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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gb__index_8cpp_source.html below:

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

51 #define THIS_FILE "gb_index.cpp" 104 for

(p = line; *p !=

'\0'

&& *p !=

' '

&& *p !=

'\t'

;)

106

gi = (*p ==

'\0'

) ?

false

true

;

115

entry->

drop

true

;

120 for

(

= q + 1; *

'0'

&& *

'9'

;)

126

entry->

drop

true

;

137

entry->

drop

true

;

147

entry->

drop

true

;

152 for

(*p++ =

ch1

; *p ==

' '

|| *p ==

'\t'

;)

156 if

(*p !=

'\0'

&& ! ign_toks) {

167

entry->

drop

true

;

171 for

(q = p; *q >=

'0'

&& *q <=

'9'

;)

175

entry->

drop

true

;

191 for

(p = line; *p ==

' '

|| *p ==

'\t'

;)

211 for

(q =

str

+ 5; *q >=

'0'

&& *q <=

'9'

;)

217 for

(q = p + 5; *q >=

'0'

&& *q <=

'9'

;)

224 for

(q =

str

+ 5; *q ==

'0'

;)

227 for

(q = p + 5; *q ==

'0'

;)

236

ibp->

bases

= to - from + 1;

278 auto

tibnp = ibl.before_begin();

281 while

(! end_of_file) {

285

tibnp = ibl.emplace_after(tibnp, entry);

293

after_LOCUS =

false

;

294

after_DEFNTN =

false

;

295

after_SOURCE =

false

;

296

after_REFER =

false

;

298

after_ORIGIN =

false

;

299

after_COMMENT =

false

;

300

after_VERSION =

false

;

306

line_locus =

nullptr

;

313 while

(currentKeyword !=

ParFlat_END

&& ! end_of_file) {

314 switch

(currentKeyword) {

318

entry->

drop

true

;

327

entry->

drop

true

;

329

after_COMMENT =

true

;

334 if

(p && atol(p + 3) > 0)

336 if

(pp->

accver

false

)

340

entry->

drop

true

;

343

after_VERSION =

true

;

345 while

(*p ==

' '

|| *p ==

'\t'

)

347 for

(q = p; *q !=

'\0'

&& *q !=

'\r'

&& *q !=

'\n'

;)

351 if

(*q !=

' '

&& *q !=

'\t'

) {

356

line_ver =

StringSave

(string_view(p, q - p));

362 while

(*p ==

' '

|| *p ==

'\t'

)

364 for

(q = p; *q !=

'\0'

&& *q !=

' '

&& *q !=

'\t'

365

*q !=

'\r'

&& *q !=

'\n'

;)

367

line_nid =

StringSave

(string_view(p, q - p));

372

entry->

drop

true

;

373

}

else if

(after_LOCUS ==

false

) {

375

entry->

drop

true

;

377

after_DEFNTN =

true

;

383

entry->

drop

true

;

384

}

else if

(after_LOCUS ==

false

|| after_DEFNTN ==

false

) {

386

entry->

drop

true

;

388

after_SOURCE =

true

;

397

entry->

drop

true

;

402 if

(entry->

is_mga

false

) {

404

entry->

drop

true

;

408

entry->

drop

true

;

415

entry->

drop

true

;

417

(after_LOCUS ==

false

418

after_DEFNTN ==

false

419

after_SOURCE ==

false

)) {

421

entry->

drop

true

;

429

entry->

drop

true

;

432

(after_LOCUS ==

false

433

after_DEFNTN ==

false

434

after_SOURCE ==

false

435

after_FEAT ==

false

)) {

437

entry->

drop

true

;

439

after_ORIGIN =

true

;

444 if

(acwflag ==

false

)

456 "Error at linenum %d. Segmented sets are not supported."

458

entry->

drop

true

;

463

entry->

drop

true

;

467 if

(entry->

is_tpa

false

478

kwds.push_front(finfo.

str

+ 8);

483

dbl.push_front(finfo.

str

+ 8);

492 while

(! end_of_file && (finfo.

str

[0] ==

' '

|| finfo.

str

[0] ==

'\t'

)) {

494

kwds.push_back(finfo.

str

);

499

dbl.push_back(finfo.

str

);

511 if

(! kwds.empty()) {

525 if

(finfo.

str

[0] !=

' '

&& finfo.

str

[0] !=

'\t'

527

entry->

drop

true

;

533 if

(! entry->

drop

) {

538

entry->

drop

true

;

540 if

(entry->

is_mga

&& after_MGA ==

false

)

543 if

(after_LOCUS ==

false

)

546 if

(after_VERSION ==

false

&& pp->

accver

)

549 if

(after_DEFNTN ==

false

)

552 if

(after_SOURCE ==

false

)

556

entry->

is_wgs

false

562 if

(after_FEAT ==

false

) {

581

line_locus =

nullptr

;

593 if

(acwflag ==

false

601

(*fun)(entry,

data

->mBuf.ptr,

static_cast<Int4>

(

data

->mBuf.len));

620 for

(

auto

& it : ibl) {

624 return

(end_of_file);

bool QSIndex(ParserPtr pp, const TIndBlkList &ibl, unsigned ibl_size)

DataBlk * LoadEntry(ParserPtr pp, size_t offset, size_t len)

#define ERR_FORMAT_LineTypeOrder

std::list< std::string > TKeywordList

int fta_atoi(string_view sv)

bool fta_StartsWith(const char *s1, string_view s2)

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

bool StringEqu(const char *s1, const char *s2)

size_t StringLen(const char *s)

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

void FtaDeletePrefix(int prefix)

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

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

vector< string > genbankKeywords

static void ParseGenBankVersion(IndexblkPtr entry, char *line, char *nid, Parser::ESource source, Parser::EMode mode, bool ign_toks)

static bool gb_err_field(const char *str)

bool GenBankIndex(ParserPtr pp, void(*fun)(IndexblkPtr entry, char *offset, Int4 len))

static bool fta_check_mga_line(char *line, IndexblkPtr ibp)

int32_t Int4

4-byte (32-bit) signed integer

char Char

Alias for char.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

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

IndexblkPtr InitialEntry(ParserPtr pp, FinfoBlk &finfo)

bool FindNextEntryBuf(bool end_of_file, FileBuf &fbuf, FinfoBlk &finfo, string_view keyword)

bool XReadFileBuf(FileBuf &fbuf, FinfoBlk &finfo)

bool CkLocusLinePos(char *offset, Parser::ESource source, LocusContPtr lcp, bool is_mga)

void MsgSkipTitleFail(const char *flatfile, FinfoBlk &finfo)

bool SkipTitleBuf(FileBuf &fbuf, FinfoBlk &finfo, string_view keyword)

forward_list< unique_ptr< Indexblk > > TIndBlkList

#define ERR_VERSION_NonDigitVerNum

#define ERR_VERSION_MissingVerNum

#define ERR_ACCESSION_NoAccessNum

#define ERR_FORMAT_IncorrectMGALine

#define ERR_VERSION_IncorrectGIInVersion

#define ERR_VERSION_NonDigitGI

#define ERR_VERSION_BadVersionLine

#define ERR_VERSION_InvalidVersion

#define ERR_FORMAT_MissingField

#define ERR_ENTRY_InvalidLineType

#define ERR_VERSION_AccessionsDontMatch

if(yy_accept[yy_current_state])

const CharType(& source)[N]

static const BitmapCharRec ch1

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

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

vector< IndexblkPtr > entrylist

void check_est_sts_gss_tpa_kwds(const TKeywordList &kwds, size_t len, IndexblkPtr entry, bool tpa_check, bool &specialist_db, bool &inferential, bool &experimental, bool &assembly)

bool CheckLineType(string_view str, Int4 type, const vector< string > &keywordList, bool after_origin)

int SrchKeyword(string_view str, const vector< string > &keywordList)

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