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

clean_i.BasicCleanupSeqEntry(se);

clean_i.BasicCleanupSeqSubmit(ss);

clean_i.BasicCleanupSubmitblock(block);

clean_i.BasicCleanupBioseqSet(bss);

clean_i.BasicCleanupSeqAnnot(sa);

clean_i.BasicCleanupSeqFeat(sf);

clean_i.BasicCleanupBioSource(src);

clean_i.BasicCleanup(desc);

(

& it : desc.

()) {

clean_i.BasicCleanup(*it);

clean_i.ExtendedCleanupSeqEntry(se);

clean_i.ExtendedCleanupSeqSubmit(ss);

clean_i.ExtendedCleanupSeqAnnot(sa);

vector<string_view>

;

constexpr std::array<string_view, CCleanupChangeCore::eNumberofChangeTypes>

= {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

;

;

;

;

;

new_feat->

().push_back(q);

CSeq_feat::TQual::iterator it = feat.

().begin();

(it != feat.

().end()) {

((*it)->IsSetQual() &&

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

((*it)->GetVal())) {

feat.

().SetProt().SetName().push_back((*it)->GetVal());

it = feat.

().erase(it);

(feat.

().empty()) {

feat_by_product =

;

(cdsScores.empty()) {

(

cdsScore : cdsScores) {

cdsScore.second;

cdsScores.front().second;

(parent_bsh.

()) {

matched_by_product =

;

matched_by_product =

;

(!matched_by_product) {

require_frame =

;

(!require_frame) {

((*id_it)->IsEmbl() || (*id_it)->IsDdbj()) {

require_frame =

;

new_feat->

(*orig_feat);

new_feat->

().SetProt().SetProcessed(processed);

new_feat->

().SetProt().SetName().push_back(

);

(matched_by_product) {

((*annot_it)->IsFtable()) {

any_change =

;

(

prot_it(*bi, sel); prot_it; ++prot_it) {

(scores.size() == 1) {

}

(scores.size() == 0) {

(

->second.GetPointer() != gene.

() &&

(!

.IsSetXref()) {

any_removed =

;

CSeq_feat::TXref::iterator xit =

.SetXref().begin();

(xit !=

.SetXref().end()) {

((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&

xit =

.SetXref().erase(xit);

(

.IsSetXref() &&

.GetXref().empty()) {

any_change =

;

(fi->IsSetXref()) {

new_feat->

(*(fi->GetOriginalSeq_feat()));

(!

.IsSetXref()) {

any_removed =

;

CSeq_feat::TXref::iterator xit =

.SetXref().begin();

(xit !=

.SetXref().end()) {

((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&

!(*xit)->GetData().GetGene().IsSuppressed()) {

xit =

.SetXref().erase(xit);

(

.IsSetXref() &&

.GetXref().empty()) {

has_xref =

;

((*xit)->IsSetId() && (*xit)->GetId().IsLocal()) {

((*xit)->GetId().Equals(src.

())) {

(!

.IsSetId() || !

.IsSetXref()) {

((*xit)->IsSetId() && (*xit)->GetId().IsLocal()) {

(far_feats.size() == 1) {

( !

.Equals(*feat_ci->GetSeq_feat()) && feat_ci->GetSeq_feat()->IsSetData() && feat_ci->GetSeq_feat()->GetData().IsGene()

&& feat_ci->GetSeq_feat()->GetData().GetGene().IsSetLocus())

locus2 = feat_ci->GetSeq_feat()->GetData().GetGene().GetLocus();

(!locus1.empty() && !locus2.empty() && locus1 == locus2)

(!

.IsSetXref()) {

any_removed =

;

CSeq_feat::TXref::iterator xit =

.SetXref().begin();

(xit !=

.SetXref().end()) {

((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&

!(*xit)->GetData().GetGene().IsSuppressed() && !

(

, (*xit)->GetData().GetGene(), bsh)) {

xit =

.SetXref().erase(xit);

(

.IsSetXref() &&

.GetXref().empty()) {

( !

.Equals(*feat_ci->GetSeq_feat()) && feat_ci->GetSeq_feat()->IsSetData() && feat_ci->GetSeq_feat()->GetData().IsGene()

&& feat_ci->GetSeq_feat()->GetData().GetGene().IsSetLocus_tag())

locus_tag2 = feat_ci->GetSeq_feat()->GetData().GetGene().GetLocus_tag();

(!locus_tag1.empty() && !locus_tag2.empty() && locus_tag1 == locus_tag2)

(!

.IsSetXref()) {

any_removed =

;

CSeq_feat::TXref::iterator xit =

.SetXref().begin();

(xit !=

.SetXref().end()) {

((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&

xit =

.SetXref().erase(xit);

any_removed =

;

(

.IsSetXref() &&

.GetXref().empty()) {

changed =

;

(pos < loc_start) {

->Assign(*(loc.

()));

}

(pos > loc_stop) {

->Assign(*(loc.

()));

(new_loc->

()) {

last_interval = new_loc->

().SetLastLoc();

last_interval = new_loc;

last_interval->

().SetFrom(new_start);

last_interval->

().SetTo(new_stop);

last_interval->

().SetId().Assign(*

);

& loc =

.GetLocation();

(

.IsSetData() &&

.GetData().IsCdregion())

(

.GetData().GetCdregion().IsSetCode())

= &(

.GetData().GetCdregion().GetCode());

(

.GetData().GetCdregion().IsSetFrame())

frame =

.GetData().GetCdregion().GetFrame();

= orig_len;

vector_loc->

().SetId().Assign(*(bsh.

().front().GetSeqId()));

vector_loc->

().SetFrom(0);

vector_loc->

().SetTo(stop +

- 1);

vector_loc->

().SetFrom(stop -

+ 1);

usable_size = seq.

();

(limit > 0 && usable_size > limit) {

usable_size = limit;

length = usable_size / 3;

(

= 0;

< length; ++

) {

(k = 0; k < 3; ++k, ++start) {

changed =

;

(frame != new_frame) {

cds.

().SetCdregion().SetFrame(new_frame);

( (seq_len % 3) + 1 ) {

(frame != desired_frame) {

frame = desired_frame;

(!

.GetData().IsCdregion()) {

(check_for_stop) {

prot_ref.

().front() +=

;

prot_ref.

().front() += protein_name;

prot_ref.

().push_back(protein_name);

used_qual =

;

(

it = mrna.

().begin(); it != mrna.

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

(*it)->SetVal(protein_name);

mrna.

().SetRna().SetRnaProductName(protein_name, remainder);

(

it = cds.

().begin(); it != cds.

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

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

(

it = cds.

().begin(); it != cds.

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

(

it = feat.

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

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

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

(

it = feat.

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

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

(*it)->SetVal((*it)->GetVal() +

+ protein_name);

(*it)->SetVal(protein_name);

added =

;

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

xref->SetData().SetProt().SetName().push_back(protein_name);

cds.

().push_back(xref);

(

.IsSetName() && !

.GetName().empty()) {

.GetName().front();

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

(

it = cds.

().begin(); it != cds.

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

((*it)->IsSetQual() && (*it)->IsSetVal() &&

((*it)->GetQual(),

)) {

(*it)->GetVal();

any_change =

;

}

(

runtime_error&) {

(loc.

()) {

this_is_last = is_last && (*it == mix.

().back());

((*it)->IsMix() || (*it)->IsPacked_int()) {

(!this_is_last &&

this_is_last = is_last && (*it == pint.

().back());

new_feat->

(*(

->GetSeq_feat()));

(!

.IsSetLocation()) {

partial =

;

(li && !partial) {

changed =

;

(

.IsSetPartial() &&

.GetPartial()) {

.SetPartial(

);

changed =

;

& ec_num = *ec_num_iter;

tlen = ec_num.length();

(tlen != ec_num.length()) {

changed =

;

CProt_ref::TEc::iterator ec_num_iter = ec_num_list.begin();

(ec_num_iter != ec_num_list.end()) {

& ec_num = *ec_num_iter;

tlen = ec_num.length();

(tlen != ec_num.length()) {

ec_num_iter = ec_num_list.erase(ec_num_iter);

any_change =

;

(

->GetData().GetProt().IsSetEc()) {

this_change =

;

new_feat->

(*(

->GetSeq_feat()));

new_feat->

().SetProt().ResetEc();

this_change =

;

check_outer_gene =

;

check_outer_gene =

;

(check_outer_gene) {

(

> longest) {

changed =

;

needs_molinfo =

;

((*it)->IsMolinfo()) {

needs_molinfo =

;

(!(*it)->GetMolinfo().IsSetBiomol() ||

(needs_molinfo) {

seq.

().Set().push_back(m);

seq.

().Set().push_back(m);

needs_molinfo =

;

needs_molinfo;

(it->Which()) {

new_defline = sequence::CDeflineGenerator().GenerateDefline(bsh, sequence::CDeflineGenerator::fIgnoreExisting);

modified = title_desc.

().

() != new_defline;

title_desc.

().

().swap(new_defline);

(desc.

() &&

(!descr.

() || descr.

().empty()) {

& elements = descr.

();

it = elements.begin();

(it != elements.end()) {

it = elements.erase(it);

(rval && seq_entry.

().

().empty()) {

(seq_entry.

()) {

(seq_entry.

()) {

(descr.

()) {

(

pDesc : descr.

()) {

pDesc->SetUser().UpdateNcbiCleanup(ncbi_cleanup_version);

& user = pCleanupObject->SetUser();

user.UpdateNcbiCleanup(ncbi_cleanup_version);

descr.

().push_back(pCleanupObject);

((*it)->IsSource() && (*it)->GetSource().IsSetOrg()) {

src_descs.push_back(*it);

any_changes =

;

vector<CRef<COrg_ref> > rq_list;

vector<const CSeqdesc* > src_descs;

vector<CConstRef<CSeq_feat> > src_feats;

vector<const CSeqdesc* >::iterator desc_it = src_descs.begin();

(desc_it != src_descs.end()) {

org->

((*desc_it)->GetSource().GetOrg());

rq_list.push_back(org);

rq_list.push_back(org);

(rq_list.size() > 0) {

CTaxon3_reply::TReply::const_iterator reply_it = reply->GetReply().begin();

desc_it = src_descs.begin();

(reply_it != reply->GetReply().end()

&& desc_it != src_descs.end()) {

((*reply_it)->IsData() &&

!(*desc_it)->GetSource().GetOrg().Equals((*reply_it)->GetData().GetOrg())) {

any_changes =

;

desc->

().

().Assign((*reply_it)->GetData().GetOrg());

vector<CConstRef<CSeq_feat> >::iterator feat_it = src_feats.begin();

(reply_it != reply->GetReply().end()

&& feat_it != src_feats.end()) {

((*reply_it)->IsData() &&

!(*feat_it)->GetData().GetBiosrc().GetOrg().Equals((*reply_it)->GetData().GetOrg())) {

any_changes =

;

new_feat->

(**feat_it);

new_feat->

().SetBiosrc().SetOrg().Assign((*reply_it)->GetData().GetOrg());

(new_product.

()) {

new_product->

().Set().push_back(molinfo);

new_product->

().push_back(prot_id);

prot_entry->

(*new_product);

(!eh.

()) {

(!eh.

()) {

(

&&

->IsSetSeq_set()) {

(

->IsSetDescr()) {

it =

->GetDescr().Get().begin();

(it !=

->GetDescr().Get().end()) {

(!(*it)->IsMolinfo() && !(*it)->IsTitle() && !(*it)->IsCreate_date()) {

->Assign(**it);

neh.RemoveSeqdesc(**it);

(

->IsSetDescr()) {

it =

->GetDescr().Get().begin();

(!bsh.

()) {

(!bsrc.IsSetOrg() || !bsrc.IsSetOrgname()) {

(!orgname.IsSetGcode() && !orgname.IsSetMgcode() && !orgname.IsSetPgcode()) {

any_changed =

;

(; feat_ci; ++feat_ci) {

cdregionGenCode = (cds.

() ?

(cdregionGenCode != bioseqGenCode)

new_feat->

(feat);

new_cds.

().SetId(bioseqGenCode);

edit_handle.

(*new_feat);

any_changed =

;

& sTitle,

& sOrganism,

OrganellePos =

;

sPattern =

+ sOrganism +

;

answer = sTitle.length() - sPattern.length();

(answer < 1 || answer ==

) {

(answer !=

) {

(possible_organelle_start_pos !=

&&

OrganellePos = possible_organelle_start_pos;

& sTitle,

organelle_pos =

;

is_cross_kingdom =

;

(first_kingdom.empty()) {

first_kingdom = te.

();

is_cross_kingdom =

;

second_kingdom = te.

();

is_cross_kingdom;

first_kingdom, second_kingdom;

& sTitle,

organelle_pos =

;

((*it)->IsSetSubtype() && (*it)->IsSetSubname() &&

(suffixPos !=

) {

(suffixPos !=

) {

(suffixPos !=

) {

(sep != string::npos) {

(

.empty()) {

suffix_len = suffix.length();

change_made{

};

(

& name :

) {

name.erase(

- suffix_len);

change_made =

;

(

(taxname) || taxname.starts_with(

sv)) {

taxname_in_brackets{

+ taxname +

};

change_made{

};

(; annot_it; ++annot_it) {

(; feat_it; ++feat_it) {

change_made =

;

pEditedFeat->SetData().SetProt().SetName() = move(temp_names);

(

id_handle : bsh.

()) {

pId = id_handle.GetSeqId();

eCompleteness_partial:

eCompleteness_no_left:

eCompleteness_no_right:

eCompleteness_no_ends:

((! seq_descr.

()) || (pMolinfoDesc && pSrcDesc)) {

(

pDesc : seq_descr.

()) {

((! pMolinfoDesc) && pDesc->IsMolinfo()) {

pMolinfoDesc = pDesc;

}

((! pSrcDesc) && pDesc->IsSource()) {

((! pMolinfoDesc) || (! pSrcDesc)) {

(pParentSet && pParentSet.IsSetDescr()) {

make_pair(pMolinfoDesc, pSrcDesc);

(partialPos ==

) {

partialPos =

(sTitle,

);

(suffixPos ==

) {

sTitle.resize(suffixPos);

(penult !=

) {

sTitle.resize(penult);

partialPos != string::npos &&

(partialPos == (sTitle.length() - 9)))

sTitle.resize(partialPos);

(bPartial && partialPos ==

) {

sTitle +=

;

(genome >= eGenome_chloroplast &&

genome <= eGenome_chromatophore &&

genome != eGenome_extrachrom &&

genome != eGenome_transposon &&

genome != eGenome_insertion_seq &&

genome != eGenome_proviral &&

genome != eGenome_virion &&

genome != eGenome_chromosome) {

sTitle +=

+

(organelle) +

;

& org = src.

();

first_kingdom, second_kingdom;

sTitle +=

+ first_kingdom +

+ second_kingdom +

;

(org.IsSetTaxname()) {

& desc_list = descr.

();

(

it = desc_list.rbegin(); it != desc_list.rend(); ++it) {

((*it)->IsTitle()) {

molinfo_desc = molinfo_and_src.first;

src_desc = molinfo_and_src.second;

& org =

.GetOrg();

(org.IsSetTaxname()) {

title = title_desc->

();

(title != title_desc->

()) {

pNewTitleDesc->SetTitle() = move(title);

(

->GetData().GetProt().IsSetName() &&

!

->GetData().GetProt().GetName().empty()) {

=

->GetData().GetProt().GetName().front();

}

(

->GetData().GetProt().IsSetDesc()) {

=

->GetData().GetProt().GetDesc();

any_change =

;

((*xit)->IsSetId() && (*xit)->GetId().IsLocal()) {

(f_start < gene_start) {

gene_start = f_start;

(f_stop > gene_stop) {

{

, { 1000,

} },

{

, { 1000,

} },

{

, { 2000,

} },

{

, { 1000,

} },

{

, { 1000,

} },

{

, { 3300,

} },

{

, { 1000,

} },

{

, { 1000,

} },

{

, { 130,

} },

{

, { 90,

} }

is_bad =

;

& rrna =

.GetData().GetRna();

(rrna_name.empty()) {

(

.IsSetQual()) {

(

qit :

.GetQual()) {

rrna_name = gbq.

();

(pos != string::npos && len < it->second.first && !(it->second.second &&

.IsSetPartial() &&

.GetPartial()) ) {

any_changes =

;

protein_id_counter = 1;

(

cds_it(entry, sel); cds_it; ++cds_it) {

change_this_cds =

;

new_cds->

(*(cds_it->GetSeq_feat()));

new_cds->

().SetWhole().Assign(*new_id);

change_this_cds =

;

(new_cds->

() && instantiate_missing_proteins) {

any_changes =

;

new_inst->

().SetNcbieaa().Set(current);

any_changes =

;

current_name =

;

change_this_cds =

;

change_mrna =

;

new_mrna->

(*mrna);

(

it = new_mrna->

().begin(); it != new_mrna->

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

((*it)->IsSetQual() && (*it)->IsSetVal() &&

((*it)->GetQual(),

)) {

mrna_name = (*it)->GetVal();

|| (!

(current_name,

) &&

change_mrna =

;

any_changes =

;

(change_this_cds) {

any_changes =

;

& rna_feat = *(rna_it->GetSeq_feat());

change_this_rrna =

;

new_rrna->

(*(rna_it->GetSeq_feat()));

change_this_rrna =

;

change_this_rrna =

;

change_this_rrna =

;

change_this_rrna =

;

(change_this_rrna) {

any_changes =

;

change_this_gene =

;

new_gene->

(*(gene_it->GetSeq_feat()));

(change_this_gene) {

any_changes =

;

(run_extended_cleanup) {

(pChanged->ChangeCount()>0) {

(li && li.

()) {

(li && li.

()) {

(this_strand == prev_strand) {

(

((

)this_start - (

)prev_end) < min_len) {

any_change =

;

any_changes =

;

(

cds_it(entry, sel); cds_it; ++cds_it) {

change_this_cds =

;

new_cds->

(*(cds_it->GetSeq_feat()));

(change_this_cds) {

any_changes =

;

unknown_seqdesc =

(1 + sc_SeqdescOrderMap.size());

(find_iter == sc_SeqdescOrderMap.end()) {

unknown_seqdesc;

find_iter->second;

chs1 = desc1->

();

chs2 = desc2->

();

(

.IsSetDescr()) {

removed =

;

((*d)->IsTitle()) {

last_title.

(d->GetPointer());

removed =

;

(

.IsSetDescr()) {

((*d)->IsTitle()) {

.RemoveSeqdesc(*last_title);

last_title.

(d->GetPointer());

& auth_str = *out_authors;

vector<string> name_list;

((*auth_it)->IsSetName()) {

(*auth_it)->GetName().GetLabel(&

);

name_list.push_back(

);

back_inserter(name_list));

back_inserter(name_list));

(name_list.size() == 0) {

}

(name_list.size() == 1) {

auth_str = name_list.back();

last_author.swap(name_list.back());

name_list.pop_back();

(name_list,

).swap(auth_str);

auth_str +=

;

auth_str += last_author;

*out_authors_string,

& pd)

& authors_string = *out_authors_string;

authors_string.clear();

((*pub)->IsSetAuthors()) {

vector<TEntrezId>& pmids, vector<TEntrezId>& muids, vector<int>& serials,

vector<string>& published_labels,

vector<string>& unpublished_labels)

is_published =

;

need_label =

;

((*it)->IsPmid()) {

pmids.push_back((*it)->GetPmid());

is_published =

;

}

((*it)->IsMuid()) {

muids.push_back((*it)->GetMuid());

is_published =

;

}

((*it)->IsGen()) {

((*it)->GetGen().IsSetCit()

((*it)->GetGen().IsSetSerial_number()) {

serials.push_back((*it)->GetGen().GetSerial_number());

((*it)->GetGen().IsSetCit()

|| (*it)->GetGen().IsSetJournal()

|| (*it)->GetGen().IsSetDate()) {

}

((*it)->IsArticle() && (*it)->GetArticle().IsSetIds()) {

is_published =

;

((*id)->IsPubmed()) {

pmids.push_back((*id)->GetPubmed());

is_published =

;

}

((*id)->IsMedline()) {

muids.push_back((*id)->GetMedline());

published_labels.push_back(

);

unpublished_labels.push_back(

);

vector<CConstRef<CPub> > pub_list;

vector<TEntrezId> pmids;

vector<TEntrezId> muids;

vector<int> serials;

vector<string> published_labels;

vector<string> unpublished_labels;

(pmids.size() > 0) {

pub_list.push_back(pub);

}

(muids.size() > 0) {

pub_list.push_back(pub);

}

(serials.size() > 0) {

pub_list.push_back(pub);

}

(published_labels.size() > 0) {

pub_list.push_back(pub);

}

(unpublished_labels.size() > 0) {

pub_list.push_back(pub);

vector<TEntrezId> pmids;

vector<TEntrezId> muids;

vector<int> serials;

vector<string> published_labels;

vector<string> unpublished_labels;

(pmids.size() > 0) {

pub_list.push_back(pub);

}

(muids.size() > 0) {

pub_list.push_back(pub);

}

(serials.size() > 0) {

pub_list.push_back(pub);

}

(published_labels.size() > 0) {

pub_list.push_back(pub);

}

(unpublished_labels.size() > 0) {

pub_list.push_back(pub);

any_change =

;

CSeq_descr::Tdata::iterator it1 = descr.

().begin();

(it1 != descr.

().end()) {

((*it1)->IsPub()) {

CSeq_descr::Tdata::iterator it2 = it1;

(it2 != descr.

().end()) {

((*it2)->IsPub() && (*it1)->GetPub().Equals((*it2)->GetPub())) {

it2 = descr.

().erase(it2);

(pd1.

().

().front()->Equals(**it)) {

is_embl_or_ddbj =

;

((*id)->IsEmbl() || (*id)->IsDdbj()) {

is_embl_or_ddbj =

;

!is_embl_or_ddbj;

}

(parent && parent.

() &&

any_change =

;

(p->GetLocation().IsInt() &&

(p->IsSetComment()) {

found_non_minimal =

;

((*it)->IsMuid() || (*it)->IsPmid()) {

(is_refseq_prot) {

found_non_minimal =

;

}

((*it)->IsGen()) {

(

.IsSetCit() && !

.IsSetJournal() &&

!

.IsSetAuthors() && !

.IsSetVolume() &&

!

.IsSetPages()) {

found_non_minimal =

;

found_non_minimal =

;

!found_non_minimal;

found_site_ref =

;

(

&& !found_site_ref) {

found_site_ref =

;

(!found_site_ref) {

any_change =

;

is_refseq_prot =

;

((*id_it)->IsOther()) {

is_refseq_prot =

;

is_site_ref =

(*(p->GetSeq_feat()));

((*c)->IsEquiv()) {

(chs1 < chs2)

;

(chs1 > chs2)

;

& n1 = s1.

();

& n2 = s2.

();

CBioSource::TSubtype::iterator s = biosrc.

().begin();

CBioSource::TSubtype::iterator s_next = s;

(s_next != biosrc.

().end()) {

any_change =

;

any_change =

;

on1.

().push_back(

);

any_change =

;

(!

(org1, *it)) {

org1.

().push_back(*it);

org1.

().push_back(

);

org1.

().push_back(*it);

any_change =

;

CSeq_descr::Tdata::iterator src1 = seq_descr.

().begin();

(src1 != seq_descr.

().end()) {

((*src1)->IsSource() && (*src1)->GetSource().IsSetOrg() && (*src1)->GetSource().GetOrg().IsSetTaxname()) {

CSeq_descr::Tdata::iterator src2 = src1;

(src2 != seq_descr.

().end()) {

((*src2)->IsSource() &&

src2 = seq_descr.

().erase(src2);

any_change =

;

vector<CConstRef<CBioSource> > src_list;

CSeq_descr::Tdata::iterator d = descr.

().begin();

(d != descr.

().end()) {

((*d)->IsSource()) {

found =

;

((*d)->GetSource().Equals(**s)) {

d = descr.

().erase(d);

src_list.push_back(src);

(!

.IsSetData() || !

.GetData().IsBiosrc()) {

src->

(

.GetData().GetBiosrc());

(

.IsSetComment()) {

(

.IsSetDbxref()) {

src->

().SetDb().push_back(

);

any_change =

;

transgenic_or_focus =

;

(existing_src && !transgenic_or_focus) {

transgenic_or_focus =

;

(transgenic_or_focus) {

(p->GetLocation().IsInt() &&

num_gene_locus = 0;

num_gene_locus_tag = 0;

num_gene_xref_locus = 0;

num_gene_xref_locus_tag = 0;

num_gene_locus_tag++;

(

->IsSetLocus()) {

num_gene_xref_locus++;

(

->IsSetLocus_tag()) {

num_gene_xref_locus_tag++;

(num_gene_locus > 0) {

(num_gene_locus_tag > 0) {

(num_gene_xref_locus > 0) {

(num_gene_locus_tag > 0) {

(num_gene_locus > 0) {

(num_gene_xref_locus_tag > 0) {

any_change =

;

(num_gene_locus == 0 && num_gene_locus_tag > 0) {

(num_gene_xref_locus > 0 && num_gene_xref_locus_tag == 0) {

this_change =

;

((*it)->IsSetData() && (*it)->GetData().IsGene()

&& (*it)->GetData().GetGene().IsSetLocus()) {

(*it)->SetData().SetGene().SetLocus_tag((*it)->GetData().GetGene().GetLocus());

(*it)->SetData().SetGene().ResetLocus();

this_change =

;

}

(num_gene_locus > 0 && num_gene_locus_tag == 0) {

(num_gene_xref_locus == 0 && num_gene_xref_locus_tag > 0) {

this_change =

;

((*it)->IsSetData() && (*it)->GetData().IsGene()

&& (*it)->GetData().GetGene().IsSetLocus_tag()) {

(*it)->SetData().SetGene().SetLocus((*it)->GetData().GetGene().GetLocus_tag());

(*it)->SetData().SetGene().ResetLocus_tag();

this_change =

;

strip_serial =

;

(sid.

()) {

& acc =

(tsid, Accession);

(acc.length() == 6) {

strip_serial =

;

strip_serial =

;

strip_serial =

;

strip_serial;

change_made =

;

change_made =

;

change_made =

;

(

== amp ) {

{

} transformations[] = {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

(

idx = 0; idx <

(transformations); ++idx) {

searcher.

(transformations[idx].src_word, idx);

.reserve( str_len );

back_inserter(

) );

( amp !=

&& amp < str_len ) {

(

[search_pos] ==

) {

( ; search_pos < str_len ; ++search_pos ) {

ch =

[search_pos];

( ch ==

&&

== 0 ) {

& result_word = transformations[match_idx].result_word;

( result_word.begin(), result_word.end(),

back_inserter(

) );

change_made =

;

( search_pos >= str_len ) {

back_inserter(

) );

& result_word = transformations[match_idx].result_word;

( result_word.begin(), result_word.end(),

back_inserter(

) );

change_made =

;

(

.begin() + amp,

.begin() + search_pos + 1,

back_inserter(

) );

(

[search_pos] ==

) {

(

== next_amp ) {

(

.begin() + search_pos + 1,

.end(),

back_inserter(

) );

( (search_pos + 1) < next_amp ) {

(

.begin() + search_pos + 1,

.begin() + next_amp,

back_inserter(

) );

(require_inframe) {

is_ok =

;

(is_in_frame) {

new_loc = nuc2prot_mapper->

(nuc_loc);

(!sid || (orig_id && sid->

(*orig_id))) {

(!new_loc->

() && !new_loc->

()) {

changed =

;

((*annot_it)->IsSetData() && (*annot_it)->IsFtable()) {

((*feat_it)->IsSetData() && (*feat_it)->GetData().IsCdregion()) {

any_change =

;

(

bi(seh, filter); bi; ++bi) {

(!feat_loc_seq_id) {

string::size_type

= 0;

string::size_type loc_pos, end_pos;

protein_letter =

;

(aa_pos == string::npos) {

(aa_pos != string::npos) {

(aa_pos != string::npos) {

(aa_pos != string::npos) {

[pMessageListener](

, TSubcode subcode) {

(loc_pos == string::npos) {

(pMessageListener) {

=

+

+

;

postMessage(

, TSubcode::eParseError);

(loc_pos <

.length() &&

(

[loc_pos])) {

(end_pos ==

) {

(end_pos ==

) {

end_pos =

.length();

(pos.find_first_of(

) != string::npos) {

pos =

+ pos +

;

(pMessageListener) {

=

+

+

;

postMessage(

, TSubcode::eParseError);

(pMessageListener) {

=

;

postMessage(

, TSubcode::eBadLocation);

((break_loc->

() || break_loc->

()) &&

(pMessageListener) {

=

;

postMessage(

, TSubcode::eBadLocation);

newCodeBreak->

(*break_loc);

orig_list.push_back(newCodeBreak);

any_removed =

;

CSeq_feat::TQual::iterator it = feat.

().begin();

(it != feat.

().end()) {

((*it)->IsSetQual() &&

(*it)->IsSetVal() &&

it = feat.

().erase(it);

any_removed =

;

(feat.

().size() == 0) {

it = flu_map.

(

);

(it == flu_map.

()) {

new_set->AddBioseq(*bi);

flu_map[

] = new_set;

it->second->AddBioseq(*bi);

(

& entry : flu_map) {

(entry.second->OkToMakeSet()) {

entry.second->MakeSet();

(; annot_ci; ++annot_ci) {

((*annot_ci).IsFtable()) {

->SetData().SetImp().SetKey(

);

->SetLocation().SetInt().SetFrom(0);

->SetLocation().SetInt().SetId().Assign(*(bh.

()));

->SetDbxref().push_back(xref);

suppress->SetData().SetGene();

->SetXref().push_back(suppress);

COrg_ref::TDb::iterator db = org->

().begin();

(db != org->

().end()) {

((*db)->IsSetDb() &&

((*db)->GetDb(),

)) {

db = org->

().erase(db);

(org->

().size() == 0) {

default : frame = 0;

;

(cb->IsSetLoc()) {

((

- frame) / 3 ) + 1 == pos) {

start =

((pos-1)*3);

default : frame = 0;

;

frame_shift = (start - frame) % 3;

(frame_shift < 0) {

(frame_shift == 1)

(frame_shift == 2)

= loc_iter.GetRange().GetLength();

(offset <= start && offset + len > start) {

->SetId().Assign(loc_iter.GetSeq_id());

->SetTo(loc_iter.GetRange().GetTo() - (start -

) );

->SetFrom(loc_iter.GetRange().GetFrom() + start -

);

(offset <= start + 2 && offset + len > start + 2) {

->SetFrom(loc_iter.GetRange().GetTo() - (start -

+ 2) );

->SetTo(loc_iter.GetRange().GetFrom() + start -

+ 2);

->SetFrom(loc_iter.GetRange().GetFrom());

->SetTo(loc_iter.GetRange().GetTo());

->SetId().Assign(loc_iter.GetSeq_id());

->SetTo(loc_iter.GetRange().GetTo());

->SetFrom(loc_iter.GetRange().GetTo() - (start -

+ 2) );

->SetFrom(loc_iter.GetRange().GetFrom());

->SetFrom(loc_iter.GetRange().GetFrom());

->SetTo(loc_iter.GetRange().GetFrom() + start -

+ 2);

->SetTo(loc_iter.GetRange().GetTo());

any_change =

;

any_changes =

;

vector<CRef<COrg_ref> > rq_list;

vector<const CSeqdesc* > src_descs;

vector<CConstRef<CSeq_feat> > src_feats;

vector<const CSeqdesc* >::iterator desc_it = src_descs.begin();

(desc_it != src_descs.end()) {

((*desc_it)->GetSource().IsSetSubtype()) {

&& s->IsSetName()) {

month_ambiguous =

;

s->SetName(new_date);

any_changes =

;

local_change =

;

(

s : new_feat->

().SetBiosrc().SetSubtype()) {

&& s->IsSetName()) {

month_ambiguous =

;

s->SetName(new_date);

local_change =

;

any_changes =

;

removed =

;

(

->GetUser().IsAutodefOptions()) {

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

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

CSeqdesc & Set(bool skip_lookup=false)

static CRef< CUser_object > CreateIDOptions(CSeq_entry_Handle seh)

static bool RegenerateSequenceDefLines(CSeq_entry_Handle se)

static string GetOrganelleByGenome(unsigned int genome)

int GetGenCode(int def=1) const

bool HasSubtype(CSubSource::TSubtype subtype) const

CBioseq_set_EditHandle –.

vector< EChanges > GetAllChanges() const

vector< string_view > GetDescriptions() const

static string_view GetDescription(EChanges e)

static bool RescueSiteRefPubs(CSeq_entry_Handle seh)

Rescue pubs from Site-ref features.

static bool ConvertDeltaSeqToRaw(CSeq_entry_Handle seh, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set)

static bool RenormalizeNucProtSets(CSeq_entry_Handle seh)

Convert nuc-prot sets with just one sequence to just the sequence can't be done during the explore ph...

static bool ShouldStripPubSerial(const CBioseq &bs)

static char ValidAminoAcid(string_view abbrev)

static bool RemoveOrphanLocus_tagGeneXrefs(CSeq_feat &f, CBioseq_Handle bsh)

Removes orphaned locus_tag Gene-xrefs.

static bool FixGeneXrefSkew(CSeq_entry_Handle seh)

Examine all genes and gene xrefs in the Seq-entry.

static void MoveOneFeatToPubdesc(CSeq_feat_Handle feat, CRef< CSeqdesc > d, CBioseq_Handle b, bool remove_feat=true)

static bool AddGenBankWrapper(CSeq_entry_Handle seh)

Add GenBank Wrapper Set.

static bool ConvertPubFeatsToPubDescs(CSeq_entry_Handle seh)

Convert full-length publication features to publication descriptors.

static void SetProteinName(CProt_ref &prot, const string &protein_name, bool append)

static void s_SetProductOnFeat(CSeq_feat &feat, const string &protein_name, bool append)

static bool RemovePseudoProduct(CSeq_feat &cds, CScope &scope)

Removes protein product from pseudo coding region.

static bool FixECNumbers(CSeq_entry_Handle entry)

Fix EC numbers.

static bool AddMissingMolInfo(CBioseq &seq, bool is_product)

Adds missing MolInfo descriptor to sequence.

static void SetMrnaName(CSeq_feat &mrna, const string &protein_name)

static CRef< CSeq_entry > AddProtein(const CSeq_feat &cds, CScope &scope)

static bool OkToPromoteNpPub(const CPubdesc &pd)

Some pubs should not be promoted to nuc-prot set from sequence.

static void GetPubdescLabels(const CPubdesc &pd, vector< TEntrezId > &pmids, vector< TEntrezId > &muids, vector< int > &serials, vector< string > &published_labels, vector< string > &unpublished_labels)

For Publication Citations Get labels for a pubdesc.

static bool DecodeXMLMarkChanged(std::string &str)

decodes various tags, including carriage-return-line-feed constructs

static bool SetFeaturePartial(CSeq_feat &f)

Set feature partial based on feature location.

static bool AddProteinTitle(CBioseq_Handle bsh)

Creates missing protein title descriptor.

static size_t MakeSmallGenomeSet(CSeq_entry_Handle entry)

static bool ExtendToStopIfShortAndNotPartial(CSeq_feat &f, CBioseq_Handle bsh, bool check_for_stop=true)

Extends a coding region up to 50 nt.

static bool IsGeneXrefUnnecessary(const CSeq_feat &sf, CScope &scope, const CGene_ref &gene_xref)

Calculates whether a Gene-xref is unnecessary (because it refers to the same gene as would be calcula...

static bool ClearInternalPartials(CSeq_loc &loc, bool is_first=true, bool is_last=true)

Clear internal partials.

static bool RepackageProteins(CSeq_entry_Handle seh)

Find proteins that are not packaged in the same nuc-prot set as the coding region for which they are ...

CCleanup(CScope *scope=nullptr, EScopeOptions scope_handling=eScope_Copy)

static bool WGSCleanup(CSeq_entry_Handle entry, bool instantiate_missing_proteins=true, Uint4 options=0, bool run_extended_cleanup=true, bool also_fix_location=true)

Performs WGS specific cleanup.

static bool ParseCodeBreaks(CSeq_feat &feat, CScope &scope)

Parses all valid transl_except Gb-quals into code-breaks for cdregion, then removes the transl_except...

static bool SetMolinfoTech(CBioseq_Handle seq, CMolInfo::ETech tech)

Sets MolInfo::tech for a sequence.

static bool AddLowQualityException(CSeq_entry_Handle entry)

For table2asn -c s Adds an exception of "low-quality sequence region" to coding regions and mRNAs tha...

static bool RemoveUnseenTitles(CSeq_entry_EditHandle::TSeq seq)

Remove all titles in Seqdescr except the last, because it is the only one that would be displayed in ...

static bool RemoveDupBioSource(CSeq_descr &descr)

Remove duplicate biosource descriptors.

static bool ExtendStopPosition(CSeq_feat &f, const CSeq_feat *cdregion, size_t extension=0)

TChanges ExtendedCleanup(CSeq_entry &se, Uint4 options=0)

Cleanup a Seq-entry.

static bool s_IsProductOnFeat(const CSeq_feat &cds)

static bool SetGenePartialByLongestContainedFeature(CSeq_feat &gene, CScope &scope)

Set partialness of gene to match longest feature contained in gene.

static CConstRef< CCode_break > GetCodeBreakForLocation(size_t pos, const CSeq_feat &cds)

utility function for finding the code break for a given amino acid position pos is the position of th...

TChanges BasicCleanup(CSeq_entry &se, Uint4 options=0)

static bool SetCDSPartialsByFrameAndTranslation(CSeq_feat &cds, CScope &scope)

1.

static bool RemoveBadECNumbers(CProt_ref::TEc &ec_num_list)

Delete EC numbers.

static bool AddPartialToProteinTitle(CBioseq_Handle bsh)

Adjusts protein title to reflect partialness.

void SetScope(CScope *scope)

static bool RepairXrefs(const CSeq_feat &f, const CTSE_Handle &tse)

Repairs non-reciprocal xref pairs for specified feature if xrefs between subtypes are permitted and f...

static bool ExtendToStopCodon(CSeq_feat &f, CBioseq_Handle bsh, size_t limit)

Extends a feature up to limit nt to a stop codon, or to the end of the sequence if limit == 0 (partia...

static CRef< CSeq_loc > GetProteinLocationFromNucleotideLocation(const CSeq_loc &nuc_loc, CScope &scope)

static bool ParseCodeBreak(const CSeq_feat &feat, CCdregion &cds, const CTempString &str, CScope &scope, IObjtoolsListener *pMessageListener=nullptr)

Parse string into code break and add to coding region.

static void SetCodeBreakLocation(CCode_break &cb, size_t pos, const CSeq_feat &cds)

utility function for setting code break location given offset pos is the position of the amino acid w...

static bool x_AddLowQualityException(CSeq_feat &feat)

static const string & GetProteinName(const CProt_ref &prot)

static CRef< CBioSource > BioSrcFromFeat(const CSeq_feat &f)

Get BioSource from feature to use for source descriptor.

static bool MergeDupBioSources(CSeq_descr &descr)

static bool SetFrameFromLoc(CCdregion &cdregion, const CSeq_loc &loc, CScope &scope)

Chooses best frame based on location 1.

static bool SetMolinfoBiomol(CBioseq_Handle seq, CMolInfo::EBiomol biomol)

Sets MolInfo::biomol for a sequence.

static bool MoveProteinSpecificFeats(CSeq_entry_Handle seh)

Moves protein-specific features from nucleotide sequences in the Seq-entry to the appropriate protein...

static bool TaxonomyLookup(CSeq_entry_Handle seh)

Looks up Org-refs in the Seq-entry.

static bool PubAlreadyInSet(const CPubdesc &pd, const CSeq_descr &descr)

static bool NormalizeDescriptorOrder(CSeq_descr &descr)

Normalize Descriptor Order on a specific Seq-entry.

static bool ConvertSrcFeatsToSrcDescs(CSeq_entry_Handle seh)

Convert full-length source features to source descriptors.

static bool SetBestFrame(CSeq_feat &cds, CScope &scope)

Translates coding region and selects best frame (without stops, or longest)

static bool x_MergeDupOrgNames(COrgName &on1, const COrgName &add)

static bool FindMatchingLocusGene(CSeq_feat &f, const CGene_ref &gene_xref, CBioseq_Handle bsh)

Detects gene features with matching locus.

static bool MoveFeatToProtein(CSeq_feat_Handle fh)

Moves one feature from nucleotide bioseq to the appropriate protein sequence.

static bool RemoveOrphanLocusGeneXrefs(CSeq_feat &f, CBioseq_Handle bsh)

Removes orphaned locus Gene-xrefs.

static void AddNcbiCleanupObject(int ncbi_cleanup_version, CSeq_descr &descr)

Adds NcbiCleanup User Object to Seq-descr.

static bool AreBioSourcesMergeable(const CBioSource &src1, const CBioSource &src2)

static bool ExpandGeneToIncludeChildren(CSeq_feat &gene, CTSE_Handle &tse)

Expands gene to include features it cross-references.

static vector< CConstRef< CPub > > GetCitationList(CBioseq_Handle bsh)

Get list of pubs that can be used for citations for Seq-feat on a Bioseq-handle.

static bool LocationMayBeExtendedToMatch(const CSeq_loc &orig, const CSeq_loc &improved)

Checks whether it is possible to extend the original location up to improved one.

static bool UpdateECNumbers(CProt_ref::TEc &ec_num_list)

Update EC numbers.

static bool FixRNAEditingCodingRegion(CSeq_feat &cds)

From GB-7563 An action has been requested that will do the following: 1.

static bool x_HasShortIntron(const CSeq_loc &loc, size_t min_len=11)

static bool RemoveNcbiCleanupObject(CSeq_descr &descr)

Removes NcbiCleanup User Objects in the Seq-descr.

static bool SetGeneticCodes(CBioseq_Handle bsh)

Sets genetic codes for coding regions on Bioseq-Handle.

static bool RemoveUnnecessaryGeneXrefs(CSeq_feat &f, CScope &scope)

Removes unnecessary Gene-xrefs.

static bool CleanupCollectionDates(CSeq_entry_Handle seh, bool month_first)

static bool MakeIRDFeatsFromSourceXrefs(CSeq_entry_Handle entry)

From SQD-4329 For each sequence with a source that has an IRD db_xref, create a misc_feature across t...

static bool IsMinPub(const CPubdesc &pd, bool is_refseq_prot)

Is this a "minimal" pub? (If yes, do not rescue from a Seq-feat.cit)

static bool FindMatchingLocus_tagGene(CSeq_feat &f, const CGene_ref &gene_xref, CBioseq_Handle bsh)

Detects gene features with matching locus_tag.

static bool x_MergeDupOrgRefs(COrg_ref &org1, const COrg_ref &add)

static void AutodefId(CSeq_entry_Handle seh)

static bool RemoveNonsuppressingGeneXrefs(CSeq_feat &f)

Removes non-suppressing Gene-xrefs.

static bool RemoveDuplicatePubs(CSeq_descr &descr)

Remove duplicate publications.

static bool IsMethionine(const CCode_break &cb)

static bool SeqLocExtend(CSeq_loc &loc, size_t pos, CScope &scope)

Extends a location to the specificed position.

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

static const CTrans_table & GetTransTable(int id)

bool RefersToSameGene(const CGene_ref &xref) const

bool IsSuppressed(void) const

static string GetKey(const COrg_ref &org)

void BasicCleanupBioseqHandle(const CBioseq_Handle &bsh)

void BasicCleanupSeqFeat(CSeq_feat &sf)

void ExtendedCleanup(CSeq_entry_Handle &seh)

void BasicCleanupBioseqSetHandle(CBioseq_set_Handle &bssh)

void SetScope(CScope &scope)

Main methods.

void ExtendedCleanupSeqEntryHandle(CSeq_entry_Handle &seh)

void BasicCleanupSeqEntryHandle(CSeq_entry_Handle &seh)

static bool ShouldRemoveAnnot(const CSeq_annot &annot)

void BasicCleanup(CPubdesc &pd, bool strip_serial)

void BasicCleanupSeqAnnotHandle(CSeq_annot_Handle &sah)

void BasicCleanupSeqFeatHandle(CSeq_feat_Handle &sfh)

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

bool IsSetOrgMod(void) const

static bool IsECNumberSplit(const string &old_ecno)

static const string & GetECNumberReplacement(const string &old_ecno)

Return a replaced EC number's replacement.

EECNumberStatus

Enzyme Commission number status.

@ eEC_replaced

Obsolete synonym for some other EC number.

@ eEC_unknown

Unrecognized; possibly malformed.

@ eEC_deleted

Withdrawn, with no (single?) replacement.

static EECNumberStatus GetECNumberStatus(const string &ecno)

Determine an EC number's validity and specificity.

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

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

string GetRnaProductName(void) const

ESubtype GetSubtype(void) const

static bool AllowXref(CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)

SeqMap related exceptions.

SeqVector related exceptions.

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

const CSeq_descr & GetDescr(void) const

void SetDescr(CSeq_descr &value)

bool IsSetDescr(void) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

bool HasExceptionText(const string &exception_text) const

Returns whether or not the given exception_text is set for this feature.

bool AddSeqFeatXref(const CSeqFeatXref::TId &id)

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

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

static string FixDateFormat(const string &orig_date)

Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from this TSE.

TSeq_feat_Handles GetFeaturesWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

vector< CSeq_feat_Handle > TSeq_feat_Handles

virtual CRef< CTaxon3_reply > SendOrgRefList(const vector< CRef< COrg_ref > > &list, COrg_ref::fOrgref_parts result_parts=COrg_ref::eOrgref_default, fT3reply_parts t3result_parts=eT3reply_default)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

char GetCodonResidue(int state) const

static int NextCodonState(int state, unsigned char ch)

EObjectType GetObjectType() const

@ fLabel_Unique

Append a unique tag [V1].

constexpr size_t size() const

const_iterator end() const

const_iterator find(const key_type &key) const

const unsigned int methionine_encoded

void s_GetAuthorsString(string *out_authors, const CAuth_list &auth_list)

SStaticPair< CSeqdesc::E_Choice, int > TSeqdescOrderElem

static CConstRef< CSeq_feat > s_GetCdsByLocation(CScope &scope, const CSeq_loc &feat_loc)

static bool s_NameCloseEnoughC(const CSubSource &s1, const CSubSource &s2)

void RescueProtProductQual(CSeq_feat &feat)

void GetSourceDescriptors(const CSeq_entry &se, vector< const CSeqdesc * > &src_descs)

bool s_IsLocationEndAtOtherLocationInternalEndpoint(const CSeq_loc &loc, const CSeq_loc &other_loc)

DEFINE_STATIC_ARRAY_MAP(TSeqdescOrderMap, sc_SeqdescOrderMap, sc_seqdesc_order_map)

static bool s_SameSubtypeC(const CSubSource &s1, const CSubSource &s2)

static const TRNALengthMap kTrnaLengthMap

static bool s_RemoveTaxnameFromProtRef(const string &taxname, CBioseq_Handle bsh)

string s_KeyFromProcessed(CProt_ref::EProcessed processed)

bool s_SubSourceListUniqued(CBioSource &biosrc)

static CConstRef< CSeqdesc > s_GetTitleDesc(const CSeq_descr &descr)

static int s_SeqDescToOrdering(CSeqdesc::E_Choice chs)

static const string & s_GetProteinNameFromXrefOrQual(const CSeq_feat &cds)

static SIZE_TYPE s_TitleEndsInOrganism(const string &sTitle, const string &sOrganism, SIZE_TYPE &OrganellePos)

bool HasMod(const COrg_ref &org, const string &mod)

static bool s_SubsourceCompareC(const CRef< CSubSource > &st1, const CRef< CSubSource > &st2)

static const TSeqdescOrderElem sc_seqdesc_order_map[]

bool IsSiteRef(const CSeq_feat &sf)

CProt_ref::EProcessed s_ProcessedFromKey(const string &key)

void AddIRDMiscFeature(CBioseq_Handle bh, const CDbtag &tag)

static void s_UpdateTitleString(const CBioSource &src, bool bPartial, string &sTitle)

map< string, TRNALength > TRNALengthMap

static constexpr std::array< string_view, CCleanupChangeCore::eNumberofChangeTypes > sm_ChangeDesc

pair< size_t, bool > TRNALength

CStaticPairArrayMap< CSeqdesc::E_Choice, int > TSeqdescOrderMap

static bool s_IsSwissProt(const CBioseq_Handle &bsh)

static CConstRef< CSeq_feat > s_GetCdsByProduct(CScope &scope, const CSeq_loc &product)

static bool s_RemoveSuffixFromNames(const string &suffix, list< string > &names)

static CRef< CCleanupChange > makeCleanupChange(Uint4 options)

bool s_FirstPubMatchesSecond(const CPubdesc &pd1, const CPubdesc &pd2)

static void s_GetMolInfoAndSrcDescriptors(const CSeq_descr &seq_descr, CConstRef< CSeqdesc > &pMolinfoDesc, CConstRef< CSeqdesc > &pSrcDesc)

const string kLowQualitySequence

bool s_IsPreprotein(CSeq_feat_Handle fh)

static bool s_IsPartial(const CMolInfo &molInfo)

static bool s_SeqDescLessThan(const CRef< CSeqdesc > &desc1, const CRef< CSeqdesc > &desc2)

bool ConvertProteinToImp(CSeq_feat_Handle fh)

bool IsCrossKingdom(const COrg_ref &org, string &first_kingdom, string &second_kingdom)

static bool s_CleanupIsShortrRNA(const CSeq_feat &f, CScope *scope)

static bool s_IsCleanupObject(const CSeqdesc &desc)

CRef< CSeq_loc > ReadLocFromText(const string &text, const CSeq_id *id, CScope *scope)

char x_ValidAminoAcid(string_view abbrev)

bool CleanVisStringJunk(string &str, bool allow_ellipses)

bool Asn2gnbkCompressSpaces(string &val)

weird space compression from C Toolkit

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char si[8][64]

static const struct name_t names[]

static void DLIST_NAME() append(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

constexpr size_t ArraySize(const Element(&)[Size])

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

@ eDiag_Error

Error message.

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

Set object to copy of another one.

const TPrim & Get(void) const

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

Check if both objects contain the same values.

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

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

void SetPacked_int(TPacked_int &v)

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

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.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsSetStrand(void) const

Get strand.

const CInt_fuzz * GetFuzzFrom(void) const

const CInt_fuzz * GetFuzzTo(void) const

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.

bool IsEmpty(void) const

True if the current location is empty.

const CSeq_id * GetId(void) const

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

TRange GetRange(void) const

Get the range.

void ResetStrand(void)

Reset the strand on this location.

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

ENa_strand GetStrand(void) const

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

bool RetranslateCDS(const CSeq_feat &cds, CScope &scope)

RetranslateCDS A function to replace the protein Bioseq pointed to by cds.product with the current tr...

bool CopyFeaturePartials(CSeq_feat &dst, const CSeq_feat &src)

CopyFeaturePartials A function to copy the start and end partialness from one feature to another.

void AddProteinFeature(const CBioseq &seq, const string &protein_name, const CSeq_feat &cds, CScope &scope)

AddProteinFeature A function to create a protein feature with the specified protein name.

ELocationInFrame IsLocationInFrame(const CSeq_feat_Handle &cds, const CSeq_loc &loc)

Determines whether location loc is in frame with coding region cds.

bool AdjustFeaturePartialFlagForLocation(CSeq_feat &new_feat)

AdjustFeaturePartialFlagForLocation A function to ensure that Seq-feat.partial is set if either end o...

bool AdjustForCDSPartials(const CSeq_feat &cds, CSeq_entry_Handle seh)

AdjustForCDSPartials A function to make all of the necessary related changes to a Seq-entry after the...

@ eLocationInFrame_InFrame

@ eLocationInFrame_BadStart

@ eLocationInFrame_BadStop

@ eLocationInFrame_BadStartAndStop

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

TSeqPos LocationOffset(const CSeq_loc &outer, const CSeq_loc &inner, EOffsetType how=eOffset_FromStart, CScope *scope=0)

returns (TSeqPos)-1 if the locations don't overlap

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

Returns the sequence::ECompare containment relationship between CSeq_locs.

CRef< CSeq_loc > Seq_loc_Subtract(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Subtract the second seq-loc from the first one.

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eOverlap_Contained

2nd contained within 1st extremes

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

CConstRef< CSeq_feat > GetOverlappingCDS(const CSeq_loc &loc, CScope &scope)

static CCdregion::EFrame FindBestFrame(const CSeq_feat &cds, CScope &scope)

Find "best" frame for a coding region.

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

vector< TFeatScore > TFeatScores

void GetOverlappingFeatures(const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, CSeqFeatData::ESubtype feat_subtype, EOverlapType overlap_type, TFeatScores &feats, CScope &scope, const TBestFeatOpts opts=0, CGetOverlappingFeaturesPlugin *plugin=NULL)

Find all features overlapping the location.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

CSeq_annot_Handle GetSeq_annotHandle(const CSeq_annot &annot, EMissing action=eMissing_Default)

void AddScope(CScope &scope, TPriority pri=kPriority_Default)

Add the scope's datasources as a single group with the given priority All data sources (data loaders ...

CSeq_entry_EditHandle GetSeq_entryEditHandle(const CSeq_entry &entry)

@ eLocationToProduct

Map from the feature's location to product.

vector< CSeq_id_Handle > TId

const CSeq_feat::TXref & GetXref(void) const

bool IsSetInst_Mol(void) const

TSeq ConvertSetToSeq(void) const

Do the same as CollapseSet() when sub-entry is of type bioseq.

const CTSE_Handle & GetTSE_Handle(void) const

void SetDescr(TDescr &v) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

bool IsFtable(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &v) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

void SetDescr(TDescr &v) const

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CBioseq_set_EditHandle GetParentBioseq_set(void) const

Get parent bioseq-set edit handle.

void Remove(void) const

Remove current annot.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

bool IsSetDescr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

bool AddSeqdesc(CSeqdesc &d) const

CSeq_entry_EditHandle TakeEntry(const CSeq_entry_EditHandle &entry, int index=-1) const

Remove seq-entry from its location and attach to current one.

bool IsSetXref(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

TSet ConvertSeqToSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the entry from Bioseq to Bioseq-set.

void Remove(void) const

Remove the feature from Seq-annot.

const CTSE_Handle & GetTSE_Handle(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

TInst_Mol GetInst_Mol(void) const

CSeq_feat_EditHandle AddFeat(const CSeq_feat &new_obj) const

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

virtual const CSeq_loc & GetProduct(void) const

bool IsSetProduct(void) const

bool HasAnnots(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

virtual const CSeq_loc & GetLocation(void) const

void SetInst(TInst &v) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

CRef< CSeqdesc > ReplaceSeqdesc(const CSeqdesc &old_desc, CSeqdesc &new_desc) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from the TSE of this Seq-entry.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const TDescr & GetDescr(void) const

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

TInst_Length GetInst_Length(void) const

bool IsSetInst(void) const

bool IsSetClass(void) const

bool AddSeqdesc(CSeqdesc &d) const

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

const TDescr & GetDescr(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_feat_EditHandle TakeFeat(const CSeq_feat_EditHandle &handle) const

CSeq_annot_EditHandle GetAnnot(void) const

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

CSeq_entry_EditHandle AttachEntry(CSeq_entry &entry, int index=-1) const

Attach an existing seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

bool IsSetDescr(void) const

const CGene_ref * GetGeneXref(void) const

get gene (if present) from Seq-feat.xref list

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

bool AddSeqdesc(CSeqdesc &v) const

const TId & GetId(void) const

bool IsSetData(void) const

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

@ fIncludeGivenEntry

Include the top (given) entry.

@ fRecursive

Iterate recursively.

const_iterator begin(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

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 Empty(void) const THROWS_NONE

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

void AddWord(const string &word, const MatchType &match)

int GetNextState(int state, char letter) const

const vector< MatchType > & GetMatches(int state) const

bool IsMatchFound(int state) const

bool IsPrimed(void) const

int GetInitialState(void) const

NCBI_NS_STD::string::size_type SIZE_TYPE

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

@ eReverseSearch

Search in a backward direction.

@ eNocase

Case insensitive compare.

static const char label[]

void SetSerial_number(TSerial_number value)

Assign a value to Serial_number data member.

list< CRef< CAuthor > > TStd

list< CRef< CArticleId > > Tdata

bool IsSetNames(void) const

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

void SetCit(const TCit &value)

Assign a value to Cit data member.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

const TNames & GetNames(void) const

Get the Names member data.

bool IsMl(void) const

Check if variant Ml is selected.

const TStd & GetStd(void) const

Get the variant data.

const TMl & GetMl(void) const

Get the variant data.

bool IsStd(void) const

Check if variant Std is selected.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

TGenome GetGenome(void) const

Get the Genome member data.

TOrigin GetOrigin(void) const

Get the Origin 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.

list< CRef< CSubSource > > TSubtype

bool IsSetSubtype(void) const

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

void SetIs_focus(void)

Set NULL data member (assign 'NULL' value to Is_focus data member).

void SetOrigin(TOrigin value)

Assign a value to Origin data member.

const TOrg & GetOrg(void) const

Get the Org member data.

bool IsSetOrigin(void) const

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

void SetGenome(TGenome value)

Assign a value to Genome data member.

TSubtype GetSubtype(void) const

Get the Subtype member data.

bool IsSetGenome(void) const

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

bool IsSetSubtype(void) const

Check if a value has been assigned to Subtype 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.

const TName & GetName(void) const

Get the Name member data.

bool IsSetIs_focus(void) const

to distinguish biological focus Check if a value has been assigned to Is_focus data member.

EGenome

biological context

bool IsSetName(void) const

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

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

@ eSubtype_collection_date

DD-MMM-YYYY format.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From 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.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

TId GetId(void) const

Get the variant data.

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

const TLineage & GetLineage(void) const

Get the Lineage member data.

const TDiv & GetDiv(void) const

Get the Div member data.

TFixed_level GetFixed_level(void) const

Get the Fixed_level member data.

TMgcode GetMgcode(void) const

Get the Mgcode member data.

TGcode GetGcode(void) const

Get the Gcode member data.

TDb & SetDb(void)

Assign a value to Db data member.

bool IsSetFixed_level(void) const

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

bool IsSetLineage(void) const

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

vector< CRef< CDbtag > > TDb

bool IsSetMod(void) const

unstructured modifiers Check if a value has been assigned to Mod data member.

bool IsPartial(void) const

Check if variant Partial is selected.

void SetDiv(const TDiv &value)

Assign a value to Div data member.

TSyn & SetSyn(void)

Assign a value to Syn data member.

const TName & GetName(void) const

Get the Name member data.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

bool IsSetMgcode(void) const

mitochondrial genetic code Check if a value has been assigned to Mgcode data member.

const TLevel & GetLevel(void) const

Get the Level member data.

bool IsSetName(void) const

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

const TBinomial & GetBinomial(void) const

Get the variant data.

const TDb & GetDb(void) const

Get the Db member data.

const TSyn & GetSyn(void) const

Get the Syn member data.

bool IsSetDiv(void) const

GenBank division code Check if a value has been assigned to Div data member.

bool IsSetMod(void) const

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

const Tdata & Get(void) const

Get the member data.

const TName & GetName(void) const

Get the Name member data.

list< CRef< COrgMod > > TMod

void SetGcode(TGcode value)

Assign a value to Gcode data member.

bool IsSetGenus(void) const

required Check if a value has been assigned to Genus data member.

void SetMgcode(TMgcode value)

Assign a value to Mgcode data member.

const TSpecies & GetSpecies(void) const

Get the Species member data.

list< CRef< CTaxElement > > Tdata

void ResetDb(void)

Reset Db data member.

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.

bool IsSetLevel(void) const

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

TMod & SetMod(void)

Assign a value to Mod data member.

bool IsSetGcode(void) const

genetic code (see CdRegion) Check if a value has been assigned to Gcode data member.

TMod & SetMod(void)

Assign a value to Mod data member.

void SetOrgname(TOrgname &value)

Assign a value to Orgname data member.

const TGenus & GetGenus(void) const

Get the Genus member data.

const TPartial & GetPartial(void) const

Get the variant data.

bool IsSet(void) const

Check if a value has been assigned to data member.

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetSyn(void) const

synonyms for taxname or common Check if a value has been assigned to Syn data member.

bool IsSetSpecies(void) const

species required if subspecies used Check if a value has been assigned to Species data member.

bool IsSetName(void) const

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

void SetLineage(const TLineage &value)

Assign a value to Lineage data member.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

bool IsBinomial(void) const

Check if variant Binomial is selected.

EProcessed

processing status

const TName & GetName(void) const

Get the Name member data.

TProcessed GetProcessed(void) const

Get the Processed member data.

bool IsSetProcessed(void) const

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

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

const TEc & GetEc(void) const

Get the Ec member data.

TName & SetName(void)

Assign a value to Name data member.

@ eProcessed_signal_peptide

@ eProcessed_transit_peptide

TPmid & SetPmid(void)

Select the variant.

list< CRef< CPub > > Tdata

TMuid & SetMuid(void)

Select the variant.

const Tdata & Get(void) const

Get the member data.

list< CRef< CPub > > TPub

TGen & SetGen(void)

Select the variant.

bool IsSetExt(void) const

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

void SetAa(TAa &value)

Assign a value to Aa data member.

const TVal & GetVal(void) const

Get the Val member data.

TXref & SetXref(void)

Assign a value to Xref data member.

void SetQual(const TQual &value)

Assign a value to Qual data member.

const TKey & GetKey(void) const

Get the Key member data.

bool IsSetComment(void) const

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

vector< CRef< CDbtag > > TDbxref

const TPub & GetPub(void) const

Get the variant data.

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.

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

bool IsProt(void) const

Check if variant Prot is selected.

TNcbi8aa GetNcbi8aa(void) const

Get the variant data.

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.

void ResetCode(void)

Reset Code data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetKey(void) const

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

const TId & GetId(void) const

Get the Id member data.

void SetCode(TCode &value)

Assign a value to Code data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

void SetExcept(TExcept value)

Assign a value to Except data member.

bool IsLocal(void) const

Check if variant Local is selected.

void ResetLoc(void)

Reset Loc data member.

bool IsGene(void) const

Check if variant Gene is selected.

list< CRef< CCode_break > > TCode_break

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TCode & GetCode(void) const

Get the Code member data.

void SetData(TData &value)

Assign a value to Data data member.

TCode_break & SetCode_break(void)

Assign a value to Code_break data member.

void ResetComment(void)

Reset Comment data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetAa(void) const

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

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool IsSetId(void) const

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

const TAa & GetAa(void) const

Get the Aa member data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetQual(void) const

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

TNcbieaa GetNcbieaa(void) const

Get the variant data.

const TComment & GetComment(void) const

Get the Comment member data.

void SetVal(const TVal &value)

Assign a value to Val data member.

const TGene & GetGene(void) const

Get the variant data.

void SetExcept_text(const TExcept_text &value)

Assign a value to Except_text data member.

const TProt & GetProt(void) const

Get the variant data.

void ResetLocation(void)

Reset Location data member.

TExcept GetExcept(void) const

Get the Except member data.

const TXref & GetXref(void) const

Get the Xref member data.

TNcbieaa & SetNcbieaa(void)

Select the variant.

vector< CRef< CSeqFeatXref > > TXref

void ResetProduct(void)

Reset Product data member.

const TQual & GetQual(void) const

Get the Qual member data.

const TRna & GetRna(void) const

Get the variant data.

TNcbistdaa GetNcbistdaa(void) const

Get the variant data.

TQual & SetQual(void)

Assign a value to Qual data member.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsRna(void) const

Check if variant Rna is selected.

void SetFrame(TFrame value)

Assign a value to Frame data member.

void ResetQual(void)

Reset Qual data member.

bool IsSetCode_break(void) const

individual exceptions Check if a value has been assigned to Code_break data member.

const TImp & GetImp(void) const

Get the variant data.

bool IsSetFrame(void) const

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

bool IsSetLocation(void) const

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

@ e_not_set

No variant selected.

@ e_Pub

publication applies to this seq

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

@ e_Ncbi8aa

NCBI8aa code.

@ e_Ncbieaa

ASCII value of NCBIeaa code.

bool IsMix(void) const

Check if variant Mix is selected.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

Tdata & Set(void)

Assign a value to data member.

const TWhole & GetWhole(void) const

Get the variant data.

list< CRef< CSeq_loc > > Tdata

E_Choice Which(void) const

Which variant is currently selected.

E_Choice Which(void) const

Which variant is currently selected.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

Tdata & Set(void)

Assign a value to data member.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TPacked_int & GetPacked_int(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 IsSetSeq_set(void) const

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

list< CRef< CSeq_annot > > TAnnot

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

void ResetDescr(void)

Reset Descr data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_wgs_set

whole genome shotgun project

@ eClass_mut_set

set of mutations

@ eClass_eco_set

ecological sample study

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_genbank

converted genbank

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

const TIupacaa & GetIupacaa(void) const

Get the variant data.

bool IsSetComment(void) const

any comment on this pub in context Check if a value has been assigned to Comment data member.

bool IsSetCompleteness(void) const

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

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

const TUser & GetUser(void) const

Get the variant data.

void ResetDescr(void)

Reset Descr data member.

bool IsSetSeq_data(void) const

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

void SetPub(TPub &value)

Assign a value to Pub data member.

const TInst & GetInst(void) const

Get the Inst member data.

TTitle & SetTitle(void)

Select the variant.

TPub & SetPub(void)

Select the variant.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

const TComment & GetComment(void) const

Get the Comment member data.

bool IsSetAnnot(void) const

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

bool IsSetMol(void) const

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

const TTitle & GetTitle(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSetFig(void) const

figure in paper Check if a value has been assigned to Fig data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

void SetReftype(TReftype value)

Assign a value to Reftype data member.

TTech GetTech(void) const

Get the Tech member data.

const Tdata & Get(void) const

Get the member data.

bool IsSetInst(void) const

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

bool IsSetName(void) const

name used in paper Check if a value has been assigned to Name data member.

list< CRef< CSeq_id > > TId

TMol GetMol(void) const

Get the Mol member data.

TSource & SetSource(void)

Select the variant.

bool IsSetDescr(void) const

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

E_Choice

Choice variants.

bool IsSet(void) const

Check if a value has been assigned to data member.

TBiomol GetBiomol(void) const

Get the Biomol member data.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

EMol

molecule class in living organism

void SetDescr(TDescr &value)

Assign a value to Descr data member.

bool IsSetTech(void) const

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

bool IsSetPub(void) const

the citation(s) Check if a value has been assigned to Pub data member.

TUser & SetUser(void)

Select the variant.

bool IsSetNum(void) const

numbering from paper Check if a value has been assigned to Num data member.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

list< CRef< CSeq_feat > > TFtable

E_Choice Which(void) const

Which variant is currently selected.

void SetComment(const TComment &value)

Assign a value to Comment data member.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_annot > > TAnnot

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TPub & GetPub(void) const

Get the Pub member data.

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 TMolinfo & GetMolinfo(void) const

Get the variant data.

TMolinfo & SetMolinfo(void)

Select the variant.

bool IsUser(void) const

Check if variant User is selected.

@ eReftype_sites

refers to unspecified features

@ eReftype_feats

refers to specified features

@ eTech_concept_trans

conceptual translation

@ eTech_standard

standard sequencing

@ e_Embl

EMBL specific information.

@ e_Het

cofactor, etc associated but not bound

@ e_Org

if all from one organism

@ e_Num

a numbering system

@ e_User

user defined object

@ e_Update_date

date of last update

@ e_Pub

a reference to the publication

@ e_Pir

PIR specific info.

@ e_Genbank

GenBank specific info.

@ e_Prf

PRF specific information.

@ e_Mol_type

type of molecule

@ e_Sp

SWISSPROT specific info.

@ e_Dbxref

xref to other databases

@ e_Comment

a more extensive comment

@ e_Method

sequencing method

@ e_Modelev

model evidence for XM records

@ e_Region

overall region (globin locus)

@ e_Molinfo

info on the molecule and techniques

@ e_Maploc

map location of this sequence

@ e_Create_date

date entry first created/released

@ e_Title

a title for this sequence

@ e_Pdb

PDB specific information.

@ e_Name

a name for this sequence

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

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

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

const CharType(& source)[N]

static unsigned int ud(time_t one, time_t two)

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

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

#define FOR_EACH_PUB_ON_PUBDESC(Itr, Var)

FOR_EACH_PUB_ON_PUBDESC EDIT_EACH_PUB_ON_PUBDESC.

CSubSource::TSubtype TSUBSOURCE_SUBTYPE

#define SUBSOURCE_ON_BIOSOURCE_IS_SORTED(Var, Func)

SUBSOURCE_ON_BIOSOURCE_IS_SORTED.

#define SORT_SUBSOURCE_ON_BIOSOURCE(Var, Func)

SORT_SUBSOURCE_ON_BIOSOURCE.

#define NCBI_SEQID(Type)

@NAME Convenience macros for NCBI objects

Utility macros and typedefs for exploring NCBI objects from seqset.asn.

#define RESET_FIELD(Var, Fld)

RESET_FIELD base macro.

#define FIELD_IS_SET(Var, Fld)

FIELD_IS_SET base macro.

#define GET_FIELD(Var, Fld)

GET_FIELD base macro.

bool seq_mac_is_sorted(Iter first, Iter last, Comp comp)

#define BEGIN_COMMA_END(container)

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

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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

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