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

,

,

,

,

,

,

,

,

,

,

,

,

,

tsfbp = sfbl.before_begin();

(; dbp != dbp_end; ++dbp) {

(dbp->mType !=

)

(

& tdbp : dbp->GetSubBlocks()) {

* fbp = tdbp.GetFeatData();

(! fbp || fbp->

!=

)

tsfbp = sfbl.emplace_after(tsfbp);

tsfbp->quals = fbp->

;

(! line || *line ==

)

(p = line, q = line; *p !=

; p++)

(*p !=

&& *p !=

)

(

sfbp = sfbl.begin(); sfbp != sfbl.end(); ++sfbp) {

(

& cur : sfbp->quals) {

(cur->IsSetQual()) {

(cur->IsSetVal()) {

(

sfbp = sfbl.begin(); sfbp != sfbl.end(); ++sfbp) {

(

& cur : sfbp->quals) {

(cur->GetQual() == *

)

namstr.append(

);

namstr.append(

);

->SetSubtype(subtype);

mods.push_front(

);

(

& sfbp,

use_what,

* name,

* cultivar,

* isolate,

* serotype,

* serovar,

* specimen_voucher,

* strain,

* sub_species,

* sub_strain,

* variety,

* ecotype)

s.reserve(s.size() +

);

* cultivar;

* isolate;

* organelle;

* serotype;

* serovar;

* ecotype;

* specimen_voucher;

* sub_species;

* sub_strain;

* variety;

(

sfbp = sfbl.begin(); sfbp != sfbl.end(); ++sfbp) {

organelle =

;

specimen_voucher =

;

sub_species =

;

sub_strain =

;

genomename =

;

(

& cur : sfbp->quals) {

(! cur->IsSetQual())

& qual_str = cur->GetQual();

* val_ptr = cur->IsSetVal() ? cur->SetVal().data() :

;

(qual_str ==

) {

(! q || q[1] ==

)

(qual_str ==

) {

(qual_str ==

) {

(qual_str ==

) {

(qual_str ==

) {

(qual_str ==

) {

(qual_str ==

) {

(qual_str ==

) {

(qual_str ==

) {

(qual_str ==

) {

(qual_str ==

) {

specimen_voucher = val_ptr;

(qual_str ==

) {

(qual_str ==

) {

sub_species = val_ptr;

(qual_str ==

) {

sub_strain = val_ptr;

(qual_str ==

) {

(qual_str ==

) {

(sfbp->submitter_seqid) {

(sfbp->submitter_seqid);

(qual_str !=

||

! val_ptr || val_ptr[0] ==

)

str_to_find.assign(val_ptr, p);

str_to_find.assign(val_ptr);

sfbp->name = name ?

(name) :

;

(sfbp->genomename)

sfbp->genomename = genomename;

(strain && ! sfbp->strain)

(isolate && ! sfbp->isolate)

(organelle && ! sfbp->organelle)

(*sfbp, use_what, name, cultivar, isolate, serotype, serovar, specimen_voucher, strain, sub_species, sub_strain, variety, ecotype);

sfbp = sfbl.cbegin();

(; sfbp != sfbl.cend(); ++sfbp) {

(sfbp->focus && sfbp->skip)

(sfbp != sfbl.cend())

(sfbp->location);

sfbp = sfbl.cbegin();

(; sfbp != sfbl.cend(); ++sfbp) {

(sfbp != sfbl.cend())

(sfbp->location);

(

sfbp = sfbl.cbegin(); sfbp != sfbl.cend(); ++sfbp) {

(! sfbp->location || sfbp->location[0] ==

)

(

& cur : sfbp->quals) {

(cur->GetQual() !=

)

(p > sfbp->location)

((p == sfbp->location || *p ==

|| *p ==

||

*p ==

|| *p ==

|| *p ==

) &&

(*q ==

|| *q ==

|| *q ==

|| *q ==

||

*q ==

|| *q ==

)) {

(

= 0, p = sfbp->location; *p !=

; p++) {

(*p ==

|| *p ==

)

(*p ==

&& p[1] ==

)

(*p ==

&& p[1] !=

) {

(q = p + 1; *q >=

&& *q <=

;)

(q == p || *q !=

)

(invalid ||

!= 0) {

sfbp = sfbl.cbegin();

(; sfbp != sfbl.cend(); ++sfbp) {

(! sfbp->location || sfbp->location[0] ==

)

(p = sfbp->location + 1; *p !=

; p++) {

(

=

, q = p - 1;; q--) {

(q == sfbp->location) {

(*q !=

&& (*q < '0' || *q >

) &&

(*q < 'a' || *q >

) && (*q < 'A' || *q >

))

(*q !=

&& (*q < '0' || *q >

) &&

(*q < 'a' || *q >

) && (*q < 'A' || *q >

)) {

(sfbp == sfbl.cend())

(sfbp->location);

(! name || *name ==

)

(

tsfbp = sfbl.begin(); tsfbp != sfbl.end(); ++tsfbp) {

(! tsfbp->location || tsfbp->location[0] ==

||

! tsfbp->name || tsfbp->name[0] ==

)

(p = loc; *p !=

; p++)

(*p ==

|| *p ==

|| *p ==

|| *p ==

||

*p ==

|| *p ==

)

(p = loc, q = loc; *p !=

;) {

(*p ==

|| *p ==

) {

(q > loc && *(q - 1) ==

)

q = (*loc ==

) ? (loc + 1) : loc;

(

= q; *

>=

&& *

<=

;)

}

(*

==

&&

[1] ==

) {

(q = ++

; *

>=

&& *

<=

;)

(

> 0 &&

> 0) {

(

tmmp = mml.begin();; ++tmmp) {

(min < tmmp->

) {

mml.insert_after(tmmp, *tmmp);

(

(tmmp) == mml.end()) {

mml.insert_after(tmmp, newval);

mmp = mml.begin();

(mmp == mml.end() || mmp->min != 1)

(

= mmp->max; mmp != mml.end(); ++mmp)

(mmp->max >

&& mmp->min <=

+ 1)

((

)

<

)

(

tsfbp = sfbl.begin(); tsfbp != sfbl.end(); ++tsfbp,

++) {

(

> 2 ||

>

|| (tgs != 1 && sporg != 1))

* p =

;

=

;

(

sfbp = sfbl.cbegin(); sfbp != sfbl.cend(); ++sfbp) {

(sfbp->focus)

(div && *div !=

) {

(

sfbp = sfbl.cbegin(); sfbp != sfbl.cend(); ++sfbp) {

(syntgndiv == 0) {

(syntgndiv == 2 && ! got)

focus =

;

(

tsfbp = sfbl.cbegin(); tsfbp != sfbl.cend(); ++tsfbp) {

(

tsfbp = sfbl.cbegin(); tsfbp != sfbl.cend(); ++tsfbp) {

taxname = tsfbp->name;

(tsfbp->tg && tsfbp->full)

(same ==

&& tgfull ==

&& focus ==

)

tsfbp =

(sfbl.cbegin());

(tsfbp == sfbl.cend() || ! tgs)

(; tsfbp != sfbl.cend(); ++tsfbp)

(tsfbp == sfbl.cend())

(

tsfbp = sfbl.cbegin(); tsfbp != sfbl.cend(); ++tsfbp) {

(same &&

> 0)

tsfbp = sfbl.cbegin();

(; tsfbp != sfbl.cend(); ++tsfbp) {

(! tsfbp->focus || ! tsfbp->name)

(tsfbp != sfbl.cend())

(same ||

!= 0)

pat =

+ to_string(

);

(tsfbp = sfbl.cbegin(); tsfbp != sfbl.cend(); ++tsfbp) {

(! tsfbp->name || ! tsfbp->location || tsfbp->skip)

(tsfbp->location, pat.c_str()))

(tsfbp == sfbl.cend())

(tsfbp = sfbl.cbegin(); tsfbp != sfbl.cend(); ++tsfbp) {

(tsfbp->full && tsfbp->tg && ! tsfbp->skip)

(tsfbp != sfbl.cend())

((mmp.

== 1 && (

)mmp.

==

) || mmp.

)

MinMaxList::const_iterator tmmp;

mmp = mml.begin();

(; mmp != mml.end(); ++mmp) {

(tmmp =

(mmp); tmmp != mml.end(); ++tmmp) {

(tmmp->min <= mmp->max && tmmp->max >= mmp->min)

(tmmp != mml.end())

(mmp == mml.end())

ss <<

<< mmp->orgname <<

<< mmp->min <<

<< mmp->max

<<

<< tmmp->orgname <<

<< tmmp->min <<

<< tmmp->max;

(sfbl.empty() ||

(sfbl.cbegin()) == sfbl.cend())

tsfbp =

(sfbl.cbegin());

(; tsfbp != sfbl.cend(); ++tsfbp)

(tsfbp == sfbl.cend())

(tsfbp = sfbl.cbegin(); tsfbp != sfbl.cend(); ++tsfbp)

(tsfbp->full && tsfbp->tg)

(tsfbp != sfbl.cend())

sfbp = sfbl.cbegin();

(; sfbp != sfbl.cend(); ++sfbp) {

(! sfbp->full || sfbp->tg)

(sfbp == sfbl.cend())

(sfbp->name);

* cultivar;

* isolate;

* serotype;

* serovar;

* ecotype;

* specimen_voucher;

* strain;

* sub_species;

* sub_strain;

* variety;

(

sfbp = sfbl.begin(); sfbp != sfbl.end(); ++sfbp) {

(sfbp->bio_src.NotEmpty())

(sfbp->orgname.NotEmpty()) {

t_org_ref->

(*org_ref);

(t_org_ref->

(*org_ref))

sfbp->lookup =

;

sfbp->lookup =

;

sfbp->orgname.Reset();

cultivar =

;

serotype =

;

specimen_voucher =

;

sub_species =

;

sub_strain =

;

(

->GetSubtype()) {

cultivar =

->GetSubname().c_str();

isolate =

->GetSubname().c_str();

serotype =

->GetSubname().c_str();

serovar =

->GetSubname().c_str();

ecotype =

->GetSubname().c_str();

specimen_voucher =

->GetSubname().c_str();

strain =

->GetSubname().c_str();

sub_species =

->GetSubname().c_str();

sub_strain =

->GetSubname().c_str();

variety =

->GetSubname().c_str();

(*sfbp, use_what, sfbp->name, cultivar, isolate, serotype, serovar, specimen_voucher, strain, sub_species, sub_strain, variety, ecotype);

sfbp->bio_src->SetOrg(*org_ref);

(

tsfbp =

(sfbp); tsfbp != sfbl.end(); ++tsfbp) {

tsfbp->lookup = sfbp->lookup;

tsfbp->bio_src->Assign(*sfbp->bio_src);

SourceFeatBlkList::iterator what)

(what == sfbl.begin())

= sfbl.begin();

(; tsfbp != sfbl.end(); ++tsfbp) {

(tsfbp == what) {

sfbl.splice_after(sfbl.before_begin(), sfbl,

);

(

= sfbl.begin(), tsfbp =

(

); tsfbp != sfbl.end();) {

(! tsfbp->useit) {

different =

;

(

& cur : tsfbp->quals) {

& cur_qual = cur->GetQual();

(cur_qual ==

)

found =

;

(

&

: sfbl.front().quals) {

& next_qual =

->GetQual();

(next_qual ==

|| next_qual != cur_qual)

(! cur->IsSetVal() && !

->IsSetVal()) {

(cur->IsSetVal() &&

->IsSetVal() &&

cur->GetVal() ==

->GetVal()) {

tsfbp = sfbl.erase_after(

);

SourceFeatBlkList::iterator res)

(res == sfbl.end())

sfbp = sfbl.begin();

& sfb = sfbl.emplace_front();

sfb.name = res->name ?

(res->name) :

;

sfb.namstr = res->namstr ?

(res->namstr) :

;

sfb.location = res->location ?

(res->location) :

;

sfb.full = res->full;

sfb.focus = res->focus;

sfb.lookup = res->lookup;

sfb.genome = res->genome;

sfb.bio_src->Assign(*res->bio_src);

(res->orgname.NotEmpty())

sfb.orgname->Assign(*res->orgname);

sfb.quals = res->quals;

(TQualVector::iterator cur = sfb.quals.begin(); cur != sfb.quals.end();) {

& cur_qual = (*cur)->GetQual();

(cur_qual ==

) {

(; tsfbp != sfbl.end(); ++tsfbp) {

(tsfbp == res || ! tsfbp->useit)

found =

;

(

&

: tsfbp->quals) {

& next_qual =

->GetQual();

(next_qual ==

|| next_qual != cur_qual)

(! (*cur)->IsSetVal() && !

->IsSetVal()) {

((*cur)->IsSetVal() &&

->IsSetVal() &&

(*cur)->GetVal() ==

->GetVal()) {

(tsfbp == sfbl.end())

cur = sfb.quals.erase(cur);

SourceFeatBlkList::iterator res;

(

(sfbl.begin()) == sfbl.end()) {

(! sfbl.front().full) {

count_noskip = 0;

(

tsfbp = sfbl.begin(); tsfbp != sfbl.end(); ++tsfbp) {

(! tsfbp->skip) {

(count_noskip == 1) {

(

tsfbp = sfbl.begin(); tsfbp != sfbl.end(); ++tsfbp) {

(count_noskip != 0 && tsfbp->skip)

tsfbp->useit =

;

(res == sfbl.end())

tsfbp = sfbl.begin();

(; tsfbp != sfbl.end(); ++tsfbp) {

(tsfbp != sfbl.end()) {

(tsfbp = sfbl.begin(); tsfbp != sfbl.end(); ++tsfbp) {

(res != sfbl.end()) {

(tsfbp = sfbl.begin(); tsfbp != sfbl.end(); ++tsfbp) {

tsfbp->useit =

;

(count_noskip > 0) {

(tsfbp = sfbl.begin(); tsfbp != sfbl.end(); ++tsfbp) {

(res != tsfbp && tsfbp->skip)

tsfbp->useit =

;

(tsfbp = sfbl.begin(); tsfbp != sfbl.end(); ++tsfbp) {

(res != sfbl.end()) {

found =

;

(

& subtype : bio.

()) {

(subtype->GetSubtype() ==

) {

vector<string> modnames;

(it.num !=

->GetSubtype())

modnames.push_back(it.name);

(

& cur : quals) {

(! cur->IsSetQual() || cur->GetQual() ==

)

& cur_qual = cur->GetQual();

* val_ptr = cur->IsSetVal() ? cur->GetVal().c_str() :

;

(cur_qual ==

) {

(cur_qual != *

)

(! val_ptr || val_ptr[0] ==

)

(**

!=

&& cur_qual == *

) {

(cur_qual ==

||

(taxserver != 0 && cur_qual ==

))

(find(modnames.begin(), modnames.end(), cur_qual) != modnames.end())

(cur_qual == it.name) {

(qual->

() !=

)

& val_buf(qual->

());

pos = val_buf.find(

);

(pos == string::npos)

db(val_buf.substr(0, pos));

(val_buf.substr(pos + 1));

qual->

(db +

+

);

(

.front() !=

&&

.find_first_not_of(

) == string::npos)

->SetTag().SetStr(

);

is_syn =

;

is_pat =

;

sfbp = sfbl.begin();

(; sfbp != sfbl.end(); ++sfbp) {

(sfbp->bio_src.Empty())

(! sfbp->lookup) {

(is_syn && ! sfbp->tg)

(is_syn ==

&& is_pat ==

) {

* taxname =

;

dropped =

;

(

& cur : sfbp->quals) {

(! cur->IsSetQual() || cur->GetQual().empty())

& cur_qual = cur->GetQual();

cq = cur_qual;

(cq ==

) {

(cq ==

) {

(dbtag.

())

bio.

().SetDb().push_back(dbtag);

* val_ptr = cur->IsSetVal() ? cur->GetVal().c_str() :

;

(cq ==

) {

(! val_ptr || val_ptr[0] ==

)

* p =

(val_ptr,

);

string_view val_str(val_ptr, p - val_ptr);

(cq !=

||

! val_ptr || val_ptr[0] ==

)

(p = tco; *p ==

|| *p ==

;)

(q = p + 1; *q !=

;)

(q--; *q ==

|| *q ==

;)

(! valid_country) {

(! valid_country)

(oldgen > -1)

(sfbp != sfbl.end())

c ==

|| c ==

;

(

& descr : bioseq.

().

()) {

(! descr->IsSource())

& bio_src = descr->GetSource();

std::remove_copy_if(taxname.begin(), taxname.end(), std::back_inserter(orgdescr),

);

std::remove_copy_if(common.begin(), common.end(), std::back_inserter(commdescr),

);

tsfbp = sfbl.cbegin();

(; tsfbp != sfbl.cend(); ++tsfbp) {

(tsfbp->name ==

|| tsfbp->name[0] ==

)

name_len = strlen(tsfbp->name);

std::remove_copy_if(tsfbp->name, tsfbp->name + name_len, std::back_inserter(orgfeat),

);

(orgdescr == orgfeat || commdescr == orgfeat) {

(tsfbp == sfbl.cend()) {

sfbp = sfbl.cbegin();

(; sfbp != sfbl.cend(); ++sfbp) {

(! sfbp->lookup || sfbp->bio_src.Empty() || ! sfbp->bio_src->IsSetOrg())

(sfbp->bio_src->GetOrg().IsSetOrgname() &&

sfbp->bio_src->GetOrg().GetOrgname().IsSetLineage())

p = sfbp->bio_src->GetOrg().GetOrgname().GetLineage().c_str();

(! p || *p ==

) {

(sfbp == sfbl.cend())

(

sfbp = sfbl.begin(); sfbp != sfbl.end(); ++sfbp) {

(sfbp->lookup || sfbp->bio_src.Empty() ||

! sfbp->bio_src->IsSetOrg() || ! sfbp->bio_src->GetOrg().IsSetTaxname() ||

! sfbp->name || *sfbp->name ==

||

sfbp->bio_src->GetOrg().GetTaxname().empty())

& orgname = sfbp->bio_src->SetOrg().SetOrgname();

& taxname = sfbp->bio_src->GetOrg().GetTaxname();

found =

;

(

& descr : bioseq.

().

()) {

(! descr->IsSource())

& bio_src = descr->GetSource();

,

p =

;

(lineage.empty()) {

,

p =

;

p = lineage.c_str();

(

tsfbp =

(sfbp); tsfbp != sfbl.end(); ++tsfbp) {

(tsfbp->lookup || tsfbp->bio_src.Empty() ||

! tsfbp->bio_src->IsSetOrg() || ! tsfbp->bio_src->GetOrg().IsSetTaxname() ||

! tsfbp->name || *tsfbp->name ==

||

tsfbp->bio_src->GetOrg().GetTaxname().empty() ||

& torgname = tsfbp->bio_src->SetOrg().SetOrgname();

tsfbp = sfbl.cbegin();

(; tsfbp != sfbl.cend(); ++tsfbp)

(tsfbp == sfbl.cend())

name = tsfbp->moltype;

(ret =

, tsfbp = sfbl.cbegin(); tsfbp != sfbl.cend(); ++tsfbp) {

(! tsfbp->moltype) {

p = tsfbp->location;

}

(ret && !

(name, tsfbp->moltype))

(sfbl.empty() || ! ibp)

sfbp = sfbl.cbegin();

(envs = 0, sources = 0; sfbp != sfbl.cend(); ++sfbp, sources++) {

env_found =

;

(

& cur : sfbp->quals) {

(cur->IsSetQual() && cur->GetQual() ==

) {

(! sfbp->full || ! sfbp->name || sfbp->name[0] ==

)

(! skip && envs != sources) {

(ppp.empty() ||

< 1)

& pp = ppp.front();

subs.push_back(sub);

subs.push_back(sub);

(! pp.fwd_name.empty()) {

subs.push_back(sub);

(! pp.rev_name.empty()) {

subs.push_back(sub);

(

& tppp : ppp) {

len_fs += (tppp.fwd_seq.size() + 1);

len_rs += (tppp.rev_seq.size() + 1);

(! tppp.fwd_name.empty()) {

len_fn += (tppp.fwd_name.size() + 1);

(! tppp.rev_name.empty()) {

len_rn += (tppp.rev_name.size() + 1);

str_fs.reserve(len_fs);

str_rs.reserve(len_rs);

str_fn.reserve(len_fn +

- num_fn + 1);

str_rn.reserve(len_rn +

- num_rn + 1);

(

& tppp : ppp) {

str_fs.append(

);

str_fs.append(tppp.fwd_seq);

str_rs.append(

);

str_rs.append(tppp.rev_seq);

str_fn.append(

);

(! tppp.fwd_name.empty())

str_fn.append(tppp.fwd_name);

str_rn.append(

);

(! tppp.rev_name.empty())

str_rn.append(tppp.rev_name);

(! str_fs.empty()) {

subs.push_back(sub);

(! str_rs.empty()) {

subs.push_back(sub);

(! str_fn.empty()) {

subs.push_back(sub);

(! str_rn.empty()) {

subs.push_back(sub);

got_problem =

;

tppp = ppp.before_begin();

sfbp = sfbl.begin();

(; sfbp != sfbl.end(); ++sfbp) {

(sfbp->quals.empty() || sfbp->bio_src.Empty())

(

& cur : sfbp->quals) {

(cur->GetQual() !=

||

! cur->IsSetVal() || cur->GetVal().empty())

tppp = ppp.emplace_after(tppp);

std::vector<Char> val_buf(cur->GetVal().begin(), cur->GetVal().end());

val_buf.push_back(0);

(comma =

, bad_start =

, p = &val_buf[0]; *p !=

;) {

(p != &val_buf[0]) {

(

> q && *(

- 1) ==

)

(! q || *q ==

)

(! tppp->fwd_name.empty())

tppp->fwd_name +=

;

tppp->fwd_name += q;

(tppp->fwd_seq.empty())

tppp->fwd_seq +=

;

tppp->fwd_name +=

;

(! tppp->rev_name.empty())

tppp->rev_name +=

;

tppp->rev_name += q;

(tppp->rev_seq.empty())

tppp->rev_seq +=

;

tppp->rev_name +=

;

got_problem =

;

got_problem =

;

got_problem =

;

got_problem =

;

got_problem =

;

(tppp->fwd_seq.empty() || tppp->rev_seq.empty()) {

got_problem =

;

(sfbp == sfbl.end())

* Mmm[] = {

,

,

,

,

,

,

,

,

,

,

,

,

};

(

sfbp = sfbl.cbegin(); sfbp != sfbl.cend(); ++sfbp) {

(sfbp->quals.empty() || sfbp->bio_src.Empty())

(

& cur : sfbp->quals) {

(cur->GetQual() !=

||

! cur->IsSetVal() || cur->GetVal().empty())

= (

*)cur->GetVal().c_str();

(num_slash = 0, p =

; *p !=

; p++)

(num_slash > 1) {

(

= (

*)cur->GetVal().c_str();;) {

(q =

; *q ==

;)

(p = (

*)q; *p !=

; p++)

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

)

}

(

== 8) {

(

[3] !=

)

(p[0] >=

&& p[0] <=

)

(p[1] >=

&& p[1] <=

)

(p[2] >=

&& p[2] <=

)

(

= Mmm, month = 1; *

;

++, month++)

(q =

+ 4; *q ==

;)

(p = (

*)q; *p !=

; p++)

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

)

(year > date.

() ||

}

(

== 11) {

(

[2] !=

||

[6] !=

)

(p[0] <

|| p[0] >

|| p[1] <

|| p[1] >

)

(p[0] >=

&& p[0] <=

)

(p[1] >=

&& p[1] <=

)

(p[2] >=

&& p[2] <=

)

(

= Mmm, month = 1; *

;

++, month++)

(day < 1 || day > 31)

(month == 2 && day > 29)

((month == 4 || month == 6 || month == 9 || month == 11) && day > 30)

(q =

+ 7; *q ==

;)

(p = (

*)q; *p !=

; p++)

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

)

(year > date.

() ||

}

(

== 7 ||

== 10 ||

== 14 ||

== 17 ||

(p =

; *p !=

; p++) {

((*p < 'a' || *p >

) && (*p < 'A' || *p >

) &&

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

) && *p !=

&& *p !=

&&

(*p ==

)

(*p ==

)

(

== 7 ||

== 10) {

((

== 14 && num_colon > 0) ||

(

== 17 && num_colon > 1) ||

(

== 20 && num_colon > 2))

q =

;

q =

;

q =

;

q =

;

q =

;

q =

;

q =

;

(sfbl.empty() ||

(sfbl.cbegin()) == sfbl.cend())

sfbp = sfbl.cbegin();

(; sfbp != sfbl.cend(); ++sfbp) {

(sfbp != sfbl.cend())

metatax =

;

metalin =

;

(! metalin && ! metatax)

(! taxname || taxname[0] == 0)

taxname =

;

(metalin && metatax) {

}

(! metalin)

tsfbp = sfbl.cbegin();

(; tsfbp != sfbl.cend(); ++tsfbp) {

(! tsfbp->submitter_seqid)

(tsfbp->submitter_seqid[0] ==

) {

ssid = tsfbp->submitter_seqid;

(!

(ssid, tsfbp->submitter_seqid)) {

(tsfbp != sfbl.cend())

(count_feat == count_qual)

mml.emplace_front();

(sev,

,

);

}

(

> 0) {

}

(

== 2) {

}

(

== 3) {

}

(

== 2) {

(

tsfbp = sfbl.cbegin(); tsfbp != sfbl.cend(); ++tsfbp)

(sfbl.front().lookup ==

)

(sfbl.front().focus)

sfbl.front().bio_src->SetIs_focus();

sfbl.front().bio_src->ResetIs_focus();

tsfbp = sfbl.begin();

(; tsfbp != sfbl.end(); ++tsfbp) {

feat->

().SetBiosrc(*tsfbp->bio_src);

(*feat, tsfbp->location, seqid, &err, pp,

);

(! tsfbp->quals.empty()) {

seq_feats.push_back(feat);

(tsfbp != sfbl.end())

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

void ShrinkSpaces(char *line)

void fta_sort_biosource(objects::CBioSource &bio)

const COrgName & GetOrgname(void) const

bool IsSetOrgname(void) const

static bool WasValid(const string &country)

static bool IsValid(const string &country)

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

bool IsSetOrgMod(void) const

namespace ncbi::objects::

#define ERR_SOURCE_InconsistentMolType

#define ERR_SOURCE_MissingMolType

#define ERR_SOURCE_FocusAndTransposonNotAllowed

#define ERR_SOURCE_ExcessCoverage

#define ERR_SOURCE_IncompleteCoverage

#define ERR_SOURCE_InvalidDbXref

#define ERR_SOURCE_TransSingleOrgName

#define ERR_QUALIFIER_PCRprimerEmbeddedComma

#define ERR_SOURCE_OrganelleQualMultToks

#define ERR_SOURCE_UnwantedQualifiers

#define ERR_SOURCE_PartialLocation

#define ERR_SOURCE_DifferentSubmitterSeqids

#define ERR_SOURCE_FormerCountry

#define ERR_SOURCE_OrganismIncomplete

#define ERR_SOURCE_MultipleOrganismWithFocus

#define ERR_SOURCE_UnusualOrgName

#define ERR_ORGANISM_UnclassifiedLineage

#define ERR_SERVER_NoLineageFromTaxon

#define ERR_SOURCE_MissingSourceFeatureForDescr

#define ERR_SOURCE_MissingEnvSampQual

#define ERR_DIVISION_TGNnotTransgenic

#define ERR_SOURCE_MultipleSubmitterSeqids

#define ERR_ORGANISM_OrgNameLacksMetagenome

#define ERR_SOURCE_ManySourceFeats

#define ERR_SOURCE_FocusQualMissing

#define ERR_SOURCE_InvalidCollectionDate

#define ERR_SOURCE_UnusualLocation

#define ERR_DIVISION_TransgenicNotSYN_TGN

#define ERR_QUALIFIER_InvalidPCRprimer

#define ERR_SOURCE_LackingSubmitterSeqids

#define ERR_SOURCE_OrganelleIllegalClass

#define ERR_SOURCE_MultipleMolTypes

#define ERR_SOURCE_BadLocation

#define ERR_SOURCE_FocusQualNotFullLength

#define ERR_SOURCE_MultiOrgOverlap

#define ERR_FEATURE_Dropped

#define ERR_SOURCE_MultipleTransgenicQuals

#define ERR_SOURCE_InconsistentEnvSampQual

#define ERR_ORGANISM_SynOrgNameNotSYNdivision

#define ERR_QUALIFIER_MissingPCRprimerSeq

#define ERR_SOURCE_FocusQualNotNeeded

#define ERR_SOURCE_PartialQualifier

#define ERR_SOURCE_FocusAndTransgenicQuals

#define ERR_ORGANISM_NoSourceFeatMatch

#define ERR_SOURCE_TransgenicTooShort

#define ERR_ORGANISM_LineageLacksMetagenome

#define ERR_SOURCE_ObsoleteDbXref

#define ERR_SOURCE_InvalidLocation

#define ERR_SOURCE_FeatureMissing

#define ERR_SOURCE_SingleSourceTooShort

#define ERR_SOURCE_InvalidCountry

#define ERR_SOURCE_NoOrganismQual

forward_list< PcrPrimers > PcrPrimersList

static void RemoveSourceFeatSpaces(SourceFeatBlkList &sfbl)

static bool CheckMoltypeConsistency(const SourceFeatBlkList &sfbl, string &moltype)

static void FTASubSourceAdd(CBioSource &bio, const Char *val, CSubSource::ESubtype type)

static void SourceFeatRemoveDups(SourceFeatBlkList &sfbl)

static void CheckCollectionDate(const SourceFeatBlkList &sfbl, Parser::ESource source)

static void PopulateSubNames(string &namstr, const Char *name, const Char *value, COrgMod::ESubtype subtype, TOrgModList &mods)

static const char * GenomicSourceFeatQual[]

static const char * OrganelleFirstToken[]

static Int4 CheckFocusInOrgs(const SourceFeatBlkList &sfbl, size_t len, int *status)

static const char * unusual_toks[]

static const char * special_orgs[]

static void CheckQualsInSourceFeat(CBioSource &bio, TQualVector &quals, Uint1 taxserver)

static const char * SourceSubSources[]

static const char * DENLRSourceDbxrefTag[]

#define USE_SPECIMEN_VOUCHER

static void PropagateSuppliedLineage(const CBioseq &bioseq, SourceFeatBlkList &sfbl, Uint1 taxserver)

static void PickTheDescrSource(SourceFeatBlkList &sfbl)

static const char * NullTermValues[]

static void CheckMetagenome(CBioSource &bio)

static Int4 CheckTransgenicSourceFeats(const SourceFeatBlkList &sfbl)

static void SourceFeatDerive(SourceFeatBlkList &sfbl, SourceFeatBlkList::iterator res)

static bool CompareDescrFeatSources(const SourceFeatBlkList &sfbl, const CBioseq &bioseq, const string &source)

static const char * NLRSourceDbxrefTag[]

static void CollectSubNames(SourceFeatBlk &sfbp, Int4 use_what, const Char *name, const Char *cultivar, const Char *isolate, const Char *serotype, const Char *serovar, const Char *specimen_voucher, const Char *strain, const Char *sub_species, const Char *sub_strain, const Char *variety, const Char *ecotype)

static bool CheckSubmitterSeqidQuals(const SourceFeatBlkList &sfbl, char *acc)

#define BIOSOURCES_THRESHOLD

static const char * exempt_quals[]

static const char * SourceBadQuals[]

static const char * source_genomes[]

static bool UpdateRawBioSource(SourceFeatBlkList &sfbl, Parser::ESource source, IndexblkPtr ibp, Uint1 taxserver)

static bool ParsePcrPrimers(SourceFeatBlkList &sfbl)

static bool CheckSourceFeatLocFuzz(const SourceFeatBlkList &sfbl)

static SourceFeatBlkList CollectSourceFeats(DataBlkCIter dbp, DataBlkCIter dbp_end, Int2 type)

static void SourceFeatMoveOneUp(SourceFeatBlkList &sfbl, SourceFeatBlkList::iterator what)

static const char * ObsoleteSourceDbxrefTag[]

static void PopulatePcrPrimers(CBioSource &bio, PcrPrimersList &ppp, Int4 count)

static bool CheckNeedSYNFocus(const SourceFeatBlkList &sfbl)

static const char * DESourceDbxrefTag[]

static const CharUInt1 SourceOrgMods[]

static void CheckForExemption(SourceFeatBlkList &sfbl)

static char * CheckPcrPrimersTag(char *str)

static char * CheckForUnusualFullLengthOrgs(const SourceFeatBlkList &sfbl)

static bool IfSpecialFeat(const MinMax &mmp, size_t len)

static void CreateRawBioSources(ParserPtr pp, SourceFeatBlkList &sfbl, Int4 use_what)

static char * CheckSourceFeatFocusAndTransposon(const SourceFeatBlkList &sfbl)

static const char * ESourceDbxrefTag[]

static char * CheckSourceFeatLocAccs(const SourceFeatBlkList &sfbl, char *acc)

bool fta_if_special_org(const Char *name)

static bool CheckForENV(const SourceFeatBlkList &sfbl, IndexblkPtr ibp, Parser::ESource source)

forward_list< MinMax > MinMaxList

forward_list< SourceFeatBlk > SourceFeatBlkList

static void RemoveStringSpaces(char *line)

static bool is_a_space_char(Char c)

static bool SourceFeatStructFillIn(IndexblkPtr ibp, SourceFeatBlkList &sfbl, Int4 use_what)

static bool CheckSYNTGNDivision(const SourceFeatBlkList &sfbl, char *div)

static CRef< CDbtag > GetSourceDbtag(CRef< CGb_qual > &qual, Parser::ESource source)

static Int4 CheckSourceFeatCoverage(SourceFeatBlkList &sfbl, MinMaxList &mml, size_t len)

static void AddOrgMod(COrg_ref &org_ref, const Char *val, COrgMod::ESubtype type)

static bool CheckSourceLineage(const SourceFeatBlkList &sfbl, Parser::ESource source, bool is_pat)

static char * CheckWholeSourcesVersusFocused(const SourceFeatBlkList &sfbl)

static char * CheckSourceOverlap(const MinMaxList &mml, size_t len)

void ParseSourceFeat(ParserPtr pp, DataBlkCIter dbp, DataBlkCIter dbp_end, const CSeq_id &seqid, Int2 type, const CBioseq &bioseq, const string &source, TSeqFeatList &seq_feats)

static char * CheckSourceFeatOrgs(const SourceFeatBlkList &sfbl, int *status)

std::list< CRef< objects::COrgMod > > TOrgModList

std::list< CRef< objects::CSeq_feat > > TSeqFeatList

TDataBlkList::const_iterator DataBlkCIter

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)

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

void fta_fix_orgref(ParserPtr pp, COrg_ref &org_ref, bool *drop, char *organelle)

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

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

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

static const char location[]

#define TAX_ID_FROM(T, value)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

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.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

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

Case-insensitive equality of a substring with another string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eNocase

Case insensitive compare.

@ eCurrent

Use current time. See also CCurrentTime.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

bool IsSetOrg(void) const

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

bool CanGetOrg(void) const

Check if it is safe to call GetOrg method.

list< CRef< CSubSource > > TSubtype

void SetOrigin(TOrigin value)

Assign a value to Origin data member.

const TOrg & GetOrg(void) const

Get the Org member data.

void SetGenome(TGenome value)

Assign a value to Genome data member.

void SetOrg(TOrg &value)

Assign a value to Org data member.

void SetName(const TName &value)

Assign a value to Name data member.

EGenome

biological context

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

@ eSubtype_fwd_primer_seq

sequence (possibly more than one; semicolon-separated)

@ eSubtype_rev_primer_name

@ eSubtype_fwd_primer_name

@ eSubtype_rev_primer_seq

sequence (possibly more than one; semicolon-separated)

@ eOrigin_artificial

artificially engineered

TYear GetYear(void) const

Get the Year member data.

TMonth GetMonth(void) const

Get the Month member data.

TDay GetDay(void) const

Get the Day member data.

const TMod & GetMod(void) const

Get the Mod member data.

bool CanGetMod(void) const

Check if it is safe to call GetMod method.

const TLineage & GetLineage(void) const

Get the Lineage member data.

bool CanGetDiv(void) const

Check if it is safe to call GetDiv method.

const TDiv & GetDiv(void) const

Get the Div member data.

void ResetLineage(void)

Reset Lineage data member.

bool IsSetCommon(void) const

common name Check if a value has been assigned to Common data member.

bool IsSetLineage(void) const

lineage with semicolon separators Check if a value has been assigned to Lineage data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TCommon & GetCommon(void) const

Get the Common member data.

bool CanGetTaxname(void) const

Check if it is safe to call GetTaxname method.

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

bool CanGetOrgname(void) const

Check if it is safe to call GetOrgname method.

bool IsSetOrgname(void) const

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

bool IsSetTaxname(void) const

preferred formal name Check if a value has been assigned to Taxname data member.

TMod & SetMod(void)

Assign a value to Mod data member.

void SetOrgname(TOrgname &value)

Assign a value to Orgname data member.

void SetLineage(const TLineage &value)

Assign a value to Lineage data member.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSubtype_nat_host

natural host of this specimen

@ eSubtype_metagenome_source

@ eSubtype_specimen_voucher

@ eSubtype_culture_collection

const TVal & GetVal(void) const

Get the Val member data.

void SetData(TData &value)

Assign a value to Data data member.

void SetExp_ev(TExp_ev value)

Assign a value to Exp_ev data member.

void SetVal(const TVal &value)

Assign a value to Val data member.

const TQual & GetQual(void) const

Get the Qual member data.

@ eExp_ev_experimental

any reasonable experimental check

@ eExp_ev_not_experimental

similarity, pattern, etc

const Tdata & Get(void) const

Get the member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is whole

bool GetSeqLocation(CSeq_feat &feat, string_view location, const CSeq_id &seqid, bool *hard_err, ParserPtr pp, string_view name)

constexpr bool empty(list< Ts... >) noexcept

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

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

optional< string > location

MinMax(const char *o, Int4 i, Int4 x, bool s)

vector< IndexblkPtr > entrylist

CBioSource::EGenome genome

CRef< CBioSource > bio_src

optional< string > GetTheQualValue(TQualVector &qlist, const Char *qual)

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

Int2 MatchArrayString(const char **array, string_view text)

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

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

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