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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/add_8cpp_source.html below:

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

(

c :

) {

(

= 0;

<

.length(); ++

) {

(

[

] !=

)

(

k =

+ 1; k <

.length() &&

(

[k]); ++k)

.erase(

+ 1, j);

(!

.empty()) {

c =

.back();

(c ==

|| c ==

|| c ==

|| c ==

|| c ==

)

no_create =

;

no_update =

;

(

& desc : descrs) {

(desc->IsCreate_date())

(desc->IsUpdate_date())

(no_create ==

&& no_update ==

)

(no_create || no_update);

(

& desc : bioseq.

().

()) {

(

& annot : bioseq.

()) {

(! annot->IsFtable())

(

& feat : annot->GetData().GetFtable()) {

(feat->IsSetData() && feat->GetData().IsPub())

(

& feat : annot->GetData().GetFtable()) {

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

& imp = feat->GetData().GetImp();

(imp.

() ==

) {

temp = chain.cbegin();

(; temp != chain.cend(); ++temp) {

& dblk = *temp;

(dblk.mType !=

)

& subblocks = dblk.GetSubBlocks();

(

& dbp : subblocks)

dbp = subblocks.cbegin();

(temp == chain.cend())

temp = ibp->

;

(accver && ibp->

> 0) {

temp += to_string(ibp->

);

& gapType(gfp.

);

(gapType ==

|| gapType ==

|| gapType ==

) {

CDelta_ext::Tdata::iterator

= deltas.begin();

(! (*delta)->IsLiteral())

(

.GetLength() !=

(gfp->to - gfp->from + 1)) {

,

(*drop || (

== deltas.end() && gfp == gf.end()))

(

== deltas.end() && gfp != gf.end()) {

,

}

(

!= deltas.end() && gfp == gf.end()) {

((*delta)->IsLiteral())

(

== deltas.end())

(sequence.empty() || sequence.size() != bioseq.

())

(

tgfp = gf.begin(); tgfp != gf.end(); ++tgfp) {

nxt =

(tgfp);

(nxt != gf.end()) {

p = sequence.c_str() + tgfp->to;

(

= tgfp->to + 1; i < nxt->from; p++,

++)

(

== nxt->from && nxt->from > tgfp->to + 1) {

,

tgfp->from, tgfp->to, nxt->from, nxt->to);

tgfp->rightNs =

;

nextfrom = nxt->from;

(tgfp->leftNs ==

&& tgfp->from - prevto > 10) {

(p = sequence.c_str() + tgfp->from - 11,

= 0;

< 10; p++,

++)

,

tgfp->from, tgfp->to);

(tgfp->rightNs ==

&& nextfrom - tgfp->to > 10) {

(p = sequence.c_str() + tgfp->to,

= 0;

< 10; p++,

++)

,

tgfp->from, tgfp->to);

(

= tgfp->from - 1, p = sequence.c_str() +

; i < tgfp->to; p++,

++)

,

tgfp->from, tgfp->to);

(tgfp->from - prevto - 1 > 0) {

= tgfp->from - prevto - 1;

->SetLiteral().SetLength(

);

->SetLiteral().SetSeq_data().SetIupacna().Set() = sequence.substr(prevto,

);

deltas.push_back(

);

= tgfp->to - tgfp->from + 1;

->SetLiteral().SetLength(

);

(tgfp->estimated_length == -100) {

->SetLiteral().SetFuzz().SetLim();

}

(tgfp->estimated_length !=

) {

->SetLiteral().SetFuzz().SetRange().SetMin(tgfp->estimated_length);

->SetLiteral().SetFuzz().SetRange().SetMax(

);

(tgfp->assembly_gap)

deltas.push_back(

);

(tgfp == gf.end()) {

->SetLiteral().SetLength(

);

->SetLiteral().SetSeq_data().SetIupacna().Set() = sequence.substr(prevto,

);

deltas.push_back(

);

(! deltas.empty()) {

bioseq.

().SetExt().SetDelta().Set().swap(deltas);

bioseq.

().ResetSeq_data();

(sequence.empty() || sequence.size() != bioseq.

())

vector<Char>

(sequence.begin(), sequence.end());

(q = p; *p !=

;) {

(

= p, p++,

= 1; *p ==

;

++)

j = (

)(

- q);

->SetLiteral().SetLength(j);

->SetLiteral().SetSeq_data().SetIupacna().Set(

(q,

));

deltas.push_back(

);

->SetLiteral().SetLength(

);

->SetLiteral().SetFuzz().SetLim();

deltas.push_back(

);

->SetLiteral().SetLength(j);

->SetLiteral().SetSeq_data().SetIupacna().Set(

(q, p));

deltas.push_back(

);

(deltas.size() > 1) {

bioseq.

().SetExt().SetDelta().Set().swap(deltas);

bioseq.

().ResetSeq_data();

);

);

);

(extra_accs.empty())

(extra_accs.size() != 2)

CGB_block::TExtra_accessions::const_iterator it = extra_accs.begin();

acc1 = ppacc1.data();

acc2 = ppacc2.data();

(! acc1 && ! acc2)

(! acc1 || ! acc2)

(p = master; *p !=

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

);)

(q = range; *q !=

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

);)

ret = (master == range);

ext.GetDelta().IsSet()) {

&

= ext.GetDelta().Get();

any_of(begin(

),

[](

pDeltaSeq) {

(pDeltaSeq && pDeltaSeq->IsLoc()); });

idType =

.Which();

primaryType = primary.

();

primaryIsGi = primaryIsAccession ?

: (primaryType ==

);

unique_ptr<string> pPrimaryAccessionString;

(

& pDeltaSeq : delta_ext.

()) {

(pDeltaSeq && pDeltaSeq->IsLoc()) {

pId = pDeltaSeq->GetLoc().GetId();

& deltaIdType = pId->Which();

(deltaIdType == primaryType) {

(pId->GetSeqIdString() == primaryString) {

deltaAccessionHandle = scope.

(deltaHandle);

(! deltaAccessionHandle) {

(deltaAccessionHandle.GetSeqId()->GetSeqIdString() ==

(! pPrimaryAccessionString) {

primaryAccessionHandle = scope.

(primaryGiHandle);

(! primaryAccessionHandle) {

pPrimaryAccessionString =

make_unique<string>(primaryAccessionHandle.GetSeqId()->GetSeqIdString());

(*pPrimaryAccessionString == pId->GetSeqIdString()) {

it = find_if(begin(accession),

[](

c) {

! (

(c) || c ==

); });

(it != accession.end());

(distance(accession.begin(), it));

string_view primaryAccession(acc);

vector<string> candidatesAccs;

vector<CRef<CSeq_id>> candidatesIds;

vector<CSeq_id_Handle> candidatesIdhs;

list<CRef<CSeq_id>> replaces;

(

& accessionString : hist) {

(accessionString.empty())

(pri_acc == 0 || pri_acc == 2) {

(prefixLength <= 0) {

((accessionString.length() <= prefixLength ||

!

(accessionString, 0, prefixLength, primaryAccession.substr(0, prefixLength)) ||

!

(accessionString[prefixLength])) &&

candidatesAccs.push_back(accessionString);

candidatesIds.push_back(

);

(

= 0;

< candidatesIdhs.size(); ++

) {

& accessionString = candidatesAccs[

];

= candidatesIds[

];

idChoice =

->Which();

secondaryBsh = secondaryBshs[

];

IsConOrScaffold =

;

,

(! IsConOrScaffold && pricon && idChoice == acctype) {

(IsConOrScaffold && ! pricon) {

replaces.push_back(

);

replaces.push_back(

);

(! replaces.empty()) {

& hist_replaces_ids = bioseq.

().SetHist().SetReplaces().SetIds();

hist_replaces_ids.splice(hist_replaces_ids.end(), replaces);

(! s1 || ! s2 || !

(s1, s2))

deldiv =

;

(TKeywordList::iterator

= kwds.begin();

!= kwds.end();) {

delnode =

;

errpost =

;

(*

==

) {

(ibp->

!= 0 && ibp->

!= 5) {

(ibp->

== 1 || ibp->

== 2 || ibp->

== 3)

}

(*

==

) {

(ibp->

!= 0 && ibp->

!= 5) {

(ibp->

== 2 || ibp->

== 3 || ibp->

== 4)

}

(*

==

) {

(ibp->

!= 0 && ibp->

!= 5) {

(ibp->

== 1 || ibp->

== 3 || ibp->

== 4)

}

(*

==

) {

(ibp->

!= 0 && ibp->

!= 5) {

(ibp->

== 1 || ibp->

== 2 || ibp->

== 4)

}

(*

==

) {

(ibp->

== 0) {

forward_list<FTATpaSpan> ftsp;

(ftbp.empty() || length < 1)

ftsp.emplace_front(ftbp.front().from1, ftbp.front().to1);

tftsp = ftsp.begin();

(

tftbp = ftbp.begin(); tftbp != ftbp.end(); ++tftbp) {

i1 = tftbp->to1 - tftbp->from1;

i2 = tftbp->to2 - tftbp->from2;

j = (i2 > i1) ? (i2 - i1) : (i1 - i2);

(i1 < 3000 && j * 10 > i1) {

,

tftbp->from1, tftbp->to1, tftbp->from2, tftbp->to2);

,

tftbp->from1, tftbp->to1, tftbp->from2, tftbp->to2);

(i1 >= 3000 && j > 300) {

,

tftbp->from1, tftbp->to1, tftbp->from2, tftbp->to2);

,

tftbp->from1, tftbp->to1, tftbp->from2, tftbp->to2);

(tftbp->from1 <= tftsp->to + 1) {

(tftbp->to1 > tftsp->to)

tftsp->to = tftbp->to1;

tftsp = ftsp.emplace_after(tftsp, tftbp->from1, tftbp->to1);

(ftsp.front().from - 1 > 50) {

(

,

,

, ftsp.front().from - 1);

(

,

,

, ftsp.front().from - 1);

(

it = ftsp.begin(); it != ftsp.end();) {

it_next =

(it);

(it_next != ftsp.end() && it_next->from - it->to - 1 > 50) {

(

,

,

, it->to + 1, it_next->from - 1);

(

,

,

, it->to + 1, it_next->from - 1);

}

(it_next == ftsp.end() && length - it->to > 50) {

(

,

,

, it->to + 1, length);

(

,

,

, it->to + 1, length);

* bad_accession;

(p =

; *p !=

; p++)

.append(

);

ftbp.emplace_front(0, 0);

bad_interval =

;

bad_accession =

;

(p += col_data; *p ==

;)

(

= p; *p >=

&& *p <=

;)

bad_interval =

;

(

= p; *p >=

&& *p <=

;)

(*p !=

&& *p !=

&& *p !=

) {

bad_interval =

;

bad_interval =

;

ft = ftbp.begin();

it_next =

(ft);

(it_next == ftbp.end() || (it_next->from1 > from1) ||

(it_next->from1 == from1 && it_next->to1 > to1))

tftbp = ftbp.emplace_after(ft, from1, to1);

(

= p; *p !=

&& *p !=

&& *p !=

;)

(

=

; *

>=

&& *

<=

;)

bad_accession = tftbp->accession;

(

= tftbp->accession + 2; *

==

;)

bad_accession = tftbp->accession;

(*

>=

&& *

<=

)

bad_accession = tftbp->accession;

bad_accession = tftbp->accession;

(

= p; *p >=

&& *p <=

;)

bad_interval =

;

(

= p; *p >=

&& *p <=

;)

(*p !=

&& *p !=

&& *p !=

) {

bad_interval =

;

(tftbp->from2 >= tftbp->to2) {

bad_interval =

;

(p++; *p ==

;)

(bad_line || bad_interval || bad_accession) {

}

(bad_accession) {

(! assembly.empty())

(

it = ftbp.begin(); it != ftbp.end(); ++it) {

len1 = it->to1 - it->from1 + 1;

len2 = it->to2 - it->from2 + 1;

seg.SetNumseg((len1 == len2) ? 1 : 2);

seg.SetStarts().push_back(it->from1 - 1);

seg.SetStarts().push_back(it->from2 - 1);

seg.SetStarts().push_back(-1);

seg.SetStarts().push_back(it->from2 - 1 + len1);

seg.SetStarts().push_back(it->from1 - 1 + len2);

seg.SetStarts().push_back(-1);

seg.SetLens().push_back(len1);

(len1 < len2) {

seg.SetLens().push_back(len1);

seg.SetLens().push_back(len2 - len1);

seg.SetLens().push_back(len2);

seg.SetLens().push_back(len1 - len2);

seg.SetStrands().push_back(it->strand);

seg.SetStrands().push_back(it->strand);

text_id->SetAccession(acnum);

text_id->SetVersion(vernum);

seg.SetIds().push_back(

);

(

= it->accession + 2; *

==

;)

.SetTag().SetStr(

);

seg.SetIds().push_back(gen_id);

otext_id->SetAccession(it->accession);

(it->version > 0)

otext_id->SetVersion(it->version);

(it->sicho, *aux_id, *otext_id);

seg.SetIds().push_back(aux_id);

align_set.

().push_back(align);

assembly.push_back(root_align);

(! where || ! what || *where ==

|| *what ==

)

* res =

;

(

* p = where; *p !=

; p++)

interval.

().Assign(seq_id);

bad_format =

;

is_digit = [](

c) {

<= c && c <=

; };

(name.empty() || name.size() < 7)

(name[0] !=

|| name[1] !=

|| (name[2] !=

&& name[2] !=

) ||

name[3] !=

|| ! is_digit(name[4]))

p = name.begin() + 5;

e = name.end();

(p < e && is_digit(*p))

(! (p < e && *p ==

)) {

(! (p < e && is_digit(*p)))

(! std::all_of(p, e, is_digit))

bad_format =

;

is_digit = [](

c) {

<= c && c <=

; };

(name.size() < 6)

(name[0] !=

|| name[1] !=

|| name[2] !=

||

(name[3] !=

&& name[3] !=

&& name[3] !=

) ||

name[4] <

|| name[4] >

|| ! is_digit(name[5]))

(! std::all_of(name.begin() + 6, name.end(), is_digit))

(name[3] !=

|| name[4] !=

)) ||

(name[3] !=

|| name[4] !=

)))

(

.empty()) {

(

& c :

) {

(c ==

|| c ==

|| c ==

)

forward_list<string> res;

tail = res.before_begin();

(

p =

.begin(); p !=

.end();) {

(p !=

.end() && *p ==

)

(p ==

.end())

(p !=

.end() && *p !=

)

string_view name(q, p);

(! std::all_of(name.begin(), name.end(), [](

c) { return

<= c && c <=

; })) {

tail = res.insert_after(tail,

(name));

newstyle =

;

name =

sv;

name =

sv;

= name.size();

=

.find(ch);

(

!= string_view::npos)

(!

.starts_with(name)) {

.remove_prefix(

);

(

& descr : descrs) {

(! descr->IsUser() || ! descr->GetUser().IsSetData())

user_obj_ptr = &(descr->SetUser());

obj_id = &(user_obj_ptr->

());

(obj_id && obj_id->

() && obj_id->

() ==

) {

(

& tvnp : vnp)

.SetStr(

);

user_field->

().SetStr(

);

(

& tvnp : vnp)

user_field->

().SetStrs().push_back(tvnp);

user_obj_ptr->

().push_back(user_field);

.SetStr(

);

(

& tvnp : vnp) {

user_field->

().SetStr(

);

user_obj_ptr->

().push_back(user_field);

user_field->

().SetStr(

);

user_field->

().SetInt(0);

user_obj_ptr->

().push_back(user_field);

descr->

(*user_obj_ptr);

descrs.push_back(descr);

(

.

() > 3 &&

(

[0] ==

||

[0] ==

||

[0] ==

) &&

[1] ==

&&

(

[2] ==

||

[2] ==

||

[2] ==

||

[2] ==

||

[2] ==

||

[2] ==

)) {

(std::all_of(

.begin() + 3,

.end(), [](

c) {

<= c && c <=

; }))

(

.

() > 5 &&

[0] ==

&&

[1] ==

&&

[2] ==

&& (

[3] ==

||

[3] ==

||

[3] ==

)) {

p =

.begin() + 4;

(*p ==

|| *p ==

)

(std::all_of(p,

.end(), [](

c) {

<= c && c <=

; }))

(

.empty()) {

(

& c :

)

(c ==

|| c ==

)

forward_list<string> res;

tvnp = res.before_begin();

tagvnp = res.end();

bioproject =

;

nl =

.begin();

(

p =

.begin(); p !=

.end(); got_nl =

) {

(p !=

.end() && (*p ==

|| *p ==

|| *p ==

|| *p ==

)) {

= std::find(p,

.end(),

);

(

!=

.end()) {

((

.find(

) == string::npos) && (

.find(

) == string::npos)) {

(! (

==

) &&

! (

==

) &&

! (

==

) &&

! (

==

) &&

! (

==

) &&

! (

==

)) {

bioproject = (

==

);

sra = (

==

);

biosample = (

==

);

assembly = (

==

);

(! res.empty() && tvnp->find(

) != string::npos) {

(

uvnp = res.cbegin(); uvnp != res.cend(); ++uvnp)

(*uvnp ==

) {

tvnp = res.insert_after(tvnp, std::move(

));

(p !=

.end() && *p !=

&& *p !=

&& *p !=

)

(p !=

.end() && *p ==

) {

(p !=

.end() && *p !=

)

(tagvnp != res.end() && ! tagvnp->empty()) {

(

uvnp =

(tagvnp); uvnp != res.end(); ++uvnp) {

(! uvnp->empty() && *uvnp == name) {

tvnp = res.insert_after(tvnp, std::move(name));

(! res.empty() && tvnp->find(

) != string::npos) {

(

tvnp = vnp.begin(); tvnp != vnp.end(); ++tvnp) {

(tvnp->find(

) != string::npos) {

(*tvnp ==

) {

.SetStr(

);

(user_obj.

())

*

= tvnp->c_str();

(!

|| *

==

)

(*

>=

&& *

<=

)

(*

!=

) {

user_field->

().SetStr(

);

user_obj->

().push_back(user_field);

user_field->

().SetStr(

);

user_field->

().SetInt(0);

user_obj->

().push_back(user_field);

descrs.push_back(descr);

user_field.

();

(

tvnp = vnp.begin(); tvnp != vnp.end(); ++tvnp) {

(tvnp->find(

) != string::npos) {

(*tvnp ==

) {

(user_obj.

()) {

user_obj->

().SetStr(

);

(

uvnp =

(tvnp); uvnp != vnp.end(); ++uvnp, ++

)

(uvnp->find(

) != string::npos)

user_field->

().SetStr(lstr);

user_field->

().SetStrs();

user_obj->

().push_back(user_field);

}

(! inpr && user_obj.

()) {

user_field->

().SetStrs().push_back(*tvnp);

descrs.push_back(descr);

finished =

;

(!

->IsLoc())

*

=

;

* text_id =

->GetTextseq_Id();

(good && finished)

(

.IsLocal()) {

(name.empty() &&

.IsGeneral()) {

(

.GetDb() ==

||

.GetDb() ==

)

(!

.IsGenbank() && !

.IsEmbl() && !

.IsPir() &&

!

.IsSwissprot() && !

.IsOther() && !

.IsDdbj() && !

.IsPrf() &&

!

.IsTpg() && !

.IsTpe() && !

.IsTpd()) {

* text_id =

.GetTextseq_Id();

slip->

= accession;

}

(

== 7) {

slip->

= accession;

(

!=

.Which()) {

new_text_id->Assign(*text_id);

.SetGeneral().SetDb(

);

.SetGeneral().SetTag().SetStr(accession);

.SetPatent(*pat_id);

(

.IsGenbank()) {

}

(

.IsEmbl()) {

}

(

.IsPir()) {

}

(

.IsSwissprot()) {

}

(

.IsOther()) {

}

(

.IsDdbj()) {

}

(

.IsPrf()) {

}

(

.IsTpg()) {

}

(

.IsTpe()) {

}

(

.IsTpd()) {

(

& loc : locs) {

(loc->IsEmpty()) {

}

(loc->IsWhole()) {

}

(loc->IsInt()) {

}

(loc->IsPnt()) {

(iscon && ! loc->GetPnt().IsSetFuzz()) {

point = loc->GetPnt().GetPoint();

interval->

(point);

(loc->GetPnt().IsSetStrand())

interval->

(loc->GetPnt().GetStrand());

interval->

(loc->SetPnt().SetId());

loc->SetInt(*interval);

}

(loc->IsPacked_int()) {

(

& interval : loc->SetPacked_int().Set()) {

}

(loc->IsPacked_pnt()) {

}

(loc->IsMix()) {

}

(loc->IsEquiv()) {

* p =

;

((tpa > 0 && non_tpa > 0) || tpa > 1 || non_tpa > 1 ||

(tpa > 0 && non_tpa > 0) {

(tpa > 1 || non_tpa > 1) {

p =

;

msga[4] = msgb[4] = 0;

(

== 3 ||

== 7) {

(sli.

);

(p =

.data(); *p !=

; p++) {

(p++; *p ==

|| *p ==

; p++)

forward_list<string> res;

vnp = res.before_begin();

(start =

.data();;) {

vnp = res.insert_after(vnp, s);

s(start,

);

vnp = res.insert_after(vnp, s);

(

.empty() || scomment.empty())

.SetStr(

);

field->

().SetStr(

);

field->

().SetStr() +=

;

obj->

().push_back(field);

(

& tvnp : vnp) {

q = tvnp.find(

);

(q == string::npos)

(q > 0 && tvnp[q - 1] ==

)

(q < tvnp.size() && (tvnp[q] ==

|| tvnp[q] ==

))

(q == tvnp.size())

field->

().SetStr(tvnp.substr(0, qq));

field->

().SetStr(tvnp.substr(q));

obj->

().push_back(field);

(obj->

().size() < 2) {

field->

().SetStr(

);

field->

().SetStr() +=

;

obj->

().push_back(field);

forward_list<string> tagvnp;

(!

|| *

==

)

(*q ==

|| (*q ==

&& q >

&& *--q ==

) || q ==

)

(q[0] !=

|| q[1] !=

) {

=

.size();

(tagvnp.empty()) {

tagvnp.push_front(

);

(

vnp = tagvnp.begin(); vnp != tagvnp.end(); ++vnp) {

(vnp->substr(2) ==

.substr(2)) {

(vnp->front() !=

) {

vnp->front() =

;

(

(vnp) == tagvnp.end()) {

tagvnp.insert_after(vnp,

);

(

==

) {

string_view scomment(p, q);

(scomment.find(

) == string_view::npos) {

(cur.

()) {

objs.push_back(cur);

(fgets(

, 1023, fd)) {

(

[0] ==

&& ret[0] !=

)

(seq_entry.

()) {

}

(seq_entry.

()) {

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

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

descr = descrs->erase(descr);

got_comment =

;

got_dblink =

;

(

& descr : bioseq.

().

()) {

(! descr->IsUser())

& user_type_str = user_obj.

().

();

(user_type_str ==

)

got_comment =

;

(user_type_str ==

)

(user_type_str ==

) {

(

& field : user_obj.

()) {

(! field->IsSetLabel() || ! field->GetLabel().IsStr() ||

field->GetLabel().GetStr() !=

)

(

& descr : bioseq.

().Set()) {

(descr->IsMolinfo()) {

mol_info = &descr->SetMolinfo();

bioseq.

().Set().push_back(descr);

(

,

,

, num);

field->

().SetStr(

);

field->

().SetStr(

);

bsp.

().Set().push_back(descr);

(

=

.find(

);

!= string::npos;

=

.find(

,

)) {

j =

.find(

,

);

(j == string::npos)

(

> 0 &&

[

- 1] ==

)

(

> 0 && j <

.size()) {

((

[

- 1] ==

&&

[j] ==

) ||

(

[

- 1] ==

&&

[j] ==

)) {

.erase(

, j -

);

(

& field : uop->

()) {

(! field->IsSetData() || ! field->GetData().IsStrs() || ! field->IsSetNum() || field->GetNum() < 1 ||

! field->IsSetLabel() || ! field->GetLabel().IsStr() || field->GetLabel().GetStr() !=

)

(

.size() > 2 &&

(

[0] ==

||

[0] ==

||

[0] ==

) &&

[1] ==

&&

(

[2] ==

||

[2] ==

||

[2] ==

)) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static bool s_IsConOrScaffold(CBioseq_Handle bsh)

void AssemblyGapsToDelta(CBioseq &bioseq, TGapFeatsList &gf, bool *drop)

static bool fta_validate_bioproject(string_view name, Parser::ESource source)

bool no_reference(const CBioseq &bioseq)

void SeqToDelta(CBioseq &bioseq, Int2 tech)

CMolInfo::TTech fta_check_con_for_wgs(CBioseq &bioseq)

bool fta_check_htg_kwds(TKeywordList &kwds, IndexblkPtr ibp, CMolInfo &mol_info)

void fta_set_molinfo_completeness(CBioseq &bioseq, const Indexblk *ibp)

void fta_add_hist(ParserPtr pp, CBioseq &bioseq, CGB_block::TExtra_accessions &extra_accs, Parser::ESource source, CSeq_id::E_Choice acctype, bool pricon, const char *acc)

static bool fta_ranges_to_hist(const CGB_block::TExtra_accessions &extra_accs)

static int sGetPrefixLength(string_view accession)

bool fta_parse_tpa_tsa_block(CBioseq &bioseq, char *offset, char *acnum, Int2 vernum, size_t len, Int2 col_data, bool tpa)

bool g_DoesNotReferencePrimary(const CDelta_ext &delta_ext, const CSeq_id &primary, CScope &scope)

Int4 fta_fix_seq_loc_id(TSeqLocList &locs, ParserPtr pp, string_view location, string_view name, bool iscon)

static forward_list< string > fta_tokenize_project(string str, Parser::ESource source, bool newstyle)

string GetQSFromFile(FILE *fd, const Indexblk *ibp)

CRef< CSeq_loc > fta_get_seqloc_int_whole(const CSeq_id &seq_id, size_t len)

static void CreateSeqGap(CSeq_literal &seq_lit, GapFeats &gfp)

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

static void fta_check_tpa_tsa_coverage(const FTATpaBlockList &ftbp, Int4 length, bool tpa)

bool check_cds(const DataBlk &entry, Parser::EFormat format)

static bool s_IsAccession(const CSeq_id &id)

bool fta_if_valid_sra(string_view id, bool dblink)

static void fta_validate_assembly(string_view name)

void fta_create_far_fetch_policy_user_object(CBioseq &bsp, Int4 num)

void fta_tsa_tls_comment_dblink_check(const CBioseq &bioseq, bool is_tsa)

void fta_remove_cleanup_user_object(CSeq_entry &seq_entry)

bool fta_dblink_has_sra(const CRef< CUser_object > &uop)

static forward_list< string > fta_tokenize_dblink(string str, Parser::ESource source)

static void fta_do_fix_seq_loc_id(TSeqLocList &locs, IndexblkPtr ibp, string_view location, string_view name, SeqLocIdsPtr slip, bool iscon, Parser::ESource source)

void GapsToDelta(CBioseq &bioseq, TGapFeatsList &gf, bool *drop)

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

void fta_get_project_user_object(TSeqdescList &descrs, const char *offset, Parser::EFormat format, bool *drop, Parser::ESource source)

void fta_get_dblink_user_object(TSeqdescList &descrs, char *offset, size_t len, Parser::ESource source, bool *drop, CRef< CUser_object > &dbuop)

bool fta_number_is_huge(const Char *s)

void err_install(const Indexblk *ibp, bool accver)

static void fta_fix_seq_id(CSeq_loc &loc, CSeq_id &id, IndexblkPtr ibp, string_view location, string_view name, SeqLocIdsPtr slip, bool iscon, Parser::ESource source)

string tata_save(string_view t)

bool no_date(Parser::EFormat format, const TSeqdescList &descrs)

static CRef< CUser_object > fta_build_structured_comment(string_view tag, string_view scomment)

bool fta_if_valid_biosample(string_view id, bool dblink)

static forward_list< string > fta_vnp_structured_comment(string buf)

void fta_parse_structured_comment(char *str, bool &bad, TUserObjVector &objs)

forward_list< FTATpaBlock > FTATpaBlockList

void StripECO(string &str)

CRef< CPatent_seq_id > MakeUsptoPatSeqId(const char *acc)

void ShrinkSpaces(char *line)

TSeqPos GetLength(void) const

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

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

#define ParFlat_COL_DATA_EMBL

#define ERR_REFERENCE_Illegalreference

#define ERR_LOCATION_TpaAndNonTpa

#define ERR_TPA_SpanLengthDiff

#define ERR_COMMENT_SameStructuredCommentTags

#define ERR_TSA_SpanLengthDiff

#define ERR_TPA_InvalidPrimarySeqId

#define ERR_TSA_SpanDiffOver300bp

#define ERR_ENTRY_TLSLacksBioProjectLink

#define ERR_FORMAT_InvalidBioProjectAcc

#define ERR_TPA_IncompleteCoverage

#define ERR_DBLINK_InvalidIdentifier

#define ERR_SEQUENCE_HasManyComponents

#define ERR_LOCATION_CrossDatabaseFeatLoc

#define ERR_COMMENT_StructuredCommentLacksDelim

#define ERR_TPA_InvalidPrimarySpan

#define ERR_ENTRY_TSALacksStructuredComment

#define ERR_FORMAT_WrongBioProjectPrefix

#define ERR_LOCATION_SeqIdProblem

#define ERR_SEQUENCE_MultipleWGSProjects

#define ERR_TSA_IncompleteCoverage

#define ERR_ACCESSION_CannotGetDivForSecondary

#define ERR_ENTRY_TSALacksBioProjectLink

#define ERR_TPA_SpanDiffOver300bp

#define ERR_FORMAT_ContigVersusAssemblyGapMissmatch

#define ERR_TSA_InvalidPrimaryBlock

#define ERR_TSA_InvalidPrimarySpan

#define ERR_FEATURE_AllNsBetweenGaps

#define ERR_FEATURE_InvalidGapSequence

#define ERR_FORMAT_IncorrectDBLINK

#define ERR_FEATURE_NsAbutGap

#define ERR_ENTRY_TLSLacksStructuredComment

#define ERR_LOCATION_ContigAndScaffold

#define ERR_ACCESSION_WGSPrefixMismatch

#define ERR_DBLINK_DuplicateIdentifierRemoved

#define ERR_SEQUENCE_HTGPossibleShortGap

#define ERR_TPA_InvalidPrimaryBlock

#define ERR_SEQUENCE_HTGPhaseZeroHasGap

#define ERR_COMMENT_InvalidStructuredComment

#define ERR_KEYWORD_MultipleHTGPhases

#define ERR_SEQUENCE_HTGWithoutGaps

#define ERR_TSA_InvalidPrimarySeqId

forward_list< GapFeats > TGapFeatsList

std::list< std::string > TKeywordList

forward_list< GapFeats >::iterator GapFeatsPtr

std::list< CRef< objects::CSeqdesc > > TSeqdescList

std::vector< CRef< objects::CUser_object > > TUserObjVector

int fta_atoi(string_view sv)

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

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

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

void StringNCpy(char *d, const char *s, size_t n)

size_t StringLen(const char *s)

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

void FtaInstallPrefix(int prefix, string_view name, string_view location)

#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)

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

static E_Choice GetAccType(EAccessionInfo info)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

CSeq_id_Handle GetAccVer(const CSeq_id_Handle &idh, TGetFlags flags=0)

Get accession.version Seq-id Returns null CSeq_id_Handle if the sequence is not found or if it doesn'...

TBioseqHandles GetBioseqHandles(const TIds &ids)

Get bioseq handles for all ids.

const TInst_Ext & GetInst_Ext(void) const

bool IsSetInst_Ext(void) const

bool IsSetInst_Repr(void) const

TInst_Repr GetInst_Repr(void) const

TObjectType * GetNCPointer(void) const THROWS_NONE

Get pointer,.

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.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

CTempString literal(const char(&str)[Size])

Templatized initialization from a string literal.

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

Case-insensitive equality of a substring with another string.

static const char label[]

list< string > TExtra_accessions

bool IsSetData(void) const

the object itself Check if a value has been assigned to Data data member.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

TData & SetData(void)

Assign a value to Data data member.

void SetNum(TNum value)

Assign a value to Num data member.

const TStr & GetStr(void) const

Get the variant data.

void SetLabel(TLabel &value)

Assign a value to Label data member.

const TData & GetData(void) const

Get the Data member data.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

const TType & GetType(void) const

Get the Type member data.

Tdata & Set(void)

Assign a value to data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

@ eType_partial

mapping pieces together

const TKey & GetKey(void) const

Get the Key member data.

void SetTo(TTo value)

Assign a value to To data member.

bool IsGenbank(void) const

Check if variant Genbank is selected.

TGeneral & SetGeneral(void)

Select the variant.

bool IsSetAccession(void) const

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

bool IsTpg(void) const

Check if variant Tpg is selected.

bool IsEmpty(void) const

Check if variant Empty is selected.

ENa_strand

strand of nucleic acid

bool IsPacked_pnt(void) const

Check if variant Packed_pnt is selected.

bool IsTpd(void) const

Check if variant Tpd is selected.

bool IsOther(void) const

Check if variant Other is selected.

void SetId(TId &value)

Assign a value to Id data member.

bool IsEmbl(void) const

Check if variant Embl is selected.

E_Choice Which(void) const

Which variant is currently selected.

void SetFrom(TFrom value)

Assign a value to From data member.

TGi GetGi(void) const

Get the variant data.

E_Choice

Choice variants.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

void SetStrand(TStrand value)

Assign a value to Strand data member.

bool IsTpe(void) const

Check if variant Tpe is selected.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TAccession & GetAccession(void) const

Get the Accession member data.

bool IsDdbj(void) const

Check if variant Ddbj is selected.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_Named_annot_track

Internal named annotation tracking ID.

@ e_not_set

No variant selected.

@ e_Tpg

Third Party Annot/Seq Genbank.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetDescr(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TSeq & SetSeq(void)

Select the variant.

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

TRepr GetRepr(void) const

Get the Repr member data.

list< CRef< CSeq_align > > TAssembly

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

const TInst & GetInst(void) const

Get the Inst member data.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

TTopology GetTopology(void) const

Get the Topology member data.

const TIupacna & GetIupacna(void) const

Get the variant data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

const Tdata & Get(void) const

Get the member data.

void SetType(TType value)

Assign a value to Type data member.

bool IsDelta(void) const

Check if variant Delta is selected.

void SetInst(TInst &value)

Assign a value to Inst data member.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSetDescr(void) const

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

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TDelta & GetDelta(void) const

Get the variant data.

TUser & SetUser(void)

Select the variant.

const Tdata & Get(void) const

Get the member data.

list< CRef< CDelta_seq > > Tdata

TLinkage_evidence & SetLinkage_evidence(void)

Assign a value to Linkage_evidence data member.

void SetLinkage(TLinkage value)

Assign a value to Linkage data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

void SetTech(TTech value)

Assign a value to Tech data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

TMolinfo & SetMolinfo(void)

Select the variant.

@ eRepr_delta

sequence made by changes (delta) to others

@ eCompleteness_complete

complete biological entity

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_htgs_0

single genomic reads for coordination

unsigned int

A callback function used to compare two keys in a database.

int fta_if_wgs_acc(string_view accession)

bool isSupportedAccession(CSeq_id::E_Choice type)

Int4 IsNewAccessFormat(const Char *acnum)

CSeq_id::E_Choice GetNucAccOwner(string_view acc)

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

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::KEY key

const CharType(& source)[N]

static const BitmapCharRec ch1

static const BitmapCharRec ch2

std::list< SeqLoc > TSeqLocList

Int4 delta(size_t dimension_, const Int4 *score_)

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

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

FTATpaBlock(Int4 f, Int4 t)

FTATpaSpan(Int4 f, Int4 t)

objects::CLinkage_evidence::TLinkage_evidence asn_linkage_evidence

objects::CSeq_gap::TType asn_gap_type

vector< IndexblkPtr > entrylist

bool allow_crossdb_featloc

char * SrchTheChar(string_view sv, Char letter)

bool SetTextId(Uint1 seqtype, CSeq_id &seqId, CTextseq_id &textId)

TDataBlkList & TrackNodes(const DataBlk &entry)

char * SrchTheStr(string_view sv, string_view leadstr)

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

void UnwrapAccessionRange(const CGB_block::TExtra_accessions &extra_accs, CGB_block::TExtra_accessions &hist)

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