set

()) {

2389

muid = pub->GetMuid();

2391

pmid = pub->GetPmid().Get();

2392  else if

(pub->IsArticle() && ! cit_art)

2393

cit_art = &pub->SetArticle();

2401  id

->SetMedline().Set(muid);

2402

cit_art->

SetIds

().Set().push_front(

id

);

2407  id

->SetPubmed().Set(pmid);

2408

cit_art->

SetIds

().Set().push_front(

id

);

2423  bool

soft_report =

false

;

2426  bool

no_auth =

false

;

2429

soft_report =

true

;

2434

desc =

sp_refs

(pp, dbp, col_data);

2436

desc =

XMLRefs

(pp, dbp, no_auth, rej);

2438

desc =

gb_refs_common

(pp, dbp, col_data,

true

,

nullptr

, no_auth);

2440

desc =

embl_refs

(pp, dbp, col_data, no_auth);

2442  if

(desc && desc->IsSetComment()) {

2460  if

(desc.

NotEmpty

() && desc->IsSetPub()) {

2463  for

(

const auto

& pub : desc->GetPub().Get()) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

char * StringRStr(char *where, const char *what)

string tata_save(string_view t)

void ShrinkSpaces(char *line)

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

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

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

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

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

const TXmlIndexList & GetXmlData() const

struct DataBlk::@1166 mBuf

#define ERR_FORMAT_MultiplePatRefs

#define ERR_REFERENCE_Illegalreference

#define ERR_REFERENCE_InvalidInPress

#define ERR_REFERENCE_GsdbRefDropped

#define ERR_REFERENCE_Fail_to_parse

#define ERR_REFERENCE_LongAuthorName

#define ERR_REFERENCE_NoContactInfo

#define ERR_REFERENCE_MissingAuthors

#define ERR_REFERENCE_UnusualBookFormat

#define ERR_REFERENCE_Thesis

#define ERR_REFERENCE_IllegalDate

#define ERR_REFERENCE_InvalidMuid

#define INSDREFERENCE_REMARK

unique_ptr< string > XMLFindTagValue(const char *entry, const TXmlIndexList &xil, Int4 tag)

#define INSDREFERENCE_PUBMED

unique_ptr< string > XMLGetTagValue(const char *entry, const XmlIndex &xip)

#define INSDREFERENCE_AUTHORS

#define INSDREFERENCE_XREF

unique_ptr< string > XMLConcatSubTags(const char *entry, const TXmlIndexList &xil, Int4 tag, Char sep)

#define INSDREFERENCE_TITLE

#define INSDREFERENCE_JOURNAL

#define INSDREFERENCE_MEDLINE

#define INSDREFERENCE_CONSORTIUM

#define INSDREFERENCE_REFERENCE

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

forward_list< XmlIndex > TXmlIndexList

int fta_atoi(string_view sv)

bool fta_StartsWith(const char *s1, string_view s2)

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

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

void StringCpy(char *d, const char *s)

size_t StringLen(const char *s)

char * StringRChr(char *s, const char c)

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

CRef< CCit_art > FetchPubPmId(TEntrezId pmid)

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.

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

Convert string to int.

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

Check if a string starts with a specified prefix value.

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

Sanitize a string, allowing only specified classes of characters.

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

Case-insensitive equality of a substring with another string.

@ fAllowTrailingSymbols

Ignore trailing non-numerics characters.

@ eNocase

Case insensitive compare.

bool IsProc(void) const

Check if variant Proc is selected.

bool IsSetVolume(void) const

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

const TAuthors & GetAuthors(void) const

Get the Authors member data.

const TPart_supi & GetPart_supi(void) const

Get the Part_supi member data.

const TCit & GetCit(void) const

Get the Cit member data.

void SetPages(const TPages &value)

Assign a value to Pages data member.

void SetIds(TIds &value)

Assign a value to Ids data member.

const TBook & GetBook(void) const

Get the Book 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 SetTitle(TTitle &value)

Assign a value to Title data member.

void SetDate(TDate &value)

Assign a value to Date 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 IsSetApplicants(void) const

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

const TAuthors & GetAuthors(void) const

Get the Authors member data.

bool IsSetAssignees(void) const

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

void SetIssue(const TIssue &value)

Assign a value to Issue 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.

const TIssue & GetIssue(void) const

Get the Issue member data.

void SetAffil(TAffil &value)

Assign a value to Affil 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 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 ResetPart_supi(void)

Reset Part_supi data member.

TPrepub GetPrepub(void) const

Get the Prepub member data.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void ResetPrepub(void)

Reset Prepub data member.

const TProc & GetProc(void) const

Get the variant data.

void SetImp(TImp &value)

Assign a value to Imp data member.

TStr & SetStr(void)

Select the variant.

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.

void SetVolume(const TVolume &value)

Assign a value to Volume data member.

void SetNames(TNames &value)

Assign a value to Names data member.

bool IsSetIssue(void) const

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

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

void SetDate(TDate &value)

Assign a value to Date data member.

const TApplicants & GetApplicants(void) const

Get the Applicants member data.

bool IsSetDate(void) const

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

EPrepub

for prepublication citations

bool IsBook(void) const

Check if variant Book is selected.

void SetPubstatus(TPubstatus value)

Assign a value to Pubstatus data member.

bool IsSetAuthors(void) const

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

void SetMedium(TMedium value)

Assign a value to Medium data member.

bool IsSetBook(void) const

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

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.

const TStd & GetStd(void) const

Get the variant data.

void SetPart_sup(const TPart_sup &value)

Assign a value to Part_sup data member.

EMedium

medium of submission

void SetPrepub(TPrepub value)

Assign a value to Prepub data member.

bool IsSetPart_supi(void) const

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

const TAuthors & GetAuthors(void) const

Get the Authors member data.

const TAssignees & GetAssignees(void) const

Get the Assignees member data.

const TImp & GetImp(void) const

Get the Imp member data.

bool IsSetPages(void) const

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

void SetPart_supi(const TPart_supi &value)

Assign a value to Part_supi data member.

bool IsStd(void) const

Check if variant Std is selected.

const TBook & GetBook(void) const

Get the variant data.

@ ePubStatus_aheadofprint

epublish, but will be followed by print

@ ePubStatus_epublish

published electronically by publisher

@ ePrepub_in_press

accepted, not published

@ ePrepub_submitted

submitted, not accepted

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.

void SetDay(TDay value)

Assign a value to Day data member.

bool IsSetLast(void) const

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

const TLast & GetLast(void) const

Get the Last member data.

const TStd & GetStd(void) const

Get the variant data.

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 IsMedline(void) const

Check if variant Medline is selected.

TPmid & SetPmid(void)

Select the variant.

bool IsBook(void) const

Check if variant Book is selected.

const TMedline & GetMedline(void) const

Get the variant data.

const TMan & GetMan(void) const

Get the variant data.

TMuid & SetMuid(void)

Select the variant.

TBook & SetBook(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

const TArticle & GetArticle(void) const

Get the variant data.

const TSub & GetSub(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.

TMan & SetMan(void)

Select the variant.

bool IsEquiv(void) const

Check if variant Equiv is selected.

bool IsProc(void) const

Check if variant Proc is selected.

TSub & SetSub(void)

Select the variant.

bool IsSub(void) const

Check if variant Sub is selected.

TGen & SetGen(void)

Select the variant.

const TGen & GetGen(void) const

Get the variant data.

TPatent & SetPatent(void)

Select the variant.

bool IsPatent(void) const

Check if variant Patent 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.

bool IsMan(void) const

Check if variant Man is selected.

void SetQual(const TQual &value)

Assign a value to Qual data member.

bool IsSetQual(void) const

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

void SetVal(const TVal &value)

Assign a value to Val data member.

const TQual & GetQual(void) const

Get the Qual member data.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Tpg

Third Party Annot/Seq Genbank.

@ eReftype_no_target

nothing specified (EMBL)

void ind_subdbp(DataBlk &dbp, DataBlk *ind[], int maxkw, Parser::EFormat bank)

Int4 IsNewAccessFormat(const Char *acnum)

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

User-defined methods of the data storage class.

static CRef< CPub > get_muid(char *str, Parser::EFormat format)

static char * get_embl_str_pub_id(char *str, const Char *tag)

static CRef< CCit_art > get_book(char *bptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, CImprint::EPrepub pre, Parser::EFormat format, string_view jour)

Int4 fta_remark_is_er(const string &str)

static const char * ERRemarks[]

static void fta_check_long_name_in_article(const CCit_art &cit_art, bool soft_report)

static CRef< CPub > get_num(char *str)

static CRef< CPubdesc > embl_refs(ParserPtr pp, DataBlk &dbp, Uint2 col_data, bool &no_auth)

static void fta_check_long_last_name(const CAuth_list &authors, bool soft_report)

static string clean_up(const char *str)

static void fta_propagate_pmid_muid(CPub_equiv &pub_equiv)

static CRef< CCit_let > get_thesis(char *bptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, CImprint::EPrepub pre)

static TEntrezId get_embl_pmid(char *str)

static void fta_sort_pubs(TPubList &pubs)

static CRef< CCit_pat > get_pat(ParserPtr pp, char *bptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, char *eptr)

static const char * strip_sub_str[]

static CRef< CCit_sub > get_sub_gsdb(char *bptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, ParserPtr pp)

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

static void fta_add_article_ids(CPub &pub, const string &doi, const string &agricola)

static CRef< CCit_sub > get_sub(ParserPtr pp, char *bptr, CRef< CAuth_list > &auth_list)

static CRef< CCit_book > get_whole_book(char *bptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, CImprint::EPrepub pre)

static CRef< CPubdesc > gb_refs_common(ParserPtr pp, DataBlk &dbp, Uint2 col_data, bool bParser, DataBlk ***ppInd, bool &no_auth)

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 void fta_check_long_names(const CPub &pub, bool soft_report)

static void normalize_comment(string &comment)

static CRef< CCit_gen > fta_get_citgen(char *bptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title)

static void fta_get_part_sup(char *parts, CImprint &imp)

static CRef< CCit_art > get_art(ParserPtr pp, char *bptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, CImprint::EPrepub pre, bool has_muid, bool *all_zeros, Int4 er)

static char * ExtractErratum(char *comm)

static char * FindSemicolon(char *str)

static char * check_book_tit(char *title)

static bool get_parts(char *bptr, char *eptr, CImprint &imp)

static CRef< CPubdesc > XMLRefs(ParserPtr pp, const DataBlk &dbp, bool &no_auth, bool &rej)

static CRef< CDate > get_lanl_date(char *s)

static CRef< CCit_gen > get_unpub(char *bptr, char *eptr, CRef< CAuth_list > &auth_list, const Char *title)

static void XMLGetXrefs(char *entry, const TXmlIndexList &xil, TQualVector &quals)

static char * FindBackSemicolon(char *pchStart, char *pchCurrent)

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

@ ParFlat_PATENT_CITATION

@ ParFlat_ONLINE_CITATION

@ ParFlat_MONOGRAPH_NOT_JOURNAL

@ ParFlat_THESIS_CITATION

@ ParFlat_MISSING_JOURNAL

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

CRef< objects::CPatent_seq_id > psip

vector< IndexblkPtr > entrylist

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

void fta_StringCpy(char *dst, const char *src)

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

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)

CRef< CCit_gen > get_error(char *bptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title)

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

int XDateCheck(const CDate_std &date)


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