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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/em__index_8cpp_source.html below:

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

52 #define THIS_FILE "em_index.cpp" 77 "ID"

"AC"

"NI"

"DT"

"DE"

"KW"

"OS"

"OC"

"OG"

"RN"

"RP"

"RX"

"RC"

"RG"

"RA"

"RT"

"RL"

"DR"

"FH"

"FT"

"SQ"

"CC"

"SV"

"CO"

"XX"

"AH"

"AS"

"PR"

"//" 91 size_t

p = line.rfind(

'.'

);

92 if

(p == string_view::npos) {

97 string

acc(line.substr(0, p));

99 string

ver(line.substr(p));

100 for

(

size_t

q = p; q < line.size(); ++q) {

101 if

(line[q] <

'0'

|| line[q] >

'9'

) {

103

entry->

drop

true

;

107 if

(entry->

acnum

!= acc) {

109

entry->

drop

true

;

115

entry->

drop

true

;

122 if

(locus.empty() ||

str

.empty())

124 auto

p =

str

.find(

';'

);

125 if

(p == string_view::npos)

128 while

(p <

str

.size() &&

str

[p] ==

' '

)

130 if

(p + 2 >=

str

.size() ||

str

[p] !=

'S'

str

[p + 1] !=

'V'

)

133 while

(p <

str

.size() &&

str

[p] ==

' '

)

135 auto

q =

str

.find(

';'

, p);

136 if

(q == string_view::npos)

141

res +=

str

.substr(p, q - p);

180 auto

tibnp = ibl.before_begin();

182 while

(! end_of_file) {

187

tibnp = ibl.emplace_after(tibnp, entry);

203

optional<string> line_sv;

214 while

(! end_of_file &&

216 const

string_view line = finfo.

str

;

217 if

(line.starts_with(keywordKw)) {

222

}

else if

(line.starts_with(keywordId)) {

225

entry->

drop

true

;

231

}

else if

(line.starts_with(keywordAh)) {

236 if

(after_SQ &&

isalpha

(line.front())) {

238

entry->

drop

true

;

241 if

(line.starts_with(keywordNi)) {

244

entry->

drop

true

;

248

}

else if

(line.starts_with(keywordSq)) {

251

}

else if

(line.starts_with(keywordOs)) {

258

line.starts_with(keywordSv)) {

261

entry->

drop

true

;

265

entry->

drop

true

;

270 while

(*p ==

' '

|| *p ==

'\t'

)

273 for

(; *q !=

'\0'

&& *q !=

' '

&& *q !=

'\t'

279 if

(line.starts_with(

"OC"

sv))

283 if

(line.starts_with(keywordRn))

287 if

(line.starts_with(keywordCo))

292 if

(line.starts_with(keywordAc)) {

293 if

(after_AC ==

false

) {

297

}

else if

(! entry->

drop

300

}

else if

(line.starts_with(keywordDt)) {

302 if

(tokens.num > 2) {

311 if

(finfo.

str

[0] !=

' '

&& finfo.

str

[0] !=

'\t'

) {

313

entry->

drop

true

;

324 if

(! entry->

drop

) {

325 if

(after_AC ==

false

) {

327

entry->

drop

true

;

330 if

(after_ID ==

false

)

333 if

(after_SV ==

false

&& pp->

accver

337 if

(after_OS ==

false

)

340 if

(after_OC ==

false

)

343 if

(after_RN ==

false

)

346 if

(after_DT ==

false

)

349 if

(after_SQ ==

false

&& entry->

is_contig

false

)

361

(*fun)(entry,

data

->mBuf.ptr,

static_cast<Int4>

(

data

->mBuf.len));

382 for

(

auto

& it : ibl) {

386 return

(end_of_file);

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

const list< string > KeywordList() const

void AddDataLine(const string &line)

static optional< string > EmblGetNewIDVersion(string_view locus, string_view str)

vector< string > emblKeywords

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

static void ParseEmblVersion(IndexblkPtr entry, string_view line)

static bool em_err_field(const char *str)

vector< string > checkedEmblKeywords

#define ParFlat_COL_DATA_EMBL

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

#define ERR_FORMAT_MissingEnd

int fta_atoi(string_view sv)

bool fta_StartsWith(const char *s1, string_view s2)

void FtaDeletePrefix(int prefix)

#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)

int32_t Int4

4-byte (32-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IndexblkPtr InitialEntry(ParserPtr pp, FinfoBlk &finfo)

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

CRef< CDate_std > GetUpdateDate(string_view str, Parser::ESource source)

bool XReadFileBuf(FileBuf &fbuf, FinfoBlk &finfo)

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_ORGANISM_Multiple

#define ERR_VERSION_MissingVerNum

#define ERR_ACCESSION_NoAccessNum

#define ERR_FORMAT_Multiple_SV

#define ERR_VERSION_InvalidVersion

#define ERR_FORMAT_MissingField

#define ERR_FORMAT_Multiple_NI

#define ERR_ENTRY_InvalidLineType

#define ERR_VERSION_AccessionsDontMatch

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

CRef< objects::CDate_std > date

vector< IndexblkPtr > entrylist

CKeywordParser & KeywordParser()

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

TokenStatBlk TokenString(string_view str, Char delimiter)

void xCheckEstStsGssTpaKeywords(const list< string > keywordList, bool tpa_check, IndexblkPtr entry)

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