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

*

[] = {

,

,

,

};

vector<CConstRef<CSeq_loc>> to_remove;

}

(cur_loc->

()) {

}

(cur_loc->

()) {

}

(cur_loc->

()) {

to_remove.push_back(cur_loc);

(vector<

>::const_iterator it = to_remove.begin(); it != to_remove.end(); ++it)

(bond->IsSetB() && !

(bond->GetB().GetId(), acnum,

))

(acnum && *acnum !=

&& *acnum !=

)

TSynSet::const_iterator it1 = syn1.begin(),

(; it1 != syn1.end() && it2 != syn2.end(); ++it1, ++it2) {

(it1 == syn1.end() && it2 == syn2.end())

(it1 == syn1.end())

(it2 == syn2.end())

syn1.insert(grp1.

().begin(), grp1.

().end());

syn2.insert(grp2.

().begin(), grp2.

().end());

(g1.

.empty() && g2.

.empty()) {

(g1.

.empty())

(g2.

.empty())

status = slip1->

- slip2->

;

status = slip1->

- slip2->

;

(cur_loc->

()) {

= &interval.

();

to = interval.

();

}

(cur_loc->

()) {

= &point.

();

slibp->

.push_back(sid);

(slibp->

> from) {

(slibp->

< to) {

(! gnp ||

->to >= second->

)

glp = gnp->

.cbegin();

(; glp != gnp->

.cend(); ++glp) {

(glp->leave != 0 || slp->

!=

->strand ||

glp != gnp->

.cend();

(

& clp : cdsl)

(clp.from > cloc->

&& clp.to < to)

(!

.locus.empty()) {

(!

.locus_tag.empty()) {

(! maploc.empty()) {

(!

.syn.empty()) {

gene_ref.

().assign(

.syn.begin(),

.syn.end());

(

.loc.NotEmpty())

(!

.pseudogene.empty()) {

qual->

(

);

qual->

(

.pseudogene);

feat->

().push_back(qual);

(!

.wormbase.empty()) {

(

.wormbase.size() > 1)

(TWormbaseSet::const_iterator it =

.wormbase.begin(); it !=

.wormbase.end(); ++it) {

->SetDb(

);

->SetTag().SetStr(*it);

(!

.olt.empty()) {

(

.olt.size() > 1)

(TLocusTagSet::const_iterator it =

.olt.begin(); it !=

.olt.end(); ++it) {

qual->

(

);

feat->

().push_back(qual);

feats.push_back(feat);

(! pId1 && ! pId2) {

(! pId1 || ! pId2) {

(

.empty() && second.empty())

tres = res.before_begin();

(

mlp = either.cbegin(); mlp != either.cend(); ++mlp) {

tres = res.insert_after(tres, *mlp);

(!

.empty() && ! second.empty()) {

(

mlp = second.cbegin(); mlp != second.cend(); ++mlp) {

it = res.begin();

(; it != res.cend(); ++it) {

it->strand != nxt.strand)

res.insert_after(it, nxt);

= res.before_begin();

it =

(mlp);

(; it != res.cend(); ++it) {

it->strand == ttt->strand)

(it != res.cend())

res.insert_after(

, nxt);

(

got =

; got;) {

(

tres = res.begin(); tres != res.end(); ++tres) {

(

mlp =

(tres); mlp != res.end(); ++mlp) {

tres->strand != mlp->strand)

(tres->min == mlp->min && tres->max == mlp->max) {

(tres->noleft ==

)

tres->noleft = mlp->noleft;

(tres->noright ==

)

tres->noright = mlp->noright;

(

==

||

(tres->min <= mlp->max + 1 && tres->max + 1 >= mlp->min)) {

(tres->min == mlp->min) {

(tres->noleft ==

)

tres->noleft = mlp->noleft;

}

(tres->min > mlp->min) {

tres->min = mlp->min;

tres->noleft = mlp->noleft;

(tres->max == mlp->max) {

(tres->noright ==

)

tres->noright = mlp->noright;

}

(tres->max < mlp->max) {

tres->max = mlp->max;

tres->noright = mlp->noright;

(

= res.before_begin(), tres = res.begin(); tres != res.end();) {

tres = res.erase_after(

);

(

.empty() && second.empty())

tres = res.before_begin();

(

mlp =

.cbegin(); mlp !=

.cend(); ++mlp) {

tres = res.insert_after(tres, *mlp);

(

mlp = second.cbegin(); mlp != second.cend(); ++mlp) {

tres = res.insert_after(tres, *mlp);

tog.

.insert(fromg.

.begin(), fromg.

.end());

(tg.

.empty() &&

.pseudogene.empty())

(! tg.

.empty() && !

.pseudogene.empty()) {

(

,

,

, (

.locus.empty()) ?

:

.locus, (

.locus_tag.empty()) ?

:

.locus_tag, tg.

,

.pseudogene);

.pseudogene.clear();

}

(

.pseudogene.empty()) {

= (ml.

> from) ? from : ml.

;

gelop = gelocs.begin();

(; gelop != gelocs.end(); ++gelop) {

(

> gelop->verymax) {

((gelop->strand > -1 &&

.slibp->strand != gelop->strand) ||

< gelop->verymin)

(

.locus == gelop->gene &&

.locus_tag == gelop->locus)

it = gelop->ammp.begin();

(; it != gelop->ammp.end(); ++it) {

ammp.pId->GetLabel(&label1, &ver1);

(max < ammp.min || min > ammp.max || ver1 != ver2)

(label1 == label2)

(it != gelop->ammp.end()) {

gelop != gelocs.end();

(mll.empty() ||

(mll.begin()) == mll.end())

tmlp = mll.begin();

(;

(tmlp) != mll.end(); ++tmlp)

(tmlp->min >

(tmlp)->min)

(;

(tmlp) != mll.end(); ++tmlp)

(tmlp->min <

(tmlp)->min)

(

(tmlp) != mll.end())

(tmlp = mll.begin(); tmlp != mll.end(); ++tmlp) {

(

.feat.Empty() || !

.feat->IsSetLocation()) {

(

pId :

.slibp->ids) {

& ml =

.mlp.emplace_front();

ml.min =

.slibp->from;

ml.max =

.slibp->to;

ml.strand =

.slibp->strand;

ml.noleft =

.slibp->noleft;

ml.noright =

.slibp->noright;

(

.leave == 1) {

.loc.Reset(&

.feat->SetLocation());

& locs =

.feat->GetLocation();

(cur_loc->

()) {

}

(cur_loc->

()) {

(! pId || from < 0 || to < 0) {

(

.mlp.empty()) {

& ml =

.mlp.emplace_front();

ml.noright = noright;

(

tmlp =

.mlp.begin();; ++tmlp) {

(

(pId, tmlp->pId) && tmlp->strand == strand) {

(tempcirc ==

&& ((tmlp->min <= to && tmlp->max >= from) ||

(tmlp->min > from) {

tmlp->noleft = noleft;

(tmlp->max < to) {

tmlp->noright = noright;

(

(tmlp) !=

.mlp.end())

tmlp =

.mlp.emplace_after(tmlp);

ml.noright = noright;

(ml.

|| noleft) {

point.

().SetLim(lim);

(

(mll.begin()) == mll.end()) {

(mll.front().min == mll.front().max)

(

mlp = mll.begin(); mlp != mll.end(); ++mlp) {

(mlp->min == mlp->max) {

(

mlp = second.cbegin(); mlp != second.cend(); ++mlp) {

seen_before =

;

(

tmlp = second.cbegin(); tmlp != mlp; ++tmlp)

(tmlp->pId &&

(tmlp->pId, mlp->pId)) {

seen_before =

;

(

mlp =

.cbegin(); mlp !=

.cend(); ++mlp) {

seen_before =

;

(

tmlp =

.cbegin(); tmlp != mlp; ++tmlp)

(tmlp->pId &&

(tmlp->pId, mlp->pId)) {

seen_before =

;

(count2 - count1);

(

.mlp.empty() ||

(

.mlp.begin()) ==

.mlp.end())

(

got =

; got;) {

(

mlp =

.mlp.begin(); mlp !=

.mlp.end(); ++mlp) {

(mlp->numint == -1)

(

tmlp =

(mlp); tmlp !=

.mlp.end(); ++tmlp) {

(tmlp->numint == -1 || mlp->strand != tmlp->strand)

(mlp->numint == 0 && tmlp->numint == 0) {

((tmlp->min >= mlp->min && tmlp->min <= mlp->max) ||

(tmlp->max >= mlp->min && tmlp->max <= mlp->max) ||

(mlp->min > tmlp->min && mlp->max < tmlp->max)) {

(mlp->min == tmlp->min) {

mlp->noleft =

;

}

(mlp->min > tmlp->min) {

mlp->min = tmlp->min;

mlp->noleft = tmlp->noleft;

(mlp->max == tmlp->max) {

mlp->noright =

;

}

(mlp->max < tmlp->max) {

mlp->max = tmlp->max;

mlp->noright = tmlp->noright;

(mlp->min != tmlp->min || mlp->max != tmlp->max)

(tmlp->numint == 0) {

mlp->noleft =

;

mlp->noright =

;

}

(mlp->numint == 0) {

tmlp->noleft =

;

tmlp->noright =

;

}

(tmlp->numint >= mlp->numint) {

mlp->noleft =

;

mlp->noright =

;

tmlp->noleft =

;

tmlp->noright =

;

mlpprev =

.mlp.before_begin();

(

mlp =

.mlp.begin(); mlp !=

.mlp.end();) {

mlpnext =

(mlp);

(mlp->numint != -1) {

.mlp.erase_after(mlpprev);

mlpprev =

.mlp.before_begin();

mlp =

.mlp.begin();

(; mlp !=

.mlp.end(); mlpprev = mlp++)

(mlp->numint == 1)

(mlp !=

.mlp.end() && mlp !=

.mlp.begin()) {

.mlp.splice_after(

.mlp.before_begin(),

.mlp, mlpprev,

.mlp.end());

(mll.empty() ||

(mll.begin()) == mll.end())

(

mlp = mll.begin(); mlp != mll.end(); ++mlp) {

(

tmlp =

(mlp); tmlp != mll.end(); ++tmlp) {

mlp->strand != tmlp->strand)

(tmlp->min < mlp->min)

(tmlp->min == mlp->min) {

(tmlp->noleft == mlp->noleft) {

(tmlp->max < mlp->max)

(tmlp->max == mlp->max) {

(tmlp->noright == mlp->noright || mlp->noright)

}

(mlp->noleft)

(tmlp->min > mlp->min)

(tmlp->min == mlp->min) {

(tmlp->noleft == mlp->noleft) {

(tmlp->max > mlp->max)

(tmlp->max == mlp->max) {

(tmlp->noright == mlp->noright || tmlp->noright)

}

(tmlp->noleft)

noleft = mlp->noleft;

noright = mlp->noright;

numint = mlp->numint;

mlp->min = tmlp->min;

mlp->max = tmlp->max;

mlp->noleft = tmlp->noleft;

mlp->noright = tmlp->noright;

mlp->numint = tmlp->numint;

tmlp->noleft = noleft;

tmlp->noright = noright;

tmlp->numint = numint;

(

c = gnp->

.cbegin();

(c) != gnp->

.cend(); ++c) {

(

cn =

(c); cn != gnp->

.cend(); ++cn) {

(c->feat.NotEmpty() && cn->feat.NotEmpty() &&

c->feat->IsSetData() && c->feat->GetData().IsCdregion() &&

cn->feat->IsSetData() && c->feat->GetData().IsCdregion() &&

circular =

;

(

c = gnp->

.begin(); c != gnp->

.end(); ++c, j++) {

(

c = gnp->

.begin();

(c) != gnp->

.end();) {

c->leave != 0 || cn->leave != 0 ||

c->slibp->strand != cn->slibp->strand ||

(c->slibp->from > cn->slibp->from) {

c->slibp->from = cn->slibp->from;

c->slibp->noleft = cn->slibp->noleft;

(c->slibp->to < cn->slibp->to) {

c->slibp->to = cn->slibp->to;

c->slibp->noright = cn->slibp->noright;

cp = gnp->

.begin();

(; cp != gnp->

.end(); ++cp) {

(cp->leave == 1 || cp->circular)

cp->slibp->strand != c->slibp->strand)

(c->slibp->from <= cp->slibp->to &&

c->slibp->to >= cp->slibp->from)

= (cp != gnp->

.end());

(! cn->allpseudo)

c->allpseudo =

;

c->noleft = c->slibp->noleft;

c->noright = c->slibp->noright;

gnp->

.erase_after(c);

(

c = gnp->

.begin(); c != gnp->

.end(); ++c) {

(

c = gnp->

.begin(); c != gnp->

.end(); ++c)

(c->loc.Empty() && ! c->mlp.empty())

c->loc =

(c->mlp, c->noleft, c->noright);

(

c = gnp->

.begin(); c != gnp->

.end(); ++c) {

(

cn = gnp->

.begin(); cn != gnp->

.end(); ++cn) {

(cn->loc.Empty() || loc == cn->loc ||

cn->slibp->strand != c->slibp->strand ||

(cn->leave == 1 || c->leave == 0)

c->leave = cn->leave;

(! cn->allpseudo)

c->allpseudo =

;

cp = gnp->

.before_begin();

(

c = gnp->

.begin(); c != gnp->

.end();) {

c = gnp->

.erase_after(cp);

(

c = gnp->

.begin(); c != gnp->

.end();) {

(cn = c; cn != gnp->

.end(); ++cn) {

(cn->maploc.empty())

(maploc.empty()) {

maploc = cn->maploc;

(cn = c; cn != gnp->

.end(); ++cn) {

new_id->Assign(

);

* pTextId = new_id->GetTextseq_Id();

*

(pTextId)->ResetVersion();

(

.IsRna()) {

(

&& *

!= -1)

}

(

.IsImp()) {

(

.GetImp().IsSetKey()) {

(

.GetImp().GetKey() == *

)

(

& qual : quals) {

(! qual->IsSetQual() || ! qual->IsSetVal() ||

qual->GetQual() !=

||

syns.insert(qual->GetVal());

(

& qual : quals) {

(! qual->IsSetQual() || ! qual->IsSetVal() ||

qual->GetQual() !=

||

syns.insert(qual->GetVal());

(

==

||

==

||

==

||

==

)

(rna_ref.

()) {

p =

;

(loc_str.empty())

(loc_str.size() > 55) {

loc_str = loc_str.substr(0, 50);

list<AccMinMax> ammps;

(cur_loc->

()) {

to = interval.

();

(gelop->

== -2)

(gelop->

!= strand)

}

(cur_loc->

()) {

(gelop->

== -2)

(gelop->

!= strand)

found_id =

;

it = ammps.begin();

(! found_id && it != ammps.end()) {

(from < ammp.min) {

(to > ammp.max) {

ammps.push_back(ammp);

& geloc = gnp->

.emplace_front();

geloc.locus = locus_tag;

(

& dbxref : feat.

()) {

(! dbxref->IsSetTag() || ! dbxref->IsSetDb() ||

dbxref->GetDb() !=

s ||

! dbxref->GetTag().GetStr().starts_with(

sv)) {

dbxrefs.push_back(dbxref);

.wormbase.insert(dbxref->GetTag().GetStr());

(dbxrefs.empty())

(TQualVector::iterator qual = feat.

().begin(); qual != feat.

().end(); ++qual) {

(! (*qual)->IsSetQual() || ! (*qual)->IsSetVal() ||

(*qual)->GetQual() !=

) {

quals.push_back(*qual);

.olt.insert((*qual)->GetVal());

(

& feat : feats) {

locus_tag =

(feat->GetQual(),

);

* cur_loc = feat->IsSetLocation() ? &feat->GetLocation() :

;

(gene.empty() && locus_tag.empty()) {

pseudogene =

(feat->GetQual(),

);

& newg = gnp->

.emplace_front();

(! newg.

) {

gnp->

.pop_front();

(gnp->

==

&& feat->IsSetData() &&

(feat->IsSetQual()) {

newg.

=

;

newg.

= feat->IsSetPseudo() ? feat->GetPseudo() :

;

newg.

= feat->IsSetPseudo() ? feat->GetPseudo() :

;

(! gnp->

.empty())

(

& feat : feats) {

* cur_loc = feat->IsSetLocation() ? &feat->GetLocation() :

;

& newclp = cdsl.emplace_front();

newclp.from = slip->

;

newclp.to = slip->

;

* first_id =

;

(! bioseq.

().empty())

first_id = *bioseq.

().begin();

(

& annot : bioseq.

()) {

(! annot->IsFtable())

(annot->SetData().SetFtable(), gene_node, bioseq.

(), *

);

(annot->SetData().SetFtable(), gene_node->

, *

);

(! gene_node->

.empty() && gene_node->

==

) {

gene_node->

= &bioseq;

gene_node->

=

;

glp = gl.cbegin();

(glp != gl.cend()) {

(glp->locus.empty() && glp->locus_tag.empty())

tglp =

(glp);

(; tglp != gl.cend(); ++tglp) {

(tglp->locus.empty() && tglp->locus_tag.empty())

(! got && glp->slibp && tglp->slibp &&

glp->slibp->strand != tglp->slibp->strand)

(

,

,

, (glp->locus.empty()) ?

:

, (glp->locus.empty()) ? glp->locus_tag : glp->locus);

TGeneList::iterator glpstart;

TGeneList::iterator glpstop;

(gl.empty() ||

(gl.begin()) == gl.end())

(

glp = gl.begin(); glp != gl.end(); glp =

(glpstop)) {

(glp->locus.empty() && glp->locus_tag.empty())

(

tglp =

(glp); tglp != gl.end(); ++tglp) {

(

tglp =

(glpstop); tglp != gl.end(); ++tglp) {

(tglp->locus.empty() && tglp->locus_tag.empty())

((same_gn ==

&& same_lt ==

) || (same_gn && same_lt) ||

same_gn || glpstart->locus_tag.empty())

(glp = glpstart;; ++glp) {

(

,

,

, (glp->locus.empty()) ?

: glp->locus, (glp->locus_tag.empty()) ?

: glp->locus_tag, glp->fname, glp->location, (tglp->locus.empty()) ?

: tglp->locus, (tglp->locus_tag.empty()) ?

: tglp->locus_tag, tglp->fname, tglp->location);

(! glpstart->locus.empty() && ! glpstart->locus_tag.empty() &&

glpstart->locus == glpstart->locus_tag) {

(glp = glpstart;; ++glp) {

(! gnp || gnp->

.empty())

(

glp = gnp->

.begin(); glp != gnp->

.end(); ++glp) {

(glp->locus_tag.empty() || ! glp->locus.empty() ||

(glp->fname !=

))

(

tglp = gnp->

.begin(); tglp != gnp->

.end(); ++tglp) {

(tglp->fname.empty() ||

(tglp->fname ==

)) {

(tglp->locus.empty() || tglp->locus[0] ==

||

glp->locus = tglp->locus;

(! gnp || gnp->

.empty())

(

glp = gnp->

.begin(); glp != gnp->

.end(); ++glp) {

(glp->todel || ! glp->syn.empty() || (glp->fname !=

))

(

tglp = gnp->

.begin(); tglp != gnp->

.end(); ++tglp) {

(tglp->todel || (tglp->fname ==

))

(tglp->syn.empty()) {

(glp->todel && got)

glp->todel =

;

glpprev = gnp->

.before_begin();

(

glp = gnp->

.begin(); glp != gnp->

.end();) {

glp = gnp->

.erase_after(glpprev);

(TSeqFeatList::const_iterator feat = feats.begin(); feat != feats.end(); ++feat) {

& gene_ref1 = (*feat)->GetData().GetGene();

TSeqFeatList::const_iterator feat_next = feat,

(++feat_next; feat_next != feats.end(); ++feat_next, ++feat_cur) {

& gene_ref2 = (*feat_next)->GetData().GetGene();

loc1_str, loc2_str;

(diff_lt ==

) {

,

,

(

glp = gnp->

.begin(); glp != gnp->

.end(); ++glp) {

(! gnp->

.empty()) {

(! gnp->

.empty()) {

(

& cur_annot : annots) {

(! cur_annot->IsFtable())

advance = cur_annot->GetData().GetFtable().size();

cur_annot->SetData().SetFtable().splice(cur_annot->SetData().SetFtable().end(), gnp->

);

gene_refs.

= cur_annot->SetData().SetFtable().begin();

std::advance(gene_refs.

, advance);

gene_refs.

= cur_annot->SetData().SetFtable().end();

gene_refs.

=

;

(annots.empty()) {

annot->

().SetFtable().assign(gnp->

.begin(), gnp->

.end());

gene_refs.

= annot->

().SetFtable().begin();

gene_refs.

= annot->

().SetFtable().end();

gene_refs.

=

;

(strand1 != strand2) {

& intv1 = loc1.

();

& intv2 = loc2.

();

(intv1.GetFrom() >= intv2.GetFrom() && intv1.GetTo() <= intv2.GetTo());

TSeqLocInfoList::const_iterator cur_loc = llocs.begin();

stopped =

;

(gene_refs.

) {

(

cur_feat = gene_refs.

; cur_feat != gene_refs.

; ++cur_feat) {

(gene_ref.

()) {

gene_ref.

(&(*cur_feat)->GetData().GetGene());

xref->SetData().SetGene(gerep);

(CBioseq::TAnnot::iterator annot = annots.begin(); annot != annots.end();) {

(! (*annot)->IsSetData() || ! (*annot)->GetData().IsFtable()) {

(TSeqFeatList::iterator feat = feat_table.begin(); feat != feat_table.end();) {

((*feat)->IsSetData() && (*feat)->GetData().IsImp()) {

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

(imp.

() ==

) {

feat = feat_table.erase(feat);

optional<string> gene, locus_tag;

((*feat)->IsSetQual()) {

(! gene && ! locus_tag) {

gene_ref->

().assign(syns.begin(), syns.end());

(*feat)->SetXref().push_back(xref);

((*feat)->SetQual(),

);

((*feat)->SetQual(),

);

((*feat)->GetQual().empty())

(*feat)->ResetQual();

(feat_table.empty())

annot = annots.erase(annot);

(gene_refs.

) {

(TSeqFeatList::iterator feat = gene_refs.

; feat != gene_refs.

; ++feat) {

.strand = (*feat)->GetLocation().IsSetStrand() ? (*feat)->GetLocation().GetStrand() :

;

llocs.push_back(

);

(bio_set->IsSetAnnot())

(bio_set->SetAnnot(), acnum, gene_refs, llocs);

(bioseq->IsSetAnnot())

(bioseq->SetAnnot(), acnum, gene_refs, llocs);

(

& annot : bioseq.

()) {

(! annot->IsFtable())

(

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

(

& qual : feat->GetQual()) {

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

||

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

genes.insert(qual->GetVal());

(

& annot : bioseq.

()) {

(! annot->IsFtable())

(

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

(! feat->IsSetQual())

(CSeq_feat::TQual::iterator qual = feat->SetQual().begin(); qual != feat->SetQual().end(); ++qual) {

(! (*qual)->IsSetQual() || (*qual)->GetQual() !=

||

! (*qual)->IsSetVal() || (*qual)->GetVal().empty())

& cur_val = (*qual)->GetVal();

std::set<string>::const_iterator ci = genes.lower_bound(cur_val);

(*ci == cur_val) {

new_qual->

(

);

new_qual->

(cur_val);

feat->SetQual().insert(qual, new_qual);

std::set<string> genes;

(! genes.empty()) {

gene_refs.

=

;

(gene_refs.

) {

(TSeqFeatList::iterator feat = gene_refs.

; feat != gene_refs.

; ++feat) {

((*feat)->IsSetLocation()) {

(*feat)->SetPartial(

);

(! pp->

|| ! (*feat)->GetLocation().IsMix())

& mix_loc = (*feat)->SetLocation().SetMix();

CSeq_loc_mix::Tdata::iterator it_loc = mix_loc.

().begin();

(; it_loc != mix_loc.

().end(); ++it_loc) {

it_loc = mix_loc.

().insert(it_loc, null_loc);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

TSeqPos GetLength(void) const

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

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

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

namespace ncbi::objects::

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

void AddSeqLoc(const CSeq_loc &other)

Template class for iteration on objects of class C.

#define ERR_FEATURE_InconsistentPseudogene

#define ERR_FEATURE_InconsistentLocusTagAndGene

#define ERR_FEATURE_MultipleOldLocusTags

#define ERR_FEATURE_MultipleWBGeneXrefs

#define ERR_GENEREF_BothStrands

#define ERR_FEATURE_MultipleGenesDifferentLocusTags

#define ERR_GENEREF_NoUniqMaploc

std::list< CRef< objects::CSeq_id > > TSeqIdList

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

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

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

static char * join(int argc, char *argv[], const char sep[])

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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[]

const char * leave_imp_feat[]

static bool WeDontNeedToJoinThis(const CSeqFeatData &data)

static bool CompareGeneLocsMinMax(const GeneLoc &sp1, const GeneLoc &sp2)

forward_list< MixLoc > TMixLocList

static void GetGeneSyns(const TQualVector &quals, const string &name, TSynSet &syns)

forward_list< Gene > TGeneList

static void ScannGeneName(GeneNodePtr gnp, Int4 seqlen)

static void GeneQuals(CSeq_entry &entry, const char *acnum, GeneRefFeats &gene_refs)

static bool ConfirmCircular(TMixLocList &mll)

static Int4 fta_cmp_gene_syns(const TSynSet &syn1, const TSynSet &syn2)

static void fta_make_seq_int(MixLoc &ml, bool noleft, bool noright, CSeq_interval &interval)

static bool fta_rnas_cds_feat(const CSeq_feat &feat)

const char * feat_no_gene[]

static void fta_append_feat_list(GeneNodePtr gnp, const CSeq_loc *location, const string &gene, const string &locus_tag)

bool GenelocContained(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

static void SrchGene(CSeq_annot::C_Data::TFtable &feats, GeneNodePtr gnp, Int4 length, const CSeq_id &id)

static void fta_collect_genes(const CBioseq &bioseq, std::set< string > &genes)

static bool GetFeatNameAndLoc(Gene *glp, const CSeq_feat &feat, GeneNodePtr gnp)

static void CircularSeqLocFormat(Gene &g)

static void GetLocationStr(const CSeq_loc &loc, string &str)

forward_list< Cds > TCdsList

static void FixMixLoc(Gene &g, const TGeneLocList &gelocs)

static void AddGeneFeat(Gene &g, const string &maploc, TSeqFeatList &feats)

static CRef< CSeq_loc > MakeCLoc(TMixLocList &mll, bool noleft, bool noright)

static void SortMixLoc(TMixLocList &mll)

static void fta_fix_labels(CBioseq &bioseq, const std::set< string > &genes)

static void RemoveUnneededMiscFeats(GeneNodePtr gnp)

std::set< string > TWormbaseSet

static bool DoWeHaveCdssInBetween(const Gene &g, Int4 to, const TCdsList &cdsl)

static TMixLocList EasySeqLocMerge(const TMixLocList &first, const TMixLocList &second, bool join)

static Int2 GetMergeOrder(const TMixLocList &first, const TMixLocList &second)

static bool fta_check_feat_overlap(const TGeneLocList &gelocs, Gene &g, const MixLoc &ml, Int4 from, Int4 to)

static void fta_add_olt(Gene &fromg, Gene &tog)

static void CheckGene(CRef< CSeq_entry > entry, ParserPtr pp, GeneRefFeats &gene_refs)

static void fta_seqloc_del_far(CSeq_loc &locs, const Char *acnum, const CSeq_id *id)

static void fta_collect_olts(Gene &g, CSeq_feat &feat)

static void fta_make_seq_pnt(MixLoc &ml, bool noleft, bool noright, CSeq_point &point)

static bool CompareGeneListName(const Gene &g1, const Gene &g2)

static Int4 fta_cmp_gene_refs(const CGene_ref &grp1, const CGene_ref &grp2)

static SeqlocInfoblkPtr GetLowHighFromSeqLoc(const CSeq_loc *origslp, Int4 length, const CSeq_id &orig_id)

static bool fta_seqid_same(const CSeq_id &sid, const Char *acnum, const CSeq_id *id)

static Int4 fta_cmp_locusyn(const Gene &g1, const Gene &g2)

std::set< string > TSynSet

static TMixLocList CircularSeqLocCollect(const TMixLocList &first, const TMixLocList &second)

static void fta_check_pseudogene(Gene &tg, Gene &g)

forward_list< GeneLoc > TGeneLocList

static bool DoWeHaveGeneInBetween(Gene &g, SeqlocInfoblkPtr second, const GeneNode *gnp)

static bool s_IdsMatch(const CRef< CSeq_id > &pId1, const CRef< CSeq_id > &pId2)

static void fta_add_wormbase(Gene &fromg, Gene &tog)

static CRef< CSeq_loc > fta_seqloc_local(const CSeq_loc &orig, const Char *acnum)

static void SrchCDSs(CSeq_annot::C_Data::TFtable &feats, TCdsList &cdsl, const CSeq_id &id)

void DealWithGenes(CRef< CSeq_entry > &pEntry, ParserPtr pp)

static bool GeneLocusCheck(const TSeqFeatList &feats, bool diff_lt)

std::set< string > TLocusTagSet

static void FixAnnot(CBioseq::TAnnot &annots, const char *acnum, GeneRefFeats &gene_refs, TSeqLocInfoList &llocs)

static CRef< CSeq_id > CpSeqIdAcOnly(const CSeq_id &id, bool accver)

static void FindGene(CBioseq &bioseq, GeneNodePtr gene_node)

static void GeneCheckForStrands(const TGeneList &gl)

static bool LocusTagCheck(TGeneList &gl, bool &resort)

static bool IfCDSGeneFeat(const CSeq_feat &feat, Uint1 choice, const char *key)

static list< AccMinMax > fta_get_acc_minmax_strand(const CSeq_loc *location, GeneLoc *gelop)

static void MiscFeatsWithoutGene(GeneNodePtr gnp)

static CRef< CSeqFeatXref > GetXrpForOverlap(const char *acnum, GeneRefFeats &gene_refs, const TSeqLocInfoList &llocs, const CSeq_feat &feat, CGene_ref &gerep)

static void fta_collect_wormbases(Gene &g, CSeq_feat &feat)

list< SeqLocInfo > TSeqLocInfoList

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

Set object to copy of another one.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_NO

different SeqId types-can't compare

@ e_YES

SeqIds compared, but are different.

ENa_strand GetStrand(void) const

Get the location's strand.

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

Override Assign() to incorporate cache invalidation.

const_iterator end(void) const

const_iterator begin(void) const

CRef< CSeq_loc > Subtract(const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper, ILengthGetter *len_getter) const

Subtract seq-loc from this, merge/sort resulting ranges depending on flags.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void GetLabel(string *label) const

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

void SetNull(void)

Override all setters to incorporate cache invalidation.

@ eEmpty_Allow

ignore empty locations

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

int SeqLocPartialCheck(const CSeq_loc &loc, CScope *scope)

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

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 NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-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 CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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

Case-sensitive equality of a substring with another string.

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

Case-insensitive equality of a substring with another string.

TSyn & SetSyn(void)

Assign a value to Syn data member.

bool IsSetSyn(void) const

synonyms for locus Check if a value has been assigned to Syn data member.

const TSyn & GetSyn(void) const

Get the Syn member data.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

void SetLocus(const TLocus &value)

Assign a value to Locus data member.

void SetLocus_tag(const TLocus_tag &value)

Assign a value to Locus_tag data member.

void SetMaploc(const TMaploc &value)

Assign a value to Maploc data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

bool IsLim(void) const

Check if variant Lim is selected.

TLim GetLim(void) const

Get the variant data.

TType GetType(void) const

Get the Type member data.

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

bool IsSetType(void) const

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

const TName & GetName(void) const

Get the variant data.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsName(void) const

Check if variant Name is selected.

void SetQual(const TQual &value)

Assign a value to Qual data member.

const TKey & GetKey(void) const

Get the Key member data.

vector< CRef< CDbtag > > TDbxref

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

bool IsSetData(void) const

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

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

E_Choice Which(void) const

Which variant is currently selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

bool IsImp(void) const

Check if variant Imp is selected.

bool IsSetKey(void) const

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

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

void SetVal(const TVal &value)

Assign a value to Val data member.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

void SetPseudo(TPseudo value)

Assign a value to Pseudo data member.

const TRna & GetRna(void) const

Get the variant data.

void ResetDbxref(void)

Reset Dbxref data member.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsRna(void) const

Check if variant Rna is selected.

void ResetQual(void)

Reset Qual data member.

const TImp & GetImp(void) const

Get the variant data.

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

void SetTo(TTo value)

Assign a value to To data member.

const TFuzz_from & GetFuzz_from(void) const

Get the Fuzz_from member data.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

const TId & GetId(void) const

Get the Id member data.

bool IsSetPoint(void) const

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

bool IsPacked_pnt(void) const

Check if variant Packed_pnt is selected.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

const TFuzz_to & GetFuzz_to(void) const

Get the Fuzz_to member data.

bool IsSetA(void) const

connection to a least one residue Check if a value has been assigned to A data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

TFrom GetFrom(void) const

Get the From member data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

bool IsSetFuzz(void) const

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

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

const TId & GetId(void) const

Get the Id member data.

const TId & GetId(void) const

Get the Id member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TStrand GetStrand(void) const

Get the Strand member data.

bool IsBond(void) const

Check if variant Bond is selected.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

void SetFuzz_to(TFuzz_to &value)

Assign a value to Fuzz_to data member.

void SetFuzz_from(TFuzz_from &value)

Assign a value to Fuzz_from data member.

const TA & GetA(void) const

Get the A member data.

bool IsSetTo(void) const

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

bool IsSetStrand(void) const

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

Tdata & Set(void)

Assign a value to data member.

bool IsSetFuzz_to(void) const

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

bool IsSetStrand(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

TTo GetTo(void) const

Get the To member data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsSetFrom(void) const

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

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsSetVersion(void) const

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

bool IsSetFuzz_from(void) const

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

void SetStrand(TStrand value)

Assign a value to Strand data member.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TBond & GetBond(void) const

Get the variant data.

void SetData(TData &value)

Assign a value to Data data member.

const TInst & GetInst(void) const

Get the Inst member data.

TTopology GetTopology(void) const

Get the Topology member data.

bool IsSetAnnot(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

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 orig

if(yy_accept[yy_current_state])

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

TSeqFeatList::iterator first

TSeqFeatList::iterator last

vector< IndexblkPtr > entrylist

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

bool DeleteQual(TQualVector &qlist, const Char *qual)

string CpTheQualValue(const TQualVector &qlist, const Char *qual)

void MakeLocStrCompatible(string &str)

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

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

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

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