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NCBI C++ ToolKit: src/misc/hgvs/variation_util2.cpp Source File

& message,

e->SetMessage(message);

<

T>

}

(

.IsGeneral() ||

.IsLocal()) {

found_in_starts = exon_biostarts.

(exon_anchor_pos)

!= exon_biostarts.

();

found_in_stops = exon_biostops.

(exon_anchor_pos)

!= exon_biostops.

();

(offset_pos < 0 && found_in_starts)

|| (offset_pos > 0 && found_in_stops)

|| (offset_pos == 0 && (found_in_starts || found_in_stops));

!fuzz.

() ? 0

start_offset_sign =

stop_offset_sign =

start_ok =

start_offset_sign * sign);

stop_offset_sign * sign);

start_ok && stop_ok;

(

ci(bsh, sel); ci; ++ci) {

& fuzz = (minus_strand == is_start) ? loc.

().SetFuzz_to()

: loc.

().SetFuzz_from();

(!fuzz.

()) {

fuzz.

(offset_fuzz);

& bio_start_ref = minus_strand ? loc->

().SetTo()

: loc->

().SetFrom();

: loc->

().SetTo();

p.

().Assign(*loc);

);

closest_start = ss.

().front()->GetGenomic_start();

closest_stop = ss.

().front()->GetGenomic_start();

closest_start = start;

(start != closest_start || stop != closest_stop) {

int_loc->

().SetFrom(closest_start);

int_loc->

().SetTo(closest_stop);

(start != closest_start) {

= (start - closest_start);

(stop != closest_stop) {

= (stop - closest_stop);

(

= 0;

< 2;

++) {

(target_row == -1) {

source_loc_is_projected =

,

= 5000;

far_start = start_offset +

< 0

far_stop = stop_offset >

(far_start || far_stop) {

,

(check_placements) {

se->SetGenomic_start(ci.GetRange().GetFrom());

se->SetGenomic_end(ci.GetRange().GetTo());

se->SetProduct_start().SetNucpos(product_pos);

se->SetProduct_end().SetNucpos(product_pos + ci.GetRange().GetLength() - 1);

product_pos += ci.GetRange().GetLength();

->SetLoc().SetNull();

(

->GetLoc().IsNull()) {

(

ci(bsh, sel); ci; ++ci) {

aln = SerialClone<CSeq_align>(current_aln);

(!

->GetLoc().IsNull()) {

(!

->GetLoc().IsNull()) {

->Assign(*mapped_placement);

->SetLoc().Assign(*loc);

<

T>

(c !=

&& c !=

&& c !=

&& c !=

) {

had_ambiguities =

;

had_ambiguities =

;

had_ambiguities;

invalid_location =

;

out_of_order =

;

invalid_location =

;

out_of_order =

;

out_of_order =

;

invalid_location =

;

(invalid_location) {

out_of_order ?

:

,

,

invalid_location;

);

,

equal_offsets = (

merge_single_range =

&& mapped_loc->

()

(mapped_loc->

()

mapped_loc->

().ResetFuzz_to();

loc1->

().SetTo() += 500;

(tmp_mapped_loc->

()) {

p2->

(*mapped_loc);

(mapped_len == 0) {

}

(mapped_len < orig_len) {

}

(!orig_is_compound && mapped_is_compound) {

exception->SetMessage(

);

,

p.

().SetLength(length);

,

}

(length > max_len) {

,

,

,

had_exceptions =

;

(!

.GetData().IsInstance() || (

.GetConsequenceParent() && &v != &

)) {

&& inst.

().front()->IsSetSeq()

&& inst.

().front()->GetSeq().IsLiteral()) {

(!asserted_literal

}

(!variant_literal

&& (!inst.

().front()->IsSetMultiplier() && !inst.

().front()->IsSetMultiplier_fuzz())

(variant_literal) {

(

);

(

);

,

had_exceptions =

;

&& variant_literal->Equals(p.

())) {

,

had_exceptions =

;

v.

().SetSet().SetVariations())

had_exceptions = had_exceptions ||

(

, max_len);

!had_exceptions;

&& ((

.GetTextseq_Id()->

() >=

&&

.GetTextseq_Id()->

() <=

)

|| (

.GetTextseq_Id()->

() >=

&&

.GetTextseq_Id()->

() <=

))) {

(!loc.

()) {

.SetInt().SetTo(start - 1);

(stop == max_pos) {

second.

().SetFrom(stop + 1);

(prot_str.size() != 1) {

* alphabet =

;

codon =

;

(

i0 = 0; i0 < 4; i0++) {

codon[0] = alphabet[i0];

(

i1 = 0; i1 < 4; i1++) {

codon[1] = alphabet[i1];

(

i2 = 0; i2 < 4; i2++) {

codon[2] = alphabet[i2];

(

== prot_str) {

.push_back(codon);

(

= 0;

<

(

.size(),

.size());

++) {

(

[

] ==

[

]) {

& codon_from,

& prot_to,

vector<string>& codons_to)

vector<string> candidates1;

max_matches(0);

have_silent =

;

(vector<string>, it1, candidates1)

have_silent =

;

(matches >= max_matches) {

(matches > max_matches) {

codons_to.push_back(*it1);

max_matches = matches;

(codons_to.empty() && have_silent) {

codons_to.push_back(codon_from);

collapsed_seq;

vector<string> TConstStrs;

(TConstStrs, it, seqs)

& seq = *it;

(seq.size() > bits.size()) {

bits.resize(seq.size());

(

= 0;

< seq.size();

++) {

m = (nt ==

? 1

: nt ==

? 8 : 0);

* iupac_nuc_ambiguity_codes =

;

collapsed_seq.resize(bits.size());

(

= 0;

< collapsed_seq.size();

++) {

collapsed_seq[

] = iupac_nuc_ambiguity_codes[bits[

]];

collapsed_seq;

v.

().SetSet().SetVariations().clear();

(

->GetData().IsInstance()

&&

->GetData().GetInstance().IsSetObservation()

v.

().SetSet().SetVariations().push_back(

);

(!placements || placements->size() == 0) {

(!prot2precursor_mapper) {

->SetPlacements().push_back(p);

(!nuc_loc->

()

|| !

->IsSetSeq()

|| !

->GetSeq().IsLiteral()

||

->GetSeq().GetLiteral().GetLength() != 1)

->SetData().SetUnknown();

->SetPlacements().push_back(p);

original_allele_codon;

variant_codon;

->GetSeq().GetLiteral().GetSeq_data(),

vector<string> variant_codons;

original_allele_codon,

&& variant_codon != original_allele_codon) {

(variant_codon.length() > 0

&& original_allele_codon.length() > 0

&& variant_codon.at(0) == original_allele_codon.at(0)) {

variant_codon = variant_codon.substr(1);

original_allele_codon = original_allele_codon.substr(1);

nuc_loc->

().SetTo()--;

nuc_loc->

().SetFrom()++;

(variant_codon.length() > 0

&& original_allele_codon.length() > 0

&& variant_codon.at(variant_codon.length() - 1)

== original_allele_codon.at(original_allele_codon.length() - 1)) {

variant_codon.resize(variant_codon.length() - 1);

original_allele_codon.resize(original_allele_codon.length() - 1);

nuc_loc->

().SetFrom()++;

nuc_loc->

().SetTo()--;

delta2->SetSeq().SetLiteral().SetLength(variant_codon.length());

delta2->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(variant_codon);

->SetPlacements().push_back(p2);

->SetData().SetUnknown();

inst2.

().push_back(delta2);

(cached_literal) {

->SetSeq_data().SetNcbieaa().Set().push_back(

->SetLength(seq.size());

->SetSeq_data().SetNcbieaa().Set(seq);

->SetSeq_data().SetIupacna().Set(seq);

(

.GetLength() == 0) {

}

(

.GetLength() == 0) {

(

.IsSetFuzz() ||

.IsSetFuzz()) {

(

.IsSetSeq_data() &&

.IsSetSeq_data()) {

.GetSeq_data(), 0,

.GetLength(),

.GetSeq_data(), 0,

.GetLength());

v.

().SetSet().SetVariations())

(!this_literal) {

);

di->SetSeq().SetLiteral().Assign(*this_literal);

(inst.

().size() == 0) {

di->SetSeq().SetLiteral().SetLength(0);

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

);

}

(inst.

().size() > 1) {

di.

().SetLiteral().SetLength(0);

di.

().SetLiteral().SetSeq_data().SetIupacna().Set(

);

(!this_literal) {

di.

().SetLiteral().Assign(*this_literal);

(!

.IsSetSeq_data() || !

.GetSeq_data().IsIupacna()) {

str_kernel =

.GetSeq_data().GetIupacna().Get();

.SetSeq_data().SetIupacna().Set(

);

.SetSeq_data().SetIupacna().Set() += str_kernel;

(!this_literal) {

}

(this_literal->GetLength() == 0) {

this_literal->GetLength() - 1);

ignore_genomic)

v.

().SetSet().SetVariations())

(!placements || placements->size() == 0) {

consequence->SetVariation(*prot_variation);

(

& nuc_str,

is_mito)

.SetId(is_mito ? 2 : 1);

(prot_str.size() * 3 < nuc_str.size()) {

prot_str.push_back(

);

stop_pos = prot_str.find(

);

(stop_pos !=

) {

prot_str.resize(stop_pos + 1);

& prot_ref_str,

& prot_delta_str)

& prot_ref_str,

& prot_delta_str)

(

= 0;

< prot_ref_str.size() &&

< prot_delta_str.size();

++) {

(prot_ref_str[

] == prot_delta_str[

]) {

}

(prot_ref_str[

] ==

) {

}

(prot_delta_str[

] ==

) {

& prot_ref_str,

& prot_variant_str)

stop_gain =

;

stop_loss =

;

(

= 0;

<

(prot_ref_str.size(), prot_variant_str.size());

++) {

=

>= prot_ref_str.size() ?

: prot_ref_str[

];

v =

>= prot_variant_str.size() ?

: prot_variant_str[

];

(

==

&& v !=

) {

(

!=

&& v ==

) {

(nuc_delta_len == 0) {

(!stop_gain && !stop_loss) {

}

(nuc_delta_len % 3 == 0) {

vp.

().FlipStrand();

vp.

().SetSeq_data(),

&vp.

().SetSeq_data(),

(

->IsSetStart_offset()) {

(

->IsSetStop_offset()) {

(

->IsSetStart_offset_fuzz()) {

(

->IsSetStop_offset_fuzz()) {

v.

().SetSet().SetVariations())

di.

().SetLoc().FlipStrand();

di.

().GetLiteral().GetSeq_data(),

&di.

().SetLiteral().SetSeq_data(),

sub_loc->

(*range_loc);

(!suffix_loc->

()) {

sub_loc->

(*range_loc);

(!prefix_loc->

()) {

(prefix_loc, suffix_loc);

(inst.

().size() != 1) {

(!

.IsSetSeq() || !

.GetSeq().IsLiteral()) {

.SetSeq().SetLiteral(*tmp_literal2);

p->

().SetWhole().Assign(

);

v->SetData().SetUnknown();

v->SetPlacements().push_back(p);

is_frameshifting,

prot_loc = nuc2prot_mapper->

(nuc_p.

());

codons_loc = prot2nuc_mapper->

(*prot_loc);

(codons_loc->

()) {

v->SetData().SetUnknown();

prot_p->

(*prot_loc);

,

v->SetPlacements().push_back(prot_p);

codons_p->

(*codons_loc);

v->SetPlacements().push_back(codons_p);

(is_frameshifting) {

(

<

.size() &&

<

.size() &&

[

] ==

[

]) {

(

<

.size() &&

<

.size() &&

[

.size() - 1 -

] ==

[

.size() - 1 -

]) {

v->SetData().SetInstance().Assign(nuc_inst);

v->ResetPlacements();

v->SetPlacements().push_back(p);

& nuc_delta = *v->GetData().GetInstance().GetDelta().front();

prot_loc = nuc2prot_mapper->

(p->

());

codons_loc = prot2nuc_mapper->

(*prot_loc);

&& !codons_loc.

()

&& !codons_loc->

()

frameshift_phase = nuc_delta_len % 3;

(frameshift_phase < 0) {

frameshift_phase += 3;

frameshift_phase != 0,

downstream_cds_suffix_seq_str;

downstream_cds_loc = ext_cds_loc->

(

(

->GetLength() > 0) {

downstream_cds_suffix_seq_str =

->GetSeq_data().GetIupacna().Get();

(!v->GetPlacements().front()->GetSeq().IsSetSeq_data()) {

frameshift_phase != 0,

nuc_ref_prefix = v->GetPlacements().front()->GetSeq().GetSeq_data().GetIupacna().Get();

& nuc_var_literal = v->GetData().GetInstance().GetDelta().front()->GetSeq().GetLiteral();

nuc_ref_str = nuc_ref_prefix + downstream_cds_suffix_seq_str;

nuc_var_str = nuc_var_prefix + downstream_cds_suffix_seq_str;

num_ref_codons = (nuc_ref_prefix.size() + 2) / 3;

num_var_codons = (nuc_var_prefix.size() + 2) / 3;

<<

<< nuc_var_str <<

;

<<

<< prot_var_str <<

;

common_prot_prefix_len(0);

(prot_ref_str == prot_var_str) {

prot_ref_str.resize(

(

(prot_ref_str.size()), num_ref_codons));

prot_var_str.resize(prot_ref_str.size());

(prot_ref_str.size() > 0 && *prot_ref_str.rbegin() ==

) {

frameshift_phase = 0;

(common_prot_prefix_len > 0

&& common_prot_prefix_len ==

(prot_ref_str.size())) {

common_prot_prefix_len -= 1;

prot_ref_str = prot_ref_str.substr(common_prot_prefix_len);

prot_var_str = prot_var_str.substr(common_prot_prefix_len);

(

)

<<

<< prot_ref_str <<

<< prot_ref_str.size() <<

<<

<< prot_var_str <<

<< prot_var_str.size() <<

;

(frameshift_phase == 0) {

min_len =

(prot_ref_str.size(), prot_var_str.size());

ref_stop_pos = prot_ref_str.find(

);

var_stop_pos = prot_var_str.find(

);

min_stop_pos =

(ref_stop_pos, var_stop_pos);

truncate_at_stop = min_stop_pos < min_len

&& ref_stop_pos != var_stop_pos

&& nuc_delta_len == 0;

(truncate_at_stop) {

prot_ref_str.resize(min_stop_pos + 1);

prot_var_str.resize(min_stop_pos + 1);

prot_ref_str.resize(prot_ref_str.size() - suffix_len);

prot_var_str.resize(prot_var_str.size() - suffix_len);

prot_ref_str.resize(

(

(1), prot_ref_str.size()));

prot_var_str.resize(

(

(1), prot_var_str.size()));

(prot_ref_str.size() == 0) {

prot_loc->

().SetFrom() += common_prot_prefix_len - 1;

prot_loc->

().SetTo(prot_loc->

().SetFrom() + 1);

prot_loc->

().SetFrom() += common_prot_prefix_len;

prot_loc->

().SetTo(prot_loc->

().SetFrom() + prot_ref_str.size() - 1);

codons_loc = prot2nuc_mapper->

(*prot_loc);

(codons_loc->

()) {

frameshift_phase != 0,

(

)

<<

<< prot_ref_str <<

<< prot_ref_str.size() <<

<<

<< prot_var_str <<

<< prot_var_str.size() <<

;

<<

<< num_var_codons

<<

<< common_prot_prefix_len <<

;

prot_p->

().SetLength(prot_ref_str.size());

prot_p->

().SetSeq_data().SetNcbieaa().Set(prot_ref_str);

prot_p->

(*prot_loc);

prot_v->SetPlacements().push_back(prot_p);

codons_p->

(*codons_loc);

prot_v->SetPlacements().push_back(codons_p);

(frameshift_phase == 0 && prot_ref_str.size() == prot_var_str.size()) {

prot_v->SetVariant_prop().SetEffect(prop);

(so_terms.begin(), so_terms.end(), back_inserter(prot_v->SetSo_terms()));

prot_v->SetData().SetInstance().SetType(

(prot_ref_str, prot_var_str));

prot_v->SetData().SetInstance().SetDelta().push_back(di);

(prot_var_str.size() > 0) {

(

&& common_prot_prefix_len == 0) {

di->SetSeq().Assign(v->GetData().GetInstance().GetDelta().front()->GetSeq());

<<

<< prot_v->GetData().GetInstance().GetType()

<<

<< nuc_var_str.size()

<<

<< nuc_var_str

<<

<< common_prot_prefix_len * 3

<<

<< prot_var_str.size() * 3 <<

;

adjusted_codons_str = nuc_var_str.substr(

min<int>(nuc_var_str.size(), common_prot_prefix_len * 3),

prot_var_str.size() * 3);

(adjusted_codons_str.size() > 0) {

di->SetSeq().SetLiteral().SetLength(adjusted_codons_str.size());

di->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set() = adjusted_codons_str;

di->SetSeq().SetThis();

(prot_ref_str.size() == 0) {

di->SetSeq().SetThis();

(frameshift_phase != 0) {

prot_v->SetVariant_prop().SetEffect(

| (prot_v->IsSetVariant_prop()

&& prot_v->GetVariant_prop().IsSetEffect()

? prot_v->GetVariant_prop().GetEffect() : 0));

prot_v->SetFrameshift().SetPhase(frameshift_phase);

(parent ==

) {

(p1.size() != p2.size()) {

CVariation::TPlacements::const_iterator it1 = p1.begin();

CVariation::TPlacements::const_iterator it2 = p2.begin();

(; it1 != p1.end() && it2 != p2.end(); ++it1, ++it2) {

v.

().SetSet().SetVariations())

v.

().SetSet().SetVariations())

(!

.IsSetPlacements()) {

p1 = &

.SetPlacements();

(!

(*p1,

.GetPlacements())) {

v.

().SetSet().SetVariations())

.ResetPlacements();

CVariation::TConsequence::value_type::TObjectType& cons = **it;

(cons.IsVariation()

&& cons.GetVariation().IsSetPlacements()) {

cons_v.

(&cons.GetVariation());

& dbtag = **it;

(dbtag.

() ==

dbtag->

(

);

dbtag->

().SetId(gene_id);

is_completely_intronic =

;

&& (is_start_offset || is_stop_offset);

is_completely_intronic = is_case1 || is_case2;

(

= 0;

< 3;

++) {

gene_id = it->first;

(loc_prop &

[

]) {

(!is_completely_intronic) {

genomic_query_loc = mapper->

(query_loc);

genomic_query_loc.

(&query_loc);

TIdRangeMap loc_map;

loc_map[ci.GetSeq_id_Handle()][ci.GetRange()] = term;

(!rna_loc && !cds_loc) {

& main_loc = rna_loc ? *rna_loc : *cds_loc;

*ci.GetRangeAsSeq_loc());

SPropsMap::TRangeMap& rm = props_map.loc_map[ci.GetSeq_id_Handle()];

(SPropsMap::TRangeMap::const_iterator it2 = rm.begin(ci.GetRange()); it2.Valid(); ++it2) {

terms_set.

(it2->second);

(terms_set.

(), terms_set.

(), back_inserter(terms));

(

ci(bsh, sel); ci; ++ci) {

last_exon_pos ? last_exon_pos + 1

: last_polyA_pos ? last_polyA_pos + 1

(offset < 0 && offset >= -2) {

(!

.IsSetPlacements()) {

(!

.SetVariant_prop().IsSetGene_location()) {

.SetVariant_prop().SetGene_location(0);

(

.GetConsequenceParent()) {

gene_id = gene_id_and_prop.first;

(m.find(gene_id) == m.end()) {

m[gene_id] |= properties;

m_loc2prop[ci.GetSeq_id_Handle()][ci.GetRange()].push_back(

(gene_id, prop));

m_rangemap[ci.GetSeq_id_Handle()][ci.GetRange()] = ci.GetRangeAsSeq_loc();

(it2 == m_rangemap.end()) {

(std::find(k.begin(), k.end(),

) != k.end()) {

(

ci(bsh, sel); ci; ++ci) {

(transcript_seq_ids.

(product_id) == transcript_seq_ids.

()) {

& dbtag = **it;

(dbtag.

() ==

|| dbtag.

() ==

) {

feature::CFeatTree ft(ci);

(ci.

(); ci; ++ci) {

s_GetGeneID(mf, ft);

feature::CFeatTree ft(ci);

m_loc2prop[idh].size();

(ci.

(); ci; ++ci) {

gene_id = s_GetGeneID(mf, ft);

is_focus_locus = focus_loci.

()

|| focus_loci.count(gene_id);

(is_focus_locus ? focus_gene_ranges

: non_focus_gene_ranges)

->SetMix().Set().push_back(

found_some_gene_ids =

;

(ci.

(); ci; ++ci) {

gene_id = s_GetGeneID(mf, ft);

(!focus_loci.

()

&& focus_loci.

(gene_id) == focus_loci.

()) {

(!parent_mf && gene_id) {

found_some_gene_ids =

;

p.first->ResetStrand();

p.second->ResetStrand();

subtract_gene_ranges_from(*p.first);

subtract_gene_ranges_from(*p.second);

all_gene_neighborhoods->

().Set().push_back(p.first);

all_gene_neighborhoods->

().Set().push_back(p.second);

x_Add(*ci.GetRangeAsSeq_loc(),

(ft.GetChildren(mf).size() == 0) {

genes_and_neighborhoods_loc =

*genes_and_neighborhoods_loc,

*non_focus_gene_ranges,

*genes_and_neighborhoods_loc,

x_Add(*intergenic_loc,

&& !found_some_gene_ids) {

gene_id = s_GetGeneIdForProduct(bsh);

x_Add(*whole_range_loc, gene_id, 0);

feature::CFeatTree& ft)

& dbtag = **it;

(dbtag.

() ==

|| dbtag.

() ==

) {

& dbtag = **it;

(dbtag.

() ==

|| dbtag.

() ==

) {

parent ? s_GetGeneID(parent, ft) : gene_id;

p.second->Assign(*p.first);

p.first->SetInt().SetTo(p.first->GetInt().GetFrom() + 2);

p.second->SetInt().SetFrom(p.second->GetInt().GetTo() - 2);

(p.first, p.second);

p.second->SetNull();

sub_loc2->

(*sub_loc1);

(p.first, p.second);

flank1_len(2000), flank2_len(500);

(flank1_len, flank2_len);

p.second->Assign(*p.first);

(p.first->GetTotalRange().GetFrom() == 0) {

p.first->SetInt().SetTo(p.first->GetTotalRange().GetFrom() - 1);

p.first->SetInt().SetFrom(p.first->GetTotalRange().GetFrom() < flank1_len ? 0 : p.first->GetTotalRange().GetFrom() - flank1_len);

(p.second->GetTotalRange().GetTo() == max_pos) {

p.second->SetNull();

p.second->SetInt().SetFrom(p.second->GetTotalRange().GetTo() + 1);

p.second->SetInt().SetTo(p.second->GetTotalRange().GetTo() > max_pos ? max_pos : p.second->GetTotalRange().GetTo() + flank2_len);

(p.first, p.second);

introns_loc_without_splice_sites->

(*introns_loc_with_splice_sites);

seqint.

() -= 2;

p.first = introns_loc_without_splice_sites;

*introns_loc_without_splice_sites,

m_seq_data_map[idh].mapper.

();

(

ci(bsh, sel); ci; ++ci) {

m_data[ci.GetSeq_id_Handle()][ci.GetRange()].push_back(s);

x_CacheSeqData(*all_rna_loc, idh);

& d = m_seq_data_map[idh2];

target_loc->

().SetId().SetLocal().SetStr(

);

target_loc->

().SetFrom(0);

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

);

(m_seq_data_map.find(ci.GetSeq_id_Handle()) == m_seq_data_map.end()) {

& d = m_seq_data_map.find(ci.GetSeq_id_Handle())->second;

((!mapped_loc->

() && !mapped_loc->

())

->SetSeq_data().SetIupacna().Set() += seq_chunk;

(m_data.find(idh) == m_data.end()) {

(it == m_data.end()) {

cdregions.push_back(*it);

(!v->IsSetId() && parent.

()) {

v->SetId().Assign(parent.

());

feat->

().SetVariation(*vr);

feats.push_back(feat);

feat.

().push_back(uo);

out_feats.insert(out_feats.end(), feats.begin(), feats.end());

vr->SetId().Assign(v.

());

vr->SetSample_id().Assign(*v.

().front());

vr->SetPhenotype().push_back(p);

CVariation_ref::TConsequence::value_type::TObjectType);

vr->SetConsequence().push_back(fr_cons);

fr_cons->SetFrameshift();

vr->SetData().SetComplex();

vr->SetData().SetUniparental_disomy();

vr->SetData().SetUnknown();

vr->SetConsequence();

CVariation::TConsequence::value_type::TObjectType& v_cons = **it;

CVariation_ref::TConsequence::value_type::TObjectType);

vr->SetConsequence().push_back(vr_cons);

vr_cons->SetUnknown();

(v_cons.IsSplicing()) {

vr_cons->SetSplicing();

}

(v_cons.IsNote()) {

vr_cons->SetNote(v_cons.GetNote());

}

(v_cons.IsVariation()) {

vr_cons->SetVariation(*cons_variation);

}

(v_cons.IsLoss_of_heterozygosity()) {

vr_cons->SetLoss_of_heterozygosity();

(v_cons.GetLoss_of_heterozygosity().IsSetReference()) {

vr_cons->SetLoss_of_heterozygosity().SetReference(

v_cons.GetLoss_of_heterozygosity().GetReference());

(v_cons.GetLoss_of_heterozygosity().IsSetTest()) {

vr_cons->SetLoss_of_heterozygosity().SetTest(

v_cons.GetLoss_of_heterozygosity().GetTest());

vr->SetSomatic_origin();

CVariation::TSomatic_origin::value_type::TObjectType& v_so = **it;

CVariation_ref::TSomatic_origin::value_type::TObjectType);

(v_so.IsSetSource()) {

vr_so->SetSource().Assign(v_so.GetSource());

(v_so.IsSetCondition()) {

vr_so->SetCondition();

(v_so.GetCondition().IsSetDescription()) {

vr_so->SetCondition().SetDescription(

v_so.GetCondition().GetDescription());

(v_so.GetCondition().IsSetObject_id()) {

vr_so->SetCondition().SetObject_id();

(CVariation::TSomatic_origin::value_type::TObjectType::TCondition::TObject_id,

v_so.GetCondition().GetObject_id())

vr_so->SetCondition().SetObject_id().push_back(dbtag);

vr->SetSomatic_origin().push_back(vr_so);

->SetMultiplier(-1);

->SetSeq().SetLiteral().SetFuzz().Assign(*fuzz);

v->SetPlacements().push_back(p);

v->SetPub().Assign(variation_feat.

());

v->SetExt().push_back(uo);

v->SetExt().push_back(uo);

v->SetId().Assign(vr.

());

v->SetPhenotype().push_back(p);

v->SetMethod().SetMethod() = vr.

();

v->SetData().SetComplex();

v->SetData().SetUniparental_disomy();

v->SetData().SetUnknown();

v->SetConsequence();

CVariation_ref::TConsequence::value_type::TObjectType& vr_cons = **it;

(vr_cons.IsFrameshift()) {

(vr_cons.GetFrameshift().IsSetPhase()) {

cons_variation.

().SetPhase(vr_cons.GetFrameshift().GetPhase());

(vr_cons.GetFrameshift().IsSetX_length()) {

cons_variation.

().SetX_length(vr_cons.GetFrameshift().GetX_length());

(vr_cons.IsUnknown()) {

v_cons->SetUnknown();

}

(vr_cons.IsSplicing()) {

v_cons->SetSplicing();

}

(vr_cons.IsNote()) {

v_cons->SetNote(vr_cons.GetNote());

}

(vr_cons.IsVariation()) {

v_cons->SetVariation(*cons_variation);

}

(vr_cons.IsLoss_of_heterozygosity()) {

v_cons->SetLoss_of_heterozygosity();

(vr_cons.GetLoss_of_heterozygosity().IsSetReference()) {

v_cons->SetLoss_of_heterozygosity().SetReference(vr_cons.GetLoss_of_heterozygosity().GetReference());

(vr_cons.GetLoss_of_heterozygosity().IsSetTest()) {

v_cons->SetLoss_of_heterozygosity().SetTest(vr_cons.GetLoss_of_heterozygosity().GetTest());

v->SetConsequence().push_back(v_cons);

(v->GetConsequence().empty()) {

v->ResetConsequence();

v->SetSomatic_origin();

CVariation_ref::TSomatic_origin::value_type::TObjectType& vr_so = **it;

(vr_so.IsSetSource()) {

v_so->SetSource().Assign(vr_so.GetSource());

(vr_so.IsSetCondition()) {

v_so->SetCondition();

(vr_so.GetCondition().IsSetDescription()) {

v_so->SetCondition().SetDescription(vr_so.GetCondition().GetDescription());

(vr_so.GetCondition().IsSetObject_id()) {

v_so->SetCondition().SetObject_id();

(CVariation_ref::TSomatic_origin::value_type::TObjectType::TCondition::TObject_id,

vr_so.GetCondition().GetObject_id())

v_so->SetCondition().SetObject_id().push_back(dbtag);

v->SetSomatic_origin().push_back(v_so);

.GetSeq().GetLiteral().GetLength()

* (

.IsSetMultiplier() ?

.GetMultiplier() : 1);

.GetSeq().GetLiteral().IsSetFuzz() ?

&

.GetSeq().GetLiteral().GetFuzz() :

;

v.

().SetSet().SetVariations())

(delta_first->IsSetAction()

v.

().SetInstance().SetDelta().pop_front();

(delta_last != delta_first

&& delta_last->IsSetAction()

v.

().SetInstance().SetDelta().pop_back();

* asserted_out,

* actual_out)

s_PropagateLocsInPlace(vr);

have_asserted_seq =

;

asserted_seq;

(

.GetSeq_data().IsIupacna()) {

asserted_seq =

.GetSeq_data().GetIupacna();

have_asserted_seq =

;

}

(

.GetSeq_data().IsNcbieaa()) {

asserted_seq =

.GetSeq_data().GetNcbieaa();

have_asserted_seq =

;

prefix, suffix;

str_tmp =

(asserted_seq,

,

);

v.GetSeqData(v.begin(), v.end(), actual_seq);

*asserted_out = asserted_seq;

*actual_out = actual_seq;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool IsReverse(ENa_strand s)

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

bool SameOrientation(ENa_strand a, ENa_strand b)

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

ESubtype GetSubtype(void) const

TSeqPos GetSeqStop(TDim row) const

CRef< CSeq_loc > CreateRowSeq_loc(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

TSeqPos GetSeqStart(TDim row) const

namespace ncbi::objects::

TSeqPos GetLength(void) const

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

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

static TSeqPos Keep(CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static TSeqPos ReverseComplement(CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static TSeqPos Append(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2)

Template class for iteration on objects of class C (non-medifiable version)

Template class for iteration on objects of class C.

Set of related Variations.

Set of related Variations.

const TLocation & GetLocation(void) const

void SetLocation(TLocation &value)

bool IsSetLocation(void) const

NOTE: THESE ARE GOING AWAY SOON!!

const CVariation * GetParent() const

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

void Get(const CSeq_loc &loc, TCdregions &cdregions)

vector< SCdregion > TCdregions

void x_Index(const CSeq_id_Handle &idh)

CRef< CSeq_literal > GetCachedLiteralAtLoc(const CSeq_loc &loc)

void x_CacheSeqData(const CSeq_loc &loc, const CSeq_id_Handle &idh)

static TLocsPair s_GetIntronsAndSpliceSiteLocs(const CSeq_loc &rna_loc)

pair< CRef< CSeq_loc >, CRef< CSeq_loc > > TLocsPair

static int s_GetGeneIdForProduct(CBioseq_Handle bsh)

void GetLocationProperties(const CSeq_loc &loc, TGeneIDAndPropVector &v)

pair< int, CVariantProperties::TGene_location > TGeneIDAndProp

static TLocsPair s_GetNeighborhoodLocs(const CSeq_loc &gene_loc, TSeqPos max_pos)

static TLocsPair s_GetUTRLocs(const CSeq_loc &cds_loc, const CSeq_loc &parent_loc)

static TLocsPair s_GetStartAndStopCodonsLocs(const CSeq_loc &cds_loc)

static int s_GetGeneID(const CMappedFeat &mf, feature::CFeatTree &ft)

void x_Add(const CSeq_loc &loc, int gene_id, CVariantProperties::TGene_location prop)

void x_Index(const CSeq_id_Handle &idh)

vector< TGeneIDAndProp > TGeneIDAndPropVector

CRef< CVariantPlacement > RemapToAnnotatedTarget(const CVariation &v, const CSeq_id &target)

Remap variation from product coordinates onto a nucleotide sequence on which this product is annotate...

static void s_AddInstOffsetsFromPlacementOffsets(CVariation_inst &vi, const CVariantPlacement &p)

static const CVariation::TPlacements * s_GetPlacements(const CVariation &v)

@ fAA2NA_truncate_common_prefix_and_suffix

void FindLocationProperties(const CSeq_align &transcript_aln, const CSeq_loc &query_loc, TSOTerms &terms)

Find location properties based on alignment.

CRef< CSeq_literal > GetLiteralAtLoc(const CSeq_loc &loc)

CRef< CVariation > x_AsVariation(const CVariation_ref &vr)

SFlankLocs CreateFlankLocs(const CSeq_loc &loc, TSeqPos len)

vector< ESOTerm > TSOTerms

CRef< CVariation > x_CreateUnknownVariation(const CSeq_id &id, CVariantPlacement::TMol mol)

bool CheckAmbiguitiesInLiterals(CVariation &v)

if variation.data contains a seq-literal with non-ACGT residues, attach VariationException to the fir...

static size_t s_CountMatches(const string &a, const string &b)

void x_AdjustDelinsToInterval(CVariation &v, const CSeq_loc &loc)

ETestStatus CheckExonBoundary(const CVariantPlacement &p, const CSeq_align &aln)

static void s_FactorOutPlacements(CVariation &v)

If at any level in variation-set all variations have all same placements, move them to the parent lev...

static CConstRef< CVariation > s_FindConsequenceForPlacement(const CVariation &v, const CVariantPlacement &p)

Find attached consequence variation in v that corresponds to p (has same seq-id).

CRef< CVariation > TranslateNAtoAA(const CVariation_inst &nuc_inst, const CVariantPlacement &p, const CSeq_feat &cds_feat)

Evaluate protein effect of a single-inst @ single-placement.

static string AsString(ESOTerm term)

static CRef< CSeq_literal > s_SpliceLiterals(const CSeq_literal &payload, const CSeq_literal &ref, TSeqPos pos)

insert seq-literal payload into ref before pos (pos=0 -> prepend; pos=ref.len -> append)

void x_SetVariantPropertiesForIntronic(CVariantPlacement &p, int offset, const CSeq_loc &loc, CBioseq_Handle &bsh)

bool AttachSeq(CVariantPlacement &p, TSeqPos max_len=kMaxAttachSeqLen)

If have offsets (intronic) or too long, return false; else set seq field on the placement and return ...

CRef< CVariation > AsVariation(const CSeq_feat &variation_ref)

@ fOpt_cache_exon_sequence

Use when there will be many calls to calculate protein consequnece per sequence.

bool CheckPlacement(CVariantPlacement &p)

if placement is invalid SeqLocCheck fails, or offsets out of order, attach VariationException and ret...

static void s_AddIntronicOffsets(CVariantPlacement &p, const CSpliced_seg &ss, CScope *scope)

CVariantPlacement::TMol GetMolType(const CSeq_id &id)

void x_InferNAfromAA(CVariation &v, TAA2NAFlags flags)

static string s_CollapseAmbiguities(const vector< string > &seqs)

static void s_FindLocationProperties(CConstRef< CSeq_loc > rna_loc, CConstRef< CSeq_loc > cds_loc, const CSeq_loc &query_loc, TSOTerms &terms)

void ChangeToDelins(CVariation &v)

static void s_ResolveIntronicOffsets(CVariantPlacement &p)

static void s_UntranslateProt(const string &prot_str, vector< string > &codons)

void AsSOTerms(const CVariantProperties &p, TSOTerms &terms)

static void s_AttachGeneIDdbxref(CVariantPlacement &p, int gene_id)

static const CConstRef< CSeq_literal > s_FindFirstLiteral(const CVariation &v)

CRef< CSeq_literal > x_GetLiteralAtLoc(const CSeq_loc &loc)

CRef< CVariation > InferNAfromAA(const CVariation &prot_variation, TAA2NAFlags flags=fAA2NA_default)

void FlipStrand(CVariation &v) const

Other utility methods:

void SetPlacementProperties(CVariantPlacement &placement)

Methods to compute properties.

CVariantPropertiesIndex m_variant_properties_index

CRef< CVariation_ref > x_AsVariation_ref(const CVariation &v, const CVariantPlacement &p)

CRef< CVariantPlacement > Remap(const CVariantPlacement &p, const CSeq_align &aln, bool check_placements=true)

Methods to remap a VariantPlacement.

static bool s_IsInstStrandFlippable(const CVariation &v, const CVariation_inst &inst)

CCdregionIndex m_cdregion_index

static TSeqPos s_GetLength(const CVariantPlacement &p, CScope *scope)

ESOTerm

Supported SO-terms.

@ eSO_splice_acceptor_variant

@ eSO_nc_transcript_variant

@ eSO_initiator_codon_variant

@ eSO_coding_sequence_variant

@ eSO_2KB_upstream_variant

@ eSO_splice_donor_variant

@ eSO_3_prime_UTR_variant

@ eSO_5_prime_UTR_variant

@ eSO_500B_downstream_variant

@ eSO_terminator_codon_variant

TSeqPos GetEffectiveTranscriptLength(const CBioseq_Handle &bsh)

Length up to last position of the last exon (i.e.

void AttachProteinConsequences(CVariation &nuc_variation, const CSeq_id *=NULL, bool ignore_genomic=false)

Find the CDSes for the first placement; Compute prot consequence using TranslateNAtoAA for each and a...

CConstRef< CSeq_literal > x_FindOrCreateLiteral(const CVariation &v)

static void s_ConvertInstOffsetsToPlacementOffsets(CVariation &v, CVariantPlacement &p)

static const CConstRef< CSeq_literal > s_FindAssertedLiteral(const CVariation &v)

void AsVariation_feats(const CVariation &v, CSeq_annot::TData::TFtable &feats)

void SetVariantProperties(CVariation &v)

static CRef< CSeq_literal > s_CatLiterals(const CSeq_literal &a, const CSeq_literal &b)

join two seq-literals

int TAA2NAFlags

Methods to convert between nucleotide and protein.

void s_CalcPrecursorVariationCodon(const string &codon_from, const string &prot_to, vector< string > &codons_to)

CRef< CVariantPlacement > x_Remap(const CVariantPlacement &p, CSeq_loc_Mapper &mapper)

Note: this is strand-agnostic.

CRangeMap< CConstRef< CSeq_loc >, TSeqPos > TRangeMap

map< CSeq_id_Handle, TRangeMap > TIdRangeMap

SFastLocSubtract(const CSeq_loc &loc)

void operator()(CSeq_loc &container_loc) const

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

const TResidue codons[4][4]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_USER_THROW(message)

Throw a quick-and-dirty runtime exception of type 'CException' with the given error message and error...

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define NCBI_RETHROW_SAME(prev_exception, message)

Generic macro to re-throw the same exception.

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

Set object to copy of another one.

const TPrim & Get(void) const

C * SerialClone(const C &src)

Create on heap a clone of the source object.

#define MSerial_AsnText

I/O stream manipulators –.

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

Check if both objects contain the same values.

const string AsFastaString(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

CSeq_id::EAccessionInfo IdentifyAccession(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

@ eAcc_refseq_contig_ncbo

@ eAcc_refseq_mrna_predicted

@ eAcc_refseq_prot_predicted

@ eAcc_refseq_ncrna_predicted

@ eAcc_refseq_wgs_intermed

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.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsTruncatedStop(ESeqLocExtremes ext) const

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

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 IsTruncatedStart(ESeqLocExtremes ext) const

check if parts of the seq-loc are missing

const CSeq_id * GetId(void) const

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

void ResetStrand(void)

Reset the strand on this location.

CRef< CSeq_loc > Intersect(const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const

Find the intersection with the seq-loc, merge/sort resulting ranges depending on flags.

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.

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

@ eOrder_Biological

Iterate sub-locations in positional order.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

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

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

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

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.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

ESeqLocCheck SeqLocCheck(const CSeq_loc &loc, CScope *scope)

Checks that a CSeq_loc is all on one strand on one CBioseq.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eContains

First CSeq_loc contains second.

const CMolInfo * GetMolInfo(const CBioseq &bioseq)

Retrieve the MolInfo object for a given bioseq handle.

const CBioseq * GetNucleotideParent(const CBioseq &product, CScope *scope)

Get the encoding nucleotide sequnce of a protein.

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.

@ fIs5PrimePartial

= 0x4 Translate first codon even if not start codon (because sequence is 5' partial)

@ eGetId_ForceAcc

return only an accession based seq-id

@ eGetId_ForceGi

return only a gi-based seq-id

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_loc_Mapper_Base & SetMergeAll(void)

Merge any abutting or overlapping intervals.

@ eSeqMap_Up

map from segments to the top level bioseq

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

const TDescr & GetDescr(void) const

TBioseqStateFlags GetState(void) const

Get state of the bioseq.

bool IsSetDbxref(void) const

const CSeqFeatData & GetData(void) const

TInst_Mol GetInst_Mol(void) const

bool IsSetProduct(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.

const TDescr & GetDescr(void) const

TInst_Length GetInst_Length(void) const

void Reset(void)

Reset handle and make it not to point to any bioseq.

bool IsSetDescr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeq_feat::TDbxref & GetDbxref(void) const

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TMol GetBioseqMolType(void) const

Get some values from core:

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

bool CanGetDescr(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetResolveTSE(void)

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

const CSeq_loc & GetLocation(void) const

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

const CSeq_loc & GetProduct(void) const

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

bool IsProtein(void) const

const_iterator begin(void) const

bool IsNucleotide(void) const

const_iterator end(void) const

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

position_type GetLength(void) const

const_iterator begin(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Templatized initialization from a string literal.

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

Check if a string ends with a specified suffix value.

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 & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

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 SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

size_type size(void) const

Return the length of the represented array.

const TKeywords & GetKeywords(void) const

Get the Keywords member data.

TGenome GetGenome(void) const

Get the Genome member data.

bool IsSetGenome(void) const

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

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetDb(void) const

ids in other dbases Check if a value has been assigned to Db data member.

const TDb & GetDb(void) const

Get the Db member data.

vector< CRef< CDbtag > > TDb

bool IsLim(void) const

Check if variant Lim is selected.

const TTag & GetTag(void) const

Get the Tag member data.

void SetTag(TTag &value)

Assign a value to Tag data member.

bool IsId(void) const

Check if variant Id is selected.

const TDb & GetDb(void) const

Get the Db member data.

TLim GetLim(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

TLim & SetLim(void)

Select the variant.

bool IsRange(void) const

Check if variant Range is selected.

void SetDb(const TDb &value)

Assign a value to Db data member.

TId GetId(void) const

Get the variant data.

@ eLim_tl

space to left of position

@ eLim_tr

space to right of position

const TProtpos & GetProtpos(void) const

Get the variant data.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

void SetProduct_id(TProduct_id &value)

Assign a value to Product_id data member.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TExons & SetExons(void)

Assign a value to Exons data member.

void SetProduct_strand(TProduct_strand value)

Assign a value to Product_strand data member.

TAmin GetAmin(void) const

Get the Amin member data.

void SetType(TType value)

Assign a value to Type data member.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

void SetProduct_type(TProduct_type value)

Assign a value to Product_type data member.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

void SetGenomic_id(TGenomic_id &value)

Assign a value to Genomic_id data member.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

void SetGenomic_strand(TGenomic_strand value)

Assign a value to Genomic_strand data member.

bool IsSpliced(void) const

Check if variant Spliced is selected.

bool IsNucpos(void) const

Check if variant Nucpos is selected.

TNucpos GetNucpos(void) const

Get the variant data.

const TSegs & GetSegs(void) const

Get the Segs member data.

@ eProduct_type_transcript

vector< CRef< CDbtag > > TDbxref

const TExts & GetExts(void) const

Get the Exts member data.

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

list< CRef< CUser_object > > TExts

const TCit & GetCit(void) const

Get the Cit member data.

void SetCit(TCit &value)

Assign a value to Cit data member.

TExts & SetExts(void)

Assign a value to Exts 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.

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.

void SetData(TData &value)

Assign a value to Data data member.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetExts(void) const

set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.

bool IsSetCit(void) const

citations for this feature Check if a value has been assigned to Cit data member.

bool IsVariation(void) const

Check if variant Variation is selected.

const TGene & GetGene(void) const

Get the variant data.

TExcept GetExcept(void) const

Get the Except member data.

const TExt & GetExt(void) const

Get the Ext member data.

const TVariation & GetVariation(void) const

Get the variant data.

bool IsRna(void) const

Check if variant Rna is selected.

void SetTo(TTo value)

Assign a value to To data member.

bool IsMix(void) const

Check if variant Mix is selected.

bool IsEmpty(void) const

Check if variant Empty is selected.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

void SetFrom(TFrom value)

Assign a value to From data member.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool IsSetFuzz_to(void) const

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

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

bool IsSetFuzz_from(void) const

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

bool IsPnt(void) const

Check if variant Pnt is selected.

const TIupacaa & GetIupacaa(void) const

Get the variant data.

void SetLength(TLength value)

Assign a value to Length data member.

bool IsGenbank(void) const

Check if variant Genbank is selected.

bool IsSetCompleteness(void) const

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

list< CRef< CSeqdesc > > Tdata

bool IsMolinfo(void) const

Check if variant Molinfo is selected.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TIupacna & GetIupacna(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

const Tdata & Get(void) const

Get the member data.

TLength GetLength(void) const

Get the Length member data.

const TGenbank & GetGenbank(void) const

Get the variant data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

TBiomol GetBiomol(void) const

Get the Biomol member data.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

list< CRef< CSeq_feat > > TFtable

bool IsSetSeq_data(void) const

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

const TMolinfo & GetMolinfo(void) const

Get the variant data.

bool IsIupacna(void) const

Check if variant Iupacna is selected.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

E_Choice Which(void) const

Which variant is currently selected.

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ e_Iupacaa

IUPAC 1 letter amino acid code.

@ eBiomol_pre_RNA

precursor RNA of any sort really

@ eBiomol_cRNA

viral RNA genome copy intermediate

@ eBiomol_snoRNA

small nucleolar RNA

@ eBiomol_genomic_mRNA

reported a mix of genomic and cdna sequence

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

@ eBiomol_other_genetic

other genetic material

void SetStop_offset_fuzz(TStop_offset_fuzz &value)

Assign a value to Stop_offset_fuzz data member.

void SetGene_location(TGene_location value)

Assign a value to Gene_location data member.

TMol GetMol(void) const

Get the Mol member data.

bool IsSetName(void) const

names and synonyms some variants have well-known canonical names and possible accepted synonyms Check...

bool IsSetStop_offset_fuzz(void) const

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

TMethod & SetMethod(void)

Assign a value to Method data member.

void SetFrame(TFrame value)

Assign a value to Frame data member.

void SetFrameshift(TFrameshift &value)

Assign a value to Frameshift data member.

TPlacement_method GetPlacement_method(void) const

Get the Placement_method member data.

TDbxrefs & SetDbxrefs(void)

Assign a value to Dbxrefs data member.

bool IsSetOther_ids(void) const

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

bool IsComplex(void) const

Check if variant Complex is selected.

list< CRef< CVariantPlacement > > TPlacements

bool IsSetPhenotype(void) const

phenotype Check if a value has been assigned to Phenotype data member.

bool IsSetFrameshift(void) const

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

void SetPlacement_method(TPlacement_method value)

Assign a value to Placement_method data member.

void SetStop_offset(TStop_offset value)

Assign a value to Stop_offset data member.

bool IsSetMol(void) const

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

list< CRef< CVariation > > TVariations

const TStop_offset_fuzz & GetStop_offset_fuzz(void) const

Get the Stop_offset_fuzz member data.

bool IsSetPlacements(void) const

where this beast is seen note that this is a set of locations, and there are no restrictions to the c...

bool IsSetGene_location(void) const

Same semantics as VariantProperties.gene-location, except placement-specific Check if a value has bee...

void SetName(const TName &value)

Assign a value to Name data member.

const TName & GetName(void) const

Get the Name member data.

bool IsUnknown(void) const

Check if variant Unknown is selected.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetPub(void) const

publication support; same type as in seq-feat Check if a value has been assigned to Pub data member.

TX_length GetX_length(void) const

Get the X_length member data.

void ResetStop_offset(void)

Reset Stop_offset data member.

bool IsInstance(void) const

Check if variant Instance is selected.

void ResetStart_offset_fuzz(void)

Reset Start_offset_fuzz data member.

const TSample_id & GetSample_id(void) const

Get the Sample_id member data.

const TExt & GetExt(void) const

Get the Ext member data.

list< CRef< CPhenotype > > TPhenotype

const TPhenotype & GetPhenotype(void) const

Get the Phenotype member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetSeq(void) const

for situations in which a raw location isn't sufficient Check if a value has been assigned to Seq dat...

bool IsSetId(void) const

ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP|rs12334',...

const TInstance & GetInstance(void) const

Get the variant data.

const TOther_ids & GetOther_ids(void) const

Get the Other_ids member data.

bool IsSetParent_id(void) const

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

const TDescription & GetDescription(void) const

Get the Description member data.

bool IsSetStart_offset_fuzz(void) const

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

const TSomatic_origin & GetSomatic_origin(void) const

Get the Somatic_origin member data.

list< CRef< CObject_id > > TSample_id

TExceptions & SetExceptions(void)

Assign a value to Exceptions data member.

const TNote & GetNote(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the Pub member data.

const TVariations & GetVariations(void) const

Get the Variations member data.

TStop_offset GetStop_offset(void) const

Get the Stop_offset member data.

void SetSeq(TSeq &value)

Assign a value to Seq data member.

const TFrameshift & GetFrameshift(void) const

Get the Frameshift member data.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

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

void ResetStop_offset_fuzz(void)

Reset Stop_offset_fuzz data member.

bool IsNote(void) const

Check if variant Note is selected.

const TMethod & GetMethod(void) const

Get the Method member data.

const TPlacements & GetPlacements(void) const

Get the Placements member data.

bool IsSetVariant_prop(void) const

variant properties bit fields Check if a value has been assigned to Variant_prop data member.

bool IsSetSample_id(void) const

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

list< CRef< CUser_object > > TExt

TGene_location GetGene_location(void) const

Get the Gene_location member data.

void ResetStart_offset(void)

Reset Start_offset data member.

void SetType(TType value)

Assign a value to Type data member.

const TSynonyms & GetSynonyms(void) const

Get the Synonyms member data.

list< CRef< CDbtag > > TDbxrefs

const TSeq & GetSeq(void) const

Get the Seq member data.

TPlacements & SetPlacements(void)

Assign a value to Placements data member.

void SetStart_offset(TStart_offset value)

Assign a value to Start_offset data member.

void ResetPlacements(void)

Reset Placements data member.

void ResetSeq(void)

Reset Seq data member.

bool IsSetPhase(void) const

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

const TData & GetData(void) const

Get the Data member data.

void SetMol(TMol value)

Assign a value to Mol data member.

bool IsSetSynonyms(void) const

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

bool IsSetExt(void) const

Additional undescribed extensions Check if a value has been assigned to Ext data member.

bool IsSetMethod(void) const

sequencing / acuisition method Check if a value has been assigned to Method data member.

const TParent_id & GetParent_id(void) const

Get the Parent_id member data.

bool IsSetX_length(void) const

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

bool IsSetStop_offset(void) const

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

list< CRef< CDbtag > > TOther_ids

const TStart_offset_fuzz & GetStart_offset_fuzz(void) const

Get the Start_offset_fuzz member data.

TVariations & SetVariations(void)

Assign a value to Variations data member.

bool IsSetSomatic_origin(void) const

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

const TId & GetId(void) const

Get the Id member data.

list< CRef< C_E_Somatic_origin > > TSomatic_origin

const TMethod & GetMethod(void) const

Get the Method member data.

const TVariant_prop & GetVariant_prop(void) const

Get the Variant_prop member data.

bool IsSetStart_offset(void) const

location refinements, describing offsets into introns from product coordinates.

const TLoc & GetLoc(void) const

Get the Loc member data.

bool IsSet(void) const

Check if variant Set is selected.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TConsequence & GetConsequence(void) const

Get the Consequence member data.

bool IsUniparental_disomy(void) const

Check if variant Uniparental_disomy is selected.

TType GetType(void) const

Get the Type member data.

void SetStart_offset_fuzz(TStart_offset_fuzz &value)

Assign a value to Start_offset_fuzz data member.

TStart_offset GetStart_offset(void) const

Get the Start_offset member data.

bool IsSetDescription(void) const

tag for comment and descriptions Check if a value has been assigned to Description data member.

TConsequence & SetConsequence(void)

Assign a value to Consequence data member.

void ResetGene_location(void)

Reset Gene_location data member.

bool IsSetPlacement_method(void) const

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

list< CRef< C_E_Consequence > > TConsequence

bool IsSetConsequence(void) const

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

TPhase GetPhase(void) const

Get the Phase member data.

@ eMol_cdna

"c." coordinates in HGVS

@ eMol_mitochondrion

"mt." coordinates in HGVS

@ eMol_rna

"n." coordinates in HGVS

@ eMol_protein

"p." coordinates in HGVS

@ eMol_genomic

"g." coordinates in HGVS

@ eCode_ambiguous_sequence

@ eCode_inconsistent_consequence

consequence protein variation attached to precursor variation's consequence could not be derived from...

@ eCode_seqfetch_intronic

can't fetch sequence for an intronic (anchor+offset)-based location

@ eCode_ref_same_as_variant

reference sequence at the location is same as variant sequence in the variation

@ eCode_source_location_overhang

The source location overhangs the alignment by at least 5kb (VAR-1307)

@ eCode_hgvs_exon_boundary

anchor position in an intronic HGVS expression is not at an exon boundary

@ eCode_split_mapping

a source interval maps to multiple non-abutting intervals.

@ eCode_hgvs_exon_boundary_induced

Similar to (2), except induced by 5'/3'-terminal or an exon extension (VAR-1309)

@ eCode_inconsistent_asserted_allele

asserted allele is inconsistent with the reference

@ eCode_mismatches_in_mapping

the source sequence differs from sequence at mapped loc

@ eCode_seqfetch_too_long

can't fetch sequence because location is longer than specified threshold

@ eCode_partial_mapping

mapped location is shorter than the query

@ eCode_seqfetch_invalid

can't fetch sequence because location is invalid (e.g. extends past the end)

@ eCode_hgvs_parsing

invalid hgvs expression

@ eCode_no_mapping

could not remap

@ ePlacement_method_projected

@ eMethod_E_computational

TType GetType(void) const

Get the Type member data.

const TInstance & GetInstance(void) const

Get the variant data.

const TVariant_prop & GetVariant_prop(void) const

Get the Variant_prop member data.

TAction GetAction(void) const

Get the Action member data.

bool IsSetSomatic_origin(void) const

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

list< CRef< CVariation_ref > > TVariations

TObservation GetObservation(void) const

Get the Observation member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

bool IsSetSample_id(void) const

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

bool IsSetVariant_prop(void) const

variant properties bit fields Check if a value has been assigned to Variant_prop data member.

list< CRef< CDbtag > > TOther_ids

TType GetType(void) const

Get the Type member data.

const TSample_id & GetSample_id(void) const

Get the Sample_id member data.

void SetType(TType value)

Assign a value to Type data member.

bool IsSetOther_ids(void) const

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

bool IsSetSeq(void) const

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

bool IsSetAction(void) const

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

list< CRef< CPhenotype > > TPhenotype

const TNote & GetNote(void) const

Get the variant data.

const TLoc & GetLoc(void) const

Get the variant data.

TEffect GetEffect(void) const

Get the Effect member data.

void SetObservation(TObservation value)

Assign a value to Observation data member.

const TId & GetId(void) const

Get the Id member data.

const TDelta & GetDelta(void) const

Get the Delta member data.

list< CRef< C_E_Somatic_origin > > TSomatic_origin

void SetMultiplier_fuzz(TMultiplier_fuzz &value)

Assign a value to Multiplier_fuzz data member.

bool IsSetConsequence(void) const

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

const TData & GetData(void) const

Get the Data member data.

const TPhenotype & GetPhenotype(void) const

Get the Phenotype member data.

bool IsSetPhenotype(void) const

phenotype Check if a value has been assigned to Phenotype data member.

const TSeq & GetSeq(void) const

Get the Seq member data.

const TDescription & GetDescription(void) const

Get the Description member data.

bool IsInstance(void) const

Check if variant Instance is selected.

const TName & GetName(void) const

Get the Name member data.

list< CRef< C_E_Consequence > > TConsequence

const TLiteral & GetLiteral(void) const

Get the variant data.

const TSomatic_origin & GetSomatic_origin(void) const

Get the Somatic_origin member data.

const TConsequence & GetConsequence(void) const

Get the Consequence member data.

void ResetAction(void)

Reset Action data member.

bool IsSetDescription(void) const

tag for comment and descriptions Check if a value has been assigned to Description data member.

bool IsSetSynonyms(void) const

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

bool IsUniparental_disomy(void) const

Check if variant Uniparental_disomy is selected.

bool IsSet(void) const

Check if variant Set is selected.

bool IsSetMethod(void) const

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

bool IsSetParent_id(void) const

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

void SetName(const TName &value)

Assign a value to Name data member.

void SetType(TType value)

Assign a value to Type data member.

void SetSeq(TSeq &value)

Assign a value to Seq data member.

TMultiplier GetMultiplier(void) const

Get the Multiplier member data.

bool IsSetMultiplier_fuzz(void) const

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

const TParent_id & GetParent_id(void) const

Get the Parent_id member data.

bool IsSetName(void) const

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

list< CRef< CDelta_item > > TDelta

bool IsUnknown(void) const

Check if variant Unknown is selected.

TVariations & SetVariations(void)

Assign a value to Variations data member.

bool IsLiteral(void) const

Check if variant Literal is selected.

const TName & GetName(void) const

Get the Name member data.

bool IsSetId(void) const

ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP|rs12334',...

bool IsSetMultiplier(void) const

Multiplier allows representing a tandem, e.g.

void ResetMultiplier(void)

Reset Multiplier data member.

bool IsSetObservation(void) const

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

const TOther_ids & GetOther_ids(void) const

Get the Other_ids member data.

bool IsSetName(void) const

names and synonyms some variants have well-known canonical names and possible accepted synonyms Check...

TDelta & SetDelta(void)

Assign a value to Delta data member.

const TMethod & GetMethod(void) const

Get the Method member data.

bool IsNote(void) const

Check if variant Note is selected.

bool IsThis(void) const

Check if variant This is selected.

TGene_location GetGene_location(void) const

Get the Gene_location member data.

bool IsLoc(void) const

Check if variant Loc is selected.

const TVariations & GetVariations(void) const

Get the Variations member data.

const TSynonyms & GetSynonyms(void) const

Get the Synonyms member data.

bool IsComplex(void) const

Check if variant Complex is selected.

@ eType_snv

delta=[morph of length 1] NOTE: this is snV not snP; the latter requires frequency-based validation t...

@ eType_inv

delta=[del, ins.seq= RevComp(variation-location)]

@ eType_mnp

delta=[morph of length >1]

@ eType_delins

delta=[del, ins]

@ eType_prot_nonsense

delta=[del]; variation-location is the tail of the protein being truncated

@ eType_prot_other

delta=any

@ eType_prot_silent

delta=[morph of length 1, same AA as at variation-location]

@ eType_prot_missense

delta=[morph of length 1]

@ eEffect_stop_gain

reference codon is not stop codon, but the snp variant allele changes the codon to a terminating codo...

@ eEffect_missense

one allele in the set changes protein peptide (0x4)

@ eEffect_nonsense

one allele in the set changes to STOP codon (TER). (0x2)

@ eEffect_stop_loss

reverse of STOP-GAIN: reference codon is a stop codon, but a snp variant allele changes the codon to ...

@ eEffect_synonymous

one allele in the set does not change the encoded amino acid (0x1)

@ eEffect_frameshift

one allele in the set changes all downstream amino acids (0x8)

@ eGene_location_in_start_codon

the variant is observed in a start codon (0x100)

@ eGene_location_acceptor

In acceptor splice-site (0x20)

@ eGene_location_near_gene_5

Within 2kb of the 5' end of a gene feature.

@ eGene_location_near_gene_3

Within 0.5kb of the 3' end of a gene feature.

@ eGene_location_utr_3

In 3' UTR (0x80)

@ eGene_location_in_gene

Sequence intervals covered by a gene ID but not having an aligned transcript (0x01)

@ eGene_location_utr_5

In 5' UTR (0x40)

@ eGene_location_intron

In Intron (0x08)

@ eGene_location_intergenic

variant located between genes (0x400)

@ eGene_location_donor

In donor splice-site (0x10)

@ eGene_location_in_stop_codon

the variant is observed in a stop codon (0x200)

@ eGene_location_conserved_noncoding

variant is located in a conserved non-coding region (0x800)

@ eAction_offset

go downstream by distance specified by multiplier (upstream if < 0), in genomic context.

@ eAction_morph

replace len(seq) positions starting with location.start with seq

@ eAction_del_at

excise sequence at location if multiplier is specified, delete len(location)*multiplier positions dow...

@ eAction_ins_before

insert seq before the location.start

@ eObservation_variant

inst represent the observed variant at a given position

@ eObservation_asserted

inst represents the asserted base at a position

unsigned int

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

double value_type

The numeric datatype used by the parser.

static void ChangeIdsInPlace(T &container, sequence::EGetIdType id_type, CScope &scope)

static set< int > GetFocusLocusIDs(const CBioseq_Handle &bsh)

static CVariantProperties::TEffect CalcEffectForProt(const string &prot_ref_str, const string &prot_delta_str)

static bool IsRightPartial(CBioseq_Handle bsh)

static bool HasProblematicExceptions(const CSeq_feat &cds_feat)

static CRef< CDelta_item > CreateDeltaForOffset(int offset, const CInt_fuzz *fuzz)

static bool Equals(const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)

static void ApplyOffsetFuzz(CSeq_loc &loc, const CInt_fuzz &offset_fuzz, bool is_start)

static bool IsRefSeqGene(const CBioseq_Handle &bsh)

static CRef< CVariationException > CreateException(const string &message, CVariationException::ECode code=static_cast< CVariationException::ECode >(0))

static string Translate(const string &nuc_str, bool is_mito)

static int GetFuzzSign(const CInt_fuzz &fuzz, int loc_sign)

static void SwapLtGtFuzz(CInt_fuzz &fuzz)

CVariation_inst::EType CalcInstTypeForAA(const string &prot_ref_str, const string &prot_delta_str)

CRef< CVariation > InheritParentAttributes(const CVariation &child, const CVariation &parent)

static CRef< CVariation > CreateUnknownProtConsequenceVariation(const CVariantPlacement &nuc_p, const CSeq_feat &cds_feat, bool is_frameshifting, CScope &scope)

static CVariationUtil::TSOTerms CalcSOTermsForProt(TSignedSeqPos nuc_delta_len, const string &prot_ref_str, const string &prot_variant_str)

static CRef< CSeq_align > CreateSplicedSeqAlignFromFeat(const CSeq_feat &rna_feat)

static bool ValidExonTerminal(const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, TSeqPos exon_anchor_pos, int offset_pos)

static int GetSignedOffset(const CDelta_item &delta)

static bool ContainsIupacNaAmbiguities(const T &obj)

static bool Contains(const CSeq_loc &a, const CSeq_loc &b, CScope *scope)

static bool ValidExonTerminals(const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, const CVariantPlacement &p)

static size_t GetCommonSuffixLen(const string &a, const string &b)

static const CInt_fuzz * GetFuzz(const CDelta_item &delta)

static size_t GetCommonPrefixLen(const string &a, const string &b)

Int4 delta(size_t dimension_, const Int4 *score_)

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

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

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

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

CConstRef< CSeq_feat > cdregion_feat

CRef< CSeq_loc_Mapper > mapper

Calculate upstream (first) and downstream(second) flanks for loc.

CRef< CSeq_loc > upstream

CRef< CSeq_loc > downstream

CRef< CTestThread > thr[k_NumThreadsMax]

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