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;

345 const string

s = to_string(bases);

346 const string str

"(bases 1 to "

+ s +

")"

;

347 const string

str1 =

"(bases 1 to "

+ s +

";"

;

348 const string

str2 =

"(residues 1 to "

+ s +

"aa)"

;

350 string

ref(bptr, bptr + dbp.

);

352 while

(bptr < eptr && *bptr !=

'\n'

&& *bptr !=

'('

)

354 while

(*bptr ==

' '

)

385

eptr = bptr + dbp.

;

386

ptr =

(string_view(bptr, eptr),

'\n'

);

392 while

(bptr < eptr) {

398

bptr =

(string_view(bptr, eptr),

'\n'

);

402 if

(! string_view(bptr, eptr - bptr).starts_with(

"XX"

sv))

406

}

while

((*ptr ==

' '

&& ptr < eptr) || skip);

418 if

(! dbp.

ptr

|| (mtag.empty() && ptag.empty()))

426 for

(p = dbp.

ptr

;; p++) {

456 auto

& src_blk = *dbp;

462 for

(

auto

& ref_blk : chain) {

479 for

(

auto

& feat_blk : chain) {

493 auto

secType = secPtr->mType;

512

secPtr->xBuildFeatureBlocks();

546 bool

seen_oc =

false

;

554 for

(; ptr < eptr && *ptr !=

'\n'

; ptr++)

563

string_view sv(ptr, eptr);

567 if

(sv.starts_with(

"RN"

sv))

569 if

(sv.starts_with(

"ID"

sv))

572 if

(sv.starts_with(

"OC"

sv))

575 if

(seen_oc && sv.starts_with(

"OS"

sv))

578

}

while

(nextkw == curkw);

606

eptr = bptr + dbp.

;

607

ptr =

(string_view(bptr, eptr),

'\n'

);

609 while

(ptr && ptr + 1 < eptr) {

610 if

(ptr[2] ==

'H'

) {

615

eptr = bptr + dbp.

;

619 if

(bptr[1] ==

'T'

) {

626

ptr =

(string_view(bptr, eptr),

'\n'

);

644 while

(bptr < eptr) {

645

string_view sv(bptr, eptr - bptr);

646 if

(sv.starts_with(subkw))

649 auto i

= sv.find(

'\n'

);

650 if

(

!= string_view::npos)

677

eptr = bptr + dbp.

;

687 const string str

" 1-"

+ to_string(bases);

694 if

(

(string_view(bptr, eptr),

" 0-0"

)) {

702 for

(sptr = bptr + 1; sptr < eptr && *sptr !=

'R'

;)

704 if

(

(string_view(bptr, sptr),

"sites"

))

726 for

(

auto

& os_blk : chain) {

735 for

(

auto

& ref_blk: chain) {

751 auto

predbp = chain.begin();

752 auto

curdbp =

(predbp);

753 while

(curdbp != chain.end()) {

770

curdbp = chain.erase_after(predbp);

790

eptr = bptr + dbp.

;

816 if

(holds_alternative<monostate>(dbp.

mData

))

819 if

(subblocks.empty())

827 auto

ldbp = subblocks.cend();

828 for

(

auto

ndbp = subblocks.cbegin(); ndbp != subblocks.cend(); ++ndbp) {

829 size_t l

= ndbp->mBuf.ptr -

offset

;

836 if

(ldbp != subblocks.cbegin() && ldbp != subblocks.cend()) {

841 for

(

auto

curdbp = subblocks.begin();

(curdbp) != subblocks.end(); ++curdbp) {

842 offset

= curdbp->mBuf.ptr;

843

ldbp = subblocks.end();

844 for

(

auto

ndbp = subblocks.begin(); ndbp != subblocks.end(); ++ndbp) {

845 size_t l

= ndbp->mBuf.ptr -

offset

;

846 if

(

> 0 && l < curdbp->mBuf.len) {

847

curdbp->mBuf.len =

;

851 if

done

&& ldbp !=

(curdbp) && ldbp != subblocks.end()) {

864 if

(! acc || *acc ==

'\0'

)

872

pat_id->SetCit().SetCountry(

string

(p + 1, q));

875

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

string

(q + 1, p));

878

pat_id->SetCit().SetDoc_type(

string

(p + 1, q));

880

pat_id->SetSeqid(

fta_atoi

(q + 1));

938 if

(! acc || *acc ==

'\0'

)

947

text_id->SetAccession(acc);

949 if

(accver && vernum > 0)

950

text_id->SetVersion(vernum);

967 if

(! locus || *locus ==

'\0'

)

971

text_id->SetName(locus);

999 auto

sdbp = sdb.cbegin();

1000 while

(sdbp != sdb.cend() && sdbp->mType != subtype)

1002 if

(sdbp == sdb.cend())

1005

= sdbp->mBuf.len;

1006 return

(sdbp->mBuf.ptr);

1018

bioseq.

().push_back(seqId);

1042 id

->SetPatent(*psip);

1043

res->

().push_back(

id

);

1054

res->

().push_back(std::move(pId));

1057

res->

().push_back(std::move(pId));

1061

}

else if

((! locus || *locus ==

'\0'

) && (! acc || *acc ==

'\0'

)) {

1066 if

(ibp->

embl_new_ID

false

&& locus && *locus !=

'\0'

1068

textId->SetName(locus);

1070 if

(acc && *acc !=

'\0'

)

1071

textId->SetAccession(acc);

1074

textId->SetVersion(ibp->

vernum

);

1077 if

(

SetTextId

(seqtype, *seqId, *textId))

1078

res->

().push_back(seqId);

1114 bool

within =

false

;

1116 char

* eptr = bptr +

;

1119 for

(

= com; bptr < eptr; bptr = p + 1) {

1123 if

((is_htg && bptr[col_data] ==

'*'

) ||

1124

string_view(bptr, eptr - bptr).starts_with(

"XX"

sv))

1128 if

(

(string_view(bptr, p),

"-START##"

))

1140 if

(*(

- 1) !=

'~'

)

1146 if

(p - bptr < col_data)

1150 size_t size

= p - bptr;

1152 if

(*bptr ==

' '

&& *(

- 1) !=

'~'

)

1156 if

(is_pat &&

size

> 4 &&

1157

q[0] >=

'A'

&& q[0] <=

'Z'

&& q[1] >=

'A'

&& q[1] <=

'Z'

1160 else if

(

size

< 50 || within)

1166 if

(

ERR_ACCESSION_WGSWithNonWGS_Sec

(string_view(bptr, p),

"-END##"

))

1175 for

(p += 2, eptr = p; *eptr ==

' '

;)

1180 for

(p = com; *p ==

' '

;)

1184 for

(p = com; *p !=

'\0'

;)

1188 if

(*p ==

' '

|| *p ==

'\t'

|| *p ==

';'

|| *p ==

','

1189

*p ==

'.'

|| *p ==

'~'

) {

1216 auto

it1 = secondaries.begin();

1217 if

(it1 == secondaries.end() || it1->empty())

1219 auto

it2 =

(it1);

1220 if

(it2 == secondaries.end() || *it2 !=

"-"

fta_if_wgs_acc

(*it1) != 0)

1223 auto

tbp = secondaries.insert_after(it1, *it1);

1246 bool

unusual_wgs_msg;

1257

is_cp = (acc[0] ==

'C'

&& acc[1] ==

'P'

);

1260 if

(pri_acc == 1 || pri_acc == 4) {

1262 for

(p = acc; (*p >=

'A'

&& *p <=

'Z'

) || *p ==

'_'

;)

1272

unusual_wgs =

false

;

1273 for

(

auto

tbp = ibp->

secaccs

.begin(); tbp != ibp->

secaccs

.end(); ++tbp) {

1274 if

(*tbp ==

"-"

s) {

1276 if

(tbp == ibp->

secaccs

.end())

1278 if

(! accessions.empty()) {

1279

accessions.back() +=

'-'

;

1280

accessions.back() += *tbp;

1286 const string

= *tbp;

1289

unusual_wgs_msg =

true

;

1290 if

(sec_acc == 0 || sec_acc == 3 ||

1291

sec_acc == 4 || sec_acc == 6 ||

1292

sec_acc == 10 || sec_acc == 12)

1301

unusual_wgs_msg =

false

;

1302 if

(ibp->

wgssec

.empty())

1308 if

(sec_acc < 0 || sec_acc == 2) {

1309 if

(pri_acc == 1 || pri_acc == 5 || pri_acc == 11) {

1310 if

(! allow_uwsec) {

1311 FtaErrPost

(

SEV_REJECT

"This WGS/TSA/TLS record has non-WGS/TSA/TLS secondary accession \"{}\". WGS/TSA/TLS records are not currently allowed to replace finished sequence records, scaffolds, etc. without human review and confirmation."

);

1318

accessions.push_back(

);

1322 if

(sec_acc == 3 || sec_acc == 6)

1325

(pri_acc == 1 || pri_acc == 5 || pri_acc == 11) &&

1336 if

(pri_acc == 1 || pri_acc == 5 || pri_acc == 11)

1339 i

.starts_with(

"NZ_"

sv) ? 7 : 4;

1340 if

.starts_with(string_view(ibp->

acnum

))) {

1341 if

(! allow_uwsec) {

1342 FtaErrPost

(

SEV_REJECT

ERR_ACCESSION_UnusualWGS_Secondary

"This record has one or more WGS/TSA/TLS secondary accession numbers which imply that a WGS/TSA/TLS project is being replaced (either by another project or by finished sequence). This is not allowed without human review and confirmation."

);

1345 FtaErrPost

(

SEV_WARNING

ERR_ACCESSION_UnusualWGS_Secondary

"This record has one or more WGS/TSA/TLS secondary accession numbers which imply that a WGS/TSA project is being replaced (either by another project or by finished sequence). This is being allowed via the use of a special parser flag."

);

1348

}

else if

(pri_acc == 2)

1350 if

(sec_acc == 1 || sec_acc == 5 || sec_acc == 11)

1356

}

else if

(unusual_wgs_msg) {

1357 if

(! allow_uwsec) {

1358 if

(! unusual_wgs) {

1359 if

(sec_acc == 1 || sec_acc == 5 || sec_acc == 11)

1360 text

"WGS/TSA/TLS contig secondaries are present, implying that a scaffold is replacing a contig"

;

1362 text

"This record has one or more WGS/TSA/TLS secondary accession numbers which imply that a WGS/TSA/TLS project is being replaced (either by another project or by finished sequence)"

;

1365

unusual_wgs =

true

;

1368 if

(! unusual_wgs) {

1369 if

(sec_acc == 1 || sec_acc == 5 || sec_acc == 11)

1370 text

"WGS/TSA/TLS contig secondaries are present, implying that a scaffold is replacing a contig"

;

1372 text

"This record has one or more WGS/TSA/TLS secondary accession numbers which imply that a WGS/TSA/TLS project is being replaced (either by another project or by finished sequence)"

;

1375

unusual_wgs =

true

;

1379 if

(pri_acc == 1 || pri_acc == 5 || pri_acc == 11) {

1380 if

(

StringEquN

(acc,

.c_str(),

) &&

[

] >=

'0'

[

] <=

'9'

) {

1381 if

(sec_acc == 1 || sec_acc == 5 || pri_acc == 11)

1382

accessions.push_back(

);

1383

}

else if

(allow_uwsec) {

1384

accessions.push_back(

);

1386

}

else if

(pri_acc == 2) {

1387 if

(sec_acc == 0 || sec_acc == 4)

1388

accessions.push_back(

);

1390

accessions.push_back(

);

1402 for

(

string

key

: keywords) {

1409 string buf

(

"TPA:"

);

1411 for

(p =

key

.c_str() + 4; *p ==

' '

|| *p ==

'\t'

;)

1416 for

(string::iterator p =

buf

.begin() + 4; p !=

buf

.end(); ++p) {

1417 if

(*p >=

'A'

&& *p <=

'Z'

)

1429 string

& keywordData)

1432 const string

problematic(

"WGS Third Party Data"

);

1433 const string

desired(

"WGS; Third Party Data"

);

1435 if

(keywordData.empty()) {

1439 if

(wgsStart == string::npos) {

1442 auto

afterProblematic = keywordData[wgsStart + problematic.size()];

1443 if

(afterProblematic !=

';'

&& afterProblematic !=

'.'

) {

1447 string

fixedKeywords;

1449 auto

semiBefore = keywordData.rfind(

';'

, wgsStart - 1);

1450 if

(semiBefore == string::npos) {

1453 for

(

auto i

= semiBefore + 1;

< wgsStart; ++

) {

1454 if

(keywordData[

] !=

' '

) {

1458

fixedKeywords = keywordData.substr(0, wgsStart - 1);

1460

fixedKeywords += desired;

1461

fixedKeywords += keywordData.substr(wgsStart + problematic.size());

1462

keywordData = fixedKeywords;

1478 if

(

.empty()) {

1488 auto

it = keywords.begin();

1489 auto last

= --keywords.end();

1490 while

(it != keywords.end()) {

1491 auto

& keyword = *it;

1497 if

(keyword.empty()) {

1498

keywords.erase(it++);

1551 while

(*ptr !=

'\n'

&& *ptr !=

'\0'

&& blank < 6 &&

< 100) {

1552 if

(numns && (*ptr ==

'n'

|| *ptr ==

'N'

))

1563

}

else if

(residue == 1 && (warn ||

isalpha

(*ptr) != 0)) {

1565

*bu++ = replacechar;

1617 for

(

char

& c : *

)

1618 if

(c >=

'A'

&& c <=

'Z'

)

1629

endptr = seqptr +

;

1639 while

(*seqptr ==

' '

|| *seqptr ==

'\n'

|| *seqptr ==

'\t'

)

1642 while

(*seqptr !=

'\n'

)

1644 while

(

isalpha

(*seqptr) == 0)

1648

std::vector<char>

buf

;

1650 for

(numns = 0; seqptr < endptr;) {

1659 while

(

isalpha

(*seqptr) == 0 && seqptr < endptr)

1677 "This sequence for this patent record falls below the minimum length requirement of 4 amino acids."

);

1684 if

(ibp->

is_pat

false

)

1689 if

(ibp->

is_pat

false

)

1696 if

(seqlen ==

static_cast<Uint4>

(numns)) {

1718

unique_ptr<unsigned char[]> dnaconv(

new unsigned char

[255]());

1719 MemSet

((

char

*)dnaconv.get(), (

)1, (

size_t

)255);

1727

dnaconv[

static_cast<int>

(

[0])] =

[0];

1738 static

unique_ptr<unsigned char[]> dnaconv;

1740 if

(! dnaconv.get()) {

1742 if

(! dnaconv.get()) {

1743

dnaconv.reset(

new unsigned char

[255]());

1744 MemSet

((

char

*)dnaconv.get(), (

)1, (

size_t

)255);

1749

dnaconv[

static_cast<int>

(

[0])] =

[0];

1755 return

dnaconv.get();

1770

unique_ptr<unsigned char[]> protconv(

new unsigned char

[255]());

1773 MemSet

((

char

*)protconv.get(), (

)1, (

size_t

)255);

1793 static

unique_ptr<unsigned char[]> protconv;

1794 if

(! protconv.get()) {

1796 if

(! protconv.get()) {

1797

protconv.reset(

new unsigned char

[255]());

1798 MemSet

((

char

*)protconv.get(), (

)1, (

size_t

)255);

1808 return

protconv.get();

1828 if

(

id

.NotEmpty()) {

1849 bool check_div

(

bool

pat_acc,

bool

pat_ref,

bool

est_kwd,

bool

sts_kwd,

bool

gss_kwd,

bool

if_cds,

string

& div,

CMolInfo::TTech

* tech,

size_t

bases,

Parser::ESource source

bool

& drop)

1854 if

(pat_acc || pat_ref || div ==

"PAT"

) {

1855 if

(pat_ref ==

false

) {

1871 if

(div !=

"PAT"

) {

1878

}

else if

(est_kwd) {

1880 if

(div ==

"EST"

) {

1887

}

else if

(bases > 1000) {

1888 if

(div ==

"EST"

) {

1901

}

else if

(div ==

"EST"

) {

1909

}

else if

(sts_kwd) {

1911 if

(div ==

"STS"

) {

1918

}

else if

(bases > 1000) {

1919 if

(div ==

"STS"

) {

1932

}

else if

(div ==

"STS"

) {

1937

}

else if

(gss_kwd) {

1939 if

(div ==

"GSS"

) {

1946

}

else if

(bases > 2500) {

1947 if

(div ==

"GSS"

) {

1960

}

else if

(div ==

"GSS"

) {

1965

}

else if

(div ==

"TSA"

) {

1970 return

! div.empty();

1982 if

(*pch ==

'd'

|| *pch ==

'e'

) {

1985

lID = strtol(pch + 1, &pchEnd, 10);

1987 if

(! ((lID == 0 && pch + 1 == pchEnd) || (lID == LONG_MAX && errno == ERANGE))) {

1992 tag

->SetStr(

string

(pch, pchEnd - pch));

1996

dbtag->

SetDb

(pid ?

"PID"

"NID"

);

1998 id

->SetGeneral(*dbtag);

2018

bioseq.

().push_back(sid);

2026 for

(

auto

& entry : seq_entries) {

2029 if

(bioseq->IsSetId())

2031 for

(

const auto

id

: bioseq->GetId())

2040 if

(bioseq->IsSetDescr()) {

2045 for

(

auto

& descr : bioseq->SetDescr().Set()) {

2046 if

(descr->IsGenbank() && ! gb_block)

2047

gb_block = &descr->SetGenbank();

2048 else if

(descr->IsMolinfo() && ! molinfo) {

2049

molinfo = &descr->SetMolinfo();

2053 if

(gb_block && molinfo)

2066 if

(! gb_block->

() && (!ispat ||

2071 else if

(gb_block->

() && ispat &&

2085 for

(

const auto

& descr : descrs) {

2086 if

(descr->IsSource())

2087 return

&(descr->GetSource());

2109 if

(seq_entries.empty())

2132 for

(q =

; *q !=

'\0'

; q++) {

2135 else if

(*q ==

'\n'

|| *q ==

'\t'

)

2138 for

(q =

, p =

; *p !=

'\0'

; p++) {

2139 if

(*p ==

' '

&& p[1] ==

' '

)

2151

! p && ! cancelled) {

2163 r

new char

[dbp->

+ 1];

2168 for

(p =

, q =

; *p !=

'\0'

; p++)

2169 if

(*p >=

'a'

&& *p <=

'z'

)

2173 for

(

= 0, p =

; *p !=

'\0'

; p++) {

2176 else if

(++

> 10) {

2194 if

(! entry || xil.empty())

2201 for

(q =

; *q !=

'\0'

; q++)

2202 if

(*q ==

'\n'

|| *q ==

'\t'

)

2204 for

(q =

, p =

; *p !=

'\0'

; p++) {

2205 if

(*p ==

' '

&& p[1] ==

' '

)

2217

! p && ! cancelled) {

2230 for

(

= 0, p =

; *p !=

'\0'

; p++) {

2233 else if

(++

> 10) {

2246

}

else if

((! div || !

StringEqu

(div,

"HTG"

)) &&

2256 if

(entry.

IsSeq

())

2268 size_t

start_pos = 0;

2269 for

(; start_pos >

.size() &&

[start_pos] <=

' '

; ++start_pos)

2272 if

(start_pos ==

.size()) {

2277 str

.substr(start_pos);

2278 size_t

end_pos =

.size() - 1;

2279 for

(;; --end_pos) {

2280 if

(

[end_pos] ==

';'

[end_pos] <=

' '

) {

2289 if

(

[end_pos] !=

';'

|| end_pos == 0) {

2293 str

.substr(0, end_pos);

2298 size_t

amp_pos = end_pos - 1;

2299 for

(; amp_pos; --amp_pos) {

2300 if

(

[amp_pos] ==

' '

[amp_pos] ==

'&'

[amp_pos] ==

';'

)

2304 if

(

[amp_pos] ==

'&'

)

2307 str

.substr(0, end_pos);

2313 for

(list<string>::iterator it = str_list.begin(); it != str_list.end();) {

2317

it = str_list.erase(it);

2326 const Char

* div =

nullptr

;

2328 for

(

const auto

& descr : descrs) {

2329 if

(! descr->IsEmbl())

2332 if

(! descr->GetEmbl().IsSetDiv() || descr->GetEmbl().GetDiv() > 15)

2335

div =

GetEmblDiv

(descr->GetEmbl().GetDiv());

2339 for

(TSeqdescList::iterator descr = descrs.begin(); descr != descrs.end();) {

2340 if

(! (*descr)->IsGenbank()) {

2345 CGB_block

& gb_block = (*descr)->SetGenbank();

2351

}

else if

(gb_block.

() && gb_block.

GetDiv

() !=

"PAT"

2352

gb_block.

GetDiv

() !=

"SYN"

) {

2401

descr = descrs.erase(descr);

2413 for

(

auto

& entry : seq_entries) {

2415 if

(bioseq->IsSetDescr())

2420 if

(bio_set->IsSetDescr())

2432 for

(

const auto

& pub : pub_eq.

Get

()) {

2434 if

(pub->GetGen().IsSetSerial_number()) {

2435

ret = pub->GetGen().GetSerial_number();

2471 if

(

strcmp

(str1, str2) < 0)

2483 for

(

auto

& entry : seq_entries) {

2485 if

(bioseq->IsSetDescr())

2486

bioseq->SetDescr().Set().sort(

descr_cmp

);

2490 if

(bio_set->IsSetDescr())

2491

bio_set->SetDescr().Set().sort(

descr_cmp

);

2502

}

else if

(pub1->

IsGen

()) {

2517 for

(

auto

& annot : annots) {

2518 if

(annot->IsFtable()) {

2519 for

(

auto

& feat : annot->SetData().SetFtable()) {

2520 if

(feat->IsSetCit() && feat->GetCit().IsPub()) {

2523 TPubList

& pubs = feat->SetCit().SetPub();

2524 for

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

2525

TPubList::iterator next_pub = pub;

2526 for

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

2527 if

(

pub_cmp

(*next_pub, *pub))

2528 swap

(*next_pub, *pub);

2540 for

(

auto

& entry : seq_entries) {

2542 if

(bioseq->IsSetAnnot())

2547 if

(bio_set->IsSetAnnot())

2556 for

(

const auto

: dbtags) {

2557 if

(

->IsSetDb() &&

->IsSetTag() &&

2558

->GetTag().IsStr() &&

->GetTag().GetId() > 0 &&

2559 tag

->GetDb() ==

"taxon"

)

2570 if

(! org_ref || ! gbb.

())

2580 for

(

const auto

& annot : annots) {

2581 if

(! annot->IsFtable())

2585 for

(

const auto

& feat : feats) {

2586 if

(! feat->IsSetData() || ! feat->GetData().IsBiosrc())

2591 const CBioSource

& bio_src = feat->GetData().GetBiosrc();

2608 if

(! entry || xil.empty())

2611 auto

xip = xil.begin();

2612 for

(; xip != xil.end(); ++xip)

2615 if

(xip == xil.end())

2618 auto

txip = xip->subtags.begin();

2619 for

(; txip != xip->subtags.end(); ++txip) {

2620 if

(txip->subtags.empty())

2622 auto

fxip = txip->subtags.begin();

2623 for

(; fxip != txip->subtags.end(); ++fxip)

2627 if

(fxip != txip->subtags.end())

2631 if

(txip == xip->subtags.end())

2639 for

(

auto

& entry : seq_entries) {

2641 if

(bioseq->IsSetInst() && bioseq->GetInst().IsSetStrand())

2644 if

(bioseq->GetInst().IsSetMol()) {

2658 for

(

const auto

& entry : seq_entries) {

2660 if

(bioseq->IsSetId()) {

2661 for

(

const auto

id

: bioseq->GetId()) {

2662 if

(id->IsSwissprot())

2687 for

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

2688 if

((*pub)->IsGen()) {

2689 if

((*pub)->GetGen().IsSetSerial_number())

2690

(*pub)->SetGen().ResetSerial_number();

2693

pub = pubs.erase(pub);

2705 for

(

auto

& entry : seq_entries) {

2707 if

(pubdesc->IsSetPub()) {

2709 if

(pubdesc->GetPub().Get().empty())

2710

pubdesc->ResetPub();

2715 if

(feat->IsSetData()) {

2716 if

(feat->GetData().IsPub()) {

2718 if

(feat->GetData().GetPub().GetPub().Get().empty())

2719

feat->SetData().SetPub().ResetPub();

2720

}

else if

(feat->GetData().IsImp()) {

2721 CImp_feat

& imp = feat->SetData().SetImp();

2722 if

(imp.

IsSetKey

() && imp.

GetKey

() ==

"Site-ref"

&& feat->IsSetCit() && feat->GetCit().IsPub()) {

2724 if

(feat->GetCit().GetPub().empty())

2725

feat->SetCit().Reset();

2737 const string

* seq_str =

nullptr

;

2738 const

vector<Char>* seq_vec =

nullptr

;

2741 size_t

old_size = 0;

2747

old_size = seq_str->size();

2753

old_size = seq_vec->size();

2759

old_size = seq_vec->size();

2765

std::vector<Char> new_seq(old_size);

2766 size_t

new_size = 0;

2772 if

(! new_seq.empty()) {

2773

seq_data.

SetNcbieaa

().

Set

().assign(new_seq.begin(), new_seq.begin() + new_size);

2793 for

(

auto

: bioseq.

SetInst

().SetExt().SetDelta().Set()) {

2794 if

(

->IsLiteral() &&

->GetLiteral().IsSetSeq_data() && !